title: polyA depleted RNA-seq from GM12878 (ENCLB555AVM)

description:
https://www.encodeproject.org/experiments/ENCSR000CQE/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line GM12878. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQE
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AVM
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens GM12878 immortalized cell line cytosolic fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bae4e081-671c-42d7-9af6-2dcf306d68b0/@@download/attachment/LID18547.pdf

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

value: unknown

value: Thomas Gingeras, CSHL

value: ENCBS727AAA at ENCODE; https://www.encodeproject.org/ENCBS727AAA/

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

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

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

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


title: EB+0hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me2.rep2

status: Public on Dec 07 2016

type: SRA

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

country: USA

institute: Penn State University

description: ChIP-seq H3K4me2 in EB+0hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

library_source: genomic

data_processing:
Basecalling conversion to fastq files was performed using bcl2fastq for HiSeq runs and Picard for NextSeq runs
Alignment: All transcription factor ChIP-Seq fastq files were aligned to mouse genome (version mm10) using Bowtie (1.0.1) (Langmead et al., 2009) with options “-q --best --strata -m 1 --chunkmbs 1024”.  Only uniquely mapped reads were considered for further analysis.
All histone modification ChIP-Seq fastq files were aligned to mm10 genome build using bowtie2 (Ben Langmead & Salzberg, 2012) with default parameters. After filtering for uniquely-aligned reads that had 2 or less mismatches, potential PCR duplicates were removed using samtools rmdup (parameters: -s) (H. Li et al., 2009). Resulting BAM files were converted to BED format using bedtools bamtobed command when necessary (Quinlan & Hall, 2010). For H3K4me1, replicates files were concatenated for all further analysis. JAMM was used to obtain the average fragment length for each experiment (Ibrahim et al. 2015).
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-Seq replicate experiments were concatenated and converted to bigwig files using deepTools bamCoverage at 10bp resolution (parameters: --normalizeUsingRPKM)(Ramirez et al. 2014), using the average fragment length predicted by JAMM (Ibrahim et al. 2015).

molecule: genomic DNA

organism: Mus musculus

source_name: ES-derived embryoid bodies with induced transcription factors

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

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

tag: strain

tag: chip target

tag: chip antibody

value: Abcam ab7766

tag: treatment

tag: cell type

value: Embryoid Bodies


title: polyA depleted RNA-seq from HepG2 (ENCLB555APN)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR000CQK/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQK
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555APN
size range: >200
spikeins used: /references/ENCSR402QNO/

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens HepG2 immortalized cell line nuclear fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2cdfa4f2-cbb9-4fff-88b9-905563d55ccc/@@download/attachment/LID9203.pdf

tag: line

value: immortalized cell line

tag: description

value: hepatocellular carcinoma

tag: biosample encode accession

tag: dev stage

value: child

tag: Sex

value: male

tag: age

value: 15 year

tag: health state

tag: lab

tag: subcellular fraction term name

value: nucleus

tag: link

value: ENCBS745AAA at ENCODE; https://www.encodeproject.org/ENCBS745AAA/

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

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

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

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


title: polyA depleted RNA-seq from foreskin fibroblast (ENCLB555ATA)

description:
https://www.encodeproject.org/experiments/ENCSR000CQD/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of foreskin fibroblast cells. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQD
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ATA
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens foreskin fibroblast primary cell male newborn

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/01f454f8-aa4f-4f11-a5fe-55976775dbf1/@@download/attachment/LID9008.pdf

value: foreskin fibroblast

value: primary cell

value: skin fibroblast, The line was established from skin taken from normal foreskin. - ATCC. (PMID:9916803)

value: newborn

value: unknown

value: normal

value: Thomas Gingeras, CSHL

value: ENCBS754AAA at ENCODE; https://www.encodeproject.org/ENCBS754AAA/

value: Derived from ENCODE donor ENCDO000AAG; https://www.encodeproject.org/ENCDO000AAG/

value: ENCODE dbxrefs Cellosaurus CVCL_3653; http://web.expasy.org/cellosaurus/CVCL_3653

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


title: EB+12hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me1.rep2

description: ChIP-seq H3K4me1 in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

value: Abcam ab8895

value: Embryoid Bodies


title: polyA depleted RNA-seq from HeLa-S3 (ENCLB555AOB)

description:
https://www.encodeproject.org/experiments/ENCSR000CQJ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQJ
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AOB
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens HeLa-S3 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/acfd468f-b22c-47f7-a9f4-a2ac3b6dcf1b/@@download/attachment/LID8790.pdf

value: immortalized cell line

value: Cervical adenocarcinoma

value: 31 year

value: adult

value: female

value: cervical adenocarcinoma

value: ENCBS737AAA at ENCODE; https://www.encodeproject.org/ENCBS737AAA/

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

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

value: ENCODE dbxrefs HeLa-S3; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HeLa-S3

value: ATCC sample source; http://www.atcc.org/products/all/CCL-2.2.aspx


title: EB+0hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27me3.rep1

description: ChIP-seq H3K27me3 in EB+0hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1

value: Active motif 39155, 39157


title: polyA depleted RNA-seq from GM12878 (ENCLB555AVN)

description:
https://www.encodeproject.org/experiments/ENCSR000CQE/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line GM12878. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQE
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AVN
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/cc600ee4-85ca-4fa0-9d20-7cd80420707b/@@download/attachment/LID18548.pdf

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

value: unknown

value: Thomas Gingeras, CSHL

value: cytosol

value: ENCBS729AAA at ENCODE; https://www.encodeproject.org/ENCBS729AAA/

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

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

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

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


title: EB+24hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me1.rep2

description: ChIP-seq H3K4me1 in EB+24hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

value: Abcam ab8895

value: Embryoid Bodies


title: polyA depleted RNA-seq from foreskin fibroblast (ENCLB555ATB)

description:
https://www.encodeproject.org/experiments/ENCSR000CQD/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of foreskin fibroblast cells. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQD
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ATB
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0b276fc8-435c-498f-87c6-165df698ff72/@@download/attachment/LID9007.pdf

value: foreskin fibroblast

value: primary cell

value: skin fibroblast, The line was established from skin taken from normal foreskin. - ATCC. (PMID:9916803)

value: newborn

value: male

value: normal

value: ENCBS753AAA at ENCODE; https://www.encodeproject.org/ENCBS753AAA/

value: Derived from ENCODE donor ENCDO000AAG; https://www.encodeproject.org/ENCDO000AAG/

value: ENCODE dbxrefs Cellosaurus CVCL_3653; http://web.expasy.org/cellosaurus/CVCL_3653

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


title: EB+0hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me1.rep2

description: ChIP-seq H3K4me1 in EB+0hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2


title: polyA depleted RNA-seq from GM12878 (ENCLB555AKH)

description:
https://www.encodeproject.org/experiments/ENCSR000CQF/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line GM12878. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQF
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AKH
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens GM12878 immortalized cell line nuclear fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b3987649-a838-4a74-9dea-496a94e73bb1/@@download/attachment/LID9198.pdf

value: immortalized cell line

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

value: adult

value: female

value: unknown

value: Thomas Gingeras, CSHL

value: nucleus

value: ENCBS730AAA at ENCODE; https://www.encodeproject.org/ENCBS730AAA/


title: polyA depleted RNA-seq from GM12878 (ENCLB555AKG)

description:
https://www.encodeproject.org/experiments/ENCSR000CQF/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line GM12878. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQF
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AKG
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/518a0fd6-473f-4ec6-a3ee-f295aedfcbe7/@@download/attachment/LID9197.pdf

value: ENCBS728AAA at ENCODE; https://www.encodeproject.org/ENCBS728AAA/

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

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

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

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


title: EB+48hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27me3.rep1b

description: ChIP-seq H3K27me3 in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1b

value: Active motif 39155, 39157

value: Embryoid Bodies


title: EB+48hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27me3.rep1a

description: ChIP-seq H3K27me3 in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1a


title: polyA depleted RNA-seq from A549 (ENCLB555AOU)

description:
https://www.encodeproject.org/experiments/ENCSR000CQC/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from whole cell fractions of independent growths of cell line A549. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQC
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AOU
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens A549 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/e44e9b17-3d1d-4f39-9999-686545f57d3c/@@download/attachment/LID9006.pdf

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

value: 58 year

value: male

value: ENCBS445ENC at ENCODE; https://www.encodeproject.org/ENCBS445ENC/

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

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

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

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


title: polyA depleted RNA-seq from MCF-7 (ENCLB555AOJ)

description:
https://www.encodeproject.org/experiments/ENCSR000CQB/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line MCF-7. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQB
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AOJ
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens MCF-7 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/963e56f0-2d62-41f1-8ab0-bddf3a862bd2/@@download/attachment/LID8825.pdf

value: immortalized cell line

value: Whole cell fraction of MCF-7 mammary gland, adenocarcinoma.

value: adult

value: female

value: 69 year

value: breast cancer (adenocarcinoma)

value: Thomas Gingeras, CSHL

value: ENCBS567IJO at ENCODE; https://www.encodeproject.org/ENCBS567IJO/

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

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

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

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


title: EB+24hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27me3.rep1b

description: ChIP-seq H3K27me3 in EB+24hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1b

value: Active motif 39155, 39157

value: Embryoid Bodies


title: polyA depleted RNA-seq from A549 (ENCLB555ALO)

description:
https://www.encodeproject.org/experiments/ENCSR000CQC/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from whole cell fractions of independent growths of cell line A549. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQC
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ALO
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/83248e5e-f9c4-4276-a151-da41dcec43ef/@@download/attachment/LID9005.pdf

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

value: 58 year

value: male

value: ENCBS444ENC at ENCODE; https://www.encodeproject.org/ENCBS444ENC/

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: EB+12hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27me3.rep1

description: ChIP-seq H3K27me3 in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1


title: polyA depleted RNA-seq from MCF-7 (ENCLB555AOH)

description:
https://www.encodeproject.org/experiments/ENCSR000CQB/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line MCF-7. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQB
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AOH
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bc2cf3a3-d088-406d-8fbf-458a98413476/@@download/attachment/LID8824.pdf

value: immortalized cell line

value: Whole cell fraction of MCF-7 mammary gland adenocarcinoma.

value: adult

value: female

value: ENCBS102ENC at ENCODE; https://www.encodeproject.org/ENCBS102ENC/


title: EB+24hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27me3.rep1a

description: ChIP-seq H3K27me3 in EB+24hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1a


title: EB+48hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27ac.rep1b

description: ChIP-seq H3K27ac in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1b

value: Abcam ab4729


title: total RNA-seq from K562 (ENCLB555AML)

description:
https://www.encodeproject.org/experiments/ENCSR000CQA/
***************
biological replicate number: 3
technical replicate number: 1
description: The libraries contained in this experiment come from the nucleoplasm fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQA
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AML
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens K562 immortalized cell line nucleoplasmic fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d4251756-f8e6-4533-bdc1-ca8cca7e326a/@@download/attachment/LID9189.pdf

value: Nucleoplasm fraction of K562

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Thomas Gingeras, CSHL

value: nucleoplasm

value: ENCBS749AAA at ENCODE; https://www.encodeproject.org/ENCBS749AAA/

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

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

value: ENCODE dbxrefs K562; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=K562

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


title: EB+48hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27ac.rep1a

description: ChIP-seq H3K27ac in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1a

value: Embryoid Bodies


title: total RNA-seq from K562 (ENCLB555AMM)

description:
https://www.encodeproject.org/experiments/ENCSR000CQA/
***************
biological replicate number: 4
technical replicate number: 1
description: The libraries contained in this experiment come from the nucleoplasm fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQA
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AMM
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5f0159a6-eb67-4b2d-a7bf-20d994adc770/@@download/attachment/LID9190.pdf

value: immortalized cell line

value: leukemia, The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: ENCBS752AAA at ENCODE; https://www.encodeproject.org/ENCBS752AAA/


title: total RNA-seq from K562 (ENCLB555ANQ)

description:
https://www.encodeproject.org/experiments/ENCSR000CPZ/
***************
biological replicate number: 4
technical replicate number: 1
description: The libraries contained in this experiment come from the nucleolar fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPZ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ANQ
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens K562 immortalized cell line nucleolus fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/1ceb6fd0-803e-4df5-aa8f-13182f575533/@@download/attachment/LID9188.pdf

value: adult

value: female

value: nucleolus

value: ENCBS751AAA at ENCODE; https://www.encodeproject.org/ENCBS751AAA/


title: EB+12hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27ac.rep1

description: ChIP-seq H3K27ac in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1

value: Abcam ab4729


title: EB+24hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27ac.rep1b

description: ChIP-seq H3K27ac in EB+24hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1b


title: total RNA-seq from K562 (ENCLB555ANR)

description:
https://www.encodeproject.org/experiments/ENCSR000CPZ/
***************
biological replicate number: 3
technical replicate number: 1
description: The libraries contained in this experiment come from the nucleolar fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPZ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ANR
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/e1740f62-4ae2-45f5-b661-d218547ca56c/@@download/attachment/LID9187.pdf

value: Nucleolus fraction of K562

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS748AAA at ENCODE; https://www.encodeproject.org/ENCBS748AAA/


title: total RNA-seq from K562 (ENCLB555APY)

description:
https://www.encodeproject.org/experiments/ENCSR000CPY/
***************
biological replicate number: 3
technical replicate number: 1
description: The libraries contained in this experiment come from the chromatin fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPY
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555APY
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens K562 immortalized cell line chromatin fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/890286c7-5ff2-49dc-945a-91eaeeeffaa8/@@download/attachment/LID9185.pdf

value: Chromatin fraction of K562

value: Thomas Gingeras, CSHL

value: chromatin

value: ENCBS747AAA at ENCODE; https://www.encodeproject.org/ENCBS747AAA/

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


title: EB+0hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27ac.rep1

description: ChIP-seq H3K27ac in EB+0hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1

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

value: Embryoid Bodies


title: EB+24hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27ac.rep1a

description: ChIP-seq H3K27ac in EB+24hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1a


title: EB+12hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me3.rep1

description: ChIP-seq H3K4me3 in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1

value: Active motif 39159, 39160


title: total RNA-seq from K562 (ENCLB555ARJ)

description:
https://www.encodeproject.org/experiments/ENCSR000CPY/
***************
biological replicate number: 4
technical replicate number: 1
description: The libraries contained in this experiment come from the chromatin fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPY
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ARJ
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/3ab0e232-85c0-4d96-8f26-402c87df1c0d/@@download/attachment/LID9186.pdf

value: immortalized cell line

value: leukemia, The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: ENCBS750AAA at ENCODE; https://www.encodeproject.org/ENCBS750AAA/

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

value: ENCODE dbxrefs K562; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=K562

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


title: EB+48hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me2.rep1

description: ChIP-seq H3K4me2 in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1

value: Abcam ab7766


title: EB+24hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me3.rep1

description: ChIP-seq H3K4me3 in EB+24hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1


title: polyA mRNA RNA-seq from K562 (ENCLB555ALX)

description:
https://www.encodeproject.org/experiments/ENCSR000CPS/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPS
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ALX
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens K562 immortalized cell line nuclear fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ce19cd4a-f215-4740-a74a-ffb42a16f799/@@download/attachment/LID8557.pdf

value: adult

value: female

value: 53 year

value: nucleus

value: ENCBS725AAA at ENCODE; https://www.encodeproject.org/ENCBS725AAA/


title: EB+48hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me3.rep1

description: ChIP-seq H3K4me3 in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1


title: EB+12hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me2.rep1

description: ChIP-seq H3K4me2 in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1


title: polyA mRNA RNA-seq from MCF-7 (ENCLB555AQN)

description:
https://www.encodeproject.org/experiments/ENCSR000CPT/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line MCF-7. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPT
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AQN
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bab8f637-481e-41fd-8267-af3b90d0698c/@@download/attachment/LID8686.pdf

value: Whole cell fraction of MCF-7 mammary gland adenocarcinoma.

value: 69 year

value: breast cancer (adenocarcinoma)

value: Thomas Gingeras, CSHL

value: ENCBS102ENC at ENCODE; https://www.encodeproject.org/ENCBS102ENC/

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

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

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

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


title: EB+0hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me3.rep1

description: ChIP-seq H3K4me3 in EB+0hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1

value: Active motif 39159, 39160

value: Embryoid Bodies


title: polyA mRNA RNA-seq from HeLa-S3 (ENCLB555ASM)

description:
https://www.encodeproject.org/experiments/ENCSR000CPQ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPQ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ASM
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens HeLa-S3 immortalized cell line nuclear fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b4556402-c8b8-430a-92f0-a937391418c7/@@download/attachment/LID8559.pdf

value: immortalized cell line

value: Cervical adenocarcinoma

value: 31 year

value: cervical adenocarcinoma

value: ENCBS736AAA at ENCODE; https://www.encodeproject.org/ENCBS736AAA/

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

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

value: ENCODE dbxrefs HeLa-S3; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HeLa-S3

value: ATCC sample source; http://www.atcc.org/products/all/CCL-2.2.aspx


title: EB+24hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me2.rep1

description: ChIP-seq H3K4me2 in EB+24hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1

value: Abcam ab7766


title: polyA mRNA RNA-seq from HeLa-S3 (ENCLB555ALK)

description:
https://www.encodeproject.org/experiments/ENCSR000CPP/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPP
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ALK
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens HeLa-S3 immortalized cell line cytosolic fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d2b6a3f0-eba7-4776-a993-5d980c183493/@@download/attachment/LID8470.pdf

value: adult

value: female

value: Thomas Gingeras, CSHL

value: cytosol

value: ENCBS738AAA at ENCODE; https://www.encodeproject.org/ENCBS738AAA/


title: polyA mRNA RNA-seq from MCF-7 (ENCLB555AQO)

description:
https://www.encodeproject.org/experiments/ENCSR000CPT/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line MCF-7. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPT
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AQO
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f31149f4-a491-4a90-96ea-7c39649ac6fa/@@download/attachment/LID8687.pdf

value: Whole cell fraction of MCF-7 mammary gland, adenocarcinoma.

value: 69 year

value: breast cancer (adenocarcinoma)

value: ENCBS567IJO at ENCODE; https://www.encodeproject.org/ENCBS567IJO/

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

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

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

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


title: EB+0hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me2.rep1

description: ChIP-seq H3K4me2 in EB+0hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1

value: Embryoid Bodies


title: polyA mRNA RNA-seq from GM12878 (ENCLB555ALI)

description:
https://www.encodeproject.org/experiments/ENCSR000CPO/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line GM12878. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPO
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ALI
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0f1620f3-5d2f-4d7f-bddc-c20fe3951833/@@download/attachment/LID8533.pdf

value: immortalized cell line

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

value: unknown

value: nucleus

value: ENCBS730AAA at ENCODE; https://www.encodeproject.org/ENCBS730AAA/

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

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

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

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


title: polyA mRNA RNA-seq from HeLa-S3 (ENCLB555ALJ)

description:
https://www.encodeproject.org/experiments/ENCSR000CPP/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPP
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ALJ
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/e39859f3-e394-499d-852d-793199dc7837/@@download/attachment/LID8469.pdf

value: Cervical adenocarcinoma

value: adult

value: female

value: 31 year

value: cervical adenocarcinoma

value: Thomas Gingeras, CSHL

value: cytosol

value: ENCBS735AAA at ENCODE; https://www.encodeproject.org/ENCBS735AAA/

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

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

value: ENCODE dbxrefs HeLa-S3; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HeLa-S3

value: ATCC sample source; http://www.atcc.org/products/all/CCL-2.2.aspx


title: polyA mRNA RNA-seq from GM12878 (ENCLB555ANP)

description:
https://www.encodeproject.org/experiments/ENCSR000CPO/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line GM12878. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPO
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ANP
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0431fedc-29f8-4947-b0c1-3b59c91b48c4/@@download/attachment/LID8532.pdf

value: immortalized cell line

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

value: unknown

value: nucleus

value: ENCBS728AAA at ENCODE; https://www.encodeproject.org/ENCBS728AAA/


title: EB+48hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me1.rep1b

description: ChIP-seq H3K4me1 in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1b

value: Abcam ab8895

value: Embryoid Bodies


title: EB+48hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me1.rep1a

description: ChIP-seq H3K4me1 in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1a


title: EB+24hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me1.rep1

description: ChIP-seq H3K4me1 in EB+24hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1


title: polyA mRNA RNA-seq from K562 (ENCLB555ALY)

description:
https://www.encodeproject.org/experiments/ENCSR000CPS/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPS
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ALY
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/dc0aea91-da61-4c9f-b391-aac2b02802db/@@download/attachment/LID8556.pdf

value: leukemia, The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS722AAA at ENCODE; https://www.encodeproject.org/ENCBS722AAA/

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

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

value: ENCODE dbxrefs K562; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=K562

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


title: polyA mRNA RNA-seq from SK-N-SH (ENCLB555AOG)

description:
https://www.encodeproject.org/experiments/ENCSR000CPN/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line SK-N-SH that has been treated with retinoic acid. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPN
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AOG
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens SK-N-SH immortalized cell line treated with 6 ?M all-trans-retinoic acid for 48 hours

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/cb3339fe-e4c8-4f00-989c-1e192350b97f/@@download/attachment/LID8967.pdf

value: SK-N-SH

value: immortalized cell line

value: neuroblastoma cell line, treatment:differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

value: child

tag: treatments

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: 4 year

value: Thomas Gingeras, CSHL

value: ENCBS366ENC at ENCODE; https://www.encodeproject.org/ENCBS366ENC/

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

value: ENCODE dbxrefs Cellosaurus CVCL_D044; http://web.expasy.org/cellosaurus/CVCL_D044

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

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


title: EB+0hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me1.rep1

description: ChIP-seq H3K4me1 in EB+0hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1

value: Abcam ab8895

value: Embryoid Bodies


title: polyA mRNA RNA-seq from SK-N-SH (ENCLB555ARW)

description:
https://www.encodeproject.org/experiments/ENCSR000CPN/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line SK-N-SH that has been treated with retinoic acid. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPN
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ARW
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/839d1ddc-117c-4e2c-8708-c392d6d3403e/@@download/attachment/LID8968.pdf

value: female

value: ENCBS367ENC at ENCODE; https://www.encodeproject.org/ENCBS367ENC/


title: ChIP-seq Onecut2 in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

description:
Onecut2_48h_iNIL.bed
Onecut2_48h_iNIL.events

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

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

value: anti-Onecut2 (R&D Systems AF294)


title: polyA depleted RNA-seq from K562 (ENCLB555AND)

description:
https://www.encodeproject.org/experiments/ENCSR000CPG/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPG
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AND
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens K562 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2aa212e2-01a1-43b2-b187-eeec02015a45/@@download/attachment/LID8660.pdf

value: leukemia, The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: 53 year

value: adult

value: chronic myelogenous leukemia (CML)

value: ENCBS726AAA at ENCODE; https://www.encodeproject.org/ENCBS726AAA/

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

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

value: ENCODE dbxrefs K562; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=K562

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


title: ChIP-seq Onecut2 in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1


title: ChIP-seq Lhx3.V5 in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

description:
Lhx3_48h_iNIL.bed
Lhx3_48h_iNIL.events

value: anti-V5 (Abcam ab15828)


title: ChIP-seq Lhx3.V5 in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1

description:
Lhx3_48h_iNIL.bed
Lhx3_48h_iNIL.events


title: polyA mRNA RNA-seq from HepG2 (ENCLB555AOO)

description:
https://www.encodeproject.org/experiments/ENCSR000CPF/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPF
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AOO
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens HepG2 immortalized cell line cytosolic fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/731f59a6-fcc5-4e6b-9b0c-3af2a3f175dd/@@download/attachment/LID8472.pdf

value: immortalized cell line

value: hepatocellular carcinoma

value: child

value: male

value: 15 year

value: Thomas Gingeras, CSHL

value: cytosol

value: ENCBS744AAA at ENCODE; https://www.encodeproject.org/ENCBS744AAA/

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

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

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

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


title: polyA mRNA RNA-seq from HeLa-S3 (ENCLB555ASN)

description:
https://www.encodeproject.org/experiments/ENCSR000CPQ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPQ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ASN
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/c78c7d88-610b-4268-b75b-3bfc64f89f8e/@@download/attachment/LID8560.pdf

value: Cervical adenocarcinoma

value: adult

value: female

value: 31 year

value: cervical adenocarcinoma

value: nucleus

value: ENCBS739AAA at ENCODE; https://www.encodeproject.org/ENCBS739AAA/

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

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

value: ENCODE dbxrefs HeLa-S3; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HeLa-S3

value: ATCC sample source; http://www.atcc.org/products/all/CCL-2.2.aspx


title: polyA mRNA RNA-seq from HepG2 (ENCLB555AOP)

description:
https://www.encodeproject.org/experiments/ENCSR000CPF/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPF
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AOP
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b63a07e2-ebb5-4f06-9ac7-9a7552aec3ef/@@download/attachment/LID8471.pdf

value: immortalized cell line

value: hepatocellular carcinoma

value: child

value: male

value: 15 year

value: Thomas Gingeras, CSHL

value: cytosol

value: ENCBS741AAA at ENCODE; https://www.encodeproject.org/ENCBS741AAA/


title: polyA depleted RNA-seq from K562 (ENCLB555ANC)

description:
https://www.encodeproject.org/experiments/ENCSR000CPG/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPG
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ANC
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/63cf09c2-659b-41f2-b20f-45e88c771877/@@download/attachment/LID8659.pdf

value: leukemia, The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS723AAA at ENCODE; https://www.encodeproject.org/ENCBS723AAA/

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

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

value: ENCODE dbxrefs K562; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=K562

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


title: polyA depleted RNA-seq from HepG2 (ENCLB555AMK)

description:
https://www.encodeproject.org/experiments/ENCSR000CPD/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPD
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AMK
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens HepG2 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/3249963c-6c6b-496d-8331-0d583e8bc4c2/@@download/attachment/LID8792.pdf

value: immortalized cell line

value: hepatocellular carcinoma

value: ENCBS743AAA at ENCODE; https://www.encodeproject.org/ENCBS743AAA/

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

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

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

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


title: polyA mRNA RNA-seq from HepG2 (ENCLB555AWN)

description:
https://www.encodeproject.org/experiments/ENCSR000CPC/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPC
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AWN
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6c89de4b-e462-436e-8f4b-f53779fd2a70/@@download/attachment/LID8534.pdf

value: child

value: male

value: 15 year

value: Thomas Gingeras, CSHL

value: nucleus

value: ENCBS742AAA at ENCODE; https://www.encodeproject.org/ENCBS742AAA/


title: ChIP-seq Isl1 in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

description:
Isl1_48h_iNIL.bed
Isl1_48h_iNIL.events

source_name: ES-derived embryoid bodies with induced transcription factors

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

value: anti-Isl1 combination (DSHB 40.3A4, 39.3F7, 40.206)

value: Embryoid Bodies


title: ChIP-seq Lhx3.V5 in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 3

description:
Lhx3_48h_iNIL.bed
Lhx3_48h_iNIL.events

value: anti-V5 (Abcam ab15828)


title: polyA depleted RNA-seq from HepG2 (ENCLB555AMJ)

description:
https://www.encodeproject.org/experiments/ENCSR000CPD/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPD
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AMJ
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/62d8d1c2-68b2-4902-ba51-2c316ca0f1b7/@@download/attachment/LID8793.pdf

value: ENCBS746AAA at ENCODE; https://www.encodeproject.org/ENCBS746AAA/


title: Input-DNA in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1

value: Input


title: polyA mRNA RNA-seq from H1-hESC (ENCLB555AMO)

description:
https://www.encodeproject.org/experiments/ENCSR000COW/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of the human embryonic stem cell line H1-hESC. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000COW
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AMO
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens H1-hESC stem cell nuclear fraction male embryo

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6239daed-c6b6-46ff-8f6b-19dc546f80ef/@@download/attachment/LID8558.pdf

value: stem cell

value: embryonic stem cells

value: embryonic

value: unknown

value: healthy

value: ENCBS733AAA at ENCODE; https://www.encodeproject.org/ENCBS733AAA/

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

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

value: ENCODE dbxrefs H1-hESC; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=H1-hESC


title: ChIP-seq Ebf2 in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1

description:
Ebf2_48h_iNIL.bed
Ebf2_48h_iNIL.events

value: anti-Ebf2 (Abcam ab156999)


title: polyA mRNA RNA-seq from H1-hESC (ENCLB555ATY)

description:
https://www.encodeproject.org/experiments/ENCSR000COV/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of the human embryonic stem cell line H1-hESC. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000COV
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ATY
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens H1-hESC stem cell cytosolic fraction male embryo

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/c83f3793-5b6b-4c60-92bf-608d61982cbb/@@download/attachment/LID8536.pdf

value: male

value: Thomas Gingeras, CSHL

value: cytosol

value: ENCBS732AAA at ENCODE; https://www.encodeproject.org/ENCBS732AAA/


title: ChIP-seq Isl1 in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1

description:
Isl1_48h_iNIL.bed
Isl1_48h_iNIL.events

value: anti-Isl1 combination (DSHB 40.3A4, 39.3F7, 40.206)

value: Embryoid Bodies


title: ChIP-seq Ebf2 in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

description:
Ebf2_48h_iNIL.bed
Ebf2_48h_iNIL.events


title: polyA mRNA RNA-seq from H1-hESC (ENCLB555AMA)

description:
https://www.encodeproject.org/experiments/ENCSR000COU/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of the human embryonic stem cell line H1-hESC. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000COU
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AMA
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens H1-hESC stem cell male embryo

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2828ba15-f9d5-4bce-ad3c-0a7f6a18a6e5/@@download/attachment/LID8461.pdf

value: ENCBS731AAA at ENCODE; https://www.encodeproject.org/ENCBS731AAA/


title: polyA mRNA RNA-seq from H1-hESC (ENCLB555AMB)

description:
https://www.encodeproject.org/experiments/ENCSR000COU/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of the human embryonic stem cell line H1-hESC. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000COU
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AMB
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/13baf1e0-b459-496f-bf78-d32689e00e71/@@download/attachment/LID8462.pdf

value: stem cell

value: ENCBS734AAA at ENCODE; https://www.encodeproject.org/ENCBS734AAA/


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

description:
Lhx3_24h_iNIL.bed
Lhx3_24h_iNIL.events

value: anti-V5 (Abcam ab15828)


title: polyA depleted RNA-seq from H1-hESC (ENCLB555AQX)

description:
https://www.encodeproject.org/experiments/ENCSR000COT/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of the human embryonic stem cell line H1-hESC. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized  Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000COT
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AQX
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/51510051-d3e7-4570-a7ac-60185eef5c3e/@@download/attachment/LID8663.pdf

value: embryonic stem cells

value: embryonic

value: unknown


title: ChIP-seq Lhx3.V5 in EB+24hrDox(iNgn2.Isl1.Lhx3.V5) replicate 3

description:
Lhx3_24h_iNIL.bed
Lhx3_24h_iNIL.events


title: ChIP-seq Lhx3.V5 in EB+24hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

description:
Lhx3_24h_iNIL.bed
Lhx3_24h_iNIL.events


title: polyA depleted RNA-seq from H1-hESC (ENCLB555AQW)

description:
https://www.encodeproject.org/experiments/ENCSR000COT/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of the human embryonic stem cell line H1-hESC. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized  Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000COT
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AQW
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/16280088-f52e-4778-9797-1638edd356c1/@@download/attachment/LID8664.pdf

value: healthy

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


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

description:
Lhx3_24h_iNIL.bed
Lhx3_24h_iNIL.events


title: polyA depleted RNA-seq from GM12878 (ENCLB555AMC)

description:
https://www.encodeproject.org/experiments/ENCSR000COS/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line GM12878. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000COS
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AMC
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens GM12878 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/e7a7784d-e02e-4747-b6e8-b31915ed1101/@@download/attachment/LID8662.pdf

value: immortalized cell line

value: B-lymphoblastoid cell line

value: adult

value: female

value: ENCBS096RNA at ENCODE; https://www.encodeproject.org/ENCBS096RNA/

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

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

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

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


title: polyA mRNA RNA-seq from GM12878 (ENCLB555ANN)

description:
https://www.encodeproject.org/experiments/ENCSR000COR/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line GM12878. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000COR
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ANN
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens GM12878 immortalized cell line cytosolic fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b5e0ca7c-ef72-49f3-9e8f-3941233acc71/@@download/attachment/LID8468.pdf

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

value: Thomas Gingeras, CSHL

value: cytosol

value: ENCBS729AAA at ENCODE; https://www.encodeproject.org/ENCBS729AAA/


title: ChIP-seq Isl1 in EB+24hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

description:
Isl1_24h_iNIL.bed
Isl1_24h_iNIL.events

value: anti-Isl1 combination (DSHB 40.3A4, 39.3F7, 40.206)

value: Embryoid Bodies


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

description:
Isl1_24h_iNIL.bed
Isl1_24h_iNIL.events


title: polyA mRNA RNA-seq from GM12878 (ENCLB555ANM)

description:
https://www.encodeproject.org/experiments/ENCSR000COR/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line GM12878. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000COR
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ANM
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/38f11677-cf33-485a-8a90-f44beae51d4d/@@download/attachment/LID8467.pdf

value: unknown

value: ENCBS727AAA at ENCODE; https://www.encodeproject.org/ENCBS727AAA/


title: polyA mRNA RNA-seq from HepG2 (ENCLB555AWM)

description:
https://www.encodeproject.org/experiments/ENCSR000CPC/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPC
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AWM
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens HepG2 immortalized cell line nuclear fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4d8d9f75-36fc-41ea-8233-54f8027a169d/@@download/attachment/LID8535.pdf

value: immortalized cell line

value: hepatocellular carcinoma

value: child

value: male

value: 15 year

value: nucleus

value: ENCBS745AAA at ENCODE; https://www.encodeproject.org/ENCBS745AAA/

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

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

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

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


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

value: Input


title: polyA mRNA RNA-seq from foreskin fibroblast (ENCLB555ANH)

description:
https://www.encodeproject.org/experiments/ENCSR000COP/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of foreskin fibroblast cells. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000COP
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ANH
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens foreskin fibroblast primary cell male newborn

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/eb84ab16-6202-44ee-84f5-d67b241f94db/@@download/attachment/LID8970.pdf

value: foreskin fibroblast

value: primary cell

value: skin fibroblast, The line was established from skin taken from normal foreskin. - ATCC. (PMID:9916803)

value: newborn

value: normal

value: Thomas Gingeras, CSHL

value: ENCBS754AAA at ENCODE; https://www.encodeproject.org/ENCBS754AAA/

value: Derived from ENCODE donor ENCDO000AAG; https://www.encodeproject.org/ENCDO000AAG/

value: ENCODE dbxrefs Cellosaurus CVCL_3653; http://web.expasy.org/cellosaurus/CVCL_3653

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


title: polyA mRNA RNA-seq from foreskin fibroblast (ENCLB555ANG)

description:
https://www.encodeproject.org/experiments/ENCSR000COP/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of foreskin fibroblast cells. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000COP
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ANG
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/82e4c842-cba3-46f3-9660-e3c475b6ea40/@@download/attachment/LID8969.pdf

value: male

value: unknown

value: ENCBS753AAA at ENCODE; https://www.encodeproject.org/ENCBS753AAA/


title: ChIP-seq Ngn2 in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

description:
Ngn2_12h_iNIL.bed
Ngn2_12h_iNIL.events

value: anti-Ngn2 (Santa Cruz sc-19233)

value: Embryoid Bodies


title: ChIP-seq Ngn2 in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1

description:
Ngn2_12h_iNIL.bed
Ngn2_12h_iNIL.events


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

description:
Lhx3_12h_iNIL.bed
Lhx3_12h_iNIL.events

value: anti-V5 (Abcam ab15828)


title: MeRIP2

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

description: library strategy: MeRIP-Seq

data_processing:
The samples were sequenced on two flowcells on the Illumina MiSeq (MiSeq Control Software Version 2.6.1.1). Readlength was 68 bp SR
Mapping was done using Star (v. 2.4.0h), secondary alignments were filtered. Mapping was done against BDGP6 (ensembl release 79).
After mapping peaks were called using MACS (v.1.4.1, parameters: "--nomodel --shiftsize 65 --to-small -w -S --keep-dup all --call-subpeaks --nolambda -g 90464385 ).
After peakcalling peaks were split into subpeaks using PeakSplitter (v.1.0).
Consensus peaks were obtained by intersecting subpeaks of both replicates ( using BEDTools (v.2.25.0)).
For each consensus peak the coverage was calculated as counts per million (CPM) for each of the samples and averaged for input and MeRIP samples. Foldchanges for MeRIP vs Input were calculated based on these.
Genome_build: BDGP6 Ensembl release 79
Supplementary_files_format_and_content: bigwig tracks

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: MeRIP, S2R+ cells

growth_protocol: S2R+ cells were grown on standard conditions at room temperature

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen). mRNA was purified by using two rounds of purification with Dynabeads Oligo (dT)25 (Invitrogen)
NEBNext Ultra directional Kit (NEB) was used omitting RNA fragmentation step for recovered m6A-RIP samples and following the manufacturer`s protocol for input samples.

treatment_protocol: no treatment

tag: cell line

value: S2R+ cells

value: embryonic cells

tag: rip antibody


title: polyA mRNA RNA-seq from K562 (ENCLB555AQU)

description:
https://www.encodeproject.org/experiments/ENCSR000COK/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000COK
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AQU
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens K562 immortalized cell line cytosolic fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bca9a8c0-723b-4794-9d0b-667dd73d96a6/@@download/attachment/LID8466.pdf

value: immortalized cell line

value: leukemia, The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: cytosol

value: ENCBS724AAA at ENCODE; https://www.encodeproject.org/ENCBS724AAA/

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

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

value: ENCODE dbxrefs K562; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=K562

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


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

description:
Lhx3_12h_iNIL.bed
Lhx3_12h_iNIL.events

tag: strain

tag: chip target


title: Input2

description: library strategy: MeRIP-Seq

source_name: Input, S2R+ cells


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

description:
Isl1_12h_iNIL.bed
Isl1_12h_iNIL.events

tag: chip antibody

value: anti-Isl1 combination (DSHB 40.3A4, 39.3F7, 40.206)

tag: treatment


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

description:
Isl1_12h_iNIL.bed
Isl1_12h_iNIL.events

tag: cell type

value: Embryoid Bodies


title: Input1

description: library strategy: MeRIP-Seq


title: ChIP-seq Lhx3.V5 in EB+8hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

description:
Lhx3_8h_iNIL.bed
Lhx3_8h_iNIL.events

value: anti-V5 (Abcam ab15828)


title: Scerevisiae_YEPD_aF_245min

city: Hanover

first: Christina

middle: M

last: Kelliher

state: NH

address: 7400 Hinman

department: Molecular & Systems Biology

institute: Geisel School of Medicine at Dartmouth

data_processing:
Sequenced reads mapped to the respective yeast genome using STAR with parameters --outFilterType BySJout --alignIntronMin 10 --alignIntronMax 3000 --outFilterIntronMotifs RemoveNoncanonical
Transcripts were quantified in Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using Cufflinks with the respective transcriptome GTF file (i.e. quantify one transcript per annotated gene, not gene isoforms). Values were normalized by gene size and by library size.
Time point samples from the respective yeasts were normalized together using the cuffnorm feature of Cufflinks (default parameters for stranded RNA-Seq)
A value of "1" was added to every FPKM value in each dataset; see manuscript for details
Genome_build: Saccharomyces cerevisiae S288C Ensembl R64-1-1 downloaded from Illumina iGenomes on 3-2-16; Cryptococcus neoformans var. grubii H99 (Serotype A) downloaded from the Broad Institute on 3-2-16
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae culture, wild-type, 245 min

growth_protocol: YEPDextrose at 30c

extract_protocol:
Illumina TruSeq Stranded mRNA Library Prep Kit was used for the construction of sequencing libraries
Cells were removed at each time point and flash frozen on dry ice. RNA was harvested using standard yeast methods.
see SAMPLES section; RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
synchronous G1 populations collected by alpha-factor mating pheromone (30 ng/ml, 110 minutes) arrest-release
see SAMPLES section

value: BF264-15D MATa bar1

tag: genotype/variation

value: wild type

tag: time

value: 245 min


title: polyA depleted RNA-seq from GM12878 (ENCLB555ARR)

description:
https://www.encodeproject.org/experiments/ENCSR000COS/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line GM12878. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000COS
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ARR
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/19a38064-0d49-4888-a7fa-0fa81abd0000/@@download/attachment/LID8661.pdf

tag: line

value: immortalized cell line

tag: description

value: B-lymphoblastoid cell line

tag: biosample encode accession

value: unknown

tag: dev stage

value: Thomas Gingeras, CSHL

value: ENCBS095RNA at ENCODE; https://www.encodeproject.org/ENCBS095RNA/

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

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

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

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


title: Scerevisiae_YEPD_aF_235min

source_name: S. cerevisiae culture, wild-type, 235 min

value: 235 min