title: iRECs_2TF_Hnf4aWT_1

city: Zürich

first: Soeren

last: Lienkamp

state: Zürich

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zürich

description: MEFs reprogrammed to iRECs using Hnf1b, Pax8, Hnf4a WT.

data_processing:
Raw sequence analysis on the Galaxy platform and usegalaxy.org server.
Reads were trimmed with Trim Galore! version 0.4.3.
Reads were aligned to the genome build GRCm38 using RNA STAR2 version 2.5.2b.
Gene counts were calculated with featureCounts version 1.6.0.
Differentially expressed genes (DEG) between MEF and iREC WT and iREC R85W conditions were determined using DESeq2 version 1.18.1.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: *.tab: Gene raw counts calculated with featureCounts version 1.6.0, tab-delimited files.

source_name: Cell culture

growth_protocol: MEFs and iRECs were cultured in MEF medium containing DMEM (Dulbecco’s modified Eagle’s medium) supplemented with 10% (v/v) FBS (fetal bovine serum), penicillin/streptomycin and glutamine, and were maintained in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was extracted with QIAzol Lysis Reagent (Qiagen) and isolated using the RNeasy Plus Universal Mini Kit.
Library construction by Eurofinsgenomics.

treatment_protocol: Cells were seeded in MEFM and grown until confluency.

value: Induced renal epithelial tubular cells (iRECs)

tag: strain of reporter mouse

tag: transcription factors used for reprogramming

value: Hnf1b, Pax8, Hnf4a_WT


title: Slc17a6-TRAP (JX883) hypothalamus input Rep1 [981]

status: Public on Dec 16 2019

type: SRA

city: New York

first: Laura

last: Kus

state: NY

address: 1230 York Avenue # 260

department: Heintz Laboratory

country: USA

institute: The Rockefeller University

description:
Total RNA
981_Slc17a6_TRAP_JX883_hypothalamus_Input1_GTGAAA_L007

library_source: transcriptomic

data_processing:
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using default settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of counts

molecule: total RNA

organism: Mus musculus

source_name: Hypothalamus

extract_protocol:
The hypothalamus and midbrain were dissected seperately and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

tag: tissue

value: Hypothalamus

tag: animal line

value: Slc17a6-TRAP JX883

tag: application

value: RNA-seq

tag: sample type

value: Input


title: iRECs_2TF_Hnf4aWT_3

tag: cell type


title: Slc17a6-TRAP (JX883) hypothalamus IP Rep1 [980]

description:
Ribosomal-bound RNA
980_Slc17a6_TRAP_JX883_hypothalamus_IP1_ACAGTG_L007

value: Immunopurified (IP)


title: LC_1_0h_Me3

city: Southampton

first: Marta

middle: Ewa

last: Polak

state: Hampshire

address: Southampton General Hospital, Mailpoint 813, LE59,

department: Clinical and Experimental Sciences

country: United Kingdom

institute: University of Southampton

description: human skin primary migratory LCs

library_source: genomic

data_processing:
Quality control: FASTQC
ChIP-seq alignment: BioWardrobe
ChiP-seq Peak Calling: Biowardrobe (MACS2 version 2.1.1)
RNA-seq trimming: Trimmomatic
RNA-seq mapping and alignment: TopHat V 2.0.9 and HTSeq-count V.0.5.4
Genome_build: hg19
scRNA-seq: demultiplexing: bcl2fastq tool, Illumina
scRNA-seq: STAR
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq: peak files. RNA-seq: aligned Htseq Reads

molecule: genomic DNA

organism: Homo sapiens

source_name: epidermis

growth_protocol: Human primary LCs were migrated out of epidermal sheets, following digest with dispase o/n at +4C. CD1a+ cells were purified using fluorescence-activated cell sorting.

extract_protocol:
for ChIP-seq: Purified migratory LCs were fixed with 1% formaldehyde for 15 min and the reaction quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 100–200 bp (Covaris). Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat to remove crosslinks, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. Genomic DNA regions of interest were isolated using appropriate antibodies. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation (at 37 °C for 1 h, followed by 4 h at 65 °C) overnight at 65 °C, and ChIP DNA was purified by phenol–chloroform extraction and ethanol precipitation.  For RNA-seq: RNA was isolated using RNeasy mini kit (Qiagen) as per the manufacturer’s protocol. RNA concentration and integrity was determined with an Agilent Bioanalyser (Agilent Technologies, Santa Clara, CA). All the samples had a RNA integrity number of 7.0 or above and were taken forward for labelling.
for Chip-seq: Illumina sequencing libraries were prepared from the ChIP and input DNAs by the standard consecutive enzymatic steps of end- polishing, dA-addition, and adaptor ligation using TruplexTM –FD prep kit (Rubicon Genomics, USA). After a final PCR amplification step, the resulting DNA libraries were quantified using Qubit (Life technologies, USA) and 75 nucleotide single-end reads were sequenced Illumina HiSeq2500 in the DNA sequencing core of the Cincinnati Children's Hospital Medical Center.  For RNA-seq: RNA-seq libraries were generated from 300 ng total RNA with an RNA Sample Prep Kit (Illumina) according to a standard protocol. The libraries were sequenced with Illumina HiSeq2500 in the DNA sequencing core of the Cincinnati Children's Hospital Medical Center. Each sample was used to generate 2 × 107 reads with 75–base pair paired-end sequencing.

tag: condition

value: unstimulated

tag: time


title: Slc17a6-TRAP (JX883) midbrain IP Rep1 [982]

description:
Ribosomal-bound RNA
982_Slc17a6_TRAP_JX883_midbrain_IP1_ACAGTG_L008

source_name: Midbrain

value: Midbrain


title: LC_1_TNFa_2h_Me3

description: human skin primary migratory LCs

value: TNFa


title: iRECs_2TF_Hnf4aR85W_2

description: MEFs reprogrammed to iRECs using Hnf1b, Pax8, Hnf4a R85W.

value: Hnf1b, Pax8, Hnf4a_R85W


title: Chat-TRAP (DW167) Left Medial Habenula IP Rep4 [1048]

description:
Ribosomal-bound RNA
1048_Chat-TRAP (DW167) Left Medial Habenula IP Rep4_CTTGTA_L001

source_name: Medial habenula

extract_protocol:
The right side and left side of the medial habenula were dissected and homogenized separately.  Tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

value: Left Medial Habenula

value: Chat-TRAP DW167


title: iRECs_2TF_Hnf4aR85W_1


title: Chat-TRAP (DW167) Left Medial Habenula IP Rep3 [1047]

description:
Ribosomal-bound RNA
1047_Chat-TRAP (DW167) Left Medial Habenula IP Rep3_GTGAAA_L005


title: FLHSC_Capture-C_SecondBatch_Rep1

city: PHILADELPHIA

first: Kai

last: Tan

state: PA

address: 3501 CIVIC CENTER BLVD.

institute: Children's Hospital of Philadelphia

data_processing:
Library strategy: Capture-C
Capture-C data were processed using the pipeline from Hughes et al. Briefly, Illumina Truseq adaptor sequences were trimmed from raw reads using trim galore version 0.41 with default parameter setting.
Paired-end reads were merged into one single fastq file to ensure each pair of reads interleaved in strict order. Reads were mapped to the mouse genome (mm9) using Bowtie2 (v2.2.2).
Mapped reads were analyzed using the script CCanalyser2.pl (https://github. com/telenius/captureC/releases). Unique informative reads were extracted for each captured bait as the input for calling significant interactions.
Genome_build: mm9

source_name: Embryonic day 14.5 fetal liver hematopoietic stem cells

extract_protocol:
E14.5 fetal liver and adult bone marrow were dissected and HSCs were purified using cell surface marker: Lin-Sca1+cKit+CD135-. Half million FACS-sorted cells were cross-linked, lysed and nuclei were digested using DpnII (R0543T, NEB) at 37°C with shaking at 1400 rpm overnight. The digested chromatin was proximally ligated with 100 U T4 DNA ligase (10799009001, Roche) at 16°C for 8 hrs with slow rotation. The samples were de-cross-linked followed by purification using phenol-chloroform extraction and precipitated using 70% ethanol. The purified 3C DNA was was sonicated to 200~300bp using Covaris S220 ultra-sonicator (6 min; duty cycle, 10%; intensity, 5; cycle per burst, 200). Sequencing libraries were constructed using NEBNext Ultra Kit (E7370, NEB). The libraries were size-selected using AMPure XP beads (A63881, Beckman Coulter). Oligonucleotide capture was performed using the SureSelect XT2 protocol (G9621A, Agilent). The libraries were quantified with Qubit, Agilent Bioanalyzer 2100 and KAPA qPCR (KK4844, Kapabiosystems). The captured libraries were sequenced with 150 bp paired-end reads on an Illumina HiSeq platform.
Libraries constructed using NEBNext Ultra Kit (E7370, NEB). The libraries were size-selected using AMPure XP beads (A63881, Beckman Coulter). The libraries were quantified with Qubit, Agilent Bioanalyzer 2100 and KAPA qPCR (KK4844, Kapabiosystems). The captured libraries were sequenced with 150 bp paired-end reads on an Illumina HiSeq platform.

tag: strain/cell type

value: Fetal liver

tag: age

value: Embryonic day 14.5


title: iRECs_2TF_Hnf4aR85W_3


title: Chat-TRAP (DW167) Left Medial Habenula IP Rep2 [1046]

description:
Ribosomal-bound RNA
1046_Chat-TRAP (DW167) Left Medial Habenula IP Rep2_CTTGTA_L004


title: Chat-TRAP (DW167) Left Medial Habenula IP Rep5 [1049]

description:
Ribosomal-bound RNA
1049_Chat-TRAP (DW167) Left Medial Habenula IP Rep5_ACAGTG_L002


title: MEFs_3

description:
MEFs harvested from E13.5 mouse embryos.
This Sample represents two technical replicates.

value: Mouse embryonic fibroblasts (MEFs)


title: LC_2_0h_Me3

description: human skin primary migratory LCs


title: LC_2_TNFa_24h_Me3

description: human skin primary migratory LCs


title: MEFs_1

description: MEFs harvested from E13.5 mouse embryos.


title: Chat-TRAP (DW167) Right Medial Habenula IP Rep4 [1044]

description:
Ribosomal-bound RNA
1044_Chat-TRAP (DW167) Right Medial Habenula IP Rep4_GCCAAT_L001

value: Right Medial Habenula


title: Chat-TRAP (DW167) Right Medial Habenula IP Rep3 [1043]

description:
Ribosomal-bound RNA
1043_Chat-TRAP (DW167) Right Medial Habenula IP Rep3_ACAGTG_L005


title: MEFs_2


title: PαS, 2 weeks, replicate 4

city: Madrid

first: Elena

last: Piñeiro-Yáñez

address: Calle de Melchor Fernández Almagro, 3

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

data_processing:
RNA-seq data was analysed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/) as follows:
The quality of the raw data was assessed using FastQC v0.11.3 and FastQ Screen v0.5.2
Sequenced reads were trimmed to remove adaptors, first 3 bases of the reads and 3' and 5' end nucleotides with a quality cutoff of 20 using Cutadapt
Reads were aligned to the mouse genome (GRCm38/mm10) with TopHat 2.0.10 using Bowtie 1.0.0 and SAMtools 0.1.19, allowing only 2 mismatches and 20 multihits
Transcripts' abundance was calculated using Cufflinks 2.2.1 to obtain Fragments Per Kilobase of exon per Million mapped reads (FPKM), and htseq-count 0.6.1 followed by DESeq2 1.18.1 to obtain normalized counts.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and normalized counts for each sample

source_name: stromal cell types isolated from bone marrow

extract_protocol:
Enzymatic digestion of bone marrow tissues, fluorescent activated cell sorting (FACS) directly into RLT lysis buffer (Qiagen), RNA extraction using RNeasy Plus Micro Kit (Qiagen)
Clontech SMRTer Stranded total RNA-Seq Kit-Pico Input Mammalian Total RNA

value: PDGFR-alpha+ Sca-1+ mesenchymal cells

tag: strain

value: bone marrow

value: 2 weeks

tag: agent

value: no treatment


title: Chat-TRAP (DW167) Right Medial Habenula IP Rep5 [1045]

description:
Ribosomal-bound RNA
1045_Chat-TRAP (DW167) Right Medial Habenula IP Rep5_GTGAAA_L002

value: RNA-seq


title: Slc17a6-TRAP (JX883) hypothalamus input Rep3 [1015]

description:
Total RNA
1015_Slc17a6_TRAP_JX883_hypothalamus_Input3_GTGAAA_L002

value: Hypothalamus

value: Slc17a6-TRAP JX883

value: Input


title: AEC, 2 weeks, replicate 4

value: arterial endothelial cells


title: CARc, 2 weeks, replicate 4

value: CXCL12-abundant reticular cells


title: Chat-TRAP (DW167) Right Medial Habenula IP Rep1 [822]

description:
Ribosomal-bound RNA
822_Chat-TRAP (DW167) Right Medial Habenula IP Rep1_GTGAAA_L003

value: Immunopurified (IP)


title: SEC, 2 weeks, replicate 4

value: sinusoidal endothelial cells


title: PαS, 2 weeks, replicate 3


title: Cfh-EGFP/Rpl10a (NIDA092) subcortical brain regions IP [1089]

description:
Ribosomal-bound RNA
1089_Cfh-EGFP/Rpl10a (NIDA092) subcortical brain regions IP_GCCAAT_L005

source_name: Subcortical brain regions

extract_protocol:
Subcortical brain structures were dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

tag: comment

value: Cfh-TRAP NIDA092


title: pMES_4

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

description:
Chicken
processed data file: counts.txt

data_processing:
Following sequencing, Illumina Primary Analysis version RTA v1.18.64 and bcl2fastq2 v2.18 were run to demultiplex reads for all libraries and generate FASTQ files. More than 3 million total alignments were produced per sample.
Single end 51-base reads were aligned to the chicken genome galGal4 from UCSC with annotations from Ensembl 84 using STAR (2.5.2b) with options –alignEndsType EndToEnd and sjdbScore 2.
Downstream analysis was done in R (3.4.1). Differential expression analysis was performed using the edgeR package (3.18.1). Genes were denoted as differentially expressed if they had a p-value less than .05 and a fold change greater than 1.5-fold (absolute value). Gene ontology enrichment was done using a hypergeometric test on lists of differentially expressed genes.
Genome_build: Chicken genome galGal4 (Gallus_gallus-4.0) from UCSC with annotations from Ensembl 84.
Supplementary_files_format_and_content: counts.txt: Raw counts generated by STAR on genes from Ensembl 84.

organism: Gallus gallus

source_name: cranial neural crest cells

growth_protocol: Premigratory neural crest were electroporated with either AQP-1 FL or pMES and eggs re-incubated for 24hrs. The neural crest stream adjacent in rhombomere 4 was isolated from healthy ~HH15 embryos.

extract_protocol:
Cells were isolated by FACS, which included forward scatter, side scatter, pulse width, live/dead stain (7AAD) and YFP gates as previously described (McLennan 2015, Morrison 2017). Cells were sorted directly into 7ul of Clontech lysis solution containing 0.05% RNase inhibitor. Following lysis for 5 minutes at room temperature, lysates were immediately frozen on dry ice and stored at -80C.
Bulk RNA-seq lysates were thawed on ice. cDNA synthesis and library preparation were performed with SMART-seq v4 Ultra Low Input RNA-seq (634891, Takara, Kusatsu, Shiga, Japan) and Nextera XT DNA sample prep and indexing library preparation kits as recommended by the manufacturer (FC-131-2001, FC-131-2004, and FC-131-1096, Illumina, San Diego, CA). Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer (Agilent) and Qubit Fluorometer (Life Technologies). Libraries were pooled, re-quantified and sequenced as 50bp single reads on 2 lanes of the Illumina HiSeq 2500 in High Output mode using HiSeq Control Software v2.2.58 (Illumina).

treatment_protocol: Five pMES transfected embryos were pooled for each of the 3 biological replicates (n=15 total). Four AQP-1 FL embryos were pooled for each of the 3 biological replicates (n=12 total). Tissue was dissociated as previously described (McLennan 2015).

tag: breed

value: White Leghorn

value: cranial neural crest cells

tag: developmental stage (hh)

value: HH St 15

tag: treatment

value: Control overexpression


title: pMES_3

description:
Chicken
processed data file: counts.txt


title: AEC, 2 weeks, replicate 3


title: Control_DNA methylation_seq_6

city: zhangjiakou

first: wenyang

last: chen

address: zuanshi south street

country: China

institute: Hebei North University

description: control group

data_processing:
Trim_galore for quality control of RRBS raw data
Bismark for data alignment with rn6 genome
Samtools for data format conversion
Picards for duplication removing
Computation and visualization were achieved using R packages.
Genome_build: rn6
Supplementary_files_format_and_content: The .txt files report methylation level of single base

organism: Rattus norvegicus

source_name: control group

extract_protocol:
The genomic DNA (gDNA) of the testes was isolated by a TIANamp Genomic DNA Kit (TianGen), according to the instructions of the manufacturer.
One hundred nanograms of gDNA were digested with 30 U of MspI enzyme (Fermentas) in 20 μl reactions at 37℃ for 16 h. After purification, digested products were blunt ended, and dA was added, followed by methylated-adapter ligation. The obtained DNA fractions were size selected in 200-450 bp using AMPure XP beads (Beckman Coulter). Bisulfite conversion was conducted using an EZ DNA Methylation-Direct Kit (ZYMO), following the instructions of the manufacturer. The final libraries were generated by PCR amplification using a HiFi HotStart Uracil+ Kit (Kapa).

value: testis

value: wistar

value: 8 weeks


title: pMES_1

description:
Chicken
processed data file: counts.txt


title: CARc, 2 weeks, replicate 3

value: bone marrow

value: 2 weeks

value: no treatment


title: Chat-TRAP (DW167) Right Medial Habenula IP Rep2 [1042]

description:
Ribosomal-bound RNA
1042_Chat-TRAP (DW167) Right Medial Habenula IP Rep2_GCCAAT_L004

value: Right Medial Habenula

value: Chat-TRAP DW167

value: RNA-seq


title: AQP1_FL_3

description:
Chicken
processed data file: counts.txt

value: AQP1 overexpression


title: Chat-TRAP (DW167) Left Medial Habenula IP Rep1 [820]

description:
Ribosomal-bound RNA
820_Chat-TRAP (DW167) Left Medial Habenula IP Rep1 _CTTGTA_L007

value: Left Medial Habenula

value: Immunopurified (IP)


title: SEC, 2 weeks, replicate 3

value: sinusoidal endothelial cells


title: Control_DNA methylation_seq_5

description: control group


title: Cfh-EGFP/Rpl10a (NIDA092) subcortical brain regions input [1090]

description: 1090_Cfh-EGFP/Rpl10a (NIDA092) subcortical brain regions input_CTTGTA_L005

value: Cfh-TRAP NIDA092

value: Input


title: PαS, 2 weeks, replicate 2

value: PDGFR-alpha+ Sca-1+ mesenchymal cells


title: Cerebral cortex, Yoked control IP Rep2

description: 456_S100a10_TRAP_ES691_Yoked_IP_Rep2_GCCAAT_L006

source_name: Cerebral cortex

growth_protocol: Not applicable

extract_protocol:
The cerebral cortex was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

treatment_protocol: Saline self-administration. Cocaine self-administration. Yoked control

value: Cerebral cortex

value: neurons

value: Yoked control

tag: fraction

value: Ribosomal-bound RNA


title: Cerebral cortex, Yoked control IP Rep1

description: 455_S100a10_TRAP_ES691_Yoked_IP_Rep1_ACAGTG_L006


title: AEC, 2 weeks, replicate 2

value: arterial endothelial cells

value: bone marrow


title: AQP1_FL_2

description:
Chicken
processed data file: counts.txt

value: White Leghorn

value: cranial neural crest cells

value: HH St 15


title: Cerebral cortex, Cocaine self-administration IP Rep2

description: 453_S100a10_TRAP_ES691_Cocaine_IP_Rep2_GCCAAT_L005

value: Cocaine self-administration


title: Cerebral cortex, Yoked control IP Rep3

description: 457_S100a10_TRAP_ES691_Yoked_IP_Rep3_ATGTCA_L006


title: exosome in normal condition 1

type: RNA

city: Shanghai

first: Xiaoli

last: Wu

address: 2699，West Gaoke Road

department: Department of Gynecology

institute: Shanghai First Maternity and Infant Hospital, Tongji University

description: Gene expression in exosomes after 24hr under 5% O2, 90%N2,5%CO2

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 100.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were maintained

label_protocol: 1ug total RNA were dephosphorylated, denaturated and then labeled with Cyanine-3-CTP（Cy3）using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions,then followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1

growth_protocol: Skov3 cells was cultured in 10%FBS RPMI1640median ,37°C，5%CO2 until they reached logarithmic phase.

extract_protocol: total RNA was extracted by RNasey Mini Kit(Qiagen p/n 74104) following the manufacturer's instructions

treatment_protocol: Then we washed skov3 cells three times with PBS, and 10^6 cells was incubate in 10cm dish with exosome-depleted FBS RPMI1640, 37°C，hypoxia(2% O2, 90%N2,5%CO2) or normal(5% O2, 90%N2,5%CO2）condition for 72h.Then exosomes were collected by the total exosome isolation kit (Life technology) following the manufacturers instructions.

value: exosome

tag: culture condition


title: exosome in normal condition 2

tag: tissue


title: AQP1_FL_1

description:
Chicken
processed data file: counts.txt

value: AQP1 overexpression


title: exosome in hypoxia condition 2

description: Gene expression in exosomes after 24hr under 2% O2, 90%N2,5%CO2


title: iRECs_2TF_Hnf4aWT_2

description: MEFs reprogrammed to iRECs using Hnf1b, Pax8, Hnf4a WT.

value: Induced renal epithelial tubular cells (iRECs)

tag: strain of reporter mouse

tag: transcription factors used for reprogramming

value: Hnf1b, Pax8, Hnf4a_WT


title: Alveolar macrophages, WTAIR_Ia4

city: Ghent

first: Ken

middle: R

last: Bracke

address: Corneel Heymanslaan 10

department: Department of Respiratory Medicine

country: Belgium

institute: Ghent University

data_processing:
sequencing reads were mapped to the murine reference genome (GRCm38.p6) using STAR v2.6.0c and GENCODE release M18 as guidance
read counts were quantified using the "--quantMode GeneCounts" option
genomic features with a zero read count across all samples and without read count greater or equal than four in at least sixty percent of the samples from one group were discarded
raw counts were transformed into log2-counts per million using limma-voom
Genome_build: GRCm38.p6 + GENCODE release M18
Supplementary_files_format_and_content: tab-delimited text file including log-CPM transformed values

molecule: polyA RNA

source_name: FACS sorted alveolar macrophages (CD45+SiglecF+CD11c+)

extract_protocol:
RNA extraction of FACS sorted alveolar macrophages was performed with the miRNeasy Mini Kit (Qiagen).
libraries were prepared using the TruSeq mRNA library prep kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. A total of 25 ng of RNA was used as input for polyA selection, followed by fragmentation, reverse transcription and PCR amplification

treatment_protocol: wild-type and miR-155 knock-out mice to four weeks of air or cigarette smoke

tag: treatment protocol

value: air

tag: genotype

value: wild-type


title: shBECN1_1: SKOV3 cells passaged 30x, with shRNA to BECN1. Biological replicate 1

type: genomic

city: Charleston

first: Joe

last: Delaney

state: SC

address: 173 Ashley Avenue

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

description:
CEL file AT: a521191-00-977111-013118-4289464-06060.CEL
CEL file GC: a521191-00-977113-013118-4289464-06290.CEL

hyb_protocol: Sent to manufacturer

scan_protocol: Sent to manufacturer

data_processing: Sent to manufacturer

label: biotin

source_name: SKOV3 shBECN1_1

label_protocol: Sent to manufacturer

growth_protocol: All cells were grown in RPMI (Life Technologies) supplemented with 2% glucose, nonessential amino acids (Mediatech #45000-700), sodium pyruvate (Mediatech #45000-710), antibiotics (penicillin, streptomycin, and amphotericin, Mediatech #30-004-CI), and 10% FBS (Omega Scientific #FB-11).  For all shRNA experiments, puromycin (VWR #IC1005521) was added to 1ug/ml in RPMI

extract_protocol: Qiagen Blood and Tissue DNA kit

treatment_protocol: Normal passaging via 0.05% trypsin when cells reached 80% confluency, they were diluted 1:10.  All cells were passaged 30x during the course of this experiment under puromycin selection to ensure shRNA plasmid retention.  No other treatment was performed so that cells could diverge without selective pressure

tag: cell type

value: shRNA to BECN1


title: CARc, 2 weeks, replicate 2

value: CXCL12-abundant reticular cells

value: 2 weeks

value: no treatment


title: shScr_4: SKOV3 cells passaged 30x, with scrambled shRNA. Biological replicate 4

description:
CEL file AT: a521191-00-977112-013118-4289464-06237.CEL
CEL file GC: a521191-00-977105-013118-4289464-73787.CEL

source_name: SKOV3 shScr_4

value: control (shScr)


title: shBECN1_4: SKOV3 cells passaged 30x, with shRNA to BECN1. Biological replicate 4

description:
CEL file AT: a521191-00-977109-013118-4289464-75628.CEL
CEL file GC: a521191-00-977113-013118-4289464-06307.CEL

source_name: SKOV3 shBECN1_4


title: shScr_3: SKOV3 cells passaged 30x, with scrambled shRNA. Biological replicate 3

description:
CEL file AT: a521191-00-977112-013118-4289464-06227.CEL
CEL file GC: a521191-00-977103-013118-4289464-73522.CEL

source_name: SKOV3 shScr_3


title: Cerebral cortex, Saline self-administration Input

description: 451_S100a10_TRAP_ES691_Saline_Input_ACAGTG_L007

tag: animal line

value: Cerebral cortex

value: neurons

value: Saline self-administration

tag: sample type

value: Input

value: Total RNA


title: Cerebral cortex, Cocaine self-administration IP Rep3

description: 454_S100a10_TRAP_ES691_Cocaine_IP_Rep3_ATGTCA_L005

value: Cocaine self-administration

value: Immunopurified (IP)

value: Ribosomal-bound RNA


title: PαS, 2 weeks, replicate 1

value: PDGFR-alpha+ Sca-1+ mesenchymal cells

value: bone marrow

tag: age


title: Cerebral cortex, Cocaine self-administration IP Rep1

description: 452_S100a10_TRAP_ES691_Cocaine_IP_Rep1_ACAGTG_L005


title: shScr_2: SKOV3 cells passaged 30x, with scrambled shRNA. Biological replicate 2

description:
CEL file AT: a521191-00-977099-013118-4289464-99654.CEL
CEL file GC: a521191-00-977116-013118-4289464-07210.CEL

source_name: SKOV3 shScr_2


title: SEC, 2 weeks, replicate 2

value: sinusoidal endothelial cells

tag: strain


title: Cerebral cortex, Saline self-administration IP Rep3

description: 450_S100a10_TRAP_ES691_Saline_IP_Rep3_ATGTCA_L004


title: exosome in hypoxia condition 1

value: exosome


title: AEC, 2 weeks, replicate 1

value: arterial endothelial cells

tag: agent


title: Evi1 overexpressed 4

city: Singapore

first: Arsen

middle: O

last: Batagov

address: 30 Biopolis St, Matrix, 07-1

country: Singapore

institute: Bioinformatics Institute

hyb_protocol: Affymetrix 900454

scan_protocol: Affymetrix 3000 7G scanner, GCOS, Expression Console 1.1

data_processing:
Expression Console 1.1 and R (Bioconductor) software, RMA normalization, PAM and EDGE algorithms
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: SKOV3 ovarian cancer cell line

label_protocol: Affymetrix 0807009

growth_protocol: SKOV3 cells were grown in RPMI with 10% FBS, maintained at 37C, 5%CO2

extract_protocol: TRIzol RNA extraction, SuperScript II reverse transcription

treatment_protocol: the cells were transfected using Fugene 6 (Roche)

tag: gender

value: female

tag: cell line

value: Evi1 overexpressed


title: CARc, 2 weeks, replicate 1

value: CXCL12-abundant reticular cells

value: 2 weeks

value: no treatment


title: shScr_1: SKOV3 cells passaged 30x, with scrambled shRNA. Biological replicate 1

description:
CEL file AT: a521191-00-977109-013118-4289464-75647.CEL
CEL file GC: a521191-00-977106-013118-4289464-75312.CEL

source_name: SKOV3 shScr_1

value: control (shScr)


title: Evi1 overexpressed 3


title: shLC3_4: SKOV3 cells passaged 30x, with shRNA to LC3B. Biological replicate 4

description:
CEL file AT: a521191-00-977111-013118-4289464-06110.CEL
CEL file GC: a521191-00-977098-013118-4289464-99503.CEL

source_name: SKOV3 shLC3_4

value: shRNA to LC3B


title: Evi1 overexpressed 1


title: shBECN1_2: SKOV3 cells passaged 30x, with shRNA to BECN1. Biological replicate 2

description:
CEL file AT: a521191-00-977104-013118-4289464-73702.CEL
CEL file GC: a521191-00-977117-013118-4289464-07271.CEL

source_name: SKOV3 shBECN1_2

value: shRNA to BECN1


title: Control 4

value: control


title: Cerebral cortex, Saline self-administration IP Rep1

description: 448_S100a10_TRAP_ES691_Saline_IP_Rep1_ACAGTG_L004

value: Cerebral cortex

value: neurons

value: Saline self-administration


title: Whole striatum, Cocaine self-administration Rep5

description: 909_Drd2_TRAP_CP101_Cocaine_IP_Rep5_ATGTCA_L004

source_name: Whole striatum

extract_protocol:
The whole striatum was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

treatment_protocol: Saline self-administration. Cocaine self-administration.

value: Drd2-TRAP CP101

value: Whole striatum

value: medium spiny neurons

value: Cocaine self-administration

value: Immunopurified (IP)

value: Ribosomal-bound RNA


title: SEC, 2 weeks, replicate 1

value: sinusoidal endothelial cells

value: bone marrow


title: Whole striatum, Cocaine self-administration unbound

description: 911_Drd2_TRAP_CP101_Cocaine_unbound_GCCAAT_L001

value: Unbound

value: Unbound RNA


title: Whole striatum, Saline self-administration input

description: 910_Drd2_TRAP_CP101_Saline_input_ACAGTG_L001

value: Input

value: Total RNA


title: Control 3

value: female


title: shLC3_3: SKOV3 cells passaged 30x, with shRNA to LC3B. Biological replicate 3

description:
CEL file AT: a521191-00-977103-013118-4289464-73547.CEL
CEL file GC: a521191-00-977100-013118-4289464-99819.CEL

source_name: SKOV3 shLC3_3

value: shRNA to LC3B


title: Whole striatum, Cocaine self-administration Rep4

description: 908_Drd2_TRAP_CP101_Cocaine_IP_Rep4_GCCAAT_L004


title: TCF3KO_HPC7_Capture-C_Rep1

source_name: hematopoietic stem and progenitor cells

tag: strain/cell type

value: ES-derived hematopoietic stem and progenitor cells

tag: passages


title: REGINA_220316_rep2

city: Villenave d'Ornon

first: Benedicte

last: Wenden

address: 71 avenue Edouard Bourlaux

country: France

institute: INRA

data_processing:
The quality of reads was assessed using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/) and possible adaptor contaminations and low quality trailing sequences were removed using Trimmomatic (Bolger et al., 2014).
Trimmed reads were mapped to the peach (Prunus persica (L) Batsch) reference genome v.2 (Verde et al., 2017) using Tophat (Trapnell et al., 2009).
Possible optical duplicates were removed using Picard tools (https://github.com/broadinstitute/picard).
For each gene, raw reads and TPM (Transcripts Per Million) numbers were calculated (Wagner, 2003).
Genome_build: Prunus persica (L) Batsch reference genome v.2 (Verde et al., 2017)
Supplementary_files_format_and_content: Processed data files are txt files that contains the tracking_id and gene_id columns that define the gene name corresponding to the peach locus, locus information (chromosome, position), and the FPKM (fragments per million reads), TPM (transcripts per million reads) and the Raw count of reads per locus.

organism: Prunus avium

source_name: REGINA_220316_sweet cherry flower buds

growth_protocol: Branches and flower buds were collected from four different sweet cherry cultivars (Prunus avium L.) with contrasted flowering date: ‘Cristobalina’, ‘Garnet’ and ‘Regina’, which display very early, early and late flowering dates, respectively. The trees were grown in an orchard located at the Fruit Experimental Unit of INRA in the South West of France (44° 19′ 56′′ N, 0° 24′ 47′′ E), under the same agricultural practices. Ten or eleven dates spanning the entire period from flower bud organogenesis (July 2015) to bud break (March 2016) were chosen for RNA sequencing. For each date, flower buds were sampled on-site from different trees, each tree corresponding to a biological replicate. Upon harvesting, buds were flash frozen in liquid nitrogen and stored at -80°C prior to performing RNA-seq.

extract_protocol:
Total RNA was extracted from 50-60 mg of frozen and pulverised flower buds using RNeasy Plant Mini kit (Qiagen) with minor modification: 1.5% PVP-40 was added in the RLT buffer. RNA quality was evaluated using Tapestation 4200 (Agilent Genomics).
Library preparation was performed on 1 μg of high quality RNA (RNA integrity number equivalent superior or equivalent to 8.5) using the TruSeq Stranded mRNA Library Prep Kit High Throughput (Illumina cat. no. RS-122-2103) for ‘Cristobalina’, ‘Garnet’ and ‘Regina’ cultivars. DNA quality from libraries was evaluated using Tapestation 4200. The libraries were sequenced on a NextSeq500, at the Sainsbury Laboratory Cambridge University (SLCU), using paired-end sequencing of 75 bp in length.

tag: cultivar

value: REGINA

value: flower buds

tag: time point

tag: lane


title: Control 1

tag: treatment

value: control


title: shLC3_2: SKOV3 cells passaged 30x, with shRNA to LC3B. Biological replicate 2

description:
CEL file AT: a521191-00-977109-013118-4289464-75702.CEL
CEL file GC: a521191-00-977113-013118-4289464-06309.CEL

source_name: SKOV3 shLC3_2


title: PαS, 2 months, PIC, replicate 3

source_name: stromal cell types isolated from bone marrow

value: PDGFR-alpha+ Sca-1+ mesenchymal cells

tag: tissue

value: 2 months

value: poly I:C treated


title: shBECN1_3: SKOV3 cells passaged 30x, with shRNA to BECN1. Biological replicate 3

description:
CEL file AT: a521191-00-977098-013118-4289464-99577.CEL
CEL file GC: a521191-00-977098-013118-4289464-99575.CEL

source_name: SKOV3 shBECN1_3

value: shRNA to BECN1


title: Control 2


title: Evi1 overexpressed 2

value: Evi1 overexpressed


title: CARc, 2 months, PIC, replicate 4

value: CXCL12-abundant reticular cells


title: TCF3KO_HPC7_Capture-C_Rep2


title: PαS, 2 months, PIC, replicate 4

value: bone marrow


title: SEC, 2 months, PIC, replicate 4

value: sinusoidal endothelial cells


title: WT_HPC7_Capture-C_Rep2


title: Whole striatum, Cocaine self-administration Rep3

description: 907_Drd2_TRAP_CP101_Cocaine_IP_Rep3_ACAGTG_L004

value: Drd2-TRAP CP101

value: Whole striatum

value: medium spiny neurons

value: Cocaine self-administration

value: Immunopurified (IP)

tag: fraction

value: Ribosomal-bound RNA


title: WT_HPC7_Capture-C_Rep1

value: ES-derived hematopoietic stem and progenitor cells


title: Whole striatum, Cocaine self-administration Rep2

description: 906_Drd2_TRAP_CP101_Cocaine_IP_Rep2_ATGTCA_L006


title: Whole striatum, Saline self-administration Rep4

description: 904_Drd2_TRAP_CP101_Saline_IP_Rep4_ACAGTG_L006

value: Saline self-administration


title: FLHSC_Capture-C_FirstBatch_Rep2

source_name: Embryonic day 14.5 fetal liver hematopoietic stem cells

value: Fetal liver

value: Embryonic day 14.5


title: Whole striatum, Cocaine self-administration Rep1

description: 905_Drd2_TRAP_CP101_Cocaine_IP_Rep1_GCCAAT_L006


title: shLC3_1: SKOV3 cells passaged 30x, with shRNA to LC3B. Biological replicate 1

description:
CEL file AT: a521191-00-977106-013118-4289464-75295.CEL
CEL file GC: a521191-00-977099-013118-4289464-99688.CEL

source_name: SKOV3 shLC3_1

tag: genotype

value: shRNA to LC3B


title: AEC, 2 months, PIC, replicate 3

tag: cell type

value: arterial endothelial cells

value: 2 months

value: poly I:C treated


title: GARNET_220316_rep2

source_name: GARNET_220316_sweet cherry flower buds

value: GARNET

value: flower buds


title: CARc, 2 months, PIC, replicate 3

value: CXCL12-abundant reticular cells

value: bone marrow


title: SEC, 2 months, PIC, replicate 3

value: sinusoidal endothelial cells


title: GARNET_220316_rep1


title: GARNET_220316_rep3


title: REGINA_220316_rep1

value: REGINA


title: BMHSC_Capture-C_FirstBatch_Rep2

source_name: 6-8 week-old bone marrow hematopoietic stem cells

value: Adult bone marrow

value: 6-8 week-old


title: Whole striatum, Saline self-administration Rep1

description: 901_Drd2_TRAP_CP101_Saline_IP_Rep1_ACAGTG_L007

tag: animal line

value: Drd2-TRAP CP101

value: Whole striatum

value: medium spiny neurons

value: Immunopurified (IP)

value: Ribosomal-bound RNA


title: BMHSC_Capture-C_FirstBatch_Rep1


title: Whole striatum, Saline self-administration Rep2

description: 902_Drd2_TRAP_CP101_Saline_IP_Rep2_GCCAAT_L007

value: Saline self-administration

tag: sample type


title: PαS, 2 months, PIC, replicate 2

value: PDGFR-alpha+ Sca-1+ mesenchymal cells

tag: age


title: REGINA_080316_rep1

source_name: REGINA_080316_sweet cherry flower buds


title: REGINA_080316_rep2


title: FLHSC_Capture-C_FirstBatch_Rep1

value: Fetal liver

value: Embryonic day 14.5


title: CARc, 2 months, PIC, replicate 2

tag: strain

value: 2 months

value: poly I:C treated


title: REGINA_230216_rep2

source_name: REGINA_230216_sweet cherry flower buds

value: flower buds

value: February 23, 2016


title: BMHSC_K4me3_Rep1

data_processing:
Sequencing reads were mapped to the mouse genome (mm9) using Bowtie2 (v2.2.2) with default parameter setting
Uniquely mapped reads from both ChIPed and input DNA were used to compute a normalized signal for each 200 bp bin across the genome
ChIP-Seq peaks were called by MACS using default parameter setting
Genome_build: mm9

extract_protocol:
E14.5 fetal liver and adult bone marrow were dissected and HSCs were purified using cell surface marker: Lin-Sca1+cKit+CD135-. ChIP reactions were performed using 50,000 FACS-sorted cells. Iped and Input DNA were purified with MinElute PCR Purification Kit.
Libraries were constructed using Rubicom ThruPLEX DNA-Seq Kit. Libraries were size-selected at 100-700 bp by AMPure XP beads. Libraries were quantified with KAPA qPCR and bioanalyzer prior to single-end sequencing.

tag: chip antibodies

value: H3K4me3 (07-473, Millipore)


title: SEC, 2 months, PIC, replicate 2

value: sinusoidal endothelial cells

value: bone marrow

tag: agent


title: REGINA_230216_rep1

value: REGINA


title: Input [73]

source_name: Input_whole striatum

tag: strain background

value: FVB/N-Swiss Webster x C57BL/6 (mice used to generate the submitted data were at least 9 generations C57BL/6)

tag: genotype/variation

value: Drd1-TRAP CP73

value: Input

value: Input total RNA


title: BMHSC_K4me1_Rep2

value: Adult bone marrow

value: 6-8 week-old

value: H3K4me1 (ab8895, Abcam)


title: Cocaine self-administration Rep3 [71]

description: 71_Drd1_TRAP_CP73_Cocaine_IP_Rep3_ATGTCA_L001

value: Cocaine self-administration

value: Whole striatum

value: Immunopurified (IP); Ribosomal-bound RNA


title: PαS, 2 months, PIC, replicate 1

value: PDGFR-alpha+ Sca-1+ mesenchymal cells

value: 2 months

value: poly I:C treated


title: AEC, 2 months, PIC, replicate 2

value: arterial endothelial cells


title: Yoked control Rep3 [72]

description: 72_Drd1_TRAP_CP73_Yoked_IP_Rep3_ATGTCA_L002

source_name: Yoked control_whole striatum

value: Yoked control


title: AEC, 2 months, PIC, replicate 1

value: bone marrow


title: BMHSC_K4me1_Rep1


title: Saline self-administration Rep3 [70]

description: 70_Drd1_TRAP_CP73_Saline_IP_Rep3_ATGTCA_L003

value: Saline self-administration


title: Yoked control Rep2 [69]

description: 69_Drd1_TRAP_CP73_Yoked_IP_Rep2_GCCAAT_L002

value: FVB/N-Swiss Webster x C57BL/6 (mice used to generate the submitted data were at least 9 generations C57BL/6)


title: CARc, 2 months, PIC, replicate 1

value: CXCL12-abundant reticular cells


title: GARNET_230216_rep1

source_name: GARNET_230216_sweet cherry flower buds

value: GARNET

value: flower buds

value: February 23, 2016


title: GARNET_230216_rep2


title: Cocaine self-administration Rep2 [68]

description: 68_Drd1_TRAP_CP73_Cocaine_IP_Rep2_GCCAAT_L001

value: Drd1-TRAP CP73


title: Saline self-administration Rep2 [67]

description: 67_Drd1_TRAP_CP73_Saline_IP_Rep2_GCCAAT_L003


title: BMHSC_K27ac_Rep2

value: Adult bone marrow

value: 6-8 week-old

value: H3K27ac (ab4729, Abcam)


title: BMHSC_K27me3_Rep2

value: H3K27me3 (07-449, Millipore)


title: PαS, 2 months, LPS, replicate 4

value: PDGFR-alpha+ Sca-1+ mesenchymal cells

value: LPS treated


title: CRISTOBALINA_230216_rep3

description: 153B_CRISTOBALINA_230216_rep3_S3_N-40675736

source_name: CRISTOBALINA_230216_sweet cherry flower buds

value: CRISTOBALINA


title: Yoked control Rep1 [66]

description: 66_Drd1_TRAP_CP73_Yoked_IP_Rep1_ACAGTG_L002

value: Whole striatum

value: Immunopurified (IP); Ribosomal-bound RNA


title: BMHSC_K27ac_Rep1


title: BMHSC_K27me3_Rep1


title: AEC, 2 months, PIC, replicate 4

value: arterial endothelial cells

value: bone marrow

value: 2 months

value: poly I:C treated


title: BMHSC_K4me3_Rep2

value: H3K4me3 (07-473, Millipore)


title: SEC, 2 months, PIC, replicate 1

value: sinusoidal endothelial cells


title: Cocaine self-administration Rep1 [65]

description: 65_Drd1_TRAP_CP73_Cocaine_IP_Rep1_ACAGTG_L001

value: FVB/N-Swiss Webster x C57BL/6 (mice used to generate the submitted data were at least 9 generations C57BL/6)

value: Cocaine self-administration


title: CRISTOBALINA_230216_rep1

description: 152C_CRISTOBALINA_230216_rep1_S1_N-40672716

value: flower buds

value: February 23, 2016


title: CARc, 2 months, LPS, replicate 4

value: CXCL12-abundant reticular cells


title: GARNET_230216_rep3

value: GARNET


title: Saline self-administration Rep1 [64]

description: 64_Drd1_TRAP_CP73_Saline_IP_Rep1_ACAGTG_L003

value: Drd1-TRAP CP73

value: Saline self-administration


title: Cerebral cortex, Saline self-administration IP Rep2

description: 449_S100a10_TRAP_ES691_Saline_IP_Rep2_GCCAAT_L004

source_name: Cerebral cortex

value: Cerebral cortex

value: neurons

value: Immunopurified (IP)

value: Ribosomal-bound RNA


title: REGINA_260116_rep2

source_name: REGINA_260116_sweet cherry flower buds

value: REGINA

value: January 26, 2016


title: AEC, 2 months, LPS, replicate 4

value: arterial endothelial cells

value: bone marrow

value: 2 months

value: LPS treated


title: REGINA_260116_rep1


title: SKOV3 DNA rep1

hyb_protocol: Hybridization with to SNP6.0 GeneChips (Affymetrix) for 16 hours at 50oC with rotation at 60rpm. SAPE stain solution (Molecular Probes) and antibody solution (Vector Labs) were prepared fresh prior to washing and staining the arrays. Arrays were washed in an Affymetrix fluidics station using the GenomeWide SNP6_450 protocol.

scan_protocol: Affymetrix 3000 7G scanner, GCOS, Genotyping Console 2.1 software

data_processing: Genotyping Console 2.1, R (Aroma Affymetrix), RMA normalization (R, Bioconductor, Crlmm)

source_name: SKOV3 ovarian cancer cell line

label_protocol: Affymetrix 4064888

extract_protocol: Genomic DNA was extracted using Puregene Cell and Tissue Kit (Gentra). For each of the DNA samples, 500 ng of DNA was digested with Sty 1 and Nsp 1 (New England Biolabs) restriction enzymes in separate reactions

treatment_protocol: Not applicable

tag: gender

value: female

tag: cell line


title: FLHSC_K4me3_Rep2

value: Fetal liver

value: Embryonic day 14.5

value: H3K4me3 (07-473, Millipore)


title: SKOV3 DNA rep4


title: CRISTOBALINA_230216_rep2

description: 153A_CRISTOBALINA_230216_rep2_S2_N-40660955

tag: cultivar

value: CRISTOBALINA

value: flower buds

tag: time point

value: February 23, 2016


title: PαS, 2 months, LPS, replicate 3

value: PDGFR-alpha+ Sca-1+ mesenchymal cells


title: SEC, 2 months, LPS, replicate 4

value: sinusoidal endothelial cells


title: BMHSC_Input_Rep1

value: Adult bone marrow

value: 6-8 week-old


title: GARNET_260116_rep3

source_name: GARNET_260116_sweet cherry flower buds

value: GARNET

tag: lane


title: Cocaine self-administration, Unbound [912]

description: 912_Glt25d2_TRAP_DU9_Cocaine_Unbound_ATGTCA_L001

data_processing:
library strategy: Translating ribosome affinity purification (TRAP)-seq
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using default settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of counts

value: Glt25d2-TRAP DU9

tag: treatment

value: cocaine self-administration

tag: tissue

value: Cerebral cortex

value: Unbound

tag: molecule subtype

value: Unbound RNA


title: CARc, 2 months, LPS, replicate 3

tag: cell type

value: CXCL12-abundant reticular cells

value: bone marrow

value: 2 months

value: LPS treated


title: FLHSC_K4me1_Rep2

value: Fetal liver

value: Embryonic day 14.5

value: H3K4me1 (ab8895, Abcam)


title: GARNET_260116_rep2

value: flower buds

value: January 26, 2016


title: FLHSC_K4me1_Rep1


title: Yoked control Rep3 [447]

description: 447_Glt25d2_TRAP_DU9_Yoked_IP_Rep3_GTGAAA_L003

source_name: Yoked control_cerebral cortex

value: yoked control

value: Immunopurified (IP)

value: Ribosomal-bound RNA


title: SKOV3 DNA rep2

value: female


title: CRISTOBALINA_260116_rep3

description: 130C_CRISTOBALINA_260116_rep3_S5_N-40652767

source_name: CRISTOBALINA_260116_sweet cherry flower buds

value: CRISTOBALINA


title: Affymetrix reference genomic DNA 103

source_name: Control

value: male

value: Affymetrix reference genomic DNA 103


title: FLHSC_K27me3_Rep2

source_name: Embryonic day 14.5 fetal liver hematopoietic stem cells

value: H3K27me3 (07-449, Millipore)


title: PαS, 2 months, LPS, replicate 2

source_name: stromal cell types isolated from bone marrow

value: PDGFR-alpha+ Sca-1+ mesenchymal cells


title: Cocaine self-administration Rep2 [443]

description: 443_Glt25d2_TRAP_DU9_Cocaine_IP_Rep2_CAGATC_L002

value: Glt25d2-TRAP DU9

value: cocaine self-administration

value: Cerebral cortex


title: CRISTOBALINA_260116_rep2

description: 130B_CRISTOBALINA_260116_rep2_S4_N-40644826


title: Yoked control Rep1 [445]

description: 445_Glt25d2_TRAP_DU9_Yoked_IP_Rep1_CGATGT_L003


title: Yoked control Rep2 [446]

description: 446_Glt25d2_TRAP_DU9_Yoked_IP_Rep2_CAGATC_L003


title: FLHSC_K27ac_Rep2

value: Fetal liver

value: H3K27ac (ab4729, Abcam)


title: BMHSC_Input_Rep2

value: Adult bone marrow

value: 6-8 week-old


title: CARc, 2 months, LPS, replicate 2

value: CXCL12-abundant reticular cells

value: bone marrow

value: 2 months

value: LPS treated


title: Saline self-administration Input [441]

description: 441_Glt25d2_TRAP_DU9_Saline_INPUT_GTGAAA_L007

source_name: Saline self-administration Input

value: saline self-administration

value: Input

value: Total RNA


title: GARNET_130116_rep3

source_name: GARNET_130116_sweet cherry flower buds

value: GARNET

value: flower buds

value: January 13, 2016


title: FLHSC_K27ac_Rep1

value: Embryonic day 14.5


title: SEC, 2 months, LPS, replicate 3

value: sinusoidal endothelial cells


title: GARNET_130116_rep2


title: AEC, 2 months, LPS, replicate 3

value: arterial endothelial cells


title: Cocaine self-administration Rep3 [444]

description: 444_Glt25d2_TRAP_DU9_Cocaine_IP_Rep3_GTGAAA_L002

value: Glt25d2-TRAP DU9

value: cocaine self-administration

value: Cerebral cortex

value: Immunopurified (IP)

value: Ribosomal-bound RNA


title: AEC, 2 months, LPS, replicate 2

value: bone marrow


title: FLHSC_K4me3_Rep1

value: Fetal liver

value: H3K4me3 (07-473, Millipore)


title: Cocaine self-administration Rep1 [442]

description: 442_Glt25d2_TRAP_DU9_Cocaine_IP_Rep1_CGATGT_L002


title: FLHSC_K27me3_Rep1

value: H3K27me3 (07-449, Millipore)


title: REGINA_291215_rep2

source_name: REGINA_291215_sweet cherry flower buds

value: REGINA

value: December 29, 2015


title: Saline self-administration Rep3 [440]

description: 440_Glt25d2_TRAP_DU9_Saline_IP_Rep3_GTGAAA_L006

value: saline self-administration


title: BMHSC_ATAC_Rep2

data_processing:
Ilumina Nextera transposase adaptor sequences were trimmed  from raw reads using trim galore version 0.41 with default parameter setting.
Trimmed reads were mapped to the mouse genome (mm9) using Bowtie2 (v2.2.2).
ATAC-Seq peaks were called by MACS using default parameter setting
Genome_build: mm9

source_name: 6-8 week-old bone marrow hematopoietic stem cells

extract_protocol:
E14.5 fetal liver and adult bone marrow were dissected and HSCs were purified using cell surface marker: Lin-Sca1+cKit+CD135-. 50,000 FACS-sorted cells were lyzed and treated with Nextera Tn5 transposase.
Libraries were amplified using 1x NEBNext PCR master mix and custom Nextera PCR primers. Libraries were size-selected at 100-700 bp by gel extraction. Libraries were quantified with KAPA qPCR and bioanalyzer prior to pair-end sequencing.

value: Adult bone marrow

value: 6-8 week-old


title: Saline self-administration Rep1 [438]

description: 438_Glt25d2_TRAP_DU9_Saline_IP_Rep1_CGATGT_L006


title: FLHSC_Input_Rep2

value: Embryonic day 14.5


title: PαS, 2 months, LPS, replicate 1

value: PDGFR-alpha+ Sca-1+ mesenchymal cells

value: 2 months

value: LPS treated


title: REGINA_291215_rep1

value: flower buds


title: SEC, 2 months, LPS, replicate 1

value: sinusoidal endothelial cells


title: GARNET_130116_rep1

value: GARNET

value: January 13, 2016


title: Saline self-administration Rep2 [439]

description: 439_Glt25d2_TRAP_DU9_Saline_IP_Rep2_CAGATC_L006

value: Glt25d2-TRAP DU9

value: Cerebral cortex

value: Immunopurified (IP)

value: Ribosomal-bound RNA


title: FLHSC_Input_Rep1

value: Fetal liver


title: SEC, 2 months, LPS, replicate 2

value: bone marrow


title: FLHSC_ATAC_Rep1


title: AEC, 2 months, LPS, replicate 1

value: arterial endothelial cells


title: CARc, 2 months, replicate 4

value: CXCL12-abundant reticular cells

value: no treatment


title: BMHSC_ATAC_Rep1

value: Adult bone marrow

value: 6-8 week-old


title: CARc, 2 months, LPS, replicate 1

value: 2 months


title: CRISTOBALINA_291215_rep3

description: 108A_CRISTOBALINA_291215_rep3_S9_N-40637645

source_name: CRISTOBALINA_291215_sweet cherry flower buds

value: CRISTOBALINA

value: December 29, 2015


title: CRISTOBALINA_260116_rep1

description: 130A_CRISTOBALINA_260116_rep1_S3_N-40642116

value: flower buds

value: January 26, 2016


title: Cocaine self-administration Rep3

description:
Ribosomal-bound RNA
600_Chat_TRAP_DW167_Cocaine3_GTGAAA_L004

source_name: Whole Striatum

value: Cocaine self-administration

tag: animal line

value: Chat-TRAP DW167

value: Whole Striatum


title: FLHSC_ATAC_Rep2

value: Embryonic day 14.5


title: PαS, 2 months, replicate 4

value: PDGFR-alpha+ Sca-1+ mesenchymal cells


title: CRISTOBALINA_291215_rep1

description: 107B_CRISTOBALINA_291215_rep1_S7_N-40637642


title: Yoked control Rep3

description:
Ribosomal-bound RNA
603_Chat_TRAP_DW167_Yoked3_GTGAAA_L004

value: Yoked control

tag: sample type

value: Immunopurified (IP)


title: GARNET_291215_rep1

source_name: GARNET_291215_sweet cherry flower buds

value: GARNET


title: Yoked control Rep2

description:
Ribosomal-bound RNA
602_Chat_TRAP_DW167_Yoked2_L004


title: SKOV3 DNA rep3

value: female


title: CRISTOBALINA_151215_rep3

description: 96C_CRISTOBALINA_151215_rep3_S3_N-40638646

source_name: CRISTOBALINA_151215_sweet cherry flower buds

value: December 15, 2015


title: GARNET_291215_rep3


title: AEC, 2 months, replicate 4

value: arterial endothelial cells

value: bone marrow

tag: age

value: no treatment


title: Saline self-administration Input

description:
Total RNA
604_Chat_TRAP_DW167_Input_GTGAAA_L005

value: Saline self-administration

value: Input


title: Yoked control Rep1

description:
Ribosomal-bound RNA
601_Chat_TRAP_DW167_Yoked1_CGATGT_L004


title: SEC, 2 months, replicate 4

value: sinusoidal endothelial cells

tag: strain

value: 2 months


title: Saline self-administration Rep3

description:
Ribosomal-bound RNA
597_Chat_TRAP_DW167_Saline3_GTGAAA_L003


title: CARc, 2 months, replicate 3

value: CXCL12-abundant reticular cells


title: CRISTOBALINA_151215_rep2

description: 96B_CRISTOBALINA_151215_rep2_S2_N-40638634

value: CRISTOBALINA

value: flower buds


title: AEC, 2 months, replicate 3


title: SEC, 2 months, replicate 3


title: CRISTOBALINA_291215_rep2

description: 107C_CRISTOBALINA_291215_rep2_S8_N-40630837

value: December 29, 2015


title: CRISTOBALINA_151215_rep1

description: 96A_CRISTOBALINA_151215_rep1_S1_N-40629852


title: PαS, 2 months, replicate 2

value: PDGFR-alpha+ Sca-1+ mesenchymal cells


title: Saline self-administration Rep2

description:
Ribosomal-bound RNA
596_Chat_TRAP_DW167_Saline2_CAGATC_L003

value: Chat-TRAP DW167

value: Whole Striatum


title: Cocaine self-administration Rep2

description:
Ribosomal-bound RNA
599_Chat_TRAP_DW167_Cocaine2_CAGATC_L004

value: Cocaine self-administration

value: Immunopurified (IP)


title: 2D HUASMC culture rep 3

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

description: human umbilical artery smooth muscle cells - 2D

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of Mouse MoGene-2_0-type from Affymetrix. A Custom CDF Version 21 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: spheroid 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: human umbilical artery smooth muscle cells were cultured in DMEM +15% FCS and propagated 1:3

extract_protocol: RNA was extracted from HUASMCs by utilizing the Qiagen mini RNA extraction kit  following man. instr.

treatment_protocol: HUASMCs were cultured for 48h before RNA extraction

tag: phenotype

value: Control 2D


title: 3D HUASMC aggregates rep 3

description: human umbilical artery smooth muscle cells - 3D

source_name: layer 3


title: Cocaine self-administration Rep1

description:
Ribosomal-bound RNA
598_Chat_TRAP_DW167_Cocaine1_CGATGT_L004


title: REGINA_011215_rep1

source_name: REGINA_011215_sweet cherry flower buds

value: REGINA

value: December 1, 2015


title: AEC, 2 months, replicate 2

value: arterial endothelial cells

value: bone marrow

tag: agent

value: no treatment


title: LPS + BMS 3

city: Bonn

first: Eicke

last: Latz

state: NRW

address: Sigmund-Freud-Straße 25

department: Institute of Innate Immunity

institute: University Hospital Bonn

description:
normalized primary expression data
DE87NGSUKBR102688

data_processing:
Alignment against GRCm38 was performed with STAR Aligner 2.5.2b. FeatureCounts v1.5.1 was used for quantification of gene expression using the Ensembl annotation GRCm38.88 as reference. All parameters were used as recommended by the Lexogen‘s QuantSeq 3‘ mRNA-Seq Kit and integrated Data Analysis Pipeline platform. Summaries of all steps were aggregated with multiQC and checked for outliers. All samples were sufficiently covered with at least 8 M reads and included in the further analyses.
Gene expression was assessed by a limma/edgeR workflow. First uninformative transcripts were removed from analysis keeping only those with an expression above 7 counts per million in at least 4 samples. The remaining read counts, covering 12,204 genes, were log2 transformed for explorative analysis. For expression analysis, the count values were TMM normalized using edgeR and quantile normalized using the voom function of the limma package. A limma lmFit linear model was fitted to each gene.
Genome_build: mm10

source_name: bone marrow

growth_protocol: murine bone marrow was extracted and differentiation into macrophages for 6 days using 20% vol/vol L929 cell conditioned supernatant

extract_protocol:
cells wer lyzed in TRIZOL and RNA was extracted using miRNeasy Kits (Qiagen) according to instructions
Library generation for 3´ mRNA sequencing was conducted according to manufacturer´s guidelines (Quant Seq 3’ mRNA-Seq Library Prep Kit FWD for Illumina; Lexogen). Briefly, 100 ng total RNA were reversly transcripted by oligo dT priming (first strand) and random priming (second strand). After a magnetic bead-based purification step, the libraries were amplified using 16 PCR cycles.

value: bone marrow derived macrophages

value: 4 h 10 ng/ml LPS after 1 h pretreatment with 50µM BMS 303141


title: Saline self-administration Rep1

description:
Ribosomal-bound RNA
595_Chat_TRAP_DW167_Saline1_CGATGT_L003

data_processing:
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using default settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of counts

value: Saline self-administration


title: GARNET_011215_rep3

source_name: GARNET_011215_sweet cherry flower buds

value: GARNET


title: SEC, 2 months, replicate 2

value: sinusoidal endothelial cells

value: 2 months


title: 3D HUASMC aggregates rep 2

source_name: spheroid 3


title: 3D HUASMC aggregates rep 1

source_name: layer 2


title: 2D HUASMC culture rep 2

source_name: layer 1


title: LPS + BMS 1

description:
normalized primary expression data
DE44NGSUKBR102686


title: LPS + BMS 2

description:
normalized primary expression data
DE17NGSUKBR102687


title: CARc, 2 months, replicate 2

source_name: stromal cell types isolated from bone marrow

value: CXCL12-abundant reticular cells


title: PαS, 2 months, replicate 1

value: PDGFR-alpha+ Sca-1+ mesenchymal cells


title: 2D HUASMC culture rep 1

source_name: spheroid 1


title: GARNET_011215_rep2

value: flower buds


title: LPS 3

description:
normalized primary expression data
DE39NGSUKBR102679

value: 4 h 10ng/ml LPS


title: 3D HUASMC aggregates + LY2109761-1

description: human umbilical artery smooth muscle cells - 3D + LY2109761

source_name: TGF   R 2

treatment_protocol: HUASMCs were cultured/treated for 48h before RNA extraction


title: AEC, 2 months, replicate 1


title: GARNET_011215_rep1


title: GARNET_260116_rep1

source_name: GARNET_260116_sweet cherry flower buds

value: January 26, 2016


title: CRISTOBALINA_011215_rep3

description: 85B_CRISTOBALINA_011215_rep3_S13_N-40636702

source_name: CRISTOBALINA_011215_sweet cherry flower buds

value: CRISTOBALINA


title: 3D HUASMC aggregates + LY2109761-3

source_name: TGF   R 3


title: LPS 1

description:
normalized primary expression data
DE93NGSUKBR102677


title: REGINA_011215_rep2

value: REGINA


title: CRISTOBALINA_011215_rep2

description: 85A_CRISTOBALINA_011215_rep2_S12_N-40632838

value: December 1, 2015


title: UT 3

description:
normalized primary expression data
DE07NGSUKBR102673

value: untreated control


title: LPS 2

description:
normalized primary expression data
DE66NGSUKBR102678


title: SEC, 2 months, replicate 1

value: bone marrow


title: CARc, 2 months, replicate 1

value: no treatment


title: 3D HUASMC aggregates-2

source_name: TGF   R 1

value: Control 3D


title: 3D HUASMC aggregates-3

source_name: Ctrl 2


title: UT 2

description:
normalized primary expression data
DE34NGSUKBR102672

value: bone marrow derived macrophages


title: REGINA_031115_rep2

source_name: REGINA_031115_sweet cherry flower buds

value: November 3, 2015


title: REGINA_031115_rep1


title: CARc, 2 years, replicate 4

value: 2 years


title: GARNET_031115_rep3

source_name: GARNET_031115_sweet cherry flower buds

value: GARNET


title: BMHSC_RNA-Seq_Rep2

data_processing:
Sequencing reads were aligned to the mouse genome ( mm9 ) using Tophat. Only uniquely mapped reads with fewer than 2 mismatches were used for downstream analyses.
The Ensembl database (release 66 ) was used as the source of gene annotation. FPKM values were calculated by cufflinks. The featureCounts function of the Subread package was used to extract both gene-level and transcript-level read counts. Differential expression analysis was performed using the edgeR algorithm at gene-level and Ebseq at transcript-level.
Genome_build: mm9

source_name: 6-8 week-old bone marrow hematopoietic stem cells

extract_protocol:
E14.5 fetal liver and adult bone marrow were dissected and HSCs were sorted into TRIzol-LS and total RNA was purified using RNeasy micro kit. Total RNA was quantified with RNA HS Kit for Qubit fluorometer and analyzed for integrity using RNA 6000 Pico Kit for 2100 Bioanalyzer (Agilent). mRNA was purified from total RNA using NEBNext Poly(A) mRNA magnetic isolation odule ( E7490 NEB). PolyA - selected mRNA was ragented to  an  averag size of 300  nt, reverse transcribed to gnerate double -.ngth of 75 nt.
Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina according to manufacturer's instructions including the optional double size selection procedure using Agencourt AMPure XP beads. Prepared libraries were quantified with dsDNA HS Kit for Qubit and the size distribution was assessed using High Sensitivity DNA Kit for Bioanalyzer. Libraries were sequenced on Illumina HiSeq2500 in paired-end mode with the read length of 100 nt.

value: Adult bone marrow

value: 6-8 week-old


title: PαS, 2 years, replicate 4

extract_protocol:
Enzymatic digestion of bone marrow tissues, fluorescent activated cell sorting (FACS) directly into RLT lysis buffer (Qiagen), RNA extraction using RNeasy Plus Micro Kit (Qiagen)
Clontech SMRTer Stranded total RNA-Seq Kit-Pico Input Mammalian Total RNA

value: PDGFR-alpha+ Sca-1+ mesenchymal cells


title: 6hr reperfused, bio rep 3

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

hyb_protocol: Hybridization was perfromed at 45 degress C overnight with 60 rpm to RTA-1_0 arrays.

scan_protocol: Visualization utilized an Affy 3000 7G scanner

data_processing: Affymetrix Expression Console version 1.0, sst-RMA

source_name: Liver

label_protocol: Using GeneChip WT PLUS kit, 100 ng of RNA was used for an RT reaction.  After second strand synthesis, cRNA was generated in an overnight IVT reaction and purified using magnetic beads.  The cRNA was used for an RT reaction, and the resulting ss-cDNA was purified and quantified. The ss-cDNA (5.15 ug) was fragmented and biotin end-labeled

growth_protocol: All animals were housed under standard conditions with access to food and water ad libitum.

extract_protocol: RNA was extracted from flash frozen liver using the RNeasy kit according to the manufacturer's directions.

treatment_protocol: Experimental groups received 30 minutes of warm 70% ischemia followed by designated reperfusion times.  Sham animals underwent the same surgical procedures without ischemia.

value: Liver

value: Wistar

tag: condition

value: Reperfused

tag: reperfusion time


title: SEC, 2 years, replicate 4

data_processing:
RNA-seq data was analysed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/) as follows:
The quality of the raw data was assessed using FastQC v0.11.3 and FastQ Screen v0.5.2
Sequenced reads were trimmed to remove adaptors, first 3 bases of the reads and 3' and 5' end nucleotides with a quality cutoff of 20 using Cutadapt
Reads were aligned to the mouse genome (GRCm38/mm10) with TopHat 2.0.10 using Bowtie 1.0.0 and SAMtools 0.1.19, allowing only 2 mismatches and 20 multihits
Transcripts' abundance was calculated using Cufflinks 2.2.1 to obtain Fragments Per Kilobase of exon per Million mapped reads (FPKM), and htseq-count 0.6.1 followed by DESeq2 1.18.1 to obtain normalized counts.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and normalized counts for each sample

value: sinusoidal endothelial cells


title: UT 1

description:
normalized primary expression data
DE61NGSUKBR102671

source_name: bone marrow


title: GARNET_031115_rep2

value: flower buds


title: CRISTOBALINA_011215_rep1

description: 84C_CRISTOBALINA_011215_rep1_S11_N-40626852

value: CRISTOBALINA

value: December 1, 2015


title: PαS, 2 years, replicate 3

value: bone marrow


title: GARNET_031115_rep1


title: AEC, 2 years, replicate 3

value: arterial endothelial cells

value: no treatment


title: 6hr non-ischemic, bio rep 3

value: Non-ischemic


title: AEC, 2 years, replicate 4


title: 3D HUASMC aggregates-1

source_name: Ctrl 1

value: Control 3D


title: 6hr non-ischemic, bio rep 2


title: CRISTOBALINA_031115_rep3

description: 62C_CRISTOBALINA_031115_rep3_S14_N-40186335

source_name: CRISTOBALINA_031115_sweet cherry flower buds

value: November 3, 2015


title: 6hr reperfused, bio rep 1


title: 6hr reperfused, bio rep 2


title: CRISTOBALINA_031115_rep2

description: 62B_CRISTOBALINA_031115_rep2_S13_N-40176465


title: CARc, 2 years, replicate 3

value: CXCL12-abundant reticular cells

value: 2 years


title: B16

city: Suzhou

first: Ji

last: Zhou

state: Jiangsu

address: Renai Road #199

institute: Soochow university

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 17 nt.
Total clean reads were mapped to the mouse reference genome using the bwa aligner.The mapped reads were then compared to the Rfam database and  miRbase21.
The raw count for known miRNAs  were summarized and then normalized using reads per million mapped reads (RPM).
Genome_build: mm10
Supplementary_files_format_and_content: .txt file includes miRNA ID, total count and normalized value (RPM) for each Sample

source_name: melanoma cell line B16

extract_protocol:
Exosomes of B16 and JB6 were harvested by ultracentrifugation. Total RNA of B16 cells and exosomes was  harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Skin

tag: disease state

value: Melanoma

value: B16 cells


title: Exo-B

source_name: exosomes derived from B16 cells

value: melanoma cells B16-derived exosomes


title: 3D HUASMC aggregates + LY2109761-2

source_name: Ctrl 3


title: CRISTOBALINA_031115_rep1

description: 62A_CRISTOBALINA_031115_rep1_S12_N-40185331


title: SEC, 2 years, replicate 3

source_name: stromal cell types isolated from bone marrow


title: 2hr reperfused, bio rep 3

value: Liver

value: Wistar

value: Reperfused


title: 6hr non-ischemic, bio rep 1


title: REGINA_061015_rep2

source_name: REGINA_061015_sweet cherry flower buds

value: REGINA

value: flower buds

value: October 6, 2015


title: Input DNA of activated T-cells

city: Huddinge

first: Peter

last: Svensson

address: Hälsovägen 7C

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

data_processing:
ChIP-seq and input reads were aligned to the hg19 genome assembly using Bowtie2 version 2.0.6 with standard configurations.
Resulting sam files were converted to bam files using Samtools version 1.4.
Bam files were imported into SeqMonk version 0.33.0 where 1000bp probes were constructed around the 5´position of all 40147 genes of the GRCh37 assembly.
Probes were quantitated with Read Count Quantitation using All Reads correcting for total count per million reads, duplicates ignored
Bam files were converted to wig files using Samtools version 1.4 command  "mpileup input.bam | perl -ne 'BEGIN{print "track type=wiggle_0 name=fileName description=fileName\n"};($c, $start, undef, $depth) = split; if ($c ne $lastC) { print "variableStep chrom=$c\n"; };$lastC=$c;next unless $. % 10 ==0;print "$start\t$depth\n" unless $depth<3;'  > output.wig
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: wig format showing distribution of H3K27ac ChIP and input DNA.

source_name: primary CD4 T-cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were purified on Ficoll-paque PLUS (GE Healthcare, Cat#17-1440-02). CD4+ T lymphocytes were extracted (Milentyi Biotec Cat#130-096-533) by negative selection. Cells were grown in RPMI 1640 medium (Hyclone, Cat# SH30096_01), 10% FBS (Life Technologies, Cat# 10270-106), 1% Glutamax (Life Technologies, Cat# 35050), 1% Penicillin-streptomycin (Life Technologies, Cat# 15140-122).

extract_protocol:
ChIP was performed using the iDeal ChIP-qPCR Kit (Diagenode, Cat# C01010180). Each ChIP reaction was performed on 1 × 10 6 cells. Sonication was performed at 30s in eight cycles (Bioruptor Pico, Diagenode, Cat# B01060010). ChIP antibody was targeting H3K27ac (Abcam, Cat# ab4729). Input samples were taken from same sample before ChIP.
NEB Ultra II DNA library kit

treatment_protocol: T-cells were activated for 48 h in media with anti-CD28 (BD, Cat# 555725) in 6-well plates coated for 1 h with anti-CD3 (BD, Cat# 555336).

tag: chip antibody

value: primary CD4 T-cells

tag: t-cell status

value: activated


title: Input DNA of resting T-cells

value: resting


title: REGINA_061015_rep1

tag: cultivar

tag: time point


title: AEC, 2 years, replicate 2

value: arterial endothelial cells

value: bone marrow

value: no treatment


title: CARc, 2 years, replicate 2

value: CXCL12-abundant reticular cells

value: 2 years


title: SEC, 2 years, replicate 2

value: sinusoidal endothelial cells


title: H3K27ac ChIP of activated T-cells


title: GARNET_061015_rep3

source_name: GARNET_061015_sweet cherry flower buds

value: GARNET

tag: lane


title: H3K27ac ChIP of resting T-cells


title: 2hr reperfused, bio rep 2

tag: tissue


title: BMHSC_RNA-Seq_Rep1

value: Adult bone marrow

value: 6-8 week-old


title: GARNET_061015_rep2


title: 2hr non-ischemic, bio rep 2

value: Liver

value: Wistar

value: Non-ischemic


title: CRISTOBALINA_061015_rep3

description: 40A_CRISTOBALINA_061015_rep3_S6_N-40189251

source_name: CRISTOBALINA_061015_sweet cherry flower buds

value: CRISTOBALINA

value: flower buds


title: PαS, 2 years, replicate 2

value: PDGFR-alpha+ Sca-1+ mesenchymal cells


title: AEC, 2 years, replicate 1


title: 2hr non-ischemic, bio rep 3


title: 0.5hr reperfused, bio rep 3

value: Reperfused


title: 2hr non-ischemic, bio rep 1


title: 29BMS

city: London

first: Trinidad

last: Montero

address: Charterhouse Square

department: Biochemical Pharmacology

institute: Whilliam Harvey Research Institute, Bart's and The London School of Medicine; Queen Mary University of London

data_processing:
RNA-Seq reads were aligned to the human genome (hg38) using Hisat2.
Count files were generated by mapping reads the human genome (GRCh38) p5 using HTSeq
Transcript quantification was performed with htseq-count, part of the HTSeq package (version 0.6.1p1) using GENCODE v23 human gene annotation (Ensembl release 81)
The read count data was filtered to keep genes that achieve at least one read count per million (cpm) in at least four samples.
Reads per kilobase per million mapped reads (RPKM) values were calculated with the conditional quantile normalization (cqn) counting for gene length and GC content, in the R statistical environment via Bioconductor packages
Genome_build: GRCh38
Supplementary_files_format_and_content: Cpm values are provided for each sample in txt files.

source_name: Synovial fibroblast

growth_protocol: Cells were grown in RMPI 1640 medium supplemented with 10% non-heat inactivated foetal calf serum, 1% MEM non-essential amino acids, 1% sodium orthopyryvate, 2mM glutamine,100U/ml penicillin, 100μg/ml streptomycin. Cultures were maintained at 30C in 5% CO2, fed every week (i.e. replacement of two thirds of media) and split 1:3 when confluent.

extract_protocol:
RNA was extracted with Direct-zol RNA MiniPrep (Zymo research)
RNA libraries were prepared for sequencing using standard Illumina protocols, on single-read mode

treatment_protocol: BMS-470539 we added at a final concentration of 1μM.

tag: pathology

value: Rheumatoid arthritis

tag: treatment group


title: CARc, 2 years, replicate 1

tag: cell type


title: REGINA_010915_rep2

source_name: REGINA_010915_sweet cherry flower buds

value: REGINA

value: September 1, 2015


title: SEC, 2 years, replicate 1

value: bone marrow

value: no treatment


title: 13BMS


title: 25BMS


title: 2hr reperfused, bio rep 1


title: 0.5hr non-ischemic, bio rep 3


title: REGINA_010915_rep1


title: GARNET_010915_rep3

source_name: GARNET_010915_sweet cherry flower buds


title: 71BMS


title: Control_DNA methylation_seq_4

description: control group

data_processing:
Trim_galore for quality control of RRBS raw data
Bismark for data alignment with rn6 genome
Samtools for data format conversion
Picards for duplication removing
Computation and visualization were achieved using R packages.
Genome_build: rn6
Supplementary_files_format_and_content: The .txt files report methylation level of single base

source_name: control group

extract_protocol:
The genomic DNA (gDNA) of the testes was isolated by a TIANamp Genomic DNA Kit (TianGen), according to the instructions of the manufacturer.
One hundred nanograms of gDNA were digested with 30 U of MspI enzyme (Fermentas) in 20 μl reactions at 37℃ for 16 h. After purification, digested products were blunt ended, and dA was added, followed by methylated-adapter ligation. The obtained DNA fractions were size selected in 200-450 bp using AMPure XP beads (Beckman Coulter). Bisulfite conversion was conducted using an EZ DNA Methylation-Direct Kit (ZYMO), following the instructions of the manufacturer. The final libraries were generated by PCR amplification using a HiFi HotStart Uracil+ Kit (Kapa).

value: testis

value: wistar

value: 8 weeks


title: Control_DNA methylation_seq_3

description: control group


title: CRISTOBALINA_061015_rep1

description: 39B_CRISTOBALINA_061015_rep1_S4_N-40189248

value: October 6, 2015


title: GARNET_010915_rep1

value: GARNET


title: 84BMS


title: GARNET_010915_rep2


title: Control_DNA methylation_seq_2

description: control group


title: 0.5hr non-ischemic, bio rep 1

value: Liver


title: 0.5hr non-ischemic, bio rep 2

value: Wistar


title: 63BMS


title: 0hr reperfused, bio rep 3


title: CRISTOBALINA_010915_rep3

description: 28C_CRISTOBALINA_010915_rep3_S10_N-40142255

source_name: CRISTOBALINA_010915_sweet cherry flower buds


title: 25Veh

value: Vehicle


title: CRISTOBALINA_010915_rep2

description: 28B_CRISTOBALINA_010915_rep2_S9_N-40145295

value: CRISTOBALINA


title: 72Veh


title: CSR_DNA methylation_seq_6

description: CSR group

source_name: CSR group


title: 0.5hr reperfused, bio rep 1

source_name: Liver


title: 0.5hr reperfused, bio rep 2


title: CRISTOBALINA_010915_rep1

description: 28A_CRISTOBALINA_010915_rep1_S8_N-40144275

value: flower buds


title: 28BMS


title: CSR_DNA methylation_seq_5

description: CSR group


title: REGINA_040815_rep2

source_name: REGINA_040815_sweet cherry flower buds

value: August 4, 2015


title: 0hr non-ischemic, bio rep 3

value: Non-ischemic


title: 13Veh

value: Rheumatoid arthritis


title: REGINA_040815_rep1

value: REGINA


title: 71Veh


title: CSR_DNA methylation_seq_2

description: CSR group


title: 0hr reperfused, bio rep 2

value: Reperfused


title: PαS, 2 years, replicate 1

value: PDGFR-alpha+ Sca-1+ mesenchymal cells

value: bone marrow

value: 2 years


title: 0hr non-ischemic, bio rep 2


title: 0hr reperfused, bio rep 1


title: 0hr non-ischemic, bio rep 1


title: 84Veh


title: CSR_DNA methylation_seq_1

description: CSR group

value: testis

value: wistar


title: 29Veh


title: 28Veh


title: GARNET_040815_rep2

source_name: GARNET_040815_sweet cherry flower buds


title: Control_RNA_seq_3

description:
control group
CWY-MC3-1

data_processing:
Trimmomatic for quality control of RNA-Seq raw data
Hisat2 for data alignment with rn6 genome
StringTie for assembling transcripts, estimating their abundances, and testing for differential expression and regulation in RNA-Seq samples
Computation and visualization were achieved using the heatmap plus package in R.
Genome_build: rn6
Supplementary_files_format_and_content: The .txt files report FPKM

extract_protocol:
Total RNA was extracted from the testes with the TRIzol Plus RNA Purification Kit (Invitrogen) according to the instructions of the manufacturer and was finally eluted with 100 μl DNase/RNase-free water. Subsequently, the NanoQ Micro-volume Spectrophotometer (CapitalBio) was used to quantify RNA concentrations and to evaluate the quality of RNA by the detection of A260/A280, A260/A230 (1.8<A260/A280<2.0, 2.0<A260/A230<2.2). The RNA was evaluated using Bioptic Qsep 100 (Bioptic, Taiwan, China) to assure the integrity of the 18S and 28S ribosomal subunits (18S/28S>1.6, RNA Integrity Number (RIN)>8). The mRNA was isolated from total RNA using Poly (A) Beads (Bioo Scientific)
cDNA Library was prepared using a Rapid RNA-Seq Kit (Bioo Scientific) and RNA-Seq Barcodes 12 (Bioo Scientific), according to the instructions of the manufacturer. Each cDNA library was finally eluted with 15 μl of resuspension buffer. The libraries were quantified using a Qubit 3 Fluorometer (Invitrogen) and a dsDNA HS Assay Kit (Invitrogen) and were evaluated by means of Bioptic Qsep 100 (Bioptic).

value: 8 weeks


title: 63Veh


title: GARNET_040815_rep1

value: GARNET


title: CSR_DNA methylation_seq_4

description: CSR group


title: 72BMS


title: 6hr sham-operated, bio rep 2

value: Liver

value: Sham


title: CSR_DNA methylation_seq_3

description: CSR group


title: 6hr sham-operated, bio rep 1

value: Wistar


title: CRISTOBALINA_040815_rep3

description: 18A_CRISTOBALINA_040815_rep3_S17_N-39794535

source_name: CRISTOBALINA_040815_sweet cherry flower buds

value: CRISTOBALINA


title: GARNET_040815_rep3

value: flower buds


title: Control_RNA_seq_1

description:
control group
CWY-MC1-1


title: Control_RNA_seq_2

description:
control group
CWY-MC1-2


title: 2hr sham-operated, bio rep 3


title: 6hr sham-operated, bio rep 3


title: CRISTOBALINA_040815_rep2

description: 17C_CRISTOBALINA_040815_rep2_S16_N-39795518

value: August 4, 2015


title: H01 C0701-transduced B721.221 cells

city: Cambridge

first: Nir

last: Hacohen

state: MA

address: 415 Main Street

institute: Broad Institute

data_processing:
bowtie2-2.2.1 alignment to UCSC hg19 transcriptome; default parameters
rsem-1.2.19; default parameters
Genome_build: hg19
Supplementary_files_format_and_content: .isoforms.results.txt (RSEM transcript-level expression estimates; tab-delimited with headers)

growth_protocol: B721-221 cells were cultured in DMEM supplemented with 10% FBS, Penicillin and streptomycin.

extract_protocol:
Qiagen RNeasy mini kit protocol
The Nextera XT kit from Illumina and the Smart-seq2 protocol were employed to generate full length cDNA and sequencing libraries

tag: genotype

tag: well


title: CSR_RNA_seq_3

description:
CSR group
CWY-M5-1

tag: strain

tag: age


title: F01 C0701-transduced B721.221 cells


title: Control_DNA methylation_seq_1

description: control group


title: CSR_RNA_seq_2

description:
CSR group
CWY-M4-1


title: E01 C0701-transduced B721.221 cells


title: REGINA_070715_rep1

data_processing:
The quality of reads was assessed using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/) and possible adaptor contaminations and low quality trailing sequences were removed using Trimmomatic (Bolger et al., 2014).
Trimmed reads were mapped to the peach (Prunus persica (L) Batsch) reference genome v.2 (Verde et al., 2017) using Tophat (Trapnell et al., 2009).
Possible optical duplicates were removed using Picard tools (https://github.com/broadinstitute/picard).
For each gene, raw reads and TPM (Transcripts Per Million) numbers were calculated (Wagner, 2003).
Genome_build: Prunus persica (L) Batsch reference genome v.2 (Verde et al., 2017)
Supplementary_files_format_and_content: Processed data files are txt files that contains the tracking_id and gene_id columns that define the gene name corresponding to the peach locus, locus information (chromosome, position), and the FPKM (fragments per million reads), TPM (transcripts per million reads) and the Raw count of reads per locus.

source_name: REGINA_070715_sweet cherry flower buds


title: CSR_RNA_seq_1

description:
CSR group
CWY-M3-1


title: REGINA_070715_rep2


title: D01 C0401-transduced B721.221 cells


title: GARNET_070715_rep3

source_name: GARNET_070715_sweet cherry flower buds


title: 2hr sham-operated, bio rep 1


title: 0.5hr sham-operated, bio rep 3


title: C01 C0401-transduced B721.221 cells


title: CRISTOBALINA_040815_rep1

description: 17B_CRISTOBALINA_040815_rep1_S15_N-39798834


title: GARNET_070715_rep2


title: G01 C0701-transduced B721.221 cells


title: A01 C0401-transduced B721.221 cells


title: CRISTOBALINA_070715_rep3

description: 6C_CRISTOBALINA_070715_rep3_S6_N-39790506

source_name: CRISTOBALINA_070715_sweet cherry flower buds


title: 0hr sham-operated, bio rep 3


title: 2hr sham-operated, bio rep 2


title: GARNET_070715_rep1


title: CRISTOBALINA_070715_rep2

description: 6B_CRISTOBALINA_070715_rep2_S5_N-39788506


title: TM2_2_05_1_no_treatment

city: Dresden

first: Thorsten

last: Mascher

address: Zellescherweg 20b

institute: TU Dresden

data_processing:
reverse complement of fastq files with fastx_reverse_complement (version: FASTX Toolkit 0.0.14)
mapping with bowtie2 (cmd: bowtie2 --mm --very-sensitive; version: 2.3.4.1)
filter for mapped reads and convert to sorted bam (cmd: samtools view -F 4 -Shb {input} | samtools sort -o {output.bam}; Version: 1.8)
counting features with FeatureCounts (cmd: featureCounts -s 1 -t 'gene' -g 'ID' -a annotation.gff; version: subread=1.6.1)
DESeq2 normalized counts and differential gene expression (version: bioconductor-deseq2=1.18.1, R version 3.4)
Genome_build: Assembly ASM904v1 (RefSeq: GCF_000009045.1); Annotation based on Nicolas P et al., 2012 (https://www.ncbi.nlm.nih.gov/pubmed/22383849) supplementary table S5
Supplementary_files_format_and_content: bam files with mapped reads, tab-delimited text files with counts, log-fold changes, and adjusted p-values

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: whole cells

growth_protocol: Overnight cultures of B. subtilis W168 (Nicolas et al., 2012) were prepared in LB (Sigma L3522) and incubated at 37°C, 220rpm. On the next day, 10 ml day culture of LB (Sigma L3522) was inoculated 1:100 and grown till OD600 = 0.4. Subsequently, a second day culture of 200 ml LB (Sigma L3522) was started to an OD600 = 0.1. Once this second day culture reached OD600 = 0.5, cells were split into 25 ml aliquots and either exposed to 0.5 µM YydF* (final concertation) or remained untreated for 10 min. After that, cells were directly placed onto ice and centrifuged at 4° C and 8000 rpm for 3 min. The falcons containing the cell pellets were then frozen in liquid nitrogen and kept at -80 °C.

extract_protocol:
B. subtilis cells were disrupted using a micro-dismembrator. Total RNA isolation was performed with a phenol-chloroform isoamyl-alcohol (25:24:1, pH 5.5) extraction method.
rRNA was subtracted from the samples with the Illumina Ribo-Zero rRNA removal Kit (Bacteria) according to manufacturer instructions. The cDNA library was prepared using the NEB Ultra directional RNA library prep kit for Illumina according to instructions and sequencing was performed on an Illumina HiSeq3000 system.

treatment_protocol: Triplicates of non-induced (TM2_2_05_1 - TM2_2_05_3) and triplicates of YydF 0.5µM induced (TM2_2_07_1 - TM2_2_07_3) samples

value: trp+

tag: growth phase

value: logaritmic phase


title: TM2_2_05_2_no_treatment


title: TM2_2_07_2_YydF#60_0.5µM


title: TM2_2_07_1_YydF#60_0.5µM


title: TM2_2_05_3_no_treatment


title: 0hr sham-operated, bio rep 1

tag: condition


title: B01 C0401-transduced B721.221 cells


title: TM2_2_07_3_YydF#60_0.5µM


title: 0.5hr sham-operated, bio rep 1

tag: reperfusion time


title: 3840_Dam Liver

status: Public on Dec 15 2019

city: Indianapolis

first: Kamin

last: Johnson

state: IN

address: 9330 Zionsville Rd

institute: Corteva Agriscience

description: Day after mating designated gestation day 0. Loading dose delivered on gestation day 6 via oral gavage. Daily maintenance doses delivered from gestation day 7 to 20 via oral gavage. Samples analyzed 30 minutes following the last dosing.

data_processing:
Basecalls performed using Illumina CASAVA software version 1.8.
Raw sequencing reads were trimmed and filtered for low quality bases using the fastq-mcf tool from the ea-utils software package (v1.1.0) with the minimum remaining sequence length option set to 50 and quality threshold set to 30.
Trimmed reads were subsequently mapped to the rat reference genome (version 6.0.80) using the hisat2 mapping software (v2.0.3) run using default parameter settings and in stranded mode.
Using HTSeq (v0.7.2), the reads mapped to the antisense strand of each gene were counted.
Genome_build: Rattus norvegicus (version 6.0.80)
Supplementary_files_format_and_content: *.raw_gene_counts.txt: Tab-delimited text files include raw gene count values for each Sample.

source_name: Dam liver

extract_protocol:
Total RNA was extracted from organs stored in RNAlater using a Qiagen RNeasy kit. Samples were digested with DNase during the RNA isolation process to avoid DNA contamination. RNA quantity was measured using a NanoDrop ND-1000 spectrophotometer. Total RNA quality was examined using the HT RNA Std Sens assay on a LabChip GX instrument (PerkinElmer; Waltham, MA) according to the manufacturer’s instructions.
The Illumina TruSeq Stranded mRNA library preparation kit was used to prepare mRNA library templates following the manufacturer’s recommended protocol. In brief, poly-A containing mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Purified mRNA was fragmented to approximately 200 bp average length using divalent cations under high temperature. Following fragmentation, SuperScript II reverse transcriptase and random primers were used to copy the mRNA into first strand cDNA. The cDNA was further converted into double stranded cDNA using DNA polymerase I and RNase H. These double stranded cDNA fragments then underwent end repair, A-tailing, and ligation to indexed Illumina adapters. Finally, adapter-ligated library products were enriched with 15 cycles of PCR and purified.

tag: strain/background

value: Cr1:CD (SD); Sprague-Dawley

value: Dam liver

tag: developmental stage

value: Adult; pregnant (GD 20)

tag: Sex

value: Female

tag: molecule exposure

value: TCDD

tag: exposure

value: Gestation day 8 - 20

tag: loading dose level (ug/kg)

tag: maintenance dose level (ug/kg)

tag: experimental block

tag: sample deemed an outlier

value: No


title: 3841_Dam Liver

tag: tissue


title: 3842_Dam Liver


title: Unoperated animal, bio rep 2

value: WT


title: Unoperated animal, bio rep 3


title: 0.5hr sham-operated, bio rep 2


title: 3836_Dam Liver


title: 3839_Dam Liver


title: 3835_Dam Liver


title: shSPINK1-3

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description:
Lentiviral based shRNA mediated knockdown cells.
22RV1 shSPINK1 #971 vs. 22RV1 SCRAM

hyb_protocol: 300ng of Cy3 labeled sample and 300ng of Cy5 labeled sample were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scanned using the Agilent Microarray Scanner G2505C at 5 micron resolution. Data extraction from Images was done using Agilent Feature Extraction software v 10.5.1.1.

data_processing: Data analysis was performed using GeneSpring GX Software using LOWESS normalization (gene based analysis was performed).

source_name: 22RV1 shScrambled cells - control cells

label_protocol: Poly (A)-tails were added to the 3’-end of RNA by using A-plus Poly (A) polymerase tailing kit (Epicentre Biotechnologies). Then the samples were labeled using Agilent Quick-Amp labeling Kit (p/n:5190-0444). Five hundred nanograms each of the samples were incubated with reverse transcription mix at 42°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3-CTP (Agilent) and Cy5-CTP (Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: 22RV1 (SPINK1-positive) cells were transduced with lentiviral based shSPINK1 viral particles. Cells transduced with the viral particles were cultured in RPMI-1640 medium supplemented with 10% Fetal Bovine Serum (FBS), 0.5% Penicillin Streptomycin (Pen-Strep) and Puromycin (1µg/mL).

extract_protocol: Total RNA from each condition were isolated using Qiagen miRNeasy mini Kit (Cat: 217004) according to the manufacturer protocol.

tag: cell line

tag: cell type

value: Prostate cancer cells

tag: shRNA

value: shScrambled

source_name: 22RV1 shSPINK1 cells - shRNA mediated knockdown cells


title: shSPINK1-1

description:
Lentiviral based shRNA mediated knockdown cells.
22RV1 shSPINK1 #419 vs. 22RV1 SCRAM


title: shSPINK1-2

description:
Lentiviral based shRNA mediated knockdown cells.
22RV1 shSPINK1 #974 vs. 22RV1 SCRAM


title: Exo-J

source_name: exosomes derived from JB6 cells

tag: strain

value: BALB/c

value: Skin

tag: disease state

value: Normal

tag: sample type

value: normal cells JB6-derived exosomes


title: CRISTOBALINA_070715_rep1

description: 6A_CRISTOBALINA_070715_rep1_S4_N-39792479

extract_protocol:
Total RNA was extracted from 50-60 mg of frozen and pulverised flower buds using RNeasy Plant Mini kit (Qiagen) with minor modification: 1.5% PVP-40 was added in the RLT buffer. RNA quality was evaluated using Tapestation 4200 (Agilent Genomics).
Library preparation was performed on 1 μg of high quality RNA (RNA integrity number equivalent superior or equivalent to 8.5) using the TruSeq Stranded mRNA Library Prep Kit High Throughput (Illumina cat. no. RS-122-2103) for ‘Cristobalina’, ‘Garnet’ and ‘Regina’ cultivars. DNA quality from libraries was evaluated using Tapestation 4200. The libraries were sequenced on a NextSeq500, at the Sainsbury Laboratory Cambridge University (SLCU), using paired-end sequencing of 75 bp in length.

tag: cultivar

value: CRISTOBALINA

value: flower buds

tag: time point

tag: lane


title: Unoperated animal, bio rep 1

value: Liver

value: Wistar

tag: condition

tag: reperfusion time


title: 3833_Dam Liver

tag: strain/background

value: Cr1:CD (SD); Sprague-Dawley

value: Dam liver

tag: developmental stage

tag: Sex

tag: molecule exposure

tag: exposure


title: 0hr sham-operated, bio rep 2

tag: tissue

value: Sham


title: 3832_Dam Liver

value: Adult; pregnant (GD 20)

value: Female

value: TCDD

tag: loading dose level (ug/kg)

tag: maintenance dose level (ug/kg)

tag: experimental block

tag: sample deemed an outlier


title: 3831_Dam Liver

value: Gestation day 8 - 20

value: No


title: 3830_Dam Liver


title: 3826_Dam Liver

value: TCDF


title: 3829_Dam Liver


title: 3827_Dam Liver


title: 3825_Dam Liver


title: 3828_Dam Liver


title: 3824_Dam Liver


title: 3823_Dam Liver


title: 3837_Dam Liver


title: 3822_Dam Liver


title: 3821_Dam Liver


title: 3820_Dam Liver


title: 3838_Dam Liver


title: 3815_Dam Liver


title: 3819_Dam Liver


title: 3816_Dam Liver


title: 3817_Dam Liver


title: 3813_Dam Liver


title: 3814_Dam Liver


title: 3818_Dam Liver


title: 3834_Dam Liver


title: 3808_Dam Liver

value: Corn oil (vehicle)


title: 3810_Dam Liver


title: 3841_Fetal Female Liver

source_name: Fetal liver

value: Fetal liver

value: Gestation day 20


title: 3811_Dam Liver


title: 3812_Dam Liver


title: 3809_Dam Liver


title: 3839_Fetal Female Liver


title: 3834_Fetal Female Liver


title: 3837_Fetal Female Liver


title: 3833_Fetal Female Liver


title: 3840_Fetal Female Liver


title: 3832_Fetal Female Liver


title: 3836_Fetal Female Liver

value: Yes


title: 3831_Fetal Female Liver


title: 3826_Fetal Female Liver


title: 3828_Fetal Female Liver


title: 3830_Fetal Female Liver


title: 3821_Fetal Female Liver


title: 3825_Fetal Female Liver


title: 3819_Fetal Female Liver


title: 3818_Fetal Female Liver


title: 3820_Fetal Female Liver


title: 3811_Fetal Female Liver


title: 3810_Fetal Female Liver


title: 3842_Fetal Female Liver


title: 3813_Fetal Female Liver


title: 3841_Fetal Male Liver

value: Male


title: 3812_Fetal Female Liver


title: 3829_Fetal Female Liver


title: 3842_Fetal Male Liver


title: 3840_Fetal Male Liver


title: 3839_Fetal Male Liver


title: 3837_Fetal Male Liver


title: 3824_Fetal Female Liver


title: 3836_Fetal Male Liver


title: 3833_Fetal Male Liver


title: 3835_Fetal Male Liver


title: 3832_Fetal Male Liver


title: 3809_Fetal Female Liver


title: 3838_Fetal Male Liver


title: 3831_Fetal Male Liver


title: 3830_Fetal Male Liver


title: 3824_Fetal Male Liver


title: 3825_Fetal Male Liver


title: 3827_Fetal Male Liver


title: 3826_Fetal Male Liver


title: 3828_Fetal Male Liver


title: 3821_Fetal Male Liver


title: 3820_Fetal Male Liver


title: 3823_Fetal Male Liver


title: 3816_Fetal Male Liver


title: 3817_Fetal Male Liver


title: 3814_Fetal Male Liver


title: 3834_Fetal Male Liver


title: 3818_Fetal Male Liver


title: 3815_Fetal Male Liver


title: 3819_Fetal Male Liver


title: 3813_Fetal Male Liver


title: 3809_Fetal Male Liver


title: 3808_Fetal Male Liver


title: 3573_Testis

description: Day after mating designated gestation day 0. A single dose was administered on gestation day 15.

source_name: Fetal testis

value: Fetal testis

value: Gestation day 15 - 20

value: Not applicable


title: 3572_Testis

value: Cr1:CD (SD); Sprague-Dawley


title: 3812_Fetal Male Liver


title: 3811_Fetal Male Liver


title: 3829_Fetal Male Liver


title: 3570_Testis


title: 3822_Fetal Male Liver


title: 3553_Testis


title: 3552_Testis


title: 3571_Testis


title: 3551_Testis


title: 3550_Testis


title: 3533_Testis


title: 3534_Testis


title: 3531_Testis


title: 3569_Testis