title: DNase-seq from stomach (ENCLB248TKA)

description:
https://www.encodeproject.org/experiments/ENCSR095GWE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR095GWE
assay title: DNase-seq
assembly: hg19, GRCh38
encode release date: 2016-09-22
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB248TKA

source_name: Homo sapiens stomach tissue male fetal (76 days)

value: 76 day

value: ENCBS521MUU at ENCODE; https://www.encodeproject.org/ENCBS521MUU/

value: Derived from ENCODE donor ENCDO647EYG; https://www.encodeproject.org/ENCDO647EYG/


title: DNase-seq from MG63 (ENCLB952FTO)

status: Public on Dec 07 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/ENCSR083STA/
***************
biological replicate number: 1
technical replicate number: 2,1
description: DNase-seq on 14 year old male human MG63 immortalized cell line
experiment encode accession: ENCSR083STA
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-08-18
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB952FTO

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens MG63 immortalized cell line

tag: line

value: immortalized cell line

tag: biosample encode accession

tag: age

value: 14 year

tag: dev stage

value: child

tag: Sex

value: male

tag: lab

value: John Stamatoyannopoulos, UW

tag: link

value: ENCBS091SUW at ENCODE; https://www.encodeproject.org/ENCBS091SUW/

value: Derived from ENCODE donor ENCDO987OSE; https://www.encodeproject.org/ENCDO987OSE/

value: ENCODE dbxrefs Cellosaurus CVCL_0426; http://web.expasy.org/cellosaurus/CVCL_0426


title: genetic modification DNase-seq from K562 (ENCLB672YWT)

description:
https://www.encodeproject.org/experiments/ENCSR064EFK/
***************
biological replicate number: 1
technical replicate number: 1
description: TALEN-mediated heterozygous DHS deletion in K562.
experiment encode accession: ENCSR064EFK
assay title: genetic modification DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-07-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB672YWT

source_name: Homo sapiens K562 immortalized cell line genetically modified (deletion) using TALEs

tag: description

value: adult

value: female

value: 53 year

tag: health state

value: chronic myelogenous leukemia (CML)

value: ENCBS424RFS at ENCODE; https://www.encodeproject.org/ENCBS424RFS/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: DNase-seq from MG63 (ENCLB475XTU)

description:
https://www.encodeproject.org/experiments/ENCSR083STA/
***************
biological replicate number: 2
technical replicate number: 1,2
description: DNase-seq on 14 year old male human MG63 immortalized cell line
experiment encode accession: ENCSR083STA
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-08-18
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB475XTU

value: ENCBS462PMF at ENCODE; https://www.encodeproject.org/ENCBS462PMF/


title: DNase-seq from SJCRH30 (ENCLB336ZYZ)

description:
https://www.encodeproject.org/experiments/ENCSR000FFJ/
***************
biological replicate number: 2
technical replicate number: 1,2
description: SJCRH30 DNase-seq
experiment encode accession: ENCSR000FFJ
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB336ZYZ

source_name: Homo sapiens SJCRH30 immortalized cell line

value: This immortalized cell line was established from cells from the metastatic site of the bone marrow of a child with rhabdomyosarcoma.

value: 17 year

value: unknown

value: ENCBS517AAA at ENCODE; https://www.encodeproject.org/ENCBS517AAA/

value: Derived from ENCODE donor ENCDO339AAA; https://www.encodeproject.org/ENCDO339AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0041; http://web.expasy.org/cellosaurus/CVCL_0041


title: DNase-seq from SJCRH30 (ENCLB335ZYZ)

description:
https://www.encodeproject.org/experiments/ENCSR000FFJ/
***************
biological replicate number: 1
technical replicate number: 1
description: SJCRH30 DNase-seq
experiment encode accession: ENCSR000FFJ
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB335ZYZ

value: immortalized cell line

value: This immortalized cell line was established from cells from the metastatic site of the bone marrow of a child with rhabdomyosarcoma

value: male

value: John Stamatoyannopoulos, UW

value: ENCBS516AAA at ENCODE; https://www.encodeproject.org/ENCBS516AAA/


title: DNase-seq from induced pluripotent stem cell (ENCLB440GKD)

description:
https://www.encodeproject.org/experiments/ENCSR004SUL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR004SUL
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB440GKD
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens induced pluripotent stem cell line male adult (53 years) derived from fibroblast of arm

value: induced pluripotent stem cell

value: induced pluripotent stem cell line

value: These are induced pluripotent stem cells (iPSC) created from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS373AAA at ENCODE; https://www.encodeproject.org/ENCBS373AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F182; http://web.expasy.org/cellosaurus/CVCL_F182

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23338&PgId=166


title: total RNA-seq from mononuclear cell (ENCLB555ALH)

description:
https://www.encodeproject.org/experiments/ENCSR000CUT/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from mononuclear peripheral blood primary whole cells, hMNC-PB isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CUT
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ALH
size range: >200
spikeins used: /references/ENCSR470JZL/

library_source: transcriptomic

molecule: total RNA

source_name: Homo sapiens mononuclear primary cell female adult (52 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/28d53d5f-9170-475d-8bb4-6b6fc6b179d3/@@download/attachment/LID47807.pdf

value: mononuclear cell

value: primary cell

value: Peripherial Blood Mononuclear Cells (hMNC-PB) from a 52 year old caucasian female

value: female

value: 52 year

value: negative for Bac/Fung/Myc, negative for HIV-1/HBV/HCV

tag: passage number

value: ENCBS539ENC at ENCODE; https://www.encodeproject.org/ENCBS539ENC/

value: Derived from ENCODE donor ENCDO306AAA; https://www.encodeproject.org/ENCDO306AAA/

value: PromoCell sample source; http://www.promocell.com/fileadmin/promocell/PDF/C-12907.pdf


title: total RNA-seq from mesenchymal stem cell of Wharton's jelly (ENCLB555ARK)

description:
https://www.encodeproject.org/experiments/ENCSR000CUO/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from mesenchymal umbilical cord derived stem cells, hMSC-UC isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CUO
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ARK
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens mesenchymal of Wharton's jelly stem cell male newborn

extract_protocol:
data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a03729a1-9ff5-4b06-9454-dbf5489c0d29/@@download/attachment/LID47299.pdf

value: stem cell

value: Mesenchymal Stem Cells from Wharton's Jelly (hMSC-UC) from the umbilical cord of a newborn caucasian male

value: newborn

value: male

value: unknown

value: ENCBS462ENC at ENCODE; https://www.encodeproject.org/ENCBS462ENC/

value: Derived from ENCODE donor ENCDO136AAA; https://www.encodeproject.org/ENCDO136AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_Y483; http://web.expasy.org/cellosaurus/CVCL_Y483

value: ENCODE dbxrefs hMSC-UC; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=hMSC-UC


title: total RNA-seq from GM12878 (ENCLB555AKM)

description:
https://www.encodeproject.org/experiments/ENCSR000CVT/
***************
biological replicate number: 3
technical replicate number: 1
description: The libraries contained in this experiment come from the nucleolar fraction of independent growths of cell line GM12878. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CVT
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2013-03-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AKM
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens GM12878 immortalized cell line nucleolus fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/692833ab-d099-4cf5-b2f2-f0117fb254a3/@@download/attachment/LID47963.pdf

value: immortalized cell line

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: adult

value: Thomas Gingeras, CSHL

tag: subcellular fraction term name

value: nucleolus

value: ENCBS756AAA at ENCODE; https://www.encodeproject.org/ENCBS756AAA/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: ENCODE dbxrefs GM12878; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=GM12878

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: total RNA-seq from mesenchymal stem cell of Wharton's jelly (ENCLB555AUM)

description:
https://www.encodeproject.org/experiments/ENCSR000CUO/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from mesenchymal umbilical cord derived stem cells, hMSC-UC isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CUO
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AUM
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens mesenchymal of Wharton's jelly stem cell female newborn

extract_protocol:
data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/3c9f629c-db84-4715-ad3d-6c12edebf56f/@@download/attachment/LID47300.pdf

value: stem cell

value: Mesenchymal Stem Cells from Wharton's Jelly (hMSC-UC) from the umbilical cord of a newborn caucasian female

value: newborn

value: female

value: negative for Bac/Fung/Myc, negative for HIV-1/HBV/HCV

value: ENCBS461ENC at ENCODE; https://www.encodeproject.org/ENCBS461ENC/

value: Derived from ENCODE donor ENCDO137AAA; https://www.encodeproject.org/ENCDO137AAA/


title: total RNA-seq from mesenchymal stem cell of the bone marrow (ENCLB555ANL)

description:
https://www.encodeproject.org/experiments/ENCSR000CUD/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from mesenchymal bone marrow derived stem cells, hMSC-BM isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CUD
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ANL
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens mesenchymal of the bone marrow stem cell male adult (57 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0e55e157-f3ca-4c48-b32c-565fbcb3bbe8/@@download/attachment/LID47100.pdf

value: Mesenchymal Stem Cells from femoral head bone marrow (hMSC-BM) that were surgically ressected from a 57 year old caucasian male

value: male

value: 57 year

value: ENCBS459ENC at ENCODE; https://www.encodeproject.org/ENCBS459ENC/

value: Derived from ENCODE donor ENCDO134AAA; https://www.encodeproject.org/ENCDO134AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_Y510; http://web.expasy.org/cellosaurus/CVCL_Y510

value: ENCODE dbxrefs hMSC-BM; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=hMSC-BM


title: DNase-seq from hematopoietic multipotent progenitor cell (ENCLB162HJG)

description:
https://www.encodeproject.org/experiments/ENCSR098PTC/
***************
biological replicate number: 1
technical replicate number: 2,1
description:
experiment encode accession: ENCSR098PTC
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB162HJG

source_name: Homo sapiens hematopoietic multipotent progenitor primary cell male adult (25 years) treated with interleukin-3 , kit ligand , hydrocortisone succinate , erythropoietin

value: primary cell

value: Day 0 (T0)

value: adult

tag: treatments

value: treatment_term_id:UniprotKB:P08700; treatment_term_name:interleukin-3; treatment_type:protein; treatment_term_id:UniprotKB:P21583; treatment_term_name:kit ligand; treatment_type:protein; treatment_term_id:CHEBI:31677; treatment_term_name:hydrocortisone succinate; treatment_type:chemical; treatment_term_id:CHEBI:81579; treatment_term_name:erythropoietin; treatment_type:chemical;

value: 25 year

value: John Stamatoyannopoulos, UW

value: ENCBS736SRW at ENCODE; https://www.encodeproject.org/ENCBS736SRW/

value: Derived from ENCODE donor ENCDO937OUY; https://www.encodeproject.org/ENCDO937OUY/


title: total RNA-seq from mesenchymal stem cell of adipose (ENCLB555ATX)

description:
https://www.encodeproject.org/experiments/ENCSR000CTZ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from mesenchymal adipose derived stem cells, hMSC-AT isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTZ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ATX
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens mesenchymal of adipose stem cell female adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2eb5d790-fede-48ee-9a4c-22d93f349ed1/@@download/attachment/LID47098.pdf

value: mesenchymal stem cell of adipose

value: stem cell

value: Mesenchymal Stem Cells from subcutaneous adipose tissue (hMSC-AT) that were surgically ressected from the abdomen of a 37 year old caucasian female

value: female

value: 37 year

value: negative for Bac/Fung/Myc, negative for HIV-1/HBV/HCV

value: Thomas Gingeras, CSHL

value: ENCBS458ENC at ENCODE; https://www.encodeproject.org/ENCBS458ENC/

value: Derived from ENCODE donor ENCDO133AAA; https://www.encodeproject.org/ENCDO133AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_Y509; http://web.expasy.org/cellosaurus/CVCL_Y509

value: ENCODE dbxrefs hMSC-AT; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=hMSC-AT


title: total RNA-seq from mesenchymal stem cell of adipose (ENCLB555ALU)

description:
https://www.encodeproject.org/experiments/ENCSR000CTZ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from mesenchymal adipose derived stem cells, hMSC-AT isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTZ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ALU
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens mesenchymal of adipose stem cell female adult (42 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/51c8db2e-abda-4fb8-a489-190293cb85fa/@@download/attachment/LID47097.pdf

value: Mesenchymal Stem Cells from subcutaneous adipose tissue (hMSC-AT) that were surgically ressected from the abdomen of a 42 year old caucasian female

value: adult

value: 42 year

value: ENCBS457ENC at ENCODE; https://www.encodeproject.org/ENCBS457ENC/

value: Derived from ENCODE donor ENCDO132AAA; https://www.encodeproject.org/ENCDO132AAA/


title: total RNA-seq from mesenchymal stem cell of the bone marrow (ENCLB555AVI)

description:
https://www.encodeproject.org/experiments/ENCSR000CUD/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from mesenchymal bone marrow derived stem cells, hMSC-BM isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CUD
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AVI
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens mesenchymal of the bone marrow stem cell female adult (60 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/780060c9-dd98-4360-aa7e-344c1bb44215/@@download/attachment/LID47099.pdf

value: Mesenchymal Stem Cells from femoral head bone marrow (hMSC-BM) that were surgically ressected from a 60 year old caucasian female

value: 60 year

value: ENCBS460ENC at ENCODE; https://www.encodeproject.org/ENCBS460ENC/

value: Derived from ENCODE donor ENCDO135AAA; https://www.encodeproject.org/ENCDO135AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_Y510; http://web.expasy.org/cellosaurus/CVCL_Y510

value: ENCODE dbxrefs hMSC-BM; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=hMSC-BM


title: polyA mRNA RNA-seq from MCF-7 (ENCLB555APP)

description:
https://www.encodeproject.org/experiments/ENCSR000CTU/
***************
biological replicate number: 3
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line MCF-7. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTU
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555APP
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens MCF-7 immortalized cell line cytosolic fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/3f8b5d45-926a-4c4c-aacd-da6ffdbc1683/@@download/attachment/LID46857.pdf

value: immortalized cell line

value: Cytosol subcellular fraction of MCF-7 mammary gland, adenocarcinoma

value: female

value: 69 year

value: breast cancer (adenocarcinoma)

value: cytosol

value: ENCBS103ENC at ENCODE; https://www.encodeproject.org/ENCBS103ENC/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031

value: ENCODE dbxrefs MCF-7; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MCF-7

value: ATCC sample source; http://www.atcc.org/products/all/HTB-22.aspx


title: polyA mRNA RNA-seq from SK-N-SH (ENCLB555AXT)

description:
https://www.encodeproject.org/experiments/ENCSR000CTT/
***************
biological replicate number: 3
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line SK-N-SH. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTT
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AXT
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens SK-N-SH immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/8d00135e-e195-4c0e-aa8f-4d8857d0c2ff/@@download/attachment/LID46598.pdf

value: SK-N-SH

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

value: child

value: 4 year

value: Thomas Gingeras, CSHL

value: ENCBS362ENC at ENCODE; https://www.encodeproject.org/ENCBS362ENC/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/

value: ENCODE dbxrefs Cellosaurus CVCL_0531; http://web.expasy.org/cellosaurus/CVCL_0531

value: ENCODE dbxrefs SK-N-SH; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=SK-N-SH

value: ATCC sample source; http://www.atcc.org/products/all/HTB-11.aspx


title: polyA mRNA RNA-seq from MCF-7 (ENCLB555AQA)

description:
https://www.encodeproject.org/experiments/ENCSR000CTU/
***************
biological replicate number: 4
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line MCF-7. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTU
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AQA
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0cf55b53-f966-476d-b460-be75345729ec/@@download/attachment/LID46858.pdf

value: immortalized cell line

value: Cytosol subcellular fraction of MCF-7 mammary gland adenocarcinoma.

value: adult

value: female

value: 69 year

value: breast cancer (adenocarcinoma)

value: ENCBS581MUA at ENCODE; https://www.encodeproject.org/ENCBS581MUA/


title: polyA mRNA RNA-seq from SK-N-SH (ENCLB555AMH)

description:
https://www.encodeproject.org/experiments/ENCSR000CTS/
***************
biological replicate number: 4
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line SK-N-SH. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTS
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AMH
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens SK-N-SH immortalized cell line nuclear fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a542da6f-8da6-4ac4-864e-160a9e56e32c/@@download/attachment/LID46597.pdf

value: SK-N-SH

value: nucleus

value: ENCBS364ENC at ENCODE; https://www.encodeproject.org/ENCBS364ENC/


title: DNase-seq from PC-3 (ENCLB620TSQ)

description:
https://www.encodeproject.org/experiments/ENCSR052AWE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR052AWE
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-11-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB620TSQ

source_name: Homo sapiens PC-3 immortalized cell line

value: male

value: 62 year

value: grade IV, adenocarcinoma

value: John Stamatoyannopoulos, UW

value: ENCBS504WVV at ENCODE; https://www.encodeproject.org/ENCBS504WVV/

value: Derived from ENCODE donor ENCDO349AAA; https://www.encodeproject.org/ENCDO349AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0035; http://web.expasy.org/cellosaurus/CVCL_0035


title: polyA mRNA RNA-seq from SK-N-SH (ENCLB555AMI)

description:
https://www.encodeproject.org/experiments/ENCSR000CTS/
***************
biological replicate number: 3
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line SK-N-SH. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTS
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AMI
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b7125981-680d-4f1c-9d98-de63ba9d0517/@@download/attachment/LID46596.pdf

value: immortalized cell line

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

value: child

value: 4 year

value: Thomas Gingeras, CSHL

value: ENCBS361ENC at ENCODE; https://www.encodeproject.org/ENCBS361ENC/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/

value: ENCODE dbxrefs Cellosaurus CVCL_0531; http://web.expasy.org/cellosaurus/CVCL_0531

value: ENCODE dbxrefs SK-N-SH; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=SK-N-SH

value: ATCC sample source; http://www.atcc.org/products/all/HTB-11.aspx


title: polyA mRNA RNA-seq from SK-N-SH (ENCLB555AKZ)

description:
https://www.encodeproject.org/experiments/ENCSR000CTR/
***************
biological replicate number: 4
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line SK-N-SH. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTR
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AKZ
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens SK-N-SH immortalized cell line cytosolic fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b1b2eb78-bdb3-4447-9d82-cc7abd2eb148/@@download/attachment/LID46595.pdf

value: SK-N-SH

value: female

value: cytosol

value: ENCBS363ENC at ENCODE; https://www.encodeproject.org/ENCBS363ENC/


title: DNase-seq from induced pluripotent stem cell (ENCLB670LDI)

description:
https://www.encodeproject.org/experiments/ENCSR004SUL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR004SUL
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB670LDI

value: induced pluripotent stem cell

value: induced pluripotent stem cell line

value: These are induced pluripotent stem cells (iPSC) created from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: adult

value: male

value: ENCBS368AAA at ENCODE; https://www.encodeproject.org/ENCBS368AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F182; http://web.expasy.org/cellosaurus/CVCL_F182

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23338&PgId=166


title: polyA mRNA RNA-seq from IMR-90 (ENCLB555ATO)

description:
https://www.encodeproject.org/experiments/ENCSR000CTQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on human IMR90 whole cell long polyA+ RNA
experiment encode accession: ENCSR000CTQ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ATO
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens IMR-90 primary cell female fetal (16 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6f7de630-6f1f-42bc-a532-aedcbc764688/@@download/attachment/LID45016.pdf

value: primary cell

value: fetal lung fibroblasts, newly promoted to tier 2:not in 2011 analysis

value: fetal

value: 16 week

value: unknown

value: Thomas Gingeras, CSHL

value: ENCBS370ENC at ENCODE; https://www.encodeproject.org/ENCBS370ENC/

value: Derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/

value: ENCODE dbxrefs Cellosaurus CVCL_0347; http://web.expasy.org/cellosaurus/CVCL_0347

value: ENCODE dbxrefs IMR90; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=IMR90

value: ATCC sample source; http://www.atcc.org/products/all/CCL-186.aspx


title: polyA mRNA RNA-seq from SK-N-SH (ENCLB555AKY)

description:
https://www.encodeproject.org/experiments/ENCSR000CTR/
***************
biological replicate number: 3
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line SK-N-SH. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTR
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AKY
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/8f222ffd-8b26-4c77-9e89-a2fd1bed2b01/@@download/attachment/LID46594.pdf

value: SK-N-SH

value: immortalized cell line

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

value: child

value: female

value: 4 year

value: cytosol

value: ENCBS360ENC at ENCODE; https://www.encodeproject.org/ENCBS360ENC/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/

value: ENCODE dbxrefs Cellosaurus CVCL_0531; http://web.expasy.org/cellosaurus/CVCL_0531

value: ENCODE dbxrefs SK-N-SH; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=SK-N-SH

value: ATCC sample source; http://www.atcc.org/products/all/HTB-11.aspx


title: polyA mRNA RNA-seq from IMR-90 (ENCLB555AMS)

description:
https://www.encodeproject.org/experiments/ENCSR000CTP/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from lung fibroblasts primary nuclear extracts, IMR90. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTP
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AMS
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens IMR-90 primary cell nuclear fraction female fetal (16 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7cab1293-4d8f-42fb-aafb-5c4c89b99574/@@download/attachment/LID45613.pdf

value: primary cell

value: fetal lung fibroblasts, newly promoted to tier 2:not in 2011 analysis

value: fetal

value: 16 week

value: unknown

value: Thomas Gingeras, CSHL

value: nucleus

value: ENCBS369ENC at ENCODE; https://www.encodeproject.org/ENCBS369ENC/


title: polyA mRNA RNA-seq from IMR-90 (ENCLB555AUC)

description:
https://www.encodeproject.org/experiments/ENCSR000CTN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on human IMR90 cytosol long polyA+ RNA
experiment encode accession: ENCSR000CTN
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AUC
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens IMR-90 primary cell cytosolic fraction female fetal (16 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6731d949-7825-4c69-b67f-509b9bd6807a/@@download/attachment/LID45612.pdf

value: ENCBS371ENC at ENCODE; https://www.encodeproject.org/ENCBS371ENC/

value: Derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/

value: ENCODE dbxrefs Cellosaurus CVCL_0347; http://web.expasy.org/cellosaurus/CVCL_0347

value: ENCODE dbxrefs IMR90; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=IMR90

value: ATCC sample source; http://www.atcc.org/products/all/CCL-186.aspx


title: polyA mRNA RNA-seq from MCF-7 (ENCLB555AVS)

description:
https://www.encodeproject.org/experiments/ENCSR000CTO/
***************
biological replicate number: 4
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line MCF-7. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTO
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AVS
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens MCF-7 immortalized cell line nuclear fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f1927b46-cb79-4edf-be32-9de03243e09a/@@download/attachment/LID46860.pdf

value: immortalized cell line

value: Nuclear subcellular fraction of MCF-7 mammary gland adenocarcinoma.

value: adult

value: female

value: 69 year

value: breast cancer (adenocarcinoma)

value: ENCBS564FRY at ENCODE; https://www.encodeproject.org/ENCBS564FRY/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031

value: ENCODE dbxrefs MCF-7; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MCF-7

value: ATCC sample source; http://www.atcc.org/products/all/HTB-22.aspx


title: total RNA-seq from GM12878 (ENCLB555AKL)

description:
https://www.encodeproject.org/experiments/ENCSR000CVT/
***************
biological replicate number: 4
technical replicate number: 1
description: The libraries contained in this experiment come from the nucleolar fraction of independent growths of cell line GM12878. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CVT
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2013-03-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AKL
size range: >200
spikeins used: /references/ENCSR470JZL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/276cd12e-63d3-42bc-a34e-42bc757ac565/@@download/attachment/LID47964.pdf

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: unknown

value: Thomas Gingeras, CSHL

value: nucleolus

value: ENCBS758AAA at ENCODE; https://www.encodeproject.org/ENCBS758AAA/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: ENCODE dbxrefs GM12878; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=GM12878

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: polyA mRNA RNA-seq from MCF-7 (ENCLB555AVR)

description:
https://www.encodeproject.org/experiments/ENCSR000CTO/
***************
biological replicate number: 3
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line MCF-7. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTO
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AVR
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/9409cdf2-f525-4075-b5f1-ee92c7b36a19/@@download/attachment/LID46859.pdf

value: immortalized cell line

value: Nuclear subcellular fraction of MCF-7 mammary gland adenocarcinoma

value: adult

value: female

value: nucleus

value: ENCBS104ENC at ENCODE; https://www.encodeproject.org/ENCBS104ENC/


title: polyA mRNA RNA-seq from IMR-90 (ENCLB555ATP)

description:
https://www.encodeproject.org/experiments/ENCSR000CTQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on human IMR90 whole cell long polyA+ RNA
experiment encode accession: ENCSR000CTQ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ATP
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/461c8b9a-68a6-477f-a299-63a53054ce2d/@@download/attachment/LID45017.pdf

value: primary cell

value: fetal lung fibroblasts, newly promoted to tier 2:not in 2011 analysis

value: fetal

value: 16 week

value: ENCBS373ENC at ENCODE; https://www.encodeproject.org/ENCBS373ENC/

value: Derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/

value: ENCODE dbxrefs Cellosaurus CVCL_0347; http://web.expasy.org/cellosaurus/CVCL_0347

value: ENCODE dbxrefs IMR90; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=IMR90

value: ATCC sample source; http://www.atcc.org/products/all/CCL-186.aspx


title: polyA mRNA RNA-seq from A549 (ENCLB555ASB)

description:
https://www.encodeproject.org/experiments/ENCSR000CTM/
***************
biological replicate number: 4
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line A549. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTM
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ASB
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens A549 immortalized cell line nuclear fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bf94d175-0230-4325-9702-d2e796c129db/@@download/attachment/LID45900.pdf

value: epithelial cell line derived from a 58 year old caucasian male lung carcinoma.

value: male

value: 58 year

value: Thomas Gingeras, CSHL

value: ENCBS450ENC at ENCODE; https://www.encodeproject.org/ENCBS450ENC/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023

value: ENCODE dbxrefs A549; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=A549

value: ATCC sample source; http://www.atcc.org/products/all/CCL-185.aspx


title: polyA mRNA RNA-seq from A549 (ENCLB555AWP)

description:
https://www.encodeproject.org/experiments/ENCSR000CTL/
***************
biological replicate number: 4
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line A549. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTL
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AWP
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens A549 immortalized cell line cytosolic fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/fbb03918-6e0e-4543-8ddb-1beed80b93d5/@@download/attachment/LID45898.pdf

value: immortalized cell line

value: adult

value: cytosol

value: ENCBS449ENC at ENCODE; https://www.encodeproject.org/ENCBS449ENC/


title: total RNA-seq from IMR-90 (ENCLB555AMY)

description:
https://www.encodeproject.org/experiments/ENCSR000CTK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on human IMR90 whole cell long total RNA
experiment encode accession: ENCSR000CTK
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AMY
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/961fdf61-ad4a-47f2-946e-bb4cfcdf7575/@@download/attachment/LID45238.pdf

value: primary cell

value: fetal lung fibroblasts, newly promoted to tier 2:not in 2011 analysis

value: fetal

value: female

value: 16 week

value: unknown

value: ENCBS370ENC at ENCODE; https://www.encodeproject.org/ENCBS370ENC/

value: Derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/


title: polyA mRNA RNA-seq from U-87 MG (ENCLB285ZDC)

description:
https://www.encodeproject.org/experiments/ENCSR000BYO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on U87 greater than 200bp polyA+
experiment encode accession: ENCSR000BYO
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB285ZDC
size range: >200
spikeins used: /references/ENCSR466YMU/

source_name: Homo sapiens U-87 MG immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0f926b2b-f4ce-402a-b936-884770ed81d1/@@download/attachment/wgEncodeHaibRnaSeq.html.pdf

value: U-87 MG

value: male

value: 44 year

value: Richard Myers, HAIB

value: ENCBS424ENC at ENCODE; https://www.encodeproject.org/ENCBS424ENC/

value: Derived from ENCODE donor ENCDO000ADQ; https://www.encodeproject.org/ENCDO000ADQ/

value: ENCODE dbxrefs Cellosaurus CVCL_0022; http://web.expasy.org/cellosaurus/CVCL_0022

value: ENCODE dbxrefs U87; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=U87


title: polyA mRNA RNA-seq from A549 (ENCLB555AWO)

description:
https://www.encodeproject.org/experiments/ENCSR000CTL/
***************
biological replicate number: 3
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line A549. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTL
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AWO
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/3aa213ee-25d1-4f18-95cd-7d9ba9ab1f98/@@download/attachment/LID45897.pdf

value: immortalized cell line

value: epithelial cell line derived from a 58 year old caucasian male lung carcinoma.

value: adult

value: 58 year

value: Thomas Gingeras, CSHL

value: cytosol

value: ENCBS446ENC at ENCODE; https://www.encodeproject.org/ENCBS446ENC/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023

value: ENCODE dbxrefs A549; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=A549

value: ATCC sample source; http://www.atcc.org/products/all/CCL-185.aspx


title: polyA mRNA RNA-seq from A549 (ENCLB555ASA)

description:
https://www.encodeproject.org/experiments/ENCSR000CTM/
***************
biological replicate number: 3
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line A549. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTM
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ASA
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6315bb22-d367-4f01-b8be-b3328588c33b/@@download/attachment/LID45899.pdf

value: male

value: nucleus

value: ENCBS447ENC at ENCODE; https://www.encodeproject.org/ENCBS447ENC/


title: total RNA-seq from IMR-90 (ENCLB555AMX)

description:
https://www.encodeproject.org/experiments/ENCSR000CTK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on human IMR90 whole cell long total RNA
experiment encode accession: ENCSR000CTK
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AMX
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/8fd1aa0f-7df0-4451-ba0d-f2c68d71b0c4/@@download/attachment/LID45239.pdf

value: primary cell

value: fetal lung fibroblasts, newly promoted to tier 2:not in 2011 analysis

value: fetal

value: female

value: 16 week

value: unknown

value: ENCBS373ENC at ENCODE; https://www.encodeproject.org/ENCBS373ENC/

value: Derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/

value: ENCODE dbxrefs Cellosaurus CVCL_0347; http://web.expasy.org/cellosaurus/CVCL_0347

value: ENCODE dbxrefs IMR90; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=IMR90

value: ATCC sample source; http://www.atcc.org/products/all/CCL-186.aspx


title: shRPA1 Bru-Seq

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

description:
Library strategy: Bru-Seq
molecule: bru-labeled RNA
hr16
Bromouridine labeling RNA for sequencing

data_processing:
Paired-end reads from ChIP-seq were aligned to the human genome (hg19) using the Bowtie2 (Langmead and Salzberg, 2012) software with default parameters. After PCR duplications removed by samtools (Li et al., 2009), consistent pair reads were used for further analysis. Sequence reads from RNA-seq and Bru-seq samples were aligned to the human genome hg19 and to gene annotations from Refseq gene using TopHat v2.05.
The genome-wide read coverage was calculated by BEDTools and in-house Perl programs.
The ChIP-seq peaks were identified using MACS2 (Zhang et al., 2008) using 0.001 as the p value cutoff. For Bru-seq, the number of reads in up- and downstream of TSS was counted, then DESeq differential read count analysis was performed. For the RNA-seq, Cufflinks v2.0.2 was used to calculate FPKM values of genes. Differential gene expression was analyzed by Cuffdiff.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated, scores represent the normalization reads density.

growth_protocol: HeLa cells were grown in Dulbecco’s Modiﬁed Eagle’s medium (Gibco) supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
HeLa cells were crosslinked with 2mM DSG in PBS for 30 min at room temperature, followed by treatment with 1% formaldehyde for 15 min. After quenching with glycine, the cells were harvested and digested by Mnase (NEB, M0247S，0.5u/1000 cells) at 37°c for 20mins to produce soluble chromatin with DNA fragments in the range of 150–300 bp. This chromatin was immunoprecipitated using antibodies against  RPA1 or RPA2 overnight. Then, chromatin complexes were incubated with protein G beads for 3 h. After extensive washing steps, the DNA was recovered from the protein G complex using elution buffer (10 mM Tris at pH 8.0, 10 mM EDTA at pH 8.0, 1% SDS, 150 mM NaCL, 5 mM DTT). DNA was subsequently purified using Qiagen Mini Elute PCR purification kit. For RNA-seq, total RNA was extracted using the miRNeasy Mini kit (Qiagen, Valencia, CA). For Bru-seq, bromouridine labeling, isolation of Bru-RNA and strand specific cDNA library preparation were performed as described previously (Paulsen et al., 2014; Paulsen et al., 2013). Briefly, Bromouridine (Aldrich) was added to the media of HeLa cell to a ﬁnal concentration of 2 mM, and cells were incubated at 37 °C for 30 min. Cells were then directly lysed by Trizol and isolated total RNA. Then Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads under gentle agitation at room temperature for 1 h.
ChIP-seq libraries were prepared from 10 ng ChIP and input DNA using the Ovation ultralow DR Multiplex kit (NuGEN, San Carlos, CA). The ChIP-seq libraries were sequenced to 51 base pairs from both ends on an Illumina HiSeq 2000 instrument in the Mayo Clinic Center for Individualized Medicine Medical Genomics Facility.RNA-seq libraries were prepared with ovation RNA-seq system v2 kit (NuGEN) according to the manufacture’s instruction, and were sequenced on an Illumina HiSeq 2000 instrument in the Mayo Clinic Center for Individualized Medicine Medical Genomics Facility. For Bru-seq, Isolated Bru-labeled RNA was used to prepare strand-speciﬁc DNA libraries by using the Illumina Tru Seq Kit (Illumina) according to the manufacturer’s instructions with modiﬁcations described as (Paulsen et al., 2014).

tag: cell line

value: Hela

tag: medium

value: DMEM

tag: cell cycle stage

value: asynchronization

tag: treatment

tag: labeling agent

value: Bromouridine (Bru)


title: shRPA1 RNA-seq repeat 2


title: polyA mRNA RNA-seq from U-87 MG (ENCLB271KOP)

description:
https://www.encodeproject.org/experiments/ENCSR000BYO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on U87 greater than 200bp polyA+
experiment encode accession: ENCSR000BYO
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB271KOP
size range: >200
spikeins used: /references/ENCSR466YMU/

tag: line

value: U-87 MG

value: immortalized cell line

value: adult

value: male

value: 44 year

value: Richard Myers, HAIB

value: ENCBS424ENC at ENCODE; https://www.encodeproject.org/ENCBS424ENC/

value: Derived from ENCODE donor ENCDO000ADQ; https://www.encodeproject.org/ENCDO000ADQ/

value: ENCODE dbxrefs Cellosaurus CVCL_0022; http://web.expasy.org/cellosaurus/CVCL_0022

value: ENCODE dbxrefs U87; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=U87


title: NT RNA-seq repeat 2

source_name: NT

value: NT


title: shHIRA Bru-Seq

description:
Library strategy: Bru-Seq
molecule: bru-labeled RNA
hr15
Bromouridine labeling RNA for sequencing

source_name: shHIRA

value: shHIRA


title: shRPA1 RNA-seq


title: NT RNA-seq repeat 1


title: RPA1 ChIP

source_name: RPA1 ChIP

tag: chip antibody

value: RPA1 (gifted by Dr. Bruce Stillman)


title: RPA2 ChIP repeat 2

source_name: RPA2 ChIP

value: Hela

value: RPA2 (Abcam, catalog# ab16850, lot# GR88602-1)


title: polyA mRNA RNA-seq from IMR-90 (ENCLB555AMR)

description:
https://www.encodeproject.org/experiments/ENCSR000CTP/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from lung fibroblasts primary nuclear extracts, IMR90. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTP
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AMR
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/021bee2b-12e1-4fd7-bd5b-bd8dc4d11c84/@@download/attachment/LID45635.pdf

value: primary cell

value: fetal lung fibroblasts, newly promoted to tier 2:not in 2011 analysis

tag: biosample encode accession

value: fetal

value: female

tag: age

value: 16 week

value: unknown

value: Thomas Gingeras, CSHL

value: nucleus

value: ENCBS372ENC at ENCODE; https://www.encodeproject.org/ENCBS372ENC/

value: Derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/

value: ENCODE dbxrefs Cellosaurus CVCL_0347; http://web.expasy.org/cellosaurus/CVCL_0347

value: ENCODE dbxrefs IMR90; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=IMR90

value: ATCC sample source; http://www.atcc.org/products/all/CCL-186.aspx


title: RPA2 ChIP repeat 1

value: DMEM

value: asynchronization


title: polyA mRNA RNA-seq from IMR-90 (ENCLB555APS)

description:
https://www.encodeproject.org/experiments/ENCSR000CTN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on human IMR90 cytosol long polyA+ RNA
experiment encode accession: ENCSR000CTN
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555APS
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a81b8cb7-7e18-487a-940c-358abce2cdf6/@@download/attachment/LID45611.pdf

tag: dev stage

tag: Sex

value: cytosol

value: ENCBS368ENC at ENCODE; https://www.encodeproject.org/ENCBS368ENC/


title: hESC_siTP53_replicate2

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

description: processed data in series file hESC_siTP53_pool.fpkm.txt

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
RNA-seq reads were aligned to the hg19 genome using tophat 2.0.10
Genome_build: hg19
Supplementary_files_format_and_content: For siTP53 RNA-seq data, fpkm values were generated using cufflinks 2.2.1. For shLncRNA RNA-seq data, reads count were generated using HTSeq 0.6.1p1

source_name: H9 hESCs

growth_protocol: Human ESCs were cultured in mTeSR1 media on metrigel coated plates following standard culture protocols. Transient siRNA transfection (siControl and siT53) were performed following the procedureds described in (Jain et al, PLoS Biology, 2012. PMID: 22389628). Stable shRNA transfections (shControl and shLncRNA) were performed following the procedures as described in (Akdemir et al, Nucleic Acids Res, 2014. PMID: 26636540).

extract_protocol:
Human ESCs were harvested and RNA was isolated using Trizol reagent. Illumina TruSeq stranded total RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hESCs were treated with Retinoic Acid as described in (Jain et al, PLoS Biology, 2012. PMID: 22389628)

value: TP53 Knock Down


title: hESC_siTP53+RA_replicate2

value: TP53 Knock Down treated with Retinoic Acid (RA) for 4 days


title: hESC_siTP53_replicate1


title: hESC_siControl_replicate1

value: Control


title: input repeat 1

source_name: input

value: Hela


title: input repeat 2


title: hESC_siTP53+RA_replicate1


title: hESC_siControl+RA_replicate2

value: Control treated with Retinoic Acid (RA) for 4 days


title: NT Bru-Seq

description:
Library strategy: Bru-Seq
molecule: bru-labeled RNA
hr14
Bromouridine labeling RNA for sequencing

value: NT

value: Bromouridine (Bru)


title: polyA mRNA RNA-seq from SK-N-SH (ENCLB555AWX)

description:
https://www.encodeproject.org/experiments/ENCSR000CTT/
***************
biological replicate number: 4
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line SK-N-SH. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTT
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AWX
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens SK-N-SH immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/444a9820-a7bd-4f9c-a33d-2195e5f2739e/@@download/attachment/LID46599.pdf

value: SK-N-SH

value: immortalized cell line

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

value: child

value: female

value: 4 year

tag: lab

value: Thomas Gingeras, CSHL

tag: link

value: ENCBS365ENC at ENCODE; https://www.encodeproject.org/ENCBS365ENC/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/

value: ENCODE dbxrefs Cellosaurus CVCL_0531; http://web.expasy.org/cellosaurus/CVCL_0531

value: ENCODE dbxrefs SK-N-SH; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=SK-N-SH

value: ATCC sample source; http://www.atcc.org/products/all/HTB-11.aspx


title: shHIRA RNA-seq

value: DMEM

value: asynchronization

value: shHIRA


title: hESC_shLncRNA_replicate3

description: processed data in series file hESC_shLncRNA_pool.htseq_reads_count.txt

value: lncRNA Knock Down


title: hESC_siControl+RA_replicate1

value: Control treated with Retinoic Acid (RA) for 4 days


title: hESC_shLncRNA_replicate2


title: hESC_shControl_replicate1

value: Control


title: hESC_shControl_replicate3


title: hESC_shLncRNA_replicate1


title: polyA mRNA RNA-seq from C3H10T1/2 (ENCLB358ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AHZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of 10T1-2 polyadenlated RNA
experiment encode accession: ENCSR000AHZ
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB358ZZZ
size range: >200
spikeins used: /references/ENCSR714LOF/

organism: Mus musculus

source_name: Mus musculus C3H10T1/2 immortalized cell line

extract_protocol:
general protocol: https://www.encodeproject.org/documents/1549840e-0ec9-44c8-adb3-43ceac9d7d6b/@@download/attachment/wgEncodeCaltechRnaSeq.release1.html.pdf
extraction method: Trizol (Invitrogen 15596-026)

value: immortalized cell line

tag: description

value: Multipotential cell line that can be converted by 5-azacytidine into three mesodermal stem cell lineages.

value: unknown

value: not collected

tag: health state

value: Barbara Wold, Caltech

value: ENCBS034ENC at ENCODE; https://www.encodeproject.org/ENCBS034ENC/

value: Derived from ENCODE donor ENCDO321TZV; https://www.encodeproject.org/ENCDO321TZV/

value: ENCODE dbxrefs Cellosaurus CVCL_0190; http://web.expasy.org/cellosaurus/CVCL_0190

value: ENCODE dbxrefs 10T1/2; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=10T1/2

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-226.aspx


title: polyA mRNA RNA-seq from C2C12 (ENCLB359ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AHY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of C2C12 polyadenlated RNA
experiment encode accession: ENCSR000AHY
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB359ZZZ
size range: >200
spikeins used: /references/ENCSR714LOF/

source_name: Mus musculus C2C12 immortalized cell line

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

value: ENCBS124ENC at ENCODE; https://www.encodeproject.org/ENCBS124ENC/

value: ENCODE dbxrefs Cellosaurus CVCL_0188; http://web.expasy.org/cellosaurus/CVCL_0188

value: ENCODE dbxrefs C2C12; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=C2C12


title: polyA mRNA RNA-seq from C3H10T1/2 (ENCLB357ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AHX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse 10T1-2 treated with differentiation treatment (control) for 60 hours polyA+
experiment encode accession: ENCSR000AHX
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB357ZZZ
size range: >200
spikeins used: /references/ENCSR714LOF/

source_name: Mus musculus C3H10T1/2 immortalized cell line derived from C3H10T1/2

value: As a control, this multipotential cell line was treated with a differentiation protocol that will not induce these cells to differentiate into three mesodermal stem cell lineages.

value: ENCBS035ENC at ENCODE; https://www.encodeproject.org/ENCBS035ENC/


title: genetic modification DNase-seq from K562 (ENCLB001AHD)

description:
https://www.encodeproject.org/experiments/ENCSR967DXR/
***************
biological replicate number: 1
technical replicate number: 1
description: TALEN-mediated heterozygous DHS deletion in K562
experiment encode accession: ENCSR967DXR
assay title: genetic modification DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-07-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB001AHD
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

source_name: Homo sapiens K562 immortalized cell line genetically modified (deletion) using TALEs

value: TALEN-mediated heterozygous DHS deletion in K562.

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: John Stamatoyannopoulos, UW

value: ENCBS410EIF at ENCODE; https://www.encodeproject.org/ENCBS410EIF/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: polyA mRNA RNA-seq from myocyte (ENCLB356ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AIA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse C2C12 differentiated for 60 hours polyA+
experiment encode accession: ENCSR000AIA
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB356ZZZ
size range: >200
spikeins used: /references/ENCSR714LOF/

source_name: Mus musculus myocyte in vitro differentiated cells derived from C2C12

value: myocyte

value: in vitro differentiated cells

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury; differentiated from C2C12 cells for 60 hours

value: unknown

value: not collected

value: Barbara Wold, Caltech

value: ENCBS127ENC at ENCODE; https://www.encodeproject.org/ENCBS127ENC/

value: Derived from ENCODE donor ENCDO321TZV; https://www.encodeproject.org/ENCDO321TZV/


title: hESC_siControl_replicate2

value: Control


title: DNase-seq from thyroid gland (ENCLB659EDK)

description:
https://www.encodeproject.org/experiments/ENCSR902XFY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR902XFY
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-23
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB659EDK
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

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

value: thyroid gland

value: tissue

value: adult

value: male

value: 54 year

value: ENCBS702NUN at ENCODE; https://www.encodeproject.org/ENCBS702NUN/

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


title: polyA mRNA RNA-seq from HepG2 (ENCLB334AQY)

description:
https://www.encodeproject.org/experiments/ENCSR329MHM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on human HepG2 (paired-ended)
experiment encode accession: ENCSR329MHM
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-02-08
lab: Barbara Wold, Caltech
library encode accession: ENCLB334AQY
size range: >200

source_name: Homo sapiens HepG2 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/174fda30-39a7-4bd0-be00-7e081ff20e87/@@download/attachment/wgEncodeCaltechRnaSeq.release4.html.pdf

value: immortalized cell line

value: hepatocellular carcinoma

value: 15 year

value: child

value: ENCBS644SVK at ENCODE; https://www.encodeproject.org/ENCBS644SVK/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ENCODE dbxrefs HepG2; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HepG2


title: polyA mRNA RNA-seq from HepG2 (ENCLB267HUY)

description:
https://www.encodeproject.org/experiments/ENCSR329MHM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on human HepG2 (paired-ended)
experiment encode accession: ENCSR329MHM
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-02-08
lab: Barbara Wold, Caltech
library encode accession: ENCLB267HUY
size range: >200
spikeins used: /references/ENCSR714LOF/

value: Barbara Wold, Caltech

value: ENCBS429YJD at ENCODE; https://www.encodeproject.org/ENCBS429YJD/


title: DNase-seq from SK-N-DZ (ENCLB534QSX)

description:
https://www.encodeproject.org/experiments/ENCSR946MVP/
***************
biological replicate number: 2
technical replicate number: 1,2
description:
experiment encode accession: ENCSR946MVP
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB534QSX
instrument models: Illumina NextSeq 500,Illumina HiSeq 2000

source_name: Homo sapiens SK-N-DZ immortalized cell line

value: SK-N-DZ

value: female

value: 2 year

value: John Stamatoyannopoulos, UW

value: ENCBS478IFE at ENCODE; https://www.encodeproject.org/ENCBS478IFE/

value: Derived from ENCODE donor ENCDO340AAA; https://www.encodeproject.org/ENCDO340AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1701; http://web.expasy.org/cellosaurus/CVCL_1701


title: DNase-seq from trophoblast cell (ENCLB320YRF)

description:
https://www.encodeproject.org/experiments/ENCSR809LCE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR809LCE
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB320YRF
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

source_name: Homo sapiens trophoblast primary cell fetal (23 weeks)

value: trophoblast cell

value: primary cell

value: fetal

value: not collected

value: 23 week

value: ENCBS576QRR at ENCODE; https://www.encodeproject.org/ENCBS576QRR/

value: Derived from ENCODE donor ENCDO623MQT; https://www.encodeproject.org/ENCDO623MQT/


title: DNase-seq from heart (ENCLB491BID)

description:
https://www.encodeproject.org/experiments/ENCSR749BWV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR749BWV
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB491BID

source_name: Homo sapiens heart tissue female fetal (116 days)

value: heart

value: tissue

value: 116 day

value: ENCBS320XNN at ENCODE; https://www.encodeproject.org/ENCBS320XNN/

value: Derived from ENCODE donor ENCDO712ZBZ; https://www.encodeproject.org/ENCDO712ZBZ/


title: DNase-seq from embryonic facial prominence (ENCLB092SZP)

description:
https://www.encodeproject.org/experiments/ENCSR863XNX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR863XNX
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB092SZP
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

source_name: Homo sapiens embryonic facial prominence tissue male fetal (81 day)

value: embryonic facial prominence

value: male

value: 81 day

value: ENCBS114WOF at ENCODE; https://www.encodeproject.org/ENCBS114WOF/

value: Derived from ENCODE donor ENCDO567MNP; https://www.encodeproject.org/ENCDO567MNP/


title: DNase-seq from L1-S8R (ENCLB151KZC)

description:
https://www.encodeproject.org/experiments/ENCSR746ZPP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR746ZPP
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-07-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB151KZC
instrument models: Illumina NextSeq 500,Illumina HiSeq 2000

source_name: Homo sapiens L1-S8R induced pluripotent stem cell line

value: induced pluripotent stem cell line

value: L1-S8R is a human iPSC line derived from L1-S8 after transduction with lentiviral vector pLM-fSV2A (Papapetrou et al NBT 2011) expressing OCT4, SOX2, KLF4 and cMYC.

value: unknown

value: John Stamatoyannopoulos, UW

value: ENCBS023FES at ENCODE; https://www.encodeproject.org/ENCBS023FES/

value: Derived from ENCODE donor ENCDO430ZDZ; https://www.encodeproject.org/ENCDO430ZDZ/

value: ENCODE dbxrefs Cellosaurus CVCL_AV89; http://web.expasy.org/cellosaurus/CVCL_AV89


title: DNase-seq from heart (ENCLB434QXK)

description:
https://www.encodeproject.org/experiments/ENCSR664PKM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR664PKM
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-09-22
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB434QXK
instrument models: Illumina NextSeq 500,Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens heart tissue fetal (59 days)

value: heart

value: fetal

value: not collected

value: 59 day

value: ENCBS910QFW at ENCODE; https://www.encodeproject.org/ENCBS910QFW/

value: Derived from ENCODE donor ENCDO163CLX; https://www.encodeproject.org/ENCDO163CLX/


title: DNase-seq from ovary (ENCLB496AQJ)

description:
https://www.encodeproject.org/experiments/ENCSR855DJV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR855DJV
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB496AQJ
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

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

value: ovary

value: tissue

value: adult

value: female

value: 51 year

value: ENCBS279OPH at ENCODE; https://www.encodeproject.org/ENCBS279OPH/

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


title: hESC_shControl_replicate2

source_name: H9 hESCs

value: Control


title: DNase-seq from limb (ENCLB121VCC)

description:
https://www.encodeproject.org/experiments/ENCSR818JGZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR818JGZ
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB121VCC
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

source_name: Homo sapiens limb tissue fetal (56 days)

value: limb

value: 56 day

value: John Stamatoyannopoulos, UW

value: ENCBS845CJS at ENCODE; https://www.encodeproject.org/ENCBS845CJS/

value: Derived from ENCODE donor ENCDO114CJX; https://www.encodeproject.org/ENCDO114CJX/


title: DNase-seq from caudate nucleus (ENCLB164DNM)

description:
https://www.encodeproject.org/experiments/ENCSR015BGH/
***************
biological replicate number: 1
technical replicate number: 2,1
description:
experiment encode accession: ENCSR015BGH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB164DNM
instrument models: Illumina NextSeq 500,Illumina HiSeq 2000

source_name: Homo sapiens caudate nucleus tissue male adult (78 years)

value: caudate nucleus

value: male

value: 78 year

value: ENCBS214ENX at ENCODE; https://www.encodeproject.org/ENCBS214ENX/

value: Derived from ENCODE donor ENCDO317XRR; https://www.encodeproject.org/ENCDO317XRR/


title: DNase-seq from trophoblast cell (ENCLB171WJX)

description:
https://www.encodeproject.org/experiments/ENCSR593LTJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR593LTJ
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB171WJX
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

source_name: Homo sapiens trophoblast primary cell fetal (17 weeks)

value: trophoblast cell

value: primary cell

value: fetal

value: not collected

value: 17 week

value: ENCBS994UWD at ENCODE; https://www.encodeproject.org/ENCBS994UWD/

value: Derived from ENCODE donor ENCDO960IHW; https://www.encodeproject.org/ENCDO960IHW/


title: DNase-seq from medulla oblongata (ENCLB763GZW)

description:
https://www.encodeproject.org/experiments/ENCSR224IYD/
***************
biological replicate number: 1
technical replicate number: 2,1
description:
experiment encode accession: ENCSR224IYD
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB763GZW
instrument models: Illumina NextSeq 500,Illumina HiSeq 2000

source_name: Homo sapiens medulla oblongata tissue male adult (84 years)

value: medulla oblongata

value: tissue

value: adult

value: 84 year

value: ENCBS799XTS at ENCODE; https://www.encodeproject.org/ENCBS799XTS/

value: Derived from ENCODE donor ENCDO240JUB; https://www.encodeproject.org/ENCDO240JUB/


title: DNase-seq from G401 (ENCLB760QMB)

description:
https://www.encodeproject.org/experiments/ENCSR269SIA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR269SIA
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-08-18
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB760QMB

source_name: Homo sapiens G401 immortalized cell line

value: immortalized cell line

value: 3 month

value: child

value: male

value: John Stamatoyannopoulos, UW

value: ENCBS659PBH at ENCODE; https://www.encodeproject.org/ENCBS659PBH/

value: Derived from ENCODE donor ENCDO572LRN; https://www.encodeproject.org/ENCDO572LRN/

value: ENCODE dbxrefs Cellosaurus CVCL_0270; http://web.expasy.org/cellosaurus/CVCL_0270


title: Input-DNA  in EB+36hrDox(iIsl1.Lhx3.V5.Ebf2.Onecut2) replicate 1

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

data_processing:
Basecall conversion to fastq files was performed using bcl2fastq for HiSeq runs and Picard fpr NextSeq runs.
Alignment: All transcription factor ChIP-Seq fastq files were aligned to mouse genome (version mm10) using Bowtie (1.0.1) (Langmead et al., 2009) with options “-q --best --strata -m 1 --chunkmbs 1024”.  Only uniquely mapped reads were considered for further analysis.
Binding event detection: Isl1 and Lhx3 binding sites were profiled using MultiGPS (Mahony et al., 2014), which enables the identification of differentially-enriched TF binding sites across multiple conditions. Our initial analysis showed that Isl1 and Lhx3 mostly bind to the same sets of regions genome-wide with similar ChIP enrichment. Hence we treated Isl1 and Lhx3 datasets at each time-point as different conditions in a single MultiGPS run. The discovered binding events were required to have a significant ChIP enrichment over input samples (q-value < 0.001) as assessed using binomial tests. Binding sites for Ngn2, Onecut2, and Ebf2 were identified using MultiGPS (Mahony et al., 2014) with different runs for each transcription factor. Binding events were required to have a significant ChIP enrichment over the input samples based on a binomial test (q-value < 0.001).
Genome_build: mm10
Supplementary_files_format_and_content: MultiGPS: MultiGPS output files
Supplementary_files_format_and_content: BED: Conversion of MultiGPS output files to BED format, centered on the MultiGPS binding event location
Supplementary_files_format_and_content: BIGWIG: WIG files were generated using custom software to summarize read counts overlapping genomic regions. All reads were artificially extended out to 200bp in length. A bin size of 10bp was used for calculating overlapping read counts. WIG files were converted to bigWig using wigToBigWig (UCSC)

source_name: ES-derived embryoid bodies with induced transcription factors

growth_protocol: The inducible ESC lines were generated using the inducible cassette exchange (ICE) system (Iacovino et al., 2011). NIL (Ngn2-Isl1-Lhx3) inducible ESC line was previously generated (Mazzoni et al., 2013) (Mazzoni et al., 2011). To generate the p2lox-IL plasmid, Isl1-Lhx3 open reading frames were amplified from p2Lox-NIL and inserted into the p2Lox-V5 plasmid (Mazzoni et al., 2011). The p2lox-IL-EO and p2lox-NIL-EO plasmids were obtained by cloning Ebf2 and Onecut2 open reading frames under control of a second inducible tetracycline response element (TRE), into the p2lox-IL or p2lox-NIL plasmid, respectively. 2A peptides were used to separate Ngn2-Isl1-Lhx3, Isl1-Lhx3 and Ebf2-Onecut2 in the NIL, IL and NIL/IL-EO inducible lines, respectively. The p2lox-N plasmid was obtained by cloning the Ngn2 open reading frame into a p2lox-Flag plasmid (Mazzoni et al., 2011). Phusion polymerase (New England Biolabs) was used to minimize the introduction of mutations during PCR amplification. The inducible cell lines (iIL, iIL-EO, iNIL-EO and iN) were generated by treating the recipient ESCs for 16 h with 1 µg/ml Dox to induce Cre followed by electroporation of the respective plasmids (p2lox-IL, p2lox-IL-EO, p2lox-NIL-EO  and p2lox-N). After G418 selection (250ng/ml, Cellgro), cell lines were characterized by performing antibody staining (Hb9, Isl1/2, Chat, Vacht, Tubb3) and expanded. All the inducible ESC lines were grown in 2-inhibitors medium (Advanced DMEM/F12:Neurobasal (1:1) Medium (Gibco), supplemented with 2.5% ESC-grade fetal bovine serum (vol/vol, Corning), N2 (Gibco), B27 (Gibco), 2mM L-glutamine (Gibco), 0.1 mM β-mercaptoethanol (Gibco), 1000 U/ml leukemia inhibitory factor (Millipore), 3µM CHIR (BioVision) and 1 µM PD0325901 (Sigma). For ChIP experiments 3 x 10^6 cells were plated in each square dish (245mm x 245mm).

extract_protocol:
Cells were collected at different time points after NIL induction and fixed with 1 mM DSG (ProteoChem) followed by 1% formaldehyde (vol/vol) for 15 min at 20–25°C. Pellets containing ~25 × 10^6 cells were stored at −80 °C. Cells were thawed on ice, resuspended in 5 ml of Lysis Buffer  A (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol (vol/vol), 0.5% Igepal (vol/vol), 0.25% Triton X-100 (vol/vol)) and incubated for 10 min at 4°C in a rotating platform. Samples were spun down for 5 min at 1,350 g, resuspended in 5 ml Lysis Buffer B (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0) and incubated for 10 min at 4 °C in a rotating platform. Samples were spun down for 5 min at 1,350 g, resuspended in 3 ml of Sonication Buffer (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Trition X-100, 0.1% sodium deoxycholate (wt/vol), 0.1% SDS (wt/vol)). Nuclear extracts were sonicated on ice using a Branson 450 Sonifier (20% power amplitude; 18 cycles x 30 seconds pulses with 1 minute interval between each pulse) to sheer cross-linked DNA to an average fragment size of approximately 500 bp. Sonicated chromatin was incubated for 16 h at 4 °C with Dynabeads protein-G (Life Techologies) conjugated with either rabbit polyclonal antibody to V5 (ab15828, Abcam) to immunoprecipitate Lhx3 or a  combination of monoclonal antibodies (40.3A4, 39.3F7 and 40.206, DSHB) for Isl1. Ngn2 was immunoprecipitated by using a goat polyclonal antobody (sc-19233, Santa Cruz), whereas to immunoprecipitate Ebf2 and Onecut2, a rabbit polyclonal antibody (ab156999, Abcam) and a sheep polyclonal antibody (AF294, R&D Systems) were used, respectively. For histone modifications the following rabbit polyclonal antibodies were used: ab8895 (Abcam) for H3K4me1, ab7766 (Abcam) for H3K4me2, 39159 (Active Motif) for H3K4me3, ab4729 (Abcam) for H3K27ac and 39155 (Active Motif) for H3K27me3. After incubation, and with the aid of a magnetic device, beads were washed once with Sonication Buffer, than with Sonication buffer and 500 nM NaCl and once with LiCl Wash Buffer (20 mM Tris-HCl (pH 8.0), 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate) and 1 ml of TE (10 mM Tris, 1 mM EDTA, pH 8). Then, beads were centrifuged at 950 g for 3 min and the residual TE removed with a pipette. 210 µl of Elution Buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA (pH 8.0), 1% SDS) was added to the beads followed by incubation at 65°C for 45 min with a brief pulse of vortex every 10 min. 200 µl of supernatant was removed after a 1 min centrifugation at 16,000 g. The crosslink was reversed by 16 h incubation at 65°C. RNA was digested by the addition of 200 µl of TE and RNAse A (Sigma) at a final concentration of 0.2 mg/ml and incubated for 2 h at 37°C. Protein was digested by the addition of Proteinase K (Invitrogen) at a final concentration of 0.2 mg/ml, supplemented with CaCl2 followed by a 30-min incubation at 55°C. DNA was extracted with phenol:chloroform:isoamyl alcohol (25:24:1; vol/vol) (Invitrogen) and then recovered with an ethanol precipitation with glycogens as carrier. The pellets were suspended in 70 µl of water.
One third (24ul) of ChIP DNA was used to prepare llumina DNA sequencing libraries. Briefly, after end repair and A-tailing, Illumina-compatible Bioo Scientific multiplexed adapters were ligated and the unligated adapters removed through purification using Agencourt AmpureXP beads (Beckman Coulter). Adapter-ligated DNA was amplified by PCR using TruSeq Fw primer (AATGATACGGCGACCACCGAGATCTACAC) and TruSeq Rev primer (CAAGCAGAAGACGGCATACGAGAT), both from Sigma. DNA libraries between 300 and 500 bp in size were gel purified. KAPA SYBR FAST Roche LightCycler 480 2X qPCR Master Mix (Kapa Biosystems) was used in 20 μl reactions that were analyzed in a Roche LightCycler. Fifty base pair single-end sequencing was performed using Illumina HiSeq-2500 at the NYU Genome Core facility.

treatment_protocol: To obtain Embryoid bodies (EBs) ESC were trypsinized (Gibco) and seeded in AK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout SR (vol/vol) (Gibco), Pen/Strep (Gibco), 2mM L-glutamine and 0.1 mM 2-mercaptoethanol) (day -2).  After 2 days, EBs were passed 1:2 and the inducible cassette was induced by adding 3 µg/ml of Doxycycline (Sigma) to the culture medium (EBs 0h).

tag: strain

tag: chip target

value: Input

tag: cell type

value: Embryoid Bodies


title: DNase-seq from embryonic facial prominence (ENCLB956ATK)

description:
https://www.encodeproject.org/experiments/ENCSR435NHO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR435NHO
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB956ATK
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

source_name: Homo sapiens embryonic facial prominence tissue fetal (58 days)

value: embryonic facial prominence

value: fetal

value: not collected

value: 58 day

value: ENCBS151SUR at ENCODE; https://www.encodeproject.org/ENCBS151SUR/

value: Derived from ENCODE donor ENCDO234CBV; https://www.encodeproject.org/ENCDO234CBV/


title: DNase-seq from heart left ventricle (ENCLB652THU)

description:
https://www.encodeproject.org/experiments/ENCSR501FWC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR501FWC
assay title: DNase-seq
assembly: hg19, GRCh38
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB652THU
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

source_name: Homo sapiens heart left ventricle tissue female fetal (101 day)

value: heart left ventricle

value: tissue

value: female

value: 101 day

value: ENCBS931FTX at ENCODE; https://www.encodeproject.org/ENCBS931FTX/

value: Derived from ENCODE donor ENCDO060OTP; https://www.encodeproject.org/ENCDO060OTP/


title: DNase-seq from placenta (ENCLB257DMJ)

description:
https://www.encodeproject.org/experiments/ENCSR575VMI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR575VMI
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB257DMJ
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

source_name: Homo sapiens placenta tissue female fetal (101 day)

value: placenta

value: John Stamatoyannopoulos, UW

value: ENCBS321PDE at ENCODE; https://www.encodeproject.org/ENCBS321PDE/


title: ChIP-seq Lhx3.V5 in EB+36hrDox(iIsl1.Lhx3.V5.Ebf2.Onecut2) replicate 1

description:
Lhx3_36h_iILEO.bed
Lhx3_36h_iILEO.events.txt

value: anti-V5 (Abcam ab15828)


title: DNase-seq from trophoblast cell (ENCLB873PCM)

description:
https://www.encodeproject.org/experiments/ENCSR121ZSL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR121ZSL
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB873PCM
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

source_name: Homo sapiens trophoblast primary cell fetal (21 week)

value: trophoblast cell

value: primary cell

value: 21 week

value: ENCBS627LRI at ENCODE; https://www.encodeproject.org/ENCBS627LRI/

value: Derived from ENCODE donor ENCDO096FKE; https://www.encodeproject.org/ENCDO096FKE/


title: ChIP-seq Lhx3.V5 in EB+12hrDox(iIsl1.Lhx3.V5.Ebf2.Onecut2) replicate 2

description:
Lhx3_12h_iILEO.bed
Lhx3_12h_iILEO.events.txt

value: Embryoid Bodies


title: ChIP-seq Lhx3.V5 in EB+24hrDox(iNgn2.Isl1.Lhx3.V5.Ebf2.Onecut2) replicate 1

description:
Lhx3_24h_iNILEO.bed
Lhx3_24h_iNILEO.events.txt


title: Input-DNA  in EB+24hrDox(iNgn2.Isl1.Lhx3.V5.Ebf2.Onecut2) replicate 1

value: Input


title: ChIP-seq Lhx3.V5 in EB+12hrDox(iNgn2.Isl1.Lhx3.V5.Ebf2.Onecut2) replicate 1

description:
Lhx3_12h_iNILEO.bed
Lhx3_12h_iNILEO.events.txt


title: DNase-seq from heart (ENCLB784QGT)

description:
https://www.encodeproject.org/experiments/ENCSR749BWV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR749BWV
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB784QGT

source_name: Homo sapiens heart tissue female fetal (98 days)

value: heart

value: fetal

value: 98 day

value: ENCBS996MDU at ENCODE; https://www.encodeproject.org/ENCBS996MDU/

value: Derived from ENCODE donor ENCDO298NZG; https://www.encodeproject.org/ENCDO298NZG/


title: ChIP-seq Lhx3.V5 in EB+12hrDox(iNgn2.Isl1.Lhx3.V5.Ebf2.Onecut2) replicate 2


title: ChIP-seq Lhx3.V5 in EB+24hrDox(iIsl1.Lhx3.V5.Ebf2.Onecut2) replicate 2

description:
Lhx3_24h_iILEO.bed
Lhx3_24h_iILEO.events.txt


title: Input-DNA  in EB+12hrDox(iNgn2.Isl1.Lhx3.V5.Ebf2.Onecut2) replicate 1


title: Input-DNA  in EB+12hrDox(iIsl1.Lhx3.V5.Ebf2.Onecut2) replicate 1


title: ChIP-seq Lhx3.V5 in EB+12hrDox(iIsl1.Lhx3.V5.Ebf2.Onecut2) replicate 1


title: DNase-seq from MN1 (ENCLB792YOE)

description:
https://www.encodeproject.org/experiments/ENCSR898KAX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR898KAX
assay title: DNase-seq
assembly: mm10
encode release date: 2016-07-15
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB792YOE
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Mus musculus strain B6NCrl MN1 immortalized cell line treated with 10 nM methyltrienolone

value: immortalized cell line

value: unknown

tag: treatments

value: not collected

value: ENCBS880XXF at ENCODE; https://www.encodeproject.org/ENCBS880XXF/

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

value: ENCODE dbxrefs Cellosaurus CVCL_U508; http://web.expasy.org/cellosaurus/CVCL_U508


title: Single-cell RNA-seq in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) cell 95

description:
EB+48hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_95
esc1_48h_95_rsem

data_processing:
Basecall conversion to fastq files was performed using bcl2fastq for HiSeq runs and Picard fpr NextSeq runs.
We quantified gene expression (transcripts per million) in each library as previously described (Shalek et al., 2013). We filtered out low quality cells where we detected less than 2,000 unique genes, which typically had poor transcriptomics alignment rates (<30%, as compared to 65% for successful cells). We first ran a principal component analysis (PCA), as previously described (Shalek et al., 2013) using all detected genes, and saw that the first component perfectly separated the two experimental batches. We therefore subtracted the first PC from the data in order to remove this batch effect.
Single cell RNA-seq: Data pre-processing and filtration: We quantified gene expression (transcripts per million) in each library as previously described (Shalek et al., 2013). We filtered out low quality cells where we detected less than 2,000 unique genes, which typically had poor transcriptomics alignment rates (<30%, as compared to 65% for successful cells). We first ran a principal component analysis (PCA), as previously described (Shalek et al., 2013) using all detected genes, and saw that the first component perfectly separated the two experimental batches. We therefore subtracted the first PC from the data in order to remove this batch effect.
Calculating developmental trajectories and ‘pseudotime’: As trajectory analysis is sensitive to gene input list, we first sought to identify a set of genes whose expression changes with biological time (the timepoint during the differentiation series when the cells were collected). We used a strategy similar to (Trapnell et al., 2014), constructing a linear model for each gene as a function of its biological time. We identified 458 genes where the linear model explained a significant (p<1e-5 after Bonferroni correction) of the variance in gene expression. We next used these 458 genes as input to a diffusion map, a non-linear dimensional reduction technique that has been shown to be well-suited to reconstructing developmental trajectories for single cell data. We assigned each cell a ‘pseudotime’ value, reflecting its progression through the differentiation process, by projecting a principal curve through the first two diffusion map dimensions.
Genome_build: mm10
Supplementary_files_format_and_content: gene expression table summarizing processed per-gene read counts across all submitted experiments

growth_protocol: Generation of inducible lines: NIL (Ngn2-Isl1-Lhx3)-V5 and Flag-Ngn2 inducible ESC lines were generated as previously described (Mazzoni et al. 2013, Mazzoni et al. 2011). To generate IL (Isl1-Lhx3)-V5 inducible ESC lines, Isl1-Lhx3 open reading frames were amplified from p2Lox-NIL-V5 and inserted into the p2Lox-V5 plasmid (Iacovino M. et al., 2011). Phusion polymerase (New England Biolabs) was used to minimize the introduction of mutations during PCR amplification. Inducible cell lines were generated by treating the recipient ESCs for 16 h with 1 µg/ml Dox to induce Cre followed by electroporation of p2Lox-IL-V5 plasmid. After G418 selection (250ng/ml, Cellgro), four resistant clones were picked, characterized and expanded.   Cell culture and differentiation: All the inducible ESC lines were grown in 2-inhibitors medium (Advanced DMEM/F12:Neurobasal (1:1) Medium (Gibco), supplemented with 2.5% ESC-grade fetal bovine serum (vol/vol, Corning), N2 (Gibco), B27 (Gibco), 2mM L-glutamine (Gibco), 0.1 mM β-mercaptoethanol (Gibco), 1000 U/ml leukemia inhibitory factor (Millipore), 3µM CHIR (BioVision) and 1 µM PD0325901 (Sigma). For ChIP experiments, 3 x 10^6 cells were plated in each square dish (245mm x 245mm).

extract_protocol:
Cells were collected at different time points after NIL induction. Differentiating embryoid bodies were washed with phosphate-buffered saline and then dissociated by mild trypsinization followed by mechanical dissociation into single cell suspension. Viable cells were labeled by incubating with 1 µM Fluorescein diacetate (Sigma) at 37°C for 10 minutes. Single cells were FACS-sorted into 96-well plates containing 10 µl of 1% beta-mercaptoethanol in TCL buffer (Qiagen). Once sorting was completed, plates were sealed, centrifuged 1 min at 800 g at RT and immediately frozen on dry ice. Plates were kept at -80°C until lysate cleanup and reverse transcription of mRNA.
Single cell libraries were prepared in two overall batches using a custom version of the SMART-Seq2 protocol (Picelli et al., 2013), as previously described (Satija et al., 2015), without the use of Random Molecular Tags. Cells were sequenced with 50bp single end reads on a HiSeq 2500 at an average sequencing depth of 325,000 reads per cell.

value: ES-derived embryoid bodies with induced transcription factors


title: DNase-seq from MN1 (ENCLB287QED)

description:
https://www.encodeproject.org/experiments/ENCSR732IZK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR732IZK
assay title: DNase-seq
assembly: mm10
encode release date: 2016-07-15
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB287QED
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Mus musculus strain B6NCrl MN1 immortalized cell line

value: John Stamatoyannopoulos, UW

value: ENCBS389RBU at ENCODE; https://www.encodeproject.org/ENCBS389RBU/


title: Single-cell RNA-seq in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) cell 96

description:
EB+48hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_96
esc1_48h_96_rsem


title: Single-cell RNA-seq in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) cell 94

description:
EB+48hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_94
esc1_48h_94_rsem


title: Single-cell RNA-seq in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) cell 92

description:
EB+48hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_92
esc1_48h_92_rsem


title: Single-cell RNA-seq in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) cell 91

description:
EB+48hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_91
esc1_48h_91_rsem


title: ChIP-seq Lhx3.V5 in EB+48hrDox(iIsl1.Lhx3.V5.Ebf2.Onecut2) replicate 1

description:
Lhx3_48h_iILEO.bed
Lhx3_48h_iILEO.events.txt

value: anti-V5 (Abcam ab15828)


title: Single-cell RNA-seq in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) cell 90

description:
EB+48hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_90
esc1_48h_90_rsem


title: Single-cell RNA-seq in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) cell 89

description:
EB+48hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_89
esc1_48h_89_rsem