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Sample GSM8108765

Query DataSets for GSM8108765

Status

Public on Feb 27, 2024

Title

TF ChIP-seq from whole organism (ENCLB430GMB)

Sample type

SRA

Source name

Caenorhabditis elegans strain OP404 (unc-119(tm4063) III; wgIs404) hermaphrodite young adult insertion targeting C. elegans nfya-1

Organism

Caenorhabditis elegans

Characteristics

antibody: nfya-1
cell_type: whole organism
biomaterial_type: whole organisms
biosample encode accession: ENCBS103WCK (SAMN40084446)
collection date: not applicable
geographic location: not applicable
encode accession: ENCBS103WCK
note: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to NFYA-1
Sex: hermaphrodite
dev stage: young adult
age: unknown
donor_id: ENCDO148DCX
lab: Valerie Reinke, Yale
source: Valerie Reinke
link: ENCBS103WCK at ENCODE; https://www.encodeproject.org/ENCBS103WCK/

Extracted molecule

genomic DNA

Extraction protocol

general protocol: https://www.encodeproject.org/documents/5de8421c-b074-44ed-985c-638d2bc4a0a3/@@download/attachment/Reinke_Lab_ModENCODE_ChIP_protocol_%28revised%205-24-13%29.pdf
general protocol: https://www.encodeproject.org/documents/e7ede93f-861a-4269-aba2-d0059ffb62b1/@@download/attachment/Stanford_sequencin_ChIP_Protocol_2012WN.pdf

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina Genome Analyzer IIx

Description

https://www.encodeproject.org/experiments/ENCSR581THE/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing NFYA-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR581THE
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR116BMC
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB430GMB
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)

[email protected]

Organization name

ENCODE DCC

Street address

300 Pasteur Dr

City

Stanford

State/province

ZIP/Postal code

94305-5120

Country

USA

Platform ID

GPL13776

Series (1)

GSE257876

TF ChIP-seq from whole organism (ENCSR581THE)

Relations

BioSample

SAMN40084446

Supplementary file	Size	Download	File type/resource
GSM8108765_ENCFF060DCB_control_normalized_signal_ce10.bigWig	9.8 Mb	(ftp)(http)	BIGWIG
GSM8108765_ENCFF236UWV_read-depth_normalized_signal_ce11.bigWig	9.6 Mb	(ftp)(http)	BIGWIG
GSM8108765_ENCFF365LDP_peaks_and_background_as_input_for_IDR_ce10.bed.gz	758.8 Kb	(ftp)(http)	BED
GSM8108765_ENCFF561BEB_control_normalized_signal_ce11.bigWig	9.8 Mb	(ftp)(http)	BIGWIG
GSM8108765_ENCFF668VDZ_signal_of_unique_reads_ce11.bigWig	9.6 Mb	(ftp)(http)	BIGWIG
GSM8108765_ENCFF672KJR_peaks_and_background_as_input_for_IDR_ce10.bigBed	1.2 Mb	(ftp)(http)	BIGBED
GSM8108765_ENCFF684PNP_signal_of_unique_reads_ce10.bigWig	9.6 Mb	(ftp)(http)	BIGWIG
GSM8108765_ENCFF812DIO_read-depth_normalized_signal_ce10.bigWig	9.6 Mb	(ftp)(http)	BIGWIG
GSM8108765_ENCFF878KEH_peaks_and_background_as_input_for_IDR_ce11.bed.gz	758.7 Kb	(ftp)(http)	BED
GSM8108765_ENCFF961PHB_peaks_and_background_as_input_for_IDR_ce11.bigBed	1.2 Mb	(ftp)(http)	BIGBED
GSM8108765_ENCLB430GMB_README.txt.gz	1.9 Kb	(ftp)(http)	TXT
Raw data are available in SRA