title: rep3_smit_extended_totalRNA

description:
Total RNA
R1 - 3-end read; R2 - SMIT read
processed data files: MS2_R1.bam, MS2_U4C_EEJ.bam, MS2_U4C_EEJ_final.length, MS2_U4C_EIJ.bam, MS2_U4C_EIJ_final.length

data_processing:
Fastq files were filtered for read quality (fastq_quality_filter -Q 33 -q 20 -p 90).
The 3’ end read (R1) was filtered for 3’ end adaptor presence and Illumina sequencing primer with cutadapt (-g CATTGATGGTGCCTACAG -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGACCTCATCTCGTATGCCGTCTTCTGCTTG -n 2 -O 18 -m 23 -e 0.11 –match-read-wildcards –discard-untrimmed).
The SMIT read (R2) was filtered for the reverse-complement sequences with cutadapt (-a CTGTAGGCACCATCAATG -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -n 2 -m 28 -M <read length-21> -e 0.11 –match-read-wildcards).
PCR duplicates were removed with prinseq (prinseq-lite-0.20.4).
The 5 nt random 3’ barcode was removed with the FASTX toolkit (fastx_trimmer -Q 33 -f 6, version 0.0.13)
3’ end reads (R1) were mapped with tophat2 (2.0.13) to the S. cerevisiae genome (sacCer3) with the following settings: -p 5 -N 1 -m 0 –segment-mismatches 0 -i 30 -I 1010 -g 1 –segment-length 20 –no-coverage-search –library-type fr-firststrand –min-anchor-length 8 –min-coverage-intron 30 –max-coverage-intron 1010 –min-segment-intron 30 –max-segment-intron 1010.
The SMIT read (R2) was mapped with bowtie2 (2.2.5) to predefined junctions with the settings: -L 10 –end-to-end -N 0 -k 1 –norc.
For the 3' end sequencing data set, the 3' end linker was trimmed with cutadapt in forward and reverse read. Only reads containing the 3' end linker were kept and the 5 nt barcode was trimmed. Paired-end reads were mapped with tophat2.
Genome_build: sacCer3
Supplementary_files_format_and_content: 3'end (R1) and SMIT read (R2) mapped data (bam-format), text file containing insert length information (EEJ-spliced, EIJ-unspliced, IL-intronless)

organism: Saccharomyces cerevisiae

source_name: cells in exponential growth (Galactose)

growth_protocol: Cell cultures were grown in complete media (YPD) at 30°C and 250 rpm. For cell growth with Galactose as carbon source, cells were grown in YP containing 1% Raffinose and 2% D-Galactose. Cells were harvested in exponential growth at an OD (595nm) of 0.5-1.

extract_protocol:
Nascent RNA was prepared using a nascent RNA isolation protocol for yeast (Carrillo Oesterreich et al. 2010) and Phenol:Chloroform:IAA, 25:24:1, pH 6.6 extraction. Total RNA was extracted with Phenol:Chloroform:IAA, 25:24:1, pH 6.6 using the RiboPure RNA Purification Kit, yeast (Life technologies).
Nascent RNA was 3’ end ligated to the DNA adaptor (/5rApp/NNNNNCTGTAGGCACCATCAAT/3ddC/) and reverse transcribed into cDNA with a primer complementary to the DNA adaptor (ATTGATGGTGCCTACAG). The cDNA solution was diluted by 1:2-1:5 and used as template for gene-specific PCRs. The forward primer was designed to bind to a gene-specific sequence, whereas the reverse primer targets the cDNA 3’ end with the adaptor sequence. Both primers carried Illumina library adaptor overhangs. The individual PCRs were pooled and PCR purified. The pooled cDNA was template for a second PCR, which attached final library adaptors.
All PCRs were adjusted in their cycle numbers. Prior to sequencing the double-stranded DNA ranging from ~150 bp (no insert product) to >2 kb was purified by gel electrophoresis. This step was not necessary for size-selected short RNA samples. Final sample purification was done with AMPure beads. Paired-end sequencing of DNA > 200 bp was done after Bioanalyser, Qubit and Kappa library quantification.
For 3' end sequencing, 3’ end ligated nascent RNA was heat-fragmented and then reverse transcribed using the DNA adaptor sequence as RT primer. The final paired-end sequencing library was prepared according to in-house protocols of the Yale Center for Genome Analysis.
targeted paired-end RNA-Seq

treatment_protocol: For nascent RNA extraction, 1l of cells was pelleted, washed with ice-cold PBS, quick-frozen in liquid nitrogen in 6 aliquots and kept at -80°C. For total RNA extraction, 50ml of exponentially growing cells were pelleted and used immediately for total RNA extraction.

tag: genotype

value: MATa ade2 ade3 his3 leu2-3,112 trp1 URA3::Pgal1:pHZ18Split-MS2-GUAcGU


title: rep2_smit_extended_totalRNA

status: Public on Mar 24 2016

type: SRA

city: Berlin

first: Lydia

last: Herzel

address: Takustr. 6

department: Biology, Chemistry and Pharmacy

country: Germany

institute: Freie Universität

description:
Total RNA
R1 - 3-end read; R2 - SMIT read
processed data files: MS2_EEJ.bam, MS2_EEJ_final.length, MS2_EIJ.bam, MS2_EIJ_final.length, MS2_R1.bam

library_source: transcriptomic

molecule: total RNA

tag: strain

value: MATa ade2 ade3 his3 leu2-3,112 trp1 URA3::Pgal1:pHZ18Split-MS2


title: WTcas9_only-rep2_d6

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

country: USA

institute: University of Rochester

description: Sample 8

data_processing:
Basecalls performed using CASAVA version
Sequenced reads were trimmed for barcode sequence
RNA-seq reads were aligned to the mm10 genome assembly using Tophat v2.0.11,allowing for uniquely mapped reads and mapping both spliced and unspliced reads.
FPKM was calculated by Cufflink 2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: Expression profile in FPKM of sample

organism: Mus musculus

source_name: CJ9 mES cells (-LIF, day6)

growth_protocol:
ESCs  were cultured in ESC differentiation medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and without recombinant leukemia inhibitory factor (LIF, millipore) for six days.
Wild-type ESCs or Evx1as/Evx1 KO ESCs were maintained in standard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore). Differentiated ESCs were cultured in standard ES medium without LIF.

extract_protocol:
Differentiated ES cells were harvested at day 6 of LIF withdrawal. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
Library was prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.

tag: cell line

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: WT

tag: treatment

value: LIF withdrawal

tag: time

tag: chirp probes

tag: barcode

value: GATGTCT


title: rep1_smit_extended_totalRNA


title: WTcas9_only-rep1_d6

description: Sample 6

growth_protocol:
ESCs  were cultured in ESC differentiation medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and without recombinant leukemia inhibitory factor (LIF, millipore) for four days.
Wild-type ESCs or Evx1as/Evx1 KO ESCs were maintained in standard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore). Differentiated ESCs were cultured in standard ES medium without LIF.

value: CTGAAGT


title: rep4_smit_extended_totalRNA


title: smit_extended_shortRNA_Ind9

description:
Nascent RNA
R1 - 3-end read; R2 - SMIT read
processed data files: R1.bam, R2_EEJ.bam, R2_EIJ.bam, R2_IL.bam,R2_EEJ_final.length, R2_EIJ_final.length, IL_final.length

source_name: cells in exponential growth (Glucose)

value: MATa leu2D0 met15D0 ura3D0


title: smit_extended_shortRNA_Ind10


title: KO_EVX1_D4_1

description:
NO_6
E1-1

data_processing:
Basecalls performed using CASAVA version
Sequenced reads were trimmed for barcode sequence
RNA-seq reads were aligned to the mm10 genome assembly using Tophat v2.0.11,allowing for uniquely mapped reads and mapping both spliced and unspliced reads.
FPKM was calculated by Cufflink 2.1.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all the samples

source_name: CJ9 mES cells (-LIF, day4)

growth_protocol:
ESCs  were cultured in ESC differentiation medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and without recombinant leukemia inhibitory factor (LIF, millipore) for four days.
Wild-type ESCs or XH lncRNA-knockdown ESCs were maintained in standard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore). Differentiated ESCs were cultured in standard ES medium without LIF or N2B27 standard medium with RA.

extract_protocol:
Differentiated ES cells were harvested at day 4. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
Library was prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
Libraries were prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.

value: EVX1 KO


title: smit_extended_shortRNA_Ind8


title: smit_extended_shortRNA_Ind5


title: smit_extended_shortRNA_Ind6


title: smit_extended_shortRNA_Ind4


title: smit_extended_Ind10


title: smit_extended_shortRNA_Ind1


title: smit_extended_shortRNA_Ind3


title: smit_extended_Ind7


title: smit_extended_Ind9


title: smit_extended_Ind8


title: WTcas9_only-rep2_d4

description: Sample 7

extract_protocol:
Differentiated ES cells were harvested at day 4 of LIF withdrawal. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
Library was prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.

value: GTACCTT


title: smit_extended_Ind6


title: rep1_smit_20genes_shortRNA


title: rep3_smit_20genes_shortRNA


title: rep2_smit_20genes_shortRNA


title: smit_extended_Ind1


title: smit_extended_Ind4


title: rep6_smit_20genes


title: WTcas9_only-rep1_d4

description: Sample 5

growth_protocol:
ESCs  were cultured in ESC differentiation medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and without recombinant leukemia inhibitory factor (LIF, millipore) for two days.
Wild-type ESCs or Evx1as/Evx1 KO ESCs were maintained in standard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore). Differentiated ESCs were cultured in standard ES medium without LIF.

value: TCACGTT


title: smit_extended_shortRNA_Ind7


title: rep1_smit_20genes


title: rep4_smit_20genes


title: rep2_smit_20genes


title: rep5_smit_20genes


title: H9-derived mesendoderm rep2

city: Santa Barbara

first: Kenneth

middle: S.

last: Kosik

state: California

address: UC Santa Barbara

department: NRI

institute: UCSB

description: H

data_processing:
ion torrent proton, Torrent Suite 4.42 software used for basecalling.
Sequenced reads were aligned to human genome by using tophat TopHat v2.0.13, known transcripts of refSeq download from UCSC genome browser were provided tp tophat.
unmapped reads from Tophat were realigned by using bowtie2 --local --very-sensitive-local,version 2.1.0
alignments were conbined, reads for each refseq transcript were counted by using RPKM_count.py from RSeQC v2.6.1,stranded,exon only
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values of refSeq for each Sample ...

organism: Homo sapiens

source_name: H9 hESC

growth_protocol: H9 cells were maintained on Matrigel (BD Biosciences) in mTeSR1 medium (Stem Cell Technologies). Neuroectoderm was derived with NOGGIN (200 nM) and SB431542 (10 μM).  Mesendoderm was derived with mTeSR1 containing hBMP4 (5 ng/ml).

extract_protocol:
Total RNA was extracted using mirVana miRNA isolation kit.
Total RNA was subjected to DNase treatment using the Turbo DNA-free kit (Life Technologies #AM1907) followed by ribosomal RNA depletion with the RiboMinus Eukaryote Kit v2 (Life Technologies #A15020). Remaining RNA was used for library preparation according to the Ion Total RNA-Seq Kit v2 protocol (Life Technologies #4475936).

tag: days after differentiation

value: Day 5

value: H9 hESC


title: rep3_smit_20genes


title: H9-derived neuroectoderm rep3

description: F


title: H9-derived mesendoderm rep1

description: G


title: H9-derived neuroectoderm rep2

description: E


title: H9-derived neuroectoderm rep1

description: D


title: H9 hESC rep3

description: C

value: Day 0


title: H9 hESC rep2

description: B


title: H9 hESC rep1

description: A


title: smit_extended_Ind5


title: PacBio_YDR381W

description: Nascent RNA

data_processing:
PacBio SMRT Analysis v2.3.0 software was used to obtain CCS reads (reads of inserts protocol).
Fastq files were filtered and trimmed for the 3’ end DNA adaptor and downstream Clontech adaptor sequences with cutadapt 1.8 (-a CTGTAGGCACCATCAAT -n 1 -O 17 -e 0.1 –match-read-wildcards –discard-untrimmed -m 15).
Also the reverse-complement adaptor was trimmed (-g ATTGATGGTGCCTACAG) and the read was reverse-complemented.
Demultiplexing (MS2_reads_of_insert.fastq) was also done similarly using the sample identifier and its reverse-complement identifier.
Trimmed fastq-files were catenated and the remaining 5 nt random 3’ barcode was removed using the FASTX toolkit (fastx_trimmer -Q 33 -t 5, version 0.0.13).
Reads with 5’ and 3’ end adaptors were trimmed and retained for mapping (cutadapt -g AAGCAGTGGTATCAACGCAGAGTACATGGG -n 3 -O 30 -e 0.1 –match-read-wildcards –discard-untrimmed -m 10).
Processed fastq-data were mapped to the genome version  S. cerevisiae sacCer3 or S. pombe EF2 using gmap 2013-05-09 (-d <genome_index> –min-intronlength=30 –intronlength=1010 (850 S. pombe) –localsplicedist=1010 (850 S. pombe) –totallength=1010 ( 850 S. pombe) –trimendexons=0 –microexon-spliceprob=0.5 –direction=auto –find-shifted-canonical –allow-close-indels=2 –npaths=1 –nofails –fails-as-input –mapboth -A –format=samse).
genome build: sacCer3 and S. pombe EF2
processed data files format and content: mapped data in sam- or bed-format

extract_protocol:
Nascent RNA was prepared using a nascent RNA isolation protocol for yeast (Carrillo Oesterreich et al. 2010) and Phenol:Chloroform:IAA, 25:24:1, pH 6.6 extraction.
Nascent RNA was 3’ end ligated to the DNA adaptor (/5rApp/NNNNNCTGTAGGCACCATCAAT/3ddC/) and reverse transcribed into cDNA with a slight modification of the SMARTer PCR cDNA Synthesis Kit (Clontech).
A custom primer reverse-complement to the 3’ end adaptor was used (AAGCAGTGGTATCAACGCAGAGTACATTGATGGTGCCTACAG). Maximal 1 µg of RNA was used per reaction.
The subsequent low cycle PCR was carried out with the Advantage 2 PCR Kit according to the instructions provided by the kit.
Double-stranded cDNA was further used for Pacific Biosciences library preparation and sequencing with standard protocols and kit from Pacific Biosciences (SMRTbell™ Template Prep Kit 1.0).
SMRT DNA sequencing (Pacific Biosciences)

treatment_protocol: For nascent RNA extraction, 1l of cells was pelleted, washed with ice-cold PBS, quick-frozen in liquid nitrogen in 6 aliquots and kept at -80°C.

tag: sample identifier

value: AGGGACATTAAGCAGGATGC


title: rep1_PacBio_HZ18-SplitMS2_U4C

description: Nascent RNA

value: TGTGTGGATCTCGAGACTAG


title: pollen of wt Col with the transgene KRP6pro::22nt_mock_site-trGFP

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description: 1-pGMA148:KRP6pro::22nt_mock_site-trGFP_wt

data_processing:
Illumina Casava1.7 software was used for basecalling.
Sequenced reads de-multiplexed and were trimmed for adaptor sequence
Sequences were masked for low-complexity or low-quality sequence, filtered for reads 18-28 nt in size, only genome matching reads retained (UEA small RNA tool v 2.5.0 used)
tRNA and rRNA-matching reads were removed
Genome_build: TAIR10
Supplementary_files_format_and_content: genome-matched and filtered small RNA sequences and the number of times they were sequenced

organism: Arabidopsis thaliana

growth_protocol: Plants were grown on soil in 18 hour long days at 22C. All plants were grown side-by-side.

extract_protocol:
Mature pollen was harvested by manual collection of open flowers into a 18% sucrose collection buffer placed on ice. Tubes containing the extraction buffer and open flowers were vortexed for 5 minutes and centrifuged for 3 minutes at 3,000 rpm in a centrifuge equipped with a tilt rotor. Pollen RNA was extracted with TRIzol reagent according to manufacturer instructions. Small RNA was enriched by cutting the 17-29nt small RNA fraction from a polyacrylamide gel and subsequent elution and precipitation.
Cloning of small RNAs was performed using the Illumina TruSeq RNA Sample Preparation Kit

treatment_protocol: Mature pollen was harvested in the morning following anthesis.

tag: ecotype background

value: wild type

tag: transgene

tag: tissue

value: mature pollen

tag: molecule subtype

value: small RNA


title: pollen of dcl2/dcl4 with the transgene KRP6pro::22nt_mock_site-trGFP

description: 2-pGMA148:KRP6pro::22nt_mock_site-trGFP_dcl2dcl4

value: dcl2/dcl4 mutant


title: pollen of wt Col with the transgene KRP6pro::miR173site-trGFP


title: rep3_PacBio_HZ18-SplitMS2

description: Nascent RNA

value: MATa ade2 ade3 his3 leu2-3,112 trp1 URA3::Pgal1:pHZ18Split-MS2

value: AGGGAGGATCTCGAGACTAG


title: rep1_PacBio_HZ18-SplitMS2

description: Nascent RNA

value: TGAAAGGATCTCGAGACTAG


title: SC_nRNA_rep1_PacBio

description: Nascent RNA


title: rep2_PacBio_HZ18-SplitMS2

description: Nascent RNA

value: GTTGCGGATCTCGAGACTAG


title: pollen of dcl2/dcl4 with the transgene KRP6pro::miR173site-trGFP

description: 4-pGMA149:KRP6pro::miR173site-trGFP_dcl2dcl4


title: SC_nRNA_rep2_PacBio

description: Nascent RNA

value: MATa leu2D0 met15D0 ura3D0


title: MDA231_input_REP2

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

description: MDA231 SAMPLE 6

library_source: genomic

data_processing:
Remove adapter reads (Cutadapt v1.6)
Trim low quality base calls from both ends.  Min score >= 20, window of 10 step size of 1. (FASTQ Quality Trimmer 1.0.0)
Concatenate replicates.
Align reads with STAR v2.4, splicing disabled with '--alignIntronMax 1'.
Call peaks and generate .bdg with MACS2, p-value e-5. (MACS2 v2.1.0.20140616)
Compare treatment bedgraph to input with MACS2 bdgcmp in logFE mode.
Convert logFE.bdg to bigwig with UCSC's bedGraphToBigWig v4
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files of log fold enrichment over input from bdgcmp function of MACS2

molecule: genomic DNA

growth_protocol: MCF10a cells were grown in DMEM: F12 (Hyclone-SH30271 or SH30272 without phenol red), 5% (v/v) horse serum (Gibco #16050 lot #1075876) + 10ug/ml human insulin (Sigma I-1882)+ 20ng/ml recombinant hEGF (Peprotech AF-100-15) + 100ng/ml Cholera toxin (Sigma C-8052) + 0.5 ug/ml Hydrocortisone (Sigma H-0888) Pen/Strep (Life Technologies) and Glutamine (Life Technologies). MCF-7 cells and MDA-MB-231 were grown in DMEM: F12 (Hyclone-SH30271 or SH30272 without phenol red) + 10% (v/v) FBS (Atlanta Biologicals).

extract_protocol:
Nuclei were isolated using a modification of the Dignam method (Dignam et al Nucleic Acids Res. 1983) and pellets were sonicated using a Covaris S-220 Ultrasonic Processor to obtain sheared chromatin ranging from 200-800 bp with an average peak size of 500 bp.  For immunoprecipitation, 30 μg of sheared chromatin was incubated with 10 ug of anti-H3K4me3 (Abcam, ab1012 lot#GR80367-1) or H3K27me3 (Millipore -07-449 lot#1764447 or 2475696) overnight at 4°C and then incubated with 50 μl Protein-G Dynabeads (Life Technologies 10004D lot#123085320) for 4 h at 4°C.
Briefly, end-repair, A-tailing and paired-end adapter ligation were performed using 8 ug of ChIP-DNA at 150 pg/ul using the TruSeq ChIP sample preparation kit (Illumina cat#9235121 lot #15027084) following manufacture’s instructions. Excess adapters were removed by sequential Ampure XP (Beckman Coulter A63881 lot #1348300) purifications and recovered, ligated fragments were the amplified by PCR on a Biorad thermal cycler. Libraries were then run on a 2% agarose/TAE gel to select for fragments in the 350-400 bp range.
Barcoded libraries (Illumina TruSeq) were then loaded onto an Illumina HiSeq 1500 and single-end 100-base (SE100) sequencing was performed at the Advanced Genome Technologies Core Massively Parallel Sequencing Facility at UVM.

treatment_protocol: Cells were seeded at 1.5x10^6 cells per 100 mm dish and grown to 80% confluence. Cells were washed twice with phosphate buffered saline (PBS) and crosslinked with 0.8% formaldehyde (Thermo Scientific Cat no. 28908) in PBS for 10 minutes at room temperature with continuous shaking

tag: tissue source

value: breast

value: mammary gland/breast epithelial cell; metastatic site derived

tag: neoplasia type

value: adenocarcinoma

tag: atcc id

value: ATCC HTB-26

tag: chip antibody

value: none (input DNA control)


title: rep2_smit_fastPolII

description:
Nascent RNA
R1 - 3-end read; R2 - SMIT read
FastPolII_692_EEJ.bam, FastPolII_692_EEJ_final.length, FastPolII_692_EIJ.bam,  FastPolII_692_EIJ_final.length, FastPolII_692_R1.bam

growth_protocol: Cell cultures were grown in YPD or synthetic dropout medium (SD –LEU for fast Pol II mutants) at 30°C and 250 rpm. For cell growth with Galactose as carbon source, cells were grown in YP containing 1% Raffinose and 2% D-Galactose. Cells were harvested in exponential growth at an OD (595nm) of 0.5-1.

tag: strain

tag: genotype

value: ura3-52 his3<delta>200 leu2<delta>1 or <delta>0 trp1<delta>63 met15<delta>0 lys2-128delta gal10<delta>56 rpb1<delta>::CLONATMX RPB3::TAP::KlacTRP1

tag: plasmid

value: pCK960 rpb1 E1103G T69 corrected CEN LEU2


title: MDA231_H3K4ME3_REP1

description:
MDA231 SAMPLE 3
processed data file: MDA231_H3K4ME3_logFE.bw

tag: cell line

tag: cell type

value: anti-H3K4me3 (Abcam, ab1012 lot#GR80367-1)


title: MDA231_H3K4ME3_REP2

description:
MDA231 SAMPLE 4
processed data file: MDA231_H3K4ME3_logFE.bw


title: rep1_smit_fastPolII


title: 6456-HO4

city: Los Angeles

first: Jacqueline

middle: Gire

last: O'Rourke

state: CA

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

description: 17 mo RNA Seq C9null

data_processing:
fastq reads were alignd to the mouse genome (mm9) with tophat v2.0.8b with parameters -G --no-novel-juncs
bam files were annotated in using Partek software to generate RPKM numbers for each Refseq annotated gene
Genome_build: mm9 (3 month) and mm10 (17 month)

source_name: spinal cord (17 months)

growth_protocol: Mouse  spinal cords (lumbar region) were collected at 3 month and 17 months

extract_protocol:
Lumbar spinal cords were flash frozen on dry ice, and RNA was harvested using Trizol. Total RNA isolated using the PureLink™ RNA Mini Kit (Catalog # 12183018A) and 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard  Illumina (3 month) or Iontorrent (17 month) protocols.  RNA sequencing libraries were constructed with the TruSeq RNA Sample Prep Kits v2 from Illumina. 9 RNA samples were indexed with different adapters and pooled for sequencing.

value: lumbar spinal cord


title: 6455-HO3

description: 17 mo RNA Seq C9null


title: MDA231_H3K27ME3_REP1

description:
MDA231 SAMPLE 1
processed data file: MDA231_H3K27ME3_logFE.bw


title: 6445-HO1

description: 17 mo RNA Seq C9null


title: 6450-HO2

description: 17 mo RNA Seq C9null


title: rep3_PacBio_HZ18-SplitMS2_U4C

description: Nascent RNA

value: MATa ade2 ade3 his3 leu2-3,112 trp1 URA3::Pgal1:pHZ18Split-MS2-GUAcGU

value: TATGAGGATCTCGAGACTAG


title: MCF7_input_REP1

description: MCF7 SAMPLE 5

value: ATCC HTB-22


title: H9-derived mesendoderm rep3

description: I

value: Day 5

value: H9 hESC


title: 6457-HE4

description: 17 mo RNA Seq C9null


title: rep2_PacBio_HZ18-SplitMS2_U4C

description: Nascent RNA

value: TCACTGGATCTCGAGACTAG


title: MCF7_H3K4ME3_REP2

description:
MCF7 SAMPLE 4
processed data file: MCF7_H3K4ME3_logFE.bw


title: MDA231_H3K27ME3_REP2

description:
MDA231 SAMPLE 2
processed data file: MDA231_H3K27ME3_logFE.bw


title: 6460-HE3

description: 17 mo RNA Seq C9null


title: MCF7_H3K4ME3_REP1

description:
MCF7 SAMPLE 3
processed data file: MCF7_H3K4ME3_logFE.bw


title: MCF7_H3K27ME3_REP1

description:
MCF7 SAMPLE 1
processed data file: MCF7_H3K27ME3_logFE.bw


title: 6448-HE1

description: 17 mo RNA Seq C9null


title: MDA231_input_REP1

description: MDA231 SAMPLE 5


title: 6403-WT3

description: 17 mo RNA Seq C9null


title: MCF10A_input_REP2

description: MCF10A SAMPLE 6

value: mammary gland/breast epithelial cell; luminal ductal cells

value: fibrocystic disease

value: ATCC CRL-10317


title: MCF7_H3K27ME3_REP2

description:
MCF7 SAMPLE 2
processed data file: MCF7_H3K27ME3_logFE.bw

value: breast

value: mammary gland/breast epithelial cell; metastatic site derived


title: MCF7_input_REP2

description: MCF7 SAMPLE 6

value: adenocarcinoma


title: MCF10A_input_REP1

description: MCF10A SAMPLE 5

value: none (input DNA control)


title: MCF10A_H3K4ME3_REP2

description:
MCF10A SAMPLE 4
processed data file: MCF10A_H3K4ME3_logFE.bw


title: 6357-WT1

description: 17 mo RNA Seq C9null


title: MCF10A_H3K4ME3_REP1

description:
MCF10A SAMPLE 3
processed data file: MCF10A_H3K4ME3_logFE.bw


title: MCF10A_H3K27ME3_REP2

description:
MCF10A SAMPLE 2
processed data file: MCF10A_H3K27ME3_logFE.bw


title: 6459-HE2

description: 17 mo RNA Seq C9null


title: 3' end sequencing

description:
Nascent RNA
R1 - 3-end read
SC_R1_3end_W.bedgraph, SC_R1_3end_C.bedgraph

value: MATa leu2D0 met15D0 ura3D0


title: 6368-WT2

description: 17 mo RNA Seq C9null


title: MCF10A_H3K27ME3_REP1

description:
MCF10A SAMPLE 1
processed data file: MCF10A_H3K27ME3_logFE.bw


title: RNA-seq adult HSC TGF rep 1

status: Public on Mar 23 2016

city: Boston

first: Chan

last: Zhou

state: Massachusetts

address: 55 Fruit Street

department: gastroenterology

institute: Mass General Hospital, Harvard Medical School

data_processing:
Raw RNA-seq data were mapped into human reference genome (hg19) with tophat (V2.1.0). The mapped reads were futher assemblied into transcirptiomes using CUFFLINK (v2.2.1) and SCRIPTURE (v.beta2) softwares. CUFFMERGE tool was used to merge the transcripts assemblied by CUFFLINK and SCRIPTURE into one list of transcripts through cuffmerge
ChIP-seq data were mapped into human reference genome (hg19) by bowtie2 and then the mapped reads were processed by using MACS2 to call peaks.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

molecule: polyA RNA

source_name: hepatic stellate cells (HSCs)

growth_protocol: All HSCs were cultured ex vivo in DMEM with 10% FCS.

extract_protocol:
For RNA-seq analysis, total RNA was extracted with Trizol reagent and cleaned using the mirVana kit by following instructions for total RNA purification. For ChIP-seq analysis, cells were crosslinked with 1% formaldehyde and sheared by sonication.  Histone-DNA complexes were isolated by antibodies against H3K4me3 (Millipore 07-473, lot 2019729) and H3K27ac (Abcam Ab4729, lot GR132150-1)
RNA-seq libraries were prepared according to Iluminas instructions for the TruSeq Stranded mRNA Kit and barcoded for sequencing.  ChIP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Kit and barcoded for sequencing.

treatment_protocol: All HSC myofibroblasts were grown in DMEM with 10% FCS.  HSC myofibroblats were grown in DMEM with 0.2% BSA for 48 hours followed by the addition of 2.5 ng/ml of TGF-beta for 16 hours for TGF-beta treatment.  For serum starvation conditions (low TGF), cells were cultlures in 0.2% BSA for 48 hours and then remained in 0.2% BSA for an additiona 16 hours in parallel with cells treated with TGF-beta.

value: adult HSCs differentiated into HSC myofibroblasts

tag: passage

value: passage 7-8


title: RNA-seq adult HSC myofibroblast rep2


title: RNA-seq adult HSC serum starvation (low TGF) rep 1


title: RNA-seq adult HSC serum starvation (low TGF) rep 2


title: RNA-seq adult HSC TGF rep 2


title: Pair19_cure [19B]

city: Amsterdam

first: Monique

middle: C.

last: de Jong

address: Plesmanlaan 121

department: Dept of Biological Stress Response and Dept. of Radiation Oncology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
The FAST-Q data from the run were analyzed and quantified by comparing the data to the miR databases. Sequence reads (51bp) were mapped using the mirExpress pipeline.
The reads were trimmed for adapter sequences upon alignment. During the alignment the identity was set to 0.9.
Human mature and precursor sequences were downloaded from mirbase (version 20).
The miR expression results that were generated for each sample were combined for further analysis.
MiR counts were normalized to 100,000 reads per patient.
Genome_build: mirbase (version 20)
Supplementary_files_format_and_content: normalized miR counts

extract_protocol:
Using the Roche High Pure miRNA Isolation Kit (REF: 05080576001), miRNAs were extracted from pre-treatment biopsies. Briefly, 5 slides of 5µm thick were deparaffinized and macrodissected, assuring that the sample consisted of at least 50% tumor cells. MiRs were further purified according to the manufacturer’s instructions. The total RNA samples were quality controlled and quantified with the Agilent Technologies 2100 Bioanalyzer,  using the RNA 6000 Nano kit.
One µg of total RNA in a volume of 5 µl was used as input for the miR library preparation for Illumina sequencing (SR 50bp) using the TruSeq® Small RNA Sample Preparation kit (RS-200-0012 ) and Guide (Part # 15004197 Rev. E). Shortly, stepwise RNA ligation of 3’ and 5’ adapters to miRs introduce a specific index to every sample. The product was PCR amplified and pooled and purified using a 6% PAGE gel. Fragments of 145 – 160 bp were cut from the gel, washed and concentrated by ethanol precipitation and resuspended in nuclease free water. The small RNA library pools were quantified using a DNA 7500 chip with the Agilent Technologies 2100 Bioanalyzer. The pools were diluted to a concentration of 2 nM and passed on for sequencing onto an Illumina HiSeq2000 machine and a stretch of 50 bp was sequenced according to manufacturer’s instructions.

tag: Sex

value: M

tag: age at diagnosis (yrs)

tag: t-stage

tag: n-stage

tag: local recurrence

value: no

tag: time to local recurrence or last follow-up (years)

tag: tissue type

value: pre-radiotherapy biopsy of laryngeal carcinoma


title: Pair19_recurrence [19A]

value: yes


title: Pair18_cure [18B]


title: 6462-WT4

description: 17 mo RNA Seq C9null

tag: tissue

value: lumbar spinal cord


title: Pair18_recurrence [18A]


title: Pair17_recurrence [17A]

value: F


title: Pair16_recurrence [16A]


title: Pair14_cure [14B]


title: Pair14_recurrence [14A]


title: Pair17_cure [17B]


title: Pair13_recurrence [13A]


title: Pair16_cure [16B]


title: Pair11_recurrence [11A]


title: Pair11_cure [11B]


title: Pair10_cure [10B]


title: Pol2 ChIP in Jhd2 wild type

city: new haven

first: Zongzhi

last: Liu

state: CONNECTICUT

address: 310 Cedar Street

institute: yale university

description: Sample name: LBY038_pol2

data_processing:
Basecalls performed using CASAVA version 1.8
The sequencing reads (50 bp single ended) were trimmed for 3' adapter sequences using Trimmomatic [Bolger AM 2014], and the reads shorter than 36bp after trimming were excluded.
The remaining sequencing reads were aligned to the S. cerevisiae reference genome (SacCer3)  using bowtie  version 1.1 [Langmead B 2009]. Up to one mismatch was allowed in the 28-bp seeding region for each aligned read. Reads mapping to multiple sites were excluded.
Binding regions were identified using SICER with the following parameters: effective genome size of 0.74, window size of 200 bp, and gap size of 200 bp.
The differential binding regions between Jhd2 deletion and wild-type strains were identified with SICER-df
HOMER was used for peak annotation and coverage calculation.
Genome_build: SacCer3
Supplementary_files_format_and_content: bedgraph files were generated using HOMER; Scores represents ratio of normalized coverage (read per 10 Million mapped) ChIP vs input for each ChIP sample.

source_name: yeast cells

growth_protocol: yeast were grown to mid-log phase and crosslinked using 1% formaldehyde for 15 minutes at room temperature

extract_protocol:
Samples were washed in PBS and lysed by FA lysis buffer [50 mM Hepes (pH7.5), 150 mM NaCl, 1 mM EDTA, 1% Triton-X 100, 0.1% sodium deoxycholate, 0.1% SDS, protease inhibitors] with 500 µl glass beads.  Shearing of DNA was done using a Bioruptor sonicator (Diagenode) for 25 mins with 30 sec on, 30 sec off cycles.  TAP-tagged proteins were isolated from chromatin using Rabbit IgG-sepharose beads.  CL-4B-Sepharose beads were used for control IP (Sigma).  Data for H3K4me3 and RNA polymerase II was attained using ChIP-grade antibodies against H3K4me3 (Abcam, #) and RNA pol II (Abcam, #).  Both were isolated using Protein A-sepharose beads (Sigma).  IgG (Sigma, #) was used as a non-specific control for H3K4me3 and RNA polymerase II immunopreciptiations.  All samples were washed in FA lysis buffer, DOC buffer [10 mM Tris-HCl (pH8.0), 250 mM LiCl, 0.5% NP-40, 0.5% NaDOC, 1 mM EDTA] and TE buffer [10 mM Tris-HCl (pH8.0), 1 mM EDTA (pH8.0)].  Crosslinks were reversed at 65°C in TES [10 mM Tris-Cl(pH7.5), 1 mM EDTA, 1.0% SDS] and samples were treated with proteinase K.  DNA was precipitated using standard ethanol precipitation protocols and was resuspended in TE containing RNase.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

tag: genotype/variation

value: Jhd2 wild type

value: anti-Pol2 (Abcam, catalog# ab81859, lot# GR6094-5)


title: Pair10_recurrence [10A]


title: Pair9_recurrence [9A]


title: H3K4me3 ChIP in Jhd2 wild type

description: Sample name: LBY038_H3K4me3

value: anti-H3K4me3 (Abcam, catalog# ab8580-100, lot# GR124249-1)


title: RNA-seq adult HSC myofibroblast rep1


title: Pair9_cure [9B]


title: H3K4me3 ChIP in Jhd2 deletion

description: Sample name: LBY029_H3K4me3

value: Jhd2 deletion


title: input in Jhd2 wild type

description: Sample name: LBY038_Input

value: none (input)


title: Pol2 ChIP in Jhd2 deletion

description: Sample name: LBY029_pol2


title: Pair8_cure [8B]


title: Pair8_recurrence [8A]


title: Jhd2 Input

description: Sample name: LBY001_Input


title: Pair13_cure [13B]


title: Pair7_cure [7B]


title: Pcf11 ChIP

description:
Sample name: LBY017_IgG
TAP-tagged proteins were isolated using IgG-sepharose beads.

value: anti-IgG (Sigma-Aldrich; I5381-5MG)


title: Pair7_recurrence [7A]


title: Jhd2 ChIP

description:
Sample name: LBY001_IgG
TAP-tagged proteins were isolated using IgG-sepharose beads.


title: Pair6_recurrence [6A]


title: Pair5_recurrence [5A]


title: input in Jhd2 deletion

description: Sample name: LBY029_Input


title: Jhd2 Deletion replicate3

description: Sample name: 29_6

data_processing:
Illumina Hiseq 2000 using 50bp single end reads
The adapter sequences were trimmed off,  the remaining reads longer than 15 bp were kept
mapped to yeast genome SacCer3 using bowtie2  with the setting '-5 4 --local'
The alignments were then filtered by 1) MAPQ>=10, 2) mismatches <= 5%, 3) unaligned 5' Ts >=2 to get the PASS reads.
The last aligned positions of the PASS reads were grouped to pA clusters with a clustering size of 24 bp.  Each pA cluster was assigned to one of the genes defined by SGD [Cherry JM].  The 3' end of a gene was extended 1000bp from the end of CDS until it overlaps with another gene in the same direction.  The pA Clusters were then filtered by contains 1) >= 3 PASS reads 2) >= 5% of all PASS reads mapped to the gene.
Genome_build: SacCer3
Supplementary_files_format_and_content: CSV format, with the count of PASS reads in each pA cluster (row) for each sample (column)

growth_protocol: yeast were grown to mid-log phase

extract_protocol:
a standard hot acid phenol procedure
cDNA libraries enriched for 3’UTRs were prepared according to: Hoque, M. et al. Analysis of alternative cleavage and polyadenylation by 3' region extraction and deep sequencing. Nat Methods 10, 133-9 (2013)

value: Jhd2 Deletion


title: Jhd2 WT replicate1

description: Sample name: 38_4

value: Jhd2 WT


title: Jhd2 WT replicate2

description: Sample name: 38_5


title: Jhd2 WT replicate3

description: Sample name: 38_6


title: Pair4_cure [4B]


title: Jhd2 Deletion replicate1

description: Sample name: 29_4


title: Pair3_cure [3B]


title: Pcf11 Input

description: Sample name: LBY017_Input


title: Pair2_cure [2B]


title: Pair3_recurrence [3A]


title: edn1-36hpf-DP

first: Gage

middle: DeKoeyer

last: Crump

address: 1425 San Pablo St, BCC403

department: Broad CIRM Center for Regenerative Medicine and Stem Cell Research

institute: University of Southern California

data_processing:
Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification.
Pre-alignment QC showed that the reads from all samples had generally high quality, with the average Phred quality score for each sample being above 30.
Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25.
The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly (Ensembl_v80).
Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values.
Genome_build: GRCz10
Supplementary_files_format_and_content: csv text files include RPKM values for each gene in each sample

organism: Danio rerio

source_name: Pharyngeal arches

extract_protocol:
GFP/DsRed double-positive, double-negative, and single-positive populations were collected directly into RLT lysis buffer (Qiagen). Total RNA was immediately extracted using the RNeasy Micro kit (Qiagen) following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer (NanoDrop Products, Wilmington, DE, USA).
The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip (Agilent, Santa Clara, CA). cDNA was then made from the extracted RNA using the SMARTer V3 kit (Clontech, Mountain View, CA), according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator (Covaris, Woburn, MA) according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit (Kapa Biosystems, Wilmington, MA) and NextFlex adapters (Bioo Scientific, Austin, TX). Libraries were visualized by Bioanalyzer analysis and quantified by qPCR (Kapa library quantification kit). Sequencing was performed on Illumina HiSeq 2000 (50-bp paired end reads) and NextSeq 500 (75-bp paired end reads) machines (Illumina, San Diego, CA). DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.

value: Pharyngeal arches

tag: developmental stage

value: embryo

tag: age

value: 36 hpf

tag: treatment


title: WT-36hpf-DP

tag: genotype

value: WT


title: Pair2_recurrence [2A]

value: M


title: Pair1_cure [1B]

value: no

value: pre-radiotherapy biopsy of laryngeal carcinoma


title: Pair6_cure [6B]


title: WT-36hpf-fli1a

source_name: Mixed/Vasculature

value: Mixed/Vasculature


title: Pair5_cure [5B]

value: F


title: Pair1_recurrence [1A]

value: yes


title: ChIP-seq WCE serum starve (low TGF)

data_processing:
ChIP-seq data were mapped into human reference genome (hg19) by bowtie2 and then the mapped reads were processed by using MACS2 to call peaks.
genome build: hg19
processed data files format and content: bigWig

growth_protocol: HSCs were cultured ex vivo in DMEM with 10% FCS.

extract_protocol:
For ChIP-seq analysis, cells were crosslinked with 1% formaldehyde and sheared by sonication.  Histone-DNA complexes were isolated by antibodies against H3K4me3 (Millipore 07-473, lot 2019729) and H3K27ac (Abcam Ab4729, lot GR132150-1)
ChIP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Kit and barcoded for sequencing.

treatment_protocol: HSC myofibroblasts were grown in DMEM with 10% FCS.  HSCs myofibroblasts were cultured in Matrigel for 72 hours to induce quiescence.  HSC myofibroblasts were grown in DMEM with 0.2% BSA for 48 hours followed by the addition of 2.5 ng/ml of TGF-beta for 16 hours for TGF-beta treatment.  For serum starvation conditions (low TGF), cells were cultlures in 0.2% BSA for 48 hours and then remained in 0.2% BSA for an additional 16 hours in parallel with cells treated with TGF-beta.

value: liver

value: Primary fetal HSCs differentiated into HSC myofibroblasts

value: passage 7-8


title: ChIP-seq H3K27Ac HSC myofibroblasts

description:
Antibody: H3K27ac Abcam Ab4729, lot GR132150-1
processed data file: H3K27_nomodel_SPMR_logLR.bw
H3K27ac Histone modification density called by MACS2 (logLR ratio) for HSC myofibroblasts  after subtracting the background in whole Cell Extract (WCE)


title: ChIP-seq H3K4me3 TGF

description:
Antibody: H3K4me3 Millipore 07-473, lot 2019729
processed data file: TGFb_H3K4me3_logLR.bw
H3K4me3 histone peak density called by MACS2 (logLR ratio) for TGF HSCs  after subtracting the background in whole Cell Extract (WCE)


title: ChIP-seq WCE TGF


title: ChIP-seq H3K4me3 serum starve (low TGF)

description:
Antibody: H3K4me3 Millipore 07-473, lot 2019729
processed data file: noTGFb_H3K4me3_logLR.bw
H3K4me3 histone peak density called by MACS2 (logLR ratio) for low TGF HSCs  after subtracting the background in whole Cell Extract (WCE)


title: ChIP-seq WCE HSC myofibroblasts


title: Pair4_recurrence [4A]


title: Jhd2 Deletion replicate2

description: Sample name: 29_5


title: RNA-seq HSC serum starvation (low TGF) rep 1

description:
processed data file: noTGF.plus.bw, noTGF.minus.bw
noTGF.plus.bw = All the reads from all replicates of low TGF HSC mapped into the sense strand of the genome. noTGF.minus.bw = All the reads from all replicates of low TGF HSC mapped into the anti-sense strand of the genome.

data_processing:
Raw RNA-seq data were mapped into human reference genome (hg19) with tophat (V2.0.8). The mapped reads were futher assemblied into transcriptomes using CUFFLINK (v2.2.1) and SCRIPTURE (v.beta2) softwares. CUFFMERGE tool was used to merge the transcripts assemblied by CUFFLINK and SCRIPTURE into one list of transcripts through cuffmerge
genome build: hg19
processed data files format and content: bigWig

extract_protocol:
For RNA-seq analysis, total RNA was extracted with Trizol reagent and cleaned using the mirVana kit by following instructions for total RNA purification.
RNA-seq libraries were prepared according to Iluminas instructions for the TruSeq Stranded mRNA Kit and barcoded for sequencing.


title: ChIP-seq H3K4me3 HSC myofibroblasts rep 2

description:
Antibody: H3K4me3 Millipore 07-473, lot 2019729
processed data file: MFB_H3K4me3_SPMR_logLR.bw
H3K4me3 histone peak density called by MACS2 (logLR ratio) for HSC myofibroblasts after subtracting the background in whole Cell Extract (WCE)


title: RNA-seq HSC TGF rep 2

description:
processed data file: TGF.plus.bw, TGF.minus.bw
TGF.plus.bw = All the reads from all replicates of TGF HSC mapped into the sense strand of the genome. TGF.minus.bw = All the reads from all replicates of TGF HSC mapped into the anti-sense strand of the genome.


title: ChIP-seq H3K4me3 HSC myofibroblasts rep 1


title: RNA-seq HSC myofibroblasts rep 2B

description:
processed data file: MFB_BC.plus.bw, MFB_BC.minus.bw
MFB_BC.plus.bw = All the reads from all replicates of HSC myofibroblasts (MFB) mapped into the sense strand of the genome. MFB_BC.minus.bw =  All the reads from all replicates of HSC myofibroblasts (MFB) mapped into the anti-sense strand of the genome.


title: RNA-seq HSC TGF rep 1


title: RNA-seq HSC myofibroblasts rep 1B


title: RNA-seq HSC serum starvation (low TGF) rep 2


title: RNA-seq HSC myofibroblasts rep 2A


title: RNA-seq HSC myofibroblasts rep 1A


title: TcpP ChIP B

city: Austin

first: Bryan

last: Davies

state: TX

address: 2506 Speedway

institute: University of Texas at Austin

data_processing:
Illumina data was processed and used in fastq format
Alignments were performed using CLC genomic benchwork
ChIP peaks were called using CLC genomic benchwork
Genome_build: Genome_build: NC_002505, NC_002506
Supplementary_files_format_and_content: all files are in tab-delimited text. ChIP-seq data show locations of peaks in each sample.

organism: Vibrio cholerae O1 str. C6706

source_name: TcpP ChIP-seq

extract_protocol:
histone-DNA complexes were extracted using antibody
samples were processed according to Illumina manufacture protocols

tag: strain

tag: biotype

value: El Tor

value: wild type expressing TcpP from pBAD18-Cm

tag: chip antibody

value: Monoclonal Anti-V5 antibody produced in mouse

tag: chip antibody vendor

value: Sigma

tag: chip antibody cat #

tag: chip antibody lot #


title: CTC1_2 (ii)

city: Utrecht

first: Jean-Charles

last: Boisset

address: Uppsalalaan 8

institute: Hubrecht Institute

description:
readme_barcodes.txt
processed data file: CTCall.t.csv

data_processing:
Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases).
Genome_build: mm10
Supplementary_files_format_and_content: *t.csv: Tab separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicate the cell number of the experiment, separated by a space. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: PyMT breast tumors (CTCs and solid tumor cells)

extract_protocol:
Cells were sorted into Trizol (Life Technologies) and total RNA was isolated according to the manufacturer’s instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 2.5ug GlycoBlue (Life Technologies).
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

tag: cell types

value: TEn (Solid tumor Ecadherin negative), TEp (Solid tumor Ecadherin positive), BEn (Circulating tumor cell Ecadherin negative)


title: CTC1_4 (ii)


title: WT-36hpf-sox10

source_name: Mixed/Ear

value: Mixed/Ear

value: embryo


title: TcpP ChIP A


title: CTC1_3 (ii)


title: ToxR ChIP control

data_processing:
Illumina data was processed and used in fastq format
Alignments were performed using CLC genomic benchwork
ChIP peaks were called using CLC genomic benchwork
Genome_build: Genome_build: NC_002505, NC_002506
Supplementary_files_format_and_content: tab-delimited text files showing locations of peaks in each sample.

source_name: ToxR ChIP-seq

tag: strain background

value: wild type expressing ToxR from pBAD18-Cm


title: ToxR ChIP B


title: ToxR ChIP A


title: TcpP ChIP control


title: CTC1_1 (ii)

value: TEn (Solid tumor Ecadherin negative), TEp (Solid tumor Ecadherin positive), BEn (Circulating tumor cell Ecadherin negative), BEp (Circulating tumor cell Ecadherin positive)


title: HNS ChIP B

source_name: HNS ChIP-seq

value: wild type


title: HNS ChIP A


title: HNS ChIP control


title: mol1_replicate3

city: Heidelberg

first: Thomas

last: Greb

address: Im Neuenheimer Feld 360

department: Centre for Organismal Studies

institute: Heidelberg University

data_processing:
Basecalls performed using RTA VN:1.18.61.0
Sequenced reads were aligned to TAIR10 whole genome using CLC Genomics Workbench version 6 with the following parameters: Additional upstream bases = 0; Additional downstream bases = 0; Maximum number of mismatches allowed (applies to short reads) = 0; Minimum length fraction (applies to long reads) = 0,9; Minimum similarity fraction (applies to long reads) = 0,8; Unspecific match limit = 1; Use colorspace encoding = No; Use strand specific assembly = No; Strand = Forward; Minimum paired distance = 180; Maximum paired distance = 250; Count paired reads as two = No; Minimum exon coverage fraction = 0,2; Minimum number of reads = 10; Minimum length of putative exons = 50
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., 2008.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each Sample

growth_protocol: Arabidopsis from WT (Col-0), mol1-1 and anticle46 genotypes were grown on soil for three weeks in short days (8h light 16h dark, constant 21°C) and then transfered to long days (16h light 8h dark) to stimulate flowering.

extract_protocol:
1 cm of the infloresence stem, above the first branch was harvested from plants between 15 and 20 cm tall and frozen immediately in liquid nitrogen. Total RNA was extracted with Trizol reagent according to the manufacturer´s protocol.
Ambion Dynabeads mRNA Purification Kit for poly A RNA enrichment and the NEB RNA Ultra Kit for preparation of the libraries

value: first internode


title: UASEdn1-36hpf-DP

value: Pharyngeal arches

value: 36 hpf

value: Heat shocked


title: hspGal4-36hpf-DP


title: mol1_replicate2


title: mol1_replicate1


title: hspEdn1-36hpf-DP

value: hspGal4 ; UASEdn1


title: jag1b++-36hpf-DP

value: WT

value: Genotyped


title: WT_replicate3

source_name: WT

tag: ecotype background


title: WT_replicate2


title: mol1_replicat 2

data_processing:
Basecalls performed using RTA VN:1.18.61.0
Sequenced reads were aligned to TAIR10 whole genome using CLC Genomics Workbench version 6 with the following parameters: Additional upstream bases = 0; Additional downstream bases = 0; Maximum number of mismatches allowed (applies to short reads) = 0; Minimum length fraction (applies to long reads) = 0,9; Minimum similarity fraction (applies to long reads) = 0,8; Unspecific match limit = 1; Use colorspace encoding = No; Use strand specific assembly = No; Strand = Forward; Minimum paired distance = 180; Maximum paired distance = 250; Count paired reads as two = No; Minimum exon coverage fraction = 0,2; Minimum number of reads = 10; Minimum length of putative exons = 50
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., 2008.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files including RPKM measurement and count reads for each Sample

growth_protocol: Arabidopsis from WT (Col-0) and mol1-1 genotypes were grown on soil for three weeks in short days (8h light 16h dark, constant 21°C) and then transfered to long days (16h light 8h dark) to stimulate flowering.

extract_protocol:
1 cm of the infloresence stem, directly above the uppermost rosette leaf, was harvested from plants between 15 and 20 cm tall and frozen immediately in liquid nitrogen. Total RNA was extracted with Trizol reagent according to the manufacturer´s protocol.
Ambion Dynabeads mRNA Purification Kit for poly A RNA enrichment and the NEB RNA Ultra Kit for preparation of the libraries

value: mol1-1 mutant

value: base stem


title: hspNICD-36hpf-DP

value: hspGal4 ; UASNICD


title: DBZ-36hpf-DP

value: DBZ treated


title: jag1b-36hpf-DP


title: WT_replicate1


title: WT_replicat 2


title: WT_replicat 1


title: mol1_replicat 1


title: smit_extended_Ind3

description:
Nascent RNA
R1 - 3-end read; R2 - SMIT read
processed data files: R1.bam, R2_EEJ.bam, R2_EIJ.bam, R2_IL.bam,R2_EEJ_final.length, R2_EIJ_final.length, IL_final.length

data_processing:
Fastq files were filtered for read quality (fastq_quality_filter -Q 33 -q 20 -p 90).
The 3’ end read (R1) was filtered for 3’ end adaptor presence and Illumina sequencing primer with cutadapt (-g CATTGATGGTGCCTACAG -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGACCTCATCTCGTATGCCGTCTTCTGCTTG -n 2 -O 18 -m 23 -e 0.11 –match-read-wildcards –discard-untrimmed).
The SMIT read (R2) was filtered for the reverse-complement sequences with cutadapt (-a CTGTAGGCACCATCAATG -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -n 2 -m 28 -M <read length-21> -e 0.11 –match-read-wildcards).
PCR duplicates were removed with prinseq (prinseq-lite-0.20.4).
The 5 nt random 3’ barcode was removed with the FASTX toolkit (fastx_trimmer -Q 33 -f 6, version 0.0.13)
3’ end reads (R1) were mapped with tophat2 (2.0.13) to the S. cerevisiae genome (sacCer3) with the following settings: -p 5 -N 1 -m 0 –segment-mismatches 0 -i 30 -I 1010 -g 1 –segment-length 20 –no-coverage-search –library-type fr-firststrand –min-anchor-length 8 –min-coverage-intron 30 –max-coverage-intron 1010 –min-segment-intron 30 –max-segment-intron 1010.
The SMIT read (R2) was mapped with bowtie2 (2.2.5) to predefined junctions with the settings: -L 10 –end-to-end -N 0 -k 1 –norc.
For the 3' end sequencing data set, the 3' end linker was trimmed with cutadapt in forward and reverse read. Only reads containing the 3' end linker were kept and the 5 nt barcode was trimmed. Paired-end reads were mapped with tophat2.
Genome_build: sacCer3
Supplementary_files_format_and_content: 3'end (R1) and SMIT read (R2) mapped data (bam-format), text file containing insert length information (EEJ-spliced, EIJ-unspliced, IL-intronless)

extract_protocol:
Nascent RNA was prepared using a nascent RNA isolation protocol for yeast (Carrillo Oesterreich et al. 2010) and Phenol:Chloroform:IAA, 25:24:1, pH 6.6 extraction. Total RNA was extracted with Phenol:Chloroform:IAA, 25:24:1, pH 6.6 using the RiboPure RNA Purification Kit, yeast (Life technologies).
Nascent RNA was 3’ end ligated to the DNA adaptor (/5rApp/NNNNNCTGTAGGCACCATCAAT/3ddC/) and reverse transcribed into cDNA with a primer complementary to the DNA adaptor (ATTGATGGTGCCTACAG). The cDNA solution was diluted by 1:2-1:5 and used as template for gene-specific PCRs. The forward primer was designed to bind to a gene-specific sequence, whereas the reverse primer targets the cDNA 3’ end with the adaptor sequence. Both primers carried Illumina library adaptor overhangs. The individual PCRs were pooled and PCR purified. The pooled cDNA was template for a second PCR, which attached final library adaptors.
All PCRs were adjusted in their cycle numbers. Prior to sequencing the double-stranded DNA ranging from ~150 bp (no insert product) to >2 kb was purified by gel electrophoresis. This step was not necessary for size-selected short RNA samples. Final sample purification was done with AMPure beads. Paired-end sequencing of DNA > 200 bp was done after Bioanalyser, Qubit and Kappa library quantification.
For 3' end sequencing, 3’ end ligated nascent RNA was heat-fragmented and then reverse transcribed using the DNA adaptor sequence as RT primer. The final paired-end sequencing library was prepared according to in-house protocols of the Yale Center for Genome Analysis.
targeted paired-end RNA-Seq

value: MATa leu2D0 met15D0 ura3D0


title: WT-20hpf-DP

value: 20 hpf


title: mMSC_14

status: Public on Mar 22 2016

city: Minneapolis

first: Brenda

middle: M

last: Ogle

state: Minnesota

address: 312 Church St SE

department: Biomedical Engineering

institute: University of Minnesota-Twin Cities

description: total RNA of single-cell

data_processing:
Gene expression analysis was performed with Galaxy software (Minnesota Supercomputing Institute (MSI), University of Minnesota, Minneapolis, MN).
Reads were processed and aligned to the mouse reference genome (mm10_genes_2012_05_23.gtf and canonical_mm10.fa) using Tophat (version 2.0.12, open source software, http://ccb.jhu.edu/software/tophat/index.shtml). The default options supplied with the software were used and the aligned read files produced by Tophat were processed using Cufflinks software (version 2.2.1, open source software, http://cole-trapnell-lab.github.io/cufflinks/).
Genome_build: mm10
Supplementary_files_format_and_content: Processed data file includes FPKM values for each Sample as well as FPKMs normalized to each samples Gapdh FPKM

source_name: Mouse bone marrow mesenchymal stem cell, isolated prior to co-culture

growth_protocol: MSCs were cultured on a 0.1% gelatin (Sigma Aldrich, St. Louis, MO) pretreated flask containing a-minimum essential medium (MEM) complete. Alpha-MEM-complete consisted of a-MEM (Invitrogen, Carlsbad, CA), 10% fetal bovine serum (Hyclone, Logan, UT), 0.1 mM nonessential amino acids (Invitrogen), and 2 mM L-glutamine (Invitrogren).  MSC cultures were allowed to grow to 60-70% confluence and were replated at a concentration of 1,500 cells/cm2. HL1cms were cultured on fibronectin/gelatin (1.25 mg fibronectin/100 mL 0.02% gelatin) (Sigma Aldrich) pretreated flasks containing Claycomb-complete.  Claycomb-complete medium was comprised of Claycomb medium (SAFC Biosciences, St. Louis, MO, USA), 10% fetal bovine serum qualified for CMs (SAFC Biosciences), 100 U/mL: 100 μg/mL penicillin-streptomycin (Lonza, Walkersville, MD, USA), 0.1 mM norepinephrine (Sigma-Aldrich), and 2 mM L-glutamine (Invitrogen).  HL1cms were passaged at 100% confluence and split 1:3.  HL1cm coating and HL1cm medium was used when the two cell types were co-cultured.

extract_protocol:
Fluorescent fusion products were sorted via flow activated cell sorting and placed into the Fluidigm C1 chip (17-25 micron) for capture.  Controls were captured in a similar manner.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To induce “accidental cell fusion” between MSCs (hMSCs or mMSCs) and HL1cms, we utilized the measles virus to create a recombinant DNA fusion system. The recombinant DNA system contains three components and enables fusion only when the hemagglutinin (H) protein of the virus binds to the human signaling lymphocytic activation molecule (hSLAM) of the human cell, which then forms a trimeric complex with the fusion protein (F) of the virus to initiate fusion. HL1cms are transfected with the receptor component, hSLAM, while MSCs are transfected with the hemagglutinin (H) and fusion (F) proteins (viral fusogens provided by Yoshihiro Kawaoka of the University of Wisconsin-Madison). Fusion only occurs when all three proteins are present and we utilized this ability to induce fusion between MSCs and HL1cms. Transfection was accomplished using the Neon Transfection System (Invitrogen, Carlsbad, CA), according to the manufacturer’s protocol. Briefly, 5 x 105 HL1cms were transfected with 2 μg of hSLAM and 2 μg of the detection system plasmid with one 1,300 V pulse for 30 msec and plated into 6-well plates (Falcon, Fisher Scientific, Forest Lawn, NJ) containing Claycomb-complete medium without penicillin-streptomycin as per Neon Transfection System protocol.  The HL1cm electroporation was repeated and added to the same well to obtain approximately 1 x 106 total cells transfected.   Eighteen hours later, fresh Claycomb-complete medium without penicillin-streptomycin was added to the transfected HL1cm and 5 x 105 MSCs were transfected with 2 μg of F-H and 2 μg of the detection system plasmid  with one 1,500 V pulse for 20 msec and plated directly onto the previously electroporated HL1cms in the 6-well plate.  The co-culture was allowed to incubate overnight and the fusion products were analyzed on the following day and identified using flow cytometry for GFP.

tag: cell type

value: Bone marrow MSC

tag: passages


title: mMSC_7

description: total RNA of single-cell


title: mMSC_9

description: total RNA of single-cell


title: mMSC_D1_3

description: total RNA of single-cell

source_name: Mouse bone marrow mesenchymal stem cell, isolated 24 hours after co-culture with HL-1 cardiomyocytes


title: mMSC_4

description: total RNA of single-cell


title: mMSC_2

description: total RNA of single-cell


title: mMSC_13

description: total RNA of single-cell


title: mMSC_5

description: total RNA of single-cell


title: mMSC_D1_5

description: total RNA of single-cell


title: mMSC_12

description: total RNA of single-cell


title: mMSC_15

description: total RNA of single-cell


title: mMSC_D1_4

description: total RNA of single-cell


title: mMSC_3

description: total RNA of single-cell


title: HL1cm_D1_3

description: total RNA of single-cell

source_name: HL-1 Cardiomyocyte, isolated 24 hours after co-culture with MSCs

value: HL-1 cardiomyocyte


title: mMSC_11

description: total RNA of single-cell


title: mMSC_1

description: total RNA of single-cell


title: mMSC_10

description: total RNA of single-cell


title: mMSC_D1_2

description: total RNA of single-cell


title: mMSC_D1_1

description: total RNA of single-cell


title: HL1cm_D1_5

description: total RNA of single-cell


title: HL1cm_D1_2

description: total RNA of single-cell


title: mMSC_8

description: total RNA of single-cell


title: mMSC_PC

description: total RNA

source_name: Mouse bone marrow mesenchymal stem cell, population control

value: Bone marrow MSC, population control


title: HL1cm_D1_4

description: total RNA of single-cell


title: WT-28hpf-DP

tag: tissue

value: embryo

value: 28 hpf


title: HL1cm_PC

description: total RNA

source_name: HL-1 Cardiomyocyte Population control

value: HL-1 cardiomyocyte, population control


title: HL1cm_D1_1

description: total RNA of single-cell


title: HL1cm_15

description: total RNA of single-cell

source_name: HL-1 Cardiomyocyte, isolated prior to co-culture


title: HL1cm_14

description: total RNA of single-cell


title: mMSC_6

description: total RNA of single-cell


title: HL1cm_11

description: total RNA of single-cell


title: HL1cm_12

description: total RNA of single-cell


title: HL1cm_13

description: total RNA of single-cell


title: DC_D3_F6

description: total RNA of single-cell

source_name: Fusion of mouse bone marrow mesenchymal stem cell and a HL-1 cardiomyocyte

value: Fusion Product

value: Fused within 72 hours of capture


title: DC_D1_F16

description: total RNA of single-cell

value: Fused within 24 hours of capture


title: DC_D3_F4

description: total RNA of single-cell


title: DC_D1_F14

description: total RNA of single-cell


title: DC_D1_F12

description: total RNA of single-cell


title: DC_D3_F7

description: total RNA of single-cell


title: Mix_D1

description: total RNA

source_name: Mixture of both parental cells and fusion products obtained 24 hours after co-culture was included

value: Mixture of HL-1 cardiomyocytes, MSCs and fusion products

value: Mixture of 70-85 HL1cm, 6-11 mMSC, and newly formed fusion products


title: DC_D1_F13

description: total RNA of single-cell


title: HL1cm_4

description: total RNA of single-cell


title: HL1cm_5

description: total RNA of single-cell


title: DC_D3_F5

description: total RNA of single-cell


title: HL1cm_1

description: total RNA of single-cell


title: DC_D1_F15

description: total RNA of single-cell


title: HL1cm_10

description: total RNA of single-cell


title: DC_D3_F2

description: total RNA of single-cell


title: DC_D3_F1

description: total RNA of single-cell


title: DC_D1_F11

description: total RNA of single-cell


title: DC_D1_F8

description: total RNA of single-cell


title: HL1cm_7

description: total RNA of single-cell


title: HL1cm_9

description: total RNA of single-cell


title: HL1cm_6

description: total RNA of single-cell


title: DC_D3_F3

description: total RNA of single-cell


title: DC_D1_F10

description: total RNA of single-cell


title: HL1cm_3

description: total RNA of single-cell


title: HL1cm_8

description: total RNA of single-cell


title: HL1cm_2

description: total RNA of single-cell


title: DC_D1_F9

description: total RNA of single-cell


title: DC_D1_F3

description: total RNA of single-cell


title: DC_D1_F6

description: total RNA of single-cell


title: DC_D1_F1

description: total RNA of single-cell


title: DC_D1_F7

description: total RNA of single-cell


title: DC_D1_F2

description: total RNA of single-cell


title: SAH2

city: Luzhou

first: Jianhua

last: Peng

state: Sichuan

address: NO.25 of Taiping Street, Jiangyang District

department: Neurosurgery

country: China

institute: The Affiliated Hospital of Southwest Medical University

description: SAH

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat2 with parameters read-mismatches=2，read-gap-length=2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: brain cortex tissue

extract_protocol:
Total RNA was harvested from cortex around bleeding areas and RNA integrity was assessed and judged by A260/A280. Then the total RNA was fragmented into ~200 base pair (bp) units. RNA fragments were used to generate double-stranded cDNA, and then single strand of cDNA labeled by deoxy-UTP, which was enriched by PCR for 12 cycles.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain tissue

tag: group

value: 24 h after SAH

value: wild type


title: DC_D1_F5

description: total RNA of single-cell


title: SAH3

description: SAH


title: CC3

description: Normal

value: control


title: BiFC_D1_F5

description: total RNA of single-cell


title: BiFC_D1_F1

description: total RNA of single-cell


title: BiFC_D1_F3

description: total RNA of single-cell


title: BiFC_D1_F2

description: total RNA of single-cell


title: SAH1

description: SAH


title: DC_D1_F4

description: total RNA of single-cell


title: CC2

description: Normal


title: BiFC_D1_F4

description: total RNA of single-cell


title: A/J RNA Reversal Rep2

city: Duarte

first: Amy

last: Leung

address: 1500 E. Duarte Rd

department: Diabetes/Cancer

institute: Beckman Research Institute, City of Hope

data_processing:
FAIRE-seq: FAIRE was performed as previously described (Giresi et al., 2007). Isolated DNAs were barcoded and sequenced on the Illumina HiSeq 2500 to produced 100bp x 100bp paired-end reads. Reads were aligned to the mouse genome (version mm9, from the UCSC Genome Browser) using Bowtie2 with default options except for local alignment allowing for 1 mismatch in the seed sequence (Langmead and Salzberg, 2012). To assess the effect of sequence variation on the ability to map tags from DBA/2J liver to the mm9 reference genome, we generated a pseudo DBA/2J reference genome by substituting SNVs into the mm9 genome and performed the same analysis.
RNA-seq: RNAs were extracted from livers using Trizol (Invitrogen). RNAs were prepared for sequencing using Illumina protocols and sequenced on the HiSeq 2500 (Illumina). The reads were aligned to the mm9 reference genome with Tophat using the RefSeq gene annotation for transcript reference. Deseq2 was used to identify differentially expressed transcripts from the RefSeq gene annotation.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: Deseq2 output
Supplementary_files_format_and_content: FAIRE-seq: narrowPeaks format

source_name: Liver

growth_protocol: Livers were harvested from humanely euthanized mice

extract_protocol: Libraries were prepped according to the Illumina instructions for RNA-seq or DNA-seq

treatment_protocol: mice were fed three regimen: 1) Con: 16wk of control diet, 2) HF: 16 wks of HF diet, or 3) Reversal: 8wk of HF diet followed by 8wk of control diet

value: A/J

tag: diet

value: High Fat 8 wk, Control - 16wk


title: A/J RNA HF Rep1

value: High Fat - 16wk


title: A/J RNA Reversal Rep1


title: C57BL/6J RNA Reversal Rep2


title: A/J RNA HF Rep2


title: C57BL/6J RNA HF Rep1


title: C57BL/6J RNA HF Rep2


title: C57BL/6J RNA Control Rep2

value: Control - 16wk


title: C57BL/6J RNA Reversal Rep1


title: C57BL/6J RNA Control Rep1


title: CC1

description: Normal


title: A/J FAIRE Reversal Rep1


title: A/J FAIRE HF Rep1


title: A/J RNA Control Rep1


title: A/J FAIRE HF Rep2


title: A/J RNA Control Rep2


title: C57BL/6J FAIRE HF Rep2


title: C57BL/6J FAIRE Reversal Rep2


title: C57BL/6J FAIRE Control Rep2


title: A/J FAIRE Control Rep1


title: C57BL/6J FAIRE Reversal Rep1


title: C57BL/6J FAIRE HF Rep1


title: 56L Cortex V1 Layer 6 rep 3

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

data_processing:
Illumina Casava and BCL2FASTQ1.8.3 were used for basecalling
Sequenced reads were trimmed for NuGEN and Illumina adaptor sequences using cutadapt v1.7.1 with parameters --overlap=7 --minimum-length=30. Ribosomal RNA, mitochondrial and phiX sequences were filtered using bowtie2 v2.1.0 with default parameters. Remaining reads were then mapped to mm10 genome using STAR v2.4.0i with parameters  --chimSegmentMin 15 --outFilterMismatchNmax 3.
Uniquely mapped reads were processed with Cufflinks (v2.2.1) in the quantification mode (parameters "--max-bundle-length 10000000 --max-bundle-frags 100000000 --no-effective-length-correction -G wgEncodeGencodeBasicVM4 -p 4 -u -q --no-update-check"). GencodeVM4Basic was used as an annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab deliminated file include FPKM values

source_name: Cortex, V1, Layer 6

extract_protocol:
Mouse cortex was sliced, digested with pronase for 1 hour at RT, triturated and GFP labeled cells were sorted manually. RNA was extracted using PicoPure kit (life technologies, KIT0204).
Extracted RNA was amplified using Ovation RNA-Seq System V2 (NuGEN, #7102). 1~1.5 ug of the amplified material was used for library construction using Encore NGS Multiplex System (NuGEN, #0314).

tag: background strain

tag: age

value: postnatal day 87

tag: Sex

value: M

tag: ercc5 (10^-5 dilution of ercc in ul)


title: P139 Cortex S2 Layer 6 rep 1

source_name: Cortex, S2, Layer 6

tag: strain

value: postnatal day 38


title: P139 Cortex S2 Layer 6 rep 3

value: postnatal day 39


title: 56L Cortex V1 Layer 6 rep 4


title: P139 Cortex S2 Layer 6 rep 2


title: 56L Cortex S1 Layer 6 rep 2

source_name: Cortex, S1, Layer 6

value: postnatal day 90


title: 56L Cortex S1 Layer 6 rep 3

value: postnatal day 96


title: 56L Cortex S1 Layer 6 rep 4


title: 56L Cortex V1 Layer 6 rep 1

value: postnatal day 86


title: P139 Cortex S2 Layer 6 rep 4


title: 56L Cortex V1 Layer 6 rep 2


title: Ntsr1.GN220 Cortex V1 Layer 6 rep 1

value: Gensat GN220 (Ntsr1)

value: postnatal day 43

value: F


title: Ntsr1.GN220 Cortex V1 Layer 6 rep 2

value: postnatal day 44


title: Ntsr1.GN220 Cortex V1 Layer 6 rep 3

value: postnatal day 84


title: A/J FAIRE Reversal Rep2


title: A/J FAIRE Control Rep2


title: P162 Cortex S1 Layer 6 rep 3

value: postnatal day 41


title: P162 Cortex S1 Layer 6 rep 2

value: postnatal day 37


title: P162 Cortex S1 Layer 6 rep 4


title: P038 Cortex ECT rep 3

source_name: Cortex, ECT

value: postnatal day 35


title: 56L Cortex S1 Layer 6 rep 1


title: C57BL/6J FAIRE Control Rep1


title: P162 Cortex S1 Layer 6 rep 1


title: P038 Cortex ECT rep 1


title: P038 Cortex ECT rep 2


title: Non-progressor (107_L5.LB3)

city: Seattle

first: Daniel

middle: Edward

last: Zak

state: WA

address: 307 Westlake Ave N, Suite 5

institute: Seattle Biomedical Research Institute

description: Processed data: primarySampleJunctions.xlsx - Sheet2

data_processing:
Alignment GSNAP version 2012-06-20
Sequenced reads were filtered for low-quality sequence and the presence of 'N's, then mapped to hg19 whole genome using gsnap v0.12.2
Junctions counts were calculated by using an in house script to count the number of reads mapped to all splice junctions in the genome
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file including the raw junction counts for all the detected junctions in the genome (number of reads mapped to the splice junctions in all samples)

source_name: Blood, control

extract_protocol:
Paxgene RNA
GlobinClear Globin transcript reduction followed by Illumina mRNA-Seq

value: control (non-progressor)

tag: bin

tag: gender

value: female

tag: ethnicity

value: black

tag: previous diagnosis of tb

value: n

tag: tst

tag: qft

value: blood


title: Non-progressor (39_L1.LB10)

value: coloured

value: y


title: Non-progressor (96_L5.LB23)


title: Non-progressor (67_L1.LB15)


title: Non-progressor (31_L4.LB9)

value: male


title: Non-progressor (64_P_L4.LB13)


title: Non-progressor (82_L2.LB19)


title: Non-progressor (10_L1.LB3)


title: Non-progressor (98_L3.LB27)


title: TB progressor (97_L8.LB25)

source_name: Blood, case

value: case (TB progressor)

value: positive


title: Non-progressor (114_L1.LB4)


title: Non-progressor (29_L2.LB8)


title: Non-progressor (100_L4.LB2)


title: Non-progressor (6_L3.LB2)


title: Non-progressor (5_L1.LB11)


title: Non-progressor (71_L8.LB16)


title: Non-progressor (66_L3.LB14)


title: Non-progressor (90_L8.LB21)


title: Non-progressor (23_L6.LB6)


title: Non-progressor (19_L3.LB5)


title: Non-progressor (3_L8.LB1)


title: Non-progressor (17_P_L5.LB4)


title: Non-progressor (86_L3.LB20)


title: Non-progressor (99_L8.LB1)


title: Non-progressor (93_L7.LB21)


title: TB progressor (7_L8.LB19)


title: Non-progressor (95_L4.LB22)


title: Non-progressor (78_L2.LB18)


title: Non-progressor (50_L6.LB12)


title: Non-progressor (74_L8.LB12)


title: Non-progressor (4_L1.LB18)


title: Non-progressor (21_L4.LB23)


title: Non-progressor (18_L2.LB22)


title: Non-progressor (102_L7.LB22)


title: Non-progressor (12_L3.LB20)


title: TB progressor (30_L5.LB25)


title: Non-progressor (111_L4.LB4)


title: TB progressor (15_L3.LB21)


title: Non-progressor (106_L6.LB1)


title: Non-progressor (118_L2.LB7)


title: Non-progressor (57_L5.LB5)


title: Non-progressor (45_L3.LB1)


title: TB progressor (117_L1.LB6)


title: TB progressor (84_L1.LB18)


title: TB progressor (105_L2.LB27)


title: Non-progressor (53_L3.LB7)


title: Non-progressor (47_L2.LB4)


title: Non-progressor (41_L7.LB2)


title: Non-progressor (116_L6.LB5)


title: Non-progressor (88_P_L7.LB20)


title: Non-progressor (75_L1.LB13)


title: Non-progressor (60_L5.LB9)


title: Non-progressor (46_L6.LB3)


title: Non-progressor (85_L5.LB19)


title: Non-progressor (76_L4.LB14)


title: Non-progressor (110_L8.LB3)


title: Non-progressor (103_L5.LB23)


title: Non-progressor (62_L6.LB10)


title: Non-progressor (104_L2.LB25)


title: Non-progressor (109_L2.LB2)


title: Non-progressor (79_L5.LB15)


title: TB progressor (58_L2.LB6)


title: Non-progressor (38_L6.LB1)


title: Non-progressor (92_L7.LB20)


title: Non-progressor (43_L2.LB25)


title: Non-progressor (40_L3.LB22)


title: Non-progressor (11_L1.LB13)


title: Non-progressor (68_L7.LB9)


title: Non-progressor (108_L3.LB23)


title: Non-progressor (34_L6.LB27)


title: Non-progressor (112_L8.LB25)


title: Non-progressor (36_L5.LB21)


title: Non-progressor (9_L6.LB12)


title: Non-progressor (8_L6.LB11)


title: Non-progressor (83_L1.LB15)


title: Non-progressor (51_L8.LB2)


title: TB progressor (59_L6.LB7)


title: Non-progressor (87_L4.LB16)


title: TB progressor (25_L3.LB15)


title: Non-progressor (89_L1.LB18)


title: Non-progressor (55_L8.LB4)


title: Non-progressor (94_L1.LB21)


title: Non-progressor (70_L8.LB11)


title: Non-progressor (91_L5.LB19)


title: TB progressor (101_L7.LB22)


title: TB progressor (2_L5.LB10)


title: Non-progressor (65_L5.LB8)


title: Non-progressor (26_L2.LB16)


title: TB progressor (090789PAXGENEIC_L7.LB22)

description: Processed data: primarySampleJunctions.xlsx - Sheet1


title: Non-progressor (090818PAXGENEDAY0_L1.LB9)


title: Non-progressor (54_L4.LB3)


title: TB progressor (09_0789D020uL09_0789_L3.LB4)


title: Non-progressor (09_0721D030uL09_0721_L7.LB6)


title: Non-progressor (09_0712D025uL09_0712_L5.LB5)


title: Non-progressor (090745PAXGENEDAY0_L1.LB5)


title: TB progressor (090644PAXGENEIC_L7.LB20)


title: Non-progressor (090628PAXGENEDAY0_L4.LB1)


title: TB progressor (09_0644D030uL09_0644_L8.LB12)


title: TB progressor (090624PAXGENEIC_L7.LB18)


title: Non-progressor (09_0578D020uL09_0578_L2.LB8)


title: Non-progressor (09_0587D025uL09_0587_L5.LB4)


title: TB progressor (09_0624D020uL09_0624_L3.LB3)


title: TB progressor (09_0507D020uL09_0507_L3.LB2)


title: Non-progressor (09_0462D025uL09_0462_L5.LB3)


title: Non-progressor (090406PAXGENEDAY0_L3.LB19)


title: Non-progressor (090489PAXGENEDAY0_L2.LB12)


title: Non-progressor (09_0532D020uL09_0532_L2.LB7)


title: Non-progressor (09_0428D030uL09_0428_L6.LB11)


title: Non-progressor (090467PAXGENEDAY0_L6.LB22)


title: Non-progressor (090398PAXGENEDAY0_L1.LB8)


title: TB progressor (090507PAXGENEIC_L6.LB15)


title: Non-progressor (090796PAXGENEDAY0_L3.LB18)


title: Non-progressor (090460PAXGENEDAY0_L1.LB6)


title: Non-progressor (44_P_L6.LB27)


title: Non-progressor (090350PAXGENEDAY0_L2.LB14)


title: Non-progressor (090625PAXGENEDAY0_L4.LB25)


title: TB progressor (09_0278D025uL09_0278_L6.LB8)


title: Non-progressor (09_0397D025uL09_0397_L4.LB8)


title: Non-progressor (090226PAXGENEDAY0_L8.LB2)


title: TB progressor (090278PAXGENEIC_L6.LB13)


title: Non-progressor (071158PAXGENEDAY360_L3.LB18)


title: Non-progressor (07_1158D025uL07_1158_L4.LB9)


title: TB progressor (071153PAXGENEDAY360_L4.LB2)


title: TB progressor (071153PAXGENEDAY540_L4.LB3)


title: TB progressor (071153PAXGENEDAY180_L4.LB1)


title: Non-progressor (071158PAXGENEDAY180_L2.LB16)


title: TB progressor (07_1153D030uL07_1153_L8.LB11)


title: Non-progressor (09_0520D030uL09_0520_L7.LB4)


title: Non-progressor (071147PAXGENEDAY0_L8.LB1)


title: Non-progressor (071135PAXGENEDAY540_L8.LB27)


title: Non-progressor (071147PAXGENEDAY540_L5.LB4)


title: Non-progressor (09_0377D020uL09_0377_L1.LB5)


title: Non-progressor (071135PAXGENEDAY0_L7.LB22)


title: Non-progressor (071132PAXGENEDAY540_L6.LB11)


title: Non-progressor (071115PAXGENEDAY0_L6.LB21)


title: Non-progressor (071132PAXGENEDAY0_L5.LB8)


title: Non-progressor (071115PAXGENEDAY540_L5.LB6)


title: Non-progressor (071158PAXGENEDAY540_L3.LB19)


title: TB progressor (071153PAXGENEIC_L6.LB19)


title: Non-progressor (071112PAXGENEDAY360_L6.LB16)


title: TB progressor (071104PAXGENEDAY180_L3.LB20)


title: Non-progressor (071112PAXGENEDAY180_L5.LB13)


title: Non-progressor (071112PAXGENEDAY540_L7.LB18)


title: Non-progressor (071132PAXGENEDAY360_L5.LB10)


title: TB progressor (071104PAXGENEDAY540_L3.LB21)


title: TB progressor (071003PAXGENEDAY360_L4.LB4)


title: TB progressor (071003PAXGENEDAY180_L5.LB12)


title: Non-progressor (071132PAXGENEDAY180_L5.LB9)


title: TB progressor (070692PAXGENEDAY360_L7.LB20)

value: negative


title: TB progressor (070692PAXGENEDAY180_L5.LB14)


title: TB progressor (070663PAXGENEDAY540_L2.LB12)


title: Non-progressor (071135PAXGENEDAY180_L7.LB23)


title: Non-progressor (071112PAXGENEDAY0_L6.LB14)


title: Non-progressor (071135PAXGENEDAY360_L8.LB25)


title: TB progressor (070663PAXGENEDAY360_L2.LB11)


title: TB progressor (070663PAXGENEDAY180_L1.LB10)


title: TB progressor (070663PAXGENEIC_L6.LB16)


title: TB progressor (070630PAXGENEDAY360_L3.LB21)


title: TB progressor (070630PAXGENEDAY180_L3.LB20)


title: Non-progressor (070440PAXGENEDAY540_L4.LB16)


title: Non-progressor (07_0440D020uL07_0440_L1.LB4)


title: TB progressor (070425PAXGENEDAY540_L2.LB15)


title: TB progressor (071003PAXGENEDAY540_L4.LB5)


title: TB progressor (070425PAXGENEDAY180_L2.LB13)


title: Non-progressor (070438PAXGENEDAY540_L8.LB27)


title: TB progressor (070414PAXGENEDAY540_L1.LB7)


title: TB progressor (070414PAXGENEIC_L8.LB8)


title: TB progressor (070692PAXGENEIC_L7.LB21)


title: TB progressor (070630PAXGENEDAY540_L8.LB22)


title: Non-progressor (07_0424D020uL07_0424_L1.LB3)


title: Non-progressor (070392PAXGENEDAY360_L8.LB3)


title: TB progressor (07_0425D020uL07_0425_L3.LB1)


title: TB progressor (070425PAXGENEDAY360IC_L2.LB14)


title: Non-progressor (070392PAXGENEDAY540_L1.LB4)


title: Non-progressor (070392PAXGENEDAY180_L8.LB2)


title: Non-progressor (070391PAXGENEDAY540_L3.LB25)


title: Non-progressor (070392PAXGENEDAY0_L8.LB1)


title: TB progressor (070414PAXGENEDAY360_L1.LB6)


title: Non-progressor (070391PAXGENEDAY180_L3.LB23)


title: TB progressor (070390PAXGENEDAY540_L8.LB23)


title: TB progressor (070414PAXGENEDAY180_L1.LB5)


title: TB progressor (070386PAXGENEDAY540_L5.LB11)


title: TB progressor (070390PAXGENEDAY360_L7.LB22)


title: TB progressor (070390PAXGENEIC_L8.LB25)


title: TB progressor (070386PAXGENEDAY360_L5.LB10)


title: TB progressor (07_0386D030uL07_0386_L8.LB10)


title: Non-progressor (070369PAXGENEDAY540_L8.LB27)


title: Non-progressor (070438PAXGENEDAY0_L4.LB3)


title: Non-progressor (070369PAXGENEDAY180_L7.LB23)


title: Non-progressor (070369PAXGENEDAY360_L8.LB25)


title: Non-progressor (070361PAXGENEDAY360_L2.LB16)


title: Non-progressor (070361PAXGENEDAY180_L2.LB15)


title: Non-progressor (070361PAXGENEDAY0_L2.LB14)


title: Non-progressor (070360PAXGENEDAY540_L2.LB19)


title: Non-progressor (07_0369D025uL07_0369_L4.LB7)


title: Non-progressor (070360PAXGENEDAY360_L2.LB18)


title: Non-progressor (070360PAXGENEDAY0_L2.LB15)


title: Non-progressor (070355PAXGENEDAY180_L7.LB20)


title: Non-progressor (070308PAXGENEDAY0_L3.LB16)


title: Non-progressor (070293PAXGENEDAY540_L2.LB12)


title: Non-progressor (070293PAXGENEDAY360_L2.LB11)


title: Non-progressor (070308PAXGENEDAY540_L6.LB12)


title: Non-progressor (070355PAXGENEDAY540_L7.LB22)


title: Non-progressor (070360PAXGENEDAY180_L5.LB10)


title: Non-progressor (070293PAXGENEDAY0_L1.LB9)


title: Non-progressor (070282PAXGENEDAY360_L7.LB25)


title: Non-progressor (07_0290D025uL07_0290_L4.LB10)


title: Non-progressor (070282PAXGENEDAY540_L7.LB27)


title: Non-progressor (070282PAXGENEDAY180_L7.LB23)


title: TB progressor (070259PAXGENEDAY180_L3.LB27)


title: TB progressor (070259PAXGENEDAY360_L3.LB1)


title: Non-progressor (07_0282D025uL07_0282_L5.LB1)


title: TB progressor (070257PAXGENEDAY360_L6.LB15)


title: TB progressor (070259PAXGENEDAY0_L3.LB25)


title: Non-progressor (070293PAXGENEDAY180_L1.LB10)


title: TB progressor (070257PAXGENEDAY0_L8.LB13)


title: TB progressor (070257PAXGENEDAY180_L6.LB14)


title: Non-progressor (070355PAXGENEDAY360_L7.LB21)


title: Non-progressor (07_0236D030uL07_0236_L7.LB1)


title: Non-progressor (070218PAXGENEDAY540_L4.LB2)


title: Non-progressor (07_0355D025uL07_0355_L5.LB2)


title: TB progressor (070259PAXGENEDAY540_L4.LB2)


title: Non-progressor (070229PAXGENEDAY180_L7.LB18)


title: Non-progressor (070218PAXGENEDAY360_L4.LB1)


title: Non-progressor (070229PAXGENEDAY0_L7.LB16)


title: Non-progressor (07_0218D020uL07_0218_L1.LB2)


title: Non-progressor (070229PAXGENEDAY540_L7.LB20)


title: Non-progressor (070208PAXGENEDAY540_L7.LB19)


title: Non-progressor (070180PAXGENEDAY360_L6.LB13)


title: Non-progressor (07_0208D030uL07_0208_L7.LB3)


title: Non-progressor (070180PAXGENEDAY540_L6.LB14)


title: Non-progressor (070180PAXGENEDAY180_L5.LB12)


title: Non-progressor (07_0180D030uL07_0180_L7.LB2)


title: Non-progressor (070177PAXGENEDAY360_L6.LB11)


title: Non-progressor (070200PAXGENEDAY0_L3.LB20)


title: Non-progressor (070157PAXGENEDAY540_L4.LB4)


title: Non-progressor (07_0177D025uL07_0177_L4.LB12)


title: Non-progressor (070157PAXGENEDAY360_L4.LB3)


title: Non-progressor (070229PAXGENEDAY360_L7.LB19)


title: Non-progressor (070157PAXGENEDAY180_L4.LB2)


title: H3K9me2_Col

city: Beijing

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology

description: anti-H3K9me2 ChIPseq of Col (wild type)

data_processing:
ChIP-seq Data Analysis: The ChIP-seq reads were aligned to Arabidopsis thaliana genome TAIR10 by Bowtie v2.1.0 (Langmead and Salzberg, 2012) using default parameters with local alignment model. Duplicated reads and low-mapping-quality reads were identified and removed with SAMtools (Li et al., 2009). Enriched intervals were identified by MACS version 2.1.0(Zhang et al., 2008) with default parameters. Parameter of “--broad” was used in the calling of the enriched regions of H3K27me3, while“—call-summits” was used in the calling of peaks of REF6 binding signal. Density maps of reads for visualization were caculated with SAMtools and programs from UCSC genome, based on read counts of the 200 bp extension of sequencing reads towards the 3’ direction (as described previously described (Ernst et al., 2011)) after total reads normalization.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig(bw)

source_name: 28DAG seedlings

growth_protocol: All seeds,except for H3K9me2 ChIP-seq, were grown on 1/2MS plate (with 1% sucrose) at 23°C under long day condition (LD, 16 hours light, 8 hours dark). 12 day after germination (12DAG), whole seedling were harvested for ChIP-seq. For H3K9me2 ChIP-seq, plants were grown in soil at 23°C under long day condition. Aerial part of plants were harvested for ChIP-seq 28d after germination.

extract_protocol:
Chromatin Immunoprecipitation (ChIP) assays were performed using 1 g 12-day-old seedlings as previously described with minor modifications (Lu F. et al., 2010, Cell research 20(3):387-390).Antibodies used in ChIP were anti-H3K27me3 (Millipore, 07-449) and anti-HA (Sigma, H6908).
The ChIP-Seq libraries were constructed using NEBNext® DNA Library Prep Master Mix Set for Illumina® (NEB, E6040S). ChIPed DNA was ligated with Illumina single-end genome sequencing adaptors, size fractionated to obtain 300-bp fragments

treatment_protocol: No treatment

value: shoot (Aerial part)

tag: ecotype

value: Col

value: 28 day after germination(DAG)

tag: genotype

value: wildtype

tag: chip antibody

value: H3K9me2 (abcam, Catalog:ab1220)


title: Non-progressor (070177PAXGENEDAY180_L6.LB10)

tag: tissue


title: Non-progressor (070143PAXGENEDAY540_L5.LB9)

tag: group


title: Non-progressor (070143PAXGENEDAY360_L5.LB8)


title: Non-progressor (070157PAXGENEDAY0_L4.LB1)


title: Non-progressor (070143PAXGENEDAY0_L4.LB6)


title: Non-progressor (070218PAXGENEDAY180_L4.LB27)


title: H3K27me3_ref6

description: anti-H3K27me3 ChIPseq of ref6-1 (mutant)

source_name: 12DAG seedlings

growth_protocol: All seeds were grown on 1/2MS plate (with 1% sucrose) at 23°C under long day condition (LD, 16 hours light, 8 hours dark). 12 day after germination (12DAG), whole seedling were harvested for ChIP-seq.

value: seedling

value: 12 day after germination(DAG)

value: H3K27me3 (Millipore, Catalog:07-449)


title: H3K27me3_Col

description: anti-H3K27me3 ChIPseq of Col (wild type)


title: HA_REF6-ZnF-HA

description: anti-HA ChIPseq of REF6-ZnF-HA

value: REF6p::REF6-ZnF-HA ref6-1

value: HA (Sigma, Catalog:H6908)


title: H3K27me3_REF6-ZnF-HA

description: anti-H3K27me3 ChIPseq of REF6-ZnF-HA


title: H3K27me3_REF6-HA

description: anti-H3K27me3 ChIPseq of REF6-HA

value: REF6p::REF6-HA ref6-1


title: Non-progressor (070140PAXGENEDAY540_L6.LB14)

value: control (non-progressor)

value: female

value: coloured

value: n

value: blood


title: Non-progressor (070143PAXGENEDAY180_L5.LB7)


title: TB progressor (070135PAXGENEDAY360_L4.LB27)

value: case (TB progressor)

value: male

value: negative


title: Non-progressor (070177PAXGENEDAY540_L6.LB12)


title: TB progressor (070135PAXGENEDAY180_L4.LB25)


title: Non-progressor (070074PAXGENEDAY180_L2.LB13)


title: Non-progressor (070074PAXGENEDAY360_L2.LB14)


title: Non-progressor (070074PAXGENEDAY0_L2.LB12)


title: TB progressor (070135PAXGENEDAY0_L3.LB23)

value: positive


title: HA_Col

description: anti-HA ChIPseq of Col (negtive control)

value: Col


title: Non-progressor (07_0140D025uL07_0140_L4.LB11)


title: TB progressor (070060PAXGENEIC_L2.LB11)


title: TB progressor (070060PAXGENEDAY540_L1.LB10)


title: TB progressor (070060PAXGENEDAY360_L1.LB9)


title: CD7_RNASEQ

city: Houston

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

description: processed data file: RnaSeqCounts.txt

data_processing:
For MiGS data, all reads with MAPQ < 10 were filtered. Remaining reads were aligned to hg19 with bowtie2 (options: -N 1 -L 20 -phred33). Average coverage in non-overlapping 50 bp bins were counted genome-wide, and served as input for a differentially methylated region (DMR) detection pipeline in R.
For RNA-seq data, reads were aligned to hg19 using GSNAP. Read counts for RefSeq genes were computed using HTSeq-count.
Genome_build: hg19
Supplementary_files_format_and_content: For MiGS data, rounded average coverage values within 50 bp non-overlapping windows have been provided for each sample as text files. The first column is the chromosome (hg19) followed by start and end coordinates in the second and third columns. The fourth column provides the average coverage within the window, rounded to the nearest integer. Bins with values of zero have been omitted. These were generated in the process of differentially methylated region (DMR) discovery using iDPT (http://idpt.github.io/dptscan/).
Supplementary_files_format_and_content: For RNA-seq data, reads were counted for RefSeq transcription units using HTSeq-count. The tab-delimited text file contains one row for each gene and one column containing the DESeq normalized read counts for each sample.

source_name: human intestinal fibroblasts (HIFs)

growth_protocol: Human intestinal fibroblasts (HIFs) were cultured and their purity confirmed by established methods.

extract_protocol:
RNA was extracted using the Qiagen RNEasy mini kit.
A sequencing library for each sample (1ug RNA) was prepared using the Illumina TruSeq RNA Sample Prep Kit v2 (polyA selection).

value: Crohn's disease-associated fibrosis

value: colon

tag: cell type

value: intestinal fibroblast


title: CD8_RNASEQ

description: processed data file: RnaSeqCounts.txt


title: NL2_RNASEQ

description: processed data file: RnaSeqCounts.txt

value: control


title: HA_REF6-HA

description: anti-HA ChIPseq of REF6-HA

value: seedling

value: 12 day after germination(DAG)


title: CD6_RNASEQ

description: processed data file: RnaSeqCounts.txt


title: NL4_RNASEQ

description: processed data file: RnaSeqCounts.txt


title: TB progressor (070060PAXGENEDAY0_L1.LB7)


title: NL3_RNASEQ

description: processed data file: RnaSeqCounts.txt


title: Non-progressor (070056PAXGENEDAY540_L8.LB25)


title: Non-progressor (060231PAXGENEDAY360_L1.LB5)

value: black


title: Non-progressor (060129PAXGENEDAY540_L7.LB23)

value: control (non-progressor)


title: TB progressor (060127PAXGENEDAY540_L8.LB3)

value: female


title: Non-progressor (070056PAXGENEDAY0_L4.LB2)

value: coloured


title: Non-progressor (060231PAXGENEDAY540_L1.LB6)

value: n


title: Non-progressor (060231PAXGENEDAY180_L8.LB4)

value: blood


title: Non-progressor (06_0231D030uL06_0231_L7.LB5)


title: TB progressor (060127PAXGENEDAY180_L8.LB1)

value: case (TB progressor)


title: TB progressor (06_0127D030uL06_0127_L8.LB9)


title: Non-progressor (041140PAXGENEDAY360_L1.LB8)

value: male


title: Non-progressor (041140PAXGENEDAY540_L1.LB9)


title: TB progressor (060127PAXGENEDAY360_L8.LB2)


title: Non-progressor (041125PAXGENEDAY180_L3.LB20)


title: Non-progressor (041125PAXGENEDAY360_L3.LB21)


title: Non-progressor (041140PAXGENEDAY180_L1.LB7)


title: TB progressor (070060PAXGENEDAY180_L1.LB8)


title: Non-progressor (041120PAXGENEDAY540_L5.LB8)

value: y


title: Non-progressor (041125PAXGENEDAY0_L3.LB19)


title: Non-progressor (041120PAXGENEDAY360_L5.LB7)


title: Non-progressor (041119PAXGENEDAY360_L3.LB18)


title: Non-progressor (041120PAXGENEDAY180_L5.LB6)


title: Non-progressor (04_1104D020uL04_1104_L1.LB6)


title: Non-progressor (041104PAXGENEDAY540_L7.LB21)


title: Non-progressor (041067PAXGENEDAY540_L6.LB10)


title: Non-progressor (060129PAXGENEDAY0_L4.LB27)


title: Non-progressor (04_1058D025uL04_1058_L3.LB5)


title: Non-progressor (041058PAXGENEDAY540_L5.LB8)


title: Non-progressor (041067PAXGENEDAY0_L2.LB15)


title: Non-progressor (041125PAXGENEDAY540_L3.LB22)


title: Non-progressor (041020PAXGENEDAY360_L6.LB15)


title: TB progressor (041056PAXGENEDAY360_L1.LB9)

value: positive


title: Non-progressor (040979PAXGENEDAY360_L3.LB22)


title: Non-progressor (041003PAXGENEDAY540_L4.LB6)


title: Non-progressor (041003PAXGENEDAY360_L4.LB5)


title: Non-progressor (040979PAXGENEDAY0_L2.LB20)


title: Non-progressor (041020PAXGENEDAY180_L6.LB14)


title: Non-progressor (040979PAXGENEDAY540_L3.LB23)


title: Non-progressor (040979PAXGENEDAY180_L3.LB21)


title: Non-progressor (041003PAXGENEDAY0_L4.LB3)


title: Non-progressor (041020PAXGENEDAY0_L6.LB13)


title: Non-progressor (041003PAXGENEDAY180_L5.LB11)


title: Non-progressor (041020PAXGENEDAY540_L6.LB20)


title: TB progressor (040910PAXGENEDAY360_L5.LB6)

value: negative


title: TB progressor (040910PAXGENEDAY540_L5.LB7)


title: Non-progressor (041120PAXGENEDAY0_L5.LB5)


title: Non-progressor (040886PAXGENEDAY360_L8.LB5)


title: Non-progressor (040843PAXGENEDAY360_L8.LB2)


title: TB progressor (04_0859D020uL04_0859_L2.LB9)


title: Non-progressor (04_0843D030uL04_0843_L6.LB12)


title: Non-progressor (040843PAXGENEDAY180_L8.LB1)


title: Non-progressor (040811PAXGENEDAY540_L4.LB27)


title: Non-progressor (040886PAXGENEDAY540_L8.LB6)


title: Non-progressor (040811PAXGENEDAY180_L3.LB23)


title: Non-progressor (040811PAXGENEDAY360_L4.LB25)


title: TB progressor (041056PAXGENEDAY180_L1.LB8)


title: Non-progressor (040811PAXGENEDAY0_L6.LB18)


title: TB progressor (040779PAXGENEDAY360_L8.LB4)


title: TB progressor (040779PAXGENEDAY540_L1.LB6)


title: Non-progressor (040843PAXGENEDAY540_L5.LB15)


title: TB progressor (040779PAXGENEDAY180IC_L1.LB5)


title: TB progressor (040718PAXGENEDAY360_L8.LB4)


title: TB progressor (040718PAXGENEDAY540_L8.LB1)


title: TB progressor (04_0779D025uL04_0779_L5.LB6)


title: TB progressor (040859PAXGENEDAY540_L8.LB27)


title: TB progressor (040718PAXGENEDAY180_L8.LB3)


title: TB progressor (040695PAXGENEIC_L7.LB22)


title: TB progressor (040511PAXGENEDAY540_L6.LB13)


title: TB progressor (040695PAXGENEDAY180_L7.LB19)