title: MC18

city: Milano

first: Maurizio

last: Crestani

address: via Balzaretti 9

country: Italy

institute: University of Milano

data_processing:
Sequencing data was processed using the Illumina Pipeline Software version 1.82.
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.3, Martin 2011) and filtered for low complexity with seq_crumbs (v. 0.1.8).
Reads were aligned against Mus musculus genome (version GRCm38) using STAR (v. 2.4.2a, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1, Anders et al. 2014) using Mus musculus (Ensembl v. GRCm38.82) gene annotation.
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for each Sample.

source_name: H3atKO replicate 3

growth_protocol: Mice with selective ablation of Hdac3 in adipose tissue were obtained by crossing Hdac3 floxed mice in BL6 background with B6:FVB-Tg(Adipoq-cre)1Evdr/J (The Jackson Laboratory). Hdac3 floxed and knock out (H3atKO) were maintained in standard housing conditions and fed with chow diet.

extract_protocol:
Trizol extraction of total RNA, followed by purification with Lipid RNeasy Mini Kit (Qiagen). After quality check, 500ng of total RNA from 2/3 individual mice of the same experimental group were pooled for RNA-seq.
RNA-seq libraries were prepared using the Illumina Truseq Stranded mRNA protocol

treatment_protocol: At sacrifice, inguinal subcutaneous adipose tissue was collected from individual mice for total RNA extraction.

tag: strain

tag: age

value: 5-9 months

value: mouse inguinal subcutaneous adipose tissue


title: MC17

status: Public on Jul 17 2017

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: H3atKO replicate 2

tag: tissue


title: 1Plate1_A05_CD8_CMVtet_short_paired-end

city: Berkeley

first: Shaked

last: Afik

state: CA

address: Stanley Hall

department: Computational Biology Graduate Group

country: USA

institute: UC Berkeley

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_A05_CD8_CMVtet

data_processing:
Low quality bases were trimmed with trimmomatic using the following parameters: LEADING:15, TRAILING:15, SLIDINGWINDOW:4:15, MINLEN:16.
Trimmed reads were then aligned to the genome (hg38 or mm10 for human or mouse samples, respectively) with TopHat2 for TCR reconstruction, and aligned to the transcriptome with RSEM for transcriptome quantification.
For transcriptome analysis of the human CMV and YFV donors (donors 1 and 2), low quality cells were filtered out prior to normalization. Cells were filtered out if their read depth was less than 1 million pairs or if the cell expressed less than 20% of all expressed transcript, where a transcript was considered expressed if it had a TPM value of >10 in at least 10% of cells, leaving 353 out of 378 cells for further analysis.
Normalization of TPM values was done with our newly developed normalization framework SCONE. In our study, the chosen normalization first scaled each sample with the DEseq scaling factor to account for differences in sequencing depth. Then, we ran RUVg with k=1.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: Normalized TPM expression matrix of high quality cells from donors 1 and 2.

molecule: polyA RNA

organism: Homo sapiens

source_name: CD8+ CMV-specific T cell donor 1

growth_protocol: Mouse LCMV: Female C57BL/6 mice (The Jackson Laboratory), aged 7 weeks, were infected with 2x105 plaque forming units (PFU) LCMV Armstrong intraperitoneally i.p. or 4x106 PFU LCMV Clone 13 i.v. Human Donor 2: A healthy volunteer was vaccinated with a single dose (0.5 ml containing at least 105 PFU) of 17D live-attenuated yellow fever vaccine strain administered subcutaneously. Seroconversion after vaccination was confirmed by assaying the neutralizing antibody titers for YF-17D. Human Donor 3: Patient 355 (59yr old Male, infected with genotype 1a HCV, baseline viral load 467,000 IU/ml) received a prime vaccination of ChAd3-NSmut (2.5x1010 viral particles) and an MVA-NSmut (2x108 plaque forming units) boost vaccination 8 weeks later.

extract_protocol:
Mouse LCMV: Peripheral blood was obtained from the mice at day 7 post infection (p.i.) and lymphocytes were enriched using LSM density centrifugation. Cells were prestained with a near-IR fixable live/dead marker (Life Technologies, cat# L34976) and an APC- conjugated dextramer reagent for gp33 (Immudex, cat# A2160-APC) according to manufacturer recommendations. The cells were then stained with the following antibodies: FITC 2B4 (BioLegend, cat# 133504), PerCP-Cy5.5 CD44 (BioLegend, cat# 103032), PE KLRG1 (BioLegend, cat# 138408), PE-Cy7 PD1 (BioLegend, cat# 135215), BV421 CD127 (BioLegend, cat# 135024), BV510 CD8A (BioLegend, cat# 100752). Human Donor 1: Blood samples were obtained from a donor with detectable NLV-specific CD8+ T cell response. Lymphocytes were enriched via Ficoll gradient and prestained with a near-IR fixable live/dead marker (Life Technologies, cat# L34976) and an APC-conjugated dextramer reagent (Immudex, cat# WB2132-APC). The cells were then stained with the following antibodies: FITC CD8A (BioLegend, cat# 300906), PerCP-Cy5.5 CCR7 (BioLegend, cat# 353220), PE CD3 (BioLegend, cat# 317308), BV605 CD45RA (BioLegend, cat# 304133). Human Donor 2: A whole blood sample was obtained 9 months post-vaccination and lymphocytes were enriched from whole blood via Ficoll gradient centrifugation and a CD8 negative selection magnetic bead kit (Miltenyi Biotec). Cells were prestained with a live/dead marker (Life Technologies, cat# L34976) and an APC-labeled tetramer reagent (NS4B 214–222 LLWNGPMAV, kindly provided by Dr. Rafi Ahmed). The cells were then stained with the following antibodies: FITC CD8A (BioLegend, cat# 300906), PE CXCR3 (BioLegend, cat# 353705), PE-Cy7 CCR7 (BioLegend, cat# 353226), BV421 IL2Rb (BioLegend, cat# 339009), BV510 CD3 (BioLegend, cat# 317332), BV605 CD95 (BioLegend, cat# 305627), BV780 CD45RA (BioLegend, cat# 304140). Human Donor 3: PBMC were collected 14 weeks post-boost vaccination. PBMC were thawed and prestained with a live/dead marker (Life Technologies, cat# L34976) and a PE-conjugated pentamer reagent (PE-labeled HCV NS31406–1415 (KLSALGINAV; HLA-A*0201)). The cells were then stained with the following antibodies: FITC 2B4 (BioLegend, cat# 329505), PerCP-eFluor 710 LAG3 (eBioscience, cat# 46-2239), PE-Cy7 CCR7 (BioLegend, cat# 329919), APC CD39 (BioLegend, cat# 328209), BV421 PD1 (BioLegend, cat# 329919), BV510 CD3 (BioLegend, cat# 317332), BV605 CD8A (BioLegend, cat# 301040), BV780 CD45RA (BioLegend, cat# 304140).
Single cell lysates were converted to cDNA following capture with Agencourt RNA Clean beads using the SmartSeq2 protocol. The cDNA was amplified using 22-24 PCR enrichment cycles prior to quantification and dual-index barcoding with the Illumina Nextera XT kit. The libraries were enriched with 12 cycles of PCR, then combined in equal volumes prior to final bead cleanup and sequencing.

value: CD8+ CMV-specific T cell

tag: donor

value: Donor 1

tag: number of cells in sample


title: MC16

source_name: H3atKO replicate 1


title: 1Plate1_A05_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: MC15

source_name: floxed replicate 3


title: MC14

source_name: floxed replicate 2


title: 1Plate1_A04_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_A04_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_A03_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_A03_CD8_CMVtet


title: MC13

source_name: floxed replicate 1


title: Nb_pSUC2_Mock2

city: College Park

first: James

middle: N

last: Culver

state: MD

address: 4291 Fieldhouse Dr.

department: Plant Science and Landscape Architecture

institute: University of Maryland, College Park

description: polysomal RNA from leaf phloem tissue mock inoculated with sterile water

data_processing:
CASAVA 1.8.2 was used for bcl conversion and demultiplexing
Reads were mapped to the N. benthamiana draft genome v1.0.1 described in Bombarely et al. (Molecular Plant-Microbe Interactions 25, 1523-1530; 2012) using the CLC Genomics Workbench v 7.5.1 RNA-seq analysis tool and default parameters. (Mismatch cost 2, Insertion cost 3, Deletion Cost 3, Length fraction 0.8, Similarity fraction 0.8, Max hits for a read 10).
Genome_build: N. benthamiana draft genome v1.0.1 described in Bombarely et al. (Molecular Plant-Microbe Interactions 25, 1523-1530; 2012)
Supplementary_files_format_and_content: tab-delimited text files include Gene ID, Chromosome, Region, RPKM value, Total gene reads, and Total exon reads.

organism: Nicotiana benthamiana

growth_protocol: Transgenic plants expressing promoter:His6FLAG-RPL18 were maintained in growth chambers for a 12-h photoperiod, light 100 µmol s-1 m-2, at 24°C.  Biological replicates were grown in different months under the same growth chamber conditions.

extract_protocol:
Frozen tissue was homogenized in Polysome Extraction Buffer (PEB; 200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM ethylene glycol tetraacetic acid (EGTA) pH 8.0, 35 mM MgCl2, 1% (v/v) octylphenyl-polyethylene glycol (Igepal CA-630), 1% (v/v) polyoxyethylene 10 tridecyl ether, 1% (v/v) sodium deoxycholate, 5 mM dithiothereitol (DTT), 1 mM PMSF, 50 ug/mL cycloheximide, 50 ug/mL chloramphenicol, 0.5 mg/mL heparin) using 10 mL PEB per 5 g of tissue.  Homogenates were clarified by centrifugation at 16,000 g for 15 min and filtered with cheesecloth.  The supernatant was loaded onto an 8 mL 1.6 M sucrose cushion. Samples were ultracentrifuged at 170,000 g for 18 h at 4 C to pellet polysomes. 1 mL of PEB was used to resuspend the pellet. Anti-FLAG magnetic beads, 50 μL (Sigma Chemical Company, St. Louis, MO USA) were added to the resupsended pellet and incubated at 4oC overnight with gentle rocking.  The beads were recovered using a magnet and washed four times for 5 min with 5 mL of wash buffer (200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM EGTA, 35 mM MgCl2, 5 mM DTT, 50 μg/mL cycloheximide, 50 μg/mL chloramphenicol).  The complexes were eluted by treatment of the magnetic beads with 100 uL of elution buffer (100 uL wash buffer, 10 uL of 5mg/mL FLAG3 peptide - Sigma Chemical Company, St. Louis, MO USA, 0.5 uL of 2 U/mL RNAse OUT - Thermo Fisher Scientific Cleveland, Ohio, USA).  RLT buffer plus 2-Mercaptoethanol from the Qiagen RNeasy kit (Qiagen, Valencia, CA USA) was added to the eluted complexes.  A 0.5 X volume of 100% ethanol was then added and the sample transferred to Qiagen RNeasy columns.  Washes and RNA elutions were performed according to the manufacturer’s instructions.  Isolated RNA was measured on a NanoDrop 1000 and the quality of the RNA confirmed using a 2100 Bioanalyzer Eukaryotic Total RNA Nanochip (Agilent Technologies Palo Alto, CA USA).
cDNA libraries were prepared by the by the UM-IBBR Sequencing Core at University of Maryland, College Park (http://ibbr.umd.edu/facilities/sequencing) using the Illuminia TrueSeq RNA library kit according to the manufacturer's instructions.

treatment_protocol: Plant leaves were inoculated with tobacco mosaic virus (1 mg/ml) or mock inoculated with sterile water. Inoculated leaves were harvested 6 days post infection and immediately frozen in liquid nitrogen.

tag: developmental stage

value: 5-week-old plants

tag: genotype/variation

tag: infected with

value: Mock

value: leaf phloem


title: Nb_pSULTR22_Mock1


title: Nb_pSULTR22_Mock2


title: 1Plate1_A02_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_A03_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_A02_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: Nb_pSUC2_Mock1


title: Nb_p35S_Mock2

description: polysomal RNA from leaf tissue mock inoculated with sterile water

value: leaf


title: 1Plate1_A01_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_A01_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_A01_CD8_CMVtet


title: Nb_pSULTR22_TMV2

description: polysomal RNA from leaf phloem tissue inoculated with tobacco mosaic virus

value: Tobacco mosaic virus


title: SSB PAR-CLIP, RNase A

city: New York

first: Tasos

last: Gogakos

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description: 4SU-crosslinked RNA

data_processing:
Library strategy: PAR-CLIP-Seq
Barcoded samples (hydro-tRNAseq replicates 2-4) were demultiplexed by assigning by 5 nt barcodes using cutadapt. Adapters and barcodes were removed (cutadapt) from fastq files. Fastq files were converted to fasta using Perl scripts.
Fasta files were collapsed into a non-redundant fasta file in which the read count is contained within the read header and mapped against an in-house derived tRNA reference database based on predictions from GtRNAdb, http://gtrnadb.ucsc.edu . BWA was v0.5.9 used, with parameters aln -n 2 -t 16 -i 0 -d 0.
Multi-mapping reads are first assigned to hits with the lowest number of errors, then the count is split equally between the number of locations mapped.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-separated files. Columns represent in order: transcript name, RNA type, d0, d1, d2, and total mapped reads. All reads are split over the number of mapping positions. d0, d1, d2 refer to error distances of mapped reads with respect to reference (i.e., d0 has no mismatches, d1 and d2 have one and two mismatches, respectively). The read counts are raw.

source_name: HEK293 (Flp-In T-REx)

growth_protocol: Flp-In T-REx HEK293 cells (Invitrogen) were grown in high-glucose DMEM supplemented with 10% (v/v) fetal bovine serum (FBS), 1 mM sodium pyruvate, 100 U/mL penicillin, 100 µg/mL streptomycin, 100 µg/mL zeocin and 15 µg/mL blasticidin, at 37 °C, 95% humidity and 5% CO2. Cells were split using 0.05% Trypsin-EDTA.

extract_protocol:
Total RNA for sequencing was isolated using the TRIzol Reagent (Invitrogen) according to the manufacturer's instructions.
Crosslinked RNA was recovered as described previously (Garzia et al. 2016), with the exception that only the first RNase step was performed. In one of the two replicates (SSB_RNase_A), RNase T1 was replaced by RNase A.
For hydro-tRNAseq: 20 μg of 60-100 nt-sized total RNA were hydrolyzed in a 15 μL buffer of 10 mM in a 15 µL buffer of 10 mM Na2CO3 and 10 mM NaHCO3 at pH 9.7 either at 65 °C for 10 min (replicate 1) or 1 h (replicates 2-4). The partially hydrolyzed RNA was dephosphorylated with 10 U of calf intestinal phosphatase (NEB) in a 50 µL reaction of 100 mM NaCl, 50 mM Tris-HCl, pH 7.9 at 25 °C, 10 mM MgCl2, 1 mM DTT, 3 mM Na2CO3 and 3 mM NaHCO3, at 37 ºC for 1 h. The resulting RNA was re-phosphorylated with 10 U of T4 polynucleotide kinase (NEB) in a 20 µlL reaction of 70 mM Tris-HCl, pH 7.6, 10 mM MgCl2, 5 mM DTT and 1 mM ATP, at 37 °C for 1 h. Fragments of 19-35 nt were converted into barcoded small RNA cDNA libraries. Replicate 1 was run alone on a single lane with 3' adapter:TCGTATGCCGTCTTCTGCTTG. Replicates 2-4 were part of a barcoded library. 3' adapters used (5 first nts represent barcodes): replicate 2, TCACTTCGTATGCCGTCTTCTGCTTG; replicate 3, TCACTTCGTATGCCGTCTTCTGCTTG; replicate 4, TCTAGTCGTATGCCGTCTTCTGCTTG.
The recovered RNA was carried through a cDNA library preparation protocol as described previously (Garzia et al. 2016).

tag: cell line

value: HEK293 (Flp-In T-REx)

tag: 4su treatment

value: 100 uM for 16 hrs

tag: doxycycline induction

value: 1 ug/ mL for 24 hrs


title: Nb_p35S_Mock1


title: SSB PAR-CLIP, RNase T1

description: 4SU-crosslinked RNA


title: Nb_pSULTR22_TMV1


title: Nb_pSUC2_TMV2


title: hydro-tRNAseq, replicate 3

description:
Barcoded small RNA-seq
Size-fractionated RNA (~60-100 nt)

data_processing:
Barcoded samples (hydro-tRNAseq replicates 2-4) were demultiplexed by assigning by 5 nt barcodes using cutadapt. Adapters and barcodes were removed (cutadapt) from fastq files. Fastq files were converted to fasta using Perl scripts.
Fasta files were collapsed into a non-redundant fasta file in which the read count is contained within the read header and mapped against an in-house derived tRNA reference database based on predictions from GtRNAdb, http://gtrnadb.ucsc.edu . BWA was v0.5.9 used, with parameters aln -n 2 -t 16 -i 0 -d 0.
Multi-mapping reads are first assigned to hits with the lowest number of errors, then the count is split equally between the number of locations mapped.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-separated files. Columns represent in order: transcript name, RNA type, d0, d1, d2, and total mapped reads. All reads are split over the number of mapping positions. d0, d1, d2 refer to error distances of mapped reads with respect to reference (i.e., d0 has no mismatches, d1 and d2 have one and two mismatches, respectively). The read counts are raw.


title: hydro-tRNAseq, replicate 4


title: Nb_p35S_TMV2

description: polysomal RNA from leaf tissue inoculated with tobacco mosaic virus


title: B-Leaf-BN

city: Beijing

first: Junying

last: Liu

state: Beijing

address: yuan ming yuan weat road

department: Plant Pathology

country: China

institute: China Agricultural University

description: B-Leaf-BN: processed data "VL" columns

data_processing:
Illumina FastQC
ACGT101-miR (LC Sciences, Houston, Texas, USA)
miRBase21.0
RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi)
Genome_build: Beta vulgaris subsp. Vulgaris AYZS02000000
Supplementary_files_format_and_content: An Excel file includes identified miRNAs and their expression levels  in health and BNYVV-infected B. macrocarpa.

organism: Beta macrocarpa

source_name: leaf

growth_protocol: B. macrocarpa plants were grown in a controlled-environment chamber at 24 ± 1°C with 16 h of illumination per day.

extract_protocol:
Total RNAs were extracted from systemic leaves of virus-free and BNYVV-infected B. macrocarpa at 15 dpi using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. RNA integrity and size distribution were checked using a Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA) and agarose gel electrophoresis (1%). The RNA pool was prepared by mixing 20 μl of five RNA samples (1000 ng/μl) per group.
RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA)

treatment_protocol: BNYVV (RNAs 1+2+3+4+5) was an equal-volume mixture of total RNAs (1000 ng/μl) from ‘BN34’ (RNAs 1+2+3+4) preserved in our laboratory and in vitro transcripts of RNA5, and was rubbed onto B. macrocarpa leaves, with water as the control.

value: 5-leaf stage

tag: sample time

value: 15 dpi

tag: infection

value: Beet necrotic yellow vein virus

tag: leaf position

value: systemic leaves

tag: genotype

value: wild type


title: hydro-tRNAseq, replicate 2


title: Nb_p35S_TMV1


title: 1Plate1_E05_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: B-Leaf-MOCK

description: B-Leaf-MOCK; processed data "L" columns

value: mock


title: ChIP-seq from limb (ENCLB842GOO)

status: Public on Jul 16 2017

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR890ACP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR890ACP
assay title: ChIP-seq
possible controls: ENCSR687ALB
encode release date: 2016-07-12
lab: Bing Ren, UCSD
library encode accession: ENCLB842GOO
size range: 300-500

library_source: genomic

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

molecule: genomic DNA

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

tag: antibody

value: limb

value: tissue

tag: description

value: Limb from 69 embryonic 10.5 day mice

tag: biosample encode accession

tag: dev stage

value: embryonic

tag: Sex

value: pooled male and female

tag: lab

value: Len Pennacchio, LBNL

tag: link

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

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


title: ChIP-seq from limb (ENCLB768STI)

description:
https://www.encodeproject.org/experiments/ENCSR890ACP/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR890ACP
assay title: ChIP-seq
possible controls: ENCSR687ALB
encode release date: 2016-07-12
lab: Bing Ren, UCSD
library encode accession: ENCLB768STI
size range: 300-500

value: Limb from 51 embryonic 10.5 day mice

tag: age

tag: health state

value: healthy

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


title: ChIP-seq from heart left ventricle (ENCLB736KOR)

description:
https://www.encodeproject.org/experiments/ENCSR988JLN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR988JLN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR526EXI
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB736KOR
size range: 200-600

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

value: heart left ventricle

value: EnTEX:Heart - Left Ventricle

value: adult

value: female

value: 53 year

value: Bradley Bernstein, Broad

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

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


title: ChIP-seq from ascending aorta (ENCLB626HJU)

description:
https://www.encodeproject.org/experiments/ENCSR982QIF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR982QIF
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR494YJW
encode release date: 2017-06-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB626HJU
size range: 200-600

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

value: ascending aorta

value: tissue

value: EnTEX:Artery- Aorta

value: 51 year

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

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


title: ChIP-seq from uterus (ENCLB644JFK)

description:
https://www.encodeproject.org/experiments/ENCSR979XBX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR979XBX
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB644JFK
size range: 200-600

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

value: Control

value: uterus

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


title: ChIP-seq from thoracic aorta (ENCLB688ZDJ)

description:
https://www.encodeproject.org/experiments/ENCSR984KWT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR984KWT
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR158PLZ
encode release date: 2016-10-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB688ZDJ
size range: 200-600
nucleic acid starting quantity: 17.925
nucleic acid starting quantity units: ng

source_name: Homo sapiens thoracic aorta tissue male adult (37 years)

value: thoracic aorta

value: male

value: 37 year

value: ENCBS543OJU at ENCODE; https://www.encodeproject.org/ENCBS543OJU/

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


title: ChIP-seq from GM12878 (ENCLB267CFW)

description:
https://www.encodeproject.org/experiments/ENCSR982FSK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR982FSK
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR142REC
encode release date: 2016-11-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB267CFW
size range: 200-600
nucleic acid starting quantity: 23
nucleic acid starting quantity units: ng

source_name: Homo sapiens GM12878 immortalized cell line

tag: line

value: immortalized cell line

value: adult

value: female

value: unknown

tag: passage number

value: Bradley Bernstein, Broad

value: ENCBS900QPF at ENCODE; https://www.encodeproject.org/ENCBS900QPF/

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


title: ChIP-seq from uterus (ENCLB904QWG)

description:
https://www.encodeproject.org/experiments/ENCSR979XBX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR979XBX
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB904QWG
size range: 200-600

value: tissue

value: 53 year

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


title: ChIP-seq from tibial artery (ENCLB997DLM)

description:
https://www.encodeproject.org/experiments/ENCSR950CDM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR950CDM
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB997DLM
size range: 200-600

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

value: Control

value: tibial artery

value: EnTEX:Artery - Tibial

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


title: ChIP-seq from Peyer's patch (ENCLB075GJW)

description:
https://www.encodeproject.org/experiments/ENCSR982PLJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR982PLJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR124GAS
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB075GJW
size range: 200-600

source_name: Homo sapiens Peyer's patch tissue female adult (53 years)

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum

value: ENCBS766ILR at ENCODE; https://www.encodeproject.org/ENCBS766ILR/


title: ChIP-seq from A549 (ENCLB576JMI)

description:
https://www.encodeproject.org/experiments/ENCSR933MHJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR933MHJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB576JMI
size range: 200-600
nucleic acid starting quantity: 13.6
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line

value: immortalized cell line

value: 58 year

value: male

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

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

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


title: ChIP-seq from GM12878 (ENCLB584FZQ)

description:
https://www.encodeproject.org/experiments/ENCSR982FSK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR982FSK
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR142REC
encode release date: 2016-11-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB584FZQ
size range: 200-600
nucleic acid starting quantity: 22.4
nucleic acid starting quantity units: ng

value: adult

value: female

value: unknown

value: Bradley Bernstein, Broad

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

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


title: ChIP-seq from body of pancreas (ENCLB426EEB)

description:
https://www.encodeproject.org/experiments/ENCSR977CEC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR977CEC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR888RBQ
encode release date: 2016-10-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB426EEB
size range: 200-600

source_name: Homo sapiens body of pancreas tissue male adult (37 years)

value: body of pancreas

value: tissue

value: 37 year

value: ENCBS869MHP at ENCODE; https://www.encodeproject.org/ENCBS869MHP/

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


title: ChIP-seq from transverse colon (ENCLB554FUA)

description:
https://www.encodeproject.org/experiments/ENCSR933BVL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR933BVL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR828XQV
encode release date: 2017-01-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB554FUA
size range: 200-600

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

value: transverse colon

value: EnTEX:Colon - Transverse

value: 53 year

value: ENCBS765HGS at ENCODE; https://www.encodeproject.org/ENCBS765HGS/

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


title: ChIP-seq from A549 (ENCLB740QXD)

description:
https://www.encodeproject.org/experiments/ENCSR933MHJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR933MHJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB740QXD
size range: 200-600
nucleic acid starting quantity: 6.3
nucleic acid starting quantity units: ng

value: immortalized cell line

value: 58 year

value: male

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

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

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


title: ChIP-seq from vagina (ENCLB483YHJ)

description:
https://www.encodeproject.org/experiments/ENCSR962MYX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR962MYX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR620XWM
encode release date: 2017-01-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB483YHJ
size range: 200-600

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

value: vagina

value: adult

value: female

value: Bradley Bernstein, Broad

value: ENCBS047TWL at ENCODE; https://www.encodeproject.org/ENCBS047TWL/


title: ChIP-seq from thoracic aorta (ENCLB721HWL)

description:
https://www.encodeproject.org/experiments/ENCSR974OMC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR974OMC
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR158PLZ
encode release date: 2016-10-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB721HWL
size range: 200-600
nucleic acid starting quantity: 12.75
nucleic acid starting quantity units: ng

value: thoracic aorta

value: tissue

value: EnTEX:Artery- Aorta

value: 37 year

value: ENCBS543OJU at ENCODE; https://www.encodeproject.org/ENCBS543OJU/

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


title: hydro-tRNAseq, replicate 1

description:
Small RNA-seq
Size-fractionated RNA (~60-100 nt)

tag: cell line

value: HEK293 (Flp-In T-REx)

tag: 4su treatment


title: ChIP-seq from thyroid gland (ENCLB409QRH)

description:
https://www.encodeproject.org/experiments/ENCSR908DTR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR908DTR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR164POT
encode release date: 2016-05-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB409QRH
size range: 200-600
nucleic acid starting quantity: 545.9
nucleic acid starting quantity units: ng

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

value: thyroid gland

value: 54 year

value: ENCBS050AKF at ENCODE; https://www.encodeproject.org/ENCBS050AKF/

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


title: ChIP-seq from adrenal gland (ENCLB193KMB)

description:
https://www.encodeproject.org/experiments/ENCSR926NMC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR926NMC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR828HXJ
encode release date: 2016-06-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB193KMB
size range: 200-600

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

value: adrenal gland

value: EnTEX:Adrenal Gland

value: male

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


title: ChIP-seq from right atrium auricular region (ENCLB868TGI)

description:
https://www.encodeproject.org/experiments/ENCSR967KZJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR967KZJ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR195BZZ
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB868TGI
size range: 200-600

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

value: right atrium auricular region

value: EnTEX:Heart - Atrial Appendage

value: adult

value: Bradley Bernstein, Broad

value: 53 year

value: female

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

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


title: ChIP-seq from K562 (ENCLB654QVD)

description:
https://www.encodeproject.org/experiments/ENCSR915SJR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR915SJR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AKY
encode release date: 2017-01-31
lab: Bradley Bernstein, Broad
library encode accession: ENCLB654QVD
size range: 200-600
nucleic acid starting quantity: 16.4
nucleic acid starting quantity units: ng

source_name: Homo sapiens K562 immortalized cell line

value: immortalized cell line

value: chronic myelogenous leukemia (CML)

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

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


title: ChIP-seq from MCF-7 (ENCLB883DAD)

description:
https://www.encodeproject.org/experiments/ENCSR906IQU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR906IQU
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR768LHG
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB883DAD
size range: 200-600
nucleic acid starting quantity: 486.2
nucleic acid starting quantity units: ng

source_name: Homo sapiens MCF-7 immortalized cell line

value: mammary epithelium, doubling time ~ 29hoursATCC HTB-22

value: 69 year

value: breast cancer (adenocarcinoma)

value: ENCBS967MVZ at ENCODE; https://www.encodeproject.org/ENCBS967MVZ/

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


title: ChIP-seq from gastrocnemius medialis (ENCLB965OIZ)

description:
https://www.encodeproject.org/experiments/ENCSR899TDF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR899TDF
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR001UFN
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB965OIZ
size range: 200-600

source_name: Homo sapiens gastrocnemius medialis tissue female adult (53 years)

value: gastrocnemius medialis

value: tissue

value: i.e. REMC 6, 13, 14 and 15; EnTEX:Muscle - Skeletal

value: adult

value: ENCBS866HOM at ENCODE; https://www.encodeproject.org/ENCBS866HOM/


title: ChIP-seq from A549 (ENCLB133LGP)

description:
https://www.encodeproject.org/experiments/ENCSR892DRK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR892DRK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB133LGP
size range: 200-600
nucleic acid starting quantity: 2.1
nucleic acid starting quantity units: ng

value: REST

value: Bradley Bernstein, Broad

value: 58 year

value: male

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

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

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


title: ChIP-seq from esophagus squamous epithelium (ENCLB926RHQ)

description:
https://www.encodeproject.org/experiments/ENCSR909UAG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR909UAG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR652EPR
encode release date: 2016-11-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB926RHQ
size range: 200-600

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

value: esophagus squamous epithelium

value: EnTEX:Esophagus - Mucosa

value: female

value: 53 year

value: ENCBS054JUC at ENCODE; https://www.encodeproject.org/ENCBS054JUC/

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


title: ChIP-seq from A549 (ENCLB804HNS)

description:
https://www.encodeproject.org/experiments/ENCSR892DRK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR892DRK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB804HNS
size range: 200-600
nucleic acid starting quantity: 6.7
nucleic acid starting quantity units: ng

value: immortalized cell line

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


title: ChIP-seq from body of pancreas (ENCLB842YLY)

description:
https://www.encodeproject.org/experiments/ENCSR903GLL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR903GLL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR833HBT
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB842YLY
size range: 200-600

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

value: body of pancreas

value: tissue

value: adult

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


title: ChIP-seq from heart left ventricle (ENCLB132WBF)

description:
https://www.encodeproject.org/experiments/ENCSR901SIL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR901SIL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR526EXI
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB132WBF
size range: 200-600

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

value: heart left ventricle

value: EnTEX:Heart - Left Ventricle

value: Bradley Bernstein, Broad

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


title: ChIP-seq from bipolar neuron (ENCLB283SNO)

description:
https://www.encodeproject.org/experiments/ENCSR886KKK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR886KKK
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR001KCX
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB283SNO
size range: 200-600

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

value: bipolar neuron

value: in vitro differentiated cells

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

value: male

value: Thomas Gingeras, CSHL

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

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


title: total RNA-seq from erythroid progenitor cell (ENCLB773MPI)

description:
https://www.encodeproject.org/experiments/ENCSR847AMQ/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse CFU-E 100ng rRNA-depleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR847AMQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-01-04
lab: Ross Hardison, PennState
library encode accession: ENCLB773MPI
size range: 209-891
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

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

value: erythroid progenitor cell

value: primary cell

value: Ross Hardison, PennState

value: 5-6 week

value: unknown

value: ENCBS820CJW at ENCODE; https://www.encodeproject.org/ENCBS820CJW/

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


title: ChIP-seq from K562 (ENCLB487ERN)

description:
https://www.encodeproject.org/experiments/ENCSR915SJR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR915SJR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AKY
encode release date: 2017-01-31
lab: Bradley Bernstein, Broad
library encode accession: ENCLB487ERN
size range: 200-600
nucleic acid starting quantity: 17.74
nucleic acid starting quantity units: ng

value: immortalized cell line

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: female

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

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


title: ChIP-seq from H1-hESC (ENCLB059LGY)

description:
https://www.encodeproject.org/experiments/ENCSR882AWL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR882AWL
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR000AMI
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB059LGY
size range: 200-600

source_name: Homo sapiens H1-hESC stem cell male embryo

value: stem cell

value: embryonic

value: male

value: healthy

value: Bradley Bernstein, Broad

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

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


title: ChIP-seq from bipolar neuron (ENCLB430DDM)

description:
https://www.encodeproject.org/experiments/ENCSR886KKK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR886KKK
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR001KCX
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB430DDM
size range: 200-600

value: bipolar neuron

value: in vitro differentiated cells

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

value: Thomas Gingeras, CSHL

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

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


title: WGBS from embryonic facial prominence (ENCLB249RES)

description:
https://www.encodeproject.org/experiments/ENCSR993XPD/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR993XPD
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB249RES
size range: 180-500

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

value: embryonic facial prominence

value: tissue

value: Craniofacial prominence from 51 embryonic 10.5 day mice

value: pooled male and female

value: Len Pennacchio, LBNL

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

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


title: ChIP-seq from H1-hESC (ENCLB762VPL)

description:
https://www.encodeproject.org/experiments/ENCSR882AWL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR882AWL
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR000AMI
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB762VPL
size range: 200-600
nucleic acid starting quantity: 25.4
nucleic acid starting quantity units: ng

value: stem cell

value: embryonic

value: male

value: unknown

value: healthy

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


title: WGBS from embryonic facial prominence (ENCLB353APJ)

description:
https://www.encodeproject.org/experiments/ENCSR993XPD/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR993XPD
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB353APJ
size range: 180-500


title: ChIP-seq from upper lobe of left lung (ENCLB813VIH)

description:
https://www.encodeproject.org/experiments/ENCSR869GBP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR869GBP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR422TGJ
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB813VIH
size range: 200-600

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

value: upper lobe of left lung

value: adult

value: Bradley Bernstein, Broad

value: 53 year

value: female

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

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


title: WGBS from embryonic facial prominence (ENCLB408PAW)

description:
https://www.encodeproject.org/experiments/ENCSR993XPD/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR993XPD
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB408PAW
size range: 180-500

value: embryonic facial prominence

value: tissue

value: Craniofacial prominence from 69 embryonic 10.5 day mice

value: pooled male and female

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


title: ChIP-seq from thyroid gland (ENCLB483WUJ)

description:
https://www.encodeproject.org/experiments/ENCSR855XNQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR855XNQ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR475NOQ
encode release date: 2016-11-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB483WUJ
size range: 200-600

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

value: thyroid gland

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


title: WGBS from forebrain (ENCLB475UZJ)

description:
https://www.encodeproject.org/experiments/ENCSR888JFA/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR888JFA
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB475UZJ
size range: 180-500

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

value: forebrain

value: Forebrain from 51 embryonic 10.5 day mice

value: embryonic

value: Len Pennacchio, LBNL

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

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


title: total RNA-seq from erythroid progenitor cell (ENCLB575TRR)

description:
https://www.encodeproject.org/experiments/ENCSR847AMQ/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse CFU-E 100ng rRNA-depleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR847AMQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-01-04
lab: Ross Hardison, PennState
library encode accession: ENCLB575TRR
size range: 186-747
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: erythroid progenitor cell

value: primary cell

value: adult

value: Ross Hardison, PennState

value: 5-6 week

value: unknown

value: male

value: ENCBS074PZK at ENCODE; https://www.encodeproject.org/ENCBS074PZK/

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


title: ChIP-seq from upper lobe of left lung (ENCLB592IFV)

description:
https://www.encodeproject.org/experiments/ENCSR859MXQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR859MXQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR422TGJ
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB592IFV
size range: 200-600

value: upper lobe of left lung

value: tissue

value: Bradley Bernstein, Broad

value: 53 year

value: female

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

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


title: ChIP-seq from body of pancreas (ENCLB519VLC)

description:
https://www.encodeproject.org/experiments/ENCSR863TAL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR863TAL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR099LGH
encode release date: 2016-10-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB519VLC
size range: 200-600

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

value: body of pancreas

value: 54 year

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

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


title: WGBS from embryonic facial prominence (ENCLB967XOG)

description:
https://www.encodeproject.org/experiments/ENCSR993XPD/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR993XPD
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB967XOG
size range: 180-500

value: embryonic facial prominence

value: Craniofacial prominence from 69 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

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

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


title: WGBS from forebrain (ENCLB760COS)

description:
https://www.encodeproject.org/experiments/ENCSR888JFA/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR888JFA
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB760COS
size range: 180-500

value: forebrain

value: tissue

value: Forebrain from 51 embryonic 10.5 day mice

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


title: WGBS from forebrain (ENCLB699WSH)

description:
https://www.encodeproject.org/experiments/ENCSR888JFA/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR888JFA
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB699WSH
size range: 180-500

value: Forebrain from 69 embryonic 10.5 day mice

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


title: ChIP-seq from H1-hESC (ENCLB103ROT)

description:
https://www.encodeproject.org/experiments/ENCSR853NNZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR853NNZ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR000AMI
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB103ROT
size range: 200-600
nucleic acid starting quantity: 33.2
nucleic acid starting quantity units: ng

value: stem cell

value: male

value: unknown

value: Bradley Bernstein, Broad

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

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


title: ChIP-seq from heart left ventricle (ENCLB818WJB)

description:
https://www.encodeproject.org/experiments/ENCSR854OXF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR854OXF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR526EXI
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB818WJB
size range: 200-600

value: heart left ventricle

value: EnTEX:Heart - Left Ventricle

value: adult

value: female

value: 53 year

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

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


title: ChIP-seq from H1-hESC (ENCLB225PWG)

description:
https://www.encodeproject.org/experiments/ENCSR853NNZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR853NNZ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR000AMI
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB225PWG
size range: 200-600
nucleic acid starting quantity: 69.4
nucleic acid starting quantity units: ng

value: embryonic

value: healthy

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


title: WGBS from forebrain (ENCLB595QSS)

description:
https://www.encodeproject.org/experiments/ENCSR888JFA/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR888JFA
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB595QSS
size range: 180-500

value: forebrain

value: tissue

value: Forebrain from 69 embryonic 10.5 day mice

value: pooled male and female

value: Len Pennacchio, LBNL

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

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


title: NRPD1FL_rep2

city: Bloomington

first: Jered

last: Wendte

state: IN

address: 915 E. 3rd Street

institute: Indiana University

description: Index 13

data_processing:
Reads were trimmed of adapters and filtered for size and quality using cutadapt v. 1.91. with the commands: cutadapt -a TGGAATTCTCGGGTGCCAAG -q 20 -m 15 -M60
Reads were first filtered of all structural RNAs (tRNAs, rRNAs, snRNAs, and snoRNAs) by mapping to a genome consisting of sequences corresponding to all genomic coordinates identified as structural RNAs on TAIR (www.arabidopsis.org) using bowtie2 default commands. All unmapped reads were saved for further analysis.
Filtered and cleaned reads were mapped to the Arabidopsis TAIR10 genome using ShortStack version 3.4 default settings.  Regions classified as 24 nt siRNA clusters in both Col-0 samples with a minimum read coverage of 24 nt were analysed for expression in each line
sRNA counts for regions of interest were extracted from bam files using the ShortStack --locifile file function.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab delimited text file of raw read counts for 24 nt siRNA clusters

organism: Arabidopsis thaliana

source_name: 2.5 week above ground tissues

growth_protocol: Plants were grown in soil in long day conditions (16 hours light, 8 hours dark)

extract_protocol:
RNA was extracted using Trizol
Libraries were constructed using the Illumina TruSeq Small RNA Library prep kit with the size selection step expanded to 16-60 nt.

tag: ecotype

tag: mutant

tag: transgene


title: WGBS from heart (ENCLB504HAF)

description:
https://www.encodeproject.org/experiments/ENCSR835OJU/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR835OJU
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB504HAF
size range: 180-500

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

value: heart

value: Heart from 51 embryonic 10.5 day mice

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


title: ChIP-seq from stomach (ENCLB809SOQ)

description:
https://www.encodeproject.org/experiments/ENCSR903QBX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR903QBX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR539HNK
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB809SOQ
size range: 200-600

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

value: stomach

value: adult

value: Bradley Bernstein, Broad

value: female

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


title: ChIP-seq from tibial nerve (ENCLB758XBL)

description:
https://www.encodeproject.org/experiments/ENCSR850RVA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR850RVA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR154SJE
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB758XBL
size range: 200-600

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

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: 53 year

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

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


title: ChIP-seq from sigmoid colon (ENCLB149DLQ)

description:
https://www.encodeproject.org/experiments/ENCSR900UIP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR900UIP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR844YME
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB149DLQ
size range: 200-600

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

value: sigmoid colon

value: tissue

value: EnTEX:Colon - Sigmoid

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


title: Col_rep2

description: Index 23


title: WGBS from heart (ENCLB289ILB)

description:
https://www.encodeproject.org/experiments/ENCSR835OJU/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR835OJU
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB289ILB
size range: 180-500

value: heart

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

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


title: WGBS from heart (ENCLB849EOC)

description:
https://www.encodeproject.org/experiments/ENCSR835OJU/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR835OJU
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB849EOC
size range: 180-500

value: Heart from 69 embryonic 10.5 day mice

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


title: WGBS from heart (ENCLB950YGL)

description:
https://www.encodeproject.org/experiments/ENCSR835OJU/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR835OJU
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB950YGL
size range: 180-500


title: ChIP-seq from GM12878 (ENCLB064KHY)

description:
https://www.encodeproject.org/experiments/ENCSR849WCQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR849WCQ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR142REC
encode release date: 2017-01-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB064KHY
size range: 200-600
nucleic acid starting quantity: 4.0
nucleic acid starting quantity units: ng

source_name: Homo sapiens GM12878 immortalized cell line

value: immortalized cell line

value: adult

value: female

value: unknown

value: Bradley Bernstein, Broad

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

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


title: NRPD1FL_rep1

description: Index 11


title: ChIP-seq from sigmoid colon (ENCLB828XIB)

description:
https://www.encodeproject.org/experiments/ENCSR844YME/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR844YME
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB828XIB
size range: 200-600

value: Control

value: sigmoid colon

value: tissue

value: EnTEX:Colon - Sigmoid

value: 53 year

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


title: WGBS from midbrain (ENCLB540HFM)

description:
https://www.encodeproject.org/experiments/ENCSR803ICQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR803ICQ
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB540HFM
size range: 180-500

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

value: midbrain

value: Midbrain from 51 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

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


title: Col_rep1

description: Index 7


title: WGBS from midbrain (ENCLB868LIT)

description:
https://www.encodeproject.org/experiments/ENCSR803ICQ/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR803ICQ
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB868LIT
size range: 180-500

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


title: WGBS from midbrain (ENCLB380OJS)

description:
https://www.encodeproject.org/experiments/ENCSR803ICQ/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR803ICQ
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB380OJS
size range: 180-500

value: Midbrain from 69 embryonic 10.5 day mice

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


title: NRPE1FL rep2

description: Index 8

data_processing:
Base-calling, adapter trimming, and size selection (>35bp) was completed with bcl2fastq v2.16.0.10
Methylation end bias was removed and reads were quality filtered using cutadapt v. 1.9.1 with the commands: cutadapt -U 7 -u 2 -q 25
Filtered reads were mapped to the TAIR10 genome and mapped reads were deduplicated using Bismark 0.16.1 using default settings.
Methylation status of each cytosine was extracted from mapped reads using Bismark_methylation_extractor with the commands: bismark_methylation_extractor -p --bedGraph --CX -cutoff 5 --cytosine_report --CX
Methylation status of each cytosine in the CHH context was extracted from the bismark_methylation_extractor output and used as input to the R package, methylkit v. 0.9.5 to define differentially methylated regions (DMRs) relative to Col-0. The genome was split into 300 base pair sliding windows with a step size of 200 base pairs and a minimum coverage requirement for each window of 10 informative cytosines with at least 5 read coverage each. Only regions that had coverage in each sample were utilized for calculation of DMRs. Significant hypo-DMRs were defined as those regions with a minimum 10% or 25% decrease in methylation relative to Col-0 and a q-value of less than or equal to 0.01.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab delimited text files that include methylation status of cytosines in the CHH context with at least 5 read coverage. Format for input to R package methylkit

growth_protocol: Plants were grown in soil in long day conditions (16h light, 8 hours dark)

extract_protocol:
CTAB extraction of genomic DNA from 2.5 week above ground tissues
Illumina TruSeq DNA methylation Kit (product number: EGMK81312)

treatment_protocol: Transgenic lines were selected for by spraying with Basta herbicide

tag: mutant background


title: ChIP-seq from transverse colon (ENCLB242TQJ)

description:
https://www.encodeproject.org/experiments/ENCSR828XQV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR828XQV
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB242TQJ
size range: 200-600

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

tag: antibody

value: transverse colon

value: EnTEX:Colon - Transverse

value: adult

value: Bradley Bernstein, Broad

value: female

value: ENCBS765HGS at ENCODE; https://www.encodeproject.org/ENCBS765HGS/


title: nrpd1dDeCL_rep2

description: Index 19


title: ChIP-seq from transverse colon (ENCLB054LWD)

description:
https://www.encodeproject.org/experiments/ENCSR840VWD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR840VWD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR828XQV
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB054LWD
size range: 200-600

value: tissue

tag: description

value: 53 year

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


title: ChIP-seq from body of pancreas (ENCLB082ODG)

description:
https://www.encodeproject.org/experiments/ENCSR833HBT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR833HBT
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB082ODG
size range: 200-600

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

value: Control

value: body of pancreas

tag: biosample encode accession

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


title: nrpd1-3_rep1

description: Index 8


title: ChIP-seq from Peyer's patch (ENCLB415JQU)

description:
https://www.encodeproject.org/experiments/ENCSR837SGJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR837SGJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR124GAS
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB415JQU
size range: 200-600

source_name: Homo sapiens Peyer's patch tissue female adult (53 years)

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum

tag: dev stage

value: ENCBS766ILR at ENCODE; https://www.encodeproject.org/ENCBS766ILR/


title: WGBS from midbrain (ENCLB569KIZ)

description:
https://www.encodeproject.org/experiments/ENCSR803ICQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR803ICQ
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB569KIZ
size range: 180-500

value: midbrain

value: Midbrain from 69 embryonic 10.5 day mice

value: embryonic

tag: Sex

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

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


title: ChIP-seq from transverse colon (ENCLB617ECJ)

description:
https://www.encodeproject.org/experiments/ENCSR828XQV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR828XQV
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB617ECJ
size range: 200-600

value: transverse colon

value: EnTEX:Colon - Transverse

value: adult

tag: lab

value: Bradley Bernstein, Broad

value: female

value: ENCBS765HGS at ENCODE; https://www.encodeproject.org/ENCBS765HGS/


title: ChIP-seq from MCF-7 (ENCLB308JHC)

description:
https://www.encodeproject.org/experiments/ENCSR906IQU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR906IQU
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR768LHG
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB308JHC
size range: 200-600
nucleic acid starting quantity: 5.876
nucleic acid starting quantity units: ng

source_name: Homo sapiens MCF-7 immortalized cell line

value: immortalized cell line

value: mammary epithelium, doubling time ~ 29hoursATCC HTB-22

value: 69 year

value: breast cancer (adenocarcinoma)

tag: link

value: ENCBS789UPK at ENCODE; https://www.encodeproject.org/ENCBS789UPK/

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


title: ChIP-seq from GM12878 (ENCLB624UVT)

description:
https://www.encodeproject.org/experiments/ENCSR849WCQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR849WCQ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR142REC
encode release date: 2017-01-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB624UVT
size range: 200-600
nucleic acid starting quantity: 22.6
nucleic acid starting quantity units: ng

tag: age

value: unknown

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

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


title: nrpd1-3_rep2

description: Index 9


title: NRPE1FL rep1

description: Index 4


title: nrpd1dDeCL rep2

description: Index 7


title: ChIP-seq from B cell (ENCLB728KKD)

description:
https://www.encodeproject.org/experiments/ENCSR878JSF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR878JSF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR805DRF
encode release date: 2016-11-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB728KKD
size range: 200-600

source_name: Homo sapiens B primary cell female adult (43 years)

value: B cell

value: primary cell

value: 43 year

tag: health state

value: normal

value: ENCBS098ETX at ENCODE; https://www.encodeproject.org/ENCBS098ETX/

value: Derived from ENCODE donor ENCDO114AAA; https://www.encodeproject.org/ENCDO114AAA/


title: nrpd1dDeCL_rep1

description: Index 15


title: ChIP-seq from B cell (ENCLB214ZQY)

description:
https://www.encodeproject.org/experiments/ENCSR878JSF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR878JSF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR805DRF
encode release date: 2016-11-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB214ZQY
size range: 200-600

value: adult

value: female

value: Bradley Bernstein, Broad


title: nrpd1dDeCL rep1

description: Index 3


title: ChIP-seq from A549 (ENCLB807XEG)

description:
https://www.encodeproject.org/experiments/ENCSR817JZD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR817JZD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB807XEG
size range: 200-600
nucleic acid starting quantity: 9.8
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line

tag: line

value: immortalized cell line

value: 58 year

value: male

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

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

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


title: ChIP-seq from A549 (ENCLB459IVE)

description:
https://www.encodeproject.org/experiments/ENCSR817JZD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR817JZD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB459IVE
size range: 200-600
nucleic acid starting quantity: 9.16
nucleic acid starting quantity units: ng

tag: passage number

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


title: nrpd1-3 rep1

description: Index 2


title: 54

status: Public on Jul 15 2017

city: balice

first: Maria

last: Oczkowicz

state: malopolskie

address: krakowska 1

country: Poland

institute: National Reseach Institute of Animal Production

data_processing:
demultiplexing of samples (bcl2fastq)
quality check (fastQC)
trimming of reads (flexbar)
mapping of reads (tophat)
mapping statistics (samstat, RSeQC, RSEM) and counting of reads (HTSeq)
Genome_build: Sus scrofa 10.2

organism: Sus scrofa

source_name: (+DDGS+coconut oil)_backfat

extract_protocol:
Total RNA was isolated using "Direct-zol RNA" kit (Zymoresearch)
Libraries construction was performed using The SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara, Clontech)according to the protocol. RNA libraries were prepared for sequencing using standard Illumina protocols

tag: diet

value: (+DDGS+coconut oil)

tag: tissue

value: backfat


title: 55


title: nrpd1-3 rep2

description: Index 6

tag: ecotype


title: ChIP-seq from sigmoid colon (ENCLB492WEH)

description:
https://www.encodeproject.org/experiments/ENCSR812POE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR812POE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR844YME
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB492WEH
size range: 200-600

value: sigmoid colon

value: tissue

value: EnTEX:Colon - Sigmoid

value: 53 year

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

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


title: ChIP-seq from thoracic aorta (ENCLB571ZNZ)

description:
https://www.encodeproject.org/experiments/ENCSR803IBD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR803IBD
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR158PLZ
encode release date: 2016-10-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB571ZNZ
size range: 200-600

source_name: Homo sapiens thoracic aorta tissue male adult (37 years)

value: thoracic aorta

value: EnTEX:Artery- Aorta

value: adult

value: 37 year

value: ENCBS882JUX at ENCODE; https://www.encodeproject.org/ENCBS882JUX/

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


title: 48

value: male

value: (+DDGS+beeftallow)


title: 53

value: female


title: 43


title: 52

value: (+DDGS+coconut oil)


title: 49

value: backfat


title: 45


title: 41


title: ChIP-seq from sigmoid colon (ENCLB132QZW)

description:
https://www.encodeproject.org/experiments/ENCSR844YME/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR844YME
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB132QZW
size range: 200-600

value: Control

value: sigmoid colon

value: Bradley Bernstein, Broad


title: 24

source_name: (+DDGS+rapeseed oil)_backfat

value: (+DDGS+rapeseed oil)


title: 20


title: 22


title: 19


title: 8

source_name: (-DDGS+rapeseed oil)_backfat

value: (-DDGS+rapeseed oil)


title: 7


title: 3


title: 5


title: 2


title: 46


title: 1


title: Alpha-H2az-Rep2

city: Sherbrooke

first: Jean-Francois

last: Lucier

state: Quebec

address: 2500, boulevard de l'Université

department: Département de Biologie

country: Canada

institute: Université de Sherbrooke

description: ChIP antibody raised against CSLIGKKGQQKT

data_processing:
We based the analyses of H2AZ ChIP-Seq data on the ChIP-seq pipeline version 1.4 developed by MUGQIC. Briefly the raw reads were trimmed as for RNA-Seq reads, then aligned onto hg19 using BWA 0.7.5a with default parameters, then filtered on alignment quality using Samtools 0.1.19 with the settings view -F4 -q 20 [5]. The two biological replicates per condition were then combined using makeTagDirectory from Homer 4.7 [6]. The signal density files in BedGraph were generated using Homer 4.7 and the default settings of the command makeUCSCfile [6]. Narrow peak summits were determined using MACS2 version 2.0.10 [7] with default parameters except --fix-bimodal -f BAMPE.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: Colorectal carcinoma cells

growth_protocol: HCT116 were collected in exponential growth phase

extract_protocol:
ChIP were performed as described in Gevry N, Chan HM, Laflamme L, Livingston DM, Gaudreau L. p21 transcription is regulated by differential localization of histone H2A.Z. Genes & development. 2007;21(15):1869-81. PubMed PMID: 17671089 except for the following steps. For each treatment conditions six immuno-precipitations were performed. Immuno-precipitations were performed using Dynabeads coupled to protein A (Life Technologies) without pre-clearing.
The libraries for deep-sequencing were prepared from 10 ng ChIPed DNA using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s protocol

treatment_protocol: 250 nM daunorubicin or alpha amanitin 8 mM 8h or vehicle for non-treated

tag: cell line

tag: cell type

value: Colorectal carcinoma

value: colon

tag: culture

value: Collected in exponential growth phase

value: Epithelial


title: Dau-H2az-Rep2


title: Alpha-H2az-Rep1


title: NT-H2az-Rep1


title: Dau-H2az-Rep1


title: 21


title: NT-H2az-Rep2


title: 6


title: sav3_wHyp3h replicate-3

city: La Jolla

first: Joanne

last: Chory

state: California

address: 10010 N Torrey Pines RD

department: Plant Biology Laboratory

institute: Salk Institute for Biological Studies

data_processing:
base calling was done by RTA 1.17.20 (Illumina, CA)
demultiplexing was done by CASAVA 1.8.2 (Illumina, CA)
Sequenced reads were trimmed for adaptor sequence, then aligned to TAIR10 whole genome build using Tophat2 v2.0.8b (Kim et al. 2013 Genome Biology) on a Linux platform
FPKM were calculated for each sample using Cufflinks 2.1.1 (Trapnell et al. 2012 Nature Protocols) with parameters -u --compatible-hits-norm -G parameters on a Linux platform
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: sav3-2_hypocotyl_high R:FR_3h

growth_protocol: Seeds of the indicated genotype was stratified for 2 days in the cold and then was grown on 0.5x Linsmaier and Skoog medium under 16hL 8hD conditions at 22°C.

extract_protocol:
RNeasy Micro kit (Qiagen)
Truseq RNA Sample prep kit v2 Cat# RS-122-2001 and RS-122-2002 (Illumina, CA)

treatment_protocol: 5 day old white high R:FR grown seedlings were treated low R:FR or mock treated (high R:FR) for indicated times

value: Columbia

tag: genotype/variation

tag: exposed to

value: high R:FR

tag: treatment time

value: hypocotyl tissue


title: sav3_wCot3h replicate-2

source_name: sav3-2_cotyledon_high R:FR_3h

value: cotyledon


title: ChIP-seq from thyroid gland (ENCLB011KWB)

description:
https://www.encodeproject.org/experiments/ENCSR901BRV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR901BRV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR777VQP
encode release date: 2016-05-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB011KWB
size range: 200-600

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

tag: antibody

value: thyroid gland

value: tissue

tag: description

tag: biosample encode accession

tag: dev stage

value: adult

value: male

value: 37 year

value: ENCBS522TJW at ENCODE; https://www.encodeproject.org/ENCBS522TJW/

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


title: sav3_sCot3h replicate-1

source_name: sav3-2_cotyledon_low R:FR_3h

value: low R:FR


title: pif7_wCot3h replicate-2

source_name: pif7-1_cotyledon_high R:FR_3h


title: pif7_wHyp3h replicate-2

source_name: pif7-1_hypocotyl_high R:FR_3h


title: sav3_sHyp3h replicate-2

source_name: sav3-2_hypocotyl_low R:FR_3h


title: sav3_wCot3h replicate-3


title: sav3_sCot3h replicate-2


title: pif7_wCot3h replicate-1


title: sav3_sHyp3h replicate-1


title: pif7_wHyp3h replicate-1


title: sav3_sCot3h replicate-3


title: sav3_sHyp3h replicate-3


title: pif7_sHyp3h replicate-1

source_name: pif7-1_hypocotyl_low R:FR_3h


title: sav3_wCot3h replicate-1


title: pif7_sCot3h replicate-1

source_name: pif7-1_cotyledon_low R:FR_3h


title: sCot7h replicate-2

source_name: WT_cotyledon_low R:FR_7h

value: WT


title: sav3_wHyp3h replicate-2


title: pif7_sHyp3h replicate-2


title: sCot4h replicate-2

source_name: WT_cotyledon_low R:FR_4h


title: sav3_wHyp3h replicate-1


title: sCot4h replicate-1


title: sCot3h replicate-2

source_name: WT_cotyledon_low R:FR_3h


title: sCot30m replicate-2

source_name: WT_cotyledon_low R:FR_0.5h


title: pif7_sCot3h replicate-2


title: sCot7h replicate-1


title: sCot2h replicate-2

source_name: WT_cotyledon_low R:FR_2h


title: sCot2h replicate-1


title: sCot1h replicate-2

source_name: WT_cotyledon_low R:FR_1h


title: sCot1h replicate-1


title: sCot3h replicate-1


title: 17

source_name: (+DDGS+rapeseed oil)_backfat

tag: Sex

value: female

value: (+DDGS+rapeseed oil)

value: backfat


title: sCot30m replicate-1


title: wCot3h replicate-2

source_name: WT_cotyledon_high R:FR_3h


title: wCot30m replicate-2

source_name: WT_cotyledon_high R:FR_0.5h


title: sHyp30m replicate-2

source_name: WT_hypocotyl_low R:FR_0.5h


title: sHyp7h replicate-1

source_name: WT_hypocotyl_low R:FR_7h


title: wCot30m replicate-1


title: sHyp4h replicate-1

source_name: WT_hypocotyl_low R:FR_4h


title: sHyp4h replicate-2


title: sHyp1h replicate-2

source_name: WT_hypocotyl_low R:FR_1h


title: sHyp2h replicate-1

source_name: WT_hypocotyl_low R:FR_2h


title: sHyp1h replicate-1


title: sHyp3h replicate-2

source_name: WT_hypocotyl_low R:FR_3h


title: sHyp3h replicate-1


title: sHyp2h replicate-2


title: wCot4h replicate-1

source_name: WT_cotyledon_high R:FR_4h


title: wCot2h replicate-2

source_name: WT_cotyledon_high R:FR_2h


title: wCot7h replicate-1

source_name: WT_cotyledon_high R:FR_7h


title: wCot4h replicate-2


title: wCot2h replicate-1


title: wCot7h replicate-2


title: wCot3h replicate-1


title: wCot0h replicate-2

source_name: WT_cotyledon_high R:FR_0h


title: wHyp7h replicate-2

source_name: WT_hypocotyl_high R:FR_7h


title: wCot0h replicate-1


title: wCot1h replicate-2

source_name: WT_cotyledon_high R:FR_1h


title: wCot1h replicate-1


title: wHyp4h replicate-2

source_name: WT_hypocotyl_high R:FR_4h


title: wHyp7h replicate-1


title: wHyp30m replicate-2

source_name: WT_hypocotyl_high R:FR_0.5h


title: wHyp3h replicate-2

source_name: WT_hypocotyl_high R:FR_3h


title: wHyp3h replicate-1


title: wHyp2h replicate-2

source_name: WT_hypocotyl_high R:FR_2h


title: wHyp4h replicate-1


title: wHyp1h replicate-1

source_name: WT_hypocotyl_high R:FR_1h


title: wHyp30m replicate-1


title: wHyp1h replicate-2


title: wHyp2h replicate-1


title: Lphn2-siRNA-4 Rep 2

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Raw data files were trimmed using trimmomatic
Reads were then mapped to the genome using STAR.
FeatureCounts v1.5.0-p1 was used to assign reads to genes from the Gencode v19 annotation.
raw counts were send to DEseq2 for normalization and were used for pairwise comparison
Genome_build: hg19
Supplementary_files_format_and_content: xlsx

source_name: HUVEC

growth_protocol: Human umbilical vein endothelial cells (HUVEC) were obtained from Lonza and cultured on dishes coated with 30 µg/ml Collagen (Corning) in EBM-2 medium supplemented with EGM-2 SingleQuot Kit Suppl. & Growth Factors (both Lonza). For endothelial activation, HUVEC were stimulated with 10 ng/ml human recombinant TNF-a (Peprotech) for 10h.

extract_protocol:
RNA for cell pool Nanostring analysis and RNA sequencing was isolated with the RNeasy Micro Kit (Qiagen) according to the corresponding manufacturer`s instructions. For RNA-seq, DNA was digested on-column with DNaseI digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
RNA and library preparation integrity were verified with a BioAnalyzer 2100 (Agilent) or LabChip Gx Touch 24 (Perkin Elmer). 2µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry

treatment_protocol: siRNA for human LPHN2 (Hs_LPHN2_2, target sequence: AAGCTGGTTGACACTAATAAA; Hs_LPHN2_4, target sequence: TCGCCAAACAACAACATATAA)  and AllStars negative control siRNA were obtained from Quiagen. 8x104/ml HUVECs were cultured in 24- or 96-well plates and transfected with 28.5 nM of the corresponding siRNA using RNAiMax lipofectamine (Invitrogen). Gene expression analysis and adhesion assays were conducted 82 h after transfection.

value: umbilical vein

tag: origin

value: endothelial cell


title: wHyp0h replicate-1

source_name: WT_hypocotyl_high R:FR_0h

value: Columbia

value: high R:FR


title: MDCK_2 cm_3d

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: MDCK cells with no pressure

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the dog reference genome sequences (CanFam3.1) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: text file with FPKM

organism: Canis lupus familiaris

source_name: MDCK cells cultured in 2-cm-high medium

growth_protocol: MDCK cells (40000 cells) were plated into a culture insert placed in a 6-well plate and cultured in EMEM containing 10% FCS for 3 days.

extract_protocol:
RNA was prepared from each MDCK cells (2-5x10^6 cells) by the miRNeasy Isolation kit.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: MDCK cells were cultured using the water pressure-loadable two-chamber culture system, as described in Molecular Neurobiology by Yoneshige et al (DOI: 10.1007/s12035-016-0166-y).

tag: treatment

value: 2 cmH2O

value: MDCK


title: Lphn2-siRNA-2 Rep 2


title: Lphn2-siRNA-4 Rep 1


title: pMIR-Sox2_rep1

first: Jayanta

last: Chaudhuri

address: 415 E 68th Street Z-1464

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

description:
replicate 1
Sox2_8

data_processing:
Raw reads were trimmed and clipped for quality control in Trimmomatic v0.32 with standard settings to remove low-quality reads and adaptor contamination
Trimmed reads were aligned to the mouse genome using TopHat2 v2.0.11 implementing Bowtie2 v2.2.2 with default settings.
Read alignments were sorted with SAMtools v0.1.19 before being counted to genomic features using HTSeq v0.6.1p1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited file including a matrix of raw counts of sequencing reads for all genes

source_name: Splenic B cells

growth_protocol: B cells were isolated from mouse spleens and stimulated ex vivo with anti-CD40 (1µg/ml) and IL-4 (12.5µg/ml)

extract_protocol:
RNA was extracted with Trizol reagent. Quality control and quanitifcation was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At 24h and 48h of stimulation, B cells were spininfected with either pMIR or pMIR-Sox2 retroviral vectors. Cells were sorted at 96h using mCherry as a surrogate marker for infection.

tag: strain

value: B cells

tag: age

value: 4 months

value: infected with pMIR-Sox2


title: Lphn2-siRNA-2 Rep 1

tag: tissue


title: scrambled siRNA Rep 2


title: Nt_artificial_precursor_rep1

city: Bengaluru

first: Shivaprasad

last: Padubidri V.

state: Karnataka

address: GKVK Campus, Bellary Road

country: India

institute: National Centre for Biological Sciences, TIFR

data_processing:
3’ adapter (5’-TGGAATTCTCGGGTGCCAAGG-3’) was removed from sequenced reads using UEA small RNA workbench.
The small RNA reads of length 18nt-25nt filtered and were analyzed.
Supplementary_files_format_and_content: Text file containing 18nt-25nt long unique reads and their raw abundance after removal of adapter.

organism: Nicotiana tabacum

source_name: infiltrated leaves

extract_protocol:
Total RNA from infiltrated leaves was extracted using Trizol (Invitrogen) reagent.
Size fractionation

tag: genotype

value: Wisconsin 35

tag: material

value: Leaves transiently expressing GFP under 35s promoter

value: leaves


title: pMIR_rep3

description:
replicate 3
pMIR_12

tag: cell type

value: infected with pMIR


title: pMIR-Sox2_rep2

description:
replicate 2
Sox2_9


title: pMIR_rep2

description:
replicate 2
pMIR_9


title: scrambled siRNA Rep 1


title: MDCK_50 cm_3d

description: MDCK cells with 50 cmH2O pressure burden

source_name: MDCK cells cultured in 50-cm-high medium

value: 50 cmH2O

tag: cell line


title: pMIR-Sox2_rep3

description:
replicate 3
Sox2_12


title: Nb_pSUC2_TMV1

description: polysomal RNA from leaf phloem tissue inoculated with tobacco mosaic virus

tag: developmental stage

value: 5-week-old plants

tag: genotype/variation

tag: infected with

value: Tobacco mosaic virus

value: leaf phloem


title: Nt_artificial_precursor_rep2


title: wHyp0h replicate-2

tag: ecotype

value: WT

tag: exposed to

tag: treatment time

value: hypocotyl tissue


title: Nt_vector_control_rep1


title: UE_4_10

status: Public on Jul 14 2017

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

data_processing:
Sequencing reads were mapped to the Mus musculus reference genome (GRCm38/mm10) and the 92 ERCC spike-in sequences using TopHat (v2.1.0) with parameters “-o out_dir -G gtf --transcriptome-index trans_index bowtie2_index input_fastq”.
HTSeq (v0.6.0) was used to count the number of reads mapped to each gene with parameters “htseq-count -f bam -r pos -s no -a 30 input_bam gtf”.
TPM (Transcripts Per Million) was employed to quantify gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: values tab-delimited text files include read count and TPM values for each sample

source_name: Liver

growth_protocol: The major lobes were collected from E12.5 embryos and cultured on Nuclepore Track-Etch Membranes (Whatman, 110414) in 12-well plates containing 2 ml of RPMI 1640 medium (Invitrogen, 22400) supplemented with 10% fetal bovine serum, 50 ng/ml EGF, 1×ITS-X (Gibco, 51500) and antibiotics.

extract_protocol:
After FACS sorting, single cells were manually picked up under the microscope with a mouth pipette and transferred into 4 μl of cell lysis buffer containing 0.05 μl of a 1:300,000 dilution of ERCC Spike-in RNA (Life Technologies, 4456740). The cDNA was synthesized, amplified (18 cycles) using the Smart-seq2 protocol, and purified using VAHTS DNA Clean Beads XP beads (Vazyme, N411-03).
Two nanograms of cDNA were used to prepare the sequencing libraries using the TruePrep DNA Library Prep Kit (Vazyme, TD502) with 0.4 × of the standard reaction volume. PCR amplifications were conducted in 8 cycles. Purification and size-based selection of PCR products were performed to obtain libraries with a peak size of 350 bp.

treatment_protocol: The cultures were treated for two days with 0.5 μM TPPB (Calbiochem, 508158) and/or 10 μM U0126 (Sigma, U120) or DMSO carrier as a control.

tag: embryonic day

tag: culture time

value: 2 days

tag: sorting

value: EpCAM+

tag: putative cell type

value: cholangiocyte


title: CAY10603

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-Seq data analyzing was done with rsem(ver. 1.2.3) and Hg19 genome with UCSC known gene set to estimate raw counts and FPKM values
edgeR was used for differentail expression analysis to compare control to treated samples
Genome_build: hg19
Supplementary_files_format_and_content: Expression file contains gene raw counts and FPKM values

source_name: TOV21G cell line

growth_protocol: Ovarian clear cell carcinoma cell line TOV21G was purchased from JCRB.  Cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was isolated for RNA-Seq using Trizol reagent.
RNA-Seq library was prepared using the TruSeq Stranded Total RNA Library Preparation kit (Illumina).

treatment_protocol: ACY1215 and CAY10603 were obtained from Selleckchem. shHDAC6 (TRCN0000004839 and TRCN0000004841) were used.  Cells infected with viruses encoding the puromycin resistance gene were selected in 1 µg/ml puromycin.

tag: treatment

value: ovarian clear cell carcinoma

tag: experiment

value: repressed HDAC6

tag: experiment type

value: drug treatment


title: ACY1215


title: shControl

value: shControl

value: control

value: shRNA


title: Vehicle control

value: Vehicle control


title: shHDAC6


title: UE_4_09


title: pMIR_rep1

description:
replicate 1
pMIR_8

tag: strain

value: B cells

tag: age

value: 4 months

value: infected with pMIR


title: UE_4_07


title: UE_4_05


title: UE_4_04


title: Nt_vector_control_rep2

tag: genotype

value: Wisconsin 35

tag: material

value: Leaves transiently expressing GFP under 35s promoter

tag: tissue

value: leaves


title: UE_4_06


title: UE_4_03