title: MeDIP-Seq 5mhC Progenitors replicate 1

city: La Jolla

first: Yina

last: Zhu

address: 9500 Gilman Drive

department: Biological Sciences

institute: university of california,san diego

description: Immunoprecipitated DNA

data_processing:
The paired-end Hi-C reads were truncated at GATCGATC site, aligned separately to the mm9 genome using BOWTIE2, only keeping read pairs if both ends mapped to unique locations. The two reads were merged into pairs using HOMER (http://biowhat.ucsd.edu/homer/). Read alignment filtering and other Hi-C processing including normalization was performed using HOMER. Reads passing these filters are included in the Hi-C summary files. Principle component analysis of normalized Hi-C interaction frequency matrices was performed using HOMER and R. Hi-C statistics was processed using HiCUP(http://www.bioinformatics.babraham.ac.uk/projects/hicup/).
For ChIP-Seq, MeDIP-Seq and GRO-Seq samples (single end reads), reads were aligned to the mm9 genome using BOWTIE2, keeping only reads that mapped unique locations. Aligned read files were analyzed with HOMER to find peaks, generate bedGraph, calculate RPKM from the gene bodies of RefFlat genes, and perform other analyses in the study.
RNA-Seq reads were aligned to the mm9 reference genome using Tophat2. RPKMs for each RefFlat gene were calculated from aligned reads using Cufflink. For a gene to be considered expressed the cutoff of FPKM is 0.5.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include BED files (ChIP-Seq peak or region positions, Hi-C PC1 domain positions), FKPM CSV files (RNA-Seq expression data), RPKM CSV files (GRO-Seq expression data), BEDGRAPH (ChIP-Seq, duplicates-combined GRO-Seq and MeDIP-Seq tracks, principle component values along the genome for combined Hi-C data), and TXT files, including Hi-C summary files (filtered read pairs from combined Hi-C data processed using HOMER; filtered read pairs from each Hi-C replicates processed using HiCUP), columns: Read Name, chromosome for read 1, positions for read 1 (5' end of read, one-indexed), strand of read 1, chromosome for read 2, positions for read 2 (5' end of read, one-indexed), strand of read 2), as well as Hi-C background files from HOMER.

source_name: undifferentiated myeloid progenitor cells

growth_protocol:
GM-CSF-dependent ECOMG cells were grown in RPMI 1640 with 10% FBS and penicillin-streptomycin-glutamine, by the addition of 1:100 conditioned media (about 10 ng/mL GM-CSF) isolated from a B16 melanoma cell line stably transfected with a murine GM-CSF construct. b-estradiol where applicable, was added to the medium at a final concentration of 1 mM from a 10,000 × stock in 100% ethanol. Differentiation of ECOMG cells into granulocytes was induced by withdrawal β-estradiol for 5 days.
C57BL/6J mice were housed in specific pathogen-free conditions in accordance with the Institutional Animal Care and Use Committee of University of California, San Diego. Bone marrow derived neutrophils were separated by EasySepTM Mouse Neutrophil Enrichment Kit (Stem Cell Technologies, 19762). Bone marrow cells were harvested from femur, tibia and crista iliac. Bone marrow cells were incubated with a cocktail of biotinylated lineage specific antibodies (EasySepTM Mouse Neutrophil Enrichment Cocktail), conjugated with EasySepTM Biotin Selection Cocktail, labeled with EasySepTM D Magnetic Particles, followed by depletion of biotin-labeled cells with EasySep™ Magnet.

extract_protocol:
The in-situ Hi-C experiments were performed similarly as described (Rao SSP, et al. 2014. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159: 1665-1680).
The GRO-Seq experiments were performed as described (Core LJ, Waterfall JJ, Lis JT. 2008. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322: 1845-8).
The ChIP-Seq experiments were performed similarly as described (Lin YC, et al. 2012. Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate. Nat Immunol 13: 1196-1204).
The MeDIP-Seq experiments were performed similarly as described (Pomraning KR, Smith KM, Freitag M. 2009. Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods 47: 142-150).
For RNA-Seq: total RNA was isolated using RNeasy Mini kit (Qiagen). RNA was treated with TURBO DNase (Life Technologies). mRNA was purified from total RNA using Dynabeads mRNA purification kit (Life Technologies).cDNA was generated with the First-strand synthesis kit (Life Technologies) using a combination of random hexamers and oligo(dT) in presence of actinomycin D. Second-strand synthesis was performed with dUTP instead of dTTP. The ds-cDNA was sonicated to 200-400 bp using the S220 Focused-ultrasonicator (Covaris).
Hi-C libraries were prepared with the NEBNext primer set and were selected by size by 6% PAGE and sequenced for 50 cycles on Illumina HiSeq 2500.
GRO-Seq libraries were prepared with custom GRO-Seq PCR primers and were selected by size by 8% PAGE and sequenced for 50 cycles on Illumina HiSeq 2000.
ChIP-Seq and MeDIP-Seq libraries were prepared with the NEBNext primer set and were selected by size by 8% PAGE and sequenced for 50 cycles on Illumina HiSeq 2000 or 2500.
RNA-Seq ibraries were prepared with the TruSeq primer set and were selected by size by 8% PAGE and sequenced for 50 cycles on Illumina HiSeq 2000.

value: Ecomg myeloid progenitor cell line

tag: genotyping

value: human E2A_ER_Pbx1b

tag: chip antibody

value: 5mhC 39770 active motif


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 10

status: Public on Feb 06 2017

type: SRA

city: Boston

first: John

middle: N

last: Campbell

state: Massachusetts

address: Center for Life Science, room 7-717

department: Medicine

country: USA

institute: Beth Israel Deaconess Medical Center

library_source: transcriptomic

data_processing:
Base calls performed with bcl2fastq2.15.0.4
Alignment by TopHat v2.0.14. [Using “-M”, “--no-coverage-search”, “--segment-length 10”]
Removal of duplicates and low quality reads, indexing, and sorting: Picard 2.5.0 and samtools 0.1.19.
Assigned reads to features: featureCounts-1.4.6. [Using recommended setting and a custom meta-annotation that merges overlapping isoforms.]

Genome_build: Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: CSV file containing expression values by sample (columns) and gene ID (rows)

molecule: polyA RNA

organism: Mus musculus

source_name: Arcuate Nucleus/Median Eminence

extract_protocol:
GFP+ cells were manually isolated from a cell suspension prepared by triturating and washing papain-digested Arc-ME
Single cells were frozen at -80degC and then processed into RNA-seq libraries using Smart-Seq2 (Picelli et al., 2015) and Nextera XT

tag: strain

value: (C57BL/6 x DBA)F2

tag: tissue

value: Arcuate-Median Eminence

tag: Sex

value: M

tag: average age

value: 63 days

tag: number of mice pooled


title: N2 50 mM 2

city: Cambridge

first: Nicholas

last: Burton

state: MA

address: 77 Massachusetts Ave.

institute: MIT

data_processing:
For QC purposes, BEDTools (version 2.25.0) was used to count the reads falling into genes, coding regions, intronic regions, 5' or 3' UTRs, flanking 3-kb genic regions and intergenic regions.
The reads were first cleaned up by removing reads aligned to rRNAs (BWA 0.6.1 and BEDTools 2.25.0 were used).
RSEM (version 1.2.15) was used to estimate gene levels based on ce10 ensembl annotations downloaded from UCSC genome table browser.
The gene expression count table was then imported into Deseq (version 1.10.1) for differential gene expression test.
Genome_build: ce WS206
Supplementary_files_format_and_content: Excel file containing gene information, raw read counts computed by RSEM, gene expression FPKM values, log2 FPKM values, average of log2FPKMs and variance of log2 FPKMs

molecule: total RNA

organism: Caenorhabditis elegans

source_name: embryos

extract_protocol:
Embryos were lysed using a BeadBug and 0.5mm zirconium beads. Total RNA was collected using RNAeasy kit from Qiagen and DNAse treated with DNAseI from NEB
RNA integrity and concentration were checked on a Fragment analyzer (Advanced Analytical). The mRNA was purified by polyA-tail enrichment, fragmented, reverse transcribed into cDAN (Illumina TruSeq). cDNA samples were then end repaired and adaptor liged using the SPRI-works fragment library system I (Beckman Coulter Genomics) and indexed during amplification. Libraries were quantified using the fragment analyzer and qPCR before being loaded for paired-end sequencing using the Illumina NextSeq.

tag: timepoint

value: Embryos 3 hours post egg prep

tag: mutant

tag: parents growth condtions

value: 50 mM NaCl

tag: embryos growth condtions


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 7


title: MeDIP-Seq 5mhC Neutrophils replicate 2

state: CA

description: Immunoprecipitated DNA

library_source: genomic

molecule: genomic DNA

source_name: in-vitro differentiated neutrophils

tag: cell type

value: Ecomg derived neutrophils


title: MeDIP-Seq 5mhC Neutrophils replicate 1

description: Immunoprecipitated DNA


title: ChIP-Seq Input Neutrophils replicate 1&2

description:
input DNA
Input_Neu.ucsc.bedGraph.bz2


title: MeDIP-Seq 5mC Progenitors replicate 2

description: Immunoprecipitated DNA

value: 5mC A-1014-050 epigentek


title: ChIP-Seq Input Progenitors replicate 1&2

description:
input DNA
Input_Pro.ucsc.bedGraph.bz2


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 3


title: MeDIP-Seq 5mhC Progenitors replicate 2

description: Immunoprecipitated DNA


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 6


title: ChIP-Seq Neutrophils H3K27me3

description:
Immunoprecipitated DNA
H3K27me3_markedRegion_Pro_10k_50k.bed
H3K27me3_markedRegion_Neu_10k_50k.bed

value: H3K27me3 07-449 Millipore


title: MeDIP-Seq 5mC Progenitors replicate 1

description: Immunoprecipitated DNA


title: ChIP-Seq Progenitors H3K27me3


title: ChIP-Seq Progenitors H3K4me2

description: Immunoprecipitated DNA

value: H3K4me2 ab7766  Abcam


title: MeDIP-Seq 5mC Neutrophils replicate 1

description: Immunoprecipitated DNA


title: ChIP-Seq Neutrophils H3K4me2

description: Immunoprecipitated DNA


title: ChIP-Seq Progenitors H3K36me3

description: Immunoprecipitated DNA

value: H3K36me3 ab9050 Abcam


title: GRO-Seq Progenitors  replicate 1&2

description:
nascent RNA
GROSeq_activatedgenes_2fold.csv
GROSeq_repressedgenes_2fold.csv

molecule: nuclear RNA


title: ChIP-Seq Neutrophils H3K36me3

description: Immunoprecipitated DNA


title: ChIP-Seq Progenitors H3K9me3

description: Immunoprecipitated DNA

value: H3K9me3 ab8898 Abcam


title: RNA-Seq Neutrophils

description:
mature RNA
genes.fpkm_tracking_firststrand.csv
RNAseq_activatedgenes_2fold.csv
RNASeq_repressedgenes_2fold.csv


title: ChIP-Seq Progenitors H3K4me3

description: Immunoprecipitated DNA

value: H3K4me3 ab8580 Abcam


title: ChIP-Seq Neutrophils H3K9me3

description: Immunoprecipitated DNA


title: RNA-Seq Progenitors


title: ChIP-Seq Neutrophils H3K4me3

description: Immunoprecipitated DNA


title: ChIP-Seq Neutrophils H3K4me1

description: Immunoprecipitated DNA

value: H3K4me1 ab8895 Abcam


title: ChIP-Seq Progenitors H3K27ac

description: Immunoprecipitated DNA

value: Ecomg myeloid progenitor cell line

value: H3K27ac ab4729  Abcam


title: GRO-Seq Neutrophils replicate 1&2

value: human E2A_ER_Pbx1b


title: ChIP-seq Pax5-Etv6 [14210]

city: Vienna

first: Maria

last: Fischer

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology

data_processing:
Peaks were determined by using the MACS program version 1.3.6.1 (16) with default parameters, a cutoff of a P value of < 10-10 and a genome size of 2,654,911,517 bp (mm9). The identified peaks were then assigned to target genes as described (12). For comparisons of ChIPseq data, we down-sampled all reads before peak calling to the ChIP-seq experiment with the lowest number of aligned reads.
For analysis of differential gene expression, the number of reads per gene was counted using HTseq version 0.5.3 (19) with the overlap resolution mode set to ‘union’. The datasets were grouped according to cell type and organism and analyzed using the R package DESeq2 version 1.4.1 (20). Sample normalizations and dispersion estimations were conducted using the default DESeq2 settings. In detail, the following DESeq2 analyses were performed: all mouse pro B cell samples were analyzed together considering the genotype effects (model design formula: “~ genotype”). Mouse tumor cells and mouse wild-type large pre-B cells were also grouped and analyzed in the same manner, as were human tumor cells and human wild-type pre-B cells.
Genome_build: MM9
Supplementary_files_format_and_content: bigwig = bigWig Track format of read density coverage in reads per million after extension to 150 base pairs; text tab delim = TPM values in ASCII text format tab delimited

source_name: pro-B

extract_protocol:
phenol-chloroform extraction
About 1-5 ng of cDNA or ChIP-precipitated DNA were used as starting material for the generation of sequencing libraries with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-Tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-Tailing module. DNA fragments of the following sizes were selected for the different experiments: 200–500 bp for ChIP-seq and 150–700 bp for RNA-seq with AMPure XP beads (Beckman Coulter). For strand-specific RNA-sequencing, the uridines present in one cDNA strand were digested with uracil-N-glycosylase (New England Biolabs) as described (Parkhomchuk et al. 2009) followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems). Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS Library Quantification kit. Cluster generation and sequencing was carried out by using the Illumina HiSeq 2000/2500 system with a read length of 50 nucleotides (single-read) or 100/125 nucleotides (paired-end) according to the manufacturer’s guidelines.

tag: genotype

tag: cell preparation

value: pro-B culture

tag: cell sorting strategy

value: CD19+ MACS-sorted

value: Streptavidin


title: ChIP-Seq Progenitors H3K4me1

description: Immunoprecipitated DNA


title: RNA-seq B-ALL [17588]

description: SuperScript® VILO™ cDNA Synthesis, strand-specific

source_name: lymph node

extract_protocol:
Rneasy Plus Mini Kit, Dynabeads mRNA purification kit
About 1-5 ng of cDNA or ChIP-precipitated DNA were used as starting material for the generation of sequencing libraries with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-Tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-Tailing module. DNA fragments of the following sizes were selected for the different experiments: 200–500 bp for ChIP-seq and 150–700 bp for RNA-seq with AMPure XP beads (Beckman Coulter). For strand-specific RNA-sequencing, the uridines present in one cDNA strand were digested with uracil-N-glycosylase (New England Biolabs) as described (Parkhomchuk et al. 2009) followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems). Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS Library Quantification kit. Cluster generation and sequencing was carried out by using the Illumina HiSeq 2000/2500 system with a read length of 50 nucleotides (single-read) or 100/125 nucleotides (paired-end) according to the manufacturer’s guidelines.

value: Ex-vivo Lymph Node

value: whole Lymph Node


title: RNA-seq B-ALL [17586]


title: ChIP-seq Pax5-Etv6 [14211]


title: ChIP-Seq Neutrophils CTCF

description: Immunoprecipitated DNA

value: CTCF 07-729 Millipore


title: MeDIP-Seq 5mC Neutrophils replicate 2

description: Immunoprecipitated DNA

value: Ecomg derived neutrophils


title: ChIP-Seq Neutrophils H3K27ac

description: Immunoprecipitated DNA


title: H3K27ac [13017]


title: ChIP-Seq Progenitors RAD21

description:
Immunoprecipitated DNA
RAD21_Pro_peaks.bed
RAD21_Neu_peaks.bed
RAD21_Pro_specific_Peaks.bed

value: RAD21 ab992 Abcam


title: ChIP-Seq Progenitors CTCF

description: Immunoprecipitated DNA


title: RNA-seq Pax5Foxp1 Pro-B [12808]

value: Ex-vivo, FACS sorted


title: RNA-seq Pax5+/- Pro-B [12810]


title: ChIP-Seq Neutrophils RAD21


title: HiC BMDN replicate 2 PCR replicate 2

description:
genomic interactions
YZ12_index9_10.R1_2.hicup.sam.homer.txt.bz2

source_name: Bone marrow-derived neutrophils

value: Bone marrow-derived neutrophils

value: Wild type


title: HiC BMDN replicate 1 PCR replicate 2

description:
genomic interactions
YZ12_index7_8_R1_2.hicup.sam.homer.txt.bz2


title: 889PF shCd109 #2 rep2

city: Stanford

first: Jennifer

last: Brady

address: 269 Campus Drive

institute: Stanford University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat.
Aligned RNA-seq reads were assembled into transcripts using the Cufflinks assembler (version 0.9.3). Annotated transcripts were obtained from the UCSC genome browser (http://genome.ucsc.edu) and the Ensembl database; the category of transcripts was described at http://vega.sanger.ac.uk/info/about/gene_and_transcript_types.html. (FPKM).category of transcripts was described at http://vega.sanger.ac.uk/info/about/gene_and_transcript_types.html.
Transcript abundances were measured in Fragments Per Kilobase of exon per Million fragments mapped (FPKM). To address the common issue in the assembly that a read may align to multiple isoforms of the same gene or multiple transcripts within the same genetic locus, maximum likelihood estimation was performed by Cufflinks based on a numerical optimization algorithm for calculating FPKM.
The program Cuffdiff was used to define differential expression.
Genome_build: mm10
Supplementary_files_format_and_content: A single tab-delimited excel file, including FPKM values for each Sample. To determine gene expression changes induced by Cd109 knockdown in the highly metastatic murine 889 cell line we knocked down Cd109 with two independent shRNAs (shCd109#1 and shCd109#2). Additionally, we generated shControl and shCd109 cell lines two separate times to create Replicate A and Replicate B samples (separate virus production, infection, selection, and mRNA isolation). FKPM for shControl and average FKPM for shCd109#1 and shCd109#2 are shown for each replicate. Log2 fold change, p value and q value from CuffDiff are shown. The right most columns shown average FPKM across the four groups and the average fold change of the two replicate comparisons.We kept only genes with an average FPKM value greater than 1.

growth_protocol: Cells were grown in high glucose DMEM, supplemented with Glutamine, Sodium Pyruvate, Pen/Strep, 2ug/mL puromycin and 10% FBS

extract_protocol:
Total RNA was extracted using the Qiagen RNEasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: tumor source genotype

value: Kras G12D, p53 null

tag: cell line

value: mouse pleural fluid disseminating tumour cell-derived cell line

tag: cell line genotype

value: 889PF with shCd109 #2


title: RNA-seq B-ALL [17587]

tag: strain

tag: chip antibody


title: RNA-seq Pax5Foxp1 Pro-B [12807]


title: 889PF shGFP rep2

source_name: 889PF shGFP

value: 889PF with shLuciferase


title: 889PF shGFP rep1


title: normallung2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Using Sailfish to quantify expression
We kept only transcripts with max TPM value greater than 1 in at least one sample and with standard deviation greater than 1
We performed the inverse hyperbolic sine transformation (asinh in R) and quantile normalized the data
Genome_build: mm10
Supplementary_files_format_and_content: A single tab-delimited excel file, including FPKM values for each Sample

source_name: normal lung

growth_protocol: We initiated tumors in KrasLSL-G12D/+;p53flox/flox;R26LSL-tdTomato (KPT) mice with a pool of barcoded lentiviral-Cre vectors and purified Tomato-positive cancer cells away from the diverse and variable stromal cell populations

extract_protocol:
Total RNA was extracted using the Qiagen AllPrep DNA/RNA Micro Kit
RNA libraries were prepared for sequencing using Ovation® RNA-Seq system and Illumina TruSeq DNA kit

treatment_protocol: Tumor samples from defined stages of metastatic progression

tag: tumor genotype

tag: metastatic progression stage

value: Normal lung


title: normallung1


title: RNA-seq Pax5Etv6 Pro-B [12809]


title: DC0182KT

source_name: KT

value: KrasG12D;R26LSL-tdTomato (KT)

value: Hyperplasia


title: 889PF shCd109 #1 rep1

value: 889PF with shCd109 #1


title: CON_3

city: Cincinnati

first: Yan

last: Xu

state: Ohio

address: 3333 Burnet Avenue

department: Pulmonary Biology

institute: Cicinnati children's Hospital Medical Center

data_processing:
Dissociated single-cell preparations from peripheral lung of IPF patients (n = 3) and controls (n = 3) from cohort 2 were enriched for AT2 epithelial cells by FACS for CD326 (CD326) double positive, CD45 (hematopoietic) negative, CD31 (endothelial) negative cells, and HTII-280 after dissociation by proteases.
Cells were plated overnight and sorted. After sorting, cells were preserved in either RNAprotect Cell (QIAGEN) or RNAlater RNA stabilization (QIAGEN) reagent. Total RNA was isolated using an RNeasy Micro Kit (QIAGEN) by incorporating an on-column DNAsel digestion step.
Amplified cDNA was generated using the Ovation RNA-Seq System V2 kit (NuGEN) to amplify both polyA+ and non-polyadenylated RNA transcripts.
Next-generation sequencing of equimolar pools of cDNA libraries was performed using a single read 50 rapid flow cell on a HiSeq 2500 sequencing platform (Illumina), generating greater than 30 million raw reads per sample.
The raw sequenced reads were aligned from FASTQ files to the human genome build GRCh37/hg19 and the UCSC reference transcriptome (http://ccb.jhu.edu/software/tophat/index.shtml) using “Cufflinks” .
Genome_build: hg19
Supplementary_files_format_and_content: Excel sheet including Reads and FPKM expression

organism: Homo sapiens

source_name: Normal control

growth_protocol: IPF tissues (n = 3) were collected from lung explants of IPF patients undergoing lung transplantation, and lung lobes from adult donors that were resected on the basis of size incompatibility or that were deemed unsuitable for transplant were utilized as control tissues (n = 3) for cell sorting by FACS.

extract_protocol:
The minced cleaned tissue was then incubated in DMEM/F12 (Life Technologies) containing 2 mg/ml Dispase (Corning), incubated at 4°C with rocking for 1 hour, and incubated for another 30 minutes at 37°C. Further elastase/trypsin digestion was then accomplished by the addition of an equal volume of Ham’s F12 medium containing 5 U/ml elastase (Worthington Biochemical Corp.) and 0.125% trypsin/EDTA (Corning). The reaction was arrested by addition of HBSS containing 0.01% HEPES, 0.5 M EDTA, and 0.02% FBS. Triturated tissue solution was subjected to a final protease digestion of 1 volume DNase I for 15 minutes at 37°C. Cells were plated overnight on collagen-coated plates in bronchial epithelial growth medium (Lonza) and harvested by mild trypsin digestion.
Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation Kit (Illumina).

treatment_protocol: Peripheral human lung tissue with airways no larger than 2 mm in diameter and lacking visceral pleura was mechanically minced and enzymatically dissociated to generate a single-cell suspension. Briefly, finely minced tissues were washed in Ham’s F12 (Corning) at 4°C for 5 minutes with rocking, followed by centrifugation for 5 minutes at 600 g and 4°C.

tag: disease state

value: control

tag: tissue

value: lung

value: sorted Epithelial type2 cell


title: DC0185KT


title: CON_2


title: CON_1


title: CC1334KPT-E

source_name: KPT-Early

value: p53 deficient hyperplasia


title: IPF_3

source_name: IPF patients

value: IPF


title: CC1324KPT-E


title: IPF_2


title: CC1032ST1

source_name: Soft Tissue/Bladder

value: Distant metastasis


title: HiC BMDN replicate 2 PCR replicate 1

tag: genotyping


title: CC1032ST2

source_name: Soft Tissue/Back


title: 889PF shCd109 #2 rep1


title: 889PF shCd109 #1 rep2


title: CC1032LN

source_name: Lymph Node

value: Lymph Node metastasis


title: HiC BMDN replicate 1 PCR replicate 1

value: Bone marrow-derived neutrophils


title: CC1032T1

source_name: TMet

value: Metastatic primary tumor


title: CC1032T4

source_name: TnonMet

value: Non-metastatic primary tumor


title: CC0802ST2

source_name: Soft Tissue/Near Spine


title: IPF_1


title: KA_SEQ_60

city: Waltham

first: Katharine

last: Abruzzi

address: 415 South St.

department: Biology

institute: HHMI; Brandeis University

data_processing:
Aligned to dm3 using tophat2.0
Gene expression quantified using End Sequencing Analysis Tool Kit
Cycling gene expression identified using F24 analysis and JTK cycle (both publically available).
Genome_build: Drosophila dm3
Supplementary_files_format_and_content: processed files list gene expression quantification output from ESAT by transcript ID.

organism: Drosophila melanogaster

source_name: TH

growth_protocol: Drosophila were entrained for 2-4 days in LD cycles and then collected at specified timepoints.

extract_protocol:
Neurons were lysed and RNA extracted and purified using oligo-dT.  cDNA was made using primer (random and dT mixed) with T7 promoters.  cDNA was used as a template for 1 round of linear amplification using T7-polymerase.  Resutling cRNa used as input for RNA TruSEQ v2 library construction.
Illumina TruSeq v2

tag: timepoint

value: neurons

tag: type

value: TH


title: CC0802ST1


title: DC0179KT


title: CC0802T8

source_name: TnonMet/Lung


title: KA_SEQ_58


title: CC0802LN1


title: CC0772LN

source_name: Lymph node


title: KA_SEQ_57


title: CC0772T6


title: CC1331KPT-E


title: CC0772DTC

source_name: DTCs

value: Pleural Cavity Disseminating tumor cells


title: CC0802T1

source_name: TMet/Lung


title: CC0560ST

source_name: Soft Tissue/peritoneum


title: CC0772LIVER

source_name: Liver


title: KA_SEQ_55


title: AZ-105


title: AZ-104


title: CC0560T6


title: CC0545ST

source_name: Soft Tissue/Chin


title: KA_SEQ_56


title: AZ-103


title: CC0545T4


title: RNA-seq cntrl B-ALL [27573]

source_name: Bone Marrow

value: Trp53-/- NrasG12D/+Retroviral-Myc

value: Short-time culture

value: whole Bone Marrow


title: CC0545LN


title: CC0545T5


title: CC0543ST


title: KA_SEQ_59


title: ChIP-seq Pax5 [26598]

source_name: pro-B

value: pro-B culture

value: CD19+ MACS-sorted

value: Streptavidin


title: CC0543T4


title: AZ-101


title: RNA-seq cntrl B-ALL [27572]


title: ChIP-seq Pax5-Etv6 [26601]

source_name: lymph node

value: Rosa26BirA/+Cdkn2ab+/-Pax5Etv6/+ BirA/+

value: Ex-vivo Lymph Node

value: whole Lymph Node


title: CC0374LN


title: ChIP-seq Prd [26029]


title: CC0374DTC


title: CC0545PL

source_name: Pleura

value: Pleural metastasis


title: CC0543T6


title: 23b


title: CC0374T7


title: AZ-100


title: CC0374T5


title: AZ-102


title: RNA-seq Pax5+/- Pro-B [20761]

value: Ex-vivo, FACS sorted


title: CC0355LN

value: Lymph Node metastasis


title: ChIP-seq Pax5-Etv6 [26027]


title: RNA-seq Pax5Etv6 Pro-B [20762]


title: 19b


title: 23a


title: CC0543LIVER

value: Distant metastasis


title: CC0349PL


title: CC0355T4

value: Metastatic primary tumor


title: 19a

value: neurons


title: CC0355DTC


title: CC0302LIVER


title: CC0349T4


title: CC0349LN


title: RNA-seq Large pre-B [20759]

source_name: large pre-B

value: Wt

value: CD19+IgM/IgD-CD2+-Ckit- FSC large


title: CC0302T2


title: 15a


title: ChIP-seq Prd [26028]


title: RNA-seq Small pre-B [20760]

source_name: small pre-B

value: CD19+IgM/IgD-CD2+Ckit-FSC small


title: CC0302T4

value: Non-metastatic primary tumor


title: CC0349T5


title: 15b


title: 11b


title: RNA-seq Pro-B [20758]


title: CC0299ST

source_name: Soft Tissue/Back


title: CC0299PL


title: CC0299T1


title: 11a


title: CC0299LN


title: RNA-seq Pax5Prd Pro-B [20756]


title: 7b


title: CC0133PL


title: RNA-seq Large pre-B [17226]

value: CD19+IgM/D-Ckit-CD2lowFSC-size large


title: RNA-seq Small pre-B [17225]

value: CD19+IgM/D-Ckit-CD2lowFSC-size small


title: CC0133LN


title: RNA-seq Pax5Prd Pro-B [20757]


title: 7a


title: RNA-seq Pro-B [17224]


title: CC0299T5


title: 3b


title: 3a


title: BCR-ABL+_wt_d14_repl2

city: San Francisco

first: Hilde

last: Schjerven

address: 513 Parnassus Ave

department: Laboratory Medicine

institute: UCSF

description:
mRNA enriched from Total RNA
wt-d14-D

data_processing:
Raw data (fastq) was uploaded to the Galaxy website (http://galaxy.psu.edu/) and mapped with Tophat to the July 2007 annotation of mouse (Mus musculus) genome data (mm9), filtering for uniquely mapped reads (Giardine et al., 2005; Trapnell et al., 2009; Blankenberg et al., 2010a; Blankenberg et al., 2010b; Fujita et al., 2010; Goecks et al., 2010).
Genome coverage visualization files were created with BEDtools and uploaded to the UCSC genome browser (http://genome.ucsc.edu) (Kent et al., 2002).
Relative mRNA expression levels (RPKM) (Mortazavi et al., 2008) were calculated based on exonic reads obtained by using the software SeqMonk (Babraham Bioinformatics) and reference genome annotations from NCBI (mm9).
Filtering and calculation of Relative changes in expression levels between samples were analyzed in excel.
Attached as supplemental file is the unfiltered RPKM values for all annotated Refseq genes (as a Tab delimited .txt file)
Genome_build: mm9 [the July 2007 annotation of mouse (Mus musculus) genome data]
Supplementary_files_format_and_content: Genome coverage visualization files were created with BEDtools and uploaded to the UCSC genome browser (http://genome.ucsc.edu) (Kent et al., 2002).
Supplementary_files_format_and_content: RPKM .txt file attached as supplemental file on the Series record reports the unfiltered RPKM values for all annotated Refseq genes (as a Tab delimited .txt file)

growth_protocol: Single cell suspensions were prepared from BCR-ABL transformed in vitro cell culture cells.

extract_protocol: polyA-enriched RNA was purified with the MicroPoly(A)Purist Kit (Ambion) according to the manufacturers protocol. cDNA library was prepared for the Illumina Sequencing platform using the fragmented double-stranded cDNA protocol (Nagalakshmi et al., 2010)

treatment_protocol: Retroviral transduction of primary whole BM suspensions with BCR-ABL-p185-IRES-YFP (at day 0)

tag: genotype/variation

value: wt

tag: cell type

value: BCR-ABL+ transformed proB-ALL

tag: time (days in in vitro culture)

value: 14 days


title: BCR-ABL+_Ikaros_ZnF4-/-_d14_repl1

description:
mRNA enriched from Total RNA
dF4-d14-C

source_name: BCR-ABL transformed in vitro cell culture


title: BCR-ABL+_wt_d14_repl1

description:
mRNA enriched from Total RNA
wt-d14-A


title: BCR-ABL+_Ikaros_ZnF4-/-_d14_repl2

description:
mRNA enriched from Total RNA
dF4-d14-F


title: PDF ZT18

description: PDF ZT18

source_name: LNv

value: LNv


title: PDF ZT14

description: PDF ZT14


title: RNA-seq Pax5Etv6 Large pre-B [17223]

tag: genotype

tag: cell preparation

tag: cell sorting strategy


title: PDF ZT22

description: PDF ZT22


title: RNA-seq Pax5+/- Pro-B [17217]


title: BCR-ABL+_Ikaros_ZnF1-/-_d14_repl1

description:
mRNA enriched from Total RNA
dF1-d14-B


title: PDF ZT10

description: PDF ZT10


title: PDF ZT2

description: PDF ZT2


title: KA_SEQ_42


title: PDF ZT6

description: PDF ZT6


title: RNA-seq Pax5Etv6 Large pre-B [17220]


title: BCR-ABL+_Ikaros_ZnF1-/-_d14_repl2

description:
mRNA enriched from Total RNA
dF1-d14-E


title: KA_SEQ_41


title: Ka_SEQ_37


title: KA_SEQ_39


title: KA_SEQ_64

source_name: LNd

value: LNd


title: KA_SEQ_40


title: KA_SEQ_66


title: KA_SEQ_63


title: KA_SEQ_65


title: KA_SEQ_62


title: HighNaCl_NoFood_C

city: Eugene

first: Amy

middle: K

last: Webster

state: Oregon

address: Institute of Ecology and Evolution

institute: University of Oregon

data_processing:
Bowtie version 1.1.2 was used to map reads to the WS210 version of the genome.
Count files were generated with HTSeq using the GTF file used in Maxwell et al., 2012. This file includes features of the WS210 genome in addition to features of WS220 mapped back to WS210. This file is available on GSE33023 and is named GSE33023_GFF_for_cuffdiff.gtf.gz.
edgeR exact test was used on normalized count tables for differential expression analysis. Genes with counts per million (CPM) >1 in at least 3 libraries were included in the analysis.
Genome_build: WS210
Supplementary_files_format_and_content: Count files include the sequence identifier for each gene and the number of counts mapping to that gene (not normalized across libraries).

source_name: L1 larvae

growth_protocol: The wild-type N2 strain was maintained at 20C on E. coli OP50 on standard NGM plates prior to setting up the experiment. Worms were then bleached, and 5000 embryos were plated per 10cm plate at 25C. These were then grown for 24hr under the four NaCl/food combinations.

extract_protocol:
Total RNA was extracted using TRIzol with minor modifications to the manufacturer's protocol. 1mL of TRIzol was used per sample. Samples were homogenized using 100uL of acid-washed sand.
Libraries were prepared using the NEB Next Ultra Non-directional mRNA-seq Kit. 15 cycles of PCR were used to amplify libraries.

treatment_protocol: After 24hr at 25C, worms were washed from plates using S-basal. Samples were flash frozen in liquid nitrogen and stored at -80C until RNA extraction.

tag: nacl concentration

tag: presence or absence of food (op50)

value: no food

value: whole larvae

tag: developmental stage


title: KA_SEQ_61


title: LowNaCl_NoFood_B

tag: strain


title: LowNaCl_NoFood_C


title: HighNaCl_Food_C

value: food


title: RNA-seq Pax5Etv6 Pro-B [17221]

value: Ex-vivo, FACS sorted

tag: chip antibody


title: HighNaCl_Food_B


title: LowNaCl_Food_A


title: HighNaCl_NoFood_A


title: KA_SEQ_51


title: LowNaCl_Food_B


title: LowNaCl_NoFood_A


title: KA_SEQ_50


title: RNA-seq Pax5Etv6 Pro-B [17218]


title: HighNaCl_NoFood_B


title: KA_SEQ_53


title: KA_SEQ_49


title: KA_SEQ_38


title: HighNaCl_Food_A


title: KA_SEQ_52


title: KA_SEQ_54


title: input control

status: Public on Feb 05 2017

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: input control

data_processing:
Chip-seq files were aligned using bowtie version 0.12.9 to human genome hg19
Peak calling was done with homer (v1.0) software with options  -fdr 0.01 -style histone
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and Hg19 genome with UCSC known gene set.
edgeR was used for differential expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq processed files contain Homer peak calling output; RNA-Seq expression file contains raw counts and FPKM values for all genes

source_name: input control

growth_protocol: Ovarian cancer cell lines were cultured in RPMI1640 medium (Corning) supplemented with 10% fetal bovine serum (FBS; Sigma), 100 U/ml penicillin, 100 ug/ml streptomycin

extract_protocol:
cells were cross-linked with 1% formaldehyde for 10 min, followed by quenching with 125 mM glycine for 5 min at room temperature. Fixed cells were washed with TBS and the pellets were kept on -70 °C. The pellets were thawed and resuspended in cell lysis buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 min. The lysates were washed with MNase digestion buffer (20 mM Tris-HCl, pH7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2) once and incubated for 20 minutes at 37 °C in the presence of 1,000 Gel units of MNase (NEB, M0247S) in 250 ul reaction volume. After adding the same volume of sonication buffer (100 mM Tris-HCl, pH8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% Sodium deoxycholate), the lysates were sonicated for 5 min (30 sec-on / 30 sec-off) in Diagenode bioruptor and centrifuged at 15,000 rpm for 10 min.
Ovation Ultralow DR Multiplex system (NuGEN).

treatment_protocol: no treatment

tag: cell line

tag: agent

value: none (input)


title: BRD4 CHIP-seq in JQ1-treated cells

description: BRD4 CHIP-seq in JQ1-treated cells

source_name: JQ1-treated cells

extract_protocol:
cells were cross-linked with 1% formaldehyde for 10 min, followed by quenching with 125 mM glycine for 5 min at room temperature. Fixed cells were washed with TBS and the pellets were kept on -70 °C. The pellets were thawed and resuspended in cell lysis buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 min. The lysates were washed with MNase digestion buffer (20 mM Tris-HCl, pH7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2) once and incubated for 20 minutes at 37 °C in the presence of 1,000 Gel units of MNase (NEB, M0247S) in 250 ul reaction volume. After adding the same volume of sonication buffer (100 mM Tris-HCl, pH8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% Sodium deoxycholate), the lysates were sonicated for 5 min (30 sec-on / 30 sec-off) in Diagenode bioruptor and centrifuged at 15,000 rpm for 10 min.  ChIP performed with rabbit polyclonal anti-BRD4 (Bethyl Laboratories, catalog# A301-985A).
Ovation Ultralow DR Multiplex system (NuGEN).

treatment_protocol: cells were incubated with 0.5 mM ethidium uridine (EU) and treated with 125 nM JQ1 for 40min

value: rabbit polyclonal anti-BRD4 (Bethyl Laboratories, catalog# A301-985A, lot# A301-985A50-4)


title: LowNaCl_Food_C

tag: tissue


title: RNA-seq for JQ1-treated cells

description: RNA-seq for JQ1-treated cells

extract_protocol:
total RNA isolated using Trizol reagent
Ovation Human FFPE RNA-Seq Multiplex System 1-8 (Nugen)


title: S492A_1_RNA-Seq

city: Oxford

first: Sina

last: Wittmann

state: Oxfordshire

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
PAR-CLIP: Adapter sequences are first trimmed from the raw sequencing files. The quality filter then discards all reads containing unidentified nucleotides (N), Phreds scores below 30, reads shorter than 15 nucleotides (nt), or reads that are flagged by Illumina’s internal chastity filter. Quality-trimmed reads are aligned to the S. pombe genome (ASM294v2.25 from Pombase.org) using the short read aligner Bowtie (version 1.1.1) with a maximum of one mismatch and taking unique matches only (options: -q -p 4 -S -sam -nohead -v 1 -e 70 -l 28 -y -a -m 1 -best -strata -phred33 -quals). The resulting SAM files are then converted into BAM and PileUp files using SAMTools. Crosslinking sites were normalised to RNA abundance which was determined by RNA-Seq
ChIP-seq: Single end reads with a Phred score of less than 20 were removed using the the program Trimmomatic (version 0.36) and the remaining reads were aligned to the S. pombe genome (ASM294v2.25 from Pombase.org) using the short read aligner Bowtie (version 2.2.6). The BEDTools toolset was used to obtain coverage tracks that were used for peak calling using the software MACS2 2.1.1.20160309.
RNA-Seq: Paired-end reads were trimmed by quality (less than Phred score 20) and reads shorter than 20 nt were removed using Trimmomatic (Galaxy Version 0.32.3). The resulting reads were aligned to the S. pombe genome (ASM294v2.28) using TopHat (Galaxy version 0.9). Read-through was determined by counting the reads in a window 50 nt after the pA site which was normalised to counts obtained for the gene body using HTSeq (version 0.6.1.p1). In addition, bam files were converted to bed files using the deeptools tool bamtobed (option -bedpe -mate1) and the resulting file was used to generate a bed file that contains reads spanning both read pairs. This was then imported into R/Bioconductor and reads overlapping pA sites were counted and normalised to gene body expression levels as before.
Genome_build: S. pombe genome version ASM294v2.28
Supplementary_files_format_and_content: PAR-CLIP: Seb1 crosslinking sites are provided as .table text files; ChIP-Seq: the data is provided as bigwig or bedgraph files; RNA-Seq: Read counts within gene bodies and after pA site as well as are counts overlapping the pA site are summarised in an excel table and bedgraph files are provided to visualise the data

organism: Schizosaccharomyces pombe

source_name: Yeast cell extract

growth_protocol: S. pombe were initially grown in EMMG medium without thiamine at 30°C and then shifted to thiamine-containing YES medium for 24h at OD600 ~0.5

extract_protocol:
Total RNA was extracted from three separate cultures of WT and mutants grown to mid-log phase and DNase-treated.
Ribodepletion and library preparation were performed by the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics according to the TruSeq protocol. Note that with the TruSeq protocol the cDNA strand is sequenced. Thus all the strand information needs to be reversed after mapping the reads to the genome.

tag: method

value: RNA-Seq


title: RNA-seq for DMSO-treated cells

description: RNA-seq for DMSO-treated cells

source_name: DMSO-treated cells

treatment_protocol: cells were incubated with 0.5 mM ethidium uridine (EU) and treated with 125 nM vehicle control for 40min

value: DMSO


title: S492A_2_RNA-Seq


title: F445A_3_RNA-Seq


title: BRD4 CHIP-seq in DMSO-treated cells

description: BRD4 CHIP-seq in DMSO-treated cells


title: S2P_IP_2_ChIP-Seq

growth_protocol: S. pombe were grown in YES medium to exponential phase at 30°C

extract_protocol:
Cells were grown to mid-log phase and crosslinked using 11% formaldehyde. Cells were lysed by vortexing with glass beads and chromatin was extracted by two consecutive ultra-centrifugation steps. The DNA was sheared by sonication, S2P-Pol II was IP-ed using anti-S2P antibodies (3E10, Millipore) and DNA was extracted by phenol:chloroform.
Libraries were generated using the NEBNext fast DNA library Prep set for Ion Torrent (E6270).

value: ChIP-Seq


title: F445A_2_RNA-Seq


title: F445A_1_RNA-Seq


title: tm_3_RNA-Seq


title: S2P_Input_2_ChIP-Seq

extract_protocol:
Cells were grown to mid-log phase and crosslinked using 11% formaldehyde. Cells were lysed by vortexing with glass beads and chromatin was extracted by two consecutive ultra-centrifugation steps. The DNA was sheared by sonication and DNA was extracted by phenol:chloroform.
Libraries were generated using the NEBNext fast DNA library Prep set for Ion Torrent (E6270).


title: dm_1_RNA-Seq


title: S2P_Input_1_ChIP-Seq


title: dm_2_RNA-Seq


title: untagged_Input_2_ChIP-Seq


title: untagged_IP_2_ChIP-Seq

extract_protocol:
Cells were grown to mid-log phase and crosslinked using 11% formaldehyde. Cells were lysed by vortexing with glass beads and chromatin was extracted by two consecutive ultra-centrifugation steps. The DNA was sheared by sonication, Pcf11-TAP was IP-ed using IgG agarose and DNA was extracted by phenol:chloroform.
Libraries were generated using the NEBNext fast DNA library Prep set for Ion Torrent (E6270).


title: untagged_IP_1_ChIP-Seq


title: tm_2_RNA-Seq


title: Y64K_1_RNA-Seq

value: h+, ura4-294, leu1-32, ade6-M210, seb1::p(nmt1)-seb1-FLAG::NatMX, leu1::p(seb1)-seb1(Y64K)-HA


title: Y64K_3_RNA-Seq


title: tm_1_RNA-Seq


title: Pcf11_IP_2_ChIP-Seq

value: h+, ura4-<delta>18, leu1-32, ade6-M210, his3-<delta>1, pcf11::pcf11-TAP::KanMX


title: untagged_Input_1_ChIP-Seq


title: Y64K_2_RNA-Seq


title: Pcf11_IP_1_ChIP-Seq


title: S2P_IP_1_ChIP-Seq


title: Seb1_PAR-CLIP

growth_protocol: Cells were grown at 30 °C to OD600 ∼0.5 in CSM minimal medium (Formedium) supplemented with 10 mg/l uracil, 100 µM 4-thiouracil and 4 % glucose. After reaching OD600∼0.5, another 900 µM 4-thiouracil were added and cells were grown further for 4 h (OD600∼1.3-1.6)

extract_protocol:
Cells were UV-irradiated (12 J/cm2 at 365 nm) and lysed by bead beating and the lysate was sonicated. Immunoprecipitation was performed on a rotating wheel for 2 h at 4 °C with rabbit IgG-conjugated Protein G magnetic Dynabeads (Invitrogen). Crosslinked RNA was partially digested with RNase T1 and prepared for cDNA library preparation.
Data acquisition were performed as described by Schulz and Schwalb et al. (Cell, 2013) with minor modifications. Following adapter ligation, RNA was recovered by Proteinase K digestion for 2 h at 55 °C, and subsequent acidic phenol/chloroform extraction. Reverse transcription was done for 1 hr at 44 °C using SuperScript III RTase (Invitrogen). PCR amplification was performed using the NEXTflex barcode primer kit (Bioo Scientific).

value: h-, seb1::seb1-TAP::KanMX

value: PAR-CLIP


title: WT_2_RNA-Seq

value: h+, ura4-294, leu1-32, ade6-M210, seb1::p(nmt1)-seb1-FLAG::NatMX, leu1::p(seb1)-seb1-HA


title: WT_3_RNA-Seq


title: WT_1_RNA-Seq


title: UMB cells treated for 24h with vehicle

status: Public on Feb 04 2017

city: Ramat-Gan

first: Tomer

last: Kalsiky

state: Israel

address: Ramat-Gan

country: Israel

institute: Bar-Ilan University

data_processing:
Illumina Casava1.7 software used for basecalling
Raw reads were aligned by TopHat2 to the human hg19 genome. The reference genome and annotation files were obtained from the Illumina iGenomes collection (http://support.illumina.com/sequencing/sequencing_software/igenome.html)
Aligned reads were counted by HTSeq.
Data normalization and differential gene expression was done by DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: OP_original_count.csv: Raw counts of sequencing reads
Supplementary_files_format_and_content: OP_normal_count.csv: Normalized abundance measurements

source_name: UMB cells (angiomyolipoma cell line derived from TSC-associated renal angiomyolipoma)

growth_protocol: AML cell lines were grown in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (Invitrogen), 1% Penicillin–streptomycin 100M and 1% L‐glutamine (both from Biological Industries).

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols. TruSeq RNA-Seq.

treatment_protocol: The cells were treated for 12h or 24h with 50mM of the PPARG inhibitor GW9662 or vehicle (DMSO),

value: Kidney

value: UMB

tag: treatment

value: vehicle

tag: time


title: Pcf11_Input_1_ChIP-Seq


title: SV7 cell treated for 24h with GW9662

source_name: SV7 cells (angiomyolipoma cell line derived from sporadic renal angiomyolipoma)


title: SV7 cell treated for 24h with vehicle


title: RNA-Seq_for_PAR-CLIP

extract_protocol:
Cells were UV-irradiated (12 J/cm2 at 365 nm) and lysed by bead beating. Total RNA was isolated by acid phenol/chloroform extraction using Roti-Phenol (Carl Roth), and purified and concentrated using the RNA Clean Concentrator-5 (Zymo Research). Purified RNA was depleted of ribosomal RNAs using Ribo-Zero rRNA removal kit (Epicenter).
Multiplexed RNA-Seq library preparation was performed using the NuGEN Encore Complete RNA-Seq Library Systems. Libraries were qualified on an Agilent Bioanalyzer 2100 (Agilent Technologies) and sequenced on an Illumina machine (HiSeq 1500).

value: h-


title: UMB cells treated for 12h with vehicle


title: SV7 cell treated for 12h with GW9662


title: UMB cells treated for 12h with GW9662


title: Pcf11_Input_2_ChIP-Seq


title: 11-2043 Macular RPE/choroid/sclera

city: Phila

first: Dwight

last: Stambolian

state: Pa

address: 422 Curie Blvd

department: Ophthalmology

institute: University of Pennsylvania

data_processing:
RNA-seq data was aligned to the hg19 reference genome using GSNAP with default options. Required a mapping quality scofe of ≥30 for each read. Quality control analysis of the aligned data was performed using program RNA-SeQC.
Transcripts were assembled using Cufflinks (v2.1.1). A gene was considered differentially expressed if the false discovery rate (FDR) -adjusted p-value is <0.05.
Genes.fpkm_tracking is the output of cuffdiff that identifies the individual fpkm values for every comparison
Genome_build: hg19

source_name: Macular RPE/choroid/sclera

extract_protocol:
Donor eyes were obtained from non-diabetic Caucasians at a death-to-preservation interval of <6h. Eyes were stored in RNA later before extraction of RNA. For each eye we dissected macula and periphery from retina and RPE/choroid/sclera resulting in 4 samples per eye. RNA was extracted using the ALLPrep DNA/RNA Mini Kit (Qiagen). All RNA had an RNA integrity number of ≥8.
Strand specific RNA library was prepared from 100 ng total RNA using the Encore Complete RNA-Seq library kit (Nugen Technologies, San Carlos, CA).

value: Macular RPE/choroid/sclera

tag: age

tag: Sex

value: Male


title: SV7 cell treated for 12h with vehicle


title: 11-2043 Peripheral RPE/choroid/sclera

source_name: Peripheral RPE/choroid/sclera

value: Peripheral RPE/choroid/sclera


title: 11-2043 Peripheral Retina

source_name: Peripheral Retina

value: Peripheral Retina


title: 11-1875 Macular RPE/choroid/sclera


title: 11-1875 Macular Retina

source_name: Macular Retina

value: Macular Retina


title: LX0_EN_RNA-seq

city: Nanjing

first: Jingya

last: Yuan

address: 1 Weigang Road

country: China

institute: Nanjing Agricultural University

description:
RNA-seq of hybrid that has Longtefu as female parent.
Processed data file: LX0-1_reads_of_alleles_type.txt
Processed data file: LX0-2_reads_of_alleles_type.txt

data_processing:
Illumina CASAVA_v1.8.2 software used for basecalling.
We did resequencing of Longtefu and 02428 rice cultivars, mapped these reads to reference MSU version 7.0 using BWA by default parameter. We called SNPs using Samtools and removed the SNPs that have score lower than 50.
Raw small RNA sequence reads were parsed to remove 3' adapters and retain 18-30-nt reads using cutadapt, then mapped onto the Oryza sativa genome (MSU version 7.0) using bowtie. The sequences from ribosomal RNAs, transfer RNAs, snoRNAs, and snRNAs were excluded from the analysis using perl script.
Low-quality reads in the raw RNA-seq data were examined using NGSQCToolkit_v2.3 and eliminated, and the high-quality reads were mapped onto the Oryza sativa genome (MSU version 7.0) and assembled using TopHat, and then the Cufflink, Cuffmerge and Cuffdiff were used for producing the genes. Using perl script and SNPs between 02428 and Longtefu, we separate the reads that contain SNPs in RNA-seq.
Low-quality bases were filtered and processed reads were mapped to the O. sativa genome (MSU version 7.0) using Bismark.
Genome_build: Oryza sativa genome (MSU version 7.0)
Supplementary_files_format_and_content: 02428_Longtefu_SNPs.txt: SNPs between 02428 and Longtefu calling by resequencing of 02428 (BioSample: SAMN04441364) and resequencing of Longtefu (BioSample: SAMN04441365).
Supplementary_files_format_and_content: LX0_DNA_methylation_bismark_pe_all_genome_wide_C_report.txt: Methylated and unmethylated cytosine of sample (SAMN04441366) in the whole genome.
Supplementary_files_format_and_content: 0XL_DNA_methylation_bismark_pe_all_genome_wide_C_report.txt: Methylated and unmethylated cytosine of sample (SAMN04441367) in the whole genome.
Supplementary_files_format_and_content: LX0-1_reads_of_alleles_type.txt and LX0-2_reads_of_alleles_type.txt: Processed data files of RNA-seq data (BioSample: SAMN04441368) replication1 (SRX1546415) and replication2 (SRX1546416), which calculate alleles expression in Longtefu reads and 02428 reads.
Supplementary_files_format_and_content: 0XL-1_reads_of_alleles_type.txt and 0XL-2_reads_of_alleles_type.txt: Processed data files of RNA-seq data (BioSample: SAMN04441369) replication1 (SRX1546528) and replication2 (SRX1546538), which calculate alleles expression in longtefu reads and 02428 reads.
Supplementary_files_format_and_content: 02428-1_EN_with_SNP_map.txt and 02428-2_EN_with_SNP_map.txt: Processed data files of small RNA-seq data of 02428 endosperm (BioSample: SAMN04441370) replication1 (SRX1546555) and replication2 (SRX1546565), which contain mapped loci and expression levels of small RNA reads.
Supplementary_files_format_and_content: Long-1_EN_with_SNP_map.txt and Long-2_EN_with_SNP_map.txt: Processed data files of small RNA-seq data of Longtefu endosperm (BioSample: SAMN04441371) replication1 (SRX1546567) and replication2 (SRX1546569), which contain mapped loci and expression levels of small RNA reads.
Supplementary_files_format_and_content: LX0-1_EN_with_SNP_map.txt and LX0-2_EN_with_SNP_map.txt: Processed data files of small RNA-seq data of hybrid LX0 endosperm (BioSample: SAMN04441372) replication1 (SRX1546571) and replication2 (SRX1546576), which contain mapped loci and expression levels of small RNA reads.
Supplementary_files_format_and_content: 0XL-1_EN_with_SNP_map.txt and 0XL-2_EN_with_SNP_map.txt: Processed data files of small RNA-seq data of hybrid 0XL endosperm (BioSample: SAMN04441373) replication1 (SRX1546578) and replication2 (SRX1546579), which contain mapped loci and expression levels of small RNA reads.
Supplementary_files_format_and_content: 02428_L_sRNA_rep1_map.txt and 02428_L_sRNA_rep2_map.txt: Processed data files of small RNA-seq data of 02428 seedling (BioSample: SAMN04441374) replication1 (SRX1546582) and replication2 (SRX1546586), which contain mapped loci and expression levels of small RNA reads.
Supplementary_files_format_and_content: Longtefu_L_sRNA_rep1_map.txt and Longtefu_L_sRNA_rep2_map.txt: Processed data files of small RNA-seq data of Longtefu seedling (BioSample: SAMN04441375) replication1 (SRX1546588) and replication2 (SRX1546589), which contain mapped loci and expression levels of small RNA reads.
Supplementary_files_format_and_content: LX0_L_sRNA_rep1_map.txt and LX0_L_sRNA_rep2_map.txt: Processed data files of small RNA-seq data of LX0 seedling (BioSample: SAMN04441376) replication1 (SRX1546598) and replication2 (SRX1546599), which contain mapped loci and expression levels of small RNA reads.
Supplementary_files_format_and_content: 0XL_L_sRNA_rep1_map.txt and 0XL_L_sRNA_rep2_map.txt: Processed data files of small RNA-seq data of 0XL seedling (BioSample: SAMN04441377) replication1 (SRX1546600) and replication2 (SRX1546601), which contain mapped loci and expression levels of small RNA reads.

organism: Oryza sativa

source_name: endosperm, LX0, 7 days after pollination

extract_protocol:
Each biological replication from 5 or more endosperms and 1-2 seedlings were used for RNA and DNA extract. Total RNA was isolated using miRVana kit (Ambion 1561) and Plant RNA Isolation Aid (Ambion 9690) to be used for RNA libraries and small RNA libraries. DNA was isolated using CTAB used for resequencing and BS-seq.
RNA libraries, small RNA, resequencing and BS-seq libraries were prepared for sequencing using standard Illumina protocols.

tag: cultivar

value: endosperm

value: 7 days after pollination


title: 0XL_EN_RNA-seq

description:
RNA-seq of hybrid that has 02428 as female parent.
Processed data file: 0XL-1_reads_of_alleles_type.txt
Processed data file: 0XL-2_reads_of_alleles_type.txt

source_name: endosperm, 0XL, 7 days after pollination


title: 11-1875 Peripheral RPE/choroid/sclera


title: UMB cells treated for 24h with GW9662


title: 11-1875 Peripheral Retina


title: LX0_EN_BS-seq

description:
Bisulfite sequencing of hybrid that has Longtefu as female parent.
Processed data file: LX0_DNA_methylation_bismark_pe_all_genome_wide_C_report.txt


title: 11-1833 Macular RPE/choroid/sclera

value: Female


title: Testes-2

city: Nanchang

first: Xiaoning

last: Zhang

address: 999 Xuefu R.D., Nanchang

institute: Nanchang University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: mm10
Supplementary_files_format_and_content: .txt files include RPKM values for each Sample

source_name: Testes

extract_protocol:
Total RNAs were extracted from the purified sperm and testes samples using RNeasy® Plus Micro (Qiagen, Duesseldorf, Germany) according to the manufacturer’s instructions with some modifications. We added 1 ml of buffer RLT (a guanidine-thiocyanate lysis buffer supplemented with 10 mM DL-Dithiothreitol) to the sperm pellet and 10 mg testes tissues, and then homogenized the sample by passing the samples through a 20-G needle attached to a 1-ml syringe 10 to 15 times. After total RNA was bound to the membrane and other contaminants were efficiently washed away, on-column DNase digestion was performed to eliminate trace amounts DNA contamination. The concentration and integrity of the total RNA samples were evaluated using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE, USA) and a 2100-Bioanalyzer with the RNA 6000 Nano Chip (Applied Biosystems, Carlsbad, CA, USA), respectively.
RNase H protocol was performed to removal rRNA as previously described (Adiconis et al. 2013). The DNase digested RNA was purified with AMPure Beads and then fragmented to about 140–160 nt. The RNA fragments were further converted into a DNA library through end repair, adaptor ligation, reverse transcription circularization, and PCR amplification. The library was further purified with AMPure Beads and validated using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., CA, USA) and ABI StepOnePlus Real-Time PCR System (Applied Biosystems, CA, USA). The qualified library was sequenced by Illumina Illumina HiSeqTM 4000.

value: Testes

value: 3-5 months


title: Longtefu_reseq

description:
Resequencing of Longtefu.
Processed data file: 02428_Longtefu_SNPs.txt

source_name: seedling leaves, Longtefu, trefoil stage

value: Longtefu

value: leaves

value: trefoil stage


title: Sperm-3

source_name: Sperm

tag: cell type

value: Sperm


title: Sperm-4


title: Testes-1


title: 11-2043 Macular Retina


title: 11-1833 Macular Retina


title: 02428_reseq

description:
Resequencing of 02428.
Processed data file: 02428_Longtefu_SNPs.txt

source_name: seedling leaves, 02428, trefoil stage


title: Sperm-2


title: 11-1648 Macular RPE/choroid/sclera


title: 11-1833 Peripheral RPE/choroid/sclera


title: 11-1833 Peripheral Retina


title: 11-1648 Macular Retina


title: Single.BLA-M-2_RNA-seq

city: Shanghai

first: Denghui

last: Liu

state: Shanghai

address: ShengLi Building, 320 Yueyang Road

institute: CAS-MPG Partner Institute for Computational Biology (PICB)

description: Sample name: Single.BLA.M.2

data_processing:
Reads quality was examined by “fastQC”
Filtered reads were aligned to rhesus monkey genome database (AV et al. 2014) by tophat v2.1.0
Only uniquely mapped reads were used to calculate the counts of each gene by HTSeq (Anders et al. 2015).
Reads counts were normalized to library size by DESeq2 (Love et al. 2014), and normalized reads were then used for calculate the FPKM (Fragments Per Kilobase of transcript per Million fragments mapped).
Genome_build: MacaM
Supplementary_files_format_and_content: Contains the expression level of each gene in all samples, measured by FPKM

organism: Macaca mulatta

source_name: blastocyst

growth_protocol: Embryos were cultured at 37℃ in 50 μl drops of equilibrated HECM-9 containing 10% FBS (HyClone Laboratories Inc.) in a humidified atmosphere of 5% CO2 in air. Culture medium was changed every other day. Morphologically normal embryos with few fragments were selected for RNA-seq.

extract_protocol:
Dynabeads mRNA DIRECT kit (Invitrogen) was utilized to extract RNAs from oocytes and embryos. Oocytes or embryos were washed in PBS containing 0.03% PVP and transferred into a RNase-free Eppendorf tube (500 μl) containing 200 μl lysis/binding buffer from the Kit (Invitrogen). Complete lysis was achieved by gently flicking the tube for 2 min. The sample lysis were then temporarily stored at -80 ℃ until RNA extraction. RNA was extracted following manufactures instruction.
RNAs were subject to low input RNA-seq library construction based on Tang's protocol (Tang et al. 2010). In case of overloading, pooled RNA were aliquoted into several tubes and each tube was independently amplified, after 20 rounds of PCR amplification, all tubes contained the same stage samples were mixed together and sent to another 9 rounds of PCR amplification, PCR products was purified and the quality of library were checked by qPCR analysis of a set of house-keeping genes, Agilent 2100 bioanalyzer and QUBIT (Life Technologies) were also employed for quality control. The libraries were deep sequenced on Illumina HiSeq 2000 platform using 90-bp paired-end strategy.

value: blastocyst

tag: oocyte/embryo number

tag: donator monkey number

tag: source of female

value: M


title: Single.BLA-M-4_RNA-seq

description: Sample name: Single.BLA.M.4


title: Single.BLA-M-1_RNA-seq

description: Sample name: Single.BLA.M.1


title: Sperm-1


title: 11-1648 Peripheral RPE/choroid/sclera


title: Single.MOR-M-3_RNA-seq

description: Sample name: Single.MOR.M.3

source_name: morula

value: morula


title: 11-1648 Peripheral Retina


title: Single.MOR-L-2_RNA-seq

description: Sample name: Single.MOR.L.2

value: L


title: Single.MOR-L-1_RNA-seq

description: Sample name: Single.MOR.L.1


title: 0XL_EN_BS-seq

description:
Bisulfite sequencing of hybrid that has 02428 as female parent.
Processed data file: 0XL_DNA_methylation_bismark_pe_all_genome_wide_C_report.txt


title: 11-1624 Macular RPE/choroid/sclera

value: Macular RPE/choroid/sclera

value: Male


title: 11-1624 Macular Retina


title: Single.8C-L-6_RNA-seq

description: Sample name: Single.8C.L.6

source_name: 8-cell embryo

value: 8-cell embryo


title: Single.8C-L-4_RNA-seq

description: Sample name: Single.8C.L.4


title: Single.8C-K-3_RNA-seq

description: Sample name: Single.8C.K.3

value: K


title: 11-1614 Macular Retina

value: Macular Retina


title: Single.8C-K-2_RNA-seq

description: Sample name: Single.8C.K.2


title: 11-1614 Macular RPE/choroid/sclera


title: 11-1614 Peripheral RPE/choroid/sclera

value: Peripheral RPE/choroid/sclera


title: Single.8C-K-1_RNA-seq

description: Sample name: Single.8C.K.1


title: 11-1624 Peripheral Retina

value: Peripheral Retina


title: Single.4C-L-3_RNA-seq

description: Sample name: Single.4C.L.3

source_name: 4-cell embryo

value: 4-cell embryo


title: Blast_RNA-seq

description: Sample name: Pooled.Blast

value: multiple


title: Single.4C-K-2_RNA-seq

description: Sample name: Single.4C.K.2


title: 11-1614 Peripheral Retina


title: Single.2C-L-3_RNA-seq

description: Sample name: Single.2C.L.3

source_name: 2-cell embryo

value: 2-cell embryo


title: 8C_RNA-seq

description: Sample name: Pooled.8C


title: Morula_RNA-seq

description: Sample name: Pooled.MOR


title: 2C_RNA-seq

description: Sample name: Pooled.2C


title: Single.2C-L-2_RNA-seq

description: Sample name: Single.2C.L.2


title: 11-1556 Peripheral RPE/choroid/sclera

value: Female


title: Single.2C-L-1_RNA-seq

description: Sample name: Single.2C.L.1


title: 4C_RNA-seq

description: Sample name: Pooled.4C


title: 11-1624 Peripheral RPE/choroid/sclera


title: 11-1556 Macular Retina


title: PN_RNA-seq

description: Sample name: Pooled.PN

source_name: 1-cell embryo at pronuclear (PN) stage

value: 1-cell embryo at pronuclear (PN) stage


title: 11-1556 Peripheral Retina


title: GV _RNA-seq

description: Sample name: Pooled.GV

source_name: germinal vesicle-stage oocyte

value: germinal vesicle-stage oocyte


title: MII_RNA-seq

description: Sample name: Pooled.MII

source_name: mature oocyte

value: mature oocyte


title: 11-1556 Macular RPE/choroid/sclera

source_name: Macular RPE/choroid/sclera


title: Single.PN-K-2_RNA-seq

description: Sample name: Single.PN.K.2


title: 11-1516 Macular RPE/choroid/sclera


title: Single.PN-N-3_RNA-seq

description: Sample name: Single.PN.N.3

value: N


title: 11-1516 Macular Retina


title: Single.PN-K-1_RNA-seq

description: Sample name: Single.PN.K.1


title: 11-1516 Peripheral RPE/choroid/sclera

source_name: Peripheral RPE/choroid/sclera


title: Single.MII-K-3_RNA-seq

description: Sample name: Single.MII.K.3


title: 11-1516 Peripheral Retina

source_name: Peripheral Retina


title: 0XL_L_sRNA-seq

description:
Small RNA-seq of hybrid leaves that have 02428 as female parent.
Processed data file: 0XL_L_sRNA_rep1_map.txt
Processed data file: 0XL_L_sRNA_rep2_map.txt

source_name: seedling leaves, 0XL, trefoil stage

value: leaves

value: trefoil stage


title: Rhizophagus NPC exudate time point  24h replicate 1

city: Castanet-Tolosan

first: Christophe

last: Roux

address: Chemin de Borde Rouge

country: France

institute: University of Toulouse/CNRS

description: Sample 13

data_processing:
For gene expression analysis, we used additional triplicates Illumina libraries from treated samples (germinating spores of R.irregularis with wt/npc rice root exudates at time 0, 1h, 24h , 7d). Reads were mapped to the Gloin1 assembly (Tisserant et al., PNAS, 2013) for calculating gene expression by using RNA-seq functionality of the CLC Genomic Workbench suite. To find the genes significantly upregulated during symbiosis, RPKM (Reads Per Kilobase of exon per Million fragments mapped - Mortazavi et al., 2008) and proportion-based test statistics (Baggerly et al., 2003) with a False Discovery Rate (FDR) correction for multiple testing (Benjamini & Hochberg, 1995) were calculated (settings: minimum mapped read length fraction = 0.95; minimum similarity = 0.98). According to CLC recommendation, genes were considered as significantly up regulated when meeting the requirements of "total difference reads mapped" >10 (parameter proposed by CLC WorkBench to select only significantly expressed genes), RPKM fold change>2 and FDR corrected p value<0.05.
Genome_build: Gloin1 (GCA_000439145.2)
Supplementary_files_format_and_content: Analysis2.xlsx reports processed data.

organism: Rhizophagus irregularis

source_name: germinating spores

growth_protocol: 80 000 spores were germinated in 40ml of liquid M medium for 2 days in the dark with 2% CO2 before treatment (T0)

extract_protocol:
Spores were crushed with a motar and a pestle in liquid nitrogen and mRNA were extracted using RNeasy plant kit (Qiagen), according to the manufacturer instructions.
Samples were sequenced at the Genome and Transriptome platform (Toulouse, France - GeT). mRNA were isolated with polyT beads before processing, libraries were constructed according to the manufacturer's protocol.

treatment_protocol: germinating spores were treated with root exudates and collected 1 hour, 24 hours and 7 days  in the same previous conditions.

value: rice NPC Root exudates

tag: growth time post induction

value: 24 hours


title: Single.MII-K-1_RNA-seq

description: Sample name: Single.MII.K.1


title: Rhizophagus wt exudate time point 24h replicate 2

description: Sample 11

value: rice wt Root exudates


title: Single.GV-L-3_RNA-seq

description: Sample name: Single.GV.L.3

value: L


title: Rhizophagus wt exudate time point 24h replicate 3

description: Sample 12


title: LX0_L_sRNA-seq

description:
Small RNA-seq of hybrid leaves that have Longtefu as female parent.
Processed data file: LX0_L_sRNA_rep1_map.txt
Processed data file: LX0_L_sRNA_rep2_map.txt

source_name: seedling leaves, LX0, trefoil stage

tag: developmental stage


title: Rhizophagus NPC exudate time point 1h replicate 3

description: Sample 9

tag: strain

value: 1 hour


title: Rhizophagus wt exudate time point 7days replicate 3

description: Sample 18

value: 7 days


title: Rhizophagus NPC exudate time point 7days replicate 3

description: Sample 21


title: Rhizophagus NPC exudate time point 7days replicate 1

description: Sample 19


title: Rhizophagus wt exudate time point 7days replicate 2

description: Sample 17


title: Rhizophagus NPC exudate time point  24h replicate 3

description: Sample 15


title: Rhizophagus NPC exudate time point 7days replicate 2

description: Sample 20


title: Rhizophagus wt exudate time point 7days replicate 1

description: Sample 16


title: Single.GV-K-2_RNA-seq

description: Sample name: Single.GV.K.2

value: K


title: Long_L_sRNA-seq

description:
Small RNA-seq of Longtefu leaves.
Processed data file: Longtefu_L_sRNA_rep1_map.txt
Processed data file: Longtefu_L_sRNA_rep2_map.txt

source_name: seedling leaves, Longtefu, trefoil stage

value: Longtefu


title: Rhizophagus NPC exudate time point 1h replicate 2

description: Sample 8


title: Single.GV-K-1_RNA-seq

description: Sample name: Single.GV.K.1


title: Rhizophagus NPC exudate time point 1h replicate 1

description: Sample 7


title: Rhizophagus wt exudate time point 1h replicate 3

description: Sample 6


title: 02428_L_sRNA-seq

description:
Small RNA-seq of 02428 leaves.
Processed data file: 02428_L_sRNA_rep1_map.txt
Processed data file: 02428_L_sRNA_rep2_map.txt


title: Rhizophagus NPC exudate time point  24h replicate 2

description: Sample 14


title: 0XL_EN_sRNA-seq

description:
Small RNA-seq of hybrid endosperm that has 02428 as female parent.
Processed data file: 0XL-1_EN_with_SNP_map.txt
Processed data file: 0XL-2_EN_with_SNP_map.txt

source_name: endosperm, 0XL, 7 days after pollination

value: endosperm

value: 7 days after pollination


title: Rhizophagus wt exudate time point 1h replicate 2

description: Sample 5


title: Single.MII-K-2_RNA-seq

description: Sample name: Single.MII.K.2


title: Rhizophagus wt exudate time point 1h replicate 1

description: Sample 4


title: Rhizophagus wt exudate time point 24h replicate 1

description: Sample 10


title: Rhizophagus control time point 0 replicate 3

description: Sample 3


title: Rhizophagus control time point 0 replicate 2

description: Sample 2


title: LX0_EN_sRNA-seq

description:
Small RNA-seq of hybrid endosperm that has Longtefu as female parent.
Processed data file: LX0-1_EN_with_SNP_map.txt
Processed data file: LX0-2_EN_with_SNP_map.txt

source_name: endosperm, LX0, 7 days after pollination


title: Rhizophagus control time point 0 replicate 1

description: Sample 1


title: Long_EN_sRNA-seq

description:
Small RNA-seq of Longtefu endosperm.
Processed data file: Long-1_EN_with_SNP_map.txt
Processed data file: Long-2_EN_with_SNP_map.txt

source_name: endosperm, Longtefu, 7 days after pollination


title: Growth with ciprofloxacin (0.38 mg/L) - sample 2

city: Rennes

first: Vincent

last: Cattoir

address: 2 rue Henri Le Guilloux

institute: CHU de Rennes

data_processing:
The reads were mapped against the genomic sequence of E. faecium Aus0004 (Genbank accession no. CP003351) using the CLC Genomics Workbench software v8.1 (Qiagen).
The number of reads uniquely aligned to each genomic position was determined using the BEDTools program v2.16.2.
The expression of genes in different RNA-seq samples was compared using normalized RPKM values calculated as follows: (# reads for the gene*109)/(# total of reads*size of the gene).
Genome_build: E. faecium Aus0004 (Genbank accession no. CP003351)
Supplementary_files_format_and_content: Tab-delimited text files generated by BEDTools program v2.16.2 with RPKM values

organism: Enterococcus faecium Aus0004

source_name: Growth with ciprofloxacin (0.38 mg/L)

growth_protocol: Bacterial cells of E. faecium Aus0004 bacteria were cultured at 37°C to the late-exponential-growth phase in BHI broth

extract_protocol:
Total RNA was extracted from using the ZR Fungal/Bacterial RNA Miniprep kit (Zymo Research, Irvine, CA). Residual chromosomal DNA was removed by treating samples with the TURBO DNA-free kit (Life Technologies). The Ribo-Zero Magnetic Kit Gram-Positive Bacteria (Epicentre, Madison, WI) was used according to the manufacturer’s recommendations to remove the 23S, 16S, and 5S rRNAs from the total RNA samples.
The strand-specific library preparation was performed using the NEXTflex Directional RNA-Seq Kit (dUTP-Based) (Bio Scientific, Austin, TX) and the samples were sequenced using the Illumina HiSeq 2500 platform (multiplex protocol, single-end 50-bp reads).


title: Growth with ciprofloxacin (0.38 mg/L) - sample 1


title: Growth with no ciprofloxacin - sample 2

source_name: Growth with no ciprofloxacin


title: Growth with no ciprofloxacin - sample 1


title: 02428_EN_sRNA-seq

description:
Small RNA-seq of 02428 endosperm.
Processed data file: 02428-1_EN_with_SNP_map.txt
Processed data file: 02428-2_EN_with_SNP_map.txt

source_name: endosperm, 02428, 7 days after pollination


title: Pool2_WCE

status: Public on Feb 03 2017

first: Sharon

middle: R

last: Grossman

address: 415 Main Street

institute: Broad Institute

description:
ChIP input
processed data file: Pool2_ChIP.counts.txt

data_processing:
Reads were mapped to plasmids using BWA 0.7.12 (Li and Durbin, 2009) with default parameters. Reads with MAPQ<20 were removed.
Total reads in ChIP and WCE libraries corresponding to each oligo
Genome_build: mm9

source_name: 3T3-L1 cell line

growth_protocol: 3T3-L1 pre-adipocytes were maintained in DMEM supplemented with 10% calf serum. Two days after confluence, the cells were induced with DMEM supplemented with 10% FBS, 1uM dexamethasone, 1.7uM insulin, and 0.5mM 3-isobutyl-1-methylxanthine (IBMX). 48h later, the medium was replaced with DMEM supplemented with 10% FBS and the cells were fed every two days.

extract_protocol: ChIP-Seq libraries were prepared as described by Mikkelsen et al. (Nature 2007; 448(7153):553-60; PMID: 17603471)

tag: molecule subtype

value: genomic DNA


title: Pool1_WCE

description:
ChIP input
processed data file: Pool1_ChIP.counts.txt

tag: cell line


title: NZ502_12%Glu

city: Tianjin

first: feiyu

last: fan

state: Tianjin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

department: Key Laboratory of Systems Microbial Biotechnology

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences.

description: RNA sample prepared as the following description: single colonies were inoculated into 250 ml flasks containing 30 ml NBS mineral salts medium with 2%w/v glucose, and grown at 37°C and 250 rpm for 12 h. Cultures were then transferred to a 500 ml fermentation vessel containing 250 ml NBS mineral salts medium with 12%w/v glucose, and grown at 37°C and 250 rpm for 48 h.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli ATCC8739 genome (GenBank CP000946.1) using Bowtie 2 (version 2.2.5)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Detailed parameters for reads mapping: bowtie2 -x ATCC8739 -1 X_1.fq -2 X_2.fq --no-mixed -p 2 -S X.sam
Genome_build: ATCC8739
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample .

organism: Escherichia coli ATCC 8739

source_name: E.coli cells

extract_protocol:
Total RNA was isolated by the Trizol-Phenol-Chloroform method. An additional clean-up including the on-column DNase I treatment was performed by using the RNeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: NZ-502 (RpoB mutant)

tag: growth condition

value: osmotic stress condtion (12% w/v glucose)


title: SucT110_5%Glu

description: RNA sample prepared as the following description: single colonies were inoculated into 250 ml flasks containing 30 ml NBS mineral salts medium with 2%w/v glucose, and grown at 37°C and 250 rpm for 12 h. Cultures were then transferred to a 500 ml fermentation vessel containing 250 ml NBS mineral salts medium with 5%w/v glucose, and grown at 37°C and 250 rpm for 48 h.

value: Suc-T110 (parental strain)

value: normal condtion (5% w/v glucose)


title: SucT110_12%Glu


title: NZ502_5%Glu


title: polyA mRNA RNA-seq from G1E-ER4 (ENCLB200STD)

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR000CIH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse G1E-ER4 (single end) differentiated for 24 hours
experiment encode accession: ENCSR000CIH
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB200STD
size range: >175

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

source_name: Mus musculus G1E-ER4 immortalized cell line treated with 10 nM 17beta-estradiol for 24 hours

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d6ec08a9-8b45-424d-aad9-55cbc02d527f/@@download/attachment/wgEncodePsuRnaSeq.html.pdf

tag: line

value: immortalized cell line

tag: description

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

tag: biosample encode accession

tag: dev stage

value: postnatal

tag: treatments

value: treatment_term_id:CHEBI:16469; treatment_term_name:17beta-estradiol; treatment_type:chemical; duration:24; duration_units:hour; UCSC-ENCODE-cv:diffProtD_24hr;

value: male

value: 0 day

tag: health state

value: unknown

tag: lab

value: Ross Hardison, PennState

tag: link

value: ENCBS327ENC at ENCODE; https://www.encodeproject.org/ENCBS327ENC/

value: Derived from ENCODE donor ENCDO089AAA; https://www.encodeproject.org/ENCDO089AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_D047; http://web.expasy.org/cellosaurus/CVCL_D047


title: Pool1_ChIP

city: Cambridge

description:
Chromatin IP against PPARG
processed data file: Pool1_ChIP.counts.txt

tag: chip antibody

value: PPARG (Cell Signaling Technologies SC-7196X)


title: polyA mRNA RNA-seq from CH12.LX (ENCLB709YVV)

description:
https://www.encodeproject.org/experiments/ENCSR000CHR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse CH12 (single end)
experiment encode accession: ENCSR000CHR
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB709YVV
size range: >175

source_name: Mus musculus strain B10.H-2aH-4bp/Wts CH12.LX immortalized cell line

value: B-cell lymphoma

tag: age

tag: Sex

value: female

value: ENCBS443MXB at ENCODE; https://www.encodeproject.org/ENCBS443MXB/

value: Derived from ENCODE donor ENCDO324YEK; https://www.encodeproject.org/ENCDO324YEK/

value: ENCODE dbxrefs Cellosaurus CVCL_0211; http://web.expasy.org/cellosaurus/CVCL_0211

value: ENCODE dbxrefs CH12; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=CH12


title: ChIP-seq from MEL cell line (ENCLB103ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000ADU/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on mouse MEL treated with 2% DMSO produced by the Snyder lab
experiment encode accession: ENCSR000ADU
assay title: ChIP-seq
assembly: mm9
encode release date: 2012-06-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB103ZZZ
size range: 150-350

source_name: Mus musculus strain MEL MEL immortalized cell line treated with 2% dimethyl sulfoxide for 5 days

extract_protocol:
general protocol: https://www.encodeproject.org/documents/302689be-b110-40b6-8912-cc9d934b002e/@@download/attachment/mouse.wgEncodeSydhHist.txt
extraction method: see document
general protocol: https://www.encodeproject.org/documents/302689be-b110-40b6-8912-cc9d934b002e/@@download/attachment/mouse.wgEncodeSydhHist.txt

tag: antibody

value: Control

value: MEL cell line

value: immortalized cell line

value: Leukemia (K562 analog)

value: not collected

value: Sherman Weissman, Yale

value: treatment_term_id:CHEBI:28262; treatment_term_name:dimethyl sulfoxide; treatment_type:chemical; duration:5; duration_units:day; UCSC-ENCODE-cv:DMSO_2.0pct;

value: ENCBS047ENC at ENCODE; https://www.encodeproject.org/ENCBS047ENC/

value: Derived from ENCODE donor ENCDO073AAA; https://www.encodeproject.org/ENCDO073AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2111; http://web.expasy.org/cellosaurus/CVCL_2111

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


title: ChIP-seq from MEL cell line (ENCLB104ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000ADU/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on mouse MEL treated with 2% DMSO produced by the Snyder lab
experiment encode accession: ENCSR000ADU
assay title: ChIP-seq
assembly: mm9
encode release date: 2012-06-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB104ZZZ
size range: 150-350

value: unknown


title: ChIP-seq from MEL cell line (ENCLB095ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000ADR/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 Histone Modification by ChIP-seq on mouse MEL produced by the Snyder lab
experiment encode accession: ENCSR000ADR
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR000ADN
encode release date: 2012-08-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB095ZZZ
size range: 150-350

source_name: Mus musculus strain MEL MEL immortalized cell line

value: ENCBS046ENC at ENCODE; https://www.encodeproject.org/ENCBS046ENC/


title: ChIP-seq from MEL cell line (ENCLB092ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AEA/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 Histone Modification by ChIP-seq on mouse MEL treated with 2% DMSO produced by the Snyder lab
experiment encode accession: ENCSR000AEA
assay title: ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ADU
encode release date: 2012-08-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB092ZZZ
size range: 150-350


title: ChIP-seq from MEL cell line (ENCLB091ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AEA/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Histone Modification by ChIP-seq on mouse MEL treated with 2% DMSO produced by the Snyder lab
experiment encode accession: ENCSR000AEA
assay title: ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ADU
encode release date: 2012-08-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB091ZZZ
size range: 150-350


title: ChIP-seq from MEL cell line (ENCLB106ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000ADN/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on mouse MEL produced by the Snyder lab
experiment encode accession: ENCSR000ADN
assay title: ChIP-seq
assembly: mm9
encode release date: 2011-09-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB106ZZZ
size range: 150-350


title: ChIP-seq from MEL cell line (ENCLB082ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000ADP/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 Histone Modification by ChIP-seq on mouse MEL produced by the Snyder lab
experiment encode accession: ENCSR000ADP
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR000ADN
encode release date: 2012-08-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB082ZZZ
size range: 150-350


title: polyA mRNA RNA-seq from G1E-ER4 (ENCLB528TSK)

description:
https://www.encodeproject.org/experiments/ENCSR000CIH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse G1E-ER4 (single end) differentiated for 24 hours
experiment encode accession: ENCSR000CIH
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB528TSK
size range: >175

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

value: postnatal

value: treatment_term_id:CHEBI:16469; treatment_term_name:17beta-estradiol; treatment_type:chemical; duration:24; duration_units:hour; UCSC-ENCODE-cv:diffProtD_24hr;

value: male

value: 0 day

value: Ross Hardison, PennState

value: ENCBS327ENC at ENCODE; https://www.encodeproject.org/ENCBS327ENC/

value: Derived from ENCODE donor ENCDO089AAA; https://www.encodeproject.org/ENCDO089AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_D047; http://web.expasy.org/cellosaurus/CVCL_D047


title: polyA mRNA RNA-seq from CH12.LX (ENCLB116FBD)

description:
https://www.encodeproject.org/experiments/ENCSR000CHR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse CH12 (single end)
experiment encode accession: ENCSR000CHR
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB116FBD
size range: >175

value: immortalized cell line

value: B-cell lymphoma

value: female

value: ENCBS948OTG at ENCODE; https://www.encodeproject.org/ENCBS948OTG/

value: Derived from ENCODE donor ENCDO324YEK; https://www.encodeproject.org/ENCDO324YEK/

value: ENCODE dbxrefs Cellosaurus CVCL_0211; http://web.expasy.org/cellosaurus/CVCL_0211

value: ENCODE dbxrefs CH12; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=CH12


title: ChIP-seq from MEL cell line (ENCLB081ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000ADP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Histone Modification by ChIP-seq on mouse MEL produced by the Snyder lab
experiment encode accession: ENCSR000ADP
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR000ADN
encode release date: 2012-08-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB081ZZZ
size range: 150-350

value: MEL cell line

value: Leukemia (K562 analog)

value: unknown

value: not collected

value: Sherman Weissman, Yale

value: ENCBS046ENC at ENCODE; https://www.encodeproject.org/ENCBS046ENC/

value: Derived from ENCODE donor ENCDO073AAA; https://www.encodeproject.org/ENCDO073AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2111; http://web.expasy.org/cellosaurus/CVCL_2111

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


title: Pool2_ChIP

description:
Chromatin IP against PPARG
processed data file: Pool2_ChIP.counts.txt

value: PPARG (Cell Signaling Technologies SC-7196X)

value: genomic DNA


title: polyA mRNA RNA-seq from liver (ENCLB451FBJ)

description:
https://www.encodeproject.org/experiments/ENCSR000CHB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on 8 week adult mouse liver
experiment encode accession: ENCSR000CHB
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2011-08-04
lab: Bing Ren, UCSD
library encode accession: ENCLB451FBJ
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Mus musculus strain B6NCrl liver tissue male adult (8 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0a7c7860-4801-456d-baaa-0f3ac6d99aa7/@@download/attachment/Ren_mRNA-seq_protocols_v090113.pdf

value: liver

value: tissue

value: Liver from an individual mouses

value: adult

value: 8 week

value: male

value: Bing Ren, UCSD

value: ENCBS337ENC at ENCODE; https://www.encodeproject.org/ENCBS337ENC/

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

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


title: polyA mRNA RNA-seq from liver (ENCLB244YDJ)

description:
https://www.encodeproject.org/experiments/ENCSR000CHB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on 8 week adult mouse liver
experiment encode accession: ENCSR000CHB
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2011-08-04
lab: Bing Ren, UCSD
library encode accession: ENCLB244YDJ
size range: >200
spikeins used: /references/ENCSR866KGS/

value: ENCBS419QNR at ENCODE; https://www.encodeproject.org/ENCBS419QNR/


title: polyA mRNA RNA-seq from lung (ENCLB360CMF)

description:
https://www.encodeproject.org/experiments/ENCSR000CHC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on 8 week adult mouse lung
experiment encode accession: ENCSR000CHC
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2011-08-04
lab: Bing Ren, UCSD
library encode accession: ENCLB360CMF
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Mus musculus strain B6NCrl lung tissue male adult (8 weeks)

value: lung

value: Lung from an individual mouse

value: unknown

value: ENCBS149ENC at ENCODE; https://www.encodeproject.org/ENCBS149ENC/

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


title: polyA mRNA RNA-seq from kidney (ENCLB392UPX)

description:
https://www.encodeproject.org/experiments/ENCSR000CHA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on 8 week adult mouse kidney
experiment encode accession: ENCSR000CHA
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2011-08-04
lab: Bing Ren, UCSD
library encode accession: ENCLB392UPX
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Mus musculus strain B6NCrl kidney tissue male adult (8 weeks)

value: kidney

value: Pair of kidneys from an individual mouse

value: ENCBS333ENC at ENCODE; https://www.encodeproject.org/ENCBS333ENC/

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


title: polyA mRNA RNA-seq from cortical plate (ENCLB656QIU)

description:
https://www.encodeproject.org/experiments/ENCSR000CGY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on 8 week adult mouse cortex
experiment encode accession: ENCSR000CGY
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2011-08-04
lab: Bing Ren, UCSD
library encode accession: ENCLB656QIU
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Mus musculus strain B6NCrl cortical plate tissue male adult (8 weeks)

value: cortical plate

value: tissue

value: Cortex from an individual mouse

value: adult

value: ENCBS524PWT at ENCODE; https://www.encodeproject.org/ENCBS524PWT/

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


title: polyA mRNA RNA-seq from kidney (ENCLB867RWF)

description:
https://www.encodeproject.org/experiments/ENCSR000CHA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on 8 week adult mouse kidney
experiment encode accession: ENCSR000CHA
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2011-08-04
lab: Bing Ren, UCSD
library encode accession: ENCLB867RWF
size range: >200
spikeins used: /references/ENCSR866KGS/

value: 8 week

value: male

value: Bing Ren, UCSD

value: ENCBS601VEO at ENCODE; https://www.encodeproject.org/ENCBS601VEO/

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


title: ChIP-seq from MEL cell line (ENCLB096ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000ADR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Histone Modification by ChIP-seq on mouse MEL produced by the Snyder lab
experiment encode accession: ENCSR000ADR
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR000ADN
encode release date: 2012-08-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB096ZZZ
size range: 150-350

value: MEL cell line

value: immortalized cell line

value: Leukemia (K562 analog)

value: unknown

value: not collected

value: Sherman Weissman, Yale

value: ENCBS046ENC at ENCODE; https://www.encodeproject.org/ENCBS046ENC/

value: Derived from ENCODE donor ENCDO073AAA; https://www.encodeproject.org/ENCDO073AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2111; http://web.expasy.org/cellosaurus/CVCL_2111

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


title: polyA mRNA RNA-seq from cortical plate (ENCLB413LIS)

description:
https://www.encodeproject.org/experiments/ENCSR000CGY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on 8 week adult mouse cortex
experiment encode accession: ENCSR000CGY
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2011-08-04
lab: Bing Ren, UCSD
library encode accession: ENCLB413LIS
size range: >200
spikeins used: /references/ENCSR866KGS/

value: cortical plate

value: tissue

value: Cortex from an individual mouse

value: adult

value: ENCBS138ENC at ENCODE; https://www.encodeproject.org/ENCBS138ENC/


title: polyA mRNA RNA-seq from cerebellum (ENCLB713SBH)

description:
https://www.encodeproject.org/experiments/ENCSR000CGX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on 8 week adult mouse cerebellum
experiment encode accession: ENCSR000CGX
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2011-08-04
lab: Bing Ren, UCSD
library encode accession: ENCLB713SBH
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Mus musculus strain B6NCrl cerebellum tissue male adult (8 weeks)

value: cerebellum

value: Cerebellum from an individual mouse

value: 8 week

value: male

value: Bing Ren, UCSD

value: ENCBS132ENC at ENCODE; https://www.encodeproject.org/ENCBS132ENC/

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


title: polyA mRNA RNA-seq from heart (ENCLB820YDT)

description:
https://www.encodeproject.org/experiments/ENCSR000CGZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on 8 week adult mouse heart
experiment encode accession: ENCSR000CGZ
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2011-08-04
lab: Bing Ren, UCSD
library encode accession: ENCLB820YDT
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Mus musculus strain B6NCrl heart tissue male adult (8 weeks)

value: heart

value: Heart from an individual mouse

value: unknown

value: ENCBS141ENC at ENCODE; https://www.encodeproject.org/ENCBS141ENC/

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

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


title: polyA mRNA RNA-seq from heart (ENCLB398AUK)

description:
https://www.encodeproject.org/experiments/ENCSR000CGZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on 8 week adult mouse heart
experiment encode accession: ENCSR000CGZ
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2011-08-04
lab: Bing Ren, UCSD
library encode accession: ENCLB398AUK
size range: >200
spikeins used: /references/ENCSR866KGS/

value: tissue

value: ENCBS530SGO at ENCODE; https://www.encodeproject.org/ENCBS530SGO/


title: ChIP-seq from MEL cell line (ENCLB107ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000ADN/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on mouse MEL produced by the Snyder lab
experiment encode accession: ENCSR000ADN
assay title: ChIP-seq
assembly: mm9
encode release date: 2011-09-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB107ZZZ
size range: 150-350

value: Control

value: MEL cell line

value: immortalized cell line

value: Leukemia (K562 analog)

value: not collected

value: Sherman Weissman, Yale

value: ENCBS046ENC at ENCODE; https://www.encodeproject.org/ENCBS046ENC/

value: Derived from ENCODE donor ENCDO073AAA; https://www.encodeproject.org/ENCDO073AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2111; http://web.expasy.org/cellosaurus/CVCL_2111

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


title: polyA mRNA RNA-seq from embryonic fibroblast (ENCLB964ZGE)

description:
https://www.encodeproject.org/experiments/ENCSR000CGV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse embryonic fibroblast (MEF)
experiment encode accession: ENCSR000CGV
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2011-08-04
lab: Bing Ren, UCSD
library encode accession: ENCLB964ZGE
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Mus musculus strain C57BL/6J embryonic fibroblast primary cell male embryo (13.5 weeks)

value: embryonic fibroblast

value: primary cell

value: Mouse Embryonic Fibroblast

value: embryonic

value: 13.5 week

value: male

value: Bing Ren, UCSD

value: ENCBS153ENC at ENCODE; https://www.encodeproject.org/ENCBS153ENC/

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

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


title: polyA mRNA RNA-seq from spleen (ENCLB042EJB)

description:
https://www.encodeproject.org/experiments/ENCSR000CGW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on 8 week adult mouse spleen
experiment encode accession: ENCSR000CGW
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2011-08-04
lab: Bing Ren, UCSD
library encode accession: ENCLB042EJB
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Mus musculus strain B6NCrl spleen tissue male adult (8 weeks)

value: spleen

value: tissue

value: Spleen from a single mouse

value: adult

value: 8 week

value: unknown

value: ENCBS159ENC at ENCODE; https://www.encodeproject.org/ENCBS159ENC/

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

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