title: Endothelial

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: Total RNA (rRNA depleted with ribozero)

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to the human genome (hg19) with STAR (v2.2.0c) with default parameters.  Only uniquely alignable reads were used for downstream analysis
Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across the entire gene (both introns and exons)
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text file, Column Def: 1-ensembl ID, 2-chr, 3-gene start, 4-gene end, 5-strand, 6-gene length, 7-copies in genome, 8-gene name, 9-chr band, 10-gene type, 11-status, 12-aliases, 13-18: RPKM values

source_name: human embryonic stem cells (H1)

growth_protocol: Human ES cells, H1 (WA1, WiCell), (passage 25-40) were cultured in chemically defined hES/hiPS growth media, mTeSR on growth factor reduced matrigel (BD biosciences) coated plates. Briefly, 70-80% confluent hES/hiPS cells were treated with dispase (Invitrogen) for 7 minutes at 37¡C and the colonies were dispersed to small clusters and lifted carefully using a 5ml glass pipette, at a ratio of ~1:6. Human Umbilical Vein Endothelial Cells (HUVEC) were purchased from Promocell and cultivated in EBM medium supplemented with EGM singlequots (Lonza). iPS/ES-derived endothelial cells were cultivated in EGM-2 bullet kit (Lonza). All the endothelial cells were grown on collagen I coated plates (BD biosciences). All cell lines were maintained in an incubator (37¡C, 5% CO2) with media changes every day (hES/hiPS) or every second day (HUVEC).

extract_protocol:
Total RNA from roughly 10x106 cells was isolated using TRIzol reagent (Invitrogen). Intact total RNA samples were treated with DNase1. All the RNA samples met the following RNA quality- OD260/280 = 2-2.2; OD260/230 ³ 2.0; 28S:18S > 1.0, RIN>7.
TruSeq Stranded Total RNA with Ribo-Zero Human kit (Illumina) was used to remove ribosomal RNA and prepare strand specific paired end RNA seq libraries.

treatment_protocol: Pluripotent stem cells were differentiated as previously described (Kurian et al, 2012). Briefly, undifferentiated human ES/iPS cells were freshly split on to matrigel-coated plates, making sure the sub-colonies were of small size (~300-500 cells /colony). Cells were differentiated using the chemically defined mesodermal induction media (MIM) (DMEM:F12, 15mg/ml stem cell grade BSA (MP biomedicals), 17.5µg/ml Human Insulin, (SAFC bioscience),  275 µg/ml Human holo transferrin (Sigma Aldrich), 20ng/ml bFGF (Hymanzyme), 50ng/ml Human VEGF-165 aa (Humanzyme), 25ng/ml human BMP4 (Stemgent),  450µM monothioglycerol (Sigma Aldrich),  2.25mM  each L-Glutamine and Nonn-essential amino acids (Invitrogen).

tag: cell type

tag: differentiation time

value: Fully differentiated Endothelial cells

tag: differentiation stage

value: endothelial cells


title: H1 Day 8

status: Public on May 15 2015

type: SRA

country: USA

description: Total RNA (rRNA depleted with ribozero)

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: 8 days

value: late vascular progenitor cells


title: Colony ID 25014

city: Baton Rouge

first: Brenda

last: Richards

state: LA

address: 6400 Perkins Rd.

department: Basic Science

institute: Pennington Biomedical Research Center

description: SAGE-Seq

data_processing:
XSQ files generated from 5500XL SOLiD sequencer were converted into CSFASTA and QUAL files using XSQ Tools.
Sequenced reads were aligned to the NCBI RefSeq reference sequence and
SAGE tags were counted using SOLiD SAGE Analysis Software v1.10
SAGE tag counts were normalized to reads per million (RPM) using R.
Values of RPM were expressed as binary logarithm values (log2 RPM).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: txt file; tag hits, i.e., successfully aligned reads, were normalized according to DESeq by estimating the size factor for each sample and dividing the sample counts by the corresponding size factor. File contains: symbol, id, geneID, chr, strand, transcStart, transEnd, baseMean, baseMeanA, baseMeanB, foldChange,log2FoldChange, pval, padj; and one column per individual mouse sample/ID.

organism: Mus musculus

source_name: Hypothalamus

growth_protocol: Not applicable

extract_protocol:
Total RNAs were isolated using the AllPrep RNA/Protein kit (Qiagen, Valencia, CA) and re-suspended in Nanopure water.
Serial analysis of gene expression (SAGE) library was constructed using a SOLiD SAGE kit (Life Technologies) according to manufacturer's instructions.

treatment_protocol: Not applicable

tag: study id

tag: colony id

tag: genotype across subcongenic segment

tag: 10 sum total kcal

tag: 10 sum carbohydrate/protein kcal


title: HUVEC

description: Total RNA (rRNA depleted with ribozero)

source_name: HUVEC

value: HUVEC

value: 0 days

value: Human umbilical vein endothelial cells


title: Colony ID 26546

description: SAGE-Seq


title: Colony ID 24574

description: SAGE-Seq


title: H1 Day 4

description: Total RNA (rRNA depleted with ribozero)

value: 4 days

value: early vascular progenitor cells


title: H1 Day 0

description: Total RNA (rRNA depleted with ribozero)

value: embryonic stem cells


title: Colony ID 25907

description: SAGE-Seq


title: Colony ID 25874

description: SAGE-Seq


title: H1 Day 2

description: Total RNA (rRNA depleted with ribozero)

value: 2 days

value: mesoderm committed cells


title: Colony ID 24278

description: SAGE-Seq


title: Colony ID 26510

description: SAGE-Seq


title: Colony ID 26480

description: SAGE-Seq


title: Colony ID 25992

description: SAGE-Seq

value: cast/cast


title: Colony ID 26545

description: SAGE-Seq


title: Colony ID 25489

description: SAGE-Seq


title: Colony ID 26641

description: SAGE-Seq


title: Colony ID 25157

description: SAGE-Seq


title: Control rep1

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

description: DMSOA

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequences were aligned to the M. tuberculosis H37Rv genome (NCBI accession NC_000962.2) using Bowtie2 with default parameters. Read count for all annotated features were obtained with htseq-count program. Regions where genes overlapped were excluded from counting. Reads spanning more than one feature were counted for each feature. Since the RNA library was strand-specific, the orientation of sequence reads had to correspond to the orientation of annotated features to be counted.
Analysis of differential gene expression was carried out using the DESeq package.
Genome_build: NC_000962.2
Supplementary_files_format_and_content: Read count per gene

organism: Mycobacterium tuberculosis

source_name: bacteria

growth_protocol: Bacteria were grown at 37°C in Sauton's media to exponential phase (OD600 of 0.6)

extract_protocol:
Bacteria were resuspended in 600 µl of Trizol and lysed in with 400 µl of glass beads in a bead beater. After spinning and recovery of the supernatant, 200 ul of chloroform were added. After shaking and spinning, the supernatant was purified using the RNeasy bench protocol. DNA was removed from RNA samples using Turbo DNA free (Ambion) by incubation at 37°C for 1 h. RNA integrity was assessed by agarose gel electrophoresis and absence of contaminating DNA was checked by lack of amplification products after 30 PCR cycles. Successful preparation of primary transcriptome was confirmed by lack of 23S/16S rRNA bands and presence of intact 5S rRNA  in agarose gels.
100 ng of total RNA were mixed with 5x Fragmentation buffer (Applied Biosystems), incubated for 4 minutes at 70°C and then transferred immediately on ice. RNA was purified using RNAClean XP beads (Beckman Coulter), according to the manufacturer’s recommendations, and subsequently treated with Antarctic phosphatase (New England Biolabs). RNA was then re-phosphorylated at the 5’-end with polynucleotide kinase (New England Biolabs) and purified with Qiagen RNeasy MinElute columns. In order to ensure strand-specificity, v1.5 sRNA adapters (Illumina) were ligated at the 5’- and 3’-ends using RNA ligase. Reverse transcription was carried out using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). Twelve cycles of PCR amplification using Phusion DNA polymerase were then performed and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer’s instructions. A small aliquot (2.5 ml) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer prior to sequencing on Illumina HiSeq 2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3.

treatment_protocol: 30 ml of bacterial suspension was pelleted, resuspended in fresh Sauton's media and compounds (Cpd7 or Cpd15) were added for 8 hours. Bacteria were then harvested by centrifugation.

tag: strain

tag: treatment

value: DMSO


title: Colony ID 25105

description: SAGE-Seq


title: Colony ID 25932

description: SAGE-Seq


title: Colony ID 24596

description: SAGE-Seq


title: Colony ID 26001

description: SAGE-Seq


title: Colony ID 24297

description: SAGE-Seq


title: Colony ID 25994

description: SAGE-Seq


title: Colony ID 25127

description: SAGE-Seq


title: Colony ID 25089

description: SAGE-Seq


title: Colony ID 24550

description: SAGE-Seq


title: N21_Output

city: Ipswich

first: Ryan

middle: Timothy

last: Fuchs

state: MA

address: 240 County Road

department: RNA Biology

institute: New England Biolabs

description: processed data file: N21_primarysequence.txt, N21_CONTRAfold.txt, N21_cofold.txt

data_processing:
Adapter sequences were trimmed from the raw files using Galaxy (http://galaxyproject.org)
Trimmed sequences were annotated using Genomics Workbench 5.1 (CLC bio, Cambridge, MA) with a zero mismatch tolerance and a text file containing the sequences present in the mixture was used as the annotation reference.
Genome_build: not applicable
Supplementary_files_format_and_content: Text files were generated from Galaxy [N21_primarysequence.txt], the output of Genomics Workbench 5.1 annotation results [UniversalReferenceRawReads.txt, OligoMixesRawReads.txt] or RNA CONTRAfold (http://contra.stanford.edu/contrafold/index.html) [N21_CONTRAfold] or Vienna RNAcofold (http://rna.tbi.univie.ac.at/cgi-bin/RNAcofold.cgi) [N21_cofold] results.
more details provided in the 'readme.txt'

organism: synthetic construct

source_name: Synthetic N21 oligonucleotide mix

extract_protocol:
Samples were synthesized oligonucleotides
Protocol was adapted from the NEBNext® Small RNA Library Prep Set for Illumina® (New England Biolabs, Inc.).  Adapters and primers were substituted as needed to meet the needs of the study

tag: substrate

value: RNA oligonucleotides

tag: 3' adaptor

value: not applicable

tag: 5' adaptor


title: N21_Input


title: Mix1_v1v2v3v4_adaptors

description: processed data file: OligoMixesRawReads.txt

source_name: Synthetic oligonucleotide mix

value: IT MidRand v1+v2+v3+v4


title: IT_v1v2v3v4_adaptors

description: processed data file: UniversalReferenceRawReads.txt

source_name: miRXplore Universal Reference


title: Mix2_v1v2v3v4_adaptors


title: IT_A_adaptors


title: EqMix_A_adaptors


title: 3Rand_5A_adaptors_run2

value: Rand


title: 3Rand_5Rand_adaptors


title: EqMix_v1v2v3v4_adaptors


title: 3Rand_5Rand_adaptors_run2


title: Mix1_A_adaptors


title: 3Rand_5A_adaptors


title: 3MidRand_5C3_adaptors_run2

value: MidRand


title: 3A_5Rand_adaptors


title: 3MidRand_5A_adaptors_run2


title: 3MidRand_5C3_adaptors


title: 3A_5Rand_adaptors_run2


title: 3MidRand_5A_adaptors


title: Colony ID 25159

description: SAGE-Seq


title: 3A_5C3_adaptors


title: 3A_5A_adaptors_run2


title: 3A_5A_adaptors_replicate


title: 3A_5A_adaptors_run3


title: Illumina_v1v2_adaptors

value: Ill MidRand v1+v2


title: Mix2_A_adaptors


title: 3A_5A_adaptors_first


title: Illumina_A_adaptors


title: -C

status: Public on May 14 2015

city: Nanjing

first: Yue

last: Zhang

state: Jiangsu

address: Weigang No.1

department: Tea Science Research Institute

country: China

institute: Nanjing Agricultural University

description: processed data file: Tables S degradome.xlsx

data_processing:
Clean full-length reads were obtained from raw sequences after removing all low-quality reads, contaminants, and reads smaller than 15 nt. The extracted clean reads were used to calculate length distribution, and mapped to the P. trichocarpa genome sequence, and publicly available tea EST sequences using SOAP [PMID 18158127]. Sequence matching non-coding RNAs, including rRNA, tRNA, snRNA, and snoRNA, in the NCBI GenBank (http://www.ncbi.nih.gov/GenBank/), repeats (http://www.girinst.org/repbase/update/index.html) and Rfam (http://www.sanger.ac.uk/software/Rfam) databases were eliminated. Unique miRNA sequences were aligned with known miRNA sequences from miRBase 19.0 (http://www.mirbase.org/) with a maximum of two mismatches. The obtained sequences were used to predict secondary structures by RNAfold software (http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-1.8.1.tar.gz) to identify whether these precursors form a typical miRNA stem-loop structure. The remaining unknown sRNAs were analyzed, and novel miRNAs were predicted using Mireap (http://sourceforge.net/prejects/mireap/). The novel miRNAs were screened according to the recently published criteria of novel miRNAs [PMID:19074682]. The novel miRNAs and their corresponding miRNA*s formed a stem-loop duplex with less than four mismatched bases, derived from opposite stem-arms. The novel miRNAs were typically named using a ‘miR’ prefix to denote miRNAs, and a three-letter prefix to denote the species (e.g. ‘csn’ representing Camellia. sinensis).
Genome_build: tea plant sequences of mRNA and ESTs were downloaded from NCBI (http://www.ncbi.nlm.nih.gov/)
Supplementary_files_format_and_content: Table S.xlsx: speadsheet S1, mature sequences of conserved miRNA in C. sinensis; spreadsheet S2, novel miRNAs and potentially novel miRNAs identified from predicted RNA haipins in C. sinensis
Supplementary_files_format_and_content: Tables S degradome.xlsx: 'conservative miRNAs' spreadsheet, targets for conserved miRNAs from C. sinensis treated with cold (+C) and without cold (-C); 'Novel miRNAs' spreadsheet, targets for novel miRNAs from C. sinensis treated with cold (+C) and without cold (-C)

organism: Camellia sinensis

growth_protocol: Two tea plant cultivars, ‘Yingshuang’ (YS, a cold-tolerant tea plant cultivar) and ‘Baiye 1’ (BY, a cold-sensitive tea plant cultivar), were culture-grown under a 12-h light (28°C)/12-h dark (22°C) photoperiod (photo intensity 1800 Lx photos m-2.s-2) for 20 days.

extract_protocol: Total RNA was isolated with TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.  RQ1 RNase-Free DNase (Promega, Madison, WI, USA) was used to remove genomic DNA contamination.  The quality and integrity of RNAs were examined using an Agilent 2100 Bioanalyzer.  After taking equal amounts of controls and six-stage total RNAs (4°C for 1, 4, 8, 12, 24, and 48 h), these samples were pooled together for the construction of a cold-stressed small-RNA library (CL).  Total RNA was purified by electrophoretic separation on a 15% Tris-Borate-EDTA (TBE)-urea denaturing polyacrylamide gel, and small RNA regions (15 to 30 nucleotide bands) were excised and recovered.  The small purified RNAs were then ligated with 5’ adaptors (Illumina, San Diego, CA, USA), and the ligation products (40 to 60 bases in length) were purified on a Novex 15% TBE-Urea gel to remove unligated adaptors. Subsequently, a 3’ adaptor (Illumina) was ligated to the 5’ ligation products. After gel purification on a Novex 10% TBE-Urea gel (Invitrogen), RNA fragments with adaptors at both ends (70 to 90 bases in length) were reverse transcribed, and the resulting cDNAs were subjected to 15 PCR cycles using the adaptor primers. The resulting small RNA library was then sequenced by Hiseq 2000(Illumina, San Diego, CA, USA).

treatment_protocol: To analyze the miRNAs of tea leave under cold stress, tea plants (both cultivars) were stored at 4°C for 1, 4, 8, 12, 24, and 48 h. For the controls, tea plants were stored at 28°C for 1, 4, 8, 12, 24, and 48 h. The treated and untreated young leaves were then harvested into liquid nitrogen and stored at -80°C until total RNA extraction.

tag: cultivar

value: Yingshuang (YS, a cold-tolerant tea plant cultivar)

value: Baiye 1 (BY, a cold-sensitive tea plant cultivar)

tag: tissue

value: leaf

tag: exposed to

value: room temperature (28C)


title: ZY1

value: mixed sample (of cold-treated, not-treated)


title: Aureo-Udep-2

city: Guangzhou

first: Hongpo

last: Dong

address: West of Huangpu Road 601

department: Research Center for Harmful Algae and Marine Biology

institute: Jinan University

data_processing:
Illumina OLB software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcript of A. anophagefferens(http://genome.jgi.doe.gov/Auran1/Auran1) using SOAPaligner/SOAP2 (version 2.21) with parameters -m 0-x 10000 -s 28 -l32 -v 3 -p3.
The number of clean reads for each gene was calculated and then normalized to RPKM (number of transcripts per million clean reads) using the protocol of Morrissy et al. (2009, Genome Res 19: 1825-1835).
Genome_build: the transcript of A. anophagefferens(http://genome.jgi.doe.gov/Auran1/Auran1)
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values for each Sample.

organism: Aureococcus anophagefferens

source_name: the whole cell of Aureococcus anophagefferens

extract_protocol:
The cells were harvested by centrifugation and flash frozen in liquid nitrogen, and Total RNA was extracted from frozen cell pellets using TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s instructions. RNA-seq libraries were constructed following an Illumina gene expression sample preparation kit with 5-10 ug of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Chinese strain

tag: age

value: the onset of the stationary phase

tag: growth status

value: Cells were grown in N-depleted media

tag: genotype

value: wild type


title: Aureo-Urea

value: Cells were grown in media containing urea


title: Aureo-Urecov-3

value: Urea were added into N-depleted culture


title: Aureo-Nrecov-4

value: Nitrate were added into N-depleted culture


title: Aureo-Urep-1

value: Cells were grown in urea-replete media


title: Aureo-Nitrate

value: Cells were grown in media containing nitrate


title: Dlx3-K14cKO #4

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Reads were mapped to mm9 using TopHat 2.0.8/bowtie 2.1.0.0 with default settings
FPKM values were calculated using Partek 6.6
Genome_build: mm9
Supplementary_files_format_and_content: Excel file includes FPKM values

source_name: Enamel organ at P10

extract_protocol: cDNA was prepared using the NEBnext kit and library was generated using the NuGen kit and Mondrian automated system.

value: mixed background

value: Enamel organ

value: Post-natal day 10


title: +C

value: Yingshuang (YS, a cold-tolerant tea plant cultivar)

value: cold (4C)


title: Dlx3-K14cKO #3


title: Dlx3-K14cKO #1


title: Dlx3-K14cKO #2


title: Aureo-Mixture N

value: Cells were grown in media containing a mixture of urea and nitrate


title: Dlx3-WT #3


title: Dlx3-WT #4


title: 3A_5A_adaptors_repeat

value: RNA oligonucleotides


title: Dlx3-WT #1


title: Dlx3-WT #2


title: EZ2-2_31C_H3K27ac_ChIPSeq#2

city: Boston

first: Hun-Goo

last: Lee

address: 185 Cambridge St

department: Molecular Biology

institute: Mass General Hospital

description: H3K27ac ChIP with EZ2-2 cells from non-permissive temperature

library_source: genomic

data_processing:
HiSeq Control Software v2.0.5 and Casava v1.8.2 were used for basecalling and de-multiplexing.
ChIP-seq reads were aligned to the dm3 genome assembly (FlyBase 5.22) using Bowtie 0.12.7 with parameters -t -p 4 -a -m 1 --maxins 900 --tryhard --best --strata -S --chunkmbs 512. Sequence tags multiply matched to repetitive sequences were excluded in all ChIP-seq and RNA-seq results.
Sequence alignment information was further processed by SAMtools v0.1.18 (Li et al., 2009) to generate a pileup of read bases which was used for obtaining the genome-wide profiling data format by python scripts (SGR format with 25bp bin) compatible with the Integrated Genome Browser (Affymetrix).
Normalization between different culture conditions (25˚C and 31˚C) was done by calculating the correction factors based on ChIP-qPCR. At least five regions were used for the normalization.
Genome_build: dm3
Supplementary_files_format_and_content: sgr files with 25bp bin size were generated from a pileup of read bases using samtools v0.1.18 mpileup and python scripts; Scores represent qPCR-normalized number of reads per 25bp bin.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: EZ2-2 ; E(z) temperature sensitive cells

growth_protocol: EZ2-2 cells were grown in Schneider's medium (Gibco) supplemented with 10% FBS, 100U/ml of Penicillin G, 100ug/ml of Streptomycin sulfate and 292 ug/ml of L-glutamine.

extract_protocol:
Live cells were crosslinked with 1.8% formaldehyde for 10 min at 25°C and soluble chromatin prepared as described in Schwartz et al., 2006.
Libraries were prepared according to Illumina's instructions from TruSeq ChIP Sample Preparation Kit with some modifications. Indexed adaptors from TruSeq ChIP Sample Prep Kit were used for barcoding. After adapter ligation, 250-500bp size was selected by gel size selection, and the subsequent amplification was done with 15 cycles. With the constructed libraries, 100bp paired-end sequencing was performed by Illumina HiSeq technology

treatment_protocol: EZ2-2 cells were grown at 25°C or 31°C for 12 days.

tag: cell line

value: EZ2-2; E(z) temperature sensitive cells

tag: growth condition

value: grown at 31°C for 12 days

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: EZ2-2_25C_H3K4me1_ChIPSeq#2

description: H3K4me1 ChIP with EZ2-2 cells from permissive temperature

value: grown at 25C

value: H3K4me1 (Abcam, ab8895)


title: EZ2-2_25C_H3K27ac_ChIPSeq#2

description: H3K27ac ChIP with EZ2-2 cells from permissive temperature


title: EZ2-2_25C_H3K27me2-AB_ChIPSeq#2

description: H3K27me2 ChIP with EZ2-2 cells from permissive temperature


title: EZ2-2_31C_H3K4me1_ChIPSeq#2

description: H3K4me1 ChIP with EZ2-2 cells from non-permissive temperature


title: EZ2-2_31C_H3K27me3_ChIPSeq#2

description: H3K27me3 ChIP with EZ2-2 cells from non-permissive temperature

value: H3K27me3 (Abcam, ab6002)


title: EZ2-2_31C_H3K27me2-AB_ChIPSeq#2

description: H3K27me2 ChIP with EZ2-2 cells from non-permissive temperature


title: EZ2-2_25C_Pc_ChIPSeq

description: Pc ChIP with EZ2-2 cells from permissive temperature

value: EZ2-2 ; E(z) temperature sensitive cells

value: Pc (Pirrotta Lab; affinity purified)


title: EZ2-2_31C_H2Aub1-2_ChIPSeq

description: H2Aub1 ChIP with EZ2-2 cells from non-permissive temperature

value: H2AK118ub1 (Cell Signaling, D27C4)


title: EZ2-2_25C_H3K27me3_ChIPSeq#2

description: H3K27me3 ChIP with EZ2-2 cells from permissive temperature


title: EZ2-2_25C_H3K4me1_ChIPSeq


title: EZ2-2_31C_H3K4me1_ChIPSeq


title: EZ2-2_31C_H3K27me2-Abcam_ChIPSeq


title: EZ2-2_31C_H3K27ac_ChIPSeq


title: EZ2-2_25C_H3K27ac_ChIPSeq


title: EZ2-2_25C_H3K27me2-Abcam_ChIPSeq


title: EZ2-2_31C_H3K27me3_ChIPSeq


title: EZ2-2_25C_H2Aub1-1_ChIPSeq

description: H2Aub1 ChIP with EZ2-2 cells from permissive temperature


title: EZ2-2_31C_H2Aub1-1_ChIPSeq


title: EZ2-2_25C_H3K27me3_ChIPSeq


title: EZ2-2_totalRNAseq_31C-1

description:
rRNA-depleted total RNA from EZ2-2 cells at non-permissive temperature
Sample B

data_processing:
HiSeq Control Software v2.0.5 and Casava v1.8.2 were used for basecalling and de-multiplexing.
Raw reads in fastq format are aligned to a "filter" reference using bowtie to remove adaptor/primer, poly-A, poly-T, rRNA, tRNA, snRNA, and mitochondrial sequence (Geospiza genesifter pipeline).
RNA-seq reads were then aligned to the dm3 genome assembly using BWA (version 0.5.9; settings: aln -o 1 -e 10 -i 5 -l 32 -k 2 -t 6). An additional post-alignment process is then carried out with Picard (http://sourceforge.net/projects/picard/) to do local realignment. (Geospiza genesifter pipeline)
Sequence alignment information was further processed by BEDtools v2.17.0 and SAMtools v0.1.18 to generate a pileup of read bases which was used for obtaining the genome-wide profiling data format by python scripts (SGR format with 25bp bin) compatible with the Integrated Genome Browser (Affymetrix).
Normalization between different culture conditions (25˚C and 31˚C) was done by calculating the correction factors based on ChIP-qPCR. At least five regions were used for the normalization.
Genome_build: dm3
Supplementary_files_format_and_content: sgr files with 25bp bin size were generated from a pileup of read bases using SAMtools v0.1.18 mpileup and/or BEDtools v2.17.0 and python scripts; Scores represent qPCR-normalized number of reads per 25bp bin.

extract_protocol:
RNA was harvested using Trizol reagent. For the RNA-seq libraries, rRNA was depleted from the 5ug of DNase I-treated total RNA by RiboZero kit (Epicentre) and purified with Agencourt RNAclean XP beads.
For RNA-seq library construction, Ovation RNA-Seq System V2 kit (NuGEN) or Encore Complete RNA-Seq Library System (NuGEN) were used. Libraries were prepared according to manufacturer's instructions with indexed adapters from TruSeq ChIP Sample Prep kit. With the constructed libraries, 100bp paired-end sequencing was performed by Illumina HiSeq technology


title: EZ2-2_totalRNAseq_25C-2

description:
rRNA-depleted total RNA from EZ2-2 cells at permissive temperature
Sample X


title: EZ2-2_totalRNAseq_31C-2

description:
rRNA-depleted total RNA from EZ2-2 cells at non-permissive temperature
Sample Y


title: EZ2-2_totalRNAseq_25C-1

description:
rRNA-depleted total RNA from EZ2-2 cells at permissive temperature
Sample A


title: mES-input-24hr

first: Misook

last: Ha

address: NIH

institute: National Heart Lung Blood Institute

description:
24 hour after DOX treatment
There are two fastq files per sample; one for each replicate.

data_processing:
Basecalls performed using ELAND software
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2 allowing uniq match and at most 1 mismatch
Genome_build: mm9
Supplementary_files_format_and_content: Bed file containing coorrdinate of locus and number of reads mapped when H3.3-HA is induced and 6 hour later of H3.3-HA repression by DOX

source_name: Embryonic stem cells

growth_protocol: ESCs were maintained in medium consisting of Dulbecco’s modified Eagle’s medium (Hyclone) supplemented with 10% fetal bovine serum (FBS), 10% knockout serum replacement (Invitrogen), L -glutamine, 100 units/ml penicillin, 100 μg/ml streptomycin, 0.1mM beta-mercaptoethanol at 37 °C under 5% CO2 , supplemented with 1000 units/ml leukemia inhibitory factor (LIF) (ESGRO, Chemicon). For differentiation into embryoid bodies (EBs), ESCs were trypsinized and transferred into 15% FBS containing medium without the addition of LIF and medium was changed every second day.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody of HA.
ChIP material was blunt-ended and phosphorylated with the End-it-Repair kit (EPICENTRE). Illumina genome sequencing adaptors were ligated with T4 DNA ligase (New England Biolabs) after addition of adenosine nucleotides, using exo- Klenow. Samples were PCR amplified with multiplexed Illumina genomic DNA sequencing primers. PCR products (250 to 450 bp in size) were gel purified and submitted for Illumina deep sequencing.

treatment_protocol: For ‘TET-OFF’ experiments, ESCs were cultured over several passages (weeks) on feeder cells in the absence of DOX and were subsequently passaged onto feeder-free plates prior to the inhibition of HA-H3.3 expression. To repress HA/FLAG-H3.3 expression we treated cells with 2 μg/ml doxycycline hyclate before crosslinking with formaldehyde at various time points.

tag: cell type

value: Embryonic stem cells

tag: passages

value: no antibody (input DNA sequencing)


title: mES-input-48hr

description:
48 hour after DOX treatment
There are two fastq files per sample; one for each replicate.


title: mES-input-12hr

description:
12 hour after DOX treatment
There are two fastq files per sample; one for each replicate.


title: EZ2-2_25C_H2Aub1-2_ChIPSeq


title: mES-input-6hr

description:
6 hour after DOX treatment
There are two fastq files per sample; one for each replicate.


title: mES-input-0hr

description:
A TET-repressible ESC line, ES[MC1R(20)], with the expression cassette integrated at the ROSA26 locus. We transfected MC1R ESCs with HA/FLAG-tagged H3.3 controlled by tetracycline response elements. ESCs that were routinely cultured in the absence of DOX
There are two fastq files per sample; one for each replicate.


title: mES-H3.3HA-24hr

value: anti-HA (Roche, Basel,Switzerland)


title: SDG711RNAi-IM-RNAseq-replication2

city: Wuhan

first: shaoli

last: zhou

state: Hubei

address: shizishan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

description: RNA-seq

data_processing:
For RNA-seq, Tophat (version 2.0.13) was used to align the clean tags filtered by Trimmomatic (version 0.32) to the reference genome of Niponbarre (version 7.0). Cufflinks (version 2.2.1) was used for identification of differentially expressed genes.
For ChIP-seq, Bowtie2 (version 2.1.0) was used to align the clean tags filtered by Trimmomatic (version 0.32) to the reference genome of Niponbarre (version 7.0). MACS (Version 1.4) was used for peak identification with default paramaters.
Genome_build: RGAP version 7.0

organism: Oryza sativa Japonica Group

source_name: DongJin-IM

growth_protocol: Rice (Oryza sativa spp. japonica) material used in this study for CHIP-seq and RNA-seq analysis were from ‘DongJin’ (DJ) background, including wild type, SDG711 RNAi lines (Liu et al., 2014), and JMJ703 T-DNA insertion line (3A-00550)(Chen et al., 2013) .The germinated rice seedlings of all genotypes were transplanted in field at the beginning of May in Wuhan area, and grown till the beginning of June, which corresponded to the 6-7 leaf stage, to collect SAM (<0.5 mm, observed with a microscope, as a criteria for sampling). Rice plants were grown till mid June (about 10-12 leaf stage) to start IM collection (1-2 mm, observed with a microscope, as criteria). During the period from May to early June, the day length at Wuhan area is <13.5 h (which is SD for rice flowering), but afterward, becomes >13.5h (which is LD for rice flowering). Considering the short period of LD condition between early to mid June, which may accelerate flowering of SDG711 RNAi plants (Liu et al., 2014), so we harvested IM of the RNAi plants earlier (17-19 June) than that of wild type and jmj703 plants (21-24 June). About 400 plants were used to collect SAM and IM, and apices were hand-dissected from apices and frozen in liquid nitrogen for RNA extraction or fixed in formaldehyde for chromatin cross-linking.

extract_protocol:
Rice SAM and IM total RNA samples were isolated using TRIzol reagent (Invitrogen).SAMs and IM (about 2 mm) were crosslinked in 1% formaldehyde under vacuum. Chromatin was extracted and fragmented to 200-750 bp by sonication, and ChIP was performed using the following antibodies: H3K27me3 (a2363, AbclonalABclonal ) and H3K4me3 (07-473, Millipore).The eluted ChIP DNA was used to generate Illumina sequencing libraries following the manufacturer's protocol.
RNA libraries were prepared according to the protocol strictly (http://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqstrandedmrna/truseq-stranded-mrna-sample-prep-guide-15031047-e.pdf).  Briefly, 1-4 μg of total RNAs were used for mRNA purification and cDNA synthesis. After single ‘A’ nucleotide was added to the 3’ ends of the blunt fragments of the double strand cDNAs, indexing adapters are ligated to the ends of the cDNA. PCR are performed to amplify the DNA fragments. The amplified DNA fragments were purified and sequenced with the Illumina Hiseq-2000 system.The eluted ChIP DNA was used to generate Illumina sequencing libraries following the manufacturer's protocol.

value: IM from 10-12 leaf stage

tag: genotype/variation

value: SDG711 RNAi


title: SDG711RNAi-IM-RNAseq-replication1

description: RNA-seq


title: mES-H3.3HA-12hr

tag: strain


title: mES-H3.3HA-48hr


title: mES-H3.3HA-6hr


title: WT-IM-RNAseq-replication2

description: RNA-seq

value: DongJin


title: mES-H3.3HA-0hr


title: WT-SAM-RNAseq-replication2

description: RNA-seq

source_name: DongJin-SAM

value: SAM from 6-7 leaf stage


title: WT-IM-RNAseq-replication1

description: RNA-seq


title: jmj703-IM-H3K27me3

description: Chromatin IP against H3K27me3

tag: antibody


title: SDG711RNAi-IM-H3K27me3

description: Chromatin IP against H3K27me3


title: ChIP Sox9

status: Public on May 13 2015

city: Brussels

first: Jean-Christophe

last: Larsimont

state: Brussels

address: 808, route de Lennik

department: Faculté de médecine

country: Belgium

institute: Université Libre de Bruxelles (ULB)

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using BWA software.
Peaks were identified using MACS software using a FDR treshold of 5% and a minimal enrichment of 2.
Genome_build: mm9
Supplementary_files_format_and_content: wig file

source_name: K14CreER SmoM2 cells

growth_protocol: Mice were maintained in a certified animal house according to European guidelines

extract_protocol:
ChIP was performed using Millipore EZ-Magna ChIP kit.
Between 5-10ng of qPCR verified ChIPed DNA or input DNA was  processed with the TruSeq ChIP Sample Prep Kit (Illumina) according to manufacturer instruction.

treatment_protocol: Mice were injected with 2.5mg of tamoxifen for 10 consecutive days and sacrifice 9 weeks after the first injection. Tail epidermis was digested in trypsin and single cells were stained with the appropriate antibodies and FACS sorted before RNA extraction.

value: K14CreER SmoM2 cells

value: Sox9 (Millipore, AB5535)


title: Input

value: none (Input DNA)


title: SDG711RNAi-IM-H3K4me3

description: Chromatin IP against H3K4me3


title: WT-IM-H3K4me3

description: Chromatin IP against H3K4me3


title: Input control sample

city: Atlanta

first: Julio

middle: C.

last: Ayala

state: Georgia

address: 1600 Clifton Rd NE Rm 3-642

department: Division of STD Prevention

institute: Centers for Disease Control and Prevention

data_processing:
The raw fastq data files were aligned to the V. cholerae EL TOR N16961 reference genome (NC_002505.1 and NC_002506.1) using Bowtie, an ultrafast, memory-efficient short read aligner available on the Galaxy web-based platform. The generated sam data files were further filtered out to remove unmapped reads and converted to bam data files using the Galaxy NGS: SAM Tools. For H-NS binding sites (peaks) definition and quantitation, peak annotation reports and location of the nearest downstream genes, SeqMonk v0.27.0 was used, a program for visualizing and analyzing large set of mapped genomic regions (Babraham Institute). For peak calling, the Model-based Analysis of ChIP-Seq (MACS) algorithm within SeqMonk was used adjusting the P-value cutoff to 1.0E-05, the sonicated fragment size to 300 bp and using the input sample as a control. For peak quantitation the Read Count Quantitation panel was used correcting for total counts and log-transforming the counts.
Genome_build: NCBI Reference Sequences: NC_002505.1 and NC_002506.1
Supplementary_files_format_and_content: The excel file contains a report of the H-NS peaks detected by the peak calling analysis. It contains the genome coordinates of the peaks, the locus tag of the gene at the beginning of the peaks, the H-NS mean enrichment of the peaks, and the function associated with genes inside the peaks. The bed files contain the genome coordinates of H-NS peaks and the coordinates at the summit of the peaks. The wiggle plot files contain the wiggle plots for the Anti-FLAG and Input samples

organism: Vibrio cholerae

source_name: LB liquid medium planktonic cells

growth_protocol: V. cholerae cells were grown in 50 mL LB medium at 37°C with agitation (225 rpm) to optical densities at 600 nm (OD600) of 0.5. Culture media was supplemented with ampicillin (Amp, 100 µg/mL).

extract_protocol:
The ChIP protocol was carried out as described before (Wang H., et al. 2012. Appl Environ. Microbiol. 78(7):2482-8) with modifications. Briefly, nine 100 µl cell lysate samples were combined to perform the immunoprecipitation. The final purified IP DNA was resuspended in 30 µl for a concentration factor of 60 compare to our regular ChIP procedure. The DNA concentration of the anti-FLAG (7.2 ng/µl) and input (23.0 ng/µl) samples were determined by the Qubit® Fluorometric Quantitation System (Life Technologies).
Twenty ng of anti-FLAG and input DNA samples were used for library preparation for the Illumina sequencing using the TruSeq ChIP kit (Illumina, San Diego, CA) following manufacturer’s protocol. Briefly, DNA samples were end-repaired and phosphorylated using a combination of Klenow, T4 DNA Polymerase and T4 polynucleotide kinase.  An A base was added to the newly blunt ended molecules followed by adaptor ligation is a standard ligation reaction. Utilizing adaptors than contain a 6 bp index it was run several samples per lane in the HiSeq2000 instrument (Illumina). The ChIP-Seq libraries were then amplified using PCR, quantitated with qPCR and loaded to a standard concentration of 2.5 pM per lane. A standard paired-end sequencing reaction was done generating 50 bp of sequence from each direction of sequencing. The raw data was converted from .bcl file format to .fastq file format for downstream analysis. This was done using CASAVA v1.8.2 software from Illumina.

tag: od600 nm

tag: phenotype

value: C7258 hns::hns-flag


title: WT-IM-H3K27me3

description: Chromatin IP against H3K27me3


title: anti-FLAG sample


title: WT-SAM-H3K4me3

description: Chromatin IP against H3K4me3


title: WT-SAM-H3K27me3

description: Chromatin IP against H3K27me3


title: C_Input_hMSC_rep1

city: Beijing

first: Jingyi

last: Li

address: Yiheyuan Road, No.5, Haidian District

institute: Peking University

description: Chromatin input

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to gynab refference genome (hg19) using BWA software
RPKM of each gene was determined by the following formula: RPKM=TR/(MR(million)*EL(KB)), TR is the total reads that mapped to the reference, MR is total number of the reads that mapped to one of the transcripts of the gene, EL is the length of the longest transcript of a gene.
Unique mapping reads were used to call peaks by MACS(v1.4) software
Genome_build: hg19
Supplementary_files_format_and_content: [RNA-Seq] txt files which include the RPKM information of each RNA-Seq sample
Supplementary_files_format_and_content: [ChIP-Seq] bed files which include the peaks called by MACS(v1.4)
Supplementary_files_format_and_content: [ChIP-Seq] bedgraph files which depict the reads distribution among the genome

source_name: Mesenchymal stem cell

growth_protocol: H9 hESCs (WiCell Research) and their WRN mutant derivatives were maintained on Mitomycin C treated mouse embryonic fibroblasts (MEFs) in hESC medium or on Matrigel (BD Biosciences) coated plates in mTeSR medium (STEMCELL Technology). Human bone marrow-derived MSCs were maintained in Minimum Essential Medium (MEM) Alpha Medium supplemented with 10% FBS, and 0.1 mM NEAA with or without 1ng/ml bFGF.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody(anti-H3K9me3, abcam, ab8898).
Libraries were prepared by library construction NEBNext kit according to the manufacturer’s protocols

treatment_protocol: We sought to generate an isogenic human embryonic stem cell (hESC) line by knocking out the conserved 15th and 16th exons of WRN gene encoding for the DNA helicase domain of the WRN protein by helper-dependent adenoviral vector (HDAdV).

value: Mesenchymal stem cell

value: WT

value: none (input)


title: C_Input_hMSC_rep2

description: Chromatin input


title: C_H3K9me3_KO_hMSC_rep2

description: Chromatin IP against H3K9me3

value: H3K9me3 (Abcam, catalog# ab8898, lot# GR130994-1)


title: C_H3K9me3_KO_hMSC_rep1

description: Chromatin IP against H3K9me3

value: H3K9me3 (Abcam, catalog# ab8898, lot# GR111948-1)


title: C_H3K9me3_WT_hMSC_rep1

description: Chromatin IP against H3K9me3


title: Adj-Epi02

city: New York

first: Dingcheng

last: Gao

state: NY

address: 1300 York Ave

department: CT Surgery

institute: Weill Cornell Medical College

description: processed data file: NSCLC-Epi.xlsx

data_processing:
Illumina CASAVA v1.8.2 software was used for basescaling.
RNA sequencing reads were analyzed using FastQC to detect potential problems. Then short reads were aligned to the mm9 reference genome using TopHat with default parameters.
FPKMs (Fragments per kilobase per million mapped reads) (Mortazavi et al. 2008) were determined for all RefSeq genes using CuffLinks. Read counts were obtained using HTseq (Anders et al., 2014).
Genome_build: mm9
Supplementary_files_format_and_content: excel spreadsheet include FPKM values for each Sample.

source_name: Normal adjacent lung tissue_Epi

extract_protocol:
Tumor and normal adjacent lungs tissue were minced and dissociated to make single suspension. After staining with proper antibody of surface markers, cells were sorted usign BD Aria II sorter. The RNA was harvested from the sorted cells using Arcturus PicoPure RNA isolation kit. Illumina TruSeq RNA Sample Prep Kit v2 (Cat#RS-122-2001) was used with 16-33ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols(Illumina TruSeq RNA Sample Prep Kit v2 (Cat#RS-122-2001).

value: Normal adjacent lung tissue

value: epithelial cells (Epi)


title: CD59 screen

city: Boulder

first: Eric

middle: Michael

last: Davis

state: Colorado

address: MCDB 347 UCB, Gold A345C

department: MCDB

institute: University of Colorado, Boulder

description: CD59 screen

data_processing:
Library strategy: PhiT-Seq
FASTQ files were preprocessed to filter duplicate reads.
FASTQ files containing unique sequences were aligned to the human genome (hg19) using Bowtie software v0.12.08
Aligned sequences were intersected with gene tables obtained from the UCSC genome browser containing either exons or introns using BEDTools software v2.17.0
Unique insertions per gene were counted for exons and for introns. The total numbers of sense and antisense insertions within introns were counted for each gene. The total number of insertions were counted for exons for each gene, regardless of strand.
Genome_build: hg19
Supplementary_files_format_and_content: Uniqe insertion counts per intron (sense and antisense) and exon, per gene.

source_name: HAP1 cells

growth_protocol: HAP1 cells were cultured in Iscove’s Modified Dulbecco’s Medium supplemented with 10% fetal bovine serum (FBS, Sigma) and penicillin/streptomycin (Sigma).

extract_protocol:
Genomic DNA was extracted from HAP1 cells using a QIAamp DNA Mini Kit (Qiagen).
Linear PCR was performed using 2 mg of genomic DNA as template and the following primer: 5¢-Biotin-GGTCTCCAAATCTCGGTGGAAC-3¢. After 125 cycles of amplification, the linear PCR products were purified using Dynabeads (M280 Biotin Binder, Life Technologies). On-bead ligation of a 5¢ phosphorylated, 3¢ ddC linker was performed using Circligase II (Epicentre). The product was purified and used as a template for PCR to add Illumina adapter sequences.

treatment_protocol: Live HAP1 cells were labeled on ice with anti PrP or anti CD59 antibodies, and sorted for cells with reduced cell surface levels of the coresponding protein levels.

value: Haploid

tag: mutagenesis

value: Gene trap mutated

value: PrP


title: PrP screen

description: PrP screen


title: Adj-Epi03

description: processed data file: NSCLC-Epi.xlsx


title: WT-SAM-RNAseq-replication1

description: RNA-seq


title: DLD1V

city: Oviedo

first: Agustin

middle: F

last: Fernandez

email: affernandez@hca.es, agusff@gmail.com

state: Asturias

address: Avenida de Roma s/n

department: IUOPA

country: Spain

institute: Oviedo University-HUCA

description: Chromatin IP against mock

data_processing:
Alignment: Unfiltered 40 bp sequence reads were aligned against the human reference genome (hg18 (NCBI build 36.1, March 2006) using Illumina's ELANDv2 algorithm on its "eland_extended" mode from within CASAVA-1.7 package. Raw sequences were defined as reads passing purity filter before genome alignment. Only the reads with a unique alignment in the reference genome were used for the peak detection.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: colon cancer cell line

growth_protocol: All cell lines used in this study were maintained in Dulbecco's modified Eagle's medium containing 10% fetal bovine serum and 2 mM L-glutamine (Invitrogen, Paisley, UK).

extract_protocol: ChIP samples were processed into sequencing libraries with a ChIP-Seq sample preparation kit (Illumina) in accordance with the manufacturerâs instructions 2. Briefly,  each sample was electrophoresed on agarose gel and a fraction of 100-200 bp was taken. Extracted DNA was processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "ChIP Sequencing Sample Prep Guide" (part # 11257047 Rev. A), with the exception that gel extraction was replaced with Agencourt AMPure XP (BeckmanCoulter) bead purification. Each adapter-ligated library was PCR amplified with Illumina PE primers for 15 cycles. Independent aliquots were done with Phusion High-Fidelity DNA pol (Finnzymes Reagents) and Accuprime GC Rich pol (Invitrogen), and pooled after amplification. The resulting purified DNA libraries were applied to an Illumina flow cell for cluster generation and sequenced on the Genome Analyzer IIx (GAIIx; Illumina) by following manufacturer's protocols.

treatment_protocol: For transduction of DLD1 cells, lentiviruses at a multiplicity of infection of 10-60 were added to the culture medium in the presence of 8  g/ml polybrene (Sigma) for 8 h, typically yielding more than 95% transduced (GFP-positive) cells.

value: colon cancer cells mock

tag: vendor

value: Invitrogen

tag: catalog number

tag: lot number


title: Inputs pool

description: input DNA

value: colon cancer cells input

value: none, input


title: DLD1DK

description: Chromatin IP against DKK1

value: colon cancer cells transfected with DKK-1


title: Adj-Epi01

description: processed data file: NSCLC-Epi.xlsx

tag: tissue


title: Adj-Neu04

description: processed data file: NSCLC-Neu.xlsx

source_name: Normal adjacent lung tissue_Neu

value: neutrophils (Neu)


title: jmj703-IM-H3K4me3

description: Chromatin IP against H3K4me3

value: IM from 10-12 leaf stage


title: Adj-Neu02

description: processed data file: NSCLC-Neu.xlsx


title: Adj-IMMC02

description: processed data file: NSCLC-IMMC.xlsx

source_name: Normal adjacent lung tissue_IMMCs

value: immature monocytic myeloid cells (IMMCs)


title: Adj-IMMC03

description: processed data file: NSCLC-IMMC.xlsx


title: Adj-IMMC01

description: processed data file: NSCLC-IMMC.xlsx


title: Tum-Neu02

description: processed data file: NSCLC-Neu.xlsx

source_name: Lung tumor_Neu

value: Lung tumor


title: Tum-Neu01

description: processed data file: NSCLC-Neu.xlsx


title: Tum-Epi02

description: processed data file: NSCLC-Epi.xlsx

source_name: Lung tumor_Epi


title: Tum-IMMC02

description: processed data file: NSCLC-IMMC.xlsx

source_name: Lung tumor_IMMCs


title: C_Input_hMSC_rep3

description: Chromatin input

value: Mesenchymal stem cell

value: WT

value: none (input)


title: C_H3K9me3_WT_hMSC_rep2

description: Chromatin IP against H3K9me3

value: H3K9me3 (Abcam, catalog# ab8898, lot# GR130994-1)


title: Tum-IMMC03

description: processed data file: NSCLC-IMMC.xlsx


title: Tum-IMMC01

description: processed data file: NSCLC-IMMC.xlsx


title: m_WT_hMSC

description:
Total DNA extracted from cells
RRBS
processed data file: hMSC-WT-RRBS-TARRBS.bed.gz

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to gynab refference genome (hg19) using BWA software
RPKM of each gene was determined by the following formula: RPKM=TR/(MR(million)*EL(KB)), TR is the total reads that mapped to the reference, MR is total number of the reads that mapped to one of the transcripts of the gene, EL is the length of the longest transcript of a gene.
Unique mapping reads were used to call peaks by MACS(v1.4) software
Genome_build: hg19
Supplementary_files_format_and_content: [RNA-Seq] txt files which include the RPKM information of each RNA-Seq sample
Supplementary_files_format_and_content: [ChIP-Seq] bed files which include the peaks called by MACS(v1.4)
Supplementary_files_format_and_content: [ChIP-Seq] bedgraph files which depict the reads distribution among the genome
Supplementary_files_format_and_content: [RRBS-Seq] bed files which include the C and C+T of RRBS

extract_protocol:
Total DNA was extracted from the cells using the DNeasy Blood & Tissue Kit (Qiagen) following the manufacturer’s protocol
For RRBS, 100-200ng of genomic DNA was digested with Msp I and purified by QIAquick PCR Purification kit (Qiagen)QIAquick kit. 50-600bp fragments were selected by 2% agarose gel. After addition of spike-in controls, samples were end-repaired, A-tailed and ligated to methylated adapters employing TruSeq DNA Sample Preparation Kit (Illumina). The ligated DNA was then treated with bisulfate using MethylCode Kit (Invitrogen) converting unmethylated cytosine (C) into uracil (U). Finally, sequencing libraries were prepared by PCR amplification with PfuTurbo C× Hotstart DNA polymerase (Agilent Technologies).


title: Tum-Epi01

description: processed data file: NSCLC-Epi.xlsx

value: epithelial cells (Epi)


title: ChIP-seq_H3K27me3_KO_hMSC

description: Chromatin IP against H3K27me3

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to gynab refference genome (hg19) using BWA software
Unique mapping reads were used to call peaks by MACS(v1.4) software
The abundance measurements were determined by RPKM with the fomula: RPKM=TR/(MR(million)*EL(KB)), TR is the total reads that mapped to the reference, MR is total number of the reads that mapped to one of the transcripts of the gene, EL is the length of the longest transcript of a gene.
Genome_build: hg19
Supplementary_files_format_and_content: bed files whilch include the peaks called by MACS(v1.4)
Supplementary_files_format_and_content: bedgraph files which depict the reads distribution among the genome
Supplementary_files_format_and_content: .txt files which include abundance measurements (RPKM)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Sequencing libraries were constructed by TruSeq DNA Sample Preparation Kit (Illumina, #FC-121-2001) according to the manufacturer’s manuals.

value: WRN-KO


title: ChIP-seq_IgG_H3_hMSC

description: Chromatin IP against IgG

value: IgG (Santa Cruz, sc-2027, rabbit)


title: ChIP-seq_H3K27me3_WT_hMSC

description: Chromatin IP against H3K27me3


title: ChIP-seq_H3K4me3_WT_hMSC

description: Chromatin IP against H3K4me3

value: H3K4me3 (Abcam, ab8580)


title: Adj-Neu03

description: processed data file: NSCLC-Neu.xlsx

value: Normal adjacent lung tissue


title: RNA-seq_WRN-KO_hESC_rep1

description: Total RNA extracted from cells

source_name: Embryonic stem cell

extract_protocol:
Total RNA was extracted from the cells using the RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Embryonic stem cell


title: RNA-seq_WRN-KO_hESC_rep2

description: Total RNA extracted from cells


title: RNA-seq_WT_hMSC_rep1

description: Total RNA extracted from cells


title: RNA-seq_WT_hESC_rep2

description: Total RNA extracted from cells


title: RNA-seq_WT_hESC_rep1

description: Total RNA extracted from cells


title: RNA-seq_WRN-KO_hMSC_rep1

description: Total RNA extracted from cells


title: ChIP-seq_H3K4me3_KO_hMSC

description: Chromatin IP against H3K4me3


title: Adj-Neu01

description: processed data file: NSCLC-Neu.xlsx


title: MA2_3_G17_82_r1

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
Data were mapped to the Arabidopsis thaliana reference genome version 10 (TAIR10)
MethylC-seq analysis were performed as described in Schmtiz et al. Epigenome-wide inheritance of DNA methylation variants in a recombinant inbred population. Genome Research (2013).
Genome_build: TAIR10
Supplementary_files_format_and_content: MA[pedigreeID]_[experimentID]_G[generationsFromCommonFounder]_[lineNumberID]_r[replicate].txt.gz contains for every cytosine in the TAIR 10 genome:   Chromosome, strand, position in the genome, context, methylated coverage and  total coverage   Uncompressed data is in a tab delimited format.    Format, per column:    <chr TAIR10>  <strand TAIR10>  <C position TAIR10>  <sequence context of the cytosine> X=CG, Y=CHG and Z=CHH     <methylated coverage>  <total coverage>

organism: Arabidopsis thaliana

source_name: leaf tissue

growth_protocol: Arabidopsis thaliana were grown in long days (16 hours of light) at 24C

extract_protocol: Genomic DNA (gDNA) was purified from Arabidopsis thalina leaf tissue using a Qiagen DNease Plant Kit (Qiagen, Valencia, CA), according to the manufacturer’s instructions. MethylC-Seq libraries were constructed according to Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR. (2014) MethylC-seq: Base resolution whole genome bisulfite sequencing library preparation. Nature Protocols (in press)

tag: cultivar

value: leaf

tag: age

value: ~3 week old plants


title: m_KO_hMSC

description:
Total DNA extracted from cells
RRBS
processed data file: hMSC-KO-RRBS-TARRBS.bed.gz

value: KO


title: MA2_3_G16_82_r1


title: Liver from RYGB mouse 8wk after RYGB 3

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control to filter out bad samples and reads
Alignment to human genome (hg19) using Tophat 2
Read count quantification using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Read Count Table

source_name: Liver from RYGB mouse 8wk after RYGB

extract_protocol:
Total RNA was isolated with TRI Reagent (Molecular Research Center) and purified with the RNeasy MinElute Cleanup kit (Qiagen) using an on-column DNAse treatment to ensure absence of genomic DNA contamination according to the manufacturer’s supplied protocol.
2695 libraries were constructed using the Illumina TruSeq Stranded mRNA kit (Cat. No. RS-122-2101) following the manufacturer's supplied protocol. 2960 libraries were constructed using the Illumina TruSeq Stranded Total RNA kit (Catalog No. RS-122-2201) following the manufacturer's supplied protocol.

value: liver


title: MA2_3_G14_82_r1


title: MA2_3_G1_82_r1


title: Liver from DIO mouse 8wk after no surgery 5


title: Liver from RYGB mouse 8wk after RYGB 4


title: Liver from RYGB mouse 8wk after RYGB 5


title: MA2_3_G16_48_r1


title: MA2_3_G7_82_r1


title: Liver from RYGB mouse 8wk after RYGB 2


title: Liver from RYGB mouse 8wk after RYGB 1


title: MA2_3_G17_48_r1


title: MA2_3_G7_48_r1


title: MA2_3_G14_48_r1


title: RNA-seq_WT_hMSC_rep2

description: Total RNA extracted from cells


title: Liver from DIO mouse 8wk after no surgery 3


title: RNA-seq_WRN-KO_hMSC_rep2

description: Total RNA extracted from cells


title: Liver from DIO mouse 8wk after no surgery 2


title: MA2_3_G1_48_r1


title: Liver from DIO mouse 8wk after no surgery 1


title: Liver from DIO mouse 8wk after gallbladder-ileum anastomosis 3


title: MA1_3_G29_12_r1


title: MA1_3_G30_12_r1


title: Liver from DIO mouse 8wk after gallbladder-ileum anastomosis 2


title: MA1_3_G28_12_r1


title: MA1_3_G26_12_r1


title: Liver from DIO mouse 8wk after gallbladder-ileum anastomosis 1


title: Liver from DIO mouse 8wk after no surgery 4


title: MA1_3_G25_12_r1


title: MA1_3_G19_12_r1


title: MA1_3_G20_12_r1


title: MA1_3_G18_12_r1


title: No.8 resistant housefly strain

status: Public on May 12 2015

city: Slagelse

first: Khalid

last: Mahmood

address: Forsøgsvej 1

department: Agro-ecology

country: Denmark

institute: Aarhus University

data_processing:
After removal of adaptor sequences, data were aligned and de novo assembled using version 2.6 of the newbler assembler  (454 Life Sciences/Roche, Branford. Clustering  and assembly of all reads in contigs after the sequencing were done using MIRA 4.0 and contigs were initially analyzed by BLAST analysis.
Genome_build: de novo assembly
Supplementary_files_format_and_content: Total and normalized counts

organism: Musca domestica

source_name: 791 resistant strain

growth_protocol: The spinosad selected 791spin strain was created by selection with spinosad of the multi-resistant 791a strain strain that was collected in Denmark in 1997. The 791spin females are 21-fold spinosad-resistant to spinosad at the LC50, whereas 791spin male houseflies were 6-fold resistant. The flies were collected on private land with consent of the owner. The field collection did not involve endangered or protected species.Housefly breeding followed standard laboratory conditions. Egg laying was performed on crumpled filter paper soaked in whole milk. Breeding jars (5 L plastic buckets) containing 4 L of medium were seeded with 200 mg of eggs, corresponding to 2700 eggs. The breeding medium consisted of wheat bran 400 g, lucerne meal 200 g, baker’s yeast 10 g, malt extract 15 mL, whole milk 500 mL and water 500 mL. For adult feeding, cube sugar and water were given continuously. Feeding started after emergence with whole-milk powder mixed with icing sugar (1:1 w/w).Houseflies for transcriptome analysis were five to seven days old, adult male and female flies, which were fed sugar as the only food source.

extract_protocol:
Total RNA from whole bodies of pooled flies (approx. 1.2 g equivalent to 60 flies) was extracted using the RNeasy Maxi Kit (Qiagen). Flies were thoroughly ground with liquid nitrogen, a mortar and pestle and otherwise following the manufacturer’s protocol. Isolated RNA was DNase-treated and concentrated using the RNeasy MinElute Kit (Qiagen). Gel electrophoresis and spectrophotometry (Nanodrop; NanoDrop Technologies, Wilmington, USA) was performed to assess the integrity and the concentration of each RNA sample, which was dissolved in RNase-free water and stored at -20ºC until use.
A normalized cDNA library was prepared from 12.2 µg mRNA prepared from adult male and female houseflies. The normalized cDNA library was size fractioned to approx. 500-1,200 bp. High throughput sequencing on GS FLX Titanium of the Musca cDNA library was done according to the standard protocols using a Genome Sequencer FLX Titanium Instrument (Roche Diagnostics). Preparation of cDNA, normalization and sequencing was performed by Eurofins MWG GmbH (Ebersberg, Germany).

tag: insecticide resistance

value: Spinosad

value: 5-7 days

tag: gender

value: pooled male and female

tag: developmental stage

value: adult

value: whole fly


title: No.7 resistant housefly strain


title: No.1 resistant housefly strain


title: No.3 resistant housefly strain


title: No.5 resistant housefly strain


title: No.6 resistant housefly strain


title: No.4 resistant housefly strain


title: No.2 resistant housefly strain


title: Liver from DIO mouse 8wk after gallbladder-ileum anastomosis 4


title: Mid-level interaction poly(A)-

city: Frankfurt

first: Fabian

last: Afonso-Grunz

address: Max-von-Laue-Str. 9

country: Germany

institute: University of Frankfurt

description: rRNA-depleted poly(A)- total RNA

data_processing:
Library strategy: Dual 3'Seq coupled to deepSuperSAGE or MACE
Basecalling was performed by Illumina's CASAVA pipeline (1.7.0 and 1.8.1)
PCR duplicates identified by TrueQuant (GenXPro GmbH) were excluded from the datasets.
Barcoded reads were sorted from the bulked sequencing data, followed by clipping of the barcode and adaptor sequences.
DeepSuperSAGE reads were mapped with Bowtie allowing two mismatches, but reporting only those alignments with the lowest number of mismatches (-v2  -strata -best), and MACE reads were mapped with the short read mapper Novoalign v2.07.13 (Novocraft Technologies) using default parameter settings.
Annotated reads in each library were counted, and subsequently combined to three distinct expression matrices comprising reads from the  poly(A)+ or poly(A)− fraction of host cells as well as the poly(A)− fraction of SL1344 cells, respectively. Subsequently, the three matrices were separately processed with DESeq.
Genome_build: Hg19 from the UCSC table browser for HeLa-S3 cells and custom reference comprising the operon-structure for SL1344 cells
Supplementary_files_format_and_content: Tab-delimited text file of the expression matrices with median-normalized values for deepSuperSAGE and raw read counts for MACE libraries

organism:
Homo sapiens
Salmonella enterica

source_name: Interacting cells

growth_protocol: Culture of HeLa-S3 cells was performed in T-75 flasks using DMEM supplemented with 10% fetal calf serum, 2mM L-glutamine and 1mM sodium pyruvate at 37 °C in a humidified 5% CO_2 atmosphere. Salmonella SL1344 was streaked onto LB-plates and incubated overnight at 37 °C. A single colony was then used to inoculate an overnight culture in 3 ml LB medium. For preparation of the infection assays, cells were resuspended in DMEM.

extract_protocol:
Total RNA isolation was carried out with the mirVana miRNA Isolation Kit (Ambion) according to the manufacturer’s protocol for isolation of total RNA, followed by quality control of the isolates with the Agilent 2100 Bioanalyzer.
Library preparation was performed as described in Afonso-Grunz et al. XYZ

treatment_protocol: Infection assays were carried out with an MOI of 5. Total RNA from both HeLa-S3 and Salmonella SL1344 cells was isolated after three different points of time post infection and additionally from non-interacting cells.

tag: cell line

tag: employed library preparation method

value: DeepSuperSAGE

tag: point of time post infection

value: 4 hours post infection


title: Early interaction poly(A)- (MACE)

description: rRNA-depleted poly(A)- total RNA

tag: strain

value: Massive Analysis of cDNA Ends (MACE)

value: 0.5 hours post infection


title: Pathogen cells poly(A)+

description: rRNA-depleted poly(A)+ total RNA

organism: Salmonella enterica

source_name: Cultivated cells

value: Non-interacting cells


title: Late interaction poly(A)-

description: rRNA-depleted poly(A)- total RNA

value: 24 hours post infection


title: Pathogen cells poly(A)-

description: rRNA-depleted poly(A)- total RNA


title: Early interaction poly(A)+ (MACE)

description: rRNA-depleted poly(A)+ total RNA


title: Late interaction poly(A)+

description: rRNA-depleted poly(A)+ total RNA


title: Mid-level interaction poly(A)+

description: rRNA-depleted poly(A)+ total RNA


title: Early interaction poly(A)-

description: rRNA-depleted poly(A)- total RNA


title: R1284

city: Tampa

first: Derek

last: Wildman

state: FL

address: 3720 Spectrum Blvd

institute: University of South Florida

data_processing:
Illumina adapters trimmed
Discarded reads with Q<20
de-novo assembly generated using Trinity r2012-10-05
FKPK values were generated in Trinity using the "run_RSEM_align_n_estimate.pl"
Supplementary_files_format_and_content: .txt files with FPKM values for transcripts generated with Trinity.  FASTA files with the assembled sequences are available on the series record.

organism: Spalax carmeli

source_name: placenta

extract_protocol:
The villous portion of the tissue was homogenized in Trizol resulting in the isolation of total RNA following the manufacturer's instructions (Life Technologies, Grand Island, NY). The RNA was further purified using Qiagen’s RNeasy Midi Kit in conjunction with the RNase-Free DNase Set following the manufacturer’s protocol to remove any contaminating DNA from the sample (Valencia, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: placenta


title: Early interaction poly(A)+

description: rRNA-depleted poly(A)+ total RNA


title: MA1_3_G21_12_r1


title: Input Sample

first: Wanshi

last: Cai

address: 1 Beichen West Road, Chaoyang District

department: INSTITUTE OF ZOOLOGY

institute: CHINESE ACADEMY OF SCIENCES

data_processing:
Basecalls performed using CASAVA version 1.8
After basecalling, do data cleaning. Filter reads contaminated by adapter at 3’-end by software Cutadap and then filter reads with low quality.
Map cleaned reads to genome (dm3 from UCSC genome database) by using Bowtie.
Read counts will be normalized across input control (Sample_I) and IP sample (sample_M), taking into account of sequencing depths, and the normalized counts are used to call peaks.
A t-statistic similar to the TileMap t-statistic is computed. Bins with window statistic >= 3 are called as peaks. Peak false discovery rate (FDR<=0.01).
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited text files include
rank: peak rank
chromosome: chromosome
start: peak start
end: peak end
strand: peak strand (currently all +)
peak_length: peak length
FDR: false discovery rate
left_peakboundary: refined left peak boundary, this is the mode of the + strand peak
right_peakboundary:  refined right peak boundary, this is the mode of the - strand peak
peak_summit: position with the highest signal
bound_center: (left_peakboundary+right_peakboundary)/2
bound_width: right_peakboundary - left_peakboundary + 1
maxT: maximal window statistics in the peak
maxT_pos: position where the maxT is achieved
max_log2FC: maximal log2 fold change between normalized IP and control DNA fragment counts. Before computing the fold change, a pseudocount 1 is added to both the denominator and numerator.
maxFC_pos: position where max_log2FC is obtained
minuslog10_minPoisP: -10*log10(p-value). The p-value is obtained by the local poisson read sampling model.
minPoisP_pos: position where the minimal p-value (or the maximal minuslog10_minPoisP) is achieved.
normalized_couts_Sample_M: The normalized DNA fragment counts in the peak regions for Sample_M.
normalized_couts_Sample_I: The normalized DNA fragment counts in the peak regions for Sample_I.

source_name: adult intestines

growth_protocol: The ChIP-Seq assay was performed using Drosophila adult intestines with JAK/STAT signaling highly activated.We used esg-Gal4,Gal80ts driver to overexpress the JAK/STAT pathway ligands Upd and the transcription factor STAT92e in the progenitor cells at 29℃ for 10 days.

extract_protocol:
About 400 Drosophila adult midguts(with the hindgut and Malpighian excluded) were dissected in ice-cold PBS, and then cross-linked with 1% formaldehyde for 15 minutes. After washing process to remove the formaldehyde, intestinal tissue was lysed with RIPA buffer which contains 1% SDS on ice for 30 minutes. The sonication of chromatin was performed using the Covaris (AFA) system with 3% power output for 5 minutes each on 100μl lysates.STAT92E-bound chromatin fragments were enriched by immunoprecipitation with mouse raised STAT92E antibody. Most chromatin fragments resulting from sonication occurred between 200 and 400 bp.The process of dilution, antibody incubation, protein G pull down, beads washing, DNA complex elution, de-link, RNAse A / protease K digestion and DNA extraction all with normal ChIP protocols.The high throughput sequencing process was carried out using the Illumina solexa system.
ChIP and input libraries were prepared using NEXTflex™ Illumina ChIP-Seq Library Prep Kit (Illumina) according to the manufacturer’s protocol. The indexed libraries were pooled together, and sequenced using the Illumina HiSeq 2000 (Illumina) instrument.

tag: strain  background

tag: fly genotypes

value: esgts>Upd and STAT92E

tag: cultural condition

value: 29℃ for 10 days

value: intestines

tag: chip antibody


title: R1280

data_processing:
Illumina adapters were trimmed and reads that had Q<20 were discarded. The de-novo assembly was generated using Trinity r2012-10-05. FPKM values for each transcript were generated in Trinity using the "run_RSEM_align_n_estimate.pl".
Supplementary_files_format_and_content: .txt files with FPKM values for transcripts generated with Trinity.  FASTA files with the assembled sequences are available on the series record.

organism: Nannospalax galili


title: STAT92E ChIP

value: mouse-raised STAT92E antibody (self-made); 100-150aa polypeptides of STAT92E protein chosen as the antigen


title: mvt_cd24_pos_2

city: Oakland

first: Ravi

last: Sachidanandam

state: CA

address: 2945 Webster St

institute: Girihlet Inc.

description: MVT cells with CD24 cell surface expression

data_processing:
The data for each sample (Ran1 through Ran6) were merged from different runs
The reads were mapped to the mouse genome (mm9), only exact mappings were used. The mappings and processing were done using custom software and pipelines
The processed file shows the mappings and the annotations derived from the UCSC tables as well as the number of times (frequency) the read was found in the sequencing data.
Genome_build: mm9
Supplementary_files_format_and_content: The processed data file has the following columns Sequence, Chromosome, Start, Stop, Annotation, frequency

source_name: MVT1 cells

growth_protocol: Cells were cultured in DMEM supplemented with 10% fetal bovine serum and antibiotics (penicillin:streptomycin) at 37 c in a humidified atmosphere consisting of 5% CO2 and 95 % air.

extract_protocol:
Total RNA was extracted from cells using the Total RNA Purification Kit (NORGEN biotek corp) according to manufacturer's instructions. cDNA libraries were prepared using 1 ug of total RNA using the Truseq RNA sample preparation kit v2 (illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB/N

tag: cell type

value: mammary epithelial cancer cells

tag: cell subtype


title: mvt_cd24_neg_1

description: MVT cells witout CD24 cell surface expression


title: mvt_cd24_pos_1


title: K562.SRSF2.WT

city: Seattle

first: Janine

middle: O

last: Ilagan

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

data_processing:
Illumina Casava1.82 software used for basecalling.
Reads were mapped to the UCSC hg19 (NCBI GRCh37) human genome or UCSC mm10 (NCBI GRCm38) assemblies using Bowtie v1.0.0 and RSEM v1.2.4.
RSEM was modified to call Bowtie with the -v 2 mapping strategy.
RSEM was then invoked with the arguments --bowtie-m 100 --bowtie-chunkmbs 500 --calc-ci --output-genome- bam on the gene annotation file.
Genome_build: hg19 and mm10

source_name: erythroleukemia cells

extract_protocol:
Cells were sorted and expanded over a week, RNA were harvested using Trizol reagent. Illumino TruSeq RNA Sample Prep Kit (Cat#RS-122-2001)
RNA libraries were prepared for sequencing using standard Illumina protocols with a few modification.  After adapter ligation, AMPure XP Beads were used to select 100 – 400 bp DNA fragments by varying bead-to-library volume ratios. 0.5X beads were added to the sample library to select for fragments < 400 bp followed by 1X beads to select for > 100 bp fragments. DNA fragments were amplified using 15 cycles of PCR and separated by 2% agarose gel electrophoresis. DNA fragments (300 bp) were purified using the Qiagen MinElute gel extraction kit.

value: erythroleukemia cells


title: TF-1.siSRSF2


title: K562.mCherry


title: TF-1.siNegative


title: K562.SRSF2.P95H


title: K562.SRSF2.P95R


title: smrna-h7-day21-keb rep 3

first: Hannele

last: Ruohola-Baker

address: UW Medicine at South Lake Union, S580, 850 Republican Street

department: Department of Biochemistry

institute: University of Washington

description: results file: mirna-read-counts.tsv

data_processing:
Illumina Casava1.7 software used for basecalling.
Aligned to hg19 using rna-star 2.3.0
Reads counted for genes annotated in AceView Aug10
miRNA read counts generated with miRExpress 2.1.4
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited mRNA/miRNA read counts

extract_protocol:
Total RNA samples were extracted using RNAeasy mini kit
RNA and Small RNA libraries were prepared independently using Truseq library preparation kits (Illumina) following the manufacturer's protocols.

value: H7 hESC cell line

tag: time point

value: 21 days


title: smrna-h7-day21-dd rep 3

description: results file: mirna-read-counts.tsv


title: mvt_cd24_neg_3


title: smrna-h7-day15-dd rep 3

description: results file: mirna-read-counts.tsv

value: 15 days


title: smrna-h7-day21-keb rep 2

description: results file: mirna-read-counts.tsv


title: K562.SRSF2.P95L


title: smrna-h7-1yr-keb rep 2

description: results file: mirna-read-counts.tsv

value: 1 year


title: smrna-h7-day15-dd rep 2

description: results file: mirna-read-counts.tsv


title: smrna-h7-1yr-keb rep 3

description: results file: mirna-read-counts.tsv


title: smrna-h7-day15-dd rep 1

description: results file: mirna-read-counts.tsv


title: smrna-h7-1yr-keb rep 1

description: results file: mirna-read-counts.tsv


title: mvt_cd24_pos_3


title: let7 rep 3

description: results file: mrna-read-counts.tsv

value: 30 days


title: smrna-h7-day21-dd rep 2

description: results file: mirna-read-counts.tsv


title: ips-1yr

description: results file: mrna-read-counts.tsv

source_name: IMR90 ips

value: IMR90 iPS cell line


title: let7 rep 1

description: results file: mrna-read-counts.tsv


title: smrna-h7-day21-dd rep 1

description: results file: mirna-read-counts.tsv


title: mvt_cd24_neg_2


title: let7 rep 2

description: results file: mrna-read-counts.tsv


title: ev rep 2

description: results file: mrna-read-counts.tsv


title: ev rep 1

description: results file: mrna-read-counts.tsv


title: day20 rep 3

description: results file: mrna-read-counts.tsv

value: 20 days


title: day20 rep 2

description: results file: mrna-read-counts.tsv


title: 1yr rep 3

description: results file: mrna-read-counts.tsv


title: Host cells poly(A)-

description: rRNA-depleted poly(A)- total RNA

value: DeepSuperSAGE

value: Non-interacting cells


title: Th2 NLRP3KO Input

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

country: France

institute: CGFL

data_processing:
Data were processed thanks to galaxy website
Fastq groomer tool was applied
Alignment was performed with Bowtie2 on mm8 reference genome
MACS was applied
MACS files were used on the NEBULLA website
Genome_build: mm8
Supplementary_files_format_and_content: BED files report MACS_peaks

source_name: Naive T cells from spleen and nodes

growth_protocol: CD4 T naive cells were isolated from C57/Bl6 Wt and NLRP3-/- mice. Differentiation was induced in RPMI culture medium complemented with 10% FBS,1% antibiotics in CD3/CD28 coating plates

extract_protocol:
Crosslinking, extraction and shearing of chromatin was performed by using the Truchip chromatin shearing reagent kit from 300,000 Th2 cells by following manufacturer protocol. Then, sheared chromatin was immunoprecipitated with different antibodies by using the Active Motif's ChIP IT Kit by following manufacturer's instructions
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra DNA Library Prep Kit for Illumina. After library validation on a fragment analyzer, the purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the MiSeq device following the manufacturer's protocols.

treatment_protocol: Differentiation was induced with 10 ng/ml IL-4 in presence of IFNgamma blocking antibody for few hours,

value: 7 weeks

tag: genotype/variation

value: NLRP3 KO

value: CD4 T cells

value: none (input)


title: Th2 NLRP3KO IP with Ig antibody

value: anti-Ig (Dako, catalog# X0936, lot# 73343)


title: smrna-h7-day21-keb rep 1

description: results file: mirna-read-counts.tsv


title: Th2 WT IP with BATF antibody

value: Wild-type

value: anti-BATF (Cell Signalling, catalog# sc8638, lot# 1)


title: Th2 NLRP3KO IP with STAT6 antibody

value: anti-STAT6 (Cell Signalling, catalog# sc9362, lot# 4)


title: Th2 WT Input


title: Th2 WT IP with Ig antibody


title: Th2 NLRP3KO IP with NLRP3 antibody

value: anti-NLRP3 (Adipogen, catalog# AG-20B-0014, lot# A22141102)


title: LSK.SRSF2.P95H2

source_name: hematopoietic stem/progenitor cells

value: LSK

value: hematopoietic stem/progenitor cells


title: Th2 WT IP with IRF4 antibody

value: anti-IRF4 (Santa Cruz, catalog# sc6059, lot# B2614)


title: Naive T cells NLRP3KO

description: mRNA purified

data_processing:
Data were processed thanks to galaxy website
Fastq groomer tool was applied
Alignment was performed with TopHat on mm9 reference genome
Cufflink was applied
Genome_build: mm9
Supplementary_files_format_and_content: txt files with Cufflinks output

extract_protocol:
Total RNA was extracted from 300,000 Th2 cells with Trireagent by following manufacturer protocol. Then, 1µg of total RNA was rRNA depleted thanks to Ribominus Eukaryote kit for RNAseq or mRNA purified thanks to NEB kit
Libraries were prepared according to Bioo Scientific's instructions accompanying the Nextflex RNA Seq-Kit for Illumina. Briefly, RNA was heat fragmented and double strand cDNA synthesis was performed in 2 steps. After purification, the double strand cDNA was end repaired and then adenylated. After adapter ligation, DNA was PCR amplified for 12 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were obtained. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the MiSeq device following the manufacturer's protocols.

treatment_protocol: Differentiation was induced with 10 ng/ml IL-4 in presence of IFNgamma blocking antibody for 3 or 6 days,


title: Th2 WT IP with NLRP3 antibody


title: LSK.SRSF2.WT1


title: LSK.SRSF2.P95H1


title: MP.SRSF2.P95H2

value: MP


title: MP.SRSF2.P95H1


title: Naive T cells WT

description: mRNA purified


title: Th2 NLRP3KO IP with IRF4 antibody


title: Th2 NLRP3KO Day 6

description: rRNA depleted RNA

extract_protocol:
Total RNA was extracted from 300,000 Th2 cells with Trireagent by following manufacturer protocol. Then, 1µg of total RNA was rRNA depleted thanks to Ribominus Eukaryote kit for RNAseq
Libraries were prepared according to Bioo Scientific's instructions accompanying the Nextflex RNA Seq-Kit for Illumina. Briefly, RNA was heat fragmented and double strand cDNA synthesis was performed in 2 steps. After purification, the double strand cDNA was end repaired and then adenylated. After adapter ligation, DNA was PCR amplified for 12 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were obtained. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the MiSeq device following the manufacturer's protocols.


title: day20 rep 1

description: results file: mrna-read-counts.tsv

value: H7 hESC cell line


title: 1yr rep 2

description: results file: mrna-read-counts.tsv

value: 1 year


title: 1yr rep 1

description: results file: mrna-read-counts.tsv


title: MP.SRSF2.WT2


title: Host cells poly(A)+

description: rRNA-depleted poly(A)+ total RNA

value: DeepSuperSAGE


title: Th2 WT Day 6

description: rRNA depleted RNA


title: Th2 NLRP3KO Day 3

description: rRNA depleted RNA


title: MP.SRSF2.WT1


title: Th2 WT Day 3

description: rRNA depleted RNA


title: Th2 NLRP3KO IP with BATF antibody


title: Th2 WT IP with STAT6 antibody


title: INT_Replicate_1

status: Public on May 11 2015

city: Kansas City

first: Scott

middle: T

last: Younger

state: MO

address: 2401 Gillham Road

institute: Children's Mercy Kansas City

data_processing:
RNA-Seq Read Alignment: TopHat 2.0.13 with default options using UCSC known genes as reference transcriptome
RNA-Seq Differential Expression: Cuffdiff 2.2.1 with default options using UCSC known genes as reference transcriptome
Genome_build: hg19 (modified to incorporate sequences for Gaussia and Cypridina luciferase)
Supplementary_files_format_and_content: TXT files of expression matrices with FPKM values for each sample

growth_protocol: 125,000 HEK293FT cells were plated per well of gelatinized 12 well plates, in 0.6 mL high glucose Dulbecco’s modified Eagle’s medium (DMEM, Gibco), supplemented with 10% FBS, 1x penicillin/streptomycin and 2 mM L–Glutamine (Gibco). Cells were grown at 37°C and 5% CO2 in a humidified incubator. Cells were transfected one day later with plasmids expression dCas9 and modified sgRNA plasmid, when appropriate, using Lipofectamine 2000 (Life Technologies), following the manufacturer's protocol.  Whole cell RNA was harvested three days later.

extract_protocol:
RNA: TriZol
Illumina TruSeq

treatment_protocol: Transfection mixes comprised 59 ng of dCas9~VP, 11.6 ng of U6-driven sgRNA variant plasmid and 679.4 ng pNEB193 carrier plasmid per well, with 2.25 uL Lipofectamine 2000 (Life Technologies), in 18 uL final volume. Three days later, whole cell RNA was isolated by extraction with Trizol Reagent (Life Technologies), following the manufacturer's protocols.  RNA was precipitated with isopropanol using GlycoBlue (Life Technologies) as a carrier, and subsequently purified using RNEasy spin columns (QIAgen), following the manufacturer's "RNA Cleanup" protocol, with on-column DNase treatment. mRNA seq libraries were prepared using the TruSeq RNA sample preparation kit, v2 (Illumina).

tag: grna

value: INT


title: CasVP_Replicate_1


title: INT_Replicate_2


title: P4P6_Replicate_1


title: CasVP_Replicate_2


title: TOP1_Replicate_2


title: TOP1_Replicate_1


title: sgRNA_Replicate_2

value: sgRNA


title: P4P6_Replicate_2


title: RIP_Replicate_3

data_processing:
Sequence Identification:  Random sequences were extracted from raw fastq files by trimming leading and trailing known sequences from each individual read.
Sequence Counts: Random sequences from all samples were pooled and condensed into a list of unique sequences.  Occurrences of each sequence within individual samples was then tabulated.
Sequence Enrichment: Enrichment was determined using DESeq2.
Genome_build: N/A
Supplementary_files_format_and_content: Tab-delimited files containing random sequences and occurrences per sample.

growth_protocol: 2.1 million HEK293FT cells were plated on gelatinized 10 cm plates in high glucose Dulbecco’s modified Eagle’s medium (DMEM, Gibco), supplemented with 10% FBS, 1x penicillin/streptomycin and 2 mM L–Glutamine (Gibco). Cells were grown at 37°C and 5% CO2 in a humidified incubator. Cells were transfected one day later with plasmids expression dCas9 and the sgRNA plasmid pool, using Lipofectamine 2000 (Life Technologies), following the manufacturer's protocol.  Cells were harvested three days later.

extract_protocol:
Growth media was collected, and cells were washed twice with 10 mL of room temperature PBS (Gibco). Cells were crosslinked by incubation in 0.1% (v/v) formaldehyde in PBS for 10 minutes at room temperature, under very gentle agitation. Crosslinking was quenched by the addition of Glycine to 133 mM and gentle agitation for an additional five minutes at room temperature. The liquid phase was then aspirated; cells were washed twice with room temperature PBS, harvested by scraping, allotted into samples of 1×10^7 cells (typically three samples per 10 cm dish), and pelleted at 200 g in a swinging bucket rotor. PBS was aspirated and cell pellets were flash-frozen in liquid nitrogen and stored at –80°C until use. Cell pellets were thawed on ice, resuspended into 1 mL of ice-cold RIPA(+) buffer (standard RIPA supplemented with 0.1 U/uL RNAseOUT (Life Technologies), 1x EDTA-free Proteinase Inhibitor Cocktail (Thermo Scientific) and 0.5 mM DTT), and lysed for 10 minutes at 4°C with end-over-end agitation. Samples were then sheared using a Branson Digital Sonifier 250 (Emerson Industrial Automation) at 10% amplitude for three 30-second intervals (0.7 seconds on + 1.3 seconds off), with 30-second resting steps between intervals.  Samples were held in ice-cold metal thermal blocks throughout sonication.  Sheared samples were then clarified by ultracentrifugation and diluted with 1 mL each of ice-cold Native Lysis Buffer(+) (25 mM Tris, pH 7.4, 150 mM KCl, 5 mM ETA, 0.5% (v/v) NP-40, supplemented with inhibitors and DTT, as above), filtered through a 0.45 um syringe-mounted filter, and flash-frozen in liquid nitrogen before use. Clarified lysates were thawed on ice and pre-cleared by incubation with buffer-equilibrated magnetic Protein G beads (Life Technologies) for 30 minutes at 4°C, with end-over-end rotation. Cleared lysates corresponding to 5×10^6 cells were then incubated with 6 ug rabbit anti-FLAG antibody (SIGMA) or Rabbit normal IgG (Cell Signaling Technology), for two hours at 4°C with end-over-end rotation. Buffer-equilibrated magnetic Protein G beads were then added and the samples were again rotated end-over-end for one hour at 4°C. Resin was collected and twice washed with Native Lysis Buffer(+) for 10 minutes at 4°C, with end-over-end rotation. Beads were suspended in 56 μL nuclease-free water, and processed alongside input samples (56 μL; 5.6% of the total). All samples were brought to 100 μL in 1x PBS, 2% N-Lauroyl Sarcosine, 10 mM EDTA, 5 mM DTT, 0.4 U/μL RNaseOUT and 2 mg/mL proteinase K (Ambion), final. Formaldehyde crosslinks were reversed by incubation at 42°C for one hour, and then 55°C for one hour, in a thermocycler. RNA was purified using four volumes (400 μL) Agencourt RNAClean XP Beads (Beckman Coulter), following the manufacturer’s protocol, and eluted into 30 μL nuclease-free water.  Residual DNA was removed by treatment with 5 U RNase-free DNAs (RQ1, Promega) in 50 μL, following the manufacturer’s protocol. RNA was subsequently purified using four volumes (200 μL) Agencourt RNAClean XP beads, eluted into 20 μL nuclease-free water.
Sample 1. Five ng of template DNA was PCR amplified using Pfu Ultra II HS polymerase (Agilent), according to the manufacterer's protocol, using gene-spectific primers appended with standard Illumina adapters and multiplexing indexes.  The reaction volume was 50 uL; PCR was performed over 19 cycles. Samples 2–7. Twenty ng of RNA was reverse-transcribed using SuperScript III Reverse-transcriptase (Life Technologies) and a gene specific primer, in 20 uL, following the manufacturer's protocol. cDNA was then amplified over 26 cycles of PCR, in 200 uL reactions, using primers as described for Sample 1. All libraries were putified twice with Agencourt RNAClean XP beads, and eluted into 30 μL nuclease-free water.

tag: antibody

value: anti-FLAG


title: Library


title: RIP_Replicate_1


title: Input_Replicate_1


title: Input_Replicate_2


title: U2AF1(S34F) CMP 3

first: Matt

last: Walter

address: 4940 parkview

department: oncology

institute: washington university in st.louis school of medicine

data_processing:
Initial segmented alignment performed using bowtie (version 2.1.0)
Subsequent spliced alignment performed using TopHat (version 2.0.8) with arguments -g < GTF file of known and predicted mouse transcripts in Ensembl version 67 > and '--library-type fr-firststrand'
Expression estimates in the form of Fragments per Kilobase of exon per Million bases mapped (FPKM) were calculated by Cufflinks version 2.1.1 using default parameters except for ‘--num-threads 4 --max-bundle-length 10000000 --max-bundle-frags 10000000.’
Transcript models were supplied to Cufflinks using the ‘-g’ option and the same GTF described above.
Transcripts corresponding to mitochondrial and ribosomal genes, as indicated by Ensembl gene biotypes, were masked during calculation of transcript expression estimates.
Gene-level read counts were obtained by excluding unmapped reads or secondary read alignments from the BAM files (using samtools view –F 0x0100) and processing the resulting reads using HTseq (version 0.5.4p1; with parameters: --mode intersection-strict --minaqual 1 --stranded reverse --type exon --idattr gene_id).
Gene-level differential expression was determined from gene-level read counts using DESeq2 (version 1.6.1). DESeq2 was applied to genes having more than 20 reads in at least 2 samples. We directly tested for a condition-specific effect on gene expression by instantiating DESeqDataSetFromMatrix with design = ~condition. Results were obtained by invoking results with parameter independentFiltering=FALSE.
Exon-exon junction counts were obtained by parsing the ‘junctions.bed’ file produced by TopHat.
Junction-level differential junction was determined from junction counts using DEXSeq (version 1.12.1). DEXSeq was applied to junctions belonging to genes having at least two exons (as annotated in Ensembl version 67) and which met a minimum read threshold. This threshold required more than five junction reads in at least 2 samples.  ‘DA’, ‘NDA’, ‘D’, and ‘A’ junctions were analyzed together, with ‘N’ junctions (i.e., in which neither the 3’ nor the 5’ splice site was annotated in Ensembl) excluded from analysis. The log fold change was obtained by calling results with parameters name = ‘exonthis.conditionMT’ and independentFiltering = FALSE.
Genome_build: mm9
Supplementary_files_format_and_content: cmp1-3-geo-gene.tsv (gene-level DESeq results):  columns MT1, MT2, MT3, WT1, WT2, and WT3 hold gene-level counts
Supplementary_files_format_and_content: cmp1-3-geo-juncs.tsv (junction-level DEXSeq results): junc.MTX and junc.WTX hold junction-level counts; gene.MTX and junc.WTX hold gene-level counts; junc.chr.start.stop holds mm9 coordinates of junction; gene.FPKM.* hold cufflinks gene-level expression; gene.deseq.* hold gene-level DESeq results; junc.dexseq.* hold junction-level DEXSeq results

source_name: common myeloid progenitor cells

extract_protocol:
RNA was extracted from CMP cells sorted by flow cytometry using Qiagen miRNeasy kit.  Genomic DNA was removed by Turbo DNA free (Ambion).
Ribosomal RNA was depleted (Ribozero), followed by cDNA preparation and TruSeq stranded Illumina library production.

treatment_protocol: rtTA-dependent transgene induction occurred for 5 days using doxycycline chow.  Mice were transplanted with transgenic donor bone marrow cells, and engraftment was allowed for >6 weeks prior to transgene induction.

tag: genotype

value: common myeloid progenitor (Lineage -,c-Kit+, Sca-1-, CD34+, Fcgamma-)

tag: tissue source

value: bone marrow


title: U2AF1(WT) CMP 1


title: U2AF1(WT) CMP 3


title: U2AF1(WT) CMP 2


title: Tr. Astrocyte replicate 2

city: la jolla

first: vipul

last: bhargava

state: California

address: 9500 gilman drive

institute: ucsd

data_processing:
Basecalls performed using Illumina Casava 1.8
The libraries were sequenced as 50 bp single-end reads, except for astrocytes and in-vivo cancer samples which were sequenced with a configuration of 100 bp single-end reads. The first 7 sequencing bases of the biological samples, excluding cortical astrocytes and dedifferentiated astrocytes, were truncated as they came from our defined set of 44 heptamer primers that were used for targeted amplification using DP-seq.
In case of astrocyte samples, the first 14 sequencing bases were truncated.
The next 32 bp reads were aligned to the RefSeq mRNA database.
Genome_build: mus musculus RefSeq database of RNA version 41, May 9 2010
Supplementary_files_format_and_content: tab-delimited files include RefSeq transcript ID and Unique Reads

source_name: primary cortical astrocytes transduced in vitro

growth_protocol: Astrocytes were maintained in DMEM containing 10% FBS and neurons were cultured in Neurobasal -A medium (Gibco) containing Glutamax (Gibco) and B-27 supplement (Gibco).

extract_protocol:
Cells were harvested and total RNA was extracted using Trizol. Poly 'A' enriched mRNA was isolated using Dynabeads mRNA purification kit (Invitrogen) from each sample.
Sequencing libraries were prepared using DP-seq protocol as described by Bhargava et al. 2013

treatment_protocol: Follwing transduction of either primary astrocytes or neurons with the lentivirus, at the early passages, cells were cultured in the medium decribed above or in parallel cultured in NSCs medium.

value: cortical astorcytes post natal day 11 (PN11) transduced with H-RasV12-shp53 lentivirus, switched to NSC media


title: Tr. Astrocyte replicate 1


title: U2AF1(S34F) CMP 1


title: U2AF1(S34F) CMP 2


title: in-vivo cancer

source_name: mouse tumor sample

value: tumor induced by injection of H-RasV12-shp53 in the cortex of SynapsinI-Cre mouse


title: Astrocyte replicate 1

source_name: primary cortical astrocytes

value: cortical astrocytes PN11


title: Tr. Neuron replicate 2

source_name: primary cortical neurons transduced in vitro

value: cortical neurons post natal day 11 (PN11) transduced with H-RasV12-shp53 lentivirus, switched to NSC media


title: sgRNA_Replicate_1


title: Input_Replicate_3


title: RIP_Replicate_2


title: WT_small RNA seq

city: Boston

first: Peng

last: Du

address: 1 Blackfan Circle

institute: Boston Children’s Hospital, Harvard Medical School

data_processing:
bowtie softare is used to map reads to mRNA with two mismatches permitted, and self-developed perl scripts were used to coculate the reads of each genes
For small RNA sequencing, after removal of the adaptor sequences, bowtie software was used to mapping the small RNAs into mature miRNA sequences (miRBase).
Genome_build: mm9
Supplementary_files_format_and_content: RNAseq.txt provided a matrix table, which contained five columns including the gene's name, cDNA's name, reads number in WT, DGCR8 and Dicer samples; small RNA seq.txt provided the reads number for each miRNAs.

source_name: mESCs

growth_protocol: Mouse ESCs (V6.5, Dgcr8-/- and Dicer-/-) were cultured in DMEM with ESGRO (1000 units/mL), supplemented with 15% (v/v) FBS and antibiotics

extract_protocol:
total RNAs were extracted using Trizol reagent
200 ng polyA(+) RNA isolated as described above was used for mRNA-seq. Sample preparation was with the TruSeq Stranded mRNA Sample Prep Kits (Illumina).10ug total RNAs was used for small RNA libraries preparaion fellowing small RNA Sample Prep Kits (Illumina)

value: WT mESCs


title: ENSC_replicate 2

source_name: ESC

value: mouse embryionic stem cells E14.5


title: Neuron_replicate 1

source_name: primary cortical neurons

value: cortical neurons post natal day 11 (PN11)


title: ENSC_replicate 1


title: Tr. Neuron maintained in DMEM replicate 2

value: cortical neurons post natal day 11 (PN11) transduced with H-RasV12-shp53 lentivirus


title: Tr. Neuron replicate 1


title: Neuron_replicate 2


title: Tr. Neuron maintained in DMEM replicate 1


title: Astrocyte replicate 2


title: mouse ESC


title: Ezh2KO-Epithelium rep3

city: Parkville

first: Marie-Liesse

last: Asselin-Labat

state: VIC

address: 1G Royal Parade

department: Stem Cells and Cancer

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v1.4.8 and Real Time Analysis (RTA) v1.12.4.2, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then Illumina CASAVA1.8 pipeline was used to generate the sequence data.
Reads were aligned to the mouse reference genome mm10 and mapped to known genomic features at the gene level using the Rsubread package (version 1.14.2) (Liao et al. 2013) from the Bioconductor software project (Gentleman et al. 2004). Reads were summarized at the gene level using the featureCounts (Liao et al. 2014) function in a strand-specific manner.
Genes with low counts were discarded, retaining only those with counts per million above 0.5 in at least 3 libraries. Predicted genes, genes without annotation and genes that mapped to Y or mitochondrial chromosomes were also removed from the analysis. After filtering, 14,831 genes remained available for the differential expression analysis.
Genome_build: NCBI mm10
Supplementary_files_format_and_content: Tab delimited count matrices containing read counts at gene level before (count.matrix.txt) and after (filtered.count.matrix.txt) filtering.

growth_protocol: Lungs from ShhCre;Ezh2fl/fl and control ShhCre;Ezh2fl/+ embryos at day E16.5 were digested to a single cell suspesion, depleted by FACS for CD31 and CD45 positive cells and separated into epithelial and stromal cell populations based on expression of EpCAM marker.

extract_protocol:
EpCAM+ and EpCAM- cells from the Ezh2-deficient and control embryonic lungs at day E16.5 were pooled together as necessary to a minimum of 100000 cells per sample (3 samples per tissue-genotype combination). Total RNA was extracted and purified using Total RNA Purification Kit (Norgen) according to kit instructions.
150 ng of total RNA was subjected to NGS library preparation using TruSeq Stranded Total RNA with Ribo-Zero (Illumina) according to kit instructions. Completed libraries from different samples were pooled together at equimolar concentrations and sequenced on HiSeq 2000 with TruSeq SBS Kit v3- HS reagents (Illumina) as 100 bp single end reads at the Australian Genome Research Facility (AGRF).

tag: strain background

tag: age

tag: tissue

value: lung

tag: cell population

value: Epithelial (CD31-CD45-EpCAM+)

tag: library adapter

tag: sequencing depth

tag: mapped to genes before filtering

tag: mapped to genes after filtering


title: Control-Epithelium rep2

source_name: Control-Epithelium