title: G1 RNA-Seq Exp1 Rep3

description: 'G1 mRNA Rep3' column in RC_Data.xlsx

source_name: HeLa S3_G1_RNA-Seq Exp1


title: PyMT organoids day0 n2

status: Public on Sep 28 2016

type: SRA

city: Dunedin

first: Sarah

middle: D

last: Diermeier

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

description: polyA+ RNA

library_source: transcriptomic

data_processing:
Illumina Casava software used for basecalling.
The quality of the raw data was evaluated using FastQC.
The reads were mapped to mm10 using STAR.
The GENCODE mV5 annotation set was used as a reference and the reads per gene record were counted using the HTSeq package.
Differential gene expression was performed with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads (generated with HTSeq-count) for each sample.

molecule: total RNA

organism: Mus musculus

source_name: mammary tumor

growth_protocol: Organoids from MMTV-PyMT tumors were prepared as described previously (Ewald AJ et al, Cold Spring Harbor Protocols, 2013) and cultured in matrigel in the presence of FGF2 for 6 days. For day 0 datasets, RNA was extratced directly after organoid preparation. For tumor sections, RNA was extratced from a homogenous, 30 µm cryo-section.

extract_protocol:
Total RNA was extracted using TRIzol reagent from both organoids and homogenized tumor tissue.
Libraries for polyA+ RNA-Sequencing were prepared from 1 μg RNA per sample using TruSeq chemistry (Illumina)

tag: strain

value: FVB

tag: genotype

value: MMTV-PyMT

tag: processing

value: organoids

tag: culture time

value: 0 days


title: PyMT organoids n1

description: polyA+ RNA

value: 6 days


title: G1 RNA-Seq Exp1 Rep2

city: Tel Aviv-Yafo

first: Tamir

last: Tuller

department: Biomedical Engineering

country: Israel

institute: Tel Aviv University

description: 'G1 mRNA Rep2' column in RC_Data.xlsx

data_processing:
Reference transcriptome, rRNAs, and tRNAs, were assembled from BioMart (GRCh37.p11).
The 3’end adapter CTGTAGGCACCATCAAT was removed from the 51nt long reads using Cutadapt v1.6, retaining only reads with a minimum length of 24nt.
These reads were then initially mapped against the rRNA and tRNA databases, using Bowtie v0.12.8: -a --best --strata -n 2 --seedlen 24 --tryhard. Throughout the analysis the Bowtie mapping is executed as described. Reads which mapped against the rRNA and tRNA databases were removed.
The remaining reads are mapped against the assembled transcriptome using Bowtie as described.
Please see our paper for multi-read handling documentation.
Genome_build: GRCh37.p11
Supplementary_files_format_and_content: Excel file containing per gene read counts for each sample.

organism: Homo sapiens

extract_protocol:
Total mRNA and ribosome-protected fragments were analyzed essentially as described in [PMID:22836135]. In brief, 5x106 HeLa S3 cells synchronized to either G1 or M phase were treated with 100 ug/mL cycloheximide for 5 min, harvested on ice and washed twice in ice-cold PBS. Following cell lysis and removal of nuclei by centrifugation, one tenth of the lysate was removed for total mRNA extraction and the rest was digested with 60 units RNase I (Ambion) for 45 min at room temp. Digestion was terminated with SuperaseIN (Ambion) and monosomes were pelleted by ultracentrifugation on a sucrose cushion. Footprint fragments were purified using a 15% polyacrylamide urea gel, and rRNA fragments were removed using Ribo-Zero Magnetic Gold Kit (Epicentre) according to the manufacturer’s instructions. In parallel, mRNA was purified using Oligo (dT) cellulose (Ambion) according to the manufacturer’s instructions and fragmented for 25 min at 94°C.
Both mRNA and ribosome-protected fragments were dephosphorylated with T4 polynucleotide kinase and ligated to Universal miRNA Cloning Linker (NEB). RNA was reverse transcribed using SuperScript III and cDNA was circularized using CircLigase (both Epicentre). Libraries were amplified using indexed Illumina primers, size selected on a 1% agarose gel and extracted using High Pure PCR Purification Kit (Roche).

tag: cell type

value: HeLa S3 cells

tag: cell cycle phase

value: G1 phase

tag: molecule subtype

value: Total mRNA (RNA-seq)


title: MDA-MB-453_separate_culture

city: Boston

first: Muhammad

middle: B

last: Ekram

state: MA

address: 450 Brookline Avenue, DA 740A

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

description: cultured seperately and mixed with cancer-associated fibroblasts (CAFs)

data_processing:
Library strategy: SAGE-Seq
SAGE-Seq: Basecalls were performed using CASAVA version 1.8.2
SAGE-Seq: The sequencing tags were mapped and normalized as described in Wu et al., Genome Research, 2010 (PMID: 21045080). Tag counts used were the sums of all sense SAGE-Seq tags uniquely mapped to the same gene.
processed data files format and content: SAGE-Seq: Tab-separated file of the normalized tag counts of each samples for each gene.
Genome_build: hg18

growth_protocol: All the epithelial and fibroblast cell lines were grown in media representing 50/50 mixture of DMEM-F12, 10% FBS/MEGM with supplements, as this media fully supported growth and viability of both epithelial cells and fibroblasts. Matrigel 3d culture experiments were performed using on-top method as described in Lee et al., Nature Methods, 2007 (PMID: 17396127).

extract_protocol:
DsRED labeled carcinoma cell lines and GFP expressing primary CAFs were cultured either separately or in co-cultures for 17 hours. Colonies were released from Matrigel by 30 min incubation in PBS/EDTA, at which point separately cultured cells were combined to control for cross-contamination. Cell mixtures were washed with PBS, trypsinized for 7 min, quenched with serum containing media, washed and spun down. Epithelial cells were selected using Epithelial Enrich dynabeads (Life Technologies) following manufacturer’s protocol. Microscopic examination of captured cells revealed no detectable CAF contamination.
From each sample 5E5 cells were used to prepare SAGE-Seq (serial analysis of gene expression combined with the Illumina/Solexa 1G platform) libraries according to a detailed protocol available at http://polyaklab.dfci.harvard.edu/index.php/science/protocols

tag: cell line

tag: tissue of origin

value: breast metastatic site:pericardial effusion

tag: cell line type

value: cancer cell line

tag: sub-type

value: HER2 positive


title: MCF10DCIS_co-culture

description: co-cultured with cancer-associated fibroblasts (CAFs)

value: xenograft of breast tumorigenic cell line MCF10AT

value: triple-negative


title: MDA-MB-453_co-culture


title: G1 Ribo-Seq Exp1 Rep3

description: 'G1 RP Rep3' column in RC_Data.xlsx

data_processing:
library strategy: Ribo-seq
Reference transcriptome, rRNAs, and tRNAs, were assembled from BioMart (GRCh37.p11).
The 3’end adapter CTGTAGGCACCATCAAT was removed from the 51nt long reads using Cutadapt v1.6, retaining only reads with a minimum length of 24nt.
These reads were then initially mapped against the rRNA and tRNA databases, using Bowtie v0.12.8: -a --best --strata -n 2 --seedlen 24 --tryhard. Throughout the analysis the Bowtie mapping is executed as described. Reads which mapped against the rRNA and tRNA databases were removed.
The remaining reads are mapped against the assembled transcriptome using Bowtie as described.
Please see our paper for multi-read handling documentation.
Genome_build: GRCh37.p11
Supplementary_files_format_and_content: Excel file containing per gene read counts for each sample.

source_name: HeLa S3_G1_Ribo-Seq Exp1

value: ribosome-protected fragments  (Ribo-seq)


title: Cancer_associated_fibroblasts

description: cultured separately

source_name: Fibroblast from breast tumor

value: breast tumor


title: G1 RNA-Seq Exp1 Rep1

description: 'G1 mRNA Rep1' column in RC_Data.xlsx


title: 630∆erm-14H_rep2

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using AlienTrimmer_0.4.0. Only sequence with a minimum length of 30 were considered.
Sequenced were mapped to Peptoclostridium difficile 630 whole genome sequence complemented by the known ncRNA using bowtie v1.0.1 with parameter -k 2000
MAP2COV was used for counting genes with parameters -t RNA -b YES
Statistical analyses were performed using R version 3 and Bioconductor packages.
The whole dataset was first normalized using the normalization function of DESeq2 and with default parameters.
The statistical test function of DESeq2 was then applied on each strand coverage count with the 6 h value as a reference for reporting the expression data of 14 and 24 h.
Genome_build: Peptoclostridium difficile 630 (NC_009089.1) complemented by the known ncRNA (PMID: 23675309)
Supplementary_files_format_and_content: Genome annotation (Gene ID, Gene Name), Raw Counts (630, 630Derm, 630E, 6H, 14H, 24H), Normalized Counts (630, 630Derm, 630E, 6H, 14H, 24H), Statistics (FC, pvalue, significant)

organism: Clostridioides difficile

source_name: Erythromycin-sensitive strain 630∆erm

growth_protocol: Strains were grown aerobically in TY at 37°C for 6, 14 and 24 H)

extract_protocol:
Total RNA was extracted using phenol, Trizol reagent and chloroform/isoamylalcohol.
RNA libraries were prepared for sequencing using standard Illumina protocols
Truseq stranded RNA seq kit

tag: strain provider

value: Mullany laboratory

tag: phenotype

value: Erythromycin-sensitive


title: PyMT organoids day0 n1

description: polyA+ RNA

value: FVB


title: MCF10DCIS_separate_culture


title: T47D_co-culture

value: breast metastatic site:pleural effusion

value: luminal estrogen receptor positive


title: M Ribo-Seq Exp2 Rep1

description: 'M RP Rep4' column in RC_Data.xlsx

source_name: HeLa S3_M_Ribo-Seq Exp2

value: M phase


title: 630∆erm-6H_rep2


title: 630∆erm-6H_rep1


title: PyMT tumor n1

description: polyA+ RNA

value: MMTV-PyMT

value: tumor section


title: M Ribo-Seq Exp1 Rep3

description: 'M RP Rep3' column in RC_Data.xlsx

source_name: HeLa S3_M_Ribo-Seq Exp1

value: HeLa S3 cells


title: PyMT tumor n2

description: polyA+ RNA


title: 630∆erm-24H_rep1


title: M Ribo-Seq Exp1 Rep2

description: 'M RP Rep2' column in RC_Data.xlsx


title: T47D_separate_culture


title: WT n3

description: polyA+ RNA

source_name: mammary gland

value: wild type

value: organoids

value: 6 days


title: MCF7_co-culture

value: cancer cell line


title: 630-24H_rep2

source_name: Wild type strain 630

value: wild-type strain 630

value: Erythromycin-resistant


title: WT n2

description: polyA+ RNA


title: 630E-14H_rep2

source_name: Erythromycin-sensitive strain 630E

value: Rood laboratory


title: 630-24H_rep1


title: M Ribo-Seq Exp1 Rep1

description: 'M RP Rep1' column in RC_Data.xlsx

value: ribosome-protected fragments  (Ribo-seq)


title: MCF7_separate_culture


title: PyMT tumor n3

description: polyA+ RNA


title: WT n1

description: polyA+ RNA


title: 630∆erm-14H_rep1

value: Mullany laboratory


title: cns-ptc-rep2

city: Cambridge

first: Peter

middle: W

last: Reddien

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Basecalling was performed by Illumina CASAVA
Sequenced reads were trimmed of  mapped to transcriptome with Bowtie2 with parameters --best -S -5 5
Read counts were generated with Samtools
Differential expression was determined with DESeq2
Genome_build: Dresden S. mediterranea Transcriptome Assembly (https://idisk.mpi-cbg.de/~brandl/planaria/dd_Smed_v4.nuc.fasta.zip)
Supplementary_files_format_and_content: Comma-separated text files

molecule: polyA RNA

organism: Schmidtea mediterranea

source_name: Cephalic ganglia

growth_protocol: Standard planarian culture conditions

extract_protocol:
Total RNA extracted from cephalic ganglia or head fragments with TriZOL reagent. Extracted RNA treated with Promega RQ1 DNase and quantified by NanoDrop and Agilent Bioanalyser
Standard Illumina TruSeq RNA Library Preparation Kit v2 protocol

treatment_protocol: Animals fed dsRNA-expressing bacteria 6-12 times at 4-day intervals

tag: tissue

value: Cephalic ganglia

tag: RNAi

value: patched


title: M RNA-Seq Exp1 Rep3

description: 'M mRNA Rep3' column in RC_Data.xlsx

source_name: HeLa S3_M_RNA-Seq Exp1

value: Total mRNA (RNA-seq)


title: 630-6H_rep2


title: M RNA-Seq Exp1 Rep1

description: 'M mRNA Rep1' column in RC_Data.xlsx


title: AB042 rep2

city: Winnipeg

first: Manu

middle: Kumar

last: Singh

state: Manitoba

address: 45 Chancellors circle, 412 Buller

department: Microbiology

country: Canada

institute: University of Manitoba

data_processing: Gene annotation and chromosomal location was done using already published annotation file from the same organism.

organism: Acinetobacter baumannii ATCC 17978

source_name: KumarLab collection

growth_protocol: All samples were grown in LB and supplimented with triclosan, when required.

extract_protocol:
Cells were palleted at OD600 between 0.6 to 0.8 and total RNA were extracted using Rneasy mini kit from QIAGEN.
Illumina standard protocols were used.

value: Triclosan-resistant mutant


title: cns-hh-rep1

value: hedgehog


title: Try

city: Deagu, Korea

first: Ji-Yeon

last: Kim

address: 80 Daehakro, Bukgu

country: South Korea

institute: Kyungpook National University

data_processing:
Sequenced reads were mapped to the reference genome sequence (GenBank No. CP014334.1).
The relative transcript abundance was computed by the trimmed mean of M-values normalization (TMM) (Robinson & Oshlack, 2010).
Genome_build: GenBank accession for complete genome: CP014334.1
Supplementary_files_format_and_content: worksheet files include relative normalization value, p-value, gene annotation. The FASTA file with protein sequence is available on the series record.

organism: Fervidobacterium islandicum

source_name: Tryptone

extract_protocol:
Total RNA was isolated from bacterial samples by using a RNeasy Mini Kit (QIAGEN, Hilden, Germany) as described by the manufacturer. Illumina TruSeq RNA Sample Prep kit v2 (Illumina) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: cns-control-rep2

description:
cns-control_vs_head-control.csv
cns-control_vs_cns-hh.csv
cns-control_vs_cns-ptc.csv


title: cns-control-rep1


title: 630-14H_rep2


title: M RNA-Seq Exp2 Rep1

description: 'M mRNA Rep4' column in RC_Data.xlsx

source_name: HeLa S3_M_RNA-Seq Exp2

value: M phase


title: Fea

source_name: Feather


title: CBP-011 APK3 Sessile RNA-4

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

data_processing:
Basecall files and fastq files were created on the MiSeq instrument during the sequencing run using  MiSeq Real Time Analysis (RTA v 1.18.54.0) software and the MiSeq Reporter (MSR v 2.5.1.3).
RNAseq reads were aligned to the C. thermocellum 27045  (CP000568.1) complete genome using Fastq files imported into the CLCBio RNA-sequencing pipeline. Default settings were used for mismatch, insertion, and deletion costs.
Total gene counts from the CLCBio mapping were used for DESeq2 analysis to normalise and determine significant gene expression differences
Supplementary_files_format_and_content: PL.vs.SS - CLC - Uniquely mapped fragment reads - AD_09-26-2016.xlsx includes read counts for each gene across the 8 samples used in this study
Supplementary_files_format_and_content: PL.vs.SS - DeSeq2 - Differential expression results - AD_09-26-2016.xlsx includes dignigicant gene expression differences

organism: Acetivibrio thermocellus ATCC 27405

source_name: CBP-011 APK3 Sessile

growth_protocol: Six replicate batch fermentations in MTC medium with Whatman #3 cellulose paper at 3 g/L as the sole carbon source were carried in 3 L Applikon bioreactors (Applikon Biotechnology, CA) with a 2 L fermentation volume at constant pH of 7.00, 60.0o C temperature and 250 rpm impeller speed. Nitrogen gas at 2 mL/min was passed through the reactors and pH was adjusted by titration with 2 N potassium hydroxide. Reactors were inoculated (5% v/v) with fresh, overnight cultures. Four fermentations were ended 14 hours after inoculation with biofilm and planktonic cell fractions collected for gene expression and proteomic studies. Two fermentations were run 35 hours to completion for quantitative analysis of the fermentation process and time-course measurements of planktonic cells accumulation in the liquid medium. Three pockets made of stainless steel mesh (Spectrum Laboratories Inc., CA) with 213 µm pore size were tied to each reactor’s baffles and each housed a sheet of cellulose Whatman #3 paper for easy and fast collection of the biofilm (sessile) cell fraction.

extract_protocol:
Trizol (Invitrogen, CA) was added to each sample and the mixture was lysed  by bead beating with 0.8 g of 0.1 mm glass beads (BioSpec Products, OK) in a Retsch Tissue Lyser II (Retsch GmbH, Germany) for 3 x 20s each at 25 Hz with a 1 minute pause between each disruption.  RNA was prepared from each sample, cleaned on and RNeasy column, with on column DNaseI-treatment, and quantity and quality assessed, as previously described (Wilson CM, et al. (2013) Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass. Biotechnol Biofuels 6(1):179). High quality total RNA (RIN>8.4) was depleted of rRNA using Ribo-Zero rRNA Removal Kit for bacteria (Epicentre-Illumina, CA) following kit protocol.  The depleted sample was purified on a RNA Clean & Concentrator-5 (Zymo Research, CA) following kit protocol.
Depleted RNA was used for RNA-Seq library preparation with the Epicentre ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre-Illumina, CA) following the manufacturer’s protocol (EPILIT329 Rev.C).  Agencount AMPure beads (Beckman Coulter, IN) were used to purify the cDNA, and unique indexes were added during 13 cycles of library amplification.  The final RNA-Seq libraries were purified with Agencount AMPure beads (Beckman Coulter, IN) and quantified with a Qubit fluorometer (Life Technologies, CA).  The library quality was assessed on a Bioanalyzer DNA 7500 DNA Chip (Agilent, CA), and samples were pooled and diluted. Samples were pooled to make a stock of 6 nM.  The Library pool was further diluted and then denatured according to manufactures protocols.  Two paired end runs were completed (2 x 251 + 6 bp barcode) and (2x76 + 6 bp barcode) on an Illuimina MiSeq instrument.
Illumina\Epicentre ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre-Illumina, CA)

treatment_protocol: For RNAseq and proteomic analyses, the steel meshes housing cellulose and biofilm were first briefly rinsed in saline solution before flash freezing in liquid nitrogen and the frozen material was then stored at -80o C in plastic conical tubes. The planktonic cell fraction was collected from the aqueous medium in 40 mL aliquots, drawn through a 20 µm nylon woven net filter (EMD Millipore, MA) to prevent contamination from cellulose particulates. After centrifugation at 9000 g for 5 minutes at 4o C the supernatant was discarded and tubes containing cell pellets were flash frozen in liquid nitrogen and stored at -80o C.

tag: xylose

value: Sessile


title: head-control-rep2

source_name: Head fragment

value: Head fragment


title: Glu

source_name: Glucose


title: CBP-011 APK2 Sessile RNA-3

description: PL.vs.SS - CLC - Uniquely mapped fragment reads - AD_09-26-2016.xlsx

source_name: CBP-011 APK2 Sessile


title: cns-ptc-rep1


title: ATCC 17978 rep1

source_name: ATCC

value: Wild type


title: AB042 rep1


title: 630-14H_rep1


title: CBP-010 APK3 Sessile RNA-2

source_name: CBP-010 APK3 Sessile


title: head-control-rep1


title: 630-6H_rep1


title: CBP-010 APK2 Sessile RNA-1

source_name: CBP-010 APK2 Sessile


title: Pep

source_name: Peptone


title: ATCC 17978 rep2


title: PBMC_replicate_14 intravenous LPS low inflammation

status: Public on Sep 27 2016

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

data_processing:
Base calling was done by RTA v1.13.48.0
Sequence reads were aligned to hg19 genome using STAR with default options.
Alignment was filtered using the following specifications: 1) read was uniquely mapped, 2) reads from the same pair were mapped to the same chromosome with expected orientations and mapping distance between the read pair was < 500,000 bp
Fragments Per Kilobase of exon per Million reads mapped (FPKM) was estimated by Cufflinks 2.1.1. Differential expression was tested by Cuffdiff with options "-u --max-bundle-frags 50000000". Annotation included mRNAs from RefSeq, stringent set of lincRNAs from Cabili et al. 2011 and lincRNAs from GENCODE v19.
Genome_build: hg19
Supplementary_files_format_and_content: DIFF files were obtained from Cuffdiff output.
Supplementary_files_format_and_content: PBMC_high_pre_vs_post_gene_exp.diff contains differential expression result from PBMC high responders. Annotation included mRNAs from GENCODE, lincRNAs from GENCODE and stringent set of lincRNAs form Cabili et al. sample_1 = baseline, sample_2 = post-LPS
Supplementary_files_format_and_content: PBMC_low_pre_vs_post_gene_exp.diff contains differential expression result from PBMC low responders. Annotation included mRNAs from GENCODE, lincRNAs from GENCODE and stringent set of lincRNAs form Cabili et al. sample_1 = baseline, sample_2 = post-LPS

source_name: PBMC

extract_protocol:
PBMCs were isolated from whole blood using magnetic bead selection (Dynabeads® CD14, ThermoFisher, Waltham MA), and frozen in TRIzol reagent (ThermoFisher, Waltham MA) for subsequent RNA extraction via standard protocol. Extracted RNA samples underwent quality control (QC) assessment using the Agilent Bioanalyzer (Agilent, Santa Clara, CA) and all RNA samples submitted for sequencing had an RNA Integrity Number (RIN) >6.
Using a minimum of 300ng input RNA, Poly-A libraries were prepared using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) per standard protocols. The prepared libraries were sequenced on an Illumina HiSeq 2000 at the UPenn Next Generation Sequencing Core (NGSC). We sequenced samples at a depth of 1-2 samples per lane, which generated ~150-200 million 2×101 bp paired-end reads per sample.

value: PBMC

tag: Sex

value: Male

tag: race

value: Caucasian

tag: treatment

value: intravenous LPS

tag: inflammatory response

value: low


title: PBMC_replicate_15 intravenous LPS low inflammation

value: Female

value: African American


title: PBMC_replicate_11 intravenous LPS high inflammation

value: high


title: PBMC_replicate_12 intravenous LPS low inflammation


title: PBMC_replicate_13 intravenous LPS low inflammation


title: PBMC_replicate_9 intravenous LPS low inflammation


title: PBMC_replicate_10 intravenous LPS high inflammation


title: PBMC_replicate_6 intravenous LPS high inflammation


title: PBMC_replicate_7 intravenous LPS low inflammation


title: PBMC_replicate_1 intravenous LPS high inflammation


title: PBMC_replicate_8 intravenous LPS low inflammation


title: PBMC_replicate_4 intravenous LPS high inflammation


title: PBMC_replicate_3 intravenous LPS high inflammation


title: PBMC_replicate_15 baseline low inflammation

value: baseline


title: PBMC_replicate_2 intravenous LPS high inflammation


title: PBMC_replicate_13 baseline low inflammation


title: PBMC_replicate_12 baseline low inflammation


title: PBMC_replicate_10 baseline high inflammation


title: PBMC_replicate_11 baseline high inflammation


title: PBMC_replicate_9 baseline low inflammation


title: PBMC_replicate_8 baseline low inflammation


title: PBMC_replicate_7 baseline low inflammation


title: PBMC_replicate_6 baseline high inflammation


title: PBMC_replicate_3 baseline high inflammation


title: PBMC_replicate_4 baseline high inflammation


title: PBMC_replicate_5 baseline high inflammation


title: PBMC_replicate_2 baseline high inflammation


title: PBMC_replicate_1 baseline high inflammation


title: Overexpressed DIS3L2 D391N mutant rep3

city: Prague 4

first: Josef

last: Pasulka

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR, v. v. i.

data_processing:
alignment: Segemehl
expression level: BitSeq
differential expression analysis: BitSeq
Genome_build: hg38
Supplementary_files_format_and_content: ENSEMBL transcript expression estimation (RPKM)

extract_protocol: RNA-Seq Library-protocol

tag: condition

value: Overexpressed DIS3L2 D391N mutant


title: Overexpressed DIS3L2 D391N mutant rep2


title: control rep1

value: control


title: control rep3


title: Overexpressed DIS3L2 D391N mutant rep1


title: Overexpressed DIS3L2 D391N mutant rep2 (CLIP-Seq)

data_processing:
Library strategy: CLIP-Seq
alignment: Segemehl, Subread
analysis: Bayesian background analysis
Genome_build: hg19
Supplementary_files_format_and_content: Count table of uridylated regions

extract_protocol: crosslinking in vivo and immunoprecipitation (CLIP) method


title: control rep2


title: 2L

first: Mukund

last: Varma

address: 415 Main Street

institute: Broad Institute

data_processing:
Alignment of Reads was done using Tophat2+Bowtie1, with alignment against the transcriptome and the genome
Counting of transcripts aligned in the previous step was done with the HTSeq package
QC metrics for the data were analysed using RSeqC
Differential gene expression was calculated using a linear model with the EdgeR package
Genome_build: Mus_musculus_assembly10

source_name: LPS alone

growth_protocol: Bone-marrow was extracted from mouse tibia and femers and cultured in L929 media as a sourse of MCSF for 6 days prior to treatment.

extract_protocol:
Cells were directly lysed in RLT (500 μl) lysis buffer and stored at -80°
SmartSeq2
full length cDNA libraries were prepared using template switching and whole transcriptome amplification in a slight variation of the SmartSeq2 protocol described in PMID: 24056875

treatment_protocol: BMDMs were either left untreated or treated with succinate or dimethyl malonate for 3 h prior to treatment with or without LPS for 4 or 48 h.

tag: strain

value: Bone marrow

tag: age

value: 12 weeks

tag: number of cells

tag: total volume

tag: collection buffer

value: RLT


title: 2S

source_name: succinate alone


title: 2D

source_name: DMM alone


title: 2C

source_name: Untreated control


title: DL1B

source_name: DMM (3 h) + LPS (4 h)


title: SL1B

source_name: succinate (3 h) + LPS (4 h)


title: D1B


title: L1B


title: Overexpressed DIS3L2 D391N mutant rep3 (CLIP-Seq)

tag: cell line


title: S1B


title: C1B


title: 1DL

source_name: DMM (3 h) + LPS (48 h)


title: 1D


title: 2DL


title: DL1A


title: 1SL

source_name: succinate (3 h) + LPS (48 h)


title: L1A


title: S1A


title: D1A


title: 1S


title: KOp3C_7

city: La Jolla

first: Kun

last: Zhang

state: California

address: 9500 Gilman Drive

institute: UCSD

data_processing:
50bp single-end reads (or first 50bp of 100bp reads using parameter "--clip3pNbases 50") were mapped to the mouse genome using STAR (v2.3.0): STAR --readFilesCommand zcat --runThreadN 8  --outSAMstrandField intronMotif --genomeDir "genome dir" --readFilesIn "fastq files" --outFileNamePrefix "sample name"
Gene read counts were calculated based on exon mapping using HTSeq (v0.6.1): htseq-count -q -t exon - "gtf file" > "readCount file"
Transcripts per million mapped reads (TPM) values were calculated
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes TPM values for each Sample

source_name: Testes

extract_protocol:
Testes were decapsulated in HBSS (Mediatech  Inc.) and digested with collagenase IV (1 mg/ml in HBSS) at 37 °C for 3 min with gentle agitation.  After washing with HBSS, samples were digested with 0.25 ml of DNase I (7 mg/ml, Sigma Inc.) and 1 ml of Trypsin/EDTA (0.25%, Invitrogen Inc.) at 37 °C for 10 min.  Digestion was stopped by adding 1 ml of media (MEMa + 10% FBS) and GFP+ cells were sorted using a FACSAria II machine (BD Biosciences).
Reverse transcription and cDNA amplification was performed with C1 Single-Cell Microfluidic Auto Prep System (Fluidigm) using the SMARTer Ultra Low RNA Kit (Clontech Inc.) with modifications: 1) addition of ERCC RNA Spike-In Mix (4456740, Ambion) at 1:40,000 dilution to the lysis reaction buffer; 2) inclusion of supplemental primer (5’-AAGCAGTGGTATCAACGCAGAGTACNNNNNN, diluted to 12µM in the supplied Clontech Dilution buffer) to Lysis Mix A for a final concentration of 4.2µM.  Final libraries were prepared for sequencing using the NexteraXT dual barcoding system (Illumina, Inc.).

tag: genotype

value: Rhox10 Knockout

value: Postnatal Day 3

tag: cell type

value: Id4-eGFP Positive


title: KOp3C_9


title: KOp3C_8


title: C1A


title: KOp3C_35


title: KOp3C_33


title: KOp3C_34


title: 1L


title: KOp3C_32


title: KOp3C_28


title: KOp3C_29


title: KOp3C_30


title: KOp3C_27


title: KOp3C_4


title: KOp3C_5


title: KOp3C_26


title: KOp3C_25


title: KOp3C_22


title: KOp3C_23


title: CBP-011 APK3 Plank RNA-4

source_name: CBP-011 APK3 Plank

value: Plantonic


title: KOp3C_24


title: KOp3C_21


title: cns-hh-rep2

source_name: Cephalic ganglia

value: Cephalic ganglia

value: hedgehog


title: CBP-010 APK3 Plank RNA-2

source_name: CBP-010 APK Plank


title: KOp3C_20


title: KOp3C_2


title: KOp3C_3


title: KOp3C_19


title: KOp3C_18


title: KOp3C_17


title: KOp3C_16


title: KOp3C_14


title: KOp3C_15


title: KOp3C_12


title: KOp3C_13


title: KOp3C_10


title: KOp3C_1


title: KOp3B_9


title: KOp3B_8


title: KOp3C_11


title: KOp3B_7


title: KOp3B_6


title: KOp3B_5


title: KOp3B_3


title: KOp3B_12


title: KOp3B_2


title: KOp3B_4


title: KOp3C_36


title: KOp3B_11


title: KOp3B_1


title: KOp3B_10


title: KOp3A_9


title: KOp3A_7


title: KOp3A_6


title: KOp3A_5


title: KOp3A_3


title: KOp3A_17


title: KOp3A_21


title: KOp3A_19


title: KOp3A_18


title: KOp3A_2


title: KOp3A_20


title: KOp3A_15


title: KOp3A_16


title: KOp3A_13


title: KOp3A_12


title: M RNA-Seq Exp1 Rep2

description: 'M mRNA Rep2' column in RC_Data.xlsx

source_name: HeLa S3_M_RNA-Seq Exp1

value: HeLa S3 cells

tag: cell cycle phase

value: M phase

tag: molecule subtype

value: Total mRNA (RNA-seq)


title: KOp3A_8


title: KOp3A_10


title: KOp3A_11


title: KOp3A_1


title: WTp3B_9

value: Wildtype


title: WTp3B_8


title: KOp3A_4


title: WTp3B_7


title: WTp3B_55


title: WTp3B_6


title: KOp3A_14


title: WTp3B_5


title: WTp3B_50


title: WTp3B_47


title: WTp3B_52


title: WTp3B_51


title: WTp3B_45


title: WTp3B_54


title: WTp3B_48


title: WTp3B_49


title: WTp3B_46


title: WTp3B_41


title: WTp3B_42


title: WTp3B_43


title: WTp3B_4


title: WTp3B_40


title: WTp3B_37


title: WTp3B_38


title: WTp3B_36


title: WTp3B_39


title: WTp3B_34


title: WTp3B_53


title: Overexpressed DIS3L2 D391N mutant rep1 (CLIP-Seq)


title: PBMC_replicate_14 baseline low inflammation

tag: tissue

value: PBMC

value: Male

value: Caucasian

value: low


title: WTp3B_33


title: WTp3B_30


title: WTp3B_28


title: WTp3B_3


title: WTp3B_29


title: WTp3B_31


title: WTp3B_24


title: WTp3B_26


title: WTp3B_22


title: WTp3B_20


title: WTp3B_21


title: WTp3B_44


title: WTp3B_19


title: WTp3B_2


title: WTp3B_35


title: WTp3B_23


title: WTp3B_18


title: CBP-010 APK2 Plank RNA-1

source_name: CBP-010 APK2 Plank

tag: xylose


title: WTp3B_16


title: WTp3B_15


title: WTp3B_14


title: WTp3B_27


title: WTp3B_13


title: WTp3B_12


title: WTp3B_25


title: WTp3A_8


title: WTp3B_10


title: PBMC_replicate_5 intravenous LPS high inflammation

tag: Sex

value: intravenous LPS

value: high


title: WTp3A_9


title: WTp3B_1


title: WTp3A_6


title: WTp3A_5


title: WTp3A_15


title: WTp3A_3


title: WTp3B_17


title: WTp3A_14


title: WTp3A_2


title: WTp3A_7


title: CBP-011 APK2 Plank RNA-3

source_name: CBP-011 APK2 Plank


title: WTp3A_16


title: WTp3A_4


title: CHG419

city: Singapore

first: Aditi

last: Qamra

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: GIS

library_source: genomic

data_processing:
Sequencing reads were trimmed (10bp from front and back) and mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.6.2) ‘aln’ algorithm.
We filtered reads based on their mapping quality (MAPQ) and used uniquely mapped reads to perform peak calling using CCAT v3.0 [local FDR < 0.05]
Genome_build: hg19
Supplementary_files_format_and_content: interval format for ucsc genome browser, including 8 columns: "chromosome" "position of the peak" "start of region" "end of region" "read counts in ChIP library" "read counts in control library" "fold-change score" "local FDR"

molecule: genomic DNA

source_name: Gastric Cancer Line

extract_protocol:
Fresh-frozen cancer and normal tissues were dissected using a razor blade in liquid nitrogen to obtain ~5mg sized pieces for each ChIP. Tissue pieces were fixed in 1% formaldehyde/PBS buffer for 10 min at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Tissue pieces were washed 3 times with TBSE buffer. For cell lines, 1 million fresh harvested cells were fixed in 1% formaldehyde/medium buffer for 10 minutes (min) at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Fixed cells were washed 3 times with TBSE buffer, and centrifuged (5,000 r.p.m., 5 min). Pelleted cells and pulverized tissues were lysed in 100 µl 1% SDS lysis buffer and sonicated to 300-500bp using a Bioruptor (Diagenode). ChIP was performed using the following antibodies: H3K4me3 (07-473, Millipore); H3K4me1 (ab8895, Abcam); H3K27ac (ab4729, Abcam).
library construction protocol: 30ng of amplified DNA was used for each sequencing library preparation (New England Biolabs). 8 libraries were multiplexed (New England Biolabs) and sequenced on 2 lanes of a Hiseq2500 sequencer (Illumina) to an average depth of 20-30 million reads per library.

value: Gastric Cancer Line

tag: chip antibody


title: WTp3A_12


title: WTp3A_13


title: WTp3A_11


title: WTp3A_1


title: WTp7B_9

value: Postnatal Day 7


title: WTp7B_8


title: WTp3A_10

value: Postnatal Day 3


title: WTp7B_7

value: Id4-eGFP Positive


title: WTp7B_5


title: WTp7B_6


title: WTp7B_4


title: WTp7B_38


title: WTp7B_37


title: WTp7B_41


title: WTp7B_31


title: WTp7B_36


title: WTp7B_30


title: WTp7B_32


title: WTp7B_35


title: WTp7B_27


title: WTp7B_33


title: WTp7B_29


title: WTp7B_28


title: WTp7B_25


title: WTp7B_23


title: WTp7B_26


title: WTp3B_11


title: WTp7B_24


title: WTp7B_40


title: WTp7B_39


title: WTp7B_21


title: WTp7B_22


title: WTp7B_2


title: WTp7B_20


title: WTp7B_19


title: WTp7B_17


title: WTp7B_34


title: KOp3C_6

value: Rhox10 Knockout


title: WTp7B_3


title: WTp7B_11


title: WTp7B_10


title: WTp7B_13


title: WTp7B_12


title: WTp7B_16


title: WTp7B_18


title: Single cell 4 month old LMPP 83

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
Samples with less than 100,000 reads were removed from analysis pipeline
Samples were aligned with Bowtie(v 2.2.0) and annotated with RSEM v 1.2.12
gene set was filtered by removing genes that did not meet a threshhold of at least 25 transcripts in at least 3 samples
analysis was done using Fluidigm Singular Analysis Toolset v3.5
Genome_build: mm10
Supplementary_files_format_and_content: csv file containing transcripts per kilobase million (TPM) values of samples which passed RSEM annotation.

source_name: Mouse Primary Bone Marrow Cells

extract_protocol:
Bone marrow mononuclear cells (MNCs) from the iliac crest, femur, and tibial bones were isolated by Ficoll-Paque density gradient centrifugation (GE Healthcare). MNCs were depleted of cells expressing the mature lineage (Lin) markers CD3e, CD11b, CD45R/B220, Ly-6G/Ly-6C (Gr-1) and TER-119 using the IMag Mouse Hematopoietic Progenitor Cell Enrichment set (BD). The cells were then stained with combinations of anti c-Kit (clone 2B8), Sca-1 (clone E13-161.7), CD34 (clone RAM34), CD150 (clone mShad150), Flt3 (clone A2F10), mature Lin markers with fluorochrome-conjugated secondary antibody, and the viability dye propidium iodide (PI). LMPPs are gated as Lin- Sca-1+ c-Kit+ CD150- CD34+ Flt3hi. Isolated LMPPs from 4mo or 14mo mice were then resuspended at a concentration of 200 cells/μl and loaded onto the C1 Single-Cell Auto Prep Integrated Fluidic Circuit (Fluidigm) with freshly prepared staining buffer. Images of captured cells were collected with a Zeiss AxioObserver.Z1 microscope in the brightfield, GFP and CY3 channels using ZenPro software. Single-cell RNA extraction and mRNA amplification were performed following manufacturer’s recommendations including exogenous spike-in controls.
library construction was performed following manufacturer’s recommendations including exogenous spike-in controls.

value: 4 months

value: Female

tag: cell surface phenotype

value: Lin- Sca1+ cKit+ CD150- CD34+ Flk2hi


title: WTp7A_6


title: WTp7A_5


title: WTp7A_9


title: WTp7A_7


title: WTp7A_8


title: WTp7A_4


title: Single cell 4 month old LMPP 86


title: WTp7B_1


title: WTp7A_2


title: WTp7A_12


title: WTp7A_10


title: WTp7A_11


title: WTp7A_1


title: WTp7A_3


title: Single cell 4 month old LMPP 78


title: Single cell 4 month old LMPP 80


title: Single cell 4 month old LMPP 81


title: WTp7B_15


title: WTp7B_14


title: Single cell 4 month old LMPP 77


title: Single cell 4 month old LMPP 75


title: Single cell 4 month old LMPP 74


title: Single cell 4 month old LMPP 72


title: Single cell 4 month old LMPP 71


title: Single cell 4 month old LMPP 69


title: Single cell 4 month old LMPP 70


title: Single cell 4 month old LMPP 76


title: Single cell 4 month old LMPP 68


title: Single cell 4 month old LMPP 67


title: Single cell 4 month old LMPP 61


title: Single cell 4 month old LMPP 66


title: Single cell 4 month old LMPP 59


title: Single cell 4 month old LMPP 62


title: Single cell 4 month old LMPP 60


title: Single cell 4 month old LMPP 56


title: Single cell 4 month old LMPP 65


title: Single cell 4 month old LMPP 57


title: Single cell 4 month old LMPP 63


title: Single cell 4 month old LMPP 55


title: Single cell 4 month old LMPP 64


title: Single cell 4 month old LMPP 41


title: Single cell 4 month old LMPP 49


title: Single cell 4 month old LMPP 52


title: Single cell 4 month old LMPP 46


title: Single cell 4 month old LMPP 53


title: Single cell 4 month old LMPP 45


title: Single cell 4 month old LMPP 51


title: Single cell 4 month old LMPP 48


title: Single cell 4 month old LMPP 40


title: Single cell 4 month old LMPP 50


title: Single cell 4 month old LMPP 43


title: Single cell 4 month old LMPP 44


title: Single cell 4 month old LMPP 47


title: Single cell 4 month old LMPP 58


title: Single cell 4 month old LMPP 38


title: Single cell 4 month old LMPP 39


title: Single cell 4 month old LMPP 42


title: Single cell 4 month old LMPP 36


title: Single cell 4 month old LMPP 34


title: Single cell 4 month old LMPP 33


title: Single cell 4 month old LMPP 32


title: Single cell 4 month old LMPP 94


title: Single cell 4 month old LMPP 37


title: Single cell 4 month old LMPP 29


title: Single cell 4 month old LMPP 30


title: Single cell 4 month old LMPP 95


title: Single cell 4 month old LMPP 31


title: Single cell 4 month old LMPP 27


title: Single cell 4 month old LMPP 26


title: Single cell 4 month old LMPP 23


title: Single cell 4 month old LMPP 24


title: Single cell 4 month old LMPP 25


title: Single cell 4 month old LMPP 22


title: Single cell 4 month old LMPP 20


title: Single cell 4 month old LMPP 18


title: Single cell 4 month old LMPP 15


title: Single cell 4 month old LMPP 13


title: Single cell 4 month old LMPP 91


title: Single cell 4 month old LMPP 16


title: Single cell 4 month old LMPP 19


title: Single cell 4 month old LMPP 14


title: Single cell 4 month old LMPP 21


title: Single cell 4 month old LMPP 35


title: Single cell 4 month old LMPP 28


title: Single cell 4 month old LMPP 17


title: Single cell 4 month old LMPP 88


title: Single cell 4 month old LMPP 8


title: Single cell 4 month old LMPP 4


title: Single cell 4 month old LMPP 6


title: Single cell 4 month old LMPP 7


title: Single cell 4 month old LMPP 5


title: Single cell 4 month old LMPP 9


title: Single cell 4 month old LMPP 3


title: Single cell 4 month old LMPP 12


title: Single cell 4 month old LMPP 1


title: Single cell 14 month old LMPP 78

value: 14 months


title: Single cell 14 month old LMPP 82


title: Single cell 14 month old LMPP 77


title: Single cell 14 month old LMPP 74


title: Single cell 14 month old LMPP 73


title: Single cell 14 month old LMPP 75


title: Single cell 14 month old LMPP 84


title: Single cell 14 month old LMPP 67


title: Single cell 14 month old LMPP 70


title: Single cell 14 month old LMPP 68


title: Single cell 14 month old LMPP 69


title: Single cell 14 month old LMPP 71


title: Single cell 14 month old LMPP 76


title: Single cell 14 month old LMPP 72


title: Single cell 4 month old LMPP 11


title: Single cell 4 month old LMPP 10


title: Single cell 14 month old LMPP 64


title: Single cell 14 month old LMPP 59


title: Single cell 14 month old LMPP 61


title: Single cell 14 month old LMPP 63


title: Single cell 14 month old LMPP 60


title: Single cell 14 month old LMPP 62


title: Single cell 14 month old LMPP 58


title: Single cell 14 month old LMPP 80


title: Single cell 4 month old LMPP 2


title: Single cell 14 month old LMPP 57


title: Single cell 14 month old LMPP 54


title: Single cell 14 month old LMPP 51


title: Single cell 14 month old LMPP 56


title: Single cell 14 month old LMPP 50


title: Single cell 14 month old LMPP 53


title: Single cell 14 month old LMPP 46


title: Single cell 14 month old LMPP 65


title: Single cell 14 month old LMPP 44


title: Single cell 14 month old LMPP 43


title: Single cell 14 month old LMPP 48


title: Single cell 14 month old LMPP 52


title: Single cell 14 month old LMPP 45


title: Single cell 14 month old LMPP 55


title: Single cell 14 month old LMPP 47


title: Single cell 14 month old LMPP 66


title: Single cell 14 month old LMPP 49


title: Single cell 14 month old LMPP 41


title: Single cell 14 month old LMPP 39


title: Single cell 14 month old LMPP 42


title: Single cell 14 month old LMPP 88


title: Single cell 14 month old LMPP 40


title: Single cell 14 month old LMPP 37


title: Single cell 14 month old LMPP 38


title: Single cell 14 month old LMPP 36


title: Single cell 14 month old LMPP 35


title: Single cell 14 month old LMPP 34


title: Single cell 14 month old LMPP 32


title: Single cell 14 month old LMPP 33


title: Single cell 14 month old LMPP 31


title: Single cell 14 month old LMPP 30


title: Single cell 14 month old LMPP 29


title: Single cell 14 month old LMPP 28


title: Single cell 14 month old LMPP 27


title: Single cell 14 month old LMPP 25


title: Single cell 14 month old LMPP 24


title: Single cell 14 month old LMPP 23


title: Single cell 14 month old LMPP 16


title: Single cell 14 month old LMPP 20


title: Single cell 14 month old LMPP 21


title: Single cell 14 month old LMPP 19


title: Single cell 14 month old LMPP 13


title: Single cell 14 month old LMPP 15


title: Single cell 14 month old LMPP 22


title: Single cell 14 month old LMPP 18


title: Single cell 14 month old LMPP 86


title: Single cell 14 month old LMPP 10


title: Single cell 14 month old LMPP 11


title: Single cell 14 month old LMPP 14


title: Single cell 14 month old LMPP 5


title: Single cell 14 month old LMPP 6


title: Single cell 14 month old LMPP 8


title: Single cell 14 month old LMPP 9


title: Single cell 14 month old LMPP 3


title: Single cell 14 month old LMPP 4


title: Single cell 14 month old LMPP 2


title: Single cell 14 month old LMPP 26


title: Single cell 14 month old LMPP 1


title: Single cell 14 month old LMPP 85


title: Single cell 14 month old LMPP 17


title: 2236-Luminal-ARKO#2

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description:
LX2236
Luminal-ARKO

data_processing:
Illumina bcl2fastq 1.8.3 software used for basecalling and FASTQ file generation.
Sequenced reads in FASTQ files were mapped to mm10 whole genome using Tophat (Galaxy tool version 0.9) with parameters -r 100. UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.0) with parameters -r 100. UCSC known transcripts were supplied in GTF format file.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include UCSC transcript id and their FPKM values, along with confidence intervals for each sample.

source_name: mouse prostate luminal cells, AR KO

growth_protocol: We generated K8-CreERT2;ARfl/Y mice (hereafter referred to as the K8-AR mice) by breeding an AR conditional line with a K8-CreERT2 transgenic mouse line that harbors the tamoxifen-responding CreERT2 transgene driven by the promoter of the luminal cell marker cytokeratin 8 (K8).

extract_protocol:
NucleoSpin RNA Kit from Macherey-Nagel, using manufacturer's protocol.
Total RNA samples were made into cDNA using the NuGEN Ovation® RNA-Seq System V2 kit (using both random priming and poly d(T) priming). cDNA from the NuGEN kit were taken into the Illumina TruSeq DNA Sample Prep Kit for library construction. Completed libraries were sequenced on the Illumina HiSeq 2500.

treatment_protocol: 8-week-old K8-AR mice were treated with tamoxifen transiently to induce AR knockout in prostate luminal cells. The necessary dosage of tamoxifen (9mg/40g/day for 4 days) for effective AR disruption in a substantial number of luminal cells was determined by titration. Littermate K8-CreERT2 mice (hereafter referred to as the control) were treated likewise and used as controls.

tag: strain/background

tag: treatment

value: tamoxifen

tag: genotype/variation

value: androgen receptor (AR) knockout

value: prostate luminal cells


title: 2232-Luminal-ARKO#1

description:
LX2232
Luminal-ARKO


title: KZ10 (10019)-2

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Map Bisulfite-seq reads to converted Arabidopsis genome by using bowtie 2.0.
Remove clonal reads and Call un-converted C position
Genome_build: TAIR 10 conversion (C-T,G-A)
Supplementary_files_format_and_content: tab delimited file with chromosome, position, strain, mC, h, and sum

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
Genomic DNA was extracted using the DNeasy Plant Kit (Qiagen, Valencia, CA) from ground, frozen 10 rosette leaves, harvested just before bolting.
Two ¬µg of genomic DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 200 bp, followed by end repair (End-It, Epicenter) and addition of a 3‚Äô A base (Klenow (3'->5' exo-), dA-tailing buffer (NEB)). Cytosine-methylated adapters provided by Bio

tag: cultivar

tag: ecotype id

value: leaf


title: WalHaesB4 (10003)


title: HKT2.4 (9995)-2


title: Single cell 14 month old LMPP 7

tag: strain

tag: age


title: 2234-Luminal-ARWT#1

description:
LX2234
Luminal-ARWT

source_name: mouse prostate luminal cells, AR WT

value: wild-type androgen receptor (AR)


title: Bak-2 (9988)-2


title: Apost-1 (9982)-2


title: Sij-1 (10008)-2


title: Copac-1 (10005)


title: Shigu-2 (9959)-2


title: QUI-8 (9934)-2


title: Timpo-1 (9968)-2


title: Nemrut-1 (9993)-2


title: Voeran-1 (9979)-2


title: Stepn-2 (9955)


title: Tuescha-9 (10000)-2


title: 2238-Luminal-ARWT#2

description:
LX2238
Luminal-ARWT


title: RUM-20 (9925)


title: ARGE-1-15 (9911)-2


title: SAUL-24 (9918)-2


title: Etna-2 (9762)-2


title: ENC-2-1 (9907)-2


title: GEN-8 (9909)-2


title: TueWal-2 (10002)-2


title: Teiu-1 (9742)-2


title: Zagub-1 (9748)-2


title: Altenb-2 (9970)-2


title: Epidauros-1 (9725)-2


title: Castelfed-3-205 (9689)


title: Kidr-1 (9960)-2


title: Malak-1 (9720)-2


title: Stiav-3 (9731)-2


title: Bela-4 (9735)-2


title: Mitterberg-1-180 (9665)-2


title: Yeg-4 (9130)-2


title: Teano-1 (9663)-2


title: Bijisk-4 (9622)-2


title: Yeg-7 (9133)-2


title: Rakit-3 (9642)-2


title: K-oze-3 (9630)-2


title: Chaba-2 (9624)-2


title: Lerik1-7 (9078)-2


title: Xan-3 (9067)-2


title: Lerik2-1 (9079)-2


title: Lu-1 (8334)-2


title: PHW-2 (8243)


title: Lag1-4 (9102)-2


title: DraII-1 (8284)-2


title: Lerik2-7 (9085)-2


title: Ost-0 (8351)-2


title: Bak-5 (9121)-2


title: Ge-0 (8297)-2


title: Hod (8235)-2

value: Hod


title: KNO1.37 (7717)-2


title: Rmx-A180 (7525)


title: Petergof (7296)-2

value: Petergof


title: Tscha-1 (7372)-2


title: Yeg-2 (9128)-2


title: Lag1-2 (9100)-2


title: Edi-0 (7111)-2


title: Gul1-2 (8234)-2


title: Kent (8238)-2

value: Kent


title: Can-0 (7063)


title: Li-7 (7231)-2


title: Ler-0 (7213)


title: WTp3B_32

value: Wildtype


title: Uod-7 (6976)-2


title: Co (7081)

value: Co


title: 9_H9_NCAM_N2_1_S3

city: Los Angeles

first: Ascia

last: Eskin

address: 695 Charles Young Drive South  Gonda 5554

department: Human Genetics

institute: UCLA

description: processed data file: gene_exp_diff_fc_yes_reg_Fetal_myotubes_vs_HPSC_myotubes_and_FACS_sort.xls

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to hg19 genome using TopHat v2.0.8 with parameters  -G (using Ensembl GRCh37 GTF) and --no-novel-juncs.
Transcripts were assembled using Cufflinks v2..1. Cuffdiff was used to compare samples, using Ensembl GRCh37 GTF
Genome_build: hg19
Supplementary_files_format_and_content: Excel Cuffdif result files include FPKM values for each Sample, as well as q-value and fold change.

source_name: Pluripotent stem cell_H9 line

extract_protocol:
Total RNA was isolated using Qiagen's Rneasy Micro Kit.
RNA-Seq libraries were constructed with Roche's KAPA Stranded RNA-Seq Library Preparation Kit, using standard protocols

tag: cell line

tag: cell status

value: FACS sorted CD45-CD31-NCAM+ hPSC myotube

value: day 62 in culture

tag: rna collection post facs

value: 5 days expansion and 7 days differentiation


title: Buckhorn Pass (7033)-2

value: Buckhorn Pass


title: Ull2-3 (6973)-2


title: 7_H9_NCAM_1_S1

description: processed data file: gene_exp_diff_fc_yes_reg_Fetal_stem_cells_and_FACS_sort_vs_HPSC_stem_cells_and_FACS_sort_MH_02022016.xls

value: FACS sorted CD45-CD31-NCAM+ hPSC muscle progenitor

value: day 50 in culture

value: Immediately


title: 5_FW17_0_N2_d10_S8

description:
RNA from these samples were collected from primary human muscle tissue after being differentiated to form myotubes for 7 days in N2 media.
processed data file: gene_exp_diff_fc_yes_reg_Fetal_myotubes_vs_HPSC_myotubes_and_FACS_sort.xls, gene_exp_diff_fc_yes_reg_Fetal_stem_cells_vs_Fetal_myotubes_MH_02022016.xls

source_name: Fetal limb muscle

value: Fetal limb muscle

value: Fetal Myotubes

value: human week 17

value: No FACS


title: Nc-1 (7430)

value: leaf


title: Sq-1 (6966)-2


title: 6_FW17_1_N2_d10_S7

description:
RNA from these samples were collected from primary human muscle tissue after being differentiated to form myotubes for 7 days in N2 media.
processed data file: gene_exp_diff_fc_yes_reg_Fetal_myotubes_vs_HPSC_myotubes_and_FACS_sort.xls,gene_exp_diff_fc_yes_reg_Fetal_stem_cells_vs_Fetal_myotubes_MH_02022016.xls


title: Tamm-27 (6969)


title: 4_Fresh_W17_3_p0_S9

description: processed data file: gene_exp_diff_fc_yes_reg_Fetal_stem_cells_and_FACS_sort_vs_Fetal_stem_cells.xls

value: directly isolated fetal muscle stem cell


title: Ren-11 (6960)-2


title: 8_H9_NCAM_2_S2


title: Zu-0 (7417)


title: 3_Fresh_W17_2_p0_S10


title: Mt-0 (6939)-2


title: Knox-10 (6927)


title: Pu2-8 (6957)-2


title: LL-0 (6933)-2


title: 2_Fresh_W17_1_Imm_Sort_S5

value: FACS sorted CD45-CD31-NCAM+ fetal muscle progenitor


title: CIBC-5 (6908)-2


title: UduI 4-9 (6396)

value: UduI 4-9


title: UduI 1-11 (6296)-2

value: UduI 1-11


title: Sample_11_P3

city: Medord

first: Benjamin

middle: E

last: Wolfe

address: 200 Boston Ave.

institute: Tufts University

description: Staphylococcus equorum grown with Penicillium, Replicate 3

data_processing:
Basecalls performed using CASAVA
Transcripts were aligned to S. equorum BC9 draft genome (Accesson No. LNNB00000000) using Rockhopper Reference Assembly, using standard options: Strand-specific checked yes, max bases between paired reads: 500, allowed mismatches: 0.15, minimum seed length 0.33, minimum expression of UTRs and ncRNAs: 0.5,
Differential Gene expression and Operon identification performed by Rockhopper (http://cs.wellesley.edu/~btjaden/Rockhopper/)
Genome_build: Staphylococcus equorum BC9; LNNB00000000 private accession at NCBI Whole Genome Shotgun (WGS) archive
Supplementary_files_format_and_content: Rockhopper_analysis_FOR_GEO.xlsx

organism: Staphylococcus equorum

source_name: S. equorum_with penicillium

growth_protocol: Experimental biofilms were created by inoculating organisms onto cheese curd agar medium. See Wolfe et al. 2014 Cell 158 422-433

extract_protocol:
RNA was extracted using a phenol-chloroform
RNA libraries were prepared using the NEBNext RNA Ultra Kit for Illumina

treatment_protocol: Staphylococcus equorum was grown either alone, with a Penicillium spp., or with a Scopulariopsis spp.

tag: growth condition

value: with penicillium

value: experimental biofilm


title: Sample_10_P2

description: Staphylococcus equorum grown with Penicillium, Replicate 2


title: Sample_9_P1

description: Staphylococcus equorum grown with Penicillium, Replicate 1


title: Sample_8_S3

description: Staphylococcus equorum grown with Scopulariopsis, Replicate 3

source_name: S. equorum_with scopulariopsis

value: with scopulariopsis


title: Sample_6_S2

description: Staphylococcus equorum grown with Scopulariopsis, Replicate 2


title: Duk (6008)-2

value: Duk


title: UKID116 (5822)-2


title: Sample_5_S1

description: Staphylococcus equorum grown with Scopulariopsis, Replicate 1


title: Sample_4_A3

description: Staphylococcus equorum grown alone, Replicate 3

source_name: S. equorum_alone

value: alone


title: UKID114 (5818)-2


title: UKID107 (5811)-2


title: TFA 07 (6217)-2

value: TFA 07


title: Sample_2_A1

description: Staphylococcus equorum grown alone, Replicate 1


title: Got-22 (6920)


title: UKNW06-102 (5395)-2


title: For-2 (5741)-2


title: UKSE06-541 (5279)-2


title: UKNW06-354 (5535)-2


title: Sample_3_A2

description: Staphylococcus equorum grown alone, Replicate 2


title: Ty-1 (5784)-2


title: 1_Fresh_W17_0_Imm_Sort_S6


title: UKNW06-233 (5486)-2


title: UKSW06-240 (4840)


title: Cal-2 (5720)-2


title: UKSW06-257 (4857)


title: UKSW06-226 (4826)-2


title: SLSP-31 (2276)-2


title: Paw-26 (2171)-2


title: DraII-6 (5874)-2


title: UKSE06-362 (5165)


title: MNF-Pot-75 (1872)-2


title: MNF-Pot-21 (1853)


title: LIN S-5 (915)-2

value: LIN S-5


title: UKID74 (5779)-2


title: estradiol_12h rep2

city: Cologne

first: Barbara

last: Kracher

address: Carl-von-Linné-Weg 10

department: Plant-Microbe Interactions

country: Germany

institute: Max Planck Institute for Plant Breeding Research

description: PolyA-enriched RNA

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing read quality control was performed using FastQC version 0.11.2.
Sequenced reads were mapped to the genome of Arabidopsis thaliana (TAIR10) using TopHat v2.0.10 with parameters -a 10 -g 10 --library-type fr-unstranded
Read counts per gene per sample were obtained using the htseq-count script in the HTSeq Python package with options -s no -t exon
Genome_build: TAIR10
Supplementary_files_format_and_content: CountTable_At_0925_raw.txt: Tab-delimited text file includes read counts per gene per sample.

source_name: ED-P4E1, leaves, estradiol, 12h

growth_protocol: Plants were grown in soil in controlled environment chambers under a regime of a 10 h photoperiod (200µE m-2 s-1) at 22°C, and 65% relative humidity.

extract_protocol:
RNA-purification with the RNeasy Plant Mini Kit (Qiagen) was performed according to the manufacturer’s protocol.
RNA-seq libraries were prepared from 1 μg total RNA according to recommendations (TruSeq RNA sample preparation v2 guide; Illumina).

treatment_protocol: 10 uM estradiol or mock (0.2% DMSO) plus 0.01% slilwet-77 was sprayed onto 4-week-old plant leaves.

tag: ecotype background

value: estradiol-inducible-promoter:PAD4 35S:EDS1 eds1-2 pad4-1

value: leaves

value: estradiol

tag: time


title: mock_12h rep1

description: PolyA-enriched RNA

source_name: ED-P4E1, leaves, mock, 12h

tag: tissue

value: DMSO (mock)


title: mock_24h rep1

description: PolyA-enriched RNA

source_name: ED-P4E1, leaves, mock, 24h


title: LDV-18 (108)-2


title: estradiol_24h rep3

description: PolyA-enriched RNA

source_name: ED-P4E1, leaves, estradiol, 24h


title: estradiol_24h rep1

description: PolyA-enriched RNA


title: mock_24h rep2

description: PolyA-enriched RNA


title: estradiol_24h rep2

description: PolyA-enriched RNA


title: estradiol_6h rep1

description: PolyA-enriched RNA

source_name: ED-P4E1, leaves, estradiol, 6h

value: 6 h


title: estradiol_12h rep3

description: PolyA-enriched RNA


title: KYC-33 (801)-2

value: leaf


title: mock_24h rep3

description: PolyA-enriched RNA


title: mock_6h rep2

description: PolyA-enriched RNA

source_name: ED-P4E1, leaves, mock, 6h


title: mock_6h rep3

description: PolyA-enriched RNA


title: CYR (88)

value: CYR


title: estradiol_6h rep3

description: PolyA-enriched RNA


title: Borky1 (428)-2


title: DAI

city: Tarrytown

first: Asiel

middle: Arturo

last: Benitez

state: New York

address: 777 Old Saw Mill River Rd, 92-516A

department: Immunology & Inflammation

institute: Regeneron Pharmaceuticals, Inc

description: Processed data file: DAI_Seq.txt

data_processing:
Basecalls performed using CASAVA version 1.8.
Sequenced reads were trimmed for adaptor sequence, then mapped to the genome of A/Puerto Rico/8/1934 using Bowtie 1.1.2.
Genome_build: A/Puerto Rico/8/1934 (EF190971.1 to EF190978.1)
Supplementary_files_format_and_content: The processed data file DAI_Seq.txt is a tab-delimited text file containing the raw read numbers obtained from the alignment. The first column lists the reference sequence for each segment of A/Puerto Rico/8/1934. The other columns contain the raw read numbers for DAI and RIGI analyzed.

organism:
Homo sapiens
Influenza A virus (A/Puerto Rico/8/1934(H1N1))

source_name: 293T, FLAG-tagged DAI, influenza A/PR/8/34 virus

extract_protocol:
Total RNA was immunoprecipitated from cells using Anti-FLAG M2 Magnetic Beads from Sigma (M8823).
Libraries were made using the Illumina TruSeq Stranded Total RNA Kit.

treatment_protocol: 293T fibroblasts were transfected with pcDNA FLAG-based plasmids expressing no open read frame (vector), DAI, or RIG-I. Transfected cells were subsequently infected with influenza A/PR/8/34 virus for 6 hrs.

tag: cell type

value: Human embryonic kidney cell line

tag: expression

value: FLAG-tagged DAI

tag: infection

value: influenza A/PR/8/34 virus

tag: ip antibody

value: Anti-FLAG M2 Magnetic Beads (Sigma, Catalog# M8823)


title: estradiol_6h rep2

description: PolyA-enriched RNA

tag: treatment


title: estradiol_12h rep1

description: PolyA-enriched RNA

tag: genotype/variation


title: RIGI

description: Processed data file: DAI_Seq.txt

source_name: 293T, FLAG-tagged RIGI, influenza A/PR/8/34 virus

value: FLAG-tagged RIGI


title: spe-9, Day0, Replicate-2, Seq-2

city: Camperdown

first: Masaomi

last: Kato

state: NSW

address: Missenden Road

country: Australia

institute: Centenary Institute, The University of Sydney

description:
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt
speB_2ndSeq
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 2.17.1.14 pipeline was used to generate the sequence data. This part was done by a commercial sequencing facility.
Sequencing reads were aligned to the C. elegans genome (WS220) using Bowtie program (version 2.1.0), then incorporated into TopHat program (version 2.1.0).
Expression levels of genes were calculated using Cufflinks software (version 2.2.1), and were represented as FPKM.
The Cuffdiff program of Cufflinks was applied to FPKM values to compare expression of genes between two samples.
The DEseq program was also used to list genes with differential expression between spe-9 and mir-60;spe-9 strains at Day 0 young adult, for which the biological replicates are available.
Genome_build: C. elegans genome WS220
Supplementary_files_format_and_content: The processed data (Refseq_FPKM_matrix_2Seqs_merged.txt) shows gene expression levels represented as FPKM in all samples, which were calculated using Cufflinks software (version 2.2.1).

organism: Caenorhabditis elegans

source_name: whole animal body, spe-9, untreated, day 0

growth_protocol: Eggs for spe-9 single and mir-60;spe-9 double mutant animals were prepared by a standard bleach/NaOH treatment and directly placed on bacteria (E. coli, OP50)-seeded solid NGM (Nematode Growth Media) plates, and cultured at 23.5 °C for 68 hours until they reached young adult (defined as Day 0 adulthood). Total RNAs were purified from both strains as Day 0 adulthood.

extract_protocol:
Animals collected were first washed with M9 buffer 3 times, then incubated in M9 with rotating for 30 minutes to allow them to digest bacteria within the intestine. Total RNAs were purified using mirVana miRNA Isolation Kit (Ambion/Life Technologies), according to the manufacturer's instruction.
cDNA libraries for RNA-sequencing were established from 4 μg of total RNAs for each using TruSeq Stranded mRNA Sample Prep Kit (Illumina) with indexed adapters, according to the manufacturer's instruction.

treatment_protocol: To further purify RNAs from aged animals exposed to chronic oxidative stress, spe-9 and mir-60;spe-9 strains at Day 0 adult stage were treated with 5-fluorodeoxyuridine (FUDR, final 325 μM, preventing growth of progenies completely) and methyl viologen dichloride (paraquat, final 5 mM, inducing oxidative stress by generating superoxide from oxygen) on solid NGM plates. Total RNAs were purified at Day 7 and Day 10.

tag: strain/background

value: whole body

value: Normal condition

tag: time point

value: Day 0


title: mir-60;spe-9, Day7, Seq-2

description:
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt
s60D7_2ndSeq
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt

source_name: whole animal body, mir-60;spe-9, paraquat, day 7

value: Paraquat 5 mM

value: Day 7


title: spe-9, Day0, Replicate-1, Seq-2

description:
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt
speA_2ndSeq
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt


title: mock_12h rep2

description: PolyA-enriched RNA

value: estradiol-inducible-promoter:PAD4 35S:EDS1 eds1-2 pad4-1


title: MNF-Pin-40 (2017)-2

source_name: leaf

tag: cultivar

tag: ecotype id


title: spe-9, Day7, Seq-2

description:
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt
speD7_2ndSeq
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt

source_name: whole animal body, spe-9, paraquat, day 7


title: mock_12h rep3

description: PolyA-enriched RNA

value: leaves


title: 10_H9_NCAM_N2_2_S4

description: processed data file: gene_exp_diff_fc_yes_reg_Fetal_myotubes_vs_HPSC_myotubes_and_FACS_sort.xls

source_name: Pluripotent stem cell_H9 line

tag: cell line

value: FACS sorted CD45-CD31-NCAM+ hPSC myotube

tag: age

value: day 62 in culture

value: 5 days expansion and 7 days differentiation


title: spe-9, Day7, Seq-1

description:
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt
speD7_1stSeq
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt


title: mir-60;spe-9, Day7, Seq-1

description:
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt
s60D7_1stSeq
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt


title: mir-60;spe-9, Day0, Replicate-2, Seq-2

description:
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt
s60B_2ndSeq
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt

source_name: whole animal body, mir-60;spe-9, untreated, day 0


title: spe-9, Day0, Replicate-2, Seq-1

description:
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt
speB_1stSeq
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt


title: mir-60;spe-9, Day10, Seq-2

description:
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt
s60D10_2ndSeq
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt

source_name: whole animal body, mir-60;spe-9, paraquat, day 10

value: Day 10


title: mir-60;spe-9, Day0, Replicate-1, Seq-2

description:
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt
s60A_2ndSeq
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt


title: Nrf2_polyclonal_Ab_ChIPSeq

city: Baltimore

first: Shyam

last: Biswal

state: MD

address: 615 N. Wolfe St.

department: Environmental Health Sciences

institute: Johns Hopkins Bloomberg School of Public Health

data_processing:
Sequencing and read alignment to the mouse genome (NCBI build 37) was performed at the Genome Science Centre (Vancouver, Canada) as described previously in Robertson G et al, Nat Methods. 2007 Aug;4(8):651-7, PMID:17558387, DOI:10.1038/nmeth1068
Peaks were called with the FindPeaks software (PMID:18599518) with the following parameters: Triangle dist. = 100 low/200 median/300 high; Sub-peaks = 0.8; Trim-peaks = 0.2; Filter Duplicates = On; Filter out reads quality lower than 10. The false discovery rate estimation (FDR) was based on a Lander-Waterman calculation integrated in the FindPeaks software. An artifactual cluster of peaks was found at the beginning of chromosome 11 in all three libraries and was discarded from the analysis.
The peak height is defined by the number of tags overlapping at a specific genomic location. All peaks above a height of 5 from each of the three libraries were considered in this analysis. Peaks were considered as overlapping when their maximum heights were located within 100 bp of each other.
A total of 1256 peaks were compiled consisting of 886 monocolonal peaks with peak height >= 9 plus 370 peaks which overlapped between the monoclonal and polyclonal libraries with had a peak height >=5 in both libraries and did not overlap with any control peaks. These combined peaks are contained in the included supplementary file Nrf2_ChIP-Seq.txt.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: wig files were generated using FindPeaks software (PMID:18599518). Scores represent average read count at each position. A BED-like text file was chromosomal location plus the location of the maximum peak height the peak height was generated containing the peak coordinates, heigh and location of maximum peak height

source_name: Embryonic fibroblasts

growth_protocol: Cells were grown to 90% confluency in 100-mm plates in Iscove’s modified Dulbecco’s medium (Invitrogen, CA) containing 10% FBS.

extract_protocol:
Cells were harvested and processed for microarray and chromatin immunoprecipitation (ChIP) analyses as described below.
MEFs were fixed ∼1% formaldehyde in cell growth media for 10 min followed by glycine fixation. Cells were then sonicated in ChIP–lysis buffer containing protease inhibitor cocktail after incubation on ice for 30 min. Upon sonication, the samples were spun at maximum speed for 12 min in a cold microcentrifuge. The supernatants were then addressed to as Input samples. A part of the input sample was precleared using 50% slurry of Protein A/G beads prepared in immunoprecipitation (IP) buffer for 2 h in cold, following which the beads were centrifuged out and supernatant was used for IP. Then the precleared samples were incubated with 2 µg of either of two distinct anti-Nrf2 antibodies that recognize different portions of Nrf2 protein. The rabbit-anti-Nrf2 monoclonal antibody from Epitomics Inc., CA, recognizes the C-terminal domain in all three cell lines, while the rabbit-anti-Nrf2 polyclonal antibody from Santa Cruz Biotech., CA, recognizes domains spanning the N-terminus in all three cell lines as well. For control, we used anti-rabbit IgG antibody for 1 h in cold. These antibodies have been used extensively in our laboratory for western and EMSA analysis [Figure 1A(i) and data not shown]. Protein A/G bead slurry was added to each reaction and was rotated overnight. Next day, beads were washed extensively, DNA was reverse crosslinked and eluted in elution buffer and stored at −80°C until used for sequencing or PCR validation assays. The eluted DNA was checked for 100- to 300-bp fragment enrichments using 8% polyacrylamide gel electrophoresis (data not shown). We generated two DNA libraries using two Nrf2-specific antibodies [one monoclonal, rabbit-anti-Nrf2 (Epitomics Inc., CA), and one polyclonal, rabbit-anti-Nrf2 (Santa Cruz Biotech., CA)] incubated with crosslinked and sonicated DNA from Keap1−/− MEFs. A third control library contains the input DNA from Keap1−/− MEFs.

value: MEF

tag: strain

tag: developmental stage

value: 8-10 weeks

tag: genotype

tag: chip antibody

value: rabbit-anti-Nrf2 polyclonal


title: Control

value: anti-rabbit IgG antibody


title: spe-9, Day0, Replicate-1, Seq-1

description:
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt
speA_1stSeq
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt

tag: tissue


title: mock_6h rep1

description: PolyA-enriched RNA

tag: ecotype background

value: DMSO (mock)

tag: time

value: 6 h


title: mir-60;spe-9, Day10, Seq-1

description:
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt
s60D10_1stSeq
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt

value: whole body


title: LMPP1_batch2

data_processing:
Sequences were alinged using Bowtie v 2.2.0. Epxression estimation was performed using RSEM v 1.2.12
RSEM based expected counts from all samples were merged to from an gene by sample expression matrix
Only gene with counts greater than 1 cpm in atleast 2 samples were retained for further analysis
Trimmed Mean of M vailues normalization was performed using R/ edgeR (3.10.0)
Genome_build: mm10
Supplementary_files_format_and_content: csv file containing transcripts per kilobase million (TPM) values

source_name: Mouse Primary Bone Marrow Cells

tag: Sex

value: Female

tag: cell surface phenotype

value: Lin- Sca1+ cKit+ CD150- CD34+ Flk2hi


title: mir-60;spe-9, Day0, Replicate-2, Seq-1

description:
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt
s60B_1stSeq
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt

tag: treatment

value: Normal condition

value: Day 0


title: mir-60;spe-9, Day0, Replicate-1, Seq-1

description:
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt
s60A_1stSeq
Processed data file: Refseq_FPKM_matrix_2Seqs_merged.txt

tag: genotype/variation


title: LMPP2_batch1


title: LMPP3_batch2


title: LMPP1_batch1


title: GMP2_batch2

value: Lin- Sca1- cKit+ CD150- CD34+ FcgR+


title: GMP1_batch2


title: CLP2_batch1

value: Lin- Sca1lo cKitlo IL7Ra+ Flk2+


title: CLP2_batch2


title: CLP1_batch1


title: GMP2_batch1


title: CLP1_batch2


title: R48h_infected

city: Beijing

first: Wenxian

last: Sun

address: 2 West Yuanmingyuan Rd., Haidian District

country: China

institute: China Agricultural University

data_processing:
Raw image data were transformed into sequence data by base calling.
All sequences were filtered to remove adaptor sequences and low-quality sequences (where the percentage of the low-quality bases with quality value ≤ 5 was greater than 50% in a read)
The quality-trimmed reads were mapped to U. virens genome using SOAP aligner/SOAP2, allowing up to two base mismatches per read.
The RPKM (reads per kb per million reads) was calculated to reflect the expression level of U. virens transcripts
Genome_build: JHTR00000000
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

organism: Ustilaginoidea virens

source_name: from resistant rice variety

growth_protocol: The U. virens isolates were cultured in potato sucrose broth (PSB, fresh potato extract and 2 % sucrose) on an incubator shaker at 120 rpm and 28 °C for a week. The panicles of rice plants at the booting stage were inoculated with conidial suspensions (2 × 105 conidia ml−1) at 5 to 7 days before earing.

extract_protocol:
The pathogen-inoculated panicles were harvested at 6 hpi, 24 hpi and 48 hpi, immediately frozen in liquid nitrogen, and then kept at -70 °C for RNA isolation.
RNA-Seq libraries were constructed following the standard pipeline at Beijing Genomics Institute (BGI) in Shenzhen, China.

treatment_protocol: Rice panicles were inoculated with a mixture of conidial and hyphal fragments.

tag: growth substrate

value: Inoculated rice panicles


title: R24h_infected


title: GMP1_batch1


title: Nrf2_monoclonal_Ab_ChIPSeq

tag: cell type

value: rabbit-anti-Nrf2 monoclonal


title: S24h_infected

source_name: from susceptible rice variety


title: CK-P1

source_name: from in vitro cultures

value: In vitro cultures


title: R6h_infected


title: WT_UTC.A_3'seq

status: Public on Sep 26 2016

city: Stanford

first: Adam

last: Schmitt

address: 269 Campus Drive

department: Department of Dermatology

institute: Stanford University

data_processing:
The 3'-Seq reads were mapped to the mouse genome using Bowtie2 default parameters. The unique mapped reads have been quantified on the gene level by htseq-count with parameters: -m union -s no -t exon -i gene_id.
The raw counts for 8 samples have been merged to a table with rows representing genes and columns representing samples.
Genome_build: mm9
Supplementary_files_format_and_content: txt file; rows: genes, columns: samples

growth_protocol: Early passage MEFs from E13.5 embryos of indicated genotype were grown under standard conditions of DMEM + 10% serum.

extract_protocol:
RNA was isolated using Trizol and Qiagen Rneasy columns. RNA was DNAse treated prior to library construction.
Sequencing libraries were constructed using the TruSeq RNA Access Library Prep kit with 50ng of total RNA
3' RNA sequencing

treatment_protocol: 300,000 fibroblasts were treated with 0.2ug/mL doxorubicin or vehicle alone for 8 hours prior to RNA isolation.

value: mouse embryonic fibroblast

value: WT (DINO+/+)

tag: traeted with

value: none (control) for 8hrs


title: LOXP_UTC.B_3'seq

value: DINO MUTANT (DINO loxP/loxP)


title: WT_DOX.A_3'seq

value: 0.2ug/mL of DOXORUBICIN for 8 hrs


title: LOXP_UTC.A_3'seq


title: lnc-ASTN1-LNA1-rep3

city: Ghent

first: Farzaneh

last: Ghazavi

address: De Pintelaan 185

department: Center of medical genetics

country: Belgium

institute: Gent university hospital

data_processing:
Aligned with STAR2.4.2a to hg38, using Ensembl38v81 as guide
Genome_build: hg38
Supplementary_files_format_and_content: STAR count output

source_name: REH cell line

growth_protocol: Cells were grown in RPMI supplemented with 20% fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin

extract_protocol:
Total RNA was harvested with the miRNeasy mini kit (Qiagen) with Dnase treatment on-column.
totalRNA, ribodepletion, stranded RNA-seq

treatment_protocol: Cells were seeded at 1*10^6 cells/ml and treated with either medium or 10 µM LNA GapmeRs. Cells were harvested 72h after treatment.

value: REH

value: lnc-ASTN1-1 LNA GapmeR1


title: lnc-NKX2-LNA2-rep3

value: lnc-NKX2-3-1 LNA GapmeR2


title: LOXP_DOX.A_3'seq


title: WT_DOX.B_3'seq


title: lnc-ASTN1-LNA2-rep3

value: lnc-ASTN1-1 LNA GapmeR2


title: WT_UTC.B_3'seq


title: NTC-rep3

value: non-targeting LNA GapmeR


title: lnc-RTN4R-LNA2-rep2

value: lnc-RTN4R-1 LNA GapmeR2


title: lnc-ASTN1-LNA1-rep2


title: lnc-NKX2-LNA2-rep2


title: lnc-TIMM21-LNA2-rep3

value: lnc-TIMM21-5 LNA GapmeR2


title: lnc-TIMM21-LNA1-rep3

value: lnc-TIMM21-5 LNA GapmeR1


title: S48h_infected


title: lnc-NKX2-LNA1-rep2

value: lnc-NKX2-3-1 LNA GapmeR1


title: lnc-TIMM21-LNA2-rpe2


title: lnc-RTN4R-LNA1-rep2

value: lnc-RTN4R-1 LNA GapmeR1


title: NTC-rep2


title: lnc-TIMM21-LNA1-rep2


title: No LNA-rep2

value: medium


title: S6h_infected

value: Inoculated rice panicles


title: LOXP_DOX.B_3'seq

value: mouse embryonic fibroblast


title: lnc-ASTN1-LNA1-rep1


title: lnc-RTN4R-LNA2-rep1


title: lnc-RTN4R-LNA2-rep3


title: lnc-NKX2-LNA2-rep1


title: lnc-RTN4R-LNA1-rep1


title: lnc-NKX2-LNA1-rep1


title: No LNA-rep1


title: lnc-TIMM21-LNA2-rep1


title: 697 H3K27ac ChIP-seq

data_processing:
Aligned to hg19 using bowtie2, default settings, mapq>4
peak calling using macs2 with input DNA as control
Genome_build: hg19

source_name: 697 cell line

growth_protocol: Cells were grown in RPMI supplemented with 10% fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin

extract_protocol:
DNA was purified by phenol/chloroform extraction, assisted by phase lock gel tubes (5Prime).
TruSeq

treatment_protocol: The ChIP-protocol has been adapted from previous studies (Lee et al. 2006). In brief, 100*106 cells were cross-linked with 1,1% formaldehyde (Sigma-Aldrich, F1635) at room temperature for 10 min and the cross-linking reaction was quenched with glycine (125 mM final concentration, Sigma-Aldrich, G-8790). Nuclei were isolated and chromatin was purified by chemical lysis. Next, the purified chromatin was fragmented to 200-300 bp fragments by sonication (Covaris, S220, Focused-ultrasonicator). Chromatin immunoprecipitation was performed by incubation of the chromatin fraction overnight with 100 ul of protein-A coated beads (Thermo-Scientific, catalog number 53139) and 10 μg of H3K27ac-specific antibody (Abcam, ab4729). The next day, beads were washed to remove non-specific binding events and enriched chromatin fragments were eluted from the beads, followed by reverse cross-linking by incubation at 65°C overnight.

value: B-ALL


title: 697 input DNA


title: Tnip1+/+ plus Imiquimod-1

city: Memphis

first: David

last: Finkelstein

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Basecalling was performed using Illumina Casava 1.7
FASTQ sequences adapter trimmed (curtadapt) and mapped to the mouse mm9 genome by a pipeline that serially  employs STAR and BWA
Mapped reads were counted with HTSEQ
voom TMM normalized and contrasted using the empirical Bayes pipeline limma in R 3.2.3
Genome_build: mm9
Supplementary_files_format_and_content: count files are txt format files that contain raw read counts that map  to  transcripts for each defined gene.

source_name: skin

extract_protocol:
Skin biopsies (10 x 5 mm) were snap frozen in liquid nitrogen and pulverized using the BioPulverizer (BioSpec) that was pre-cooled in liquid nitrogen. Total RNA was isolated using TRIzol (Invitrogen) and quantified by measuring the optical density at 260 nm (OD260) using a Nanodrop spectrophotometer (Nanodrop).
For RNAseq, libraries were generated from ~1 µg total RNA using the Illumina Stranded Total RNA kit with the Human/Mouse/Rat Ribo-Zero Gold ribosomal reduction kit. Libraries were sequenced on an Illumina HiSeq 2500 using paired-end 100 bp sequencing chemistry.

treatment_protocol: imiquimod (IMQ) surface application

tag: background strain

value: skin

value: two days with imiquimod (IMQ)


title: REH input DNA

tag: cell line


title: Tnip1-/- plus Imiquimod-2


title: U2OS_RNase_Input

data_processing:
library strategy: ChIRP-seq
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie. Peaks were called using the MACS2 narrow peak mode using the default parameters.
Number of Raw reads in each peak was calculated using in house generated script, and data matrix was normalized using R
Genome_build: hg19
Supplementary_files_format_and_content: ENCODE narrowPeak; Content: chrom, chromStart, chromEnd, name, score, strand, signalValue, pValue, qValue, peak

source_name: U2OS osteosarcoma cell line

growth_protocol: p53 wildytpe U2OS cells were obtatined from ATCC and grown under standard culture condition.

extract_protocol:
Per ChIRPseq protocol. Chu C. et al. JoVE 2012.
Sequencing libraries were constructed using the NEB ChIPseq library preparation kit

treatment_protocol: U2OS cells were treated with 0.2ug/mL doxorubicin for 24 hours prior to cell crosslinking with glutaraldehyde and chromatin fragmentation.

value: U2OS osteosarcoma cell line

tag: treated with

value: 0.2ug/mL doxorubicin for 24 hours


title: Tnip1-/- plus Imiquimod-1


title: mouse pancreatic islets, sample 2

city: Cambridge

first: Adrian

last: Veres

state: Massachusetts

address: 7 Divinity Ave

institute: Harvard University

data_processing:
Reads were first filtered based on presence in read 1 of two sample barcode components separated by the W1 adaptor sequence (GAGTGATTGCTTGTGACGCCTT), as previously described (Klein et al., Cell 2015)
Read 2 was then trimmed using Trimomatic (5) (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
Barcodes for each read were matched against a list of the pre-determined barcodes, and errors of up to two nucleotides mismatch were corrected. Reads with a barcode separated by more than two nucleotides from the reference list were discarded. The reads were then split into barcode-specific files for mapping and UMI filtering.
The trimmed reads were aligned using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 80 -m 200 -best -strata -a) to the human or mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (Homo sapiens: GRCh38.82,  Mus musculus: GRCm38.84) including all annotations with "Transcript Support Levels" of 1, 2, or NA (only accepted for protein coding genes).
A custom Python and PySAM script to process mapped reads into counts of UMI-filtered transcripts per gene, as previously described (Klein et al., Cell 2015)
Genome_build: GRCh38 (human sample), GRCm38 (mouse samples)
Supplementary_files_format_and_content: Columns = gene; rows = cells. Column 1 contains cell identifier. Column 2 contains matching cell barcode. Column 3 contains cell-type assignment for analysis. Columns 4+ contain counts for each gene. Values show unique molecular identifier (UMI)-filtered counts per cell detected in the raw data. No normalization is performed.

source_name: 5 C57BL/6 mice

extract_protocol:
Cells were encapsulated using the inDrop platform, into droplets on ice and lysed  in the 4nL microfluidic droplets using a final concentration of 0.4% NP-40. Single cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015).
Cells were barcoded using the inDrop platform (Klein et al., Cell 2015), which makes use of the CEL-Seq protocol for library construction Hashimshony et al., Cell Reports 2012)

treatment_protocol: Human pancreatic islets were obtained from Prodo or NDRI and recovered in CMRLS at 37°C for 24h-48h hours after receipt. Mouse islets were prepared using gradient centrifugation and islets from the same strain were pooled, then recovered in XX for 24h.

tag: strain


title: Tnip1+/+ plus Imiquimod-3


title: U2OS_Input


title: lnc-ASTN1-LNA2-rep1

value: REH


title: Tnip1+/+ plus Imiquimod-2


title: DINO_ChIRP_RNase_EVEN


title: REH H3K27ac ChIP-seq


title: DINO_ChIRP_ODD


title: mouse pancreatic islets, sample 1

source_name: 5 ICR mice

value: ICR


title: DINO_ChIRP_RNase_ODD


title: DINO_ChIRP_EVEN


title: NTC-rep1


title: Tnip1-/- plus Imiquimod-3


title: HiC_NB_rep_2

city: New York

last: Soong

address: 1305 York Avenue

institute: Weill Cornell Medical College

description:
HiC in naïve B cells replicate 2
processed data file: hic_NB_intra.bed.txt.gz, hic_NB_inter.sif.gz

data_processing:
HiC: We aligned the two ends of the paired reads separately to the reference human genome hg18 using the BWA aligner. Reads mapped ambiguously to multiple locations on the genome were discarded. We further used an in-house pipeline and filtered out clonal reads caused by PCR artifacts based on the 5’ and 3’ read positions, removed non-ligated DNA fragments, and retained interactions with consistent expected placement relative to HindIII enzyme digestion sites.
RNA-seq: We aligned the paired-end RNA-seq reads to the RefSeq transcripts using Tophat, removed clonal reads caused by PCR artifacts, and quantified expression levels in RPKM (reads per kilobase of exon model per million mapped reads) units using an in-house program.
Genome_build: hg18
Supplementary_files_format_and_content: RPKM: tab delimited file containing the RPKM for each gene/transcript.
Supplementary_files_format_and_content: BED.TXT: intra-chromosomal interactions in UCSC BED format (to store the interactions' chromosome and start and end positions). Interactions are merged from all replicates.
Supplementary_files_format_and_content: SIF: inter-chromosomal interactions; each row consists of the start and end coordinates of each paired-end read. Interactions are merged from all replicates.

source_name: purified human naïve B cells

extract_protocol:
Primary human mature naïve B-cells (IgD+CD38lo; NB) and GCB-cells (CD77+CD38hi; GCB) were purified from tonsils of healthy individuals.
Hi-C DNA templates were generated as previously described (Lieberman-Aiden et al., 2009). RNA-seq libraries were prepared using the Illumina TruSeq RNA sample kits according to the manufacturer.

tag: subject status

value: healthy individual

value: tonsils

value: purified human naive B cells

tag: cell subtype

value: IgD+ CD38low


title: RNAseq_GCB_rep1

description: RNA-seq in Germinal Center B cells replicate 1

source_name: purified human germinal center B cells

value: purified human germinal center B cells

value: CD77+ CD38high


title: RNAseq_NB_rep2

description: RNA-seq in naïve B cells replicate 2


title: HiC_GCB_rep_2

description:
HiC in Germinal Center B cells replicate 2
processed data file: hic_GCB_intra.bed.txt.gz, hic_GCB_inter.sif.gz


title: lnc-RTN4R-LNA1-rep3

value: lnc-RTN4R-1 LNA GapmeR1


title: RNAseq_NB_rep1

description: RNA-seq in naïve B cells replicate 1


title: HiC_GCB_rep_1

description:
HiC in Germinal Center B cells replicate 1
processed data file: hic_GCB_intra.bed.txt.gz, hic_GCB_inter.sif.gz


title: Mcf10A_p53 and HRas_replicate 2

first: Carol

middle: L

last: Prives

address: 1212 Amsterdam Ave

department: Biological Sciences

institute: Columbia University

description: 2.Mcf10A Vec and Hras

data_processing:
Raw data checked using FastQC
Adaptor quality checked using Trimmomatic
Reads were aligned to GRCh37 using TopHat
Aligned reads were sorted with SamTools
Number of reads was counted using HTSeq
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel files, contains processed values and p values calculated with various methods

growth_protocol: Regular media: DME/F-12 plus growth supplements including horse serum.

extract_protocol:
Total RNA was made using TRIzol, then cDNA was extracted using oligo-dT beads
TruSeq RNA Library (Illumina)

treatment_protocol: No treatment

tag: expression

value: Has intact WT-p53 with H-RasV12 stable expression by retrovirus


title: Mcf10A_p53 and HRas_replicate 3

description: 2.Mcf10A Vec and Hras


title: RNAseq_GCB_rep2

description: RNA-seq in Germinal Center B cells replicate 2

tag: tissue


title: Mcf10A_p53 and HRas_replicate 1

description: 2.Mcf10A Vec and Hras


title: Mcf10A_p53 and Vector_replicate 3

description: 2.Mcf10A Vec and Hras

value: Has intact WT-p53 with pBabepuro Vector


title: Mcf10A_p53-del HRas_replicate 3

description: 1.Mcf10A p53delVec and p53delHras

value: targeted deletion of p53 at exon 2, with H-RasV12 stable expression by retrovirus


title: Mcf10A_p53-del Vector_replicate 3

description: 1.Mcf10A p53delVec and p53delHras

value: targeted deletion of p53 at exon 2, with pBabepuro Vector


title: Mcf10A_p53-del HRas_replicate 2

description: 1.Mcf10A p53delVec and p53delHras


title: Mcf10A_p53 and Vector_replicate 1

description: 2.Mcf10A Vec and Hras


title: REH RNA-Seq

data_processing:
samples were aligned to hg19 using STAR2.4.2a and ensembl GRCh37v75 as guide
Genome_build: hg19
Supplementary_files_format_and_content: STAR count output

treatment_protocol: Cells were seeded at 1*10^6 cells/ml.

value: B-ALL


title: 14b_DINO_ASO2_DOXORUBICIN_REP4

data_processing:
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie, duplicate fragments were then removed using Picard. Peaks were called using the ZINBA algorithm, which was first applied to each dataset independently, using the following parameters: a 300bp window, 50bp offset, background and enriched components were modeled using the intercept, while the zero-inflated component was modeled using alignability, a posterior probability of 0.99 was used to select the set of significant regions. The peak sets from the same cell-type and number of cells were merged.
Number of Raw reads in each peak was calculated using in house generated script, and data matrix was normalized using R
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are in tab seperated format, which includes the following columns: chromosome, start, stop, name, arbitrary score (1000), strand

growth_protocol: Early passeage FL3 human diploid fibroblasts were obtained from ATCC and grown in standard DMEM + 10% serum.

extract_protocol:
50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit.

treatment_protocol: 300,000 fibroblasts with transfected with 100nM ASO using lipofectamine. 24 hours later, cells were treated with 0.2ug/mL doxorubicin or vehicle alone for a total of 12 hours.

value: Early passage human diploid fibroblasts

tag: transfected with

value: antisenses oligonucleotides (ASOs) targeting lncRNA DINO

value: 0.2ug/mL doxorubicin


title: Mcf10A_p53-del Vector_replicate 2

description: 1.Mcf10A p53delVec and p53delHras


title: 697 RNA-Seq


title: lnc-TIMM21-LNA1-rep1

value: REH

value: lnc-TIMM21-5 LNA GapmeR1

tag: time


title: 12b_DINO_ASO1_DOXORUBICIN_REP4


title: 14a_DINO_ASO2_DOXORUBICIN_REP3


title: 12a_DINO_ASO1_DOXORUBICIN_REP3


title: HiC_NB_rep_1

description:
HiC in naïve B cells replicate 1
processed data file: hic_NB_intra.bed.txt.gz, hic_NB_inter.sif.gz

value: healthy individual


title: 10b_CNRTL_ASO_DOXORUBICIN_REP4

value: control antisenses oligonucleotides (ASOs)


title: 10a_CNRTL_ASO_DOXORUBICIN_REP3


title: 9b_CNRTL_ASO_VEHICLE_REP4


title: 6b_DINO_ASO2_DOXORUBICIN_REP2


title: 9a_CNRTL_ASO_VEHICLE_REP3


title: 6a_DINO_ASO2_DOXORUBICIN_REP1


title: Mcf10A_p53 and Vector_replicate 2

description: 2.Mcf10A Vec and Hras


title: 4b_DINO_ASO1_DOXORUBICIN_REP2


title: 4a_DINO_ASO1_DOXORUBICIN_REP1


title: Mcf10A_p53-del HRas_replicate 1

description: 1.Mcf10A p53delVec and p53delHras


title: 5a_DINO_ASO2_VEHICLE_REP1

value: vehicle alone


title: 2a_CNRTL_ASO_DOXORUBICIN_REP3


title: 1b_CNRTL_ASO_VEHICLE_REP4


title: 2b_CNRTL_ASO_DOXORUBICIN_REP4


title: 3a_DINO_ASO1_VEHICLE_REP1


title: 1a_CNRTL_ASO_VEHICLE_REP3


title: 3b_DINO_ASO1_VEHICLE_REP2


title: 2b_CNRTL_ASO_DOXORUBICIN_REP2


title: 1a_CNRTL_ASO_VEHICLE_REP1


title: 1b_CNRTL_ASO_VEHICLE_REP2


title: 2a_CNRTL_ASO_DOXORUBICIN_REP1


title: Tcell_person1_P1902_1565

city: Stockholm

first: Daniel

last: Ramsköld

address: Nobels väg 3

country: Sweden

institute: Karolinska Institutet

data_processing:
genome build:  hg19
Aligned reads with rna-star
Calculated expression values with rpkmforgenes.py (available at https://github.com/danielramskold/S3_species-specific_sequencing) with options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -bothendceil and gene annotation for the UCSC genome browser Ensembl track
Supplementary_files_format_and_content: Tab-delimited text files report RPKMs and read counts.

extract_protocol: SmartSeq2 (Picelli S, Nat Methods. 2013, PubMed PMID: 24056875)

tag: age

value: adult

tag: Sex

value: male

value: ex vivo single Tcell


title: Tcell_person1_P1902_1574


title: Tcell_person1_P1902_1558


title: Tcell_person1_P1902_1559


title: Tcell_person1_P1902_1573


title: person1_YFV2001_Exome_Seq_Cap

description: library strategy: Exome sequencing

source_name: peripheral blood mononuclear cells

extract_protocol:
QIAGEN, DNA isolation kit, Cat. 69581
Nextera Exome Sequencing kit and Nextera Rapid Capture Expanded Exome Kit, Illumina, Ref. FC-140-1000

value: peripheral blood mononuclear cells


title: Tcell_person1_P1902_1566


title: 5b_DINO_ASO2_VEHICLE_REP2


title: Tcell_person1_P1902_1557


title: Mcf10A_p53-del Vector_replicate 1

description: 1.Mcf10A p53delVec and p53delHras


title: Tcell_person1_P1902_1542


title: Tcell_person1_P1902_1541


title: Tcell_person1_P1902_1534


title: Tcell_person1_P1902_1533


title: Tcell_person1_P1902_1549


title: Tcell_person1_P1902_1527


title: Tcell_person1_P1902_1518


title: Tcell_person1_P1902_1525


title: Tcell_person1_P1902_1510


title: Tcell_person1_P1902_1551


title: Tcell_person1_P1902_1519


title: Tcell_person1_P1902_1511


title: Tcell_person1_P1902_1509


title: Tcell_person1_P1902_1517


title: Tcell_person1_P1902_1502


title: Tcell_person1_P1902_1503


title: Tcell_person1_P1902_1495


title: Tcell_person1_P1902_1494


title: Tcell_person1_P1902_1501


title: Tcell_person1_P1902_1486


title: Tcell_person1_P1902_1550


title: Tcell_person1_P1902_1487


title: Tcell_person1_P1902_1543


title: Tcell_person1_P1902_1493


title: Tcell_person1_P1902_1535


title: Tcell_person1_P1902_1563


title: Tcell_person1_P1902_1564


title: Tcell_person1_P1902_1569


title: Tcell_person1_P1902_1561


title: Tcell_person1_P1902_1556


title: Tcell_person1_P1902_1554


title: Tcell_person1_P1902_1562


title: Tcell_person1_P1902_1555


title: Tcell_person1_P1902_1548


title: Tcell_person1_P1902_1526


title: Tcell_person1_P1902_1545


title: Tcell_person1_P1902_1546


title: Tcell_person1_P1902_1538


title: Tcell_person1_P1902_1532


title: Tcell_person1_P1902_1537


title: Tcell_person1_P1902_1485


title: Tcell_person1_P1902_1540


title: Tcell_person1_P1902_1524


title: Tcell_person1_P1902_1530


title: Tcell_person1_P1902_1522


title: Tcell_person1_P1902_1529


title: Tcell_person1_P1902_1521


title: Tcell_person1_P1902_1515


title: Tcell_person1_P1902_1513


title: Tcell_person1_P1902_1516


title: Tcell_person1_P1902_1508


title: Tcell_person1_P1902_1514


title: Tcell_person1_P1902_1507


title: Tcell_person1_P1902_1506


title: Tcell_person1_P1902_1498


title: Tcell_person1_P1902_1547


title: Tcell_person1_P1902_1499


title: Tcell_person1_P1902_1500


title: Tcell_person1_P1902_1492


title: Tcell_person1_P1902_1497


title: Tcell_person1_P1902_1489


title: Tcell_person1_P1902_1490


title: Tcell_person1_P1902_1523


title: Tcell_person1_P1902_1491


title: Tcell_person1_P1902_1481


title: Tcell_person1_P1902_1483


title: Tcell_person1_P1902_1531


title: Tcell_person1_P1902_1480


title: Tcell_person1_P1902_1553


title: Tcell_person1_P1902_1484


title: Tcell_person1_P1902_1539


title: Tcell_person1_P1902_1478


title: Tcell_person1_P1902_1477


title: Tcell_person1_P1902_1476


title: Tcell_person1_P1902_1479


title: Tcell_person1_P1902_1505


title: Tcell_person1_P1902_1474


title: Tcell_person1_P1902_1475


title: Tcell_person1_P1902_1471


title: Tcell_person1_P1902_1472


title: Tcell_person1_P1902_1469


title: Tcell_person1_P1902_1467


title: Tcell_person1_P1902_1473


title: Tcell_person1_P1902_1468


title: Tcell_person1_P1902_1470


title: Tcell_person1_P1902_1465


title: Tcell_person1_P1902_1464


title: Tcell_person1_P1902_1459


title: Tcell_person1_P1902_1460


title: Tcell_person1_P1902_1461


title: Tcell_person1_P1902_1462


title: Tcell_person1_P1902_1457


title: Tcell_person1_P1902_1455


title: Tcell_person1_P1902_1456


title: Tcell_person1_P1902_1458


title: Tcell_person1_P1902_1482


title: Tcell_person1_P1902_1449


title: Tcell_person1_P1902_1452


title: Tcell_person1_P1902_1451


title: Tcell_person1_P1902_1453


title: Tcell_person1_P1902_1448


title: Tcell_person1_P1902_1447


title: Tcell_person1_P1902_1445


title: Tcell_person1_P1902_1466


title: Tcell_person1_P1902_1444


title: Tcell_person1_P1902_1450


title: Tcell_person1_P1902_1446


title: Tcell_person1_P1902_1440


title: Tcell_person1_P1902_1439


title: Tcell_person1_P1902_1442


title: Tcell_person1_P1902_1463


title: Tcell_person1_P1902_1437


title: Tcell_person1_P1902_1436


title: Tcell_person1_P1902_1441


title: Tcell_person1_P1902_1438


title: Tcell_person1_P1902_1434


title: Tcell_person1_P1902_1454


title: Tcell_person1_P1902_1443


title: Tcell_person1_P1902_1432


title: Tcell_person1_P1902_1427


title: Tcell_person1_P1902_1428


title: Tcell_person1_P1902_1430


title: Tcell_person1_P1902_1429


title: Tcell_person1_P1902_1422


title: Tcell_person1_P1902_1426


title: Tcell_person1_P1902_1424


title: Tcell_person1_P1902_1425


title: Tcell_person1_P1902_1421


title: Tcell_person1_P1902_1419


title: Tcell_person1_P1902_1418


title: Tcell_person1_P1902_1417


title: Tcell_person1_P1902_1420


title: Tcell_person1_P1902_1669


title: Tcell_person1_P1902_1664


title: Tcell_person1_P1902_1671


title: Tcell_person1_P1902_1672


title: Tcell_person1_P1902_1663


title: Tcell_person1_P1902_1433


title: Tcell_person1_P1902_1661


title: Tcell_person1_P1902_1670


title: Tcell_person1_P1902_1656


title: Tcell_person1_P1902_1662


title: Tcell_person1_P1902_1431


title: Tcell_person1_P1902_1654


title: Tcell_person1_P1902_1655


title: Tcell_person1_P1902_1653


title: Tcell_person1_P1902_1423


title: Tcell_person1_P1902_1648


title: Tcell_person1_P1902_1640


title: Tcell_person1_P1902_1646


title: Tcell_person1_P1902_1647


title: Tcell_person1_P1902_1631


title: Tcell_person1_P1902_1639


title: Tcell_person1_P1902_1435


title: Tcell_person1_P1902_1632


title: Tcell_person1_P1902_1630


title: Tcell_person1_P1902_1637


title: Tcell_person1_P1902_1624


title: Tcell_person1_P1902_1629


title: Tcell_person1_P1902_1615