title: ChIP-seq from A549 (ENCLB600TUB)

description:
https://www.encodeproject.org/experiments/ENCSR616MOB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR616MOB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB600TUB
size range: 200-600
nucleic acid starting quantity: 26.4
nucleic acid starting quantity units: ng

value: immortalized cell line

value: adult

value: 58 year

value: ENCBS998UBJ at ENCODE; https://www.encodeproject.org/ENCBS998UBJ/

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

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


title: microRNA-seq from forebrain (ENCLB647DTE)

status: Public on Jul 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/ENCSR552WPH/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on embryonic 16.5 day mouse forebrain
experiment encode accession: ENCSR552WPH
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB647DTE
size range: <30

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (16.5 days)

value: forebrain

value: tissue

tag: description

value: Forebrain pooled from embyonic 16.5 day mice

tag: biosample encode accession

tag: age

tag: dev stage

value: embryonic

tag: Sex

value: pooled male and female

tag: health state

value: healthy

tag: lab

value: Len Pennacchio, LBNL

tag: link

value: ENCBS156DHU at ENCODE; https://www.encodeproject.org/ENCBS156DHU/

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


title: microRNA-seq from hindbrain (ENCLB505RSP)

description:
https://www.encodeproject.org/experiments/ENCSR571RHM/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on embryonic 16.5 day mouse hindbrain
experiment encode accession: ENCSR571RHM
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB505RSP
size range: <30

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex embryo (16.5 days)

value: hindbrain

value: Hindbrain pooled from embyonic 16.5 day mice

value: ENCBS436LSH at ENCODE; https://www.encodeproject.org/ENCBS436LSH/


title: ChIP-seq from right lobe of liver (ENCLB198YHZ)

description:
https://www.encodeproject.org/experiments/ENCSR614JFD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR614JFD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR276SJT
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB198YHZ
size range: 200-600

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

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

tag: antibody

value: right lobe of liver

value: i.e. REMC 2,3,4,5 and 16; EnTEX:Liver

value: adult

value: female

value: 53 year

value: Bradley Bernstein, Broad

value: ENCBS536THV at ENCODE; https://www.encodeproject.org/ENCBS536THV/

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


title: microRNA-seq from forebrain (ENCLB557XLR)

description:
https://www.encodeproject.org/experiments/ENCSR552WPH/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on embryonic 16.5 day mouse forebrain
experiment encode accession: ENCSR552WPH
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB557XLR
size range: <30

value: forebrain

value: tissue

value: Forebrain from 41 embyonic 16.5 day mice

value: embryonic

value: ENCBS512LKA at ENCODE; https://www.encodeproject.org/ENCBS512LKA/


title: NPC single cell 55

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Reads were trimmed of adapter sequences TCGTATGCCGTCTTCTGCTTG, ATCTCGTATGCCGTCTTCTGCTTG, CGACAGGTTCAGAGTTCTACAGTCCGACGATC GATCGGAAGAGCACACGTCTGAACTCCAGTCAC using cutadapt v1.8.1
Trimmed reads were aligned to RepBase v18.05 using STAR v2.4.01
Reads that didn't align to RepBase were aligned to hg19 using STAR v2.4.01 and a splice junction database derived from GENCODE v19
Transcripts per million (TPM) per transcript was calculated from reads that didn't align to RepBase were quasi-aligned to GENCODE v19 protein coding and lincRNA transcripts using Sailfish v0.6.3
TPM per gene was calculated by summing the TPM for all transcripts of a gene
Percent spliced-in (Psi) was calculated from junction read output from STAR aligner (SJ.out.tab) were used to create a de novo splicing index in conjunction with GENCODE v19 gene annotations, using outrigger
Outlier cells were calculated using K-means clustering with k=3 on the expression matrix and omitting cells which clustered into a group consisting of a majority of other cell types
Modality was calculated using anchor on the psi scores for all events detected in at least 10 cells, for each cell type
Waypoints were calculated using bonvoyage on the psi scores for all events detected in at least 10 cells, for each cell type
Splicing events were annotated using poshsplice to annotate corresponding genes, splice site strength using MaxEntScan, intron and exon lengths, conservation of alternative splicing from Merkin et al Science 2012,
Genes were annotated with attributes available in Gencode v19, Phylostrata for the matching ENSEMBL identifiers in Domazet-Loso et al MBE 2008, and TF or RBP category from Gerstberger et al Nat Rev Gen 2014
Genome_build: hg19
Supplementary_files_format_and_content: "metadata.csv.gz" contains sample metadata, "splicing.csv.gz" contains Psi scores, "splicing_feature.csv.gz" contains metadata for splicing events, "expression.csv.gz" contains TPM values for genes, "expression_feature.csv.gz" contains metadata for genes, "mapping_stats.csv.gz" contains the number and percentages of reads mapped for each samples

molecule: polyA RNA

source_name: Neural progenitor cells

growth_protocol: iPSCs were cultured on matrigel coated plated using mTeSR(Stem Cell Technologies) media with mTeSR supplement at 37C incubator with 5% CO2.

extract_protocol:
Motor neurons were directly differentiated from iPSCs as previous described (Chambers S, Nature Biotechnology, 2009). Briefly, iPSCs were cultured on matrigel coated plates until fully confluent in mTeSR then switch to knock-out serum replacement media (KSR) containing Dorsomorphin(1uM) and SB431542(10uM). Upon day 4 of differentiation, increasing amounts of N2 media (25%, 50%) was added to the KSR. From day 7 of differentiation, 1.5uM retinoic acid and 200nM Smoothened Agonist (SAG, EMD Millipore) were added to induce patterning. Cells were dissociated on day 17 of differentiation and replated in poly-D-lysine and laminin coated plates. Maturation was performed using BDGF(2ng/ml), GDNF(2ng/ml), CNTF(2ng/ml), ascorbid acid, sonic hedgehog and retinoic acid in N2 and B27 media up until 35 days of differentiation.
Single cells were captured on C1 auto prep platform (Fluidigm, CA) according to manufacturer's instructions. C1 auto prep chips were visually inspected with a light microscopy at 20X to ensure singularity of captured cells. All non-single cells were discarded from analysis. SMARTer Ultra Low RNA cDNA Synthesis Kit (Clontech) was used to reverse transcribe polyA-tailed RNA. cDNA was amplified using Advantage 2 Polumerase Mix by PCR at 95¡C for 1 minutes, followed by 21 cylcles of 15 secondes at 95¡C, 30 seconds at 65¡C and 6 minutes at 68¡C, followed by another 10 minutes at 72¡C as a final extension. cDNAs were inspected using Agilent Bioanalyzer High Sensitivity DNA chips and quantitated by PicoGreen dsDNA Assay kit (ThermoFisher). cDNAs were diluted to 1ng to generate libraries using the Nextera XT DNA kit(Illumina, CA).  Libraries were multiplexed and sequenced on Illumina HiSeq200 to generate 100bp PE reads.

treatment_protocol: Neuron progenitor cells were differentiated from iPSCs. Briefly, iPSCs were cultured in Matrigel coated plates and dislodged by dispase. To form embryonic bodies, the dislodged colonies were cultured in DMEM/F12(invitrogen) with GlutaMax and N2 supplement in non-adhere petri dish. Media were replaced every other day for 7 days. EBs were then placed onto matrigel coated plate to allow rosette formation. Clean rosette were picked manually and maintained in EB media for 7 days and subsequently dissociated with accutase and cultured in NPC media (DMEM/F12, GlutaMax, N2 and B27 with 2ug/ml FGF) to allow neuron progenitor cell differentiation. NPCs were maintained in NPC media.

tag: cell type

value: iPSC-derived neural progenitor cells

tag: gender

value: male

tag: sample type

value: Single Cell


title: microRNA-seq from liver (ENCLB032OMQ)

description:
https://www.encodeproject.org/experiments/ENCSR489FQD/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq  on embryonic 11.5 day mouse liver
experiment encode accession: ENCSR489FQD
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-02-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB032OMQ
size range: <30

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (11.5 days)

value: liver

value: Liver from 109 embyronic 11.5 day mice

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS746POP at ENCODE; https://www.encodeproject.org/ENCBS746POP/

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


title: NPC single cell 54


title: ChIP-seq from body of pancreas (ENCLB149DDE)

description:
https://www.encodeproject.org/experiments/ENCSR596PFU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR596PFU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR099LGH
encode release date: 2016-07-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB149DDE
size range: 200-600

source_name: Homo sapiens body of pancreas tissue male adult (54 years)

value: body of pancreas

value: adult

value: 54 year

value: Bradley Bernstein, Broad

value: ENCBS209WBW at ENCODE; https://www.encodeproject.org/ENCBS209WBW/

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


title: NPC single cell 53


title: microRNA-seq from liver (ENCLB438BDQ)

description:
https://www.encodeproject.org/experiments/ENCSR489FQD/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq  on embryonic 11.5 day mouse liver
experiment encode accession: ENCSR489FQD
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-02-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB438BDQ
size range: <30

value: tissue

value: Liver from pooled embryonic 11.5 day mice

value: embryonic

value: ENCBS522YOW at ENCODE; https://www.encodeproject.org/ENCBS522YOW/


title: ChIP-seq from right atrium auricular region (ENCLB611VQY)

description:
https://www.encodeproject.org/experiments/ENCSR593KDJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR593KDJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR195BZZ
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB611VQY
size range: 200-600

source_name: Homo sapiens right atrium auricular region tissue female adult (53 years)

value: right atrium auricular region

value: EnTEX:Heart - Atrial Appendage

value: 53 year

value: female

value: ENCBS493WOF at ENCODE; https://www.encodeproject.org/ENCBS493WOF/

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


title: microRNA-seq from neural tube (ENCLB610IQP)

description:
https://www.encodeproject.org/experiments/ENCSR415KUB/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on embryonic 15.5 day mouse neural tube
experiment encode accession: ENCSR415KUB
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB610IQP
size range: <30

source_name: Mus musculus strain B6NCrl neural tube tissue mixed sex embryo (15.5 days)

value: neural tube

value: Neural tube from 62 embryonic 15.5 day mice

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS206NRE at ENCODE; https://www.encodeproject.org/ENCBS206NRE/

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


title: microRNA-seq from neural tube (ENCLB464VHT)

description:
https://www.encodeproject.org/experiments/ENCSR415KUB/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on embryonic 15.5 day mouse neural tube
experiment encode accession: ENCSR415KUB
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB464VHT
size range: <30

value: tissue

value: Neural tube from 78 embryonic 15.5 day mice

value: ENCBS944KEZ at ENCODE; https://www.encodeproject.org/ENCBS944KEZ/


title: NPC single cell 52

value: iPSC-derived neural progenitor cells

value: male

value: Single Cell


title: ChIP-seq from bipolar neuron (ENCLB060MEC)

description:
https://www.encodeproject.org/experiments/ENCSR592ETL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR592ETL
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR001KCX
encode release date: 2017-01-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB060MEC
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 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: adult

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: microRNA-seq from heart (ENCLB307DVK)

description:
https://www.encodeproject.org/experiments/ENCSR481QIP/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on embryonic 16.5 day mouse heart
experiment encode accession: ENCSR481QIP
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB307DVK
size range: <30

source_name: Mus musculus strain B6NCrl heart tissue mixed sex embryo (16.5 days)

value: heart

value: Heart from 41 embyonic 16.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS217XWR at ENCODE; https://www.encodeproject.org/ENCBS217XWR/


title: microRNA-seq from heart (ENCLB203DUX)

description:
https://www.encodeproject.org/experiments/ENCSR481QIP/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on embryonic 16.5 day mouse heart
experiment encode accession: ENCSR481QIP
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB203DUX
size range: <30

value: tissue

value: Heart pooled from embyonic 16.5 day mice

value: ENCBS955JPC at ENCODE; https://www.encodeproject.org/ENCBS955JPC/

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


title: microRNA-seq from midbrain (ENCLB958BIA)

description:
https://www.encodeproject.org/experiments/ENCSR625ESQ/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on embryonic 16.5 day mouse midbrain
experiment encode accession: ENCSR625ESQ
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB958BIA
size range: <30

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (16.5 days)

value: midbrain

value: Midbrain pooled from embyonic 16.5 day mice

value: ENCBS684MLE at ENCODE; https://www.encodeproject.org/ENCBS684MLE/


title: NPC single cell 51

value: iPSC-derived neural progenitor cells

value: male

value: Single Cell


title: SingleCell_Brain_EC_E145_S78

city: Würzburg

first: Mike

last: Hupe

address: Biocenter Am Hubland

department: Department of Developmental Biochemistry

country: Germany

institute: University of Würzburg

description:
total mRNA
RPKM_SingleCell.txt

data_processing:
TRAP and HUVEC: Sequence reads were mapped against the Mus musculus genome assembly (Genome Reference Consortium GRCm38, UCSC version mm10) using the RUM v. 2.04 pipeline (Grant et al.: Bioinformatics, 2011).
Single cell: The reads were aligned to mouse (mm10) genomes using STAR v2.2.0 (Dobin et al.: Bioinformatics, 2013).
Gene expression (reads per kilobase per million mapped reads, RPKM) calculations were performed using rpkmforgenes.py Ramskold et al.: PLoS Comput Biol, 2009).
The mm10 refGene.txt-file was downloaded from UCSC 20130114.
Differential expression analysis was performed with DESeq (Anderset al.: Genome Biol, 2010).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample generated using DESeq.

source_name: single brain cell

growth_protocol: HUVEC (PromoCell) were cultured in EBM2 bullet kit media (Lonza) on gelatin-coated flasks according to instructions provided by the supplier.

extract_protocol:
TRAP: Translated and transcribed RNA from brain (forebrain and part of the diencephalon), head (without brain), heart, kidney, limb, liver or lung was purified from one to six mCherryTRAP embryos (age-dependent) as described (Hupe et al.: Nucleic Acids Res, 2014).
HUVEC: RNA was purified using RNeasy® Micro Kit (Qiagen) following the manufacturer’s instructions.
Single cell: Forebrains of mCherryTRAP E14.5 embryos were dissected in ice-cold PBS. The tissue was diced with a scalpel and subsequently enzymatically dissociated in PBS containing 1 mg/ml collagenase typ II (Worthington) and 1 µl/ml DNase I (Roche) at 37°C for 30 min with gentle sequential trituration. The cell suspension was filtered through a 40 µm cell strainer and 20 ml of DMEM containing 10 % FBS was added. After centrifugation at 800 x g for 5 min, the cell pellet was resuspended in 2 ml PBS containing 2 % FBS. Cells were sorted on a BD FACSAria III Cell Sorting system (BD Bioscience) based on mCherry fluorescence utilizing the 488-nm laser. mCherryTRAP-negative embryos were used to define background fluorescence. Forward and side scatter analysis were used as gates to avoid cell debris and doublets. Single cells were collected in a 96 well plate contain 4 µl of a mild hypotonic lysis buffer [0.1% Triton X-100 (Sigma), 1 U/µl recombinant RNase inhibitor (Promega), 2.5 µM anchored oligo-dT primer (5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′, Biomers), and 2.5 mM dNTP mix (Fermentas)] in each well.
TRAP and HUVEC: RNA libraries were prepared for sequencing using standard Illumina protocols
Single cell: Libraries were generated following Smart-seq2 (Picelli et al.: Nat Methods, 2013) and Tn5 transposase tagmentation (Picelli et al.: Genome Res, 2014) protocols.

treatment_protocol: Lentiviral infection was carried out in gelatin-coated 12-well plates containing 5 × 10^4 cells per well in 600 µl RPMI medium with 200 µl viral supernatant for 4 h and cells were cultivated for 7 days in growth medium.

tag: mouse line

tag: tissue

value: forebrain


title: SingleCell_Brain_EC_E145_S80

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S79

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S76

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S77

description:
total mRNA
RPKM_SingleCell.txt


title: ChIP-seq from H1-hESC (ENCLB816NFY)

description:
https://www.encodeproject.org/experiments/ENCSR591AOD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR591AOD
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR000AMI
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB816NFY
size range: 200-600
nucleic acid starting quantity: 42.8
nucleic acid starting quantity units: ng

source_name: Homo sapiens H1-hESC stem cell male embryo

value: stem cell

value: unknown

value: Bradley Bernstein, Broad

value: ENCBS849HZG at ENCODE; https://www.encodeproject.org/ENCBS849HZG/

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


title: NPC single cell 49


title: SingleCell_Brain_EC_E145_S75

description:
total mRNA
RPKM_SingleCell.txt


title: ChIP-seq from spleen (ENCLB582YII)

description:
https://www.encodeproject.org/experiments/ENCSR589TCU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR589TCU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR189UPU
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB582YII
size range: 200-600

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

value: spleen

value: adult

value: 53 year

value: female

value: ENCBS913XPU at ENCODE; https://www.encodeproject.org/ENCBS913XPU/

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


title: SingleCell_Brain_EC_E145_S74

description:
total mRNA
RPKM_SingleCell.txt


title: ChIP-seq from ascending aorta (ENCLB203NXQ)

description:
https://www.encodeproject.org/experiments/ENCSR589GII/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR589GII
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR007WYC
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB203NXQ
size range: 200-600

source_name: Homo sapiens ascending aorta tissue female adult (53 years)

value: ascending aorta

value: tissue

value: EnTEX:Artery- Aorta

value: ENCBS328HPC at ENCODE; https://www.encodeproject.org/ENCBS328HPC/


title: SingleCell_Brain_EC_E145_S72

description:
total mRNA
RPKM_SingleCell.txt


title: NPC single cell 48

value: iPSC-derived neural progenitor cells

value: male

value: Single Cell


title: SingleCell_Brain_EC_E145_S71

description:
total mRNA
RPKM_SingleCell.txt

value: forebrain


title: SingleCell_Brain_EC_E145_S82

description:
total mRNA
RPKM_SingleCell.txt


title: NPC single cell 47


title: ChIP-seq from H1-hESC (ENCLB447QBL)

description:
https://www.encodeproject.org/experiments/ENCSR591AOD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR591AOD
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR000AMI
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB447QBL
size range: 200-600
nucleic acid starting quantity: 20.6
nucleic acid starting quantity units: ng

value: stem cell

value: embryonic

value: unknown

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS952IPA at ENCODE; https://www.encodeproject.org/ENCBS952IPA/


title: SingleCell_Brain_EC_E145_S69

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S68

description:
total mRNA
RPKM_SingleCell.txt


title: NPC single cell 46


title: ChIP-seq from K562 (ENCLB875TFE)

description:
https://www.encodeproject.org/experiments/ENCSR583ACG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR583ACG
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR000AKY
encode release date: 2017-01-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB875TFE
size range: 200-600
nucleic acid starting quantity: 12.2
nucleic acid starting quantity units: ng

source_name: Homo sapiens K562 immortalized cell line

tag: line

value: immortalized cell line

value: adult

tag: passage number

value: 53 year

value: chronic myelogenous leukemia (CML)

value: female

value: ENCBS658RMI at ENCODE; https://www.encodeproject.org/ENCBS658RMI/

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


title: ChIP-seq from esophagus muscularis mucosa (ENCLB108RTG)

description:
https://www.encodeproject.org/experiments/ENCSR578MTT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR578MTT
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR474WLZ
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB108RTG
size range: 200-600

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

value: esophagus muscularis mucosa

value: tissue

value: EnTEX:Esophagus - Muscularis

value: ENCBS071FUE at ENCODE; https://www.encodeproject.org/ENCBS071FUE/

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


title: SingleCell_Brain_EC_E145_S66

description:
total mRNA
RPKM_SingleCell.txt

value: forebrain


title: NPC single cell 50

value: iPSC-derived neural progenitor cells

value: male

value: Single Cell


title: NPC single cell 45


title: ChIP-seq from DOHH2 (ENCLB055KFD)

description:
https://www.encodeproject.org/experiments/ENCSR562NOP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR562NOP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR742WWB
encode release date: 2017-01-31
lab: Bradley Bernstein, Broad
library encode accession: ENCLB055KFD
size range: 200-600

source_name: Homo sapiens DOHH2 immortalized cell line

value: established from the pleural effusion of a 60-year-old man with refractory immunoblastic B cell lymphoma progressed from follicular centroblastic/centrocytic lymphoma in 1990

value: 60 year

value: Bradley Bernstein, Broad

value: ENCBS898JGF at ENCODE; https://www.encodeproject.org/ENCBS898JGF/

value: Derived from ENCODE donor ENCDO352AAA; https://www.encodeproject.org/ENCDO352AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1179; http://web.expasy.org/cellosaurus/CVCL_1179


title: SingleCell_Brain_EC_E145_S64

description:
total mRNA
RPKM_SingleCell.txt


title: NPC single cell 44


title: SingleCell_Brain_EC_E145_S65

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S63

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S62

description:
total mRNA
RPKM_SingleCell.txt


title: NPC single cell 43


title: SingleCell_Brain_EC_E145_S61

description:
total mRNA
RPKM_SingleCell.txt


title: ChIP-seq from A549 (ENCLB509CNN)

description:
https://www.encodeproject.org/experiments/ENCSR550SCU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR550SCU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB509CNN
size range: 200-600
nucleic acid starting quantity: 6.38
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line

value: immortalized cell line

value: adult

value: 58 year

value: ENCBS117POP at ENCODE; https://www.encodeproject.org/ENCBS117POP/

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

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


title: ChIP-seq from breast epithelium (ENCLB358SFF)

description:
https://www.encodeproject.org/experiments/ENCSR553IAW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR553IAW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR247XFQ
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB358SFF
size range: 200-600

source_name: Homo sapiens breast epithelium tissue female adult (53 years)

value: breast epithelium

value: tissue

value: EnTEX:Breast - Mammary Tissue

value: female

value: 53 year

value: ENCBS433LAO at ENCODE; https://www.encodeproject.org/ENCBS433LAO/

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


title: NPC single cell 42

source_name: Neural progenitor cells

value: iPSC-derived neural progenitor cells

value: male

value: Single Cell


title: SingleCell_Brain_EC_E145_S70

description:
total mRNA
RPKM_SingleCell.txt

value: forebrain


title: ChIP-seq from K562 (ENCLB207AST)

description:
https://www.encodeproject.org/experiments/ENCSR583ACG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR583ACG
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR000AKY
encode release date: 2017-01-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB207AST
size range: 200-600
nucleic acid starting quantity: 9.68
nucleic acid starting quantity units: ng

value: immortalized cell line

value: Bradley Bernstein, Broad

value: chronic myelogenous leukemia (CML)

value: ENCBS984VNR at ENCODE; https://www.encodeproject.org/ENCBS984VNR/

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


title: ChIP-seq from A549 (ENCLB580WQQ)

description:
https://www.encodeproject.org/experiments/ENCSR550SCU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR550SCU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB580WQQ
size range: 200-600
nucleic acid starting quantity: 32.8
nucleic acid starting quantity units: ng

value: adult

value: 58 year

value: ENCBS998UBJ at ENCODE; https://www.encodeproject.org/ENCBS998UBJ/

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

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


title: NPC single cell 41


title: SingleCell_Brain_EC_E145_S67

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S58

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S57

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S56

description:
total mRNA
RPKM_SingleCell.txt


title: NPC single cell 40


title: SingleCell_Brain_EC_E145_S55

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S54

description:
total mRNA
RPKM_SingleCell.txt


title: ChIP-seq from GM12878 (ENCLB227AZX)

description:
https://www.encodeproject.org/experiments/ENCSR549NPZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR549NPZ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR142REC
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB227AZX
size range: 200-600
nucleic acid starting quantity: 41.14
nucleic acid starting quantity units: ng

source_name: Homo sapiens GM12878 immortalized cell line

value: female

value: unknown

value: ENCBS830FPU at ENCODE; https://www.encodeproject.org/ENCBS830FPU/

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


title: SingleCell_Brain_EC_E145_S53

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S52

description:
total mRNA
RPKM_SingleCell.txt


title: ChIP-seq from stomach (ENCLB155PYL)

description:
https://www.encodeproject.org/experiments/ENCSR546HZF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR546HZF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR539HNK
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB155PYL
size range: 200-600

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

value: stomach

value: tissue

value: 53 year

value: ENCBS642ZQR at ENCODE; https://www.encodeproject.org/ENCBS642ZQR/

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


title: NPC single cell 38

value: iPSC-derived neural progenitor cells

value: male

value: Single Cell


title: SingleCell_Brain_EC_E145_S60

description:
total mRNA
RPKM_SingleCell.txt

value: forebrain


title: ChIP-seq from breast epithelium (ENCLB259KXY)

description:
https://www.encodeproject.org/experiments/ENCSR543YQF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR543YQF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR247XFQ
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB259KXY
size range: 200-600

value: breast epithelium

value: EnTEX:Breast - Mammary Tissue

value: adult

value: Bradley Bernstein, Broad

value: ENCBS433LAO at ENCODE; https://www.encodeproject.org/ENCBS433LAO/


title: SingleCell_Brain_EC_E145_S51

description:
total mRNA
RPKM_SingleCell.txt


title: NPC single cell 37


title: SingleCell_Brain_EC_E145_S59

description:
total mRNA
RPKM_SingleCell.txt


title: NPC single cell 36


title: SingleCell_Brain_EC_E145_S48

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S47

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S49

description:
total mRNA
RPKM_SingleCell.txt


title: ChIP-seq from GM12878 (ENCLB283SSP)

description:
https://www.encodeproject.org/experiments/ENCSR549NPZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR549NPZ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR142REC
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB283SSP
size range: 200-600
nucleic acid starting quantity: 90.86
nucleic acid starting quantity units: ng

value: immortalized cell line

value: female

value: unknown

value: ENCBS127ZRH at ENCODE; https://www.encodeproject.org/ENCBS127ZRH/


title: SingleCell_Brain_EC_E145_S46

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S44

description:
total mRNA
RPKM_SingleCell.txt


title: ChIP-seq from A549 (ENCLB202COI)

description:
https://www.encodeproject.org/experiments/ENCSR541AOQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR541AOQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB202COI
size range: 200-600
nucleic acid starting quantity: 10.4
nucleic acid starting quantity units: ng

value: 58 year

value: ENCBS998UBJ at ENCODE; https://www.encodeproject.org/ENCBS998UBJ/

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

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


title: SingleCell_Brain_EC_E145_S45

description:
total mRNA
RPKM_SingleCell.txt


title: ChIP-seq from stomach (ENCLB026KQN)

description:
https://www.encodeproject.org/experiments/ENCSR539HNK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR539HNK
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB026KQN
size range: 200-600

value: Control

value: stomach

value: tissue

value: 53 year

value: ENCBS642ZQR at ENCODE; https://www.encodeproject.org/ENCBS642ZQR/

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


title: ChIP-seq from A549 (ENCLB642SYY)

description:
https://www.encodeproject.org/experiments/ENCSR541AOQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR541AOQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB642SYY
size range: 200-600
nucleic acid starting quantity: 55.6
nucleic acid starting quantity units: ng

value: adult

value: male

value: ENCBS117POP at ENCODE; https://www.encodeproject.org/ENCBS117POP/


title: NPC single cell 34

value: iPSC-derived neural progenitor cells

value: Single Cell


title: NPC single cell 39


title: SingleCell_Brain_EC_E145_S43

description:
total mRNA
RPKM_SingleCell.txt

value: forebrain


title: ChIP-seq from stomach (ENCLB649IYW)

description:
https://www.encodeproject.org/experiments/ENCSR539HNK/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR539HNK
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB649IYW
size range: 200-600

value: Bradley Bernstein, Broad

value: female


title: NPC single cell 35


title: SingleCell_Brain_EC_E145_S41

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S50

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S42

description:
total mRNA
RPKM_SingleCell.txt


title: NPC single cell 33


title: SingleCell_Brain_EC_E145_S39

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S40

description:
total mRNA
RPKM_SingleCell.txt


title: ChIP-seq from tibial artery (ENCLB010TUT)

description:
https://www.encodeproject.org/experiments/ENCSR543DAS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR543DAS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR950CDM
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB010TUT
size range: 200-600

source_name: Homo sapiens tibial artery tissue female adult (53 years)

value: tibial artery

value: EnTEX:Artery - Tibial

value: ENCBS826SVC at ENCODE; https://www.encodeproject.org/ENCBS826SVC/


title: ChIP-seq from K562 (ENCLB306EUL)

description:
https://www.encodeproject.org/experiments/ENCSR530IUH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR530IUH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AKY
encode release date: 2017-01-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB306EUL
size range: 200-600
nucleic acid starting quantity: 6.116
nucleic acid starting quantity units: ng

value: immortalized cell line

value: chronic myelogenous leukemia (CML)

value: ENCBS979ZKW at ENCODE; https://www.encodeproject.org/ENCBS979ZKW/

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


title: SingleCell_Brain_EC_E145_S38

description:
total mRNA
RPKM_SingleCell.txt


title: MN single cell 68

source_name: Motor neurons

value: iPSC-derived motor neurons


title: SingleCell_Brain_EC_E145_S37

description:
total mRNA
RPKM_SingleCell.txt


title: ChIP-seq from K562 (ENCLB619BFK)

description:
https://www.encodeproject.org/experiments/ENCSR530IUH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR530IUH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AKY
encode release date: 2017-01-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB619BFK
size range: 200-600
nucleic acid starting quantity: 8.96
nucleic acid starting quantity units: ng

value: 53 year

value: ENCBS984VNR at ENCODE; https://www.encodeproject.org/ENCBS984VNR/


title: SingleCell_Brain_EC_E145_S34

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S33

description:
total mRNA
RPKM_SingleCell.txt


title: ChIP-seq from ascending aorta (ENCLB193POV)

description:
https://www.encodeproject.org/experiments/ENCSR494YJW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR494YJW
assay title: ChIP-seq
encode release date: 2017-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB193POV
size range: 200-600

source_name: Homo sapiens ascending aorta tissue female adult (51 year)

value: Control

value: ascending aorta

value: tissue

value: EnTEX:Artery- Aorta

value: adult

value: 51 year

value: ENCBS030SIU at ENCODE; https://www.encodeproject.org/ENCBS030SIU/

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


title: MN single cell 67

value: male

value: Single Cell


title: ChIP-seq from HCT116 (ENCLB806DGY)

description:
https://www.encodeproject.org/experiments/ENCSR494CCN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR494CCN
assay title: ChIP-seq
assembly: hg19
possible controls: ENCSR198WIH
encode release date: 2017-01-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB806DGY
size range: 200-600

source_name: Homo sapiens HCT116 immortalized cell line

value: immortalized cell line

value: cells obtained from ATCC

value: unknown

value: colorectal carcinoma

value: Bradley Bernstein, Broad

value: ENCBS847SOB at ENCODE; https://www.encodeproject.org/ENCBS847SOB/

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 SK-N-MC (ENCLB306XER)

description:
https://www.encodeproject.org/experiments/ENCSR526PZM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against H3K36me3 using SK-N-MC cell line which was previously described as a neuroepithelioma (ATCC HTB-10). However recent evidence reveals it is Ewing's Sarcoma (www.ncbi.nlm.nih.gov/pubmed/15548687, www.ncbi.nlm.nih.gov/biosample/3151999, www.ncbi.nlm.nih.gov/pubmed/25453903).
experiment encode accession: ENCSR526PZM
assay title: ChIP-seq
assembly: hg19
possible controls: ENCSR899XXQ
encode release date: 2017-01-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB306XER
size range: 200-600
nucleic acid starting quantity: 91.3
nucleic acid starting quantity units: ng

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

value: SK-N-MC

value: Please note:This cell line was previously described as a neuroepithelioma (ATCC HTB-10).  However recent evidence reveals it is Ewing's Sarcoma (http://www.ncbi.nlm.nih.gov/pubmed/15548687, http://www.ncbi.nlm.nih.gov/biosample/3151999, http://www.ncbi.nlm.nih.gov/pubmed/25453903).

value: child

value: female

value: 14 year

value: Ewing's sarcoma

value: ENCBS203EZT at ENCODE; https://www.encodeproject.org/ENCBS203EZT/

value: Derived from ENCODE donor ENCDO000ABC; https://www.encodeproject.org/ENCDO000ABC/

value: ENCODE dbxrefs Cellosaurus CVCL_0530; http://web.expasy.org/cellosaurus/CVCL_0530


title: SingleCell_Brain_EC_E145_S29

description:
total mRNA
RPKM_SingleCell.txt

source_name: single brain cell

value: forebrain


title: SingleCell_Brain_EC_E145_S31

description:
total mRNA
RPKM_SingleCell.txt


title: MN single cell 66

value: iPSC-derived motor neurons

value: male

value: Single Cell


title: SingleCell_Brain_EC_E145_S36

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S32

description:
total mRNA
RPKM_SingleCell.txt


title: MN single cell 70


title: SingleCell_Brain_EC_E145_S35

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S28

description:
total mRNA
RPKM_SingleCell.txt


title: MN single cell 64


title: SingleCell_Brain_EC_E145_S30

description:
total mRNA
RPKM_SingleCell.txt


title: ChIP-seq from right lobe of liver (ENCLB791HNK)

description:
https://www.encodeproject.org/experiments/ENCSR489DUV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR489DUV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR276SJT
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB791HNK
size range: 200-600

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

value: right lobe of liver

value: tissue

value: i.e. REMC 2,3,4,5 and 16; EnTEX:Liver

value: adult

value: 53 year

value: Bradley Bernstein, Broad

value: ENCBS536THV at ENCODE; https://www.encodeproject.org/ENCBS536THV/

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


title: SingleCell_Brain_EC_E145_S27

description:
total mRNA
RPKM_SingleCell.txt


title: MN single cell 69


title: SingleCell_Brain_EC_E145_S26

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S25

description:
total mRNA
RPKM_SingleCell.txt


title: ChIP-seq from hepatocyte (ENCLB517UEN)

description:
https://www.encodeproject.org/experiments/ENCSR484MFB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR484MFB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR107PGG
encode release date: 2017-03-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB517UEN
size range: 200-600

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

value: hepatocyte

value: in vitro differentiated cells

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

value: 5 day

value: embryonic

value: female

value: healthy

value: Richard Myers, HAIB

value: ENCBS520VFV at ENCODE; https://www.encodeproject.org/ENCBS520VFV/

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


title: MN single cell 63

value: iPSC-derived motor neurons

value: male

value: Single Cell


title: SingleCell_Brain_EC_E145_S24

description:
total mRNA
RPKM_SingleCell.txt

value: forebrain


title: MN single cell 62


title: SingleCell_Brain_EC_E145_S23

description:
total mRNA
RPKM_SingleCell.txt


title: ChIP-seq from hepatocyte (ENCLB642SUE)

description:
https://www.encodeproject.org/experiments/ENCSR484MFB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR484MFB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR107PGG
encode release date: 2017-03-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB642SUE
size range: 200-600


title: 9872_sh2-plus_GTGGCC_L999_cutadapt.bam

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

data_processing:
Illumina Casava1.8 software used for basecalling. Raw short sequence fragments were accepted if they passed the quality filtering parameters used in the Illumina GA Pipeline GERALD stage.
Sequenced reads were mapped to hg19 whole genome using tophat-v2.0.8b
Aligned reads was normalized by edgeR bioconductor package and outputed as normalized counts file
Genome_build: Genome Reference Consortium GRCh37
Supplementary_files_format_and_content: normalized counts in txt format for all samples

source_name: Cell line

growth_protocol: HCT116 cell line was mantained in DMEM. Media were supplemented with 10% heat inactivated fetal calf serum, 2 mM L-glutamine, 100 U ml-1 penicillin, and 100 μg ml-1 streptomycin.

extract_protocol:
Total microRNA were extracted from cells with SAE2 knockdown using miRNeasy RNA isolation kit (Qiagen, 207004),as per the manufacturer's protocol.
microRNA libraries were constructed with Illumina TruSeq Small RNA Library Prep Kit (RS-200-0012, Illumia, San Diego, USA) with minor modifications, added three NNNs at 3' of 5' adaptor, and added RT primer annlealing step after 3' adator ligation

treatment_protocol: Doxocycline was added to induced SAE2 knockdown for 3 days and total RNA (including small RNA) were extracted for RNAseq.

tag: sirna knockdown


title: SingleCell_Brain_EC_E145_S22

description:
total mRNA
RPKM_SingleCell.txt


title: MN single cell 61


title: MN single cell 65


title: SingleCell_Brain_EC_E145_S21

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S20

description:
total mRNA
RPKM_SingleCell.txt


title: 9871_sh2-minus_GTGAAA_L999_cutadapt.bam


title: ChIP-seq from stomach (ENCLB841YRS)

description:
https://www.encodeproject.org/experiments/ENCSR489ZLL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR489ZLL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR539HNK
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB841YRS
size range: 200-600

value: stomach

value: tissue

tag: description

value: adult

value: Bradley Bernstein, Broad

value: 53 year

value: ENCBS642ZQR at ENCODE; https://www.encodeproject.org/ENCBS642ZQR/


title: 9870_sh-plus_GTCCGC_L999_cutadapt.bam

value: sh-plus


title: SingleCell_Brain_EC_E145_S18

description:
total mRNA
RPKM_SingleCell.txt


title: MN single cell 60


title: MN single cell 59


title: MN single cell 58


title: SingleCell_Brain_EC_E145_S15

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S16

description:
total mRNA
RPKM_SingleCell.txt


title: MN single cell 57


title: 9869_sh1-minus_GTAGAG_L999_cutadapt.bam


title: SingleCell_Brain_EC_E145_S17

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S13

description:
total mRNA
RPKM_SingleCell.txt


title: ChIP-seq from thyroid gland (ENCLB010YFG)

description:
https://www.encodeproject.org/experiments/ENCSR475NOQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR475NOQ
assay title: ChIP-seq
encode release date: 2016-08-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB010YFG
size range: 200-600

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

value: Control

value: thyroid gland

tag: biosample encode accession

value: ENCBS586UUR at ENCODE; https://www.encodeproject.org/ENCBS586UUR/

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


title: MN single cell 56


title: SingleCell_Brain_EC_E145_S12

description:
total mRNA
RPKM_SingleCell.txt

tag: age


title: SingleCell_Brain_EC_E145_S14

description:
total mRNA
RPKM_SingleCell.txt


title: ChIP-seq from tibial nerve (ENCLB334YNF)

description:
https://www.encodeproject.org/experiments/ENCSR479GPU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR479GPU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR154SJE
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB334YNF
size range: 200-600

source_name: Homo sapiens tibial nerve tissue female adult (53 years)

value: tibial nerve

value: EnTEX:Nerve - Tibial

tag: dev stage

value: female

value: ENCBS248LIK at ENCODE; https://www.encodeproject.org/ENCBS248LIK/


title: MN single cell 55

value: iPSC-derived motor neurons

value: male

value: Single Cell


title: SingleCell_Brain_EC_E145_S19

description:
total mRNA
RPKM_SingleCell.txt

value: forebrain


title: ChIP-seq from thyroid gland (ENCLB787GDK)

description:
https://www.encodeproject.org/experiments/ENCSR475NOQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR475NOQ
assay title: ChIP-seq
encode release date: 2016-08-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB787GDK
size range: 200-600

value: tissue

value: adult

tag: Sex


title: SingleCell_Brain_EC_E145_S10

description:
total mRNA
RPKM_SingleCell.txt


title: MN single cell 53


title: MN single cell 54


title: MN single cell 52


title: ChIP-seq from A549 (ENCLB486ZSZ)

description:
https://www.encodeproject.org/experiments/ENCSR469WAO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR469WAO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB486ZSZ
size range: 200-600
nucleic acid starting quantity: 10.6
nucleic acid starting quantity units: ng

value: immortalized cell line

value: Bradley Bernstein, Broad

value: 58 year

value: ENCBS998UBJ at ENCODE; https://www.encodeproject.org/ENCBS998UBJ/

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

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


title: 9867_sh2-minus_GTGGCC_L999.bam

description: RNA subjected to RNAseq

data_processing:
Illumina Casava1.8 software used for basecalling. Raw short sequence fragments were accepted if they passed the quality filtering parameters used in the Illumina GA Pipeline GERALD stage.
Sequenced reads were mapped to hg19 whole genome using tophat-v2.0.8b
Aligned reads was normalized by edgeR bioconductor package and calculate rpkm table
Genome_build: Genome Reference Consortium GRCh37
Supplementary_files_format_and_content: RPKM reads in txt format for all samples

extract_protocol:
Total mRNA were extracted from cells with SAE2 knockdown using miRNeasy RNA isolation kit (Qiagen, 207004),as per the manufacturer's protocol.
ribosomal RNA removed with Ribo-Zero Gold rRNA Removal kit (Illumina, Cat MRZG12324), followed by KAPA Stranded RNA-seq library Preperation Kit (Cat KR0934)

tag: shRNA effects


title: MN single cell 51


title: ChIP-seq from A549 (ENCLB652ELI)

description:
https://www.encodeproject.org/experiments/ENCSR469WAO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR469WAO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB652ELI
size range: 200-600
nucleic acid starting quantity: 3.1
nucleic acid starting quantity units: ng

tag: lab

value: ENCBS117POP at ENCODE; https://www.encodeproject.org/ENCBS117POP/


title: 9866_sh-plus_GTGAAA_L999.bam

description: RNA subjected to RNAseq

value: sh-plus


title: SingleCell_Brain_EC_E145_S8

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S9

description:
total mRNA
RPKM_SingleCell.txt


title: MN single cell 50


title: SingleCell_Brain_EC_E145_S7

description:
total mRNA
RPKM_SingleCell.txt


title: iPSC pooled 1

source_name: Induced pluripotent cells

value: Skin fibroblast-derived induced pluripotent cells (iPSCs)

value: Pooled


title: iPSC pooled 2


title: MN single cell 49


title: SingleCell_Brain_EC_E145_S3

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S4

description:
total mRNA
RPKM_SingleCell.txt


title: SingleCell_Brain_EC_E145_S11

description:
total mRNA
RPKM_SingleCell.txt


title: 9865_sh1-minus_GTCCGC_L999.bam

description: RNA subjected to RNAseq


title: MN single cell 48


title: SingleCell_Brain_EC_E145_S2

description:
total mRNA
RPKM_SingleCell.txt


title: ChIP-seq from coronary artery (ENCLB728WPJ)

description:
https://www.encodeproject.org/experiments/ENCSR443UYU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR443UYU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR122GIL
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB728WPJ
size range: 200-600

source_name: Homo sapiens coronary artery tissue female adult (53 years)

value: coronary artery

value: EnTEX:Artery - Coronary

value: female

value: 53 year

tag: link

value: ENCBS474IPU at ENCODE; https://www.encodeproject.org/ENCBS474IPU/

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


title: 9868_sh2-plus_GTTTCG_L999.bam

description: RNA subjected to RNAseq


title: MN single cell 46

value: iPSC-derived motor neurons

value: male

value: Single Cell


title: Hi-C invitro 8-cell rep2

city: Beijing

first: Zhenhai

last: Du

address: Qinghua Yuan, Haidian District

country: China

institute: Tsinghua University

description:
processed data file:
invitro_8cell_rep12_allValidPairs.txt.gz

data_processing:
Basecalls performed using CASAVA version 1.8
Hi-C reads are  processed using HiCPro version2.7.1b and replicates of same stage were pooled together
Compartment analysis are done as previously described. (Dixon et al., 2015)
TAD calling is done using Insulation score method as previously described ( Crane et al., 2015)
RNA-Seq reads were aligned to the mm9 genome assembly using Tophat version 2.0.11, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format ;  read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]

source_name: Preimplantation embryo

extract_protocol: HiC libraries were prepared using sisHi-C similar with in situ Hi-C method developed by Rao et al.

treatment_protocol: Embryos were collected from C57BL/6N mice induced to superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours apart and mated to PWK males.

tag: strain

value: C57BL/6N x PWK/PhJ

tag: developmental stage

value: Preimplantation embryo


title: SingleCell_Brain_EC_E145_S1

description:
total mRNA
RPKM_SingleCell.txt

value: forebrain


title: ChIP-seq from ascending aorta (ENCLB591LCO)

description:
https://www.encodeproject.org/experiments/ENCSR441YQA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR441YQA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR494YJW
encode release date: 2016-11-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB591LCO
size range: 200-600

tag: antibody

value: ascending aorta

value: tissue

value: EnTEX:Artery- Aorta

value: adult

value: Bradley Bernstein, Broad

value: 51 year

value: ENCBS273PSC at ENCODE; https://www.encodeproject.org/ENCBS273PSC/

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


title: Brain_E175_Transcriptome_3

description:
total mRNA
deseq_E175_brain_EC_vs_E175_brain_total.txt

source_name: brain

value: brain


title: SingleCell_Brain_EC_E145_S5

description:
total mRNA
RPKM_SingleCell.txt


title: ChIP-seq from heart left ventricle (ENCLB373PQY)

description:
https://www.encodeproject.org/experiments/ENCSR438QZN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR438QZN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR526EXI
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB373PQY
size range: 200-600

source_name: Homo sapiens heart left ventricle tissue female adult (53 years)

value: heart left ventricle

value: EnTEX:Heart - Left Ventricle

value: female

value: 53 year

value: ENCBS861XCF at ENCODE; https://www.encodeproject.org/ENCBS861XCF/


title: Hi-C invitro late 2-cell rep2

description:
processed data file:
invitro_late_2cell_rep12_allValidPairs.txt.gz

value: C57BL/6N x PWK/PhJ


title: Hi-C PN3 zygote rep2

description:
processed data file:
PN3_rep12_allValidPairs.txt.gz, PN3_rep12_maternal_allValidPairs.txt.gz, PN3_rep12_paternal_allValidPairs.txt.gz

extract_protocol:
After removing the zona pellucida, embryonic cells were washed with PBS and fixed with 1% formaldehyde for 10min at RT.
HiC libraries were prepared using sisHi-C similar with in situ Hi-C method developed by Rao et al.

value: PN3 zygote


title: MN single cell 45

tag: cell type

value: iPSC-derived motor neurons

tag: gender

value: male

tag: sample type

value: Single Cell


title: Brain_E175_Transcriptome_1

tag: mouse line

tag: tissue


title: ChIP-seq from A673 (ENCLB631AHN)

description:
https://www.encodeproject.org/experiments/ENCSR435FGK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR435FGK
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR196CXJ
encode release date: 2016-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB631AHN
size range: 200-600

source_name: Homo sapiens A673 immortalized cell line

tag: line

value: immortalized cell line

value: Cell line is A673; this is a purchasable public domain cell type per Miguel Rivera, M.D.

value: unknown

value: 15 year

value: ENCBS615MBV at ENCODE; https://www.encodeproject.org/ENCBS615MBV/

value: Derived from ENCODE donor ENCDO027VXA; https://www.encodeproject.org/ENCDO027VXA/

value: ENCODE dbxrefs Cellosaurus CVCL_0080; http://web.expasy.org/cellosaurus/CVCL_0080


title: ChIP-seq from adrenal gland (ENCLB618KZC)

description:
https://www.encodeproject.org/experiments/ENCSR455JUO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR455JUO
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR754WVA
encode release date: 2016-10-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB618KZC
size range: 200-600

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

value: adrenal gland

value: tissue

tag: description

value: EnTEX:Adrenal Gland

value: adult

value: 37 year

value: Bradley Bernstein, Broad

value: ENCBS137LDS at ENCODE; https://www.encodeproject.org/ENCBS137LDS/

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


title: Brain_E175_Transcriptome_2

value: brain


title: ChIP-seq from body of pancreas (ENCLB485ARC)

description:
https://www.encodeproject.org/experiments/ENCSR429XBU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR429XBU
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR833HBT
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB485ARC
size range: 200-600

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

value: body of pancreas

tag: biosample encode accession

value: 53 year

value: female

value: ENCBS359OQR at ENCODE; https://www.encodeproject.org/ENCBS359OQR/

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


title: Hi-C alpha-amanitin 45h rep2

data_processing:
Library strategy: HiC-seq
Basecalls performed using CASAVA version 1.8
Hi-C reads are  processed using HiCPro version2.7.1b and replicates of same stage were pooled together
Compartment analysis are done as previously described. (Dixon et al., 2015)
TAD calling is done using Insulation score method as previously described ( Crane et al., 2015)
RNA-Seq reads were aligned to the mm9 genome assembly using Tophat version 2.0.11, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format ;  read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]

treatment_protocol: Embryos were collected from C57BL/6N mice induced to superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours apart and mated to PWK males. PN3 zygotes were treated with 100ug/ml alpha-amanitin for 45h.

value: C57BL/6N x PWK/PhJ

value: preimplantation embryo


title: MN pooled 3

source_name: Motor neurons

value: iPSC-derived motor neurons

value: male

value: Pooled


title: MN single cell 43

value: Single Cell


title: ChIP-seq from upper lobe of left lung (ENCLB007AYV)

description:
https://www.encodeproject.org/experiments/ENCSR422TGJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR422TGJ
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB007AYV
size range: 200-600

source_name: Homo sapiens upper lobe of left lung tissue female adult (53 years)

value: Control

value: upper lobe of left lung

value: tissue

value: adult

tag: age

value: ENCBS684YJH at ENCODE; https://www.encodeproject.org/ENCBS684YJH/


title: Brain_E175_EC_Translatome_2

description:
ribosome-bound mRNA
deseq_E175_brain_EC_vs_E175_brain_total.txt
deseq_E175_brain_EC_vs_E115_brain_EC.txt
deseq_E175_brain_EC_vs_E125_brain_EC.txt
deseq_E175_brain_EC_vs_E135_brain_EC.txt
deseq_E175_brain_EC_vs_E145_brain_EC.txt
deseq_E175_brain_EC_vs_E155_brain_EC.txt
deseq_E175_brain_EC_vs_E165_brain_EC.txt

value: forebrain EC


title: SingleCell_Brain_EC_E145_S6

description:
total mRNA
RPKM_SingleCell.txt

value: forebrain


title: Brain_E175_EC_Translatome_3


title: ChIP-seq from H1-hESC (ENCLB158GQW)

description:
https://www.encodeproject.org/experiments/ENCSR418RRF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR418RRF
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR000AMI
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB158GQW
size range: 200-600
nucleic acid starting quantity: 32.2
nucleic acid starting quantity units: ng

source_name: Homo sapiens H1-hESC stem cell male embryo

value: stem cell

tag: dev stage

value: embryonic

value: unknown

tag: health state

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS011NFB at ENCODE; https://www.encodeproject.org/ENCBS011NFB/

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

value: ENCODE dbxrefs Cellosaurus CVCL_9771; http://web.expasy.org/cellosaurus/CVCL_9771


title: MN single cell 42

value: iPSC-derived motor neurons

value: male


title: ChIP-seq from PC-3 (ENCLB893DXQ)

description:
https://www.encodeproject.org/experiments/ENCSR461HUD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR461HUD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR328AHC
encode release date: 2017-01-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB893DXQ
size range: 300-600
nucleic acid starting quantity: 12.512
nucleic acid starting quantity units: ng

source_name: Homo sapiens PC-3 immortalized cell line

value: immortalized cell line

value: prostate cancer cell line

tag: Sex

value: 62 year

value: grade IV, adenocarcinoma

tag: passage number

value: ENCBS596CTT at ENCODE; https://www.encodeproject.org/ENCBS596CTT/

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: MN single cell 47

value: Single Cell


title: Hi-C invitro 8-cell rep1

value: C57BL/6N x PWK/PhJ


title: ChIP-seq from GM12878 (ENCLB346TVP)

description:
https://www.encodeproject.org/experiments/ENCSR410HFN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR410HFN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR142REC
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB346TVP
size range: 200-600
nucleic acid starting quantity: 15.4
nucleic acid starting quantity units: ng

source_name: Homo sapiens GM12878 immortalized cell line

value: adult

value: female

value: unknown

tag: lab

tag: link

value: ENCBS830FPU at ENCODE; https://www.encodeproject.org/ENCBS830FPU/

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


title: Hi-C alpha-amanitin 45h rep1

tag: strain

tag: developmental stage

value: preimplantation embryo


title: Brain_E175_EC_Translatome_1

value: forebrain EC


title: Hi-C invitro late 2-cell rep1

value: late 2-cell


title: MN single cell 44

tag: cell type

value: iPSC-derived motor neurons

value: male


title: ChIP-seq from GM12878 (ENCLB758GEJ)

description:
https://www.encodeproject.org/experiments/ENCSR410HFN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR410HFN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR142REC
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB758GEJ
size range: 200-600
nucleic acid starting quantity: 18.4
nucleic acid starting quantity units: ng

tag: antibody

value: immortalized cell line

value: Bradley Bernstein, Broad

value: ENCBS330WEW at ENCODE; https://www.encodeproject.org/ENCBS330WEW/


title: Brain_E175_EC_Ctnnb1KO_Translatome_4

description:
ribosome-bound mRNA
deseq_E175_KO_brain_EC_vs_E175_KO_brain_total.txt


title: MN single cell 41

tag: gender

tag: sample type


title: MN single cell 40


title: Brain_E175_EC_Ctnnb1KO_Translatome_3

tag: mouse line

tag: tissue


title: MN single cell 39


title: ChIP-seq from SK-N-SH (ENCLB953MHE)

description:
https://www.encodeproject.org/experiments/ENCSR297MUV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR297MUV
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR185OHN
encode release date: 2017-01-15
lab: Bradley Bernstein, Broad
library encode accession: ENCLB953MHE
size range: 200-600

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

tag: line

value: SK-N-SH

value: 4 year

value: child

value: ENCBS018DDZ at ENCODE; https://www.encodeproject.org/ENCBS018DDZ/

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

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


title: Hi-C alpha-amanitin 20h rep1

treatment_protocol: Embryos were collected from C57BL/6N mice induced to superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours apart and mated to PWK males. PN3 zygotes were treated with 100ug/ml alpha-amanitin for 20h.

value: C57BL/6N x PWK/PhJ


title: Brain_E175_EC_Ctnnb1KO_Translatome_2


title: ChIP-seq from SK-N-SH (ENCLB470MXD)

description:
https://www.encodeproject.org/experiments/ENCSR297MUV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR297MUV
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR185OHN
encode release date: 2017-01-15
lab: Bradley Bernstein, Broad
library encode accession: ENCLB470MXD
size range: 200-600

tag: biosample encode accession

value: female

value: ENCBS500EWH at ENCODE; https://www.encodeproject.org/ENCBS500EWH/


title: Hi-C sperm rep3

source_name: Sperm

treatment_protocol: Mature mouse sperm cells were obtained from 8 week-old PWK/PhJ males with a swim-up procedure to avoid the somatic contamination

value: PWK/PhJ

value: Sperm


title: Brain_E175_EC_Ctnnb1KO_Translatome_1

value: forebrain EC

tag: age


title: ChIP-seq from sigmoid colon (ENCLB581BOD)

description:
https://www.encodeproject.org/experiments/ENCSR268ZCF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR268ZCF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR844YME
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB581BOD
size range: 200-600

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

value: sigmoid colon

value: tissue

tag: description

value: EnTEX:Colon - Sigmoid

tag: dev stage

value: adult

value: 53 year

value: ENCBS555KUV at ENCODE; https://www.encodeproject.org/ENCBS555KUV/

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


title: MN single cell 38

value: iPSC-derived motor neurons

value: male

value: Single Cell


title: Brain_E175_Ctnnb1KO_Transcriptome_4

description:
total mRNA
deseq_E175_KO_brain_EC_vs_E175_KO_brain_total.txt
deseq_E175_wt_brain_EC_vs_E175_KO_brain_EC.txt

value: forebrain


title: Hi-C sperm rep2


title: MN single cell 37


title: Hi-C sperm rep1


title: ChIP-seq from tibial nerve (ENCLB571VSO)

description:
https://www.encodeproject.org/experiments/ENCSR611YUJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR611YUJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR154SJE
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB571VSO
size range: 200-600

source_name: Homo sapiens tibial nerve tissue female adult (53 years)

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: Bradley Bernstein, Broad

tag: Sex

value: ENCBS248LIK at ENCODE; https://www.encodeproject.org/ENCBS248LIK/


title: MN single cell 36


title: Brain_E175_Ctnnb1KO_Transcriptome_3


title: Hi-C ICM rep3

value: C57BL/6N x PWK/PhJ

value: ICM


title: ChIP-seq from H1-hESC (ENCLB448QLT)

description:
https://www.encodeproject.org/experiments/ENCSR267YDT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR267YDT
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR000AMI
encode release date: 2017-01-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB448QLT
size range: 200-600
nucleic acid starting quantity: 41.4
nucleic acid starting quantity units: ng

value: stem cell

value: embryonic

value: unknown

tag: health state

value: healthy

value: ENCBS011NFB at ENCODE; https://www.encodeproject.org/ENCBS011NFB/

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

value: ENCODE dbxrefs Cellosaurus CVCL_9771; http://web.expasy.org/cellosaurus/CVCL_9771


title: Hi-C alpha-amanitin 20h rep2

value: preimplantation embryo


title: ChIP-seq from adrenal gland (ENCLB929PRJ)

description:
https://www.encodeproject.org/experiments/ENCSR605QAV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR605QAV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR043UWF
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB929PRJ
size range: 200-600

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

value: adrenal gland

value: tissue

value: EnTEX:Adrenal Gland

value: adult

tag: lab

value: 53 year

value: female

value: ENCBS130NHB at ENCODE; https://www.encodeproject.org/ENCBS130NHB/

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


title: Brain_E175_Ctnnb1KO_Transcriptome_1

value: forebrain


title: Hi-C 8-cell rep3

value: C57BL/6N x PWK/PhJ


title: MN single cell 35

value: iPSC-derived motor neurons

value: male

value: Single Cell


title: Hi-C late 2-cell rep4

value: late 2-cell


title: ChIP-seq from GM12878 (ENCLB337YAA)

description:
https://www.encodeproject.org/experiments/ENCSR265MJJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR265MJJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR142REC
encode release date: 2016-11-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB337YAA
size range: 200-600
nucleic acid starting quantity: 8.29
nucleic acid starting quantity units: ng

value: immortalized cell line

value: unknown

tag: passage number

value: Bradley Bernstein, Broad

tag: link

value: ENCBS830FPU at ENCODE; https://www.encodeproject.org/ENCBS830FPU/

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


title: MN single cell 34


title: Brain_E165_Transcriptome_3

description:
total mRNA
deseq_E165_brain_EC_vs_E165_brain_total.txt


title: Brain_E165_Transcriptome_2


title: Hi-C late 2-cell rep3

tag: strain

tag: developmental stage


title: ChIP-seq from hepatocyte (ENCLB069MNK)

description:
https://www.encodeproject.org/experiments/ENCSR252QYR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR252QYR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR107PGG
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB069MNK
size range: 200-600

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

tag: antibody

value: CTCF

value: hepatocyte

value: in vitro differentiated cells

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

value: 5 day

value: embryonic

value: healthy

value: Richard Myers, HAIB

value: ENCBS520VFV at ENCODE; https://www.encodeproject.org/ENCBS520VFV/

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


title: Brain_E165_Transcriptome_1

value: forebrain


title: MN single cell 32

tag: cell type

value: iPSC-derived motor neurons

tag: gender

value: male

value: Single Cell


title: ChIP-seq from hepatocyte (ENCLB753UCH)

description:
https://www.encodeproject.org/experiments/ENCSR252QYR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR252QYR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR107PGG
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB753UCH
size range: 200-600

value: female


title: Brain_E175_Ctnnb1KO_Transcriptome_2

tag: mouse line


title: Hi-C early 2-cell rep3

source_name: Preimplantation embryo

value: C57BL/6N x PWK/PhJ

value: early 2-cell


title: Brain_E165_EC_Translatome_3

description:
ribosome-bound mRNA
deseq_E165_brain_EC_vs_E165_brain_total.txt
deseq_E165_brain_EC_vs_E115_brain_EC.txt
deseq_E165_brain_EC_vs_E155_brain_EC.txt
deseq_E175_brain_EC_vs_E165_brain_EC.txt

source_name: brain

tag: tissue

value: forebrain EC


title: Hi-C PN5 zygote rep4

value: PN5 zygote


title: MN single cell 31

tag: sample type


title: ChIP-seq from GM12878 (ENCLB115ATT)

description:
https://www.encodeproject.org/experiments/ENCSR265MJJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR265MJJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR142REC
encode release date: 2016-11-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB115ATT
size range: 200-600
nucleic acid starting quantity: 26.8
nucleic acid starting quantity units: ng

tag: line

value: immortalized cell line

tag: biosample encode accession

value: adult

value: Bradley Bernstein, Broad

value: unknown

value: ENCBS155GIM at ENCODE; https://www.encodeproject.org/ENCBS155GIM/

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


title: MN single cell 30


title: Brain_E165_EC_Translatome_2

tag: age


title: ChIP-seq from hepatocyte (ENCLB590TMU)

description:
https://www.encodeproject.org/experiments/ENCSR252QYR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR252QYR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR107PGG
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB590TMU
size range: 200-600

value: CTCF

value: hepatocyte

value: in vitro differentiated cells

tag: description

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

value: 5 day

tag: dev stage

value: embryonic

value: healthy

value: Richard Myers, HAIB

value: ENCBS077RUJ at ENCODE; https://www.encodeproject.org/ENCBS077RUJ/


title: ChIP-seq from adrenal gland (ENCLB840PQG)

description:
https://www.encodeproject.org/experiments/ENCSR408ZEW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR408ZEW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR828HXJ
encode release date: 2016-10-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB840PQG
size range: 200-600

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

value: adrenal gland

value: tissue

value: EnTEX:Adrenal Gland

tag: Sex

value: male

value: 54 year

value: ENCBS078MQQ at ENCODE; https://www.encodeproject.org/ENCBS078MQQ/

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


title: Hi-C PN3 zygote rep1

value: C57BL/6N x PWK/PhJ

value: PN3 zygote


title: Brain_E165_EC_Translatome_1

value: forebrain EC


title: MN single cell 29

value: iPSC-derived motor neurons

value: Single Cell


title: MN single cell 28


title: Hi-C 500 mESCs rep2

data_processing:
Library strategy: HiC-Seq
Basecalls performed using CASAVA version 1.8
Hi-C reads are  processed using HiCPro version2.7.1b and replicates of same stage were pooled together
Compartment analysis are done as previously described. (Dixon et al., 2015)
TAD calling is done using Insulation score method as previously described ( Crane et al., 2015)
Genome_build: mm9
Supplementary_files_format_and_content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format ;  read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]

source_name: Embryonic stem cell

growth_protocol: mESCs were cultured routinely in LIF and serum medium.

extract_protocol: HiC libraries were prepared using in situ Hi-C developed by Rao et al. with some modification

value: Embryonic stem cell


title: Hi-C ICM rep2

description:
ICM_rep12_allValidPairs.txt
ICM_rep12_maternal_allValidPairs.txt
ICM_rep12_paternal_allValidPairs.txt

extract_protocol:
After removing the zona pellucida, embryonic cells were washed with PBS and fixed with 1% formaldehyde for 10min at RT.
HiC libraries were prepared using in situ Hi-C developed by Rao et al. with some modification

value: C57BL/15N x PWK

value: ICM


title: ChIP-seq from MM.1S (ENCLB925HKY)

description:
https://www.encodeproject.org/experiments/ENCSR402IDP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR402IDP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR264HOB
encode release date: 2016-08-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB925HKY
size range: 300-600
nucleic acid starting quantity: 7.854
nucleic acid starting quantity units: ng

source_name: Homo sapiens MM.1S immortalized cell line

value: CTCF

value: immortalized cell line

value: The parent cell line, MM.1, was established from peripheral blood of a multiple myeloma patient who had become resistant to steroid-based therapy. this line is sensitive to dexamethasone

value: adult

value: female

value: 42 year

tag: health state

value: immunoglobulin A lambda myeloma

tag: lab

value: Bradley Bernstein, Broad

value: ENCBS241TLI at ENCODE; https://www.encodeproject.org/ENCBS241TLI/

value: Derived from ENCODE donor ENCDO697GBW; https://www.encodeproject.org/ENCDO697GBW/

value: ENCODE dbxrefs Cellosaurus CVCL_8792; http://web.expasy.org/cellosaurus/CVCL_8792


title: MN single cell 27

value: male


title: ChIP-seq from MM.1S (ENCLB636JTM)

description:
https://www.encodeproject.org/experiments/ENCSR402IDP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR402IDP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR264HOB
encode release date: 2016-08-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB636JTM
size range: 300-600
nucleic acid starting quantity: 21.93
nucleic acid starting quantity units: ng

tag: link

value: ENCBS981ZAE at ENCODE; https://www.encodeproject.org/ENCBS981ZAE/


title: MN pooled 2

value: iPSC-derived motor neurons

value: Pooled


title: ChIP-seq from breast epithelium (ENCLB506APO)

description:
https://www.encodeproject.org/experiments/ENCSR403UOU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR403UOU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR247XFQ
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB506APO
size range: 200-600

source_name: Homo sapiens breast epithelium tissue female adult (53 years)

value: breast epithelium

value: tissue

value: EnTEX:Breast - Mammary Tissue

value: 53 year

value: ENCBS433LAO at ENCODE; https://www.encodeproject.org/ENCBS433LAO/

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


title: Brain_E155_Transcriptome_3

description:
total mRNA
deseq_E155_brain_EC_vs_E155_brain_total.txt

value: forebrain


title: Brain_E155_Transcriptome_2


title: Hi-C early 2-cell rep2

description:
early_2cell_rep12_allValidPairs.txt
early_2cell_rep12_maternal_allValidPairs.txt
early_2cell_rep12_paternal_allValidPairs.txt

tag: strain

value: C57BL/9N x PWK

value: early 2-cell


title: MN single cell 26

source_name: Motor neurons

value: Single Cell


title: Brain_E155_Transcriptome_1


title: ChIP-seq from spleen (ENCLB613QLF)

description:
https://www.encodeproject.org/experiments/ENCSR197QDK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR197QDK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR189UPU
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB613QLF
size range: 200-600

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

value: spleen

value: adult

value: Bradley Bernstein, Broad

value: female

value: ENCBS913XPU at ENCODE; https://www.encodeproject.org/ENCBS913XPU/


title: Hi-C PN5 zygote rep3

value: C57BL/6N x PWK/PhJ

tag: developmental stage

value: PN5 zygote


title: MN single cell 33

value: iPSC-derived motor neurons

value: male


title: MN single cell 25


title: Hi-C PN5 zygote rep2

description:
PN5_rep12_allValidPairs.txt
PN5_rep12_maternal_allValidPairs.txt
PN5_rep12_paternal_allValidPairs.txt

value: C57BL/7N x PWK


title: ChIP-seq from right atrium auricular region (ENCLB267ERC)

description:
https://www.encodeproject.org/experiments/ENCSR195BZZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR195BZZ
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB267ERC
size range: 200-600

source_name: Homo sapiens right atrium auricular region tissue female adult (53 years)

tag: antibody

value: Control

value: right atrium auricular region

value: tissue

value: EnTEX:Heart - Atrial Appendage

value: 53 year

value: ENCBS493WOF at ENCODE; https://www.encodeproject.org/ENCBS493WOF/


title: ChIP-seq from right atrium auricular region (ENCLB326CHV)

description:
https://www.encodeproject.org/experiments/ENCSR195BZZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR195BZZ
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB326CHV
size range: 200-600

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


title: Hi-C 500 mESCs rep1

value: Embryonic stem cell


title: Hi-C MII oocytes rep2

source_name: Oocyte

treatment_protocol: Collection of MII oocytes from superovulated C57BL/6N mice was performed 20h after hCG injection.

value: MII oocyte


title: Brain_E155_EC_Translatome_3

description:
ribosome-bound mRNA
deseq_E155_brain_EC_vs_E155_brain_total.txt
deseq_E155_brain_EC_vs_E115_brain_EC.txt
deseq_E155_brain_EC_vs_E145_brain_EC.txt
deseq_E165_brain_EC_vs_E155_brain_EC.txt
deseq_E175_brain_EC_vs_E155_brain_EC.txt

value: forebrain EC


title: Brain_E155_EC_Translatome_2


title: MN single cell 24

tag: cell type

value: Single Cell


title: MN single cell 22

tag: gender


title: ChIP-seq from spleen (ENCLB930ADO)

description:
https://www.encodeproject.org/experiments/ENCSR189UPU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR189UPU
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB930ADO
size range: 200-600

value: spleen

value: adult

value: Bradley Bernstein, Broad

value: female

value: ENCBS913XPU at ENCODE; https://www.encodeproject.org/ENCBS913XPU/


title: Brain_E155_EC_Translatome_1

tag: mouse line


title: Lung_E145_Transcriptome_3

description:
total mRNA
deseq_E145_lung_EC_vs_E145_lung_total.txt

tag: tissue

value: lung


title: MN single cell 23

value: iPSC-derived motor neurons

value: male

tag: sample type


title: Hi-C 8-cell rep2

description:
8cell_rep12_allValidPairs.txt
8cell_rep12_maternal_allValidPairs.txt
8cell_rep12_paternal_allValidPairs.txt

value: C57BL/13N x PWK


title: Hi-C ICM rep1

value: C57BL/14N x PWK

value: ICM


title: MN single cell 20


title: Lung_E145_Transcriptome_2


title: MN single cell 21


title: ChIP-seq from adrenal gland (ENCLB872HUE)

description:
https://www.encodeproject.org/experiments/ENCSR189QAD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR189QAD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR043UWF
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB872HUE
size range: 200-600

value: adrenal gland

value: tissue

value: EnTEX:Adrenal Gland

value: 53 year

value: ENCBS130NHB at ENCODE; https://www.encodeproject.org/ENCBS130NHB/


title: ChIP-seq from esophagus muscularis mucosa (ENCLB510HSR)

description:
https://www.encodeproject.org/experiments/ENCSR177CGN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR177CGN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR474WLZ
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB510HSR
size range: 200-600

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

value: esophagus muscularis mucosa

value: EnTEX:Esophagus - Muscularis

value: ENCBS071FUE at ENCODE; https://www.encodeproject.org/ENCBS071FUE/

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


title: Lung_E145_EC_Translatome_3

description:
ribosome-bound mRNA
deseq_E145_lung_EC_vs_E145_lung_total.txt
deseq_E145_lung_EC_vs_E145_brain_EC.txt
deseq_E145_lung_EC_vs_E145_head_EC.txt
deseq_E145_lung_EC_vs_E145_heart_EC.txt
deseq_E145_lung_EC_vs_E145_kidney_EC.txt
deseq_E145_lung_EC_vs_E145_limb_EC.txt
deseq_E145_lung_EC_vs_E145_liver_EC.txt

value: lung EC


title: Lung_E145_Transcriptome_1


title: Lung_E145_EC_Translatome_2


title: MN single cell 19

value: Single Cell


title: ChIP-seq from uterus (ENCLB643BVJ)

description:
https://www.encodeproject.org/experiments/ENCSR249INE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR249INE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR979XBX
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB643BVJ
size range: 200-600

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

value: uterus

value: adult

value: Bradley Bernstein, Broad

value: female

value: ENCBS469FLQ at ENCODE; https://www.encodeproject.org/ENCBS469FLQ/


title: Hi-C late 2-cell rep2

description:
late_2cell_rep12_allValidPairs.txt
late_2cell_rep12_maternal_allValidPairs.txt
late_2cell_rep12_paternal_allValidPairs.txt

value: C57BL/11N x PWK

value: late 2-cell


title: MN single cell 18

value: iPSC-derived motor neurons

value: male


title: Hi-C early 2-cell rep1

value: C57BL/8N x PWK

value: early 2-cell


title: ChIP-seq from tibial artery (ENCLB882GBE)

description:
https://www.encodeproject.org/experiments/ENCSR166VXF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR166VXF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR950CDM
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB882GBE
size range: 200-600

source_name: Homo sapiens tibial artery tissue female adult (53 years)

value: tibial artery

value: tissue

value: EnTEX:Artery - Tibial

value: 53 year

value: ENCBS826SVC at ENCODE; https://www.encodeproject.org/ENCBS826SVC/


title: GmEM_GmLEC1pep-input_br2

city: Davis

first: John

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California

description:
processed data file:
LEC1pep-EM_Gmax275_peak.bed

data_processing:
Basecalls performed using RTA version 1.12.4.2
Sequenced reads passing Illumina quality filter were aligned to the Glycine max genome (Wm82.a2.v1) using Bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Reads were filtered to remove PCR duplicates using samtools (v.0.1.19).
Peaks were identified using the PeakSeq algorithm of CisGenome (v2.0), using default parameters except min peak length=50.  Peaks were filtered further by applying an FDR threshold of 0.01.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: peak coordinates (chr, start, end) are in the standard bed format

organism: Glycine max

source_name: embryos

growth_protocol: Soybean cv Williams 82 plants were grown in 2 gallon pots containing Ron’s mix (1 part coarse sand, 1 part compost, 1 part peat moss, 3 pounds/yard Dolomite) in UC Davis greenhouses at temperatures ranging 22-30°C and under 16 hour-days.

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 3ug of an an antibody raised against a recombinant GST-GmLEC1 (GmLEC1) or a GmLEC1 peptide (GmLEC1pep).  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow DR Multiplex System, following the manufaturer's instructions and enriched by PCR using 15 cycles.  Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit

treatment_protocol: Cotyledon-stage embryos were dissected out of 2.5 to 3.5 mm long seeds, early maturation embryos from 6 to 7 mm seeds and mid-maturation, from seeds weighing between 200 and 250 mg .  Tissues were crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes.  Tissues were rinsed twice with deionized water and stored at -80C until use.

tag: cultivar

value: Williams 82

value: embryo

tag: Stage

value: Early maturation stage


title: GmEM_GmLEC1pep-input_br1


title: MN single cell 17

value: Single Cell


title: Lung_E145_EC_Translatome_1

value: lung EC

tag: age


title: MN pooled 1

value: Pooled


title: Hi-C late 2-cell rep1

value: C57BL/10N x PWK


title: GmEM_GmLEC1pep-ChIP_br2

value: anti-peptide GmLEC1


title: Hi-C PN5 zygote rep1

value: C57BL/6N x PWK/PhJ

value: PN5 zygote


title: MN single cell 16

value: iPSC-derived motor neurons

value: male


title: Liver_E145_Transcriptome_2

description:
total mRNA
deseq_E145_liver_EC_vs_E145_liver_total.txt

value: liver


title: GmEM_GmLEC1pep-ChIP_br1


title: Liver_E145_Transcriptome_3


title: Hi-C MII oocytes rep1

value: MII oocyte