|
| Status |
Public on Feb 27, 2024 |
| Title |
TF ChIP-seq from whole organism (ENCLB935ENA) |
| Sample type |
SRA |
| |
|
| Source name |
Caenorhabditis elegans strain OP620 (unc-119(tm4063) III; wgIs620) mixed sex early embryo 2 hours post synchronization using egg bleaching insertion targeting C. elegans ceh-36
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
antibody: ceh-36
cell_type: whole organism
biomaterial_type: whole organisms
biosample encode accession: ENCBS447GRK (SAMN40085004)
collection date: not applicable
geographic location: not applicable
encode accession: ENCBS447GRK
note: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to CEH-36
Sex: pooled male and female
dev stage: early embryonic
age: unknown
donor_id: ENCDO327FAE
lab: Valerie Reinke, Yale
source: Valerie Reinke
worm synchronization stage: egg bleaching
post synchronization time: 2
post synchronization time units: hour
link: ENCBS447GRK at ENCODE; https://www.encodeproject.org/ENCBS447GRK/
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
general protocol: https://www.encodeproject.org/documents/d89f19f3-31f8-4079-9635-5d3dd799471e/@@download/attachment/Reinke_Lab_ModENCODE_ChIP_protocol_%28revised%205-24-13%29_4_mg.pdf
other: https://www.encodeproject.org/documents/3e96bc0d-447f-44e8-b63b-090a35158d63/@@download/attachment/2016-1081.pdf
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
https://www.encodeproject.org/experiments/ENCSR002FCO/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing CEH-36-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR002FCO
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR646YCH
encode release date: 2016-10-11
lab: Valerie Reinke, Yale
library encode accession: ENCLB935ENA
fragmentation methods: sonication (generic microtip)
|
| Data processing |
See GSM*_README.txt supplementary file linked below
|
| |
|
| Submission date |
Feb 24, 2024 |
| Last update date |
Feb 27, 2024 |
| Contact name |
ENCODE DCC |
| E-mail(s) |
encode-help@lists.stanford.edu
|
| Organization name |
ENCODE DCC
|
| Street address |
300 Pasteur Dr
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5120 |
| Country |
USA |
| |
|
| Platform ID |
GPL22765 |
| Series (1) |
| GSE256547 |
TF ChIP-seq from whole organism (ENCSR002FCO) |
|
| Relations |
| BioSample |
SAMN40085004 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8106130_ENCFF081BYG_read-depth_normalized_signal_ce11.bigWig |
9.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM8106130_ENCFF197MOO_peaks_and_background_as_input_for_IDR_ce10.bigBed |
1.2 Mb |
(ftp)(http) |
BIGBED |
| GSM8106130_ENCFF223ZKN_control_normalized_signal_ce11.bigWig |
9.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM8106130_ENCFF266MBI_peaks_and_background_as_input_for_IDR_ce11.bed.gz |
758.8 Kb |
(ftp)(http) |
BED |
| GSM8106130_ENCFF283TPC_peaks_and_background_as_input_for_IDR_ce10.bed.gz |
759.0 Kb |
(ftp)(http) |
BED |
| GSM8106130_ENCFF305BBV_signal_of_unique_reads_ce11.bigWig |
9.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM8106130_ENCFF387YGZ_read-depth_normalized_signal_ce10.bigWig |
9.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM8106130_ENCFF524YWJ_signal_of_unique_reads_ce10.bigWig |
9.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM8106130_ENCFF761GYM_control_normalized_signal_ce10.bigWig |
9.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM8106130_ENCFF898PZY_peaks_and_background_as_input_for_IDR_ce11.bigBed |
1.2 Mb |
(ftp)(http) |
BIGBED |
| GSM8106130_ENCLB935ENA_README.txt.gz |
1.8 Kb |
(ftp)(http) |
TXT |
| Raw data are available in SRA |
