title: small RNA-seq from stomach (ENCLB209IBX)

description:
https://www.encodeproject.org/experiments/ENCSR418FVT/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's stomach tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR418FVT
assay title: small RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB209IBX
size range: <200

source_name: Homo sapiens stomach tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4afa9195-47e5-42cc-bd4f-1c24facea87e/@@download/attachment/LID296624.pdf

value: stomach

value: Stomach aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: male

value: ENCBS085LTC at ENCODE; https://www.encodeproject.org/ENCBS085LTC/


title: small RNA-seq from esophagus muscularis mucosa (ENCLB368NKG)

status: Public on Nov 08 2016

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR383PLJ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a53 year old female's muscle layer of esophagus tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR383PLJ
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB368NKG
size range: <200

library_source: transcriptomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens esophagus muscularis mucosa tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bb82ca5f-e871-43e6-9336-d81f9979adf9/@@download/attachment/LID296592.pdf

value: esophagus muscularis mucosa

value: tissue

tag: description

value: Esophagus muscle layer tissue sent from GTEx to the Gingeras lab to conduct RNA-Seq assays on.

tag: biosample encode accession

tag: age

value: 53 year

tag: dev stage

value: adult

tag: Sex

value: female

tag: lab

value: Thomas Gingeras, CSHL

tag: link

value: ENCBS571LWZ at ENCODE; https://www.encodeproject.org/ENCBS571LWZ/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: small RNA-seq from right lobe of liver (ENCLB238JDJ)

description:
https://www.encodeproject.org/experiments/ENCSR634VLA/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's right lobe of liver tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR634VLA
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB238JDJ
size range: <200

source_name: Homo sapiens right lobe of liver tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5e0eb362-deb7-46c1-900d-79db2c8f460a/@@download/attachment/LID296634.pdf

value: right lobe of liver

value: Liver tissue from a 53 year old female received by the Gingeras lab to do RNA-Seq assay on from GTEx.

value: ENCBS773RMK at ENCODE; https://www.encodeproject.org/ENCBS773RMK/


title: small RNA-seq from uterus (ENCLB871CON)

description:
https://www.encodeproject.org/experiments/ENCSR887HNW/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's uterus tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR887HNW
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB871CON
size range: <200

source_name: Homo sapiens uterus tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b7eaeeaa-38a6-44f9-bb0c-a1c0411f42f9/@@download/attachment/LID296658.pdf

value: uterus

value: Uterus aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 51 year

value: ENCBS887WTT at ENCODE; https://www.encodeproject.org/ENCBS887WTT/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: small RNA-seq from spleen (ENCLB436NOU)

description:
https://www.encodeproject.org/experiments/ENCSR593MVW/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's spleen tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR593MVW
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB436NOU
size range: <200

source_name: Homo sapiens spleen tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0aa9a0a9-adc2-48ff-b541-d6dfabf60c6a/@@download/attachment/LID296623.pdf

value: spleen

value: Spleen tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: ENCBS253SDK at ENCODE; https://www.encodeproject.org/ENCBS253SDK/


title: small RNA-seq from esophagus squamous epithelium (ENCLB348RNP)

description:
https://www.encodeproject.org/experiments/ENCSR289GGY/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's esophagus mucosa tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR289GGY
assay title: small RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB348RNP
size range: <200

source_name: Homo sapiens esophagus squamous epithelium tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/85256c4d-28b7-4bbc-b523-4316afb60d7b/@@download/attachment/LID296582.pdf

value: esophagus squamous epithelium

value: tissue

value: Esophagus mucosa tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: male

value: 37 year

value: ENCBS903FMK at ENCODE; https://www.encodeproject.org/ENCBS903FMK/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: small RNA-seq from esophagus muscularis mucosa (ENCLB871TQM)

description:
https://www.encodeproject.org/experiments/ENCSR295NAK/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's muscle layer of esophagus tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR295NAK
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB871TQM
size range: <200

source_name: Homo sapiens esophagus muscularis mucosa tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/fdadd1c8-8347-4e95-9141-b617cd01ea03/@@download/attachment/LID296593.pdf

value: esophagus muscularis mucosa

value: Esophagus muscle layer tissue sent from GTEx to the Gingeras lab to conduct RNA-Seq assays on.

value: adult

value: female

value: Thomas Gingeras, CSHL

value: ENCBS072KNR at ENCODE; https://www.encodeproject.org/ENCBS072KNR/


title: small RNA-seq from thyroid gland (ENCLB489WBR)

description:
https://www.encodeproject.org/experiments/ENCSR359CVC/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's thyroid gland tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR359CVC
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB489WBR
size range: <200

source_name: Homo sapiens thyroid gland tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/30bc992f-d065-4304-bc12-925421227005/@@download/attachment/LID296657.pdf

value: thyroid gland

value: Thyroid aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 53 year

value: ENCBS207DLU at ENCODE; https://www.encodeproject.org/ENCBS207DLU/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: small RNA-seq from prostate gland (ENCLB311TNO)

description:
https://www.encodeproject.org/experiments/ENCSR332RHR/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's prostate tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR332RHR
assay title: small RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB311TNO
size range: <200

source_name: Homo sapiens prostate gland tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f6bc4db5-b03f-4bf2-afeb-473842846053/@@download/attachment/LID296598.pdf

value: prostate gland

value: tissue

value: Prostate aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 54 year

value: ENCBS291PVP at ENCODE; https://www.encodeproject.org/ENCBS291PVP/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: small RNA-seq from gastroesophageal sphincter (ENCLB318FPY)

description:
https://www.encodeproject.org/experiments/ENCSR269YSX/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's esophagogastric junction tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR269YSX
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB318FPY
size range: <200

source_name: Homo sapiens gastroesophageal sphincter tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d946ce6f-ceec-425d-b40e-eefa33229a73/@@download/attachment/LID296541.pdf

value: gastroesophageal sphincter

value: Esophagogastric junction tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: male

value: ENCBS812ZNH at ENCODE; https://www.encodeproject.org/ENCBS812ZNH/


title: small RNA-seq from transverse colon (ENCLB893QNR)

description:
https://www.encodeproject.org/experiments/ENCSR316SXP/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's transverse colon tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR316SXP
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB893QNR
size range: <200

source_name: Homo sapiens transverse colon tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bc53c642-4cbf-4712-8a6a-12c06af54a6c/@@download/attachment/LID296537.pdf

value: transverse colon

value: Transverse colon tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: adult

value: female

value: Thomas Gingeras, CSHL

value: ENCBS974EYF at ENCODE; https://www.encodeproject.org/ENCBS974EYF/


title: small RNA-seq from tibial nerve (ENCLB057AMZ)

description:
https://www.encodeproject.org/experiments/ENCSR203DPX/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's tibial nerve tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR203DPX
assay title: small RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB057AMZ
size range: <200

source_name: Homo sapiens tibial nerve tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ca708a37-45ff-4cae-84d6-ed437fe9e454/@@download/attachment/LID296654.pdf

value: tibial nerve

value: Tibial nerve tissue from received by the Gingeras lab to do RNA-Seq assay on from GTEx.

value: 37 year

value: ENCBS986CBC at ENCODE; https://www.encodeproject.org/ENCBS986CBC/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: small RNA-seq from esophagus squamous epithelium (ENCLB970AQH)

description:
https://www.encodeproject.org/experiments/ENCSR262TBN/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's esophagus mucosa tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR262TBN
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB970AQH
size range: <200

source_name: Homo sapiens esophagus squamous epithelium tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/da57a293-e16e-4b6b-b464-a97b9e70e106/@@download/attachment/LID296583.pdf

value: esophagus squamous epithelium

value: tissue

value: Esophagus mucosa tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 54 year

value: ENCBS740AHU at ENCODE; https://www.encodeproject.org/ENCBS740AHU/


title: small RNA-seq from transverse colon (ENCLB351JFP)

description:
https://www.encodeproject.org/experiments/ENCSR183YQY/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's transverse colon tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR183YQY
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB351JFP
size range: <200

source_name: Homo sapiens transverse colon tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5d23182c-9da3-4335-939f-eb3b6be19918/@@download/attachment/LID296538.pdf

value: 51 year

value: ENCBS999VTF at ENCODE; https://www.encodeproject.org/ENCBS999VTF/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: small RNA-seq from transverse colon (ENCLB365GID)

description:
https://www.encodeproject.org/experiments/ENCSR525WFB/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's transverse colon tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR525WFB
assay title: small RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-06-13
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB365GID
size range: <200

source_name: Homo sapiens transverse colon tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/43a1c88e-b724-4599-8626-182c4556b345/@@download/attachment/LID296535.pdf

value: transverse colon

value: Transverse colon tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: adult

value: male

value: ENCBS767MGS at ENCODE; https://www.encodeproject.org/ENCBS767MGS/


title: small RNA-seq from stomach (ENCLB898TCC)

description:
https://www.encodeproject.org/experiments/ENCSR133GQJ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's stomach tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR133GQJ
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB898TCC
size range: <200

source_name: Homo sapiens stomach tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/3e794044-654d-4100-bab1-d0875dbefdb5/@@download/attachment/LID296625.pdf

value: stomach

value: Stomach aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: Thomas Gingeras, CSHL

value: ENCBS141UOA at ENCODE; https://www.encodeproject.org/ENCBS141UOA/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: small RNA-seq from Peyer's patch (ENCLB439POH)

description:
https://www.encodeproject.org/experiments/ENCSR091JNF/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's ileum tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR091JNF
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB439POH
size range: <200

source_name: Homo sapiens Peyer's patch tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6e0d2664-8993-44c1-b4db-e94cdc7309e3/@@download/attachment/LID296640.pdf

value: Peyer's patch

value: tissue

value: Small intestine aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: ENCBS943XLR at ENCODE; https://www.encodeproject.org/ENCBS943XLR/


title: small RNA-seq from body of pancreas (ENCLB244ENT)

description:
https://www.encodeproject.org/experiments/ENCSR099ACU/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's pancreas tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR099ACU
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB244ENT
size range: <200

source_name: Homo sapiens body of pancreas tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/210a7948-4214-4027-aa70-8cc54787df44/@@download/attachment/LID296596.pdf

value: body of pancreas

value: Pancreas tissue from received by the Gingeras lab to do RNA-Seq assay on from GTEx.

value: 51 year

value: female

value: ENCBS389HVX at ENCODE; https://www.encodeproject.org/ENCBS389HVX/


title: small RNA-seq from ovary (ENCLB343BMC)

description:
https://www.encodeproject.org/experiments/ENCSR024CRN/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's female gonad tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR024CRN
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB343BMC
size range: <200

source_name: Homo sapiens ovary tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/885e7356-7956-4fa4-935a-14dea5f2603a/@@download/attachment/LID296594.pdf

value: ovary

value: Ovary tissue from received by the Gingeras lab to do RNA-Seq assay on from GTEx.

value: adult

value: ENCBS711CPB at ENCODE; https://www.encodeproject.org/ENCBS711CPB/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: small RNA-seq from transverse colon (ENCLB474RLW)

description:
https://www.encodeproject.org/experiments/ENCSR168XPO/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's transverse colon tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR168XPO
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB474RLW
size range: <200

source_name: Homo sapiens transverse colon tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ee514e27-e90d-46ed-81f2-0fbddb4dab8e/@@download/attachment/LID296536.pdf

value: transverse colon

value: Transverse colon tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 54 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS668MJW at ENCODE; https://www.encodeproject.org/ENCBS668MJW/


title: small RNA-seq from body of pancreas (ENCLB874RRJ)

description:
https://www.encodeproject.org/experiments/ENCSR033TKS/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's pancreas tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR033TKS
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB874RRJ
size range: <200

source_name: Homo sapiens body of pancreas tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bd70917a-292b-46b9-8da3-d0cec697e2d6/@@download/attachment/LID296595.pdf

value: tissue

value: 53 year

value: ENCBS273XDV at ENCODE; https://www.encodeproject.org/ENCBS273XDV/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: small RNA-seq from esophagus muscularis mucosa (ENCLB748FXR)

description:
https://www.encodeproject.org/experiments/ENCSR233DGJ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's muscle layer of esophagus tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR233DGJ
assay title: small RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB748FXR
size range: <200

source_name: Homo sapiens esophagus muscularis mucosa tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ce8e4e48-823c-4184-84b9-5abea4d36b6a/@@download/attachment/LID296591.pdf

value: esophagus muscularis mucosa

value: Esophagus muscle layer tissue sent from GTEx to the Gingeras lab to conduct RNA-Seq assays on.

value: 37 year

value: ENCBS146EHL at ENCODE; https://www.encodeproject.org/ENCBS146EHL/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: small RNA-seq from testis (ENCLB448AOX)

description:
https://www.encodeproject.org/experiments/ENCSR229WIW/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's testis tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR229WIW
assay title: small RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB448AOX
size range: <200

source_name: Homo sapiens testis tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a962818e-9d39-4af0-a6f4-a25d5c30f7b4/@@download/attachment/LID296655.pdf

value: testis

value: Testis aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: adult

value: ENCBS315DHM at ENCODE; https://www.encodeproject.org/ENCBS315DHM/


title: total RNA-seq from erythroblast (ENCLB722VLH)

description:
https://www.encodeproject.org/experiments/ENCSR661TLW/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse Erythroblast 1 ng RNA-seq
experiment encode accession: ENCSR661TLW
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-21
lab: Ross Hardison, PennState
library encode accession: ENCLB722VLH
size range: 150-400
spikeins used: /references/ENCSR156CIL/, /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: ng

organism: Mus musculus

source_name: Mus musculus strain C57BL/6J erythroblast primary cell male adult (5-6 weeks)

value: erythroblast

value: primary cell

value: 5-6 week

tag: health state

value: unknown

value: Ross Hardison, PennState

value: ENCBS666WMI at ENCODE; https://www.encodeproject.org/ENCBS666WMI/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: small RNA-seq from subcutaneous adipose tissue (ENCLB932BGK)

description:
https://www.encodeproject.org/experiments/ENCSR020VES/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's adipose tissue tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR020VES
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB932BGK
size range: <200

source_name: Homo sapiens subcutaneous adipose tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/1d85c771-8f6d-40fe-ab5d-11994b9b9a68/@@download/attachment/LID296578.pdf

value: subcutaneous adipose tissue

value: tissue

value: Subcutaneous adipose tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 53 year

value: female

value: Thomas Gingeras, CSHL

value: ENCBS280PMM at ENCODE; https://www.encodeproject.org/ENCBS280PMM/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: single cell RNA-seq from Purkinje cell (ENCLB174HTP)

description:
https://www.encodeproject.org/experiments/ENCSR805QYO/
***************
biological replicate number: 2
technical replicate number: 1
description: LCMD-501,502_Mm_Castaneus_x_C57Bl-Purkinje-30-pool
experiment encode accession: ENCSR805QYO
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB174HTP
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 30.0
nucleic acid starting quantity units: cells
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Mus musculus strain B6CASTF1/J Purkinje primary cell male adult (14 months)

tag: antibody

value: Control

value: Purkinje cell

value: adult

value: male

value: 14 month

value: Barbara Wold, Caltech

value: ENCBS514SCS at ENCODE; https://www.encodeproject.org/ENCBS514SCS/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: total RNA-seq from erythroblast (ENCLB500PHK)

description:
https://www.encodeproject.org/experiments/ENCSR661TLW/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse Erythroblast 1 ng RNA-seq
experiment encode accession: ENCSR661TLW
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-21
lab: Ross Hardison, PennState
library encode accession: ENCLB500PHK
size range: 150-400
spikeins used: /references/ENCSR156CIL/, /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: ng

value: erythroblast

value: primary cell

value: 5-6 week

value: unknown

value: Ross Hardison, PennState

value: ENCBS129OMN at ENCODE; https://www.encodeproject.org/ENCBS129OMN/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: total RNA-seq from erythroid progenitor cell (ENCLB265JPE)

description:
https://www.encodeproject.org/experiments/ENCSR558PXY/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse erythroid progenitor cell (CFU-Ery) 1 ng RNA-seq
experiment encode accession: ENCSR558PXY
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-21
lab: Ross Hardison, PennState
library encode accession: ENCLB265JPE
size range: 150-400
spikeins used: /references/ENCSR156CIL/, /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: ng

source_name: Mus musculus strain C57BL/6J erythroid progenitor primary cell male adult (5-6 weeks)

value: erythroid progenitor cell

value: ENCBS949PKO at ENCODE; https://www.encodeproject.org/ENCBS949PKO/


title: single cell RNA-seq from cerebellar granule layer (ENCLB021ACJ)

description:
https://www.encodeproject.org/experiments/ENCSR822EWO/
***************
biological replicate number: 1
technical replicate number: 1
description: LCMD-503,504_Mm_Castaneus_x_C57Bl-granule-layer-area-dissection
experiment encode accession: ENCSR822EWO
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB021ACJ
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 30.0
nucleic acid starting quantity units: cell-equivalent
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Mus musculus strain B6CASTF1/J cerebellar granule layer tissue male adult (14 months)

value: Control

value: cerebellar granule layer

value: tissue

value: LCMD-503_Mm_Castaneus_x_C57Bl-granule-layer 30 cell equivalent

value: ENCBS497KQR at ENCODE; https://www.encodeproject.org/ENCBS497KQR/


title: total RNA-seq from megakaryocyte progenitor cell (ENCLB073TQT)

description:
https://www.encodeproject.org/experiments/ENCSR848LXY/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse megakaryocyte progenitor cell (CFU-Meg) 1 ng RNA-seq
experiment encode accession: ENCSR848LXY
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-21
lab: Ross Hardison, PennState
library encode accession: ENCLB073TQT
size range: 149-512
spikeins used: /references/ENCSR156CIL/, /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: ng

source_name: Mus musculus strain C57BL/6J megakaryocyte progenitor primary cell male adult (5-6 weeks)

value: megakaryocyte progenitor cell

value: adult

value: male

value: ENCBS869LMD at ENCODE; https://www.encodeproject.org/ENCBS869LMD/


title: small RNA-seq from prostate gland (ENCLB311PVN)

description:
https://www.encodeproject.org/experiments/ENCSR227FNZ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's prostate tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR227FNZ
assay title: small RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB311PVN
size range: <200

source_name: Homo sapiens prostate gland tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/9e5e14cd-27f4-4fc9-85ca-bf5ae49f6330/@@download/attachment/LID296597.pdf

value: prostate gland

value: Prostate aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 37 year

value: Thomas Gingeras, CSHL

value: ENCBS656EUB at ENCODE; https://www.encodeproject.org/ENCBS656EUB/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: total RNA-seq from megakaryocyte (ENCLB787ATZ)

description:
https://www.encodeproject.org/experiments/ENCSR340NCF/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse Megakaryocyte 1 ng RNA-seq
experiment encode accession: ENCSR340NCF
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-21
lab: Ross Hardison, PennState
library encode accession: ENCLB787ATZ
size range: 151-499
spikeins used: /references/ENCSR156CIL/, /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: ng

source_name: Mus musculus strain C57BL/6J megakaryocyte primary cell male adult (5-6 weeks)

value: megakaryocyte

value: primary cell

value: 5-6 week

value: unknown

value: Ross Hardison, PennState

value: ENCBS576MDX at ENCODE; https://www.encodeproject.org/ENCBS576MDX/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: total RNA-seq from megakaryocyte (ENCLB436FJW)

description:
https://www.encodeproject.org/experiments/ENCSR340NCF/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse Megakaryocyte 1 ng RNA-seq
experiment encode accession: ENCSR340NCF
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-21
lab: Ross Hardison, PennState
library encode accession: ENCLB436FJW
size range: 153-499
spikeins used: /references/ENCSR156CIL/, /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: ng

value: ENCBS593JCW at ENCODE; https://www.encodeproject.org/ENCBS593JCW/


title: 2-day fasting rep2

city: Dallas

first: Alec

last: Zhang

state: Texas

address: 5901 Forest Park Rd

department: Physiology

institute: UT Southwestern Medical Center

data_processing:
Before mapping, reads were trimmed to remove low-quality regions in the ends.
Trimmed reads were mapped to the mouse genome (mm10) using TopHat v2.0.1227 with the UCSC iGenomes GTF file from Illumina.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

source_name: B-Acute-Lymphoblastic-Leukemia cells

extract_protocol:
Mice bone marrow cell were collected and stained with B220-PE antibody (eBioscience), and GFP+B220+ cells were colleted by flow cytometry. RNA was purified from sorted cells with Qiagen RNeasy Mini Kit and then reverse-transcribed with SuperScript III Reverse Transcriptase (Invitrogen) according to the manufacturer’s instruction.
The cDNA was sonicated using the Covaris S2 ultrasonicator, and libraries were prepared with the KAPA High Throughput Library Preparation Kit. Samples were end-repaired, 3’ ends adenylated and barcoded with multiplex adapters. PCR-amplified libraries were purified with AmpureXP beads, and validated on the Agilent 2100 Bioanalyzer. Before being normalized and pooled, samples were quantified by Qubit (Invitrogen) and then run on a Illumina Hiseq 2500 using PE100 SBS v3 reagents to generate 51-bp single-end reads.

treatment_protocol: Mice were transplanted N-Myc / GFP-reproter expressed lineage negative  (Lin-) fetal live cells to initiate B-ALL development. At the middle stage of B-ALL development when GFP+% in PB reached about 60%, the B-ALL mice were fasted 1-day or 2-days. GFP+B220+ B-ALL cells from 1-day, 2-day fasted mice and control mice were collected by flow cytometry for RNA-seq analysis.

tag: tissue

value: Bone marrow

tag: treatment

value: 2-day fasted

tag: cell type

value: GFP+B220+ B-ALL cells

tag: strain


title: 2-day fasting rep1


title: total RNA-seq from megakaryocyte progenitor cell (ENCLB556JLH)

description:
https://www.encodeproject.org/experiments/ENCSR848LXY/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse megakaryocyte progenitor cell (CFU-Meg) 1 ng RNA-seq
experiment encode accession: ENCSR848LXY
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-21
lab: Ross Hardison, PennState
library encode accession: ENCLB556JLH
size range: 157-497
spikeins used: /references/ENCSR156CIL/, /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: ng

value: megakaryocyte progenitor cell

value: adult

value: male

value: ENCBS679HXW at ENCODE; https://www.encodeproject.org/ENCBS679HXW/


title: WT.LPS01

city: Amsterdam

first: Benjamin

last: Nota

state: Noord Holland

address: Plesmanlaan 125

department: Research Facilities

country: Netherlands

institute: Sanquin

data_processing:
Demultiplexing using Narwhal
Alignment against mm10 using Tophat version 2.0.8
For all 23,420 UCSC mm10 annotated genes the reads were counted that aligned to the exonic regions using "featureCounts" from Subread (version 1.4.3)
Only the genes with at least 1 count per million reads in at least three samples were kept for analysis in edgeR (version 3.6.8)
Significanlty differentially expressed genes were assessed in edgeR (FDR adj. P-values < 0.05)
RPKM values were calculated in edgeR for hierarchical clustering and heat maps
Genome_build: mm10
Supplementary_files_format_and_content: Raw read counts for all genes and samples

source_name: Dendritic cells

extract_protocol:
RNeasy-plus mini kit (Qiagen)
TruSeq RNA sample prep kit v2 (Illumina)

tag: genotype

value: Gata1 wild-type

value: LPS stimulated

value: dendritic cell


title: KO.LPS02

value: Gata1 knock-out


title: KO.LPS01


title: WT.LPS02


title: WT.ST01

value: Steady state


title: KO.ST02


title: 1-day fasting rep2

value: 1-day fasted


title: small RNA-seq from stomach (ENCLB762MHD)

description:
https://www.encodeproject.org/experiments/ENCSR003SZJ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's stomach tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR003SZJ
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB762MHD
size range: <200

source_name: Homo sapiens stomach tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/de21a597-ed78-43be-8523-45fb910a9005/@@download/attachment/LID296626.pdf

value: stomach

value: tissue

value: Stomach aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 53 year

value: female

value: Thomas Gingeras, CSHL

value: ENCBS607DWD at ENCODE; https://www.encodeproject.org/ENCBS607DWD/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: KO.ST01


title: 1-day fasting rep1

value: Bone marrow

value: GFP+B220+ B-ALL cells


title: Control rep2

value: Normal fed


title: Control rep1


title: WT.ST02

value: Gata1 wild-type


title: C57Bl6 Hb9::GFP MEFS day 2 (FBS) 2

city: Los Angeles

first: Justin

last: Ichida

address: 1425 San Pablo St. Bcc 307

institute: University of Southern California

description: mouse embryonic fibroblasts from E13.5 embryos

data_processing:
Reference files of the murine genome build mm10, as well as Ensembl transcript annotations, were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn). Reads were aligned to the genome using the split read aligner TopHat (v.2.0.7) and Bowtie2 (v.2.0.5) using default parameters as previously described by 14. Transcript assembly, isoform-specific quantitation and differential expression analysis was performed using Cufflinks (v.2.1.1) 14. A genome-wide corrected false discovery rate (FDR) of less than 0.05 was considered significant. Computations were performed on the Odyssey cluster supported by the FAS Science Division Research Computing Group at Harvard University.
Genome_build: Reference files of the murine genome build mm10, as well as Ensembl transcript annotations, were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn).
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

molecule: polyA RNA

source_name: mouse embryonic fibroblasts

growth_protocol: Spinal motor neurons were cultured in N3 medium, pluripotent stem cells were cultured in mouse ESC medium using 15% Hyclone FBS, and MEFs were grown in DMEM + 10% FBS or in N3 medium

extract_protocol:
RNA was extracted using Trizol LS (Life Technologies) according to the manufacturer's instructions
Illumina RNA TruSeq
RNA seq - RNA-seq libraries were generated from 100-250 ng total RNA using the Illumina TruSeq RNA kit v.2, according to the manufacturers’ directions. Libraries were sequenced at the Broad Institute’s Genomics Platform on a HiSeq 2500. A total of 20–60 million 100 bp, paired end reads were obtained for each sample.

treatment_protocol: MEFs were converted into motor neurons by retroviral transduction with vectors encoding Ascl1, Myt1l, Brn2, Lhx3, Isl1, Ngn2, and Hb9. Pluripotent stem cells were differentiated into spinal motor neurons by treatment with retinoic acid (.1 uM) and smoothened agonist (1 uM) starting at day 3 after EB formation


title: RD_fibers_4h_2_CAGGAG

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: single end protocol (R2 contain UMI of size 8 moved to fastq header):  Fastq files contain data for alignment only on read 1.  Sequencing used a short read on read 2, this read contain: 1) Sample barcodes 2) random sequence which we call UMI. Those 15 nucleotides were extracted from read 2 and concatenated to the fastq header of read 1.

data_processing:
Illumina bcl2fastq software used for basecalling.
alignment: TopHat with default parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8) from R2 file.
The raw expression levels of the genes were calculated using counts obtained using the ESAT program (http://garberlab.umassmed.edu/software/esat/)
Normalization was done using DESeq
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text file includes mRNA molecule count values for each Sample

organism: Rattus norvegicus

growth_protocol: Rat -1 fibroblasts were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen) supplemented with 2 mM L-glutamine, 1% Penicillin/Streptomycin (Invitrogen) and 10% fetal bovine serum (FBS).

extract_protocol:
Cells adhering to native or degraded ECMs were directly lysed in the presence of QIAzol and total RNA was extracted with the miRNeasy Mini Kit (Qiagen). The RNA integrity number (RIN) was determined using the TapeStation System (Agilent Technologies). Quantity of RNA was determined by Qubit Fluorometric Quantitation kit (Life Technologies).
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science
3' RNA-seq for digital gene expression quantitation

treatment_protocol: Rat-1 fibroblasts were seeded (25000 cells per well) in duplicates and incubated for 4 h  at 37°C and 5% CO2. The cells adhering to ECM were extracted and used for mRNA profiling.

tag: cell line

value: fibroblast


title: C57Bl6 Hb9::GFP MEFs day 2 (FBS) 1


title: RD_fibers_4h_1_CATAGC


title: RD_fibersMMP1_4h_2_ATTATG


title: Hb9::GFP Bl6 MEF FBS medium, passaged once, harvested day 15 1


title: Hb9::GFP Bl6 MEF N3 neuronal serum-free medium, not passaged, harvested day 15 2


title: Hb9::GFP Bl6 MEF N3 neuronal serum-free medium, not passaged, harvested day 15 1


title: Hb9::GFP Bl6 MEF FBS medium, passaged once, harvested day 15 2


title: RD_fibersMMP1_4h_1_TGTCGG


title: RD_fibersMMP13_4h_2_TACTTA


title: Hb9::GFP Bl6 iPSC OKS rep1

description: mouse iPSCs

source_name: mouse iPSCs


title: total RNA-seq from erythroid progenitor cell (ENCLB672PSC)

description:
https://www.encodeproject.org/experiments/ENCSR558PXY/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse erythroid progenitor cell (CFU-Ery) 1 ng RNA-seq
experiment encode accession: ENCSR558PXY
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-21
lab: Ross Hardison, PennState
library encode accession: ENCLB672PSC
size range: 150-400
spikeins used: /references/ENCSR156CIL/, /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: ng

value: erythroid progenitor cell

value: primary cell

value: adult

value: male

value: 5-6 week

value: unknown

value: Ross Hardison, PennState

value: ENCBS512FEW at ENCODE; https://www.encodeproject.org/ENCBS512FEW/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: Hb9::GFP Bl6 MEF FBS medium, not passaged, harvested day 15 2


title: RD_fibersMMP13_4h_1_CCTACC


title: Hb9::GFP Bl6 MEF FBS medium, not passaged, harvested day 15 1


title: Hb9::GFP Bl6 iPSC OKS rep2

description: mouse iPSCs


title: small RNA-seq from adrenal gland (ENCLB778BLV)

description:
https://www.encodeproject.org/experiments/ENCSR264COY/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's adrenal gland tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR264COY
assay title: small RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB778BLV
size range: <200

source_name: Homo sapiens adrenal gland tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/22e39578-a251-4a80-af57-746ba95a13d2/@@download/attachment/LID296580.pdf

value: adrenal gland

value: tissue

value: Adrenal gland aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 53 year

value: female

value: Thomas Gingeras, CSHL

value: ENCBS006KAW at ENCODE; https://www.encodeproject.org/ENCBS006KAW/


title: GFP+ 7F iMN day 14 12-20-11

description: spinal motor neurons derived from MEFs by lineage conversion

source_name: mouse induced motor neurons


title: Hb9::GFP Bl6 iMN 7F d15 9-24-12


title: C57Bl6 Hb9::GFP iMNs day 15 2, sorted (not stringent FACS gating)


title: C57Bl6 Hb9::GFP miPSC-MNs day 7 2, sorted

description: spinal motor neurons derived from mouse iPSCs by directed differentiation

source_name: mouse iPSC-derived motor neurons


title: Hb9::GFP Bl6 mESC rep1

description: mouse ESCS

source_name: mouse embryonic stem cells


title: C57Bl6 Hb9::GFP miPSC-MNs day 7 1, sorted


title: GFP+ mES MN sorted 9-1-11

description: spinal motor neurons derived from mouse ESCs by directed differentiation

source_name: mouse ESC-derived motor neurons


title: total RNA-seq from limb (ENCLB682KXD)

description:
https://www.encodeproject.org/experiments/ENCSR968QHO/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-seq on 10ng of embryonic 10.5 day mouse limb
experiment encode accession: ENCSR968QHO
assay title: total RNA-seq
assembly: mm10
encode release date: 2016-08-11
lab: Barbara Wold, Caltech
library encode accession: ENCLB682KXD
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (10.5 days)

value: limb

value: Limb from 51 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS892NXC at ENCODE; https://www.encodeproject.org/ENCBS892NXC/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: total RNA-seq from hindbrain (ENCLB554ZAM)

description:
https://www.encodeproject.org/experiments/ENCSR943LKA/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-seq on 10ng of embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR943LKA
assay title: total RNA-seq
assembly: mm10
encode release date: 2016-08-11
lab: Barbara Wold, Caltech
library encode accession: ENCLB554ZAM
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex embryo (10.5 days)

value: hindbrain

value: Hindbrain from 69 embryonic 10.5 day mice

value: ENCBS626UIA at ENCODE; https://www.encodeproject.org/ENCBS626UIA/


title: C57Bl6 Hb9::GFP mESC-MNs day 7 2, sorted


title: GFP+ d13.5 m Embryonic MN 12-6-11

description: spinal motor neurons harvested from E13.5 embryos

source_name: mouse embryonic motor neurons


title: single cell RNA-seq from cerebellar granule layer (ENCLB646JVH)

description:
https://www.encodeproject.org/experiments/ENCSR822EWO/
***************
biological replicate number: 2
technical replicate number: 1
description: LCMD-503,504_Mm_Castaneus_x_C57Bl-granule-layer-area-dissection
experiment encode accession: ENCSR822EWO
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB646JVH
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 30.0
nucleic acid starting quantity units: cell-equivalent
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Mus musculus strain B6CASTF1/J cerebellar granule layer tissue male adult (14 months)

value: Control

value: cerebellar granule layer

value: tissue

value: LCMD-504_Mm_Castaneus_x_C57Bl-granule-layer 30 cell equivalent

value: adult

value: male

value: 14 month

value: Barbara Wold, Caltech

value: ENCBS616ZXC at ENCODE; https://www.encodeproject.org/ENCBS616ZXC/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: total RNA-seq from embryonic facial prominence (ENCLB247JXW)

description:
https://www.encodeproject.org/experiments/ENCSR809VYL/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-seq on 10ng of embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR809VYL
assay title: total RNA-seq
assembly: mm10
encode release date: 2016-08-11
lab: Barbara Wold, Caltech
library encode accession: ENCLB247JXW
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (10.5 days)

value: embryonic facial prominence

value: Craniofacial prominence from 51 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: ENCBS199YOQ at ENCODE; https://www.encodeproject.org/ENCBS199YOQ/


title: Set 4 ShTon_NaCl

city: Philadelphia

first: Makarand

last: Risbud

state: PA

address: 1015 Walnut St.

department: Orthopaedic Surgery

institute: Thomas Jefferson University

data_processing:
Rn5 ensembl annotations (build 75 were downloaded and converted to genePred format.  Splice junction sequences were generated using USeq’s (v8.8.8 MakeTranscriptome application using a radius of 46.  These splice junction sequences were added to the rn5 chromosome sequences and run through novoindex (v2.8 to create the transcriptome index
Reads were aligned to the transcriptome reference index described above using Novoalign (v2.08.01, allowing up to 50 alignments for each read.  USeq’s SamTranscriptomeParser application was used to select the best alignment for each read and convert the coordinates of reads aligning to splices back to genomic space.
Read counts for each gene were generated using USeq’s DefinedRegionDifferentialSeq application.  These counts were used in DESeq2 (v1.10.1 to measure the differential expression between each condition, controlling for sample preparation batch.
Genome_build: Rn5
Supplementary_files_format_and_content: file containing DESeq2 normalized counts, DESeq2 log2 fold changes and DESeq2 FDR values

source_name: Rat nucleus pulposus

growth_protocol: Primary rat nucleus pulposus (NP cells were grown in explant cultures, expanded, and maintained in DMEM with 10% FBS and antibiotics

extract_protocol:
Total DNA-free RNA was extracted using RNeasy mini columns (Qiagen
Sequencing libraries (25 pM were chemically denatured and applied to an Illumina HiSeq v4 single read flow cell using an Illumina cBot.  Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR Cluster Kit v4-cBot (GD-401-4001.  Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCSv2.2.38 and RTA v1.18.61, a 50 cycle single-read sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4002.

treatment_protocol: NP cells were transduced with either control or TonEBP-specific shRNA. Cells were cultured under hypertonic conditions (110mM NaCl added to culture media for 8 hours prior to RNA isolation.

tag: culture condition

value: hypertonic

tag: genotype/variation

value: TonEBP knockdown

value: primary nucleus pulposus cells


title: total RNA-seq from midbrain (ENCLB257LEX)

description:
https://www.encodeproject.org/experiments/ENCSR764OPZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-seq on 10ng of embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR764OPZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2016-08-11
lab: Barbara Wold, Caltech
library encode accession: ENCLB257LEX
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (10.5 days)

value: midbrain

value: tissue

tag: description

value: Midbrain from 69 embryonic 10.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS491CAX at ENCODE; https://www.encodeproject.org/ENCBS491CAX/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: C57Bl6 Hb9::GFP embryo-MNs E13.5 2, sorted


title: total RNA-seq from limb (ENCLB537WPK)

description:
https://www.encodeproject.org/experiments/ENCSR968QHO/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-seq on 10ng of embryonic 10.5 day mouse limb
experiment encode accession: ENCSR968QHO
assay title: total RNA-seq
assembly: mm10
encode release date: 2016-08-11
lab: Barbara Wold, Caltech
library encode accession: ENCLB537WPK
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: limb

value: Limb from 69 embryonic 10.5 day mice

tag: biosample encode accession

value: ENCBS844FSC at ENCODE; https://www.encodeproject.org/ENCBS844FSC/


title: Set 1 ShTon_NaCl


title: total RNA-seq from hindbrain (ENCLB838FEJ)

description:
https://www.encodeproject.org/experiments/ENCSR943LKA/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-seq on 10ng of embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR943LKA
assay title: total RNA-seq
assembly: mm10
encode release date: 2016-08-11
lab: Barbara Wold, Caltech
library encode accession: ENCLB838FEJ
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: hindbrain

value: Hindbrain from 51 embryonic 10.5 day mice

tag: age

value: ENCBS723QMZ at ENCODE; https://www.encodeproject.org/ENCBS723QMZ/


title: Set 3 ShTon_NaCl


title: total RNA-seq from embryonic facial prominence (ENCLB293YOF)

description:
https://www.encodeproject.org/experiments/ENCSR809VYL/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-seq on 10ng of embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR809VYL
assay title: total RNA-seq
assembly: mm10
encode release date: 2016-08-11
lab: Barbara Wold, Caltech
library encode accession: ENCLB293YOF
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: embryonic facial prominence

value: Craniofacial prominence from 69 embryonic 10.5 day mice

tag: dev stage

value: embryonic

value: pooled male and female

value: healthy

value: ENCBS938XWJ at ENCODE; https://www.encodeproject.org/ENCBS938XWJ/


title: Set 2 ShTon_NaCl

value: hypertonic

value: TonEBP knockdown

value: primary nucleus pulposus cells


title: total RNA-seq from midbrain (ENCLB396XZV)

description:
https://www.encodeproject.org/experiments/ENCSR764OPZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-seq on 10ng of embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR764OPZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2016-08-11
lab: Barbara Wold, Caltech
library encode accession: ENCLB396XZV
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: midbrain

value: tissue

value: Midbrain from 51 embryonic 10.5 day mice

tag: Sex

value: Len Pennacchio, LBNL

value: ENCBS613YYL at ENCODE; https://www.encodeproject.org/ENCBS613YYL/


title: total RNA-seq from forebrain (ENCLB029BTN)

description:
https://www.encodeproject.org/experiments/ENCSR304RDL/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-seq on 10ng of embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR304RDL
assay title: total RNA-seq
assembly: mm10
encode release date: 2016-08-11
lab: Barbara Wold, Caltech
library encode accession: ENCLB029BTN
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (10.5 days)

value: forebrain

value: Forebrain from 69 embryonic 10.5 day mice

tag: lab

value: ENCBS152ONW at ENCODE; https://www.encodeproject.org/ENCBS152ONW/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: Set 2 PLKO1_NaCl

value: control


title: Set 3 PLKO1_NaCl


title: total RNA-seq from forebrain (ENCLB286HEN)

description:
https://www.encodeproject.org/experiments/ENCSR304RDL/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-seq on 10ng of embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR304RDL
assay title: total RNA-seq
assembly: mm10
encode release date: 2016-08-11
lab: Barbara Wold, Caltech
library encode accession: ENCLB286HEN
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: Forebrain from 51 embryonic 10.5 day mice

value: embryonic

tag: link

value: ENCBS790BBA at ENCODE; https://www.encodeproject.org/ENCBS790BBA/


title: Set 4 PLKO1_NaCl


title: Set 1 PLKO1_NaCl


title: total RNA-seq from heart (ENCLB564JOZ)

description:
https://www.encodeproject.org/experiments/ENCSR049UJU/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-seq on 10ng of embryonic 10.5 day mouse heart
experiment encode accession: ENCSR049UJU
assay title: total RNA-seq
assembly: mm10
encode release date: 2016-08-11
lab: Barbara Wold, Caltech
library encode accession: ENCLB564JOZ
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl heart tissue mixed sex embryo (10.5 days)

value: heart

value: Heart from 69 embryonic 10.5 day mice

value: pooled male and female

tag: health state

value: healthy

value: ENCBS366XOW at ENCODE; https://www.encodeproject.org/ENCBS366XOW/


title: Hb9::GFP Bl6 mESC rep2

description: mouse ESCS


title: total RNA-seq from heart (ENCLB688RET)

description:
https://www.encodeproject.org/experiments/ENCSR049UJU/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-seq on 10ng of embryonic 10.5 day mouse heart
experiment encode accession: ENCSR049UJU
assay title: total RNA-seq
assembly: mm10
encode release date: 2016-08-11
lab: Barbara Wold, Caltech
library encode accession: ENCLB688RET
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: tissue

value: Heart from 51 embryonic 10.5 day mice

value: ENCBS510GHM at ENCODE; https://www.encodeproject.org/ENCBS510GHM/


title: HH14_RNAseq_rep2

status: Public on Nov 07 2016

city: Koeln

first: Milos

last: Nikolic

state: Nordrhein-Westfalen

address: Robert Koch Str. 21

country: Germany

institute: Center for Molecular Medicine Cologne

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools
Reads were mapped to the chicken reference assembly, version galGal10, using TopHat2
Gene expression for the individual samples was calculated as TPM using custom R scripts adapted from previous reports (Wagner et al., 2012).
For calculating the expression fold changes between HH19 and HH14 SNT, we performed a differential gene expression analysis of count data using custom R script and DESeq2 (Love et al., 2014).
Genome_build: galGal4
Supplementary_files_format_and_content: Txt file containing TPMs for each ENSEMBL chicken gene.

organism: Gallus gallus

source_name: Spinal neural tube (brachial level)

growth_protocol: Fertilized chicken eggs (White Leghorn, Gallus gallus domesticus) were obtained from a local breeder (LSL Rhein-Main, Dieburg). Incubation was done at 37°C and 80% humidity in a normal poultry egg incubator (Typenreihe Thermo-de-Lux). After following microsurgical procedures, the eggs were re-incubated until the embryos reached the desired developmental stages. The developmental progress was determined according to the staging system of Hamburger Hamilton (HH) (Hamburger and Hamilton, 1992).

extract_protocol:
Fertile chicken eggs were incubated at 37°C for 48 hrs until they reached stage HH14(Hamburger and Hamilton, 1992). Embryos were isolated from the eggs, transferred into 20 ml of 1xPBS and the extraembryonic membranes were removed. Under the stereomicroscope, the transverse SNT sections from chicken embryos were collected at the brachial level, extending caudally into the thoracic region (Figure 1C). Most of the tissues that are located laterally/ventrally to the neural tube (e.g. lateral plate mesoderm, endoderm and aorta) were removed manually. Each section was immersed in 90 mm petri dish, containing 3 ml of warm (37°C) trypsin (Trypsin.EDTA solution 1:250 (IX), GIBCO) (Figure 1C). Trypsinization time was tightly controlled to avoid over-digestion and dispersion of neural tissue and to retain the structural integrity of the SNT. Once connective tissues became loosened near the outline of the neural tube, which is easily detectable under a stereomicroscope, trypsin was inactivated by rinsing with cold (4°C) DMEM containing 10% FBS and samples were transferred into cold 1 x PBS. Following trypsin treatment, mesenchymal and ectodermal tissues (e.g. paraxial mesoderm, notochord, surface ectoderm) were removed manually using forceps. After isolation, SNT fragments were pooled and total RNA was isolated using Tripure reagent according to the manufacturer’s instructions (Roche). Libraries were prepared with the RNA sample preparation kit (TruSeq v2; Ilumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: White Leghorn

value: Spinal neural tube (brachial level)

tag: developmental stage

value: WT


title: HH14_RNAseq_rep1

tag: tissue


title: HH19_input

library_source: genomic

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools
Reads were mapped to the chicken reference assembly, version galGal4, using BWA
Normalized bedGraph files were generated using DeepTools
Peaks were called using MACS2
Genome_build: galGal4

molecule: genomic DNA

extract_protocol:
Fertile chicken eggs were incubated at 37°C for 48 hrs until they reached stage HH14(Hamburger and Hamilton, 1992). Embryos were isolated from the eggs, transferred into 20 ml of 1xPBS and the extraembryonic membranes were removed. Under the stereomicroscope, the transverse SNT sections from chicken embryos were collected at the brachial level, extending caudally into the thoracic region (Figure 1C). Most of the tissues that are located laterally/ventrally to the neural tube (e.g. lateral plate mesoderm, endoderm and aorta) were removed manually. Each section was immersed in 90 mm petri dish, containing 3 ml of warm (37°C) trypsin (Trypsin.EDTA solution 1:250 (IX), GIBCO) (Figure 1C). Trypsinization time was tightly controlled to avoid over-digestion and dispersion of neural tissue and to retain the structural integrity of the SNT. Once connective tissues became loosened near the outline of the neural tube, which is easily detectable under a stereomicroscope, trypsin was inactivated by rinsing with cold (4°C) DMEM containing 10% FBS and samples were transferred into cold 1 x PBS. Following trypsin treatment, mesenchymal and ectodermal tissues (e.g. paraxial mesoderm, notochord, surface ectoderm) were removed manually using forceps.  After isolation, SNT fragments were pooled in a 1.5 ml tube, flash-frozen in liquid nitrogen and stored at -80°C. For each ChIP-seq experiment, ~25-30 SNT sections isolated from stage HH14 chicken embryos were used. Dissected neural tubes were briefly homogenized in DMEM media with 10% FBS serum/1M sodium butyrate and cross-linked with 1% formaldehyde at room temperature with rotation for 15 mins. Cross-linking was quenched with 0.125 M glycine and neural tissue was rinsed once with cold 1 X PBS and resuspended in 300 µl of sonication buffer (10mM Tris, 100mM NaCl, 1mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate and 0.5% N-lauroylsarcosine) and incubated at 4°C for 10 mins. Chromatin was then sonicated using Bioruptor plus (Diagenode) with high level settings for 11 cycles with 30-sec pulses at 4 °C (45-sec pause between pulses) to generate DNA fragments of ~200-500 bp. 30 µl of the sonicated chromatin was kept as input DNA, while the remaining chromatin was incubated overnight with 5µg of antibodies against H3K27me3 (39536, Active Motif), H3K27ac (Active Motif) or H3K4me3 (39159, Active Motif)(Rada-Iglesias et al., 2011), followed by 4-6 hours incubation with Protein G Dynabeads (Life Technologies). Beads were washed 4 times with 1ml of cold RIPA washing buffer (50mM Hepes, 500mM LiCl, 1mM EDTA, 1% NP-40 and 0.7% Na-Deoxycholate) and once with Tris/EDTA buffer (TE) containing 50mM NaCl. Immunoprecipitated chromatin was eluted from the beads by adding elution buffer (50mM Tris, 10mM EDTA and 1% SDS) and vortexing at 65°C for 15 mins. Crosslinking was reversed by incubating the eluted samples at 65°C overnight. Samples were then diluted (1:1) with TE and treated with RNase A (0.2µg/µl) for 90 mins at 37°C, followed by proteinase K (0.2µg/µl) treatment at 50°C for 90 mins. DNA was purified using Phenol:Chloroform, followed by ethanol precipitation and resuspended in water.
DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 100 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries.

treatment_protocol: Not applicable

tag: chip antibody


title: single cell RNA-seq from Purkinje cell (ENCLB765OGT)

description:
https://www.encodeproject.org/experiments/ENCSR805QYO/
***************
biological replicate number: 1
technical replicate number: 1
description: LCMD-501,502_Mm_Castaneus_x_C57Bl-Purkinje-30-pool
experiment encode accession: ENCSR805QYO
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB765OGT
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 30.0
nucleic acid starting quantity units: cells
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Mus musculus strain B6CASTF1/J Purkinje primary cell male adult (14 months)

tag: antibody

value: Control

value: Purkinje cell

value: primary cell

value: adult

value: male

value: 14 month

value: Barbara Wold, Caltech

value: ENCBS691AEG at ENCODE; https://www.encodeproject.org/ENCBS691AEG/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: HH19_RNAseq

tag: strain


title: HH14_H3K4me3_rep2

tag: genotype

value: H3K4me3 (39159, Active Motif)


title: HH19_H3K27me3

value: H3K27me3 (39155, Active Motif)


title: HH14_input_rep1


title: HH14_input_rep2


title: D21 R1

first: Larry

last: Lam

address: 610 Charles Young Drive East

department: Molecular, Cell, and Developmental Biology

institute: University of California, Los Angeles

description:
Differentiation Sample 7
21 day treatment

data_processing:
Sequenced reads were mapped to mm9 whole genome using TopHat v2.0.11 with parameter -g 1
Gene counts were generated using HTSeq 0.6.1 with parameter -s no
Gene counts normalized using DESEq
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include gene count values for each sample

source_name: D21, Cardiac Fibroblast

extract_protocol:
RNA extraction was performed using RNeasy Plus Mini Kit (Qiagen, 74134)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Cardiac Fibroblast

value: 8 weeks

value: wild type

tag: treatment

value: differentiation medium

tag: time

value: day 21


title: D7 R1

description:
Differentiation Sample 3
7 day treatment

source_name: D7, Cardiac Fibroblast

tag: genotype/variation

value: day 7


title: D7 R2

description:
Differentiation Sample 4
7 day treatment


title: HH14_H3K4me3_rep1

value: White Leghorn

value: Spinal neural tube (brachial level)

value: WT


title: CNTR R1

description:
Differentiation Sample 1
untreated

source_name: CNTR, Cardiac Fibroblast

value: before differentiation medium treatment

value: control


title: D21 R2

description:
Differentiation Sample 8
21 day treatment


title: CNTR R2

description:
Differentiation Sample 2
untreated


title: D14 R2

description:
Differentiation Sample 6
14 day treatment

source_name: D14, Cardiac Fibroblast

value: day 14


title: HH14_H3K27me3_rep1


title: HH14_H3K27ac

value: H3K27ac (39133, Active Motif)


title: HH14_H3K27me3_rep2


title: Hypothalamus, BXD95

city: Lausanne

first: Frederic

last: Burdet

address: Quartier Sorge - Batiment Amphipole

country: Switzerland

institute: Swiss Institute of Bioinformatics

description:
raw_counts.txt
normalized_counts.txt

data_processing:
100nt single-end reads from 40 mouse hypothalamii samples (mean ~40Mio reads/sample) were mapped to mm9 reference genome using Tophat software (version 2.0.8) using library-type = fr-firststrand.  Other parameters were set by default
Read counts for genes were generated using htseq-count (Version 0.5.4p3) with mm9 RefSeq genes in GTF format as a reference, with parameters stranded = reverse and mode =  union
The raw count data were first filtered for an average of 10 reads in all the samples and normalized to library size using the estimateSizeFactors method in DESeq (Anders and Huber, 2010)
Genome_build: mm9
Supplementary_files_format_and_content: The raw counts .txt file contains the counts per gene for each sample. The normalized counts .txt file are normalized using DESeq

source_name: Hypothalamus, BXD95

extract_protocol:
Total RNA extraction from hypothalamus and brainstem samples was performed using the peqGOLD TriFast method (Peqlab, Erlangen, Germany) (Mounien et al., 2010). RNA integrity was verified with a 2100 Bioanalyser (Agilent, Santa Clara, USA). For each BXD strain, equal amounts of RNAs from 3 to 6 hypothalami were pooled in a final volume of 50 μL
RNA-seq libraries were prepared using 1µg of pooled RNAs and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA) on a Sciclone liquid handling robot (PerkinElmer; Waltham, Massachusetts, USA) using a PerkinElmer-developed automated script. Cluster generation was performed with the resulting libraries using the Illumina TruSeq SR Cluster Kit v3 reagents and sequenced on the Illumina HiSeq 2000 using TruSeq SBS Kit v3 reagents. Sequencing data were processed using the Illumina Pipeline Software version 1.82. A sequencing depth of 40 millions of 100-bp single-end reads was used.

value: Hypothalamus


title: D14 R1

description:
Differentiation Sample 5
14 day treatment


title: Hypothalamus, BXD96

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD96


title: Hypothalamus, D2B6F1

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, D2B6F1 (parental strain)


title: Hypothalamus, C57BL/6J

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, C57BL/6J (parental strain)


title: Hypothalamus, BXD90

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD90


title: Hypothalamus, BXD87

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD87


title: Hypothalamus, BXD89

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD89


title: C3H 2 D7 Inj

description:
Wounding Sample 11
C3H mouse-2 Injured heart region

source_name: Heart

value: Heart

value: injured


title: Hypothalamus, BXD85

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD85


title: Hypothalamus, BXD83

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD83


title: Hypothalamus, BXD84

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD84


title: Hypothalamus, DBA/2J

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, DBA/2J (parental strain)


title: Hypothalamus, BXD79

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD79


title: C3H 1 D7 Inj

description:
Wounding Sample 10
C3H mouse-1 Injured heart region


title: Hypothalamus, BXD97

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD97


title: Hypothalamus, BXD81

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD81


title: Hypothalamus, BXD98

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD98


title: C3H 2 D7 N

description:
Wounding Sample 8
C3H mouse-2 Uninjured heart region

value: uninjured


title: B6 3 D7 Inj

description:
Wounding Sample 6
B6 mouse-3 Injured heart region


title: C3H 1 D7 N

description:
Wounding Sample 7
C3H mouse-1 Uninjured heart region


title: B6 1 D7 Inj

description:
Wounding Sample 4
B6 mouse-1 Injured heart region


title: B6 3 D7 N

description:
Wounding Sample 3
B6 mouse-3 Uninjured heart region


title: B6 2 D7 Inj

description:
Wounding Sample 5
B6 mouse-2 Injured heart region


title: Hypothalamus, BXD75

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD75


title: B6 2 D7 N

description:
Wounding Sample 2
B6 mouse-2 Uninjured heart region


title: Hypothalamus, BXD73

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD73


title: Hypothalamus, BXD71

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD71


title: Hypothalamus, BXD70

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD70


title: Hypothalamus, BXD67

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD67


title: B6 1 D7 N

description:
Wounding Sample 1
B6 mouse-1 Uninjured heart region


title: Hypothalamus, BXD61

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD61


title: Hypothalamus, BXD63

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD63


title: Hypothalamus, BXD65

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD65


title: 60448sacCer3_BY4741_5546_H2BK123ub

city: University Park

first: Alain

middle: Roger

last: Bataille

address: 453 North Frear

department: BMB

institute: Penn State University

description:
Biological replicate 2 of 2, IP with anti-H2BK123ub antibody in wildtype strain
60447-48sacCer3_BY4741_5546_H2BK123Ub_comb_READ1_shift6.tab

data_processing:
Basecalls performed using bcl2fastq ver 2.16 for NextSeq paired reads
ChIP-exo reads were aligned to Saccer3 genome assembly using bwa mem version 0.7.9a for paired reads. Read1 tags were shift 6 bp (to better reflect the crosslinking coordinates).
Genome_build: sacCer3/R64
Supplementary_files_format_and_content: tab files of shifted merge datasets used for mapping. Format: chr/index/forwardTag#/reverseTag#. The tab file of each combined dataset contains the coordinates of the shifted (6bp in the 3' direction) exo digested end (5') corresponding to the Read 1 of the sequencer.

organism: Saccharomyces cerevisiae

growth_protocol: All yeast cells were grown to an OD600 of 0.6-0.8 at 30 °C following standard procedures in indicated media.

extract_protocol:
ChIP-exo experiments were carried out essentially as described (Rhee and Pugh, 2012). Briefly, crosslinked cells were lysed, and chromatin pellets were isolated and then fragmented by sonication. Chromatin was then immunoprecipitated using antibody-conjugated magnetic beads, followed by DNA polishing, A-tailing, Illumina adaptor ligation (ExA2), and on beads digestion by lambda and recJ exonuclease. After elution of the single-stranded DNA, a primer was annealed to EXA2 and extended with phi29 DNA polymerase, then A-tailed. A second Illumina sequencing adaptor was ligated to exonuclease treated ends, and the products PCR-amplified and gel-purified.
ChIP-exo libraries were prepared for sequencing using standard Illumina protocols; Reference paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/
ChIP-exo-Seq

treatment_protocol: Cell were crosslink with 1% formaldehyde final concentration for 15 min.

tag: media

value: YPD

value: Cell Signaling 5546

tag: antibody lot#

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0

tag: protocol

value: ChIP-exo


title: 60447sacCer3_BY4741_5546_H2BK123ub

description:
Biological replicate 1 of 2, IP with anti-H2BK123ub antibody in wildtype strain
60447-48sacCer3_BY4741_5546_H2BK123Ub_comb_READ1_shift6.tab


title: 57817sacCer3_BY4741_i5006_Spt5-TAP_rep1

description:
Biological replicate 1 of 2, Spt5 IP with rabbit IgG in SPT5-TAP strain
57817-18sacCer3_BY4741_i5006_Spt5-TAP_comb_READ1_shift6.tab

value: Sigma i5006

value: MATa SPT5-TAP his3delta1 leu2delta0 ura3delta0 met15delta0

tag: tag

value: TAP


title: Hypothalamus, BXD56

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD56


title: 57814sacCer3_KY404-pKB1140_5546_H2BK123ub_rtf1D_pHMD_rep4

description:
Biological replicate 4 of 4, IP with anti-H2BK123ub antibody in rtf1D plasmid(HSV-HMD) strain
53101-02-57813-14sacCer3_KY404-pKB1140_5546_H2BK123ub_rtf1D_pHMD_comb_READ1_shift6.tab

value: Sc-Trp

value: MATa rtf1delta101::LEU2 his4-912delta lys2-128delta leu2delta1 ura3-52 trp1delta63 pKB1140(2micron, ADH1 NLS-3XHSV-HMD63-152, TRP1, KanR)


title: Hypothalamus, BXD55

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD55


title: C3H 3 D7 N

description:
Wounding Sample 9
C3H mouse-3 Uninjured heart region

source_name: Heart

tag: age

value: 8 weeks


title: 57813sacCer3_KY404-pKB1140_5546_H2BK123ub_rtf1D_pHMD_rep3

description:
Biological replicate 3 of 4, IP with anti-H2BK123ub antibody in rtf1D plamid(HSV-HMD) strain
53101-02-57813-14sacCer3_KY404-pKB1140_5546_H2BK123ub_rtf1D_pHMD_comb_READ1_shift6.tab


title: Hypothalamus, BXD50

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD50


title: 57810sacCer3_BY4741_i5006_Spt4-TAP_rep2

description:
Biological replicate 2 of 2, Spt4 IP with rabbit IgG in SPT4-TAP strain
57809-10sacCer3_BY4741_i5006_Spt4-TAP_comb_READ1_shift6.tab

value: MATa SPT4-TAP his3delta1 leu2delta0 ura3delta0 met15delta0


title: Hypothalamus, BXD49

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD49


title: 57214sacCer3_KY1652_H6030_3xHSV-Bre1_rtf1D_ref3

description:
Biological replicate 3 of 3, IP with anti-HSV antibody in rtf1D 3HSV-BRE1 strain
57212-13-14sacCer3_KY1652_H6030_3HSV-Bre1_rtf1D_comb_READ1_shift6.tab

value: Sigma H6030

value: MATalpha 3xHSV-BRE1 rtf1delta::LEU2 lys2-128delta his3delta200 leu2delta1 ura3-52

value: HSV


title: 57809sacCer3_BY4741_i5006_Spt4-TAP_rep1

description:
Biological replicate 1 of 2, Spt4 IP with rabbit IgG in SPT4-TAP strain
57809-10sacCer3_BY4741_i5006_Spt4-TAP_comb_READ1_shift6.tab


title: Hypothalamus, BXD66

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD66

value: Hypothalamus


title: Hypothalamus, BXD45

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD45


title: Hypothalamus, BXD44

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD44


title: Hypothalamus, BXD64

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD64


title: 57213sacCer3_KY1652_H6030_3xHSV-Bre1_rtf1D_rep2

description:
Biological replicate 2 of 3, IP with anti-HSV antibody in rtf1D 3HSV-BRE1 strain
57212-13-14sacCer3_KY1652_H6030_3HSV-Bre1_rtf1D_comb_READ1_shift6.tab


title: 57818sacCer3_BY4741_i5006_Spt5-TAP_rep2

description:
Biological replicate 2 of 2, Spt5 IP with rabbit IgG in SPT5-TAP strain
57817-18sacCer3_BY4741_i5006_Spt5-TAP_comb_READ1_shift6.tab


title: 57212sacCer3_KY1652_H6030_3xHSV-Bre1_rtf1D_rep1

description:
Biological replicate 1 of 3, IP with anti-HSV antibody in rtf1D 3HSV-BRE1 strain
57212-13-14sacCer3_KY1652_H6030_3HSV-Bre1_rtf1D_comb_READ1_shift6.tab


title: 57210sacCer3_KY2697_H6030_3xHSV-Bre1_rep2

description:
Biological replicate 2 of 3, IP with anti-HSV antibody in 3HSV-BRE1 strain
57209-10-11sacCer3_KY2697_H6030_3HSV-Bre1_comb_READ1_shift6.tab

value: MATalpha 3xHSV-BRE1 lys2-128delta his3delta200 leu2delta1 ura3-52


title: Hypothalamus, BXD43

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD43


title: Hypothalamus, BXD29

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD29


title: Hypothalamus, BXD32

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD32


title: 57209sacCer3_KY2697_H6030_3xHSV-Bre1_rep1

description:
Biological replicate 1 of 3, IP with anti-HSV antibody in 3HSV-BRE1 strain
57209-10-11sacCer3_KY2697_H6030_3HSV-Bre1_comb_READ1_shift6.tab


title: Hypothalamus, BXD103

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD103


title: 57211sacCer3_KY2697_H6030_3xHSV-Bre1_rep3

description:
Biological replicate 3 of 3, IP with anti-HSV antibody in 3HSV-BRE1 strain
57209-10-11sacCer3_KY2697_H6030_3HSV-Bre1_comb_READ1_shift6.tab


title: 56727sacCer3_BY4741_ab1790_H2B

description:
Biological replicate 2 of 2, IP with anti-H2B antibody in wildtype strain
52410-56727sacCer3_BY4741_ab1790_H2B_comb_READ1_shift6.tab


title: Hypothalamus, BXD51

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD51


title: Hypothalamus, BXD100

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD100


title: 53102sacCer3_KY404-pKB1140_5546_H2BK123ub_rtf1D_pHMD_rep2

description:
Biological replicate 2 of 4, H2BK123ub IP with anti-H2BK123ub antibody in rtf1D plasmid(HSV-HMD) strain
53101-02-57813-14sacCer3_KY404-pKB1140_5546_H2BK123ub_rtf1D_pHMD_comb_READ1_shift6.tab

value: MATa rtf1delta101::LEU2 his4-912delta lys2-128delta leu2delta1 ura3-52 trp1delta63


title: 54513sacCer3_BY4741_i5006_Rpb3-TAP_rep1

description:
Biological replicate 1 of 2, Rpb3 IP with rabbit IgG in RPB3-TAP strain
54513-16sacCer3_BY4741_i5006_Rpb3-TAP_comb_READ1_shift6.tab

value: YPD

value: MATa RPB3-TAP his3delta1 leu2delta0 ura3delta0 met15delta0


title: Hypothalamus, B6D2F1

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, B6D2F1 (parental strain)


title: Hypothalamus, BXD48

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD48


title: 54516sacCer3_BY4741_i5006_Rpb3-TAP_rep2

description:
Biological replicate 2 of 2, Rpb3 IP with rabbit IgG in RPB3-TAP strain
54513-16sacCer3_BY4741_i5006_Rpb3-TAP_comb_READ1_shift6.tab


title: TypeB_1

city: Durham

first: Mari

middle: L

last: Shinohara

state: NC

institute: Duke University School of Medicine

data_processing:
TrimGalore v0.4.0 for initial processing of fastq files
STAR v2.4.1d was used to align the reads ('--outFilterMultimapNmax 1' and '--alignSJoverhangMin 500' were the non-default parameters used)
HTSeq v0.6.1p1 to quantify gene expression ('-s reverse' was the non-default parameter used)
Genes were removed prior to normalization if they didn't have at least 10 reads in any one sample
EdgeR v3.8.5 was used for normalization and differential expression
Genome_build: ENSEMBL release GRCm38v73 of the mouse genome and transcriptome
Supplementary_files_format_and_content: Tab separated text files (.tsv) that contain the raw HTSeq counts as well as the EdgeR normalized expression values

source_name: CD4+ T cells

extract_protocol:
CD4+ T cells were FACS-sorted.
Illumina TruSeq RNA Stranded kit, polyA enriched mRNA (catalog number RS-122-2101) was used to generate sequencing libraries.  The quality of RNA libraries was checked by running them on a 2100 ioanalyzer instrument  (Agilent).  Average insert size is around 200bp. All samples were pooled and sequenced on 2 lanes of Illumina HiSeq 2000 50bp SR.

treatment_protocol: Type-A EAE was induced with Mtb 200 μg in CFA and MOG peptide 100 μg, 1 time of immunization.  Type-B EAE was induced with Mtb 400 μg in CFA, MOG  peptide 125 μg, 2 time of immunization.

value: spleen

value: CD4+ T cells

tag: immunization status

value: Mouse with Type-B EAE

tag: day post immunization


title: 53101sacCer3_KY404-pKB1140_5546_H2BK123ub_rtf1D_pHMD_rep1

description:
Biological replicate 1 of 4, H2BK123ub IP with anti-H2BK123ub antibody in rtf1D plamid(HSV-HMD) strain
53101-02-57813-14sacCer3_KY404-pKB1140_5546_H2BK123ub_rtf1D_pHMD_comb_READ1_shift6.tab

value: Cell Signaling 5546

value: ChIP-exo


title: TypeB_2


title: TypeA_3

value: Mouse with Type-A EAE


title: 52848sacCer3_KY404-pKB1228_5546_H2BK123ub_rtf1D_pRTF1_rep2

description:
Biological replicate 2 of 2, H2BK123ub IP with anti-H2BK123ub antibody in rtf1D plasmid(HSV-RTF1) strain
52847-48sacCer3_KY404-pKB1228_5546_H2BK123ub_rtf1D_pRTF1_comb_READ1_shift6.tab

value: Sc-Trp

value: MATa rtf1delta101::LEU2 his4-912delta lys2-128delta leu2delta1 ura3-52 trp1delta63 pKB1228(2micron, ADH1 NLS-3XHSV-Rtf1, TRP1, KanR)


title: 52847sacCer3_KY404-pKB1228_5546_H2BK123ub_rtf1D_pRTF1_rep1

description:
Biological replicate 1 of 2, H2BK123ub IP with anti-H2BK123ub antibody in rtf1D plamid(HSV-RTF1) strain
52847-48sacCer3_KY404-pKB1228_5546_H2BK123ub_rtf1D_pRTF1_comb_READ1_shift6.tab


title: TypeA_2


title: 52843sacCer3_KY404-pKB1140_39237_H2B_rtf1D_pHMD_rep1

description:
Biological replicate 1 of 2, H2B IP with anti-H2B antibody in rtf1D plamid(HSV-HMD) strain
52843-44sacCer3_KY404-pKB1140_39237_H2B_rtf1D_pHMD_comb_READ1_shift6.tab

value: Active Motif 39237

value: MATa rtf1delta101::LEU2 his4-912delta lys2-128delta leu2delta1 ura3-52 trp1delta63 pKB1140(2micron, ADH1 NLS-3XHSV-HMD63-152, TRP1, KanR)


title: 52844sacCer3_KY404-pKB1140_39237_H2B_rtf1D_pHMD_rep2

description:
Biological replicate 2 of 2, H2B IP with anti-H2B antibody in rtf1D plasmid(HSV-HMD) strain
52843-44sacCer3_KY404-pKB1140_39237_H2B_rtf1D_pHMD_comb_READ1_shift6.tab


title: Control_3

value: naïve mouse

value: naïve


title: 52842sacCer3_KY404-pKB1228_39237_H2B_rtf1D_pRTF1_rep2

description:
Biological replicate 2 of 2, H2B IP with anti-H2B antibody in rtf1D plasmid(HSV-RTF1) strain
52841-42sacCer3_KY404-pKB1228_39237_H2B_rtf1D_pRTF1_comb_READ1_shift6.tab


title: Control_2


title: Control_1


title: 52841sacCer3_KY404-pKB1228_39237_H2B_rtf1D_pRTF1_rep1

description:
Biological replicate 1 of 2, H2B IP with anti-H2B antibody in rtf1D plamid(HSV-RTF1) strain
52841-42sacCer3_KY404-pKB1228_39237_H2B_rtf1D_pRTF1_comb_READ1_shift6.tab


title: Hypothalamus, BXD101

description:
raw_counts.txt
normalized_counts.txt

source_name: Hypothalamus, BXD101

value: Hypothalamus


title: 52833sacCer3_KY404-pKB1265_H6030_3HSV-HMD-E104K_rtf1D_pHMD-E104K_rep1

description:
Biological replicate 1 of 2, HMD-E104K IP with anti-HSV antibody in rtf1D plamid(HSV-HMD-E104K) strain
52833-34sacCer3_KY404-pKB1265_H6030_3HSV-HMD-E104K_rtf1D_pHDM-E104K_comb_READ1_shift6.tab

value: Sigma H6030

value: MATa rtf1delta101::LEU2 his4-912delta lys2-128delta leu2delta1 ura3-52 trp1delta63 pKB1265(2micron, ADH1 NLS-3XHSV-HMD63-152-E104K, TRP1, KanR)

value: HSV


title: 52830sacCer3_KY404-pKB1228_H6030_3HSV-Rtf1_rtf1D_pRTF1_rep2

description:
Biological replicate 2 of 2, Rtf1 IP with anti-HSV antibody in rtf1D plasmid(HSV-RTF1) strain
52829-30sacCer3_KY404-pKB1228_H6030_3HSV-Rtf1_rtf1D_pRTF1_comb_READ1_shift6.tab

value: MATa rtf1delta101::LEU2 his4-912delta lys2-128delta leu2delta1 ura3-52 trp1delta63


title: 52818sacCer3_KY2507_ab9132_Rad6-13Myc_rtf1D_rep2

description:
Biological replicate 2 of 2, Rad6 IP with anti-Myc antibody in rtf1D RAD6-13Myc strain
52817-18sacCer3_KY2507_ab9132_Rad6-13Myc_rtf1D_comb_READ1_shift6.tab

value: YPD

value: MATa rtf1delta::KanMX4 RAD6-13xMyc::KanMX6 his3delta200 leu2delta1 ura3-52 trp1delta63

value: MYC


title: 52829sacCer3_KY404-pKB1228_H6030_3HSV-Rtf1_rtf1D_pRTF1_rep1

description:
Biological replicate 1 of 2, Rtf1 IP with anti-HSV antibody in rtf1D plamid(HSV-RTF1) strain
52829-30sacCer3_KY404-pKB1228_H6030_3HSV-Rtf1_rtf1D_pRTF1_comb_READ1_shift6.tab


title: 52831sacCer3_KY404-pKB1140_H6030_3HSV-HMD_rtf1D_pHMD_rep1

description:
Biological replicate 1 of 2, HMD IP with anti-HSV antibody in rtf1D plamid(HSV-HMD) strain
52831-32sacCer3_KY404-pKB1140_H6030_3HSV-HDM_rtf1D_pHDM_comb_READ1_shift6.tab


title: 52817sacCer3_KY2507_ab9132_Rad6-13Myc_rtf1D_rep1

description:
Biological replicate 1 of 2, Rad6 IP with anti-Myc antibody in rtf1D RAD6-13Myc strain
52817-18sacCer3_KY2507_ab9132_Rad6-13Myc_rtf1D_comb_READ1_shift6.tab


title: 595 IP

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Aligned to mm10 using STAR spliced read aligner
Count read using HT-seq using mm10 RefSeq as reference
Normalization (TMM), quantitation (FPKM and CPM) and differential expression analysis using limmavoom.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values

extract_protocol:
HA samples underwent DNA depletion and RNA purification with the RNeasy Micro Plus kit (Qiagen). Integrity of the eluted RNA was analyzed by a 2100 Bioanalyzer (Agilent) using the RNA Pico chip. RNA concentration determined by nanodrop.
Paired-end libraries for multiplexed sequencing were generated from 100ng of IP or input RNA using the KAPA Stranded RNA-Seq Kit with mRNA enrichment.

tag: developmental stage

value: brain

value: Aldh1l1-creERT2 hemi; Ribotag het

tag: rna sample type

value: HA IP


title: 52816sacCer3_KY1026_ab9132_Rad6-13Myc_rep2

description:
Biological replicate 2 of 2, Rad6 IP with anti-Myc antibody in RAD6-13Myc strain
52815-16sacCer3_KY1026_ab9132_Rad6-13Myc_comb_READ1_shift6.tab

value: MATa RAD6-13xMyc::KanMX6 his3delta200 leu2delta1 ura3-52 trp1delta63

value: ChIP-exo


title: 595 input

tag: tissue

value: input


title: 581 input


title: 52815sacCer3_KY1026_ab9132_Rad6-13Myc_rep1

description:
Biological replicate 1 of 2, Rad6 IP with anti-Myc antibody in RAD6-13Myc strain
52815-16sacCer3_KY1026_ab9132_Rad6-13Myc_comb_READ1_shift6.tab

tag: antibody


title: 52813sacCer3_GHY1092_11867431001_Leo1-3HA_rep1

description:
Biological replicate 1 of 2, Leo1 IP with anti-HA antibody in LEO1-3HA strain
52813-14sacCer3_GHY1092_11867431001_Leo1-3HA_comb_READ1_shift6.tab

value: MATa LEO1-3xHA::HIS3MX6 lys2-128delta his3delta200 leu2delta1 ura3-52 trp1delta63

value: HA


title: 580 input


title: 580 IP


title: 52809sacCer3_KY1794_11867431001_Cdc73-3HA_rep1

description:
Biological replicate 1 of 2, Cdc73 IP with anti-HA antibody in CDC73-3HA strain
52809-10sacCer3_KY1794_11867431001_Cdc73-3HA_comb_READ1_shift6.tab

value: MATalpha CDC73-3xHA::KanMX his4-912delta lys2-128delta leu2delta1 ura3-52 trp1delta63


title: 579 IP


title: 52834sacCer3_KY404-pKB1265_H6030_3HSV-HMD-E104K_rtf1D_pHMD-E104K_rep2

description:
Biological replicate 2 of 2, HMD-E104K IP with anti-HSV antibody in rtf1D plasmid(HSV-HMD-E104K) strain
52833-34sacCer3_KY404-pKB1265_H6030_3HSV-HMD-E104K_rtf1D_pHDM-E104K_comb_READ1_shift6.tab

value: Sc-Trp


title: 52810sacCer3_KY1794_11867431001_Cdc73-3HA_rep2

description:
Biological replicate 2 of 2, Cdc73 IP with anti-HA antibody in CDC73-3HA strain
52809-10sacCer3_KY1794_11867431001_Cdc73-3HA_comb_READ1_shift6.tab


title: 579 input


title: 52807sacCer3_KY1529_11867431001_3HA-Rtf1-E104K_rep1

description:
Biological replicate 1 of 2, Rtf1-E104K IP with anti-HA antibody in 3HA-rtf1-E104K (rtf1 mutant) strain
52807-08sacCer3_KY1529_11867431001_3HA-Rtf1-E104K_comb_READ1_shift6.tab

value: MATalpha 3xHA-rtf1-E104K lys2-128delta leu2delta1 ura3-52 trp1delta63