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GEO accession:
Sample GSM2191898
Query DataSets for GSM2191898
Status
Public on Jun 22, 2016
Title
ChIP-seq from neural tube (ENCLB434XIF)
Sample type
SRA
Source name
Mus musculus strain B6NCrl neural tube tissue mixed sex embryo (12.5 days)
Organism
Mus musculus
Characteristics
antibody: H3K4me3
tissue_type: neural tube
biomaterial_type: tissue
description: Neural tube from 88 embryonic 12.5 day mice
biosample encode accession: ENCBS254TSW (SAMN05202072)
age: 12.5 day
donor_id: ENCDO956IXV
dev stage: embryonic
Sex: pooled male and female
health state: healthy
lab: Len Pennacchio, LBNL
link: ENCBS254TSW at ENCODE;
https://www.encodeproject.org/ENCBS254TSW/
link: Derived from ENCODE donor ENCDO956IXV;
https://www.encodeproject.org/ENCDO956IXV/
link: excision protocol;
https://www.encodeproject.org/documents/631aa21c-8e48-467e-8cac-d40c875b3913/@@download/attachment/StandardTissueExcisionProtocol_02132017.pdf
Extracted molecule
genomic DNA
Extraction protocol
general protocol:
https://www.encodeproject.org/documents/89795b31-e65a-42ca-9d7b-d75196f6f4b3/@@download/attachment/Ren%20Lab%20ENCODE%20Chromatin%20Immunoprecipitation%20Protocol_V2.pdf
general protocol:
https://www.encodeproject.org/documents/4f73fbc3-956e-47ae-aa2d-41a7df552c81/@@download/attachment/Ren_ChIP_Library_Preparation_v060614.pdf
general protocol:
https://www.encodeproject.org/documents/3125496b-c833-4414-bf5f-84dd633eb30d/@@download/attachment/Ren_Tissue_Fixation_and_Sonication_v060614.pdf
Library strategy
ChIP-Seq
Library source
genomic
Library selection
ChIP
Instrument model
Illumina HiSeq 4000
Description
https://www.encodeproject.org/experiments/ENCSR538SRO/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 12.5 day mouse neural tube
experiment encode accession: ENCSR538SRO
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR991FSR
encode release date: 2016-03-30
lab: Bing Ren, UCSD
library encode accession: ENCLB434XIF
size range: 300-500
Data processing
See GSM*_README.txt supplementary file linked below
Submission date
Jun 07, 2016
Last update date
May 15, 2019
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
GPL21103
Series (1)
GSE82770
ChIP-seq from neural tube (ENCSR538SRO)
Relations
BioSample
SAMN05202072
SRA
SRX1833688
Named Annotation
GSM2191898_ENCFF316YDZ_signal_p-value_mm10.bigWig
Named Annotation
GSM2191898_ENCFF228QDZ_fold_change_over_control_mm10.bigWig
Named Annotation
GSM2191898_ENCFF684VFP_peaks_mm10.bed.gz
Supplementary file
Size
Download
File type/resource
GSM2191898_ENCFF228QDZ_fold_change_over_control_mm10.bigWig
525.6 Mb
(ftp)
(http)
BIGWIG
GSM2191898_ENCFF316YDZ_signal_p-value_mm10.bigWig
483.7 Mb
(ftp)
(http)
BIGWIG
GSM2191898_ENCFF375OAI_peaks_mm10.bigBed
1.8 Mb
(ftp)
(http)
BIGBED
GSM2191898_ENCFF684VFP_peaks_mm10.bed.gz
570.0 Kb
(ftp)
(http)
BED
GSM2191898_ENCLB434XIF_README.txt.gz
1.1 Kb
(ftp)
(http)
TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
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