title: ChIP-seq from induced pluripotent stem cell (ENCLB862HRK)

description:
https://www.encodeproject.org/experiments/ENCSR313NJN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR313NJN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR773IYZ
encode release date: 2017-01-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB862HRK
size range: 200-600

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: Thomas Gingeras, CSHL

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: ChIP-seq from induced pluripotent stem cell (ENCLB205AEB)

status: Public on Mar 12 2017

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/ENCSR369NGL/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on PGP1 iPSC
experiment encode accession: ENCSR369NGL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR447FVP, ENCSR655HDE
encode release date: 2016-08-09
lab: Richard Myers, HAIB
library encode accession: ENCLB205AEB

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

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

tag: antibody

tag: description

tag: biosample encode accession

tag: age

tag: dev stage

tag: Sex

tag: lab

tag: link


title: ChIP-seq from GM12878 (ENCLB472NPS)

description:
https://www.encodeproject.org/experiments/ENCSR360XQV/
***************
biological replicate number: 11
technical replicate number: 1
description: Reverse Crosslink Control ChIP-seq on human GM12878 (fragmentation date 04-19-13)
experiment encode accession: ENCSR360XQV
assay title: ChIP-seq
encode release date: 2014-07-07
lab: Richard Myers, HAIB
library encode accession: ENCLB472NPS

source_name: Homo sapiens GM12878 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6ecd8240-a351-479b-9de6-f09ca3702ac3/@@download/attachment/ChIP-seq_Protocol_v011014.pdf

value: Control

tag: line

value: immortalized cell line

value: GM12878, B-lymphocyte, lymphoblastoid.

value: female

value: unknown

tag: health state

tag: passage number

value: Richard Myers, HAIB

value: ENCBS083XJQ at ENCODE; https://www.encodeproject.org/ENCBS083XJQ/

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: Coriell sample source; https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM12878&Product=CC


title: ChIP-seq from neural cell (ENCLB181VYC)

description:
https://www.encodeproject.org/experiments/ENCSR308JFE/
***************
biological replicate number: 2
technical replicate number: 3
description:
experiment encode accession: ENCSR308JFE
assay title: ChIP-seq
encode release date: 2016-10-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB181VYC
size range: 200-600

source_name: Homo sapiens neural in vitro differentiated cells male embryo

extract_protocol: not provided

value: neural cell

value: in vitro differentiated cells

value: embryonic

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS737HIZ at ENCODE; https://www.encodeproject.org/ENCBS737HIZ/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: ChIP-seq from K562 (ENCLB446XUJ)

description:
https://www.encodeproject.org/experiments/ENCSR353HEP/
***************
biological replicate number: 1
technical replicate number: 1
description: TARDBP ChIP-seq on human K562
experiment encode accession: ENCSR353HEP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR599SPN, ENCSR996HUG
encode release date: 2014-07-07
lab: Richard Myers, HAIB
library encode accession: ENCLB446XUJ

source_name: Homo sapiens K562 immortalized cell line

extract_protocol:
general protocol: https://www.encodeproject.org/documents/6ecd8240-a351-479b-9de6-f09ca3702ac3/@@download/attachment/ChIP-seq_Protocol_v011014.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6ecd8240-a351-479b-9de6-f09ca3702ac3/@@download/attachment/ChIP-seq_Protocol_v011014.pdf

value: TARDBP

value: K562, myelogenous leukemia

value: 53 year

value: adult

value: chronic myelogenous leukemia (CML)

value: ENCBS316CKF at ENCODE; https://www.encodeproject.org/ENCBS316CKF/

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

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

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: ChIP-seq from K562 (ENCLB522MIT)

description:
https://www.encodeproject.org/experiments/ENCSR353HEP/
***************
biological replicate number: 2
technical replicate number: 1
description: TARDBP ChIP-seq on human K562
experiment encode accession: ENCSR353HEP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR599SPN, ENCSR996HUG
encode release date: 2014-07-07
lab: Richard Myers, HAIB
library encode accession: ENCLB522MIT

value: immortalized cell line

value: female

value: Richard Myers, HAIB

value: ENCBS602AAA at ENCODE; https://www.encodeproject.org/ENCBS602AAA/


title: ChIP-seq from liver (ENCLB416XPE)

description:
https://www.encodeproject.org/experiments/ENCSR350ORK/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on GABPA-human
experiment encode accession: ENCSR350ORK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR849OTN, ENCSR443AIH
encode release date: 2016-09-09
lab: Richard Myers, HAIB
library encode accession: ENCLB416XPE

source_name: Homo sapiens liver tissue female child (4 years)

value: GABPA

value: liver

value: tissue

value: Human liver tissue obtained from a healthy, 4 year old female donor

value: 4 year

value: child

value: healthy

value: Michael Snyder, Stanford

value: ENCBS401URL at ENCODE; https://www.encodeproject.org/ENCBS401URL/

value: Derived from ENCODE donor ENCDO882MMZ; https://www.encodeproject.org/ENCDO882MMZ/


title: ChIP-seq from liver (ENCLB132FIG)

description:
https://www.encodeproject.org/experiments/ENCSR350ORK/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on GABPA-human
experiment encode accession: ENCSR350ORK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR849OTN, ENCSR443AIH
encode release date: 2016-09-09
lab: Richard Myers, HAIB
library encode accession: ENCLB132FIG


title: ChIP-seq from HepG2 (ENCLB478VON)

description:
https://www.encodeproject.org/experiments/ENCSR396QWK/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR396QWK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR346XJA
encode release date: 2016-06-14
lab: Richard Myers, HAIB
library encode accession: ENCLB478VON

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-MBD1_isoform1 fusion protein

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS201IDJ at ENCODE; https://www.encodeproject.org/ENCBS201IDJ/

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

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


title: ChIP-seq from HepG2 (ENCLB942ENW)

description:
https://www.encodeproject.org/experiments/ENCSR346XJA/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2-human (fragmentation date:2015-07-21
experiment encode accession: ENCSR346XJA
assay title: ChIP-seq
encode release date: 2016-01-14
lab: Richard Myers, HAIB
library encode accession: ENCLB942ENW

source_name: Homo sapiens HepG2 immortalized cell line stably expressing N-terminal FLAG-HHEX fusion protein, C-terminal FLAG-HHEX fusion protein

value: Control

value: immortalized cell line

value: A standard Myers lab growth of HepG2, hepatocellular carcinoma

value: Richard Myers, HAIB

value: ENCBS882YXM at ENCODE; https://www.encodeproject.org/ENCBS882YXM/

value: ATCC sample source; http://www.atcc.org/products/all/HB-8065.aspx


title: ChIP-seq from neural cell (ENCLB887QUG)

description:
https://www.encodeproject.org/experiments/ENCSR308JFE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR308JFE
assay title: ChIP-seq
encode release date: 2016-10-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB887QUG
size range: 200-600

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ab9a4628-0877-468f-bdfe-78aada2fdb96/@@download/attachment/ChIP_Protocol_For_Fresh_or_Frozen_Cells_v8.2_exp.pdf

value: neural cell

value: in vitro differentiated cells

value: embryonic

value: unknown

value: Bradley Bernstein, Broad

value: ENCBS504GFW at ENCODE; https://www.encodeproject.org/ENCBS504GFW/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: ChIP-seq from liver (ENCLB899UYG)

description:
https://www.encodeproject.org/experiments/ENCSR345YWJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on ZBTB33-human
experiment encode accession: ENCSR345YWJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR849OTN, ENCSR769JUI
encode release date: 2016-09-23
lab: Richard Myers, HAIB
library encode accession: ENCLB899UYG

value: liver

value: tissue

value: Human liver tissue obtained from a healthy, 4 year old female donor

value: 4 year

value: child

value: female

value: healthy

value: Michael Snyder, Stanford

value: ENCBS401URL at ENCODE; https://www.encodeproject.org/ENCBS401URL/

value: Derived from ENCODE donor ENCDO882MMZ; https://www.encodeproject.org/ENCDO882MMZ/


title: ChIP-seq from SUDHL6 (ENCLB877ZVG)

description:
https://www.encodeproject.org/experiments/ENCSR307DQT/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR307DQT
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR179YLS
encode release date: 2016-11-17
lab: Bradley Bernstein, Broad
library encode accession: ENCLB877ZVG
size range: 200-600

source_name: Homo sapiens SUDHL6 immortalized cell line

value: immortalized cell line

value: also called SU-DHL-6 (diffuse histiocytic lymphoma) - disease:large cell lymphoma; diffuse mixed histiocytic and lymphocytic lymphoma; follicular B cell lymphoma; ATCC CRL-2959

value: adult

value: male

value: 43 year

value: ENCBS782RBW at ENCODE; https://www.encodeproject.org/ENCBS782RBW/

value: Derived from ENCODE donor ENCDO353AAA; https://www.encodeproject.org/ENCDO353AAA/


title: ChIP-seq from smooth muscle cell (ENCLB198GCM)

description:
https://www.encodeproject.org/experiments/ENCSR301VIW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR301VIW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR729MRJ
encode release date: 2016-11-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB198GCM
size range: 200-600

source_name: Homo sapiens smooth muscle in vitro differentiated cells female embryo (5 days) derived from H9

value: smooth muscle cell

value: in vitro differentiated cells

value: Frozen or fixed, in vitro differentiated smooth muscle cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

value: embryonic

value: Richard Myers, HAIB

value: ENCBS780PCJ at ENCODE; https://www.encodeproject.org/ENCBS780PCJ/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: ChIP-seq from bipolar spindle neuron (ENCLB050REL)

description:
https://www.encodeproject.org/experiments/ENCSR301AEA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR301AEA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR001KCX
encode release date: 2016-05-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB050REL
size range: 200-600

source_name: Homo sapiens bipolar spindle neuron in vitro differentiated cells male adult (53 years) derived from induced pluripotent stem cell

value: bipolar spindle neuron

value: These are bipolar neurons created from iPSC from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: Thomas Gingeras, CSHL

value: ENCBS374AAA at ENCODE; https://www.encodeproject.org/ENCBS374AAA/

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


title: ChIP-seq from liver (ENCLB406XPK)

description:
https://www.encodeproject.org/experiments/ENCSR345YWJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on ZBTB33-human
experiment encode accession: ENCSR345YWJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR849OTN, ENCSR769JUI
encode release date: 2016-09-23
lab: Richard Myers, HAIB
library encode accession: ENCLB406XPK

value: liver

value: tissue

value: Human liver tissue obtained from a healthy, 4 year old female donor

value: 4 year

value: child

value: female

value: healthy

value: Michael Snyder, Stanford

value: ENCBS401URL at ENCODE; https://www.encodeproject.org/ENCBS401URL/

value: Derived from ENCODE donor ENCDO882MMZ; https://www.encodeproject.org/ENCDO882MMZ/


title: ChIP-seq from SUDHL6 (ENCLB983FOR)

description:
https://www.encodeproject.org/experiments/ENCSR307DQT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR307DQT
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR179YLS
encode release date: 2016-11-17
lab: Bradley Bernstein, Broad
library encode accession: ENCLB983FOR
size range: 200-600

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/be2a0f12-af38-430c-8f2d-57953baab5f5/@@download/attachment/Epigenomics_Alternative_Mag_Bead_ChIP_Protocol_v1.1_exp.pdf

value: immortalized cell line

value: also called SU-DHL-6 (diffuse histiocytic lymphoma) - disease:large cell lymphoma; diffuse mixed histiocytic and lymphocytic lymphoma; follicular B cell lymphoma; ATCC CRL-2959

value: 43 year

value: adult

value: male

value: Bradley Bernstein, Broad

value: ENCBS401ZBX at ENCODE; https://www.encodeproject.org/ENCBS401ZBX/

value: Derived from ENCODE donor ENCDO353AAA; https://www.encodeproject.org/ENCDO353AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2206; http://web.expasy.org/cellosaurus/CVCL_2206


title: ChIP-seq from smooth muscle cell (ENCLB690AIR)

description:
https://www.encodeproject.org/experiments/ENCSR301VIW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR301VIW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR729MRJ
encode release date: 2016-11-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB690AIR
size range: 200-600
nucleic acid starting quantity: 38.0
nucleic acid starting quantity units: ng

value: smooth muscle cell

value: in vitro differentiated cells

value: Frozen or fixed, in vitro differentiated smooth muscle cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

value: embryonic

value: Richard Myers, HAIB

value: ENCBS899TTJ at ENCODE; https://www.encodeproject.org/ENCBS899TTJ/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: ChIP-seq from induced pluripotent stem cell (ENCLB164SGY)

description:
https://www.encodeproject.org/experiments/ENCSR369NGL/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on PGP1 iPSC
experiment encode accession: ENCSR369NGL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR447FVP, ENCSR655HDE
encode release date: 2016-08-09
lab: Richard Myers, HAIB
library encode accession: ENCLB164SGY

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: 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: microRNA High Responder Amygdala 3

city: Birmingham

first: Joshua

last: Cohen

state: AL

department: Psychiatry

institute: University of Alabama at Brmingham

description: Brain tissue from 60 day old rat

library_source: transcriptomic

data_processing:
Illumina HiSeq Control Software 2.0 was used for base calling
Raw reads were trimmed of adaptor sequences using cutadapt (version 1.3.1-rc1). Only reads greater than 15 base pairs after trimming were kept
Trimmed reads were aligned to Rattus norvegicus miRNA hairpin sequences from miRBase (version 19) using bowtie2 (version 2-2.1.0). Only reads with two or fewer mismatches were kept
Hairpin alignments were queried for overlap with mature miRNA sequences and counted using BEDTools (v2.14.2)
Genome_build: Rattus norvegicus miRBase Version 19
Supplementary_files_format_and_content: tab deliminated files contain raw miRNA counts for each sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Amygdala

extract_protocol:
Qiagen miRNeasy Extraction Kit
small RNA libraries were prepared using standard illumina protocols followed by pipin size selection

tag: tissue

value: Amygdala

tag: rat strain

value: High Responder


title: ChIP-seq from HepG2 (ENCLB121ZCU)

description:
https://www.encodeproject.org/experiments/ENCSR345EZN/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2-human (fragmentation date:2015-07-09
experiment encode accession: ENCSR345EZN
assay title: ChIP-seq
encode release date: 2016-06-13
lab: Richard Myers, HAIB
library encode accession: ENCLB121ZCU

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-CREB1 fusion protein

value: Control

value: immortalized cell line

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS727VRH at ENCODE; https://www.encodeproject.org/ENCBS727VRH/

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

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


title: ChIP-seq from HeLa-S3 (ENCLB568OSM)

description:
https://www.encodeproject.org/experiments/ENCSR340WQU/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR340WQU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AOB
encode release date: 2016-11-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB568OSM
size range: 200-600

source_name: Homo sapiens HeLa-S3 immortalized cell line

value: adult

value: female

value: 31 year

value: cervical adenocarcinoma

value: Bradley Bernstein, Broad

value: ENCBS655ARO at ENCODE; https://www.encodeproject.org/ENCBS655ARO/

value: Derived from ENCODE donor ENCDO000AAB; https://www.encodeproject.org/ENCDO000AAB/

value: ENCODE dbxrefs Cellosaurus CVCL_0058; http://web.expasy.org/cellosaurus/CVCL_0058


title: ChIP-seq from bipolar spindle neuron (ENCLB624IET)

description:
https://www.encodeproject.org/experiments/ENCSR301AEA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR301AEA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR001KCX
encode release date: 2016-05-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB624IET
size range: 200-600

value: bipolar spindle neuron

value: in vitro differentiated cells

value: These are bipolar neurons created from iPSC from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: Thomas Gingeras, CSHL

value: ENCBS369AAA at ENCODE; https://www.encodeproject.org/ENCBS369AAA/

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


title: microRNA High Responder Amygdala 1

description: Brain tissue from 60 day old rat

value: Amygdala

value: High Responder


title: microRNA High Responder Amygdala 4

description: Brain tissue from 60 day old rat


title: microRNA High Responder Amygdala 2

description: Brain tissue from 60 day old rat


title: Artificial-polyA-uncleaved

city: New York

first: Xuebing

last: Wu

state: NY

address: 630 West 168th Street

department: Medicine/Systems Biology

institute: Columbia University

data_processing:
Reads were collapsed to identify unique variants.
Supplementary_files_format_and_content: 2-column tabular: variant sequence and read count

growth_protocol: HEK293T were cultured with DMEM (VWR 45000-304) and 10% FBS (Clontech 631367).

extract_protocol:
RNA isolated using RNeasy Mini Kit, Qiagen, and DNA isolated using QIAamp DNA mini kit
The 3' end was PCR amplified and then the cleaved and uncleaved product were separated on agarose gel and extracted
Amplicon

treatment_protocol: HEK293T cells were transfected with a plasmid library encoding artificial 3' ends

tag: cell line

tag: treatment

tag: molecule subtype

value: reporter RNA 3' end


title: ChIP-seq from induced pluripotent stem cell (ENCLB425TPY)

description:
https://www.encodeproject.org/experiments/ENCSR313NJN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR313NJN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR773IYZ
encode release date: 2017-01-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB425TPY
size range: 200-600

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: adult

value: male

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

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: microRNA High Responder Dorsal Raphe 4

description: Brain tissue from 60 day old rat

source_name: Dorsal Raphe

value: Dorsal Raphe


title: Artificial-polyA-cleaved


title: ChIP-seq from neural cell (ENCLB367QBQ)

description:
https://www.encodeproject.org/experiments/ENCSR308JFE/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR308JFE
assay title: ChIP-seq
encode release date: 2016-10-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB367QBQ
size range: 200-600

value: Control

value: neural cell

value: in vitro differentiated cells

value: embryonic

value: unknown

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS737HIZ at ENCODE; https://www.encodeproject.org/ENCBS737HIZ/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: ChIP-seq from PC-3 (ENCLB316JNQ)

description:
https://www.encodeproject.org/experiments/ENCSR339ZMJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR339ZMJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR328AHC
encode release date: 2016-05-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB316JNQ
size range: 300-600
nucleic acid starting quantity: 652.8
nucleic acid starting quantity units: ng
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens PC-3 immortalized cell line

extract_protocol: extraction method: see document

value: immortalized cell line

value: prostate cancer cell line

value: 62 year

value: grade IV, adenocarcinoma

value: ENCBS451OVM at ENCODE; https://www.encodeproject.org/ENCBS451OVM/

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

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

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1435.aspx


title: microRNA High Responder Dorsal Raphe 2

description: Brain tissue from 60 day old rat

value: Dorsal Raphe

value: High Responder


title: CENPB-KO-RNA-day12

data_processing:
Reads were collapsed to identify unique variants. Variants with less than 100 DNA reads or less than 2 RNA reads were removed.
Only reads for mRNAs cleaved at the original poly(A) site (as indicated by a GCC immediately upstream of the tail) were considered in this analysis.
Supplementary_files_format_and_content: 3-column tabular: sequence, DNA count, RNA count

growth_protocol: HEK293T and HeLa cells were cultured with DMEM (VWR 45000-304) and 10% FBS (Clontech 631367).

extract_protocol:
RNA isolated using RNeasy Mini Kit, Qiagen, and DNA isolated using QIAamp DNA mini kit
The 3' end of CENPB was PCR amplified from both the genomic DNA and cDNA
Amplicon

treatment_protocol: HEK293T cells were seeded on day 0, transfected with the Cas9/gRNA plasmid on day 1, transfected again on day 2, and collected for DNA and RNA analysis on day 12.

value: CENPB 3' end cDNA


title: ChIP-seq from liver (ENCLB232FJZ)

description:
https://www.encodeproject.org/experiments/ENCSR338MMB/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on NR2F2-human
experiment encode accession: ENCSR338MMB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR931XLP, ENCSR019XRC
encode release date: 2016-08-24
lab: Richard Myers, HAIB
library encode accession: ENCLB232FJZ

source_name: Homo sapiens liver tissue male adult (32 years)

value: liver

value: tissue

value: Human liver Tissue obtained from a healthy, 32 year old Caucasian male donor

value: 32 year

value: adult

value: male

value: healthy with non-obstructive CAD (coronary artery disease)

value: Thomas Gingeras, CSHL

value: ENCBS046RNA at ENCODE; https://www.encodeproject.org/ENCBS046RNA/

value: Derived from ENCODE donor ENCDO060AAA; https://www.encodeproject.org/ENCDO060AAA/

value: ENCODE dbxrefs Liver_STL011; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=Liver_STL011


title: microRNA Low Responder Amygdala 3

description: Brain tissue from 60 day old rat

value: Amygdala

value: Low Responder


title: microRNA Low Responder Amygdala 4

description: Brain tissue from 60 day old rat


title: DMS-ctrl-rep3-paired

data_processing:
adaptor trimming: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCAC -f fastq -O 1 -m 15 --quality-base=64 -q 13,13
mapping: bowtie --phred64-quals -l 100 -n 1 -m 1 --best --strata -S
All replicates were pooled and used to calculate mutation rates, then the rate in control sample was subtracted from that of the DMS treated sample
Supplementary_files_format_and_content: difference in mutaiton rate, between DMS treated and control samples

source_name: DMS-ctrl

growth_protocol: HEK293T cells were cultured with DMEM (VWR 45000-304) and 10% FBS (Clontech 631367).

extract_protocol:
RNA isolated using Trizol
2P-seq was as described in (Spies et al., 2013) with a few modifications. Briefly, poly(A) RNA was purified from total RNA using Oligo(dT)25 Dynabeads (Life Technologies). The eluted RNA was lightly digested with RNase T1 (Life Technologies), precipitated, and then poly(A) selected again. The eluted RNA was reverse transcribed using an anchor oligo(dT)20 (Table S1). After hydrolyzing the RNA, the cDNA of lengths 150–500 nt was size-selected on a 6% TBE-Urea Gel (Life Technologies), circularized using CircLigase, PCR amplified (Table S1), size-selected, and submitted for Illumina sequencing. For 4sU-2P-seq, nascent RNA was captured based on transcriptional incorporation of 4sU (Rädle et al., 2013), and then subjected to 2P-seq, omitting the first poly(A) selection. For DIM-2P-seq, reverse transcription was performed with TGIRT for 15 minutes at 48°C, then for 2 hours at 57°C. In total, 95 and 208 million mapped reads were obtained for the DMS-treated sample and the control sample, respectively.

treatment_protocol: HEK293T cells were incubated with 3.3% DMS for 5 min

value: mRNA 3' end


title: microRNA Low Responder Amygdala 1

description: Brain tissue from 60 day old rat


title: CENPB-KO-DNA-day12

value: CENPB 3' end genomic DNA


title: microRNA Low Responder Amygdala 2

description: Brain tissue from 60 day old rat


title: microRNA Low Responder Dorsal Raphe 4

description: Brain tissue from 60 day old rat

value: Dorsal Raphe


title: DMS-ctrl-rep2-single


title: microRNA Low Responder Dorsal Raphe 3

description: Brain tissue from 60 day old rat


title: DMS-ctrl-rep2-paired


title: microRNA Low Responder Dorsal Raphe 2

description: Brain tissue from 60 day old rat


title: mRNA Low Responder Dorsal Raphe 6

description: Brain tissue from 60 day old rat

data_processing:
Illumina HiSeq Control Software 2.0 was used for base calling
Reads were trimmed with TrimGalore and aligned with STAR to rn6 (https://github.com/HudsonAlpha/aRNAPipe)
Genome_build: rn6
Supplementary_files_format_and_content: tab deliminated files contain raw mRNA counts for each sample

extract_protocol:
Qiagen miRNeasy Extraction Kit
Poly-A RNA Seq Libraries were constructed


title: mRNA Low Responder Dorsal Raphe 5

description: Brain tissue from 60 day old rat


title: ChIP-seq from GM12878 (ENCLB602THJ)

description:
https://www.encodeproject.org/experiments/ENCSR331HPA/
***************
biological replicate number: 2
technical replicate number: 1
description: GABPA ChIP-seq on human GM12878
experiment encode accession: ENCSR331HPA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000BVP
encode release date: 2014-06-30
lab: Richard Myers, HAIB
library encode accession: ENCLB602THJ

value: GABPA

value: immortalized cell line

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

value: female

value: unknown

value: Richard Myers, HAIB

value: ENCBS110ENC at ENCODE; https://www.encodeproject.org/ENCBS110ENC/

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: DMS-treated-rep2-paired

source_name: DMS-treated


title: microRNA High Responder Dorsal Raphe 1

description: Brain tissue from 60 day old rat

value: High Responder


title: mRNA Low Responder Dorsal Raphe 4

description: Brain tissue from 60 day old rat


title: mRNA Low Responder Dorsal Raphe 3

description: Brain tissue from 60 day old rat


title: mRNA Low Responder Dorsal Raphe 2

description: Brain tissue from 60 day old rat


title: ChIP-seq from HepG2 (ENCLB247IYN)

description:
https://www.encodeproject.org/experiments/ENCSR331ORD/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR331ORD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR345EZN
encode release date: 2016-06-14
lab: Richard Myers, HAIB
library encode accession: ENCLB247IYN

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS727VRH at ENCODE; https://www.encodeproject.org/ENCBS727VRH/

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

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


title: microRNA High Responder Dorsal Raphe 3

description: Brain tissue from 60 day old rat

value: Dorsal Raphe


title: ChIP-seq from GM12878 (ENCLB308HZV)

description:
https://www.encodeproject.org/experiments/ENCSR331HPA/
***************
biological replicate number: 1
technical replicate number: 1
description: GABPA ChIP-seq on human GM12878
experiment encode accession: ENCSR331HPA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000BVP
encode release date: 2014-06-30
lab: Richard Myers, HAIB
library encode accession: ENCLB308HZV

source_name: Homo sapiens GM12878 immortalized cell line

value: GABPA

value: immortalized cell line

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

value: adult

value: female


title: ChIP-seq from liver (ENCLB733SOT)

description:
https://www.encodeproject.org/experiments/ENCSR338MMB/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on NR2F2-human
experiment encode accession: ENCSR338MMB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR931XLP, ENCSR019XRC
encode release date: 2016-08-24
lab: Richard Myers, HAIB
library encode accession: ENCLB733SOT

value: liver

value: tissue

value: Human liver Tissue obtained from a healthy, 32 year old Caucasian male donor

value: 32 year

value: healthy with non-obstructive CAD (coronary artery disease)

value: Thomas Gingeras, CSHL

value: ENCBS046RNA at ENCODE; https://www.encodeproject.org/ENCBS046RNA/

value: Derived from ENCODE donor ENCDO060AAA; https://www.encodeproject.org/ENCDO060AAA/

value: ENCODE dbxrefs Liver_STL011; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=Liver_STL011


title: mRNA Low Responder Dorsal Raphe 1

description: Brain tissue from 60 day old rat

value: Low Responder


title: ChIP-seq from HCT116 (ENCLB048WZL)

description:
https://www.encodeproject.org/experiments/ENCSR333OPW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR333OPW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR198WIH
encode release date: 2016-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB048WZL
size range: 200-600

source_name: Homo sapiens HCT116 immortalized cell line

value: cells obtained from ATCC

value: unknown

value: male

value: colorectal carcinoma

value: Bradley Bernstein, Broad

value: ENCBS494OPB at ENCODE; https://www.encodeproject.org/ENCBS494OPB/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/

value: ENCODE dbxrefs Cellosaurus CVCL_0291; http://web.expasy.org/cellosaurus/CVCL_0291

value: ATCC sample source; http://www.atcc.org/products/all/CCL-247.aspx#357C3571006A4259B64650D34DF19048


title: ChIP-seq from K562 (ENCLB676ADT)

description:
https://www.encodeproject.org/experiments/ENCSR331GDC/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on K562
experiment encode accession: ENCSR331GDC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR962APM, ENCSR129NAJ
encode release date: 2016-06-28
lab: Richard Myers, HAIB
library encode accession: ENCLB676ADT

source_name: Homo sapiens K562 immortalized cell line

value: immortalized cell line

value: K562, myelogenous leukemia

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Richard Myers, HAIB

value: ENCBS577JGM at ENCODE; https://www.encodeproject.org/ENCBS577JGM/

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

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

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: mRNA Low Responder Amygdala 6

description: Brain tissue from 60 day old rat

value: Amygdala

value: Low Responder


title: DMS-treated-rep1

value: mRNA 3' end


title: ChIP-seq from K562 (ENCLB146UXU)

description:
https://www.encodeproject.org/experiments/ENCSR331GDC/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on K562
experiment encode accession: ENCSR331GDC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR962APM, ENCSR129NAJ
encode release date: 2016-06-28
lab: Richard Myers, HAIB
library encode accession: ENCLB146UXU

value: ENCBS316CKF at ENCODE; https://www.encodeproject.org/ENCBS316CKF/


title: mRNA Low Responder Amygdala 5

description: Brain tissue from 60 day old rat


title: microRNA Low Responder Dorsal Raphe 1

description: Brain tissue from 60 day old rat

value: Dorsal Raphe


title: ChIP-seq from PC-3 (ENCLB936UNC)

description:
https://www.encodeproject.org/experiments/ENCSR328AHC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR328AHC
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB936UNC
size range: 300-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/864ba3a4-4c71-4c58-bf07-b138977bf6c7/@@download/attachment/EpigenomicsMagBeadChIPv.1.2exp.pdf

value: Control

value: prostate cancer cell line

value: male

value: 62 year

value: grade IV, adenocarcinoma

value: Bradley Bernstein, Broad

value: ENCBS451OVM at ENCODE; https://www.encodeproject.org/ENCBS451OVM/

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

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

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1435.aspx


title: mRNA Low Responder Amygdala 4

description: Brain tissue from 60 day old rat


title: 4sU-60min

data_processing:
adaptor trimming: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCAC -f fastq -O 1 -m 15 --quality-base=64 -q 13,13
mapping: bowtie --phred64-quals -l 100 -n 1 -m 1 --best --strata -S
internal priming filter: mapped reads were collapsed to identify unique 3' ends, and those with more than 6 As in the first 10 nt downstream, or more than 10 As in the first 20 nt were removed
Supplementary_files_format_and_content: 2-column tabular: 3' end position, read count

source_name: nascent RNA labeled by 4sU for 60 min

treatment_protocol: HEK293T cells were incubated with 1000 mM 4sU for 30 min or 60 min

value: 4sU 60 min


title: DMS-ctrl-rep1


title: mRNA Low Responder Amygdala 2

description: Brain tissue from 60 day old rat


title: 4sU-30min-input


title: mRNA Low Responder Amygdala 1

description: Brain tissue from 60 day old rat


title: mRNA High Responder Dorsal Raphe 6

description: Brain tissue from 60 day old rat

value: High Responder


title: 4sU-30min

source_name: nascent RNA labeled by 4sU for 30 min

value: 4sU 30 min


title: ChIP-seq from HepG2 (ENCLB825XMK)

description:
https://www.encodeproject.org/experiments/ENCSR327RFM/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR327RFM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB825XMK

source_name: Homo sapiens HepG2 immortalized cell line stably expressing N-terminal FLAG-PAF1_isoform1 fusion protein, C-terminal FLAG-PAF1_isoform1 fusion protein

value: immortalized cell line

value: child

value: 15 year

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: ENCBS708MOY at ENCODE; https://www.encodeproject.org/ENCBS708MOY/

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


title: ChIP-seq from HepG2 (ENCLB508WXR)

description:
https://www.encodeproject.org/experiments/ENCSR327RFM/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR327RFM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB508WXR

value: male

value: ENCBS996RIH at ENCODE; https://www.encodeproject.org/ENCBS996RIH/


title: mRNA High Responder Dorsal Raphe 5

description: Brain tissue from 60 day old rat

value: Dorsal Raphe


title: mRNA High Responder Dorsal Raphe 2

description: Brain tissue from 60 day old rat


title: mRNA High Responder Dorsal Raphe 4

description: Brain tissue from 60 day old rat


title: CENPB-library-fixed-length-cleaved-4sU60min

data_processing:
unique sequences were counted and compared to wild-type sequences to identify mismatches
Supplementary_files_format_and_content: 4-column tabular: sequence, count, number of mismatch in the intended region, number of mismatch outside the intended region

extract_protocol:
One day after transfection of a plasmid library, cells were harvested for total RNA isolation (RNeasy Mini Kit, Qiagen)
RNA was reverse transcribed using SuperScript III (Life Technologies) and an anchor dT primer, and the RT products were amplified using Phusion HF and a forward primer that hybridized upstream of the query region

treatment_protocol: Transfection in HEK293T and HeLa cells was with Lipofectamine 2000 (Life Technologies) following the manufacture’s protocol.

tag: treated with

value: 1000 mM 4sU 60 min

value: reporter mRNA 3' end


title: CENPB-library-fixed-length-uncleaved-4sU60min


title: mRNA High Responder Dorsal Raphe 1

description: Brain tissue from 60 day old rat


title: ChIP-seq from liver (ENCLB536LGP)

description:
https://www.encodeproject.org/experiments/ENCSR324RCI/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on FOXA1-human
experiment encode accession: ENCSR324RCI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR904IXG, ENCSR849OTN
encode release date: 2016-06-30
lab: Richard Myers, HAIB
library encode accession: ENCLB536LGP

source_name: Homo sapiens liver tissue female child (4 years)

tag: antibody

value: liver

value: tissue

value: Human liver tissue obtained from a healthy, 4 year old female donor

value: 4 year

value: female

value: healthy

value: Michael Snyder, Stanford

value: ENCBS401URL at ENCODE; https://www.encodeproject.org/ENCBS401URL/

value: Derived from ENCODE donor ENCDO882MMZ; https://www.encodeproject.org/ENCDO882MMZ/


title: ChIP-seq from liver (ENCLB619XUD)

description:
https://www.encodeproject.org/experiments/ENCSR324RCI/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on FOXA1-human
experiment encode accession: ENCSR324RCI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR904IXG, ENCSR849OTN
encode release date: 2016-06-30
lab: Richard Myers, HAIB
library encode accession: ENCLB619XUD

tag: description

value: child


title: CENPB-library-fixed-length-uncleaved-4sU30min

value: 1000 mM 4sU 30 min


title: mRNA High Responder Amygdala 6

description: Brain tissue from 60 day old rat

value: Amygdala

value: High Responder


title: mRNA High Responder Amygdala 5

description: Brain tissue from 60 day old rat


title: ChIP-seq from Karpas-422 (ENCLB242EAC)

description:
https://www.encodeproject.org/experiments/ENCSR317NQG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR317NQG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR367UDO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB242EAC
size range: 200-600

source_name: Homo sapiens Karpas-422 immortalized cell line

value: immortalized cell line

value: Karpas422- Human B cell non-Hodgkin lymphoma

tag: biosample encode accession

value: 73 year

value: adult

value: human B cell non-Hodgkin's lymphoma

value: Bradley Bernstein, Broad

value: ENCBS850UIV at ENCODE; https://www.encodeproject.org/ENCBS850UIV/

value: Derived from ENCODE donor ENCDO354AAA; https://www.encodeproject.org/ENCDO354AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1325; http://web.expasy.org/cellosaurus/CVCL_1325


title: CENPB-library-fixed-length-cleaved-4sU30min

value: reporter mRNA 3' end


title: mRNA Low Responder Amygdala 3

description: Brain tissue from 60 day old rat

value: Low Responder


title: ChIP-seq from neural cell (ENCLB810TKY)

description:
https://www.encodeproject.org/experiments/ENCSR308JFE/
***************
biological replicate number: 2
technical replicate number: 8
description:
experiment encode accession: ENCSR308JFE
assay title: ChIP-seq
encode release date: 2016-10-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB810TKY
size range: 200-600

source_name: Homo sapiens neural in vitro differentiated cells male embryo

value: Control

value: neural cell

value: in vitro differentiated cells

value: embryonic

value: male

tag: age

value: unknown

value: healthy

value: ENCBS737HIZ at ENCODE; https://www.encodeproject.org/ENCBS737HIZ/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: mRNA High Responder Amygdala 4

description: Brain tissue from 60 day old rat

source_name: Amygdala

value: Amygdala

value: High Responder


title: CENPB-library-fixed-length-uncleaved-HeLa

source_name: HeLa

value: HeLa


title: mRNA High Responder Amygdala 2

description: Brain tissue from 60 day old rat


title: mRNA High Responder Amygdala 3

description: Brain tissue from 60 day old rat


title: ChIP-seq from neural cell (ENCLB394XFU)

description:
https://www.encodeproject.org/experiments/ENCSR308JFE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR308JFE
assay title: ChIP-seq
encode release date: 2016-10-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB394XFU
size range: 300-800

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/97a73f1c-6372-4dd2-b275-0b8e855cbd5a/@@download/attachment/Cell_Paper_ChIP_protocol.pdf

tag: dev stage

value: Bradley Bernstein, Broad

value: ENCBS504GFW at ENCODE; https://www.encodeproject.org/ENCBS504GFW/


title: CENPB-library-fixed-length-cleaved-HeLa


title: CENPB-library-fixed-length-cleaved


title: SPF2

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

description: Illimuna next-generation sequencing (paired-read)

data_processing:
Image processing, base calling, quality scoring (Phred), and sample demultiplexing were executed by HiSeq Control Software with Real Time Analysis (HCS v3.3.41/RTA 2.5.2) and bcl2fastq Conversion Software (Illumina; San Diego, CA)
FASTQ-formatted sequence data was analyzed using a standard HISAT (hierarchical indexing for spliced alignment of transcripts)-Cufflinks workflow. RNA-Seq sequence reads (FASTQ format) were aligned to the reference cat genome assembly (Nov. 2014, ICGSC Felis Catus 8.0) using HISAT software. Gene- and transcript-level expression were comprehensively quantified with Cufflinks software, which performed 1) transcript assembly, 2) identification of splice variants, 3) quantification of expression as FPKM (fragments per kilobase of transcript per million mapped reads) values, and 4) normalization. Normalized FPKM values (Cuffnorm output) were utilized for downstream analysis steps.
Processed data are Cufflinks-Cuffnorm output files and contain Gene_Symbol (Ensembl ID), FPKM values, and FPKM status.
Genome_build: Nov. 2014, ICGSC Felis Catus 8.0
Supplementary_files_format_and_content: Tab-delimited text files include Ensembl ID, FPKM values, and FPKM status for each transcript and were prepared from the Cufflinks-Cuffnorm gene-level output files.

organism: Felis catus

source_name: Feline adipose-derived MSCs cultured in standard tissue culture medium

growth_protocol: The MSC cultures were cultured in standard Minimum Essential Medium α [MEMα] tissue culture medium supplemented with 10% fetal bovine serum, 1% L-glutamine, and 1% penicillin/streptomycin. MSCs from passages 3–4 were used for experimentation.

extract_protocol:
Total RNA was isolated from primary ASC cultures using the RNeasy Mini Kit (Qiagen, Inc.), RNA quantity and quality were assessed on a NanoDrop spectrophotometer (Thermo Scientific) and the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), respectively.
Transcriptome profiling was performed using a directional, strand-specific mRNA-Seq approach. Briefly, indexed RNA-Seq libraries were prepared from 200 ng total RNA using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems, Inc.) according to the manufacturer’s standard protocol. Poly-adenylated mRNA was purified from total RNA and ribosomal RNA removed by binding to oligo(dT) beads, which was followed by RNA fragmentation by incubation at 94ºC in the presence of magnesium. Double-stranded cDNA was then generated by random-primed first-strand synthesis and subsequent second strand synthesis in the presence of dUTP for strand marking. The double-stranded cDNA was then 3’-A tailed and indexed, Illumina-compatible adapters were ligated. The libraries were then enriched by high-fidelity PCR amplification (15 cycles) with KAPA HiFi HotStart DNA Polymerase and adapter-specific primers.

treatment_protocol: Untreated adipose-derived MSC cultures were utilized in this study. Once cultures reached the desired density during standard passaging, the cells were harvested for isolation of toal RNA.

tag: cell type

value: feline primary adipose-derived MSC culture


title: Luna


title: mRNA High Responder Amygdala 1

description: Brain tissue from 60 day old rat


title: Gray_Boy


title: CENPB-library-fixed-length-uncleaved

value: reporter mRNA 3' end


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_75

status: Public on Mar 11 2017

city: Cincinnati

first: Steven

last: Potter

state: OH

address: 3333 Burnet Ave.

department: Developmental Biology

institute: Children's hospital Medical Center

data_processing:
TopHat version April 2012 was used for base calling and Bam files were generated
GeneSpring 12.6.1 was used to analyze Bam files and to generate nRPKM
dSeq was used, with baseline to median of all samples
GeneSpring Newgene finding option was not used
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes nRPKM for each sample.

organism: Mus musculus

source_name: Pax2 mutant Cap mesenchyme E18.5 cells

extract_protocol:
[Cell preparation protocol] Single cell suspension was made by proteolytic digestion and cells of interest enriched by FACS
[single cell RNA-seq] Standard Fluidigm C1 microfluidics/robotics were carried out
Cells were lysed after capture in the Fluidigm C1 and the resulting RNA was directly used for reverse transcription. Library was constructed according to Fluidigm protocols

tag: strain

value: mixed

value: Cap mesenchyme cells

tag: genotype/variation

value: Pax2 mutant


title: mRNA High Responder Dorsal Raphe 3

description: Brain tissue from 60 day old rat

source_name: Dorsal Raphe

value: Dorsal Raphe


title: ChIP-seq from HepG2 (ENCLB027MOU)

description:
https://www.encodeproject.org/experiments/ENCSR331ORD/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR331ORD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR345EZN
encode release date: 2016-06-14
lab: Richard Myers, HAIB
library encode accession: ENCLB027MOU

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-CREB1 fusion protein

tag: line

value: immortalized cell line

value: child

tag: Sex

value: 15 year

value: hepatocellular carcinoma

tag: lab

value: Richard Myers, HAIB

tag: link

value: ENCBS474AND at ENCODE; https://www.encodeproject.org/ENCBS474AND/

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

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


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_76


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_73


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_72


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_71


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_70


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_69


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_67


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_62


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_66


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_61


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_63


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_65


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_64


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_59


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_58


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_56


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_60


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_55


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_57


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_52


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_51


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_50


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_54


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_49


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_53


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_48


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_46


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_68


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_47


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_45


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_44


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_43


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_42


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_41


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_39


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_36


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_34


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_38


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_35


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_33


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_76

source_name: Pax2 mutant Cap mesenchyme E13.5 cells


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_78


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_75


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_37


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_77


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_71


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_73


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_68


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_69


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_40


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_67


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_65


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_63


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_74


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_70


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_66


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_62


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_59


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_64


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_60


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_61


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_58


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_57


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_54


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_53


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_55


title: Kobayashi_3_18_15_E13_5_WT_Pool03_2015_Cell_96

source_name: Cap mesenchyme and derived E13.5 wild type cells

value: Cap mesenchyme and cap mesenchyme derived kidney cells

value: wild type


title: Mouse_Kobayashi_4_28_15_E18_5_Pax2_Mutant_Pool04_2015_Cell_32


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_52


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_72


title: Kobayashi_3_18_15_E13_5_WT_Pool03_2015_Cell_94


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_51


title: Kobayashi_3_18_15_E13_5_WT_Pool03_2015_Cell_92


title: Kobayashi_3_18_15_E13_5_WT_Pool03_2015_Cell_93


title: Kobayashi_3_18_15_E13_5_WT_Pool03_2015_Cell_91


title: Kobayashi_3_18_15_E13_5_WT_Pool03_2015_Cell_90


title: Kobayashi_3_18_15_E13_5_WT_Pool03_2015_Cell_89


title: Kobayashi_3_18_15_E13_5_WT_Pool03_2015_Cell_85


title: Kobayashi_3_18_15_E13_5_WT_Pool03_2015_Cell_86


title: Kobayashi_3_18_15_E13_5_WT_Pool03_2015_Cell_87


title: Mouse_Kobayashi_3_18_15_13_5_WT_pool04_2015_Cell_31

value: Interstitial cells


title: Kobayashi_3_18_15_E13_5_WT_Pool03_2015_Cell_83


title: Kobayashi_3_18_15_E13_5_WT_Pool03_2015_Cell_81


title: Kobayashi_3_18_15_E13_5_WT_Pool03_2015_Cell_79


title: Kobayashi_3_18_15_E13_5_WT_Pool03_2015_Cell_84


title: Kobayashi_3_18_15_E13_5_WT_Pool03_2015_Cell_82


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_56


title: Kobayashi_3_18_15_E13_5_WT_Pool03_2015_Cell_80


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_96

source_name: Interstitial E18.5 wild type cells


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_95


title: Kobayashi_2_26_15_E13_5_Pax2_Mutant_2_Pool03_2015_Cell_50


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_94


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_93


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_92


title: Kobayashi_3_18_15_E13_5_WT_Pool03_2015_Cell_95


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_87


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_85


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_84


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_89


title: Kobayashi_3_18_15_E13_5_WT_Pool03_2015_Cell_88


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_88


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_91


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_90


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_86


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_83


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_79


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_78


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_81


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_76


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_80


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_75


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_47


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_46


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_48


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_49


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_45


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_44


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_42


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_43


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_40


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_77


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_41


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_38


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool02_2015_Cell_82


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_36


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_35


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_31


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_32


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_33


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_34


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_30


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_28


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_27


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_26


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_29


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_25


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_24


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_19


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_21


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_17


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_20


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_22


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_23


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_14


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_15


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_18


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_39


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_37


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_11


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_13


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_12


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_10


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_9


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_7


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_5


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_3


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_4


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_73

source_name: Cap mesenchyme and derived E18.5 wild type cells


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_72


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_16


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_74


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_70


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_69


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_71


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_67


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_65


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_60


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_62


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_61


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_66


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_63


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_57


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_8


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_56


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_55


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_6


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_54


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_1


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_59


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_52


title: Kobayashi_2_24_15_E18_5_FoxD1_GCE_Pool03_2015_Cell_2


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_51


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_50


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_49


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_48


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_68


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_44


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_64


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_47


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_43


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_42


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_41


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_46


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_58


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_39


title: Moz_sko_TAM2 rep2

city: Tokyo

first: Shuhei

last: Fujita

address: 5-1-1 Tsukiji, Chuo-ku

department: Division of Hematological Malignancy

country: Japan

institute: National Cancer Center

data_processing:
Avadis NGS Version 2.1 software was used for analysis
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Avadis NGS Version 2.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include genes up- and down-regulatedby Ezh1/2 ko with  1 fold change or 2 folds change

source_name: Bone Marrow

extract_protocol:
Bone marrow cells of femur and tibia were extracted, and RNA was harvested using IsogenⅡ reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#15026495 Rev. F) 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: Tamoxifen (10mg/kg/day) solved in corn oil was administered for 5 consecutive doses via intraperitoneal injection.

tag: tissue

value: Bone Marrow

value: 7 days after corn tamoxifen treatment

tag: genotype


title: Moz_sko_TAM1 rep1

tag: treatment


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_40

value: mixed


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_53


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_37


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_36


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_38


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_35


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_34


title: Moz_sko_oil1 rep1

value: 7 days after corn oil treatment


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_33


title: Moz_dko_TAM2 rep2


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_32


title: Moz_sko_oil2 rep2


title: Moz_dko_TAM1 rep1


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_45


title: Moz_dko_oil1 rep1


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_30


title: Moz_dko_oil2 rep2


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_29


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_27


title: G392E-NS_rep3

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

description: Processed data file: RawCountsMatrix.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were mapped to the mouse Ensembl GRCm38 build reference genome using Tophat (version 2.0.12) (Trapnell et al., 2012) using default settings plus the "—no-novel-juncs" option. Gene structure annotations corresponding to the Ensembl annotation release 75 were used to build a transcriptome index and provided to Tophat during the alignment step using the "-G" parameter.
The same gene annotations were used to quantify the gene-level read counts using HTSeq-count (version 0.6.1) script. Subsequently, differential gene expression analyses were performed using Bioconductor (Gentleman et al. 2004) R (version 3.2.2) (R Core Team, 2015) package DESeq2 (version 1.4.5) (Love et al., 2014).
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: RawCountsMatrix.txt: Tab-delimited text file includes raw counts of the gene-level reads.

source_name: Differentiated NPCs overexpressing G392E NS

extract_protocol:
Differentiated NPCs plated in T25 flasks were lysed in 400 µl/flask of RLT buffer (Qiagen RNeasy Mini kit). Total RNA was purified out using Qiagen RNeasy mini kit and eluted in 20 µl of RNase-free water.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: Neural progenitor cells (NPCs) derived from E13.5 cerebral cortex

tag: stable expression

value: G392E neuroserpin (NS)


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_28


title: G392E-NS_rep2


title: G392E-NS_rep1


title: GFP_rep2

source_name: Differentiated NPCs overexpressing GFP

value: green fluorescent protein (GFP)


title: GFP_rep1


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_25


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_24


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_23


title: H3K9me3_YA_rep2

city: Cambridge

first: Julie

last: Ahringer

address: Tennis Court Road

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Libraries were sequenced using Illumina HiSeq and de-multiplexed FASTQ files were obtained from Illumina BaseSpace.
Reads were aligned to the WS220/ce10 assembly of the C. elegans genome using BWA v. 0.7.7 with default settings (BWA-backtrack algorithm).
The SAMtools v. 0.1.19 ‘view’ utility was used to convert the alignments to BAM format.
To be able to investigate binding and expression at repetitive elements, we used all aligned reads (mapq0) to generate pileup and normalised tracks.
ChIP-seq data were normalized using summed input and the BEADS algorithm, omitting the mappability correction step (Cheung et al, 2011).
ChIP-seq signals were exported to BigWiggle tracks at 1bp native resolution.
Genome_build: ce10/WS220
Supplementary_files_format_and_content: "linear" scores in bigWig tracks represent BEADS values (signal relative to input); files were generated using BEADS normalization pipeline in R

organism: Caenorhabditis elegans

source_name: young adults

growth_protocol: About 2-7 million of adults grown in liquid culture at 20C were bleached and then hatched in M9 for 24 hrs. Hatched L1 larvae were inoculated into liquid culture (S-basal and HB101 bacteria) at a density of less than 1 million per 100ml. After 60hrs at 20C, young adults were harvested, washed in M9 buffer, cleaned by sucrose flotation and collected by freezing in liquid nitrogen.  An aliquot was stained for DAPI to confirm the stage.

extract_protocol:
Frozen worm pellets were ground, crosslinked for 10 minutes in 1.5 mM EGS in FA buffer, then formaldehyde added to 1% and cross-linking continued for an additional 10 minutes (protein factors), or fixed 10 minutes in 1% formaldehyde (histone modifications). Fixative was quenched with 125 mM glycine and cross-linked tissue washed 2X with PBS + protease inhibitors, then resuspended in FA buffer and subjected to sonication in a Bioruptor or Bioruptor pico to an average DNA size of 200bp. Extracts were  spun down and the soluble fraction used for ChIP.  For ChIPs of protein factors, 1mg of ChIP extract was incubated with 5ug antibody; for histone modifications, 500ug ChIP extract was incubated with 2ug of antibody.  After overnight incubation with rotation at 4C, 40ul of equilibrated magnetic beads (coupled to protein A or G, depending on antibody) were added and incubated for 2 hrs at room temperature with rotation. Washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer were performed and DNA was eluted in elution buffer (1% SDS in TE with 250 mM NaCl) two times with 57 ul volume each, at 65°C. Samples were treated with RNAse, proteinase K and then crosslinks were reversed overnight at 65°C. DNA was purified on Qiagen PCR purification columns and used for ChIP library preparation.
ChIP or input DNA is blunt ended, A-tailed, ligated to adaptors, amplified by PCR, then size selected using AMPure beads.  Illuimina TruSeq adaptors and barcodes were used. Samples were sequenced on a HiSeq1500

value: whole body

value: young adults

tag: chip antibody

value: H3K9me3 (Abcam, ab8898)


title: nrde2(gg91)_let-418(n3536)_YA_rep2

description: Ribosomal RNA-depleted RNA.

data_processing:
Libraries were sequenced using Illumina HiSeq and de-multiplexed FASTQ files were obtained from Illumina BaseSpace.
Reads were aligned to the WS220/ce10 assembly of the C. elegans genome using BWA v. 0.7.7 with default settings (BWA-backtrack algorithm).
The SAMtools v. 0.1.19 ‘view’ utility was used to convert the alignments to BAM format.
Pileups tracks were generated in R and normalised for depth of coverage by dividing by number of millions of reads in the library (RPM).
Genome_build: WS220/ce10
Supplementary_files_format_and_content: BigWiggle binary track file

source_name: young adults, nrde2(gg91)_let-418(n3536), condition2

growth_protocol:
Samples were grown under condition 1 or condition 2:
Condition 1: Starved L1s were grown at 20C until L4 stage, shifted to 25C, then collected as young adults.
Condition 2: Starved L1s were grown at 15C until L4 stage, shifted to 25C, then collected as young adults.

extract_protocol:
Total RNA was extracted in TriPure Reagent (Roche), treated with baseline zero DNase (Epicentre), and purified with Zymo Research RNA Clean and Concentrator-5 (Cambridge Bioscience), all according to the manufacturers' instructions. Ribosomal RNA was depleted using the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Illumina).
Ribosomal RNA-depleted RNA was used to make strand-specific libraries using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's instructions.

tag: growth condition


title: H3K9me3_YA_rep1


title: nrde2(gg91)_let-418(n3536)_YA_rep1

description: Ribosomal RNA-depleted RNA.


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_22


title: nrde2(gg91)_YA_rep1

description: Ribosomal RNA-depleted RNA.

source_name: young adults, nrde2(gg91), condition2


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_31


title: prg-1(n4357)_YA_rep2

description: Ribosomal RNA-depleted RNA.

source_name: young adults, prg-1(n4357), condition2


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_21


title: met-2(n4256)_set-25(n5021)_YA_rep1

description: Ribosomal RNA-depleted RNA.

source_name: young adults, met-2(n4256)_set-25(n5021), condition1


title: prg-1(n4357)_YA_rep1

description: Ribosomal RNA-depleted RNA.


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_19


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_20


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_26


title: let-418(n3536)_YA_rep1

description: Ribosomal RNA-depleted RNA.

source_name: young adults, let-418(n3536), condition1


title: let-418(n3536)_YA_rep2

description: Ribosomal RNA-depleted RNA.


title: lin-61(tm2649)_YA-rep1

description: Ribosomal RNA-depleted RNA.

source_name: young adults, lin-61(tm2649), condition1


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_18


title: met-2(n4256)_set-25(n5021)_YA_rep2

description: Ribosomal RNA-depleted RNA.


title: lin-61(tm2649)_YA-rep2

description: Ribosomal RNA-depleted RNA.


title: lin-13(n770)_YA_rep2

description: Ribosomal RNA-depleted RNA.

source_name: young adults, lin-13(n770), condition2


title: lin-13(n770)_YA_rep1

description: Ribosomal RNA-depleted RNA.


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_17


title: GFP_rep3


title: hpl-2(tm1489)_YA_rep1

description: Ribosomal RNA-depleted RNA.

source_name: young adults, hpl-2(tm1489), condition1


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_15


title: nrde2(gg91)_YA_rep2

description: Ribosomal RNA-depleted RNA.


title: WT_YA_condition2_rep2

description: Ribosomal RNA-depleted RNA.

source_name: young adults, WT, condition2

value: WT


title: WT_YA_condition2_rep1

description: Ribosomal RNA-depleted RNA.


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_14


title: hpl-2(tm1489)_YA_rep2

description: Ribosomal RNA-depleted RNA.


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_13


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_12


title: Summed_input_FRM

description: A mixture of input sequence from 8 formaldehyde ChIP-seq extracts.

data_processing:
Libraries were sequenced using Illumina HiSeq and de-multiplexed FASTQ files were obtained from Illumina BaseSpace.
Reads were aligned to the WS220/ce10 assembly of the C. elegans genome using BWA v. 0.7.7 with default settings (BWA-backtrack algorithm).
The SAMtools v. 0.1.19 ‘view’ utility was used to convert the alignments to BAM format.
To be able to investigate binding and expression at repetitive elements, we used all aligned reads (mapq0) to generate pileup and normalised tracks.
ChIP-seq data were normalized using summed input and the BEADS algorithm, omitting the mappability correction step (Cheung et al., 2011).
ChIP-seq signals were exported to BigWiggle tracks at 1bp native resolution.
Genome_build: WS220/ce10
Supplementary_files_format_and_content: "linear" scores in bigWig tracks represent BEADS values (signal relative to input); files were generated using BEADS normalization pipeline in R.

source_name: young adults, input FRM

growth_protocol: About 2-7 million adults grown in liquid culture at 20C were bleached and then hatched in M9 for 24 hrs. Hatched L1 larvae were inoculated into liquid culture (S-basal and HB101 bacteria) at a density of less than 1 million per 100ml. After 60hrs at 20C, young adults were harvested, washed in M9 buffer, cleaned by sucrose flotation and collected by freezing in liquid nitrogen. An aliquot was stained for DAPI to confirm the stage.

extract_protocol:
Frozen worm pellets were ground, crosslinked for 10 minutes in 1.5 mM EGS in FA buffer, then formaldehyde added to 1% and cross-linking continued for an additional 10 minutes (protein factors), or fixed 10 minutes in 1% formaldehyde (histone modifications). Fixative was quenched with 125 mM glycine and cross-linked tissue washed 2X with PBS + protease inhibitors, then resuspended in FA buffer and subjected to sonication in a Bioruptor or Bioruptor pico to an average DNA size of 200bp. Extracts were spun down and the soluble fraction used for ChIP. For ChIPs of protein factors, 1mg of ChIP extract was incubated with 5ug antibody; for histone modifications, 500ug ChIP extract was incubated with 2ug of antibody. After overnight incubation with rotation at 4C, 40ul of equilibrated magnetic beads (coupled to protein A or G, depending on antibody) were added and incubated for 2 hrs at room temperature with rotation. Washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer were performed and DNA was eluted in elution buffer (1% SDS in TE with 250 mM NaCl) two times with 57 ul volume each, at 65°C. Samples were treated with RNase, proteinase K and then crosslinks were reversed overnight at 65°C. DNA was purified on Qiagen PCR purification columns and used for ChIP library preparation.
ChIP or input DNA is blunt ended, A-tailed, ligated to adaptors, amplified by PCR, then size selected using AMPure beads. Illumina TruSeq adaptors and barcodes were used. Samples were sequenced on a HiSeq1500.


title: Summed_input_EGS

description: A mixture of input sequence from 5 EGS ChIP-seq extracts.

source_name: young adults, input EGS


title: WT_YA_condition1_rep2

description: Ribosomal RNA-depleted RNA.

source_name: young adults, WT, condition1


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_10

source_name: Cap mesenchyme and derived E18.5 wild type cells


title: MET-2_YA_rep1

source_name: young adults, MET-2 ChIP

value: MET-2 (Strategic Diagnostics Inc., Q2943)


title: LIN-61_YA_rep2

source_name: young adults, LIN-61 ChIP

value: LIN-61 (Strategic Diagnostics Inc., Q3520)


title: MET-2_YA_rep2


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_9


title: LIN-61_YA_rep1


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_7


title: LIN-13_YA_rep1

source_name: young adults, LIN-13 ChIP

value: LIN-13 (Strategic Diagnostics Inc., Q0838)


title: LIN-13_YA_rep2


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_5

value: Cap mesenchyme and cap mesenchyme derived kidney cells


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_11

value: wild type


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_6


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_4


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_16


title: HPL-2_YA_rep2

source_name: young adults, HPL-2 ChIP

value: HPL-2 (Strategic Diagnostics Inc., Q2324)


title: WT_YA_condition1_rep1

description: Ribosomal RNA-depleted RNA.


title: HPL-2_YA_rep1


title: H3K9me2_YA_rep2

source_name: young adults, H3K9me2 ChIP


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_1


title: H3K9me2_YA_rep1


title: 50PS_+_D100_y_3

status: Public on Mar 10 2017

city: Seattle

first: Allen

last: Institute

state: WA

address: 615 Westlake Ave N

institute: The Allen Institute for Brain Science

data_processing:
Read were aligned transcriptome by RSEM to RefSeq gene annotation (April 23, 2013), and unmapped reads were aligned to genome by Bowtie. The remaining reads were aligned to ERCC.
Genome_build: hg19
Supplementary_files_format_and_content: RSEM TPM gene expression matrix

molecule: polyA RNA

source_name: cultured embryonic stem cells

growth_protocol: hESCs were seeded for a 10-day cortical induction phase in NIMX media with SMAD inhibitors; reseeded for the ventralization phase at D10 in culture media containing Shh and purmorphamine, and finally at D24 for neural differentiation with neurogenic/neurotrophic factors BDNF, GDNF, NT3, and cAMP.  The protocol was ended at D125.

extract_protocol:
To generate single cell suspensions, hESC-derived cultures were dissociated from plates using Accutase  (ThermoFisher)  at  37°C.    Light  trituration  using  a P1000  pipette  was  done  every  5  min  until  nearly  all clumps  had  been  dissociated  (up  to  1  h).    Cell  suspension  was  washed  and  filtered  through  a  40  μm  cell  strainer.  Cells were washed in PBS with 1% FBS and stained with 0.5-1 μg/mL DAPI.  Single-cell suspensions were loaded onto  a  FACSAria  II  SORP  (Becton  Dickinson)  and  sorted  directly  into  PCR  strip  tubes  or  plates  held  in  chilled aluminum  blocks.    Doublets  and  dead  cells  were  excluded  based  on  forward  scatter,  side  scatter  and  DAPI fluorescence. Sorting was done using the 130  μm nozzle with the sort mode set to single cell. Accuracy of single-cell  sorts  was  confirmed  by  sorting  DAPI-stained  fixed  cells  onto  a  dry  well  of  a  96-well  plate  and  analyzing  by fluorescence microscopy. Cells were sorted into 10K cell Citrine-negative (progenitors) or Citrine-positive (neurons) populations at each timepoint. These 10K cell subpopulations were processed for RNAseq via the SmartSeq2 kit.
SmartSeq2 protocol. After  reverse  transcription  and  template  switching,  we amplified  cDNA  with  KAPA  HotStart  HIFI  2×  ReadyMix  (Kapa  Biosystems)  for  22  cycles  for  RNA  from  single primary cortical cells. We purified PCR products using Ampure XP beads (Beckman Coulter). We quantified cDNA using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 or with the Quant-iT PicoGreen dsDNA Assay   Kit  (Thermo  Fisher)  on  an  Enspire  plate  reader  (PerkinElmer).  We  used  1  ng  of  cDNA  to  generate  RNA-Seq libraries using the Nextera XT library prep system (Illumina). We carried out sequencing of human cortical cells the on Illumina HiSeq using 50 base paired-end reads

value: cultured embryonic stem cells

tag: days in culture

tag: cre line

value: DCX+

tag: batch

tag: condition

tag: co-cultured with astrocytes

value: y


title: 100PS_+_D100_y_3

tag: cell type


title: 100PS_+_D54_y_3


title: 100PS_+_D54__4


title: 50PS_+_D54_y_3


title: 50PS_+_D54_y_2


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_8

tag: strain

value: mixed

tag: genotype/variation

tag: age


title: 100PS_-_D100__2

value: DCX-


title: LET-418_YA_rep2

source_name: young adults, LET-418 ChIP

value: LET-418 (Strategic Diagnostics Inc., Q3861)


title: 100PS_+_D54_y_1


title: 50PS_-_D100__2


title: 100PS_+_D54__1


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_2


title: 50PS_-_D100__1


title: 100PS_-_D54__3


title: 50PS_-_D54__3


title: 100PS_+_D54__3


title: 50PS_+_D54__3


title: 100PS_-_D26__3


title: 100PS_+_D26__3


title: Kobayashi_2_11_15_E18_5_CTRL_2_Pool02_2015_Cell_3


title: 100PS_+_D54__2


title: 100PS_+_D100__3


title: 50PS_+_D100__3


title: 100PS_-_D26__2


title: 50PS_-_D26__3


title: 100PS_-_D54__2


title: 100PS_+_D54_y_2


title: 50PS_-_D54__2


title: 50PS_-_D54__1


title: 50PS_+_D26__3


title: 100PS_+_D26__2


title: 50PS_+_D54__2


title: 100PS_+_D100__2


title: 50PS_+_D100__2


title: 50PS_-_D26__2


title: 50PS_+_D54_y_1


title: 50PS_+_D54__1


title: 50PS_+_D100_y_2


title: 50PS_+_D100__1


title: D125Dp22H09

extract_protocol:
To generate single cell suspensions, hESC-derived cultures were dissociated from plates using Accutase  (ThermoFisher)  at  37°C.    Light  trituration  using  a P1000  pipette  was  done  every  5  min  until  nearly  all clumps  had  been  dissociated  (up  to  1  h).    Cell  suspension  was  washed  and  filtered  through  a  40  μm  cell  strainer.  Cells were washed in PBS with 1% FBS and stained with 0.5-1 μg/mL DAPI.  Single-cell suspensions were loaded onto  a  FACSAria  II  SORP  (Becton  Dickinson)  and  sorted  directly  into  PCR  strip  tubes  or  plates  held  in  chilled aluminum  blocks.    Doublets  and  dead  cells  were  excluded  based  on  forward  scatter,  side  scatter  and  DAPI fluorescence. Sorting was done using the 130  μm nozzle with the sort mode set to single cell. Accuracy of single-cell  sorts  was  confirmed  by  sorting  DAPI-stained  fixed  cells  onto  a  dry  well  of  a  96-well  plate  and  analyzing  by fluorescence microscopy.
SmartSeq2 protocol. After  reverse  transcription  and  template  switching,  we amplified  cDNA  with  KAPA  HotStart  HIFI  2×  ReadyMix  (Kapa  Biosystems)  for  22  cycles  for  RNA  from  single primary cortical cells. We purified PCR products using Ampure XP beads (Beckman Coulter). We quantified cDNA using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 or with the Quant-iT PicoGreen dsDNA Assay   Kit  (Thermo  Fisher)  on  an  Enspire  plate  reader  (PerkinElmer).  We  used  1  ng  of  cDNA  to  generate  RNA-Seq libraries using the Nextera XT library prep system (Illumina). We carried out sequencing of human cortical cells the on Illumina HiSeq using 50 base paired-end reads


title: 100PS_+_D100_y_2


title: 50PS_-_D26__1


title: D125Dp22H03


title: D125Dp22H08


title: D125Dp22H04


title: D125Dp22H06


title: D125Dp22G11


title: 50PS_+_D26__2


title: D125Dp22H07


title: D125Dp22G10


title: D125Dp22G09


title: D125Dp22G07


title: LET-418_YA_rep1


title: D125Dp22G08


title: 50PS_+_D26__1


title: D125Dp22G05


title: D125Dp22G04


title: D125Dp22G06


title: D125Dp22H01


title: D125Dp22G03


title: D125Dp22G01


title: D125Dp22G02


title: D125Dp22F10


title: D125Dp22F11


title: D125Dp22H11


title: D125Dp22F09


title: D125Dp22F04


title: D125Dp22F07


title: D125Dp22F08


title: D125Dp22F05


title: D125Dp22F03


title: D125Dp22F06


title: D125Dp22E11


title: D125Dp22E10


title: D125Dp22F02


title: D125Dp22E07


title: D125Dp22E08


title: D125Dp22E09


title: D125Dp22E03


title: D125Dp22E01


title: D125Dp22E02


title: D125Dp22E05


title: D125Dp22E04


title: D125Dp22D10


title: D125Dp22D08


title: D125Dp22D09


title: D125Dp22D05


title: D125Dp22D06


title: D125Dp22D04


title: D125Dp22D03


title: D125Dp22D02


title: D125Dp22D07


title: D125Dp22C11


title: D125Dp22C10


title: D125Dp22C06


title: D125Dp22C08


title: D125Dp22C07


title: D125Dp22C04


title: D125Dp22C05


title: D125Dp22C03


title: D125Dp22C02


title: D125Dp22C01


title: D125Dp22B08


title: D125Dp22B09


title: D125Dp22B10


title: D125Dp22B07


title: D125Dp22B05


title: D125Dp22B06


title: D125Dp22B03


title: D125Dp22B04


title: D125Dp22A09


title: D125Dp22A11


title: D125Dp22A08


title: D125Dp22B02


title: D125Dp22D01


title: D125Dp22A05


title: D125Dp22A07


title: D125Dp22A02


title: D125Dp22A04


title: D125Dp22F01


title: D125Dn23H11


title: D125Dn23H10


title: D125Dp22B11


title: D125Dn23H09


title: D125Dn23H07


title: D125Dn23H06


title: D125Dn23H04


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