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Chromatin ChIP-seq

experiment: Chromatin ChIP-seq project: Chromatin Function PI: Jason Lieb Labs: Jason Lieb, Julie Ahringer, Susan Strome
ChIP-seq analysis of elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.

All features generated by this experiment:
Feature Export
BindingSite 190586
This represents 188396 unique BindingSites
TAB CSV GFF3 (for UCSC) SEQ
NO GBROWSE TRACKS FOR THIS EXPERIMENT
All entries in public repositories generated by this experiment
There are 23 ChIP-seq submissions for this experiment:
DCC id Name developmental stage antibody strain temperature Embargoed until Features, GBrowse and Data Files
modENCODE_3563

seq-AB9050 H3K36me3 N2 L3 L3 Larval Stage [ALL]
C. elegans AB9050_H3K36ME3 rabbit polyclonal antibody [ALL] /
target: trimethylated Lys-36 of histone H3
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 16701   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-AB9050_H3K36me3_N2_L3_7_macs14_peaks.gff: 6223   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-AB9050_H3K36me3_N2_L3_1_macs14_peaks.gff: 5973   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-AB9050_H3K36me3_N2_L3_catted_peaks.gff: 4505   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM706166
GEO: GSM779422
GEO: GSM779423
GEO: GSM779424


11 files Download data files
modENCODE_3573

seq-SDQ0820 EPC1 N2 L3 EGS L3 Larval Stage [ALL]
SDQ0820-EPC1 [ALL] / epc-1
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 9924   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ0820_EPC1_N2_L3_combo_1_EGS+2_EGS_macs14_peaks.gff: 3636   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ0820_EPC1_N2_L3_1_EGS_macs14_peaks.gff: 3455   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ0820_EPC1_N2_L3_2_EGS_macs14_peaks.gff: 2833   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM713232
GEO: GSM713233
GEO: GSM713234
GEO: GSM713235


11 files Download data files
modENCODE_3570

seq-JA00011 LIN35 N2 L3 L3 Larval Stage [ALL]
JA00011-LIN35 [ALL] / lin-35
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 5973   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-JA00011_LIN35_N2_L3_2+4_catted_peaks.gff: 3303   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-JA00011_LIN35_N2_L3_2_macs14_peaks.gff: 1793   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-JA00011_LIN35_N2_L3_4_macs14_peaks.gff: 877   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM706161
GEO: GSM706164
GEO: GSM713136
GEO: GSM713137


11 files Download data files
modENCODE_3935

seq-SDQ3599 DPL1 N2 LTemb DevStageWorm:Late Embryos:JL:1 [ALL]
SDQ3599-DPL1 [ALL] / dpl-1
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 10167   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ3599_DPL1_N2_LTemb_1_peaks.gff: 4987   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ3599_DPL1_N2_LTemb_all_peaks.gff: 2724   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ3599_DPL1_N2_LTemb_2_peaks.gff: 2456   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM830458
GEO: GSM830460


11 files Download data files
modENCODE_3934

seq-SDQ3590 EFL1 N2 LTemb DevStageWorm:Late Embryos:JL:1 [ALL]
SDQ3590-EFL1 [ALL] / efl-1
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 6867   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ3590_EFL1_N2_LTemb_1_peaks.gff: 2169   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ3590_EFL1_N2_LTemb_2_peaks.gff: 2777   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ3590_EFL1_N2_LTemb_all_peaks.gff: 1921   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM830460
GEO: GSM830461


11 files Download data files
modENCODE_3572

seq-LPAR109 H4tetraac 109 N2 L3 L3 Larval Stage [ALL]
LPAR109_H4tetraac:109 [ALL] /
target: H4tetraac
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 13926   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-LPAR109_H4tetraac_109_N2_L3_1_macs14_peaks.gff: 4236   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-LPAR109_H4tetraac_109_N2_L3_2_macs14_peaks.gff: 4931   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-LPAR109_H4tetraac_109_N2_L3_combo_macs14_peaks.gff: 4759   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM706164
GEO: GSM706167
GEO: GSM713143
GEO: GSM713144


11 files Download data files
modENCODE_3571

seq-JL00001 DPY27 N2 L3 L3 Larval Stage [ALL]
JL00001_DPY27 [ALL] / dpy-27
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 3676   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-JL00001_DPY27_N2_L3_3_macs14_peaks.gff: 2755   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-JL00001_DPY27_N2_L3_2_macs14_peaks.gff: 442   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-JL00001_DPY27_N2_L3_catted_peaks.gff: 479   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM706165
GEO: GSM706166
GEO: GSM779439
GEO: GSM779440


11 files Download data files
modENCODE_3575

seq-SDQ3599 DPL1 N2 L3 L3 Larval Stage [ALL]
SDQ3599-DPL1 [ALL] / dpl-1
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 5175   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ3599_DPL1_N2_L3_1_macs14_peaks.gff: 2587   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ3599_DPL1_N2_L3_2_macs14_peaks.gff: 1174   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ3599_DPL1_N2_L3_1+2_catted_macs14_peaks.gff: 1414   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM706161
GEO: GSM706164
GEO: GSM713149
GEO: GSM713150


11 files Download data files
modENCODE_3576

seq-WA30534819 H3K4me3 N2 L3 L3 Larval Stage [ALL]
WA305-34819 H3K4me3 [ALL] /
target: H3K4me3
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 12384   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-WA30534819_H3K4me3_N2_L3_2_macs14_peaks.gff: 3280   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-WA30534819_H3K4me3_N2_L3_catted_peaks.gff: 4696   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-WA30534819_H3K4me3_N2_L3_1_macs14_peaks.gff: 4408   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM706164
GEO: GSM706167
GEO: GSM713168
GEO: GSM713169


11 files Download data files
modENCODE_3568

seq-BH00005 LIN9 N2 L3 L3 Larval Stage [ALL]
BH00005-LIN9 [ALL] / lin-9
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 10442   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00005_LIN9_N2_L3_2_macs14_peaks.gff: 4408   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00005_LIN9_N2_L3_1_macs14_peaks.gff: 2051   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00005_LIN9_N2_L3_1+2_catted_macs14_peaks.gff: 3983   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM706161
GEO: GSM706164
GEO: GSM712810
GEO: GSM712811


11 files Download data files
modENCODE_3577

seq-SDQ3590 EFL1 N2 L3 L3 Larval Stage [ALL]
SDQ3590-EFL1 [ALL] / efl-1
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 5965   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ3590_EFL1_N2_L3_1_macs14_peaks.gff: 3135   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ3590_EFL1_N2_L3_1+2_catted_macs14_peaks.gff: 1670   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ3590_EFL1_N2_L3_2_macs14_peaks.gff: 1160   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM706161
GEO: GSM706164
GEO: GSM713147
GEO: GSM713148


11 files Download data files
modENCODE_3562

seq-AB1791 H3 N2 L3 L3 Larval Stage [ALL]
C. elegans AB1791_H3 rabbit polyclonal antibody [ALL] /
target: Histone H3
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 15559   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-AB1791_H3_N2_L3_7_macs14_peaks.gff: 3037   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-AB1791_H3_N2_L3_2_macs14_peaks.gff: 3609   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-AB1791_H3_N2_L3_1_macs14_peaks.gff: 1087   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-AB1791_H3_N2_L3_catted_peaks.gff: 7826   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM706161
GEO: GSM706165
GEO: GSM706166
GEO: GSM712543
GEO: GSM712544
...All entries in public repositories generated by this submission



16 files Download data files
modENCODE_3924

seq-BH00005 LIN9 N2 LTemb DevStageWorm:Late Embryos:JL:1 [ALL]
BH00005-LIN9 [ALL] / lin-9
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 9711   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00005_LIN9_N2_LTemb_all_peaks.gff: 2160   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00005_LIN9_N2_LTemb_2_peaks.gff: 2270   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00005_LIN9_N2_LTemb_1_peaks.gff: 5281   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM830458
GEO: GSM830459


11 files Download data files
modENCODE_3565

seq-BH00001 LIN52 N2 L3 L3 Larval Stage [ALL]
BH00001_LIN52 [ALL] / lin-52
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 2817   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00001_LIN52_N2_L3_1+2_catted_macs14_peaks.gff: 723   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00001_LIN52_N2_L3_2_macs14_peaks.gff: 503   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00001_LIN52_N2_L3_1_macs14_peaks.gff: 1591   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM706161
GEO: GSM706164
GEO: GSM712709
GEO: GSM712710


11 files Download data files
modENCODE_3579

seq-SDQ4470 TAG315 N2 MXemb Mixed Stage Embryos [ALL]
SDQ4470_TAG315 [ALL] /
target: TAG315
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 4145   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ4470_TAG315_N2_MXemb_2_A_EE9_KI033_macs14_peaks.gff: 1361   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ4470_TAG315_N2_MXemb_1_A_EE8_KI032_macs14_peaks.gff: 1304   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ4470_TAG315_N2_MXemb_catted_peaks.gff: 1480   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM706160
GEO: GSM713170
GEO: GSM713171


9 files Download data files
modENCODE_3925

seq-JA00011 LIN35 N2 LTemb DevStageWorm:Late Embryos:JL:1 [ALL]
JA00011-LIN35 [ALL] / lin-35
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 5824   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-JA00011_LIN35_N2_LTemb_1_peaks.gff: 2637   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-JA00011_LIN35_N2_LTemb_2_peaks.gff: 1462   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-JA00011_LIN35_N2_LTemb_all_peaks.gff: 1725   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM830458
GEO: GSM830459


11 files Download data files
modENCODE_3566

seq-BH00003 LIN37 N2 L3 L3 Larval Stage [ALL]
BH00003_LIN37 [ALL] / lin-37
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 5801   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00003_LIN37_N2_L3_1_macs14_peaks.gff: 1693   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00003_LIN37_N2_L3_1+2_catted_macs14_peaks.gff: 1856   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00003_LIN37_N2_L3_2_macs14_peaks.gff: 2252   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM706161
GEO: GSM706164
GEO: GSM712711
GEO: GSM712712


11 files Download data files
modENCODE_3928

seq-BH00003 LIN37 N2 LTemb DevStageWorm:Late Embryos:JL:1 [ALL]
BH00003_LIN37 [ALL] / lin-37
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 8137   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00003_LIN37_N2_LTemb_2_peaks.gff: 2197   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00003_LIN37_N2_LTemb_1_peaks.gff: 3698   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00003_LIN37_N2_LTemb_all_peaks.gff: 2242   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM830458
GEO: GSM830460


11 files Download data files
modENCODE_3580

seq-SDQ4526 SFC1 N2 MXemb Mixed Stage Embryos [ALL]
SDQ4526_SFC1 [ALL] /
target: SFC-1
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 4617   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ4526_SFC1_N2_MXemb_1_A_EE8_KI034_macs14_peaks.gff: 1421   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ4526_SFC1_N2_MXemb_2_A_EE9_KI035_macs14_peaks.gff: 1369   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ4526_SFC1_N2_MXemb_catted_peaks.gff: 1827   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM706160
GEO: GSM713172
GEO: GSM713173


9 files Download data files
modENCODE_3567

seq-BH00004 LIN54 N2 L3 L3 Larval Stage [ALL]
BH00004-LIN54 [ALL] / lin-54
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 11194   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00004_LIN54_N2_L3_2_macs14_peaks.gff: 4569   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00004_LIN54_N2_L3_1_macs14_peaks.gff: 2133   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00004_LIN54_N2_L3_1+2_catted_macs14_peaks.gff: 4492   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM706161
GEO: GSM706164
GEO: GSM712713
GEO: GSM712714


11 files Download data files
modENCODE_3581

seq-SDQ4663 RPC1 N2 MXemb Mixed Stage Embryos [ALL]
SDQ4663_RPC1 [ALL] /
target: RPC-1
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 5978   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ4663_RPC1_N2_MXemb_1_A_EE8_macs14_peaks.gff: 1660   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ4663_RPC1_N2_MXemb_2_A_EE9_KI031_macs14_peaks.gff: 2096   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-SDQ4663_RPC1_N2_MXemb_catted_peaks.gff: 2222   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM706160
GEO: GSM713174
GEO: GSM713175


9 files Download data files
modENCODE_3930

seq-BH00001 LIN52 N2 LTemb DevStageWorm:Late Embryos:JL:1 [ALL]
BH00001_LIN52 [ALL] / lin-52
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 6869   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00001_LIN52_N2_LTemb_2_peaks.gff: 2490   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00001_LIN52_N2_LTemb_1_peaks.gff: 2344   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00001_LIN52_N2_LTemb_all_peaks.gff: 2035   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM830460
GEO: GSM830461


11 files Download data files
modENCODE_3932

seq-BH00004 LIN54 N2 LTemb DevStageWorm:Late Embryos:JL:1 [ALL]
BH00004-LIN54 [ALL] / lin-54
N2 [ALL]
20 degree celsius [ALL]
embargo expired
BindingSite: 8734   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00004_LIN54_N2_LTemb_1_peaks.gff: 4096   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00004_LIN54_N2_LTemb_all_peaks.gff: 2476   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
seq-BH00004_LIN54_N2_LTemb_2_peaks.gff: 2162   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GEO: GSM830458
GEO: GSM830459


11 files Download data files