|
| Status |
Public on Feb 27, 2024 |
| Title |
TF ChIP-seq from whole organism (ENCLB028PZX) |
| Sample type |
SRA |
| |
|
| Source name |
Caenorhabditis elegans strain XIL99 mixed sex L1 larva at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans vab-15
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
antibody: vab-15
cell_type: whole organism
biomaterial_type: whole organisms
biosample encode accession: ENCBS096ZAK (SAMN40084436)
collection date: not applicable
geographic location: not applicable
encode accession: ENCBS096ZAK
note: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to VAB-15
Sex: pooled male and female
dev stage: L1 larva
age: unknown
donor_id: ENCDO003JWX
lab: Valerie Reinke, Yale
source: Valerie Reinke
worm synchronization stage: L1 larva starved after bleaching
link: ENCBS096ZAK at ENCODE; https://www.encodeproject.org/ENCBS096ZAK/
|
| 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
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
https://www.encodeproject.org/experiments/ENCSR757OPC/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing VAB-15-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR757OPC
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR569VQG
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB028PZX
fragmentation methods: sonication (generic microtip)
|
| Data processing |
See GSM*_README.txt supplementary file linked below
|
| |
|
| Submission date |
Feb 25, 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) |
| GSE258406 |
TF ChIP-seq from whole organism (ENCSR757OPC) |
|
| Relations |
| BioSample |
SAMN40084436 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8109720_ENCFF068TLV_control_normalized_signal_ce11.bigWig |
9.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM8109720_ENCFF147OLJ_peaks_and_background_as_input_for_IDR_ce10.bed.gz |
763.5 Kb |
(ftp)(http) |
BED |
| GSM8109720_ENCFF157HBL_signal_of_unique_reads_ce10.bigWig |
9.6 Mb |
(ftp)(http) |
BIGWIG |
| GSM8109720_ENCFF190WUZ_peaks_and_background_as_input_for_IDR_ce10.bigBed |
1.2 Mb |
(ftp)(http) |
BIGBED |
| GSM8109720_ENCFF287USQ_read-depth_normalized_signal_ce10.bigWig |
9.6 Mb |
(ftp)(http) |
BIGWIG |
| GSM8109720_ENCFF340KQJ_control_normalized_signal_ce10.bigWig |
9.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM8109720_ENCFF356BZQ_signal_of_unique_reads_ce11.bigWig |
9.6 Mb |
(ftp)(http) |
BIGWIG |
| GSM8109720_ENCFF723GPF_peaks_and_background_as_input_for_IDR_ce11.bigBed |
1.2 Mb |
(ftp)(http) |
BIGBED |
| GSM8109720_ENCFF726MFP_peaks_and_background_as_input_for_IDR_ce11.bed.gz |
763.1 Kb |
(ftp)(http) |
BED |
| GSM8109720_ENCFF849IAA_read-depth_normalized_signal_ce11.bigWig |
9.6 Mb |
(ftp)(http) |
BIGWIG |
| GSM8109720_ENCLB028PZX_README.txt.gz |
1.8 Kb |
(ftp)(http) |
TXT |
| Raw data are available in SRA |
