title: 1A: CRC6_control

city: Chuo-ku

first: Hirokazu

last: Ohata

state: Tokyo

address: Tsukiji 5-1-1

country: Japan

institute: National Cancer Center Research Institute

description: Gene expression after 7 days in Y27632-nontreated human colon cancer spheroids (CRC6)

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°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 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanne using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1(Agilent) using default parameters (protocol GE1_105_Jan09 and Grid: 014850_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cy3-labeled cRNA was prepared from 0.2 ug RNA using Quick-Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy mini kit (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNAs from Y27632-treated and Y27632-non-treated cells were extracted using miRNeasy mini kit (QIAGEN) according to the manufacturer’s protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Human Colon spheroid cells were grown in serum-free STEMPRO hESC SFM supplemented with or without 20 microM Y-27632 for 7 days.

value: colon cancer spheroids

value: female


title: Liver - total RNA - LV-KN-210

status: Public on Apr 01 2021

type: SRA

city: Fermoy

first: Kanishka

last: Nilaweera

state: Co. Cork

address: Moorepark

department: Food Biosciences

country: Ireland

institute: Teagasc Food Research Centre

library_source: transcriptomic

data_processing:
FASTQ files were trimmed for quality and the removal of adaptors using the Cutadapt and FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) programs as implemented by Trim Galore! (V.0.61)
High-quality trimmed reads mapped to Mus musculus reference genome assembly GRCm38 using STAR RNA-seq aligner (V.2.6.1)
Gene differential expression identified with the Bioconductor R package DeSeq2 (V.1.24.0)
Genome_build: Mus musculus reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files describing sample subsetting
Supplementary_files_format_and_content: tab-delimited tables of raw gene counts for all genes and samples

molecule: total RNA

organism: Mus musculus

source_name: Liver tissue

extract_protocol:
Rneasy mini kit (Qiagen,74104)
Total RNA extracted using QIAGEN Rneasy Mini Kit (74104) following manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Liver

tag: strain

tag: treatment


title: E0771_pRetrox_Control_Rep3

city: CHICAGO

first: Ekrem Emrah

last: Er

state: IL

address: 909 S  WOLCOTT AVE

department: Physiology and Biophysics

country: USA

institute: The University of Illinois at Chicago

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s no -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, which is used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file containing normalized counts

source_name: E0771 cells

growth_protocol: RPMI with 10% FBS, L-Glut P/S 10mM HEPES

extract_protocol:
Qiagen RNeasy
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 500ng/mL Doxycycline for 48 hours to induce transgene expression

tag: cell type

value: Mammary tumor cell

tag: cell line

tag: genotype/variation

value: control


title: 2A: CRC20_control

type: RNA

description: Gene expression after 7 days in Y27632-nontreated human colon cancer spheroids (CRC20)

organism: Homo sapiens

tag: gender

value: male

tag: age


title: 1B: CRC6_Y27632

description: Gene expression after 7 days in Y27632-treated human colon cancer spheroids (CRC6)


title: EBs.index02.BC_312

city: Utrecht

first: Isabel

last: Guerreiro

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Transcriptome measurement of sample EBs.index02.BC_312

data_processing:
Demultiplexing of raw data (previously demultiplexed on Illumina index) was done using barcodes. Read1 measurements contain in read1, from 5’ to 3’: a 6nt UMI, an 8nt barcode, followed by unalignable sequence, usually polyT. Read2 of the transcriptomic measurements contains the mRNA sequence.
mRNA reads (in read2) were aligned using tophat2 (v2.1.1) using parameters ‘--segment-length 22 --read-mismatches 4 --read-edit-dist 4 --min-anchor 6 --min-intron-length 25 --max-intron-length 25000 --no-novel-juncs --no-novel-indels --no-coverage-search --b2-very-sensitive --b2-N 1 --b2-gbar 200’ to a transcriptome (options ‘--GTF’ and ‘--transcriptome-index’) obtained from GENCODE (v26) supplemented with ERCC mRNA spike-in sequences.
Reads and unique UMIs were counted per gene (according to the “intersection-strict” algorithm of `htseq-count` [http://htseq.readthedocs.io/en/master/count.html]). For each gene, the number of unique observed UMIs was trimmed by starting at the UMI with highest read count and setting UMIs with Hamming distance of 1 to zero, and iteratively filtering all UMI sequences (in case of equal read counts for a UMI, ties were broking by lexicographic sorting of the UMIs). The number of observed distinct UMIs after trimming was taken as the transcript count for that gene.
Genome_build: mm10
Supplementary_files_format_and_content: Tables are provided with the number of transcripts per gene.

molecule: polyA RNA

source_name: embryoid bodies from mouse ESCs

growth_protocol: Expansion medium: ESC were expanded for minimally 2 passages on gelatin-coated tissue-culture plastic in B27N2 medium supplemented with 3 μM CHIR99021 (AxonMed 1386), 1 μM 10 ng/mL Lif (Merck Millipore ESG1106), PD0325901 (1 μM, AxonMed 1408). PrE-induction medium: An average of 10 ESC per microwell was seeded in high-glucose DMEM containing sodium pyruvate and Glutamax (Thermo Fisher, 10569010), supplemented with 10% serum, 10 mM Non-essential amino acids, 10 mM HEPES and penicillin/streptomycin. This medium was supplemented with 10 ng/mL Lif (Merck Millipore ESG1106) and 2 µM Y27632 (AxonMed 1683). PrE-induction supplements were 3 μM CHIR99021 (AxonMed 1386), 50 ng/mL Fgf4 (RnD systems, 5846-F4-025), 10 nM RA (Sigma R2625), 1 mM 8Br-cAMP (Biolog, B007-50E), 1 µg/mL heparin (Sigma) and 50 µM 2-mercaptoethanol (Gibco 11528926).

extract_protocol:
EBs were washed twice in PBS-0 and collagenase IV (600U/ml) was added. Plates were shaken at 350RPM for 30 minutes. EBs were then transferred to TrypleE 10X (no dilution) and shaken for 20 minutes. EBs were dissociated into single cell suspensions using a small capillary. The resulting suspension was quenched using PBS with 50% FBS, centrifuged and resuspended in 230 ul of PBS0 with 10% FBS. Cells were stained with PDGFRA antibody (1:150 dilution) for 30 min at 4°C followed by three PBS (+10%FBS) washes, secondary antibody incubation (1:400) for 30 min. Cells were washed three times in PBS0 and sorted for further processing.
Library construction was done following the Sort-seq protocol as previously described [Muraro, T. et al. A Single-Cell Transcriptome Atlas of the Human Pancreas. Cell Systems 3, 385–394.e3 (2016).]
Library preparation was done as previously described[Hashimshony, T. et al. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome biology 17, 77, (2016).] using 5 μL of aRNA and 8 PCR cycles. Libraries were run on the Illumina NextSeq platform with high output 75 bp paired-end sequencing.

value: embryoid bodies from mouse ESCs

tag: celseq2 adapter

tag: pdgfra staining

value: positive


title: 2B: CRC20_Y27632

description: Gene expression after 7 days in Y27632-treated human colon cancer spheroids (CRC20)


title: EBs.index02.BC_262

description: Transcriptome measurement of sample EBs.index02.BC_262


title: Liver - total RNA - LV-KN-209


title: EBs.index02.BC_260

description: Transcriptome measurement of sample EBs.index02.BC_260


title: EBs.index02.BC_306

description: Transcriptome measurement of sample EBs.index02.BC_306


title: Liver - total RNA - LV-KN-208


title: E0771_pRetrox_Control_Rep1


title: E0771_pRetrox_Control_Rep2


title: EBs.index02.BC_304

description: Transcriptome measurement of sample EBs.index02.BC_304


title: EBs.index02.BC_258

description: Transcriptome measurement of sample EBs.index02.BC_258


title: Liver - total RNA - LV-KN-207


title: B16F10_pRetrox_MRTFB_Rep3

source_name: B16F10 cells

value: Melanoma cell

value: MRTFB


title: B16F10_pRetrox_MRTFB_Rep2


title: Liver - total RNA - LV-KN-205


title: Liver - total RNA - LV-KN-206


title: EBs.index02.BC_246

description: Transcriptome measurement of sample EBs.index02.BC_246


title: Liver - total RNA - LV-KN-204


title: EBs.index02.BC_252

description: Transcriptome measurement of sample EBs.index02.BC_252


title: Liver - total RNA - LV-KN-179


title: EBs.index02.BC_216

description: Transcriptome measurement of sample EBs.index02.BC_216


title: Liver - total RNA - LV-KN-178


title: EBs.index02.BC_242

description: Transcriptome measurement of sample EBs.index02.BC_242


title: B16F10_pRetrox_MRTFA_Rep1

value: MRTFA


title: B16F10_pRetrox_MRTFA_Rep2


title: B16F10_pRetrox_Control_Rep3


title: EBs.index02.BC_206

description: Transcriptome measurement of sample EBs.index02.BC_206


title: Liver - total RNA - LV-KN-176


title: Liver - total RNA - LV-KN-175


title: B16F10_pRetrox_Control_Rep1


title: Liver - total RNA - LV-KN-174


title: EBs.index02.BC_200

description: Transcriptome measurement of sample EBs.index02.BC_200


title: CA3 isolated from hippocampus Abx KD Hyp_6

city: Los Angeles

first: Christine

last: Olson

state: CA

address: 609 Charles E Young Dr

department: Integrative Biology and Physiology

institute: UCLA

data_processing:
Sequences were filtered using FastQC v. 0.11.9 (Andrews, 2010) for quality control
Trimmomatic (Bolger et al.)was used to remove barcodes and reads with an average phred score of 33 (parameters: illuminaclip:2:30:6, slidingwindow:5:30, leading:30, trailing:30, crop:65, minlen:20)
Parsed reads were then aligned to the mouse genome mm10 using HISAT2 (Kim et al.; Kim et al.)
Read counts were obtained using HTSeq-count (Anders et al.)
Differential gene expression was determined using DESeq2 (Love et al.). Heatmaps were constructed using the R package (Team, 2013) pheatmap (Kolde, 2015)
GO term enrichment analysis was conducted using DAVID (Huang da et al., 2009a, b)
Protein-Protein network analysis using STRING (Szklarczyk et al., 2019).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: CA3 isolated from hippocampus

extract_protocol:
Hippocampi were removed, flash frozen in liquid nitrogen, and RNA was harvested using Qiagen RNEasy Mini Kit and libraries were prepared using QuantSeq FWD’ mRNA-Seq Library Prep Kit (Lexogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CA3 isolated from hippocampus

value: Swiss Webster

tag: reared as

value: SPF, then Abx

tag: diet

value: KD

value: Hypoxia


title: EBs.index02.BC_202

description: Transcriptome measurement of sample EBs.index02.BC_202


title: EBs.index02.BC_196

description: Transcriptome measurement of sample EBs.index02.BC_196


title: EBs.index02.BC_244

description: Transcriptome measurement of sample EBs.index02.BC_244


title: Liver - total RNA - LV-KN-173


title: B16F10_pRetrox_MRTFB_Rep1


title: B16F10_pRetrox_MRTFA_Rep3


title: CA3 isolated from hippocampus Abx KD Hyp_5


title: EBs.index02.BC_194

description: Transcriptome measurement of sample EBs.index02.BC_194


title: Liver - total RNA - LV-KN-172


title: CA3 isolated from hippocampus Abx KD Hyp_4


title: CA3 isolated from hippocampus Abx KD Hyp_3


title: Liver - total RNA - LV-KN-171


title: EBs.index02.BC_210

description: Transcriptome measurement of sample EBs.index02.BC_210


title: EBs.index02.BC_160

description: Transcriptome measurement of sample EBs.index02.BC_160


title: Liver - total RNA - LV-KN-170


title: EBs.index02.BC_168

description: Transcriptome measurement of sample EBs.index02.BC_168


title: CA3 isolated from hippocampus Abx KD Hyp_2


title: CA3 isolated from hippocampus Abx KD Hyp_1


title: EBs.index02.BC_158

description: Transcriptome measurement of sample EBs.index02.BC_158


title: Liver - total RNA - LV-KN-169


title: CA3 isolated from hippocampus GF+Bilo_6

value: GF

value: Chow (Lab diet 5010)

value: Bilophila wadsworthia


title: EBs.index02.BC_156

description: Transcriptome measurement of sample EBs.index02.BC_156


title: Liver - total RNA - LV-KN-143

value: Liver


title: CA3 isolated from hippocampus GF+Bilo_5


title: B16F10_pRetrox_Control_Rep2


title: Liver - total RNA - LV-KN-177


title: EBs.index02.BC_150

description: Transcriptome measurement of sample EBs.index02.BC_150


title: EBs.index02.BC_154

description: Transcriptome measurement of sample EBs.index02.BC_154


title: Liver - total RNA - LV-KN-142


title: EBs.index02.BC_120

description: Transcriptome measurement of sample EBs.index02.BC_120


title: Liver - total RNA - LV-KN-141


title: CA3 isolated from hippocampus GF+Bilo_3


title: Liver - total RNA - LV-KN-140


title: Liver - total RNA - LV-KN-139


title: CA3 isolated from hippocampus GF+Bilo_4


title: CA3 isolated from hippocampus GF+Bilo_1


title: Liver - total RNA - LV-KN-138


title: EBs.index02.BC_116

description: Transcriptome measurement of sample EBs.index02.BC_116


title: EBs.index02.BC_118

description: Transcriptome measurement of sample EBs.index02.BC_118


title: EBs.index02.BC_110

description: Transcriptome measurement of sample EBs.index02.BC_110


title: Liver - total RNA - LV-KN-137


title: EBs.index02.BC_114

description: Transcriptome measurement of sample EBs.index02.BC_114


title: CA3 isolated from hippocampus GF+Clos_6

value: Clostridium cocleatum


title: Liver - total RNA - LV-KN-136


title: EBs.index02.BC_106

description: Transcriptome measurement of sample EBs.index02.BC_106


title: Liver - total RNA - LV-KN-135


title: CA3 isolated from hippocampus GF+Clos_5


title: mRNA EtOH_24h-2

city: Beijing

first: Xu

middle: Zhao

last: Gao

state: Beijing

address: The Summer Palace Road No. 5

department: College of Biological Sciences

country: China

institute: Peking University

data_processing:
The reads generated from RNA-seq were initially tested by fastQC and processed to remove the low-quality (Q value < 30 ) reads and adapter sequences. To get the high-quality reads, we cut the first 9bp from each read by perl script. Secondly, the high-quality reads left were mapped to the TAIR10 reference using the STAR (Spliced Transcripts Alignment to a Reference) tool (77). STAR can map the reads faster. The parameters were default, and the mapping rates was greater than 90%.
Genome_build: Tair 10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: plant

growth_protocol: The wild type plant used was Arabidopsis thaliana ecotype Col-0. The seedlings were separated into two classes for hormone processing. Half seedlings were incubated under ABA for 0.5h, 1h, 3h, 6h, 9h, 12h, and 24h time points. Simultaneously, the mock processed seedlings were curated for the same seven time points.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the seedlings were collected separately for next sequencing

value: seedling

tag: genotype

value: wild type


title: CA3 isolated from hippocampus GF+Clos_4


title: mRNA EtOH_24h-1


title: EBs.index02.BC_104

description: Transcriptome measurement of sample EBs.index02.BC_104

value: embryoid bodies from mouse ESCs


title: Liver - total RNA - LV-KN-134


title: CA3 isolated from hippocampus GF+Clos_3


title: CA3 isolated from hippocampus GF+Clos_2


title: EBs.index02.BC_098

description: Transcriptome measurement of sample EBs.index02.BC_098

value: positive


title: mRNA EtOH_12h-2


title: Liver - total RNA - LV-KN-132


title: EBs.index02.BC_072

description: Transcriptome measurement of sample EBs.index02.BC_072


title: mRNA EtOH_12h-1


title: CA3 isolated from hippocampus GF+Clos_1


title: Liver - total RNA - LV-KN-107


title: Liver - total RNA - LV-KN-133


title: mRNA EtOH_9h-2


title: Liver - total RNA - LV-KN-106


title: mRNA EtOH_9h-1


title: EBs.index02.BC_070

description: Transcriptome measurement of sample EBs.index02.BC_070


title: EBs.index02.BC_068

description: Transcriptome measurement of sample EBs.index02.BC_068


title: Liver - total RNA - LV-KN-105


title: mRNA EtOH_6h-2


title: EBs.index02.BC_060

description: Transcriptome measurement of sample EBs.index02.BC_060


title: EBs.index02.BC_064

description: Transcriptome measurement of sample EBs.index02.BC_064


title: CA3 isolated from hippocampus GF+Bilo_2


title: mRNA EtOH_6h-1


title: CA3 isolated from hippocampus GF KD Hyp_3


title: Liver - total RNA - LV-KN-104


title: EBs.index02.BC_056

description: Transcriptome measurement of sample EBs.index02.BC_056


title: Liver - total RNA - LV-KN-103


title: CA3 isolated from hippocampus GF KD Hyp_2


title: mRNA EtOH_3h-2


title: CA3 isolated from hippocampus GF KD Hyp_1


title: CA3 isolated from hippocampus GF KD Hyp_6


title: EBs.index02.BC_054

description: Transcriptome measurement of sample EBs.index02.BC_054


title: Liver - total RNA - LV-KN-102


title: CA3 isolated from hippocampus SPF KD Hyp_6

value: SPF


title: mRNA EtOH_3h-1


title: EBs.index02.BC_024

description: Transcriptome measurement of sample EBs.index02.BC_024


title: Liver - total RNA - LV-KN-101


title: mRNA EtOH_1h-2


title: EBs.index02.BC_018

description: Transcriptome measurement of sample EBs.index02.BC_018


title: CA3 isolated from hippocampus SPF KD Hyp_4


title: mRNA EtOH_0.5h-2


title: CA3 isolated from hippocampus GF KD Hyp_5


title: CA3 isolated from hippocampus SPF KD Hyp_3


title: Liver - total RNA - LV-KN-100


title: Liver - total RNA - LV-KN-99


title: mRNA EtOH_1h-1


title: Liver - total RNA - LV-KN-98


title: CA3 isolated from hippocampus GF KD Hyp_4


title: CA3 isolated from hippocampus SPF KD Hyp_5


title: mRNA EtOH_0.5h-1


title: mRNA ABA_24h-2


title: EBs.index02.BC_022

description: Transcriptome measurement of sample EBs.index02.BC_022


title: CA3 isolated from hippocampus SPF KD Hyp_1


title: EBs.index02.BC_016

description: Transcriptome measurement of sample EBs.index02.BC_016


title: mRNA ABA_24h-1


title: Liver - total RNA - LV-KN-97


title: CA3 isolated from hippocampus SPF KD Hyp_2


title: EBs.index02.BC_012

description: Transcriptome measurement of sample EBs.index02.BC_012


title: Liver - total RNA - LV-KN-96


title: EBs.index02.BC_006

description: Transcriptome measurement of sample EBs.index02.BC_006


title: CA3 isolated from hippocampus SPF KD Mock_6

value: mock


title: Liver - total RNA - LV-KN-72


title: mRNA ABA_12h-2


title: EBs.index01.BC_359

description: Transcriptome measurement of sample EBs.index01.BC_359


title: mRNA ABA_12h-1


title: CA3 isolated from hippocampus SPF KD Mock_5


title: EBs.index02.BC_014

description: Transcriptome measurement of sample EBs.index02.BC_014


title: Liver - total RNA - LV-KN-71


title: EBs.index01.BC_355

description: Transcriptome measurement of sample EBs.index01.BC_355


title: Liver - total RNA - LV-KN-70


title: Liver - total RNA - LV-KN-69


title: CA3 isolated from hippocampus SPF KD Mock_4


title: EBs.index01.BC_357

description: Transcriptome measurement of sample EBs.index01.BC_357


title: CA3 isolated from hippocampus SPF KD Mock_3


title: mRNA ABA_9h-1


title: EBs.index01.BC_353

description: Transcriptome measurement of sample EBs.index01.BC_353


title: mRNA ABA_6h-2


title: CA3 isolated from hippocampus SPF KD Mock_2


title: Liver - total RNA - LV-KN-68


title: EBs.index01.BC_349

description: Transcriptome measurement of sample EBs.index01.BC_349


title: Liver - total RNA - LV-KN-67


title: mRNA ABA_6h-1


title: EBs.index01.BC_347

description: Transcriptome measurement of sample EBs.index01.BC_347


title: Liver - total RNA - LV-KN-66


title: CA3 isolated from hippocampus SPF KD Mock_1


title: Cardiomyocytes RA4

city: Nice

first: Andreas

last: Schedl

address: Parc Valrose

department: iBV

country: France

institute: University of Nice

data_processing:
sequences were aligned using Burrows-Wheeler Aligner (bwa)  version 0.7.12-r104 using standard parameters
differential anaylsis of gene expression was calculated using DESeq2 program with Genomatix software
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: cardiomyocytes

growth_protocol: E18.5 mouse hearts were pooled, minced and trypsin digested for 3 intervals of 15 minutes. At each interval media was removed and reaction stopped with cold FBS and trypsin was replaced for non-digested material. Collected media was then pooled, pelleted and the resulting cell suspension was plated for 1 hour on uncoated plates to remove contaminating fibroblasts. Non-adherent cardiomyoctes were transferred to collagen coated 6-well plates and cells grown to desired confluency in DMEM media supplemented with 10% FBS, pen/strep and glutamine at 37°C in 10% CO2 humidified chambers. Experiment was repeated four times in total. One well used for control and one for treatment for each dissection.

extract_protocol:
Standard Trizol extraction.
Libraries were prepared on a Beckman Fxp Automation system, using the Illumina TruSeq stranded polyA chemistry kit. 500 ng sample was used as input for the library prep.

treatment_protocol: Cells were grown to around 60-70% confluency and treated with 100nM of all trans retinoic acid (sigma) for 48 hours or dmso for controls.

value: cardiomyocytes derived from E18.5 hearts

value: mixed genetic background

value: atRA (100nM)


title: Liver - total RNA - LV-KN-65


title: EBs.index01.BC_309

description: Transcriptome measurement of sample EBs.index01.BC_309


title: mRNA ABA_3h-1


title: Liver - total RNA - LV-KN-64


title: mRNA ABA_9h-2


title: EBs.index01.BC_307

description: Transcriptome measurement of sample EBs.index01.BC_307


title: Liver - total RNA - LV-KN-63


title: EBs.index01.BC_339

description: Transcriptome measurement of sample EBs.index01.BC_339


title: mRNA ABA_0.5h-2


title: Liver - total RNA - LV-KN-62


title: mRNA ABA_1h-1


title: EBs.index01.BC_305

description: Transcriptome measurement of sample EBs.index01.BC_305


title: EBs.index01.BC_299

description: Transcriptome measurement of sample EBs.index01.BC_299


title: mRNA ABA_0.5h-1


title: Liver - total RNA - LV-KN-34


title: Cardiomyocytes RA2


title: Cardiomyocytes CTL2

value: DMSO


title: Cardiomyocytes CTL4


title: mRNA ABA_3h-2


title: Liver - total RNA - LV-KN-35


title: EBs.index01.BC_293

description: Transcriptome measurement of sample EBs.index01.BC_293


title: EBs.index01.BC_295

description: Transcriptome measurement of sample EBs.index01.BC_295


title: Cardiomyocytes CTL1


title: Cardiomyocytes RA3


title: EBs.index01.BC_291

description: Transcriptome measurement of sample EBs.index01.BC_291


title: WT

city: Anam-ro 145, Seongbuk-Gu

first: Hendry

last: Susila

state: Seoul

address: Anam-ro 145

department: Life Science

country: South Korea

institute: Korea University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to TAIR 10 reference genome using tophat
Cufflinks package used for gene expression level
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Seedling

growth_protocol: Plant was grown at 16°C Long day condition on 1/2 MS plate

extract_protocol:
Total RNA was extracted using trizol reagent
mRNA libraries were prepared using TruSeq stranded mRNA sample preparation kit (illumina, San Diego, CA), according to manufacturer's instruction.

value: wildtype

tag: developmental stage

tag: sampling time

value: ZT 16

tag: media


title: pgp1


title: mRNA ABA_1h-2


title: Liver - total RNA - LV-KN-32


title: EBs.index01.BC_255

description: Transcriptome measurement of sample EBs.index01.BC_255


title: Liver - total RNA - LV-KN-33


title: Combine2_treatment2

city: Sydney

first: Chenkai

last: Ma

state: NSW

address: 11 Julius Avenue

country: Australia

institute: CSIRO

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to hg38 genome using STAR
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: co-cultured OVCAR8

extract_protocol:
Trizol
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: OVCAR8 cells and mesothelial cells were cultured alone or indirectly co-cultured in 0.4 μm pore size system for 1 week.

tag: culture type

value: coculture with mesothelial cells for 1 wk


title: Combine1_treatment1


title: EBs.index01.BC_251

description: Transcriptome measurement of sample EBs.index01.BC_251

tag: tissue


title: Cardiomyocytes RA1

tag: strain


title: Liver - total RNA - LV-KN-31

tag: treatment


title: Liver - total RNA - LV-KN-30


title: OValone2_control2

source_name: OVCAR8 alone

value: monoculture


title: EBs.index01.BC_253

description: Transcriptome measurement of sample EBs.index01.BC_253


title: Liver - total RNA - LV-KN-29


title: OValone1_control1


title: EBs.index01.BC_241

description: Transcriptome measurement of sample EBs.index01.BC_241


title: Liver - total RNA - LV-KN-28


title: Liver - total RNA - LV-KN-61


title: Liver - total RNA - LV-KN-26


title: Liver - total RNA - LV-KN-27


title: EBs.index01.BC_209

description: Transcriptome measurement of sample EBs.index01.BC_209


title: EBs.index01.BC_207

description: Transcriptome measurement of sample EBs.index01.BC_207


title: Liver - total RNA - LV-KN-25


title: Jejunum - total RNA - JEJ-215

source_name: Jejunum tissue

value: Jejunum


title: EBs.index01.BC_201

description: Transcriptome measurement of sample EBs.index01.BC_201


title: Jejunum - total RNA - JEJ-213


title: EBs.index01.BC_203

description: Transcriptome measurement of sample EBs.index01.BC_203


title: Jejunum - total RNA - JEJ-214


title: EBs.index01.BC_215

description: Transcriptome measurement of sample EBs.index01.BC_215


title: EBs.index01.BC_195

description: Transcriptome measurement of sample EBs.index01.BC_195


title: EBs.index01.BC_197

description: Transcriptome measurement of sample EBs.index01.BC_197


title: arthritis_Effector memory T cell, biological rep3

city: sinjuku-ku

first: Masaru

last: Takeshita

address: 35 shinanomachi

department: Division of Rheumatology

institute: Keio University

description: Gene expression data from Tem cells

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 18 hr at 45℃ on Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetryx GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Effector memory T cell

label_protocol: Biotinylated cDNA were prepared using NuGEN Encore Biotin Module from 5ug of amplified cDNA.

extract_protocol: Total RNA from sorted cells were extracted using miRCURY RNA Isolation Kit (Exiqon),  purified by RNeasy MinElute Cleanup Kit (Qiagen), and amplified with Ovation Pico WTA System V2 (NuGEN Technologies).

treatment_protocol: Patients with rheumatoid arthritis. Peripheral mononuclear cells were isolated by density gradient centrifugation, and CD4+ T cell were purified from them using CD4+ T Cell Isolation Kit. Cells were sorted by FACS Aria Ⅲ. Tn, Tscm, Tcm, and Tem cells were defined as CD45RO-CCR7+CD95-, CD45RO-CCR7+CD95+, CD45RO+CCR7+, and CD45RO-CCR7-, respectively.

value: blood

tag: disease state

value: rheumatoid arthritis

tag: cell type

value: Effector memory T cell

value: male


title: arthritis_Effector memory T cell, biological rep6

description: Gene expression data from Tem cells

value: female


title: EBs.index01.BC_167

description: Transcriptome measurement of sample EBs.index01.BC_167

value: embryoid bodies from mouse ESCs

value: positive


title: arthritis_Effector memory T cell, biological rep2

description: Gene expression data from Tem cells


title: arthritis_Effector memory T cell, biological rep5

description: Gene expression data from Tem cells


title: arthritis_Central memory T cell, biological rep6

description: Gene expression data from Tcm cells

source_name: Central memory T cell

value: Central memory T cell


title: arthritis_Effector memory T cell, biological rep1

description: Gene expression data from Tem cells


title: arthritis_Central memory T cell, biological rep1

description: Gene expression data from Tcm cells


title: arthritis_Effector memory T cell, biological rep4

description: Gene expression data from Tem cells


title: arthritis_Central memory T cell, biological rep4

description: Gene expression data from Tcm cells


title: arthritis_Central memory T cell, biological rep5

description: Gene expression data from Tcm cells


title: Jejunum - total RNA - JEJ-211


title: Cardiomyocytes CTL3

value: cardiomyocytes derived from E18.5 hearts


title: Jejunum - total RNA - JEJ-208


title: Jejunum - total RNA - JEJ-210


title: Jejunum - total RNA - JEJ-212


title: EBs.index01.BC_159

description: Transcriptome measurement of sample EBs.index01.BC_159


title: EBs.index01.BC_157

description: Transcriptome measurement of sample EBs.index01.BC_157


title: Jejunum - total RNA - JEJ-207


title: EBs.index01.BC_155

description: Transcriptome measurement of sample EBs.index01.BC_155


title: Jejunum - total RNA - JEJ-206


title: EBs.index01.BC_149

description: Transcriptome measurement of sample EBs.index01.BC_149


title: EBs.index01.BC_161

description: Transcriptome measurement of sample EBs.index01.BC_161


title: arthritis_Central memory T cell, biological rep3

description: Gene expression data from Tcm cells


title: arthritis_Stem cell memory T cell, biological rep5

description: Gene expression data from Tscm cells

source_name: Stem cell memory T cell

value: Stem cell memory T cell


title: arthritis_Stem cell memory T cell, biological rep6

description: Gene expression data from Tscm cells


title: Jejunum - total RNA - JEJ-205


title: arthritis_Stem cell memory T cell, biological rep2

description: Gene expression data from Tscm cells


title: Jejunum - total RNA - JEJ-204


title: arthritis_Stem cell memory T cell, biological rep3

description: Gene expression data from Tscm cells


title: arthritis_Stem cell memory T cell, biological rep4

description: Gene expression data from Tscm cells


title: Jejunum - total RNA - JEJ-179


title: arthritis_Naive T cell, biological rep6

description: Gene expression data from Tn cells

source_name: Naive T cell

value: Naive T cell


title: EBs.index01.BC_117

description: Transcriptome measurement of sample EBs.index01.BC_117


title: EBs.index01.BC_119

description: Transcriptome measurement of sample EBs.index01.BC_119


title: Jejunum - total RNA - JEJ-178


title: EBs.index01.BC_153

description: Transcriptome measurement of sample EBs.index01.BC_153


title: EBs.index01.BC_115

description: Transcriptome measurement of sample EBs.index01.BC_115


title: Jejunum - total RNA - JEJ-177


title: arthritis_Naive T cell, biological rep5

description: Gene expression data from Tn cells


title: arthritis_Central memory T cell, biological rep2

description: Gene expression data from Tcm cells


title: arthritis_Naive T cell, biological rep4

description: Gene expression data from Tn cells


title: Jejunum - total RNA - JEJ-176


title: EBs.index01.BC_145

description: Transcriptome measurement of sample EBs.index01.BC_145


title: arthritis_Stem cell memory T cell, biological rep1

description: Gene expression data from Tscm cells


title: EBs.index01.BC_109

description: Transcriptome measurement of sample EBs.index01.BC_109


title: 67_Young

city: Vienna

first: Kikuë

last: Tachibana

state: --- Select a state ---

address: Dr.-Bohr-Gasse 3

country: Austria

institute: IMBA

library_source: genomic

data_processing:
Base calling was performed by VBCF NGS unit
Mapping: iterative mapping (see Imakaev et al, 2012) using bwa
Read filtering was performed as in Flyamer et al., 2017:
Summary of filtering: If two reads map to the same strand, and each side of the read is within 500 bp of any side of the other read, we retain only one copy of the read. We separate the genome into 500 bp bins. If any two bins are interacting more than once, only one interaction is counted. Since each region is only present in the single cell up to 4 times (in oocytes), we eliminated all 500 bp bins that form more than 8 unique interactions with other bins.
Filtered reads were then binned at different resolutions (we provide 4 resolutions) using read start as a read position and stored in the Cool file format. No normalization was applied to the data.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix of whole-genome locus interaction frequencies binned at 1kb, 10kb, 40kb, and 100kb resolutions stored in the Cool file format.

molecule: genomic DNA

source_name: oocyte

extract_protocol:
snHi-C protocol according to Flyamer et al., 2017
The library preparation was done by the VBCF NGS unit (vbcf.ac.at) following the standard DNA sample preparation protocol.

tag: condition

value: Young


title: arthritis_Naive T cell, biological rep2

description: Gene expression data from Tn cells

tag: gender


title: 66_Young


title: Jejunum - total RNA - JEJ-175


title: Jejunum - total RNA - JEJ-209


title: EBs.index01.BC_105

description: Transcriptome measurement of sample EBs.index01.BC_105


title: Jejunum - total RNA - JEJ-174


title: Jejunum - total RNA - JEJ-173


title: 65_Young


title: 64_Young


title: EBs.index01.BC_199

description: Transcriptome measurement of sample EBs.index01.BC_199


title: EBs.index01.BC_097

description: Transcriptome measurement of sample EBs.index01.BC_097


title: Jejunum - total RNA - JEJ-172


title: EBs.index01.BC_111

description: Transcriptome measurement of sample EBs.index01.BC_111


title: EBs.index01.BC_099

description: Transcriptome measurement of sample EBs.index01.BC_099


title: 63_Young


title: UW426-Myc standard growth media + 100 nM AZD1152-HQPA 48hrs, rep 2

city: Montreal

first: Roberto

middle: Jose

last: Diaz

state: QC

address: 3801 Rue University, Rm 109, 3801 Rue University, Rm 122D

department: Neurosurgery

country: Canada

institute: Montreal Neurological Institute and Hospital, McGill University

hyb_protocol: 750ng of cRNA generated from amplification and labeling were hybridized into one Human HT-12 v4.0 BeadChip. See chart below for details. The BeadChip was incubated at 58°C, with rotation speed 5 for 18 hrs for hybridization.

scan_protocol: The BeadChip was washed and stained as per Illumina protocol and scanned on the iScan (Illumina).

data_processing: The data files were quantified in GenomeStudio Version 2011.1 (Illumina). All samples passed Illumina's sample dependent and independent QC metrics. Probe intensities were processed by variance stabilizing transform and robust spline normalization using the limma package (v2.8) in the R environment (v.2.15). To resolve the inconsistency of Illumina identifiers, the probes were identified and annotated by the nucleotide universal identifier (nuID). To identify differentially expressed genes, linear models were fitted using the limma package (v3.12). The t-statistics derived from pre-specified contrasts were moderated by empirical Bayes shrinkage.

label: Biotin

label_protocol: Two hundred nanograms from your 24 RNA samples were label using Illumina TotalPrep-96 RNA Amplification kit Lot # 1108030 (Ambion) as per amplification protocol

growth_protocol: Cells were cultured in Alpha modified Eagle’s media (Wisent Inc., St. Bruno, QC, Canada) with 10% v/v heat inactivated fetal bovine serum (FBS, Wisent)

extract_protocol: The cells were pelleted and solubilized in Trizol (Invitrogen, Waltham, MA, USA). Total RNA was isolated by chloroform extraction followed by clearing in phenol- chlorophorm-isoamyl alcohol (25:24:1, Sigma) and subsequent isopropyl alcohol precipitation. The total RNA was washed with 75% ethanol, air dried, and solubilized in DEPC treated water.

treatment_protocol: Cells were exposed to no drug, 0.01% Dimethylsulfoxide (DMSO) (v/v), or 100 nM AZD1152-HQPA for 48 hrs

tag: cell line background

value: Sonic hedgehog medulloblastoma cell line

tag: tumour type

value: Medulloblastoma, SHH

tag: genotype/variation

value: overexpressing Myc

value: exposed to AZD1152 auror kinase B inhibitor


title: arthritis_Naive T cell, biological rep3

description: Gene expression data from Tn cells

tag: age


title: Jejunum - total RNA - JEJ-171

value: Jejunum


title: arthritis_Naive T cell, biological rep1

description: Gene expression data from Tn cells

value: blood


title: EBs.index01.BC_071

description: Transcriptome measurement of sample EBs.index01.BC_071

tag: celseq2 adapter

tag: pdgfra staining


title: EBs.index01.BC_069

description: Transcriptome measurement of sample EBs.index01.BC_069


title: 62_Young


title: 61_Young


title: Jejunum - total RNA - JEJ-169


title: 60_Young


title: UW426-Myc standard growth media + 100 nM AZD1152-HQPA 48hrs, rep 3


title: EBs.index01.BC_067

description: Transcriptome measurement of sample EBs.index01.BC_067


title: UW426-Myc standard growth media + 100 nM AZD1152-HQPA 48hrs, rep 1


title: UW426 standard growth media + 100 nM AZD1152-HQPA 48hrs, rep 3


title: UW426 standard growth media + 100 nM AZD1152-HQPA 48hrs, rep 1


title: UW426 standard growth media + 100 nM AZD1152-HQPA 48hrs, rep 2


title: UW426-Myc standard growth media + 0.01% DMSO 48hrs, rep 3


title: Jejunum - total RNA - JEJ-143


title: 59_Young


title: EBs.index01.BC_063

description: Transcriptome measurement of sample EBs.index01.BC_063


title: UW426-Myc standard growth media + 0.01% DMSO 48hrs, rep 2


title: EBs.index01.BC_055

description: Transcriptome measurement of sample EBs.index01.BC_055


title: Jejunum - total RNA - JEJ-141


title: Jejunum - total RNA - JEJ-142


title: EBs.index01.BC_053

description: Transcriptome measurement of sample EBs.index01.BC_053


title: 58_Young


title: 57_Young


title: Jejunum - total RNA - JEJ-170


title: UW426 standard growth media + 0.01% DMSO 48hrs, rep 3


title: 56_Young


title: UW426-Myc standard growth media + 0.01% DMSO 48hrs, rep 1


title: Jejunum - total RNA - JEJ-139


title: EBs.index01.BC_019

description: Transcriptome measurement of sample EBs.index01.BC_019


title: EBs.index01.BC_023

description: Transcriptome measurement of sample EBs.index01.BC_023


title: 54_Young


title: UW426 standard growth media + 0.01% DMSO 48hrs, rep 1


title: Jejunum - total RNA - JEJ-138


title: UW426 standard growth media + 0.01% DMSO 48hrs, rep 2


title: EBs.index01.BC_017

description: Transcriptome measurement of sample EBs.index01.BC_017


title: Jejunum - total RNA - JEJ-137


title: EBs.index01.BC_013

description: Transcriptome measurement of sample EBs.index01.BC_013


title: UW426-Myc standard growth media 48hrs, rep 2

source_name: UW426-Myc standard growth media 48hrs


title: UW426-Myc standard growth media 48hrs, rep 3


title: EBs.index01.BC_049

description: Transcriptome measurement of sample EBs.index01.BC_049


title: Jejunum - total RNA - JEJ-140


title: Jejunum - total RNA - JEJ-135


title: EBs.index01.BC_001

description: Transcriptome measurement of sample EBs.index01.BC_001


title: Jejunum - total RNA - JEJ-136


title: 51_Young


title: 52_Young


title: UW426 standard growth media 48hrs, rep 3

source_name: UW426 standard growth media 48hrs


title: 50_Young


title: Jejunum - total RNA - JEJ-134


title: Single nucleus human perivascuar adipose tissue 2

city: Philadelphia

first: Patrick

last: Seale

state: PA

address: Smilow Center for Translational Research, 12th Floor 3400 Civic Center Blvd.

institute: University of Pennsylvania

description:
10X Genomics Single Nucleus RNA-Seq
hPVAT.Integrated_annotated_merged.RDS
hPVAT.Integrated_raw.rds
hPVAT.Integrated_annotated.rds
hPVAT.Subclustered_annotated.RDS
hPVAT.Subclustered_raw.RDS

data_processing:
CellRanger v3
Seurat v3
Genome_build: mm10; GRCh38
Supplementary_files_format_and_content: CellRanger Outputs (Barcodes.tsv, genes.tsv, matrix.mtx) and Seuratv3 RDS Files,

source_name: PVAT

extract_protocol:
For single cell, Aorta were isolated from mice, minced and placed into digestion medium (DMEM, Collagenase D: 6.1mg/ml (Roche), Dispase II: 2.4 mg/ml (Roche) and placed at 37oC with constant agitation at 200 rpm. To enrich for cell populations with differential sensitivity to digestion, we utilized the following procedures. For embryonic/newborn mice, 20% of the digestion was quenched at 15 minutes, 20% at 20 minutes and the remaining 60% at 25 minutes (embryos/perinatal). For adult aortas 50% of the digestion was quenched at 30 minutes, 50% at 60 minutes. Single cells were isolated from dissected aortas and flow sorted to isolate live (DAPI-) cells and remove debris. Cells were collected as either CD45+ (immune) and CD45- (non-immune) cells. For adult single cell RNA Sequencing, CD45+ cells were mixed with CD45- cells to achieve a proportion of ~20%. For single nuclei experiments, 40-80 mg of frozen human PVAT was dounce homogenized using a glass homogenizer (Sigma-Aldrich, 7 mL) on ice in 2.5 mL homogenization buffer (0.32 M sucrose (Sigma, RNase & DNase free ultra pure grade), 5 mM CaCl2 (Sigma), 3 mM MgAc2 (Sigma-Aldrich), 10 mM Tris-HCl pH 8.0 (FisherChem), 0.1% TritonX-100 (Amresco), 0.1 mM EDTA (Fischer), protease inhibitor cocktail (Roche)) and layered into ultracentrifuge tubes (Beckman Coulter) over 12 mL sucrose cushion (1.8 M sucrose, 10 mM Tris-HCl pH 8.0 (FisherChem), 3 mM MgAc2 (Sigma-Aldrich), protease inhibitor cocktail (Roche) and topped with 14.5mL homogenization buffer. Samples were ultracentrifuged (Beckman Coulter L-70K) using a swinging bucket rotor (Beckman Coulter SW28) at 25,000 rpm for 2 hrs at 4°C. The supernatant was aspirated to remove debris and the nuclear pellet was resuspended in 1 mL of DPBS (Corning) with RNase inhibitor (Lucigen). Samples were filtered and nuclei were counted before loading for snRNA-Seq
For single cell experiments, single cell transcriptomes were collected  previously using the 10X Genomics platform with v2 (perinatal) and v3 (adult) chemistry (10× Genomics, Pleasanton, CA) and sequenced on Illumina HiSeq 4000. For single nucleus experiments, single nucleus transcriptomes were collected  using the 10X Genomics platform  v3 (adult) chemistry (10× Genomics, Pleasanton, CA) and sequenced on Illumina NovaSeq 6000.

value: 65 years

value: Male

value: PVAT


title: Single nucleus human perivascuar adipose tissue 3

value: 61 years


title: 55_Young


title: 3D_WTPELP_7L_03

city: Minneapolis

first: Nuri

middle: Alpay

last: Temiz

state: MN

address: 2231 6th St SE

department: Masonic Cancer Center

institute: University of Minnesota

data_processing:
Initial QC performed using FastQC v 0.11.2
Tophat v 2.0.13 was used to align samples
Cufflinks v 2.2.1 was used to generate abundances and fpkm values with max-bundle-frans <10000000>
Genome_build: hg19
Supplementary_files_format_and_content: matrix of fpkm values per sample

extract_protocol:
RNeasy Mini Kit (Qiagen)
TruSeq RNA v2; average insert size of 200 selected

tag: cell line

value: breast cancer

tag: expression

value: wildtype PELP1


title: Jejunum - total RNA - JEJ-133


title: 49_Young


title: 3D_WTPELP_7L_02


title: Single nucleus human perivascuar adipose tissue 1


title: 48_Young


title: 3D_WTPELP_7L_01


title: 53_Young


title: Jejunum - total RNA - JEJ-132


title: Jejunum - total RNA - JEJ-107


title: UW426 standard growth media 48hrs, rep 1


title: 47_Virgin

value: Virgin

value: ICRF


title: frac_uninf_total_rep2

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description:
RNA-seq of the cytosolic, nuclear and total cell fractions.
frac_reads.txt

data_processing:
The reads were trimmed with cutadapt to remove the linker CTGTAGGCACCATCAAT in the ribo-seq libraries and the linker AGATCGGAAGAGCACACGT in the mRNA libraries. The reads of the fractionation samples were trimmed to length 50 nucleotides.
Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus.
Reads that failed to align to genome, were aligned to the host transcriptome and to the viral breaking points according to strong break point at Kim et. al, plus few breakpoints from our STAR runs.
The alignments above were made with Bowtie1. In the ribo-seq libraries the p-site was calculated as an offset (adjusted to the read length) from the read start site.
The STAR alignment was made with the flags recommended by Kim et. al. to get all the breakpoints.
Genome_build: Host : hg19 genome and annotation from UCSC, besides the mitochendria genes which are from Ensembl. Virus : Genebank NC_045512.2 with 3 changes to match the used strain, 241:C->T, 3037:C->T, 23403:A->G.
Supplementary_files_format_and_content: All processed files are tab delimited files. For the mRNA and ribo-seq samples, the files include the number of uniquely aligned reads to the transcript, coding sequence, introns of the host genes, and to the coding sequence of the virus. For the total samples (no polyA selection), and to the mRNA and ribo-seq samples, a file with the breakdown of the aligned reads to the rRNA/tRNA, viral genome, host genome, host transcriptome, etc. For the fractionation samples, the number of uniquely aligned reads to the host transcripts. For the slam-seq samples, the per gene output of the GRAND-SLAM pipeline.
Supplementary_files_format_and_content: frac_reads.txt: Number of reads aligned uniquely to host genes in the fractionation samples
Supplementary_files_format_and_content: slam_inf_params.txt: Output of the GRAND-SLAM pipeline on the Infected slam-seq samples. Includes, number of reads, NTR mean and MAP, and more.
Supplementary_files_format_and_content: slam_uninf_params.txt: Output of the GRAND-SLAM pipeline on the UnInfected slam-seq samples. Includes, number of reads, NTR mean and MAP, and more.
Supplementary_files_format_and_content: frac_abs_TPM.txt: Absolute localization TPM values (calculated based on the linear regression of the total fraction as function of the cytosolic and nuclear fractions).

source_name: Calu 3 cells, ATCC HTB-55

growth_protocol: Calu3 cells (ATCC HTB-55) were cultured in 6-well or 10cm plates with RPMI supplemented with 10% fetal bovine serum (FBS), MEM non-essential amino acids, 2mM L-Glutamine, 100Units/ml Penicillin and 1% Na-pyruvate.

extract_protocol:
For RNA-seq, cells were harvested with Tri-Reagent (Sigma-Aldrich), total RNA was extracted. poly-A selection was performed using Dynabeads mRNA DIRECT Purification Kit (Invitrogen). For ribosome profiling, medium was aspirated from dishes, which were immediately placed on ice and rinsed with 10 ml ice-cold PBS supplemented with drugs used in pretreatment of the cells. PBS was aspirated and 800 μl ice-cold lysis buffer (20 mM Tris, pH 7.4, 250 mM NaCl, 15 mM MgCl2, 1 mM dithiothreito, 0.5% Triton X-100 and 24 U / ml Turbo DNase (Ambion, AM2239), along with any drugs used for sample treatment) was dripped onto dishes. Cells were scraped and the lysate was removed and incubated 10 min on ice. The lysate was then clarified by centrifugation for 10 min at 20,000 × g, 4°C and ∼1.1 ml supernatant was recovered. For SLAM-seq libraries Cells were harvested with Tri-reagent at 1, 2, 3, and 4 hours after addition of 4sU (corresponding to 4,5,6 and 7hpi for infected cells) . RNA was extracted under reducing conditions and treated with Iodoacetamide. poly-A selection was performed using Dynabeads mRNA DIRECT Purification Kit (Invitrogen). For fractionation, first a fraction of 10% of the cells was transferred to a new tube and RNA was extracted in Tri-reagent to obtain whole cellular extract. Nuclear fraction was separated from cytoplasmic fraction by centrifugation following cell lysis. RNA was then extracted from both fraction in Tri-reagent. poly-A selection was performed using Dynabeads mRNA DIRECT Purification Kit (Invitrogen).
RNA-seq: mRNA samples were subjected to DNAseI treatment and 3’ dephpsphorylation using FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific) and T4 PNK (NEB) followed by 3’ adaptor ligation using T4 ligase (NEB). The ligated products were then used for reverse transcription with SSIII (Invitrogen) for first strand cDNA synthesis. The cDNA products were 3’ ligated with a second adaptor using T4 ligase and amplified for 8 cycles in a PCR for final library products of 200-300bp. Ribo-seq: Cells were treated with 100µg/mL CHX for 1 minute. Cells were then placed on ice, washed twice with PBS containing 100µg/mL CHX, scraped from 10cm plates, pelleted and lysed with lysis buffer (1% triton in 20mM Tris 7.5, 150mM NaCl, 5mM MgCl2, 1mM dithiothreitol supplemented with 10 U/ml Turbo DNase and 100µg/ml cycloheximide). After lysis samples stood on ice for 2h and subsequent Ribo-seq library generation was performed. Briefly, cell lysate was treated with RNAseI for 45min at room temperature followed by SUPERase-In quenching. Sample was loaded on sucrose solution (34% sucrose, 20mM Tris 7.5, 150mM NaCl, 5mM MgCl2, 1mM dithiothreitol and 100µg/ml cycloheximide) and spun for 1h at 100K RPM using TLA-110 rotor (Beckman) at 4c. Pellet was harvested using TRI reagent and the RNA was collected using chloroform phase separation. For size selection, 15uG of total RNA was loaded into 15% TBE-UREA gel for 65min, and 28-34 nt footprints were excised using 28 nt and 34 nt flanking RNA oligos, followed by RNA extraction and ribo-seq protocol (Finkel Y. et. al., 2020, ELife)
RNA-seq of whole cells as well as nuclear and cytoplasmic fractions, ribosome profiling, and SLAM-seq.

treatment_protocol: Cells were infected for indicated time points before treatment or left uninfected. For Ribo-seq libraries, samples were treated with 100μg/mL CHX for 1 minute. Cells were placed on ice immediately after treatment, washed twice with PBS containing 100μg/mL CHX. For SLAM-seq, 200μM 4sU was added to the growth media of the cells 3hpi.

value: Calu 3 cells, ATCC HTB-55

tag: hours post infection

value: uninfected


title: UW426-Myc standard growth media 48hrs, rep 1


title: Jejunum - total RNA - JEJ-106


title: 46_Virgin


title: 3D_CytoPELP_7L_03

value: cytoplasmic PELP1


title: frac_uninf_nuc_rep2


title: 3D_CytoPELP_7L_01


title: 3D_CytoPELP_7L_02


title: EBs.index01.BC_009

description: Transcriptome measurement of sample EBs.index01.BC_009

source_name: embryoid bodies from mouse ESCs

value: embryoid bodies from mouse ESCs

value: positive


title: 44_Virgin


title: Jejunum - total RNA - JEJ-104


title: UW426 standard growth media 48hrs, rep 2

value: Sonic hedgehog medulloblastoma cell line

value: Medulloblastoma, SHH


title: frac_uninf_total_rep1


title: Jejunum - total RNA - JEJ-105

value: Jejunum


title: 45_Virgin


title: frac_uninf_nuc_rep1


title: frac_uninf_cyto_rep1


title: 3D_LXSN_7L_03

value: LXSN


title: Jejunum - total RNA - JEJ-102


title: 42_Virgin


title: 3D_LXSN_7L_02


title: 43_Virgin


title: Jejunum - total RNA - JEJ-101


title: 3D_LXSN_7L_01


title: 41_Virgin


title: slam_uninf_4h_4sU

description:
RNA-seq after 4sU labeling
slam_uninf_params.txt

data_processing:
The reads were trimmed with cutadapt to remove the linker CTGTAGGCACCATCAAT in the ribo-seq libraries and the linker AGATCGGAAGAGCACACGT in the mRNA libraries. The reads of the fractionation samples were trimmed to length 50 nucleotides.
Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus.
Reads that failed to align to genome, were aligned to the host transcriptome and to the viral breaking points according to strong break point at Kim et. al, plus few breakpoints from our STAR runs.
The alignments above were made with Bowtie1. In the ribo-seq libraries the p-site was calculated as an offset (adjusted to the read length) from the read start site.
The STAR alignment was made with the flags recommended by Kim et. al. to get all the breakpoints.
Genome_build: Host : hg19 genome and annotation from UCSC, besides the mitochendria genes which are from Ensembl. Virus : Genebank NC_045512.2 with 3 changes to match the used strain, 241:C->T, 3037:C->T, 23403:A->G.
Supplementary_files_format_and_content: All processed files are tab delimited files. For the mRNA and ribo-seq samples, the files include the number of uniquely aligned reads to the transcript, coding sequence, introns of the host genes, and to the coding sequence of the virus. For the total samples (no polyA selection), and to the mRNA and ribo-seq samples, a file with the breakdown of the aligned reads to the rRNA/tRNA, viral genome, host genome, host transcriptome, etc. For the fractionation samples, the number of uniquely aligned reads to the host transcripts. For the slam-seq samples, the per gene output of the GRAND-SLAM pipeline.
Supplementary_files_format_and_content: frac_reads.txt: Number of reads aligned uniquely to host genes in the fractionation samples
Supplementary_files_format_and_content: slam_inf_params.txt: Output of the GRAND-SLAM pipeline on the Infected slam-seq samples. Includes, number of reads, NTR mean and MAP, and more.
Supplementary_files_format_and_content: slam_uninf_params.txt: Output of the GRAND-SLAM pipeline on the UnInfected slam-seq samples. Includes, number of reads, NTR mean and MAP, and more.


title: slam_uninf_3h_4sU

data_processing:
The reads were trimmed with cutadapt to remove the linker CTGTAGGCACCATCAAT in the ribo-seq libraries and the linker AGATCGGAAGAGCACACGT in the mRNA libraries. The reads of the fractionation samples were trimmed to length 50 nucleotides.
Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus.
Reads that failed to align to genome, were aligned to the host transcriptome and to the viral breaking points according to strong break point at Kim et. al, plus few breakpoints from our STAR runs.
The alignments above were made with Bowtie1. In the ribo-seq libraries the p-site was calculated as an offset (adjusted to the read length) from the read start site.
The STAR alignment was made with the flags recommended by Kim et. al. to get all the breakpoints.
Genome_build: Host : hg19 genome and annotation from UCSC, besides the mitochendria genes which are from Ensembl. Virus : Genebank NC_045512.2 with 3 changes to match the used strain, 241:C->T, 3037:C->T, 23403:A->G.
Supplementary_files_format_and_content: All processed files are tab delimited files. For the mRNA and ribo-seq samples, the files include the number of uniquely aligned reads to the transcript, coding sequence, introns of the host genes, and to the coding sequence of the virus. For the total samples (no polyA selection), and to the mRNA and ribo-seq samples, a file with the breakdown of the aligned reads to the rRNA/tRNA, viral genome, host genome, host transcriptome, etc. For the fractionation samples, the number of uniquely aligned reads to the host transcripts. For the slam-seq samples, the per gene output of the GRAND-SLAM pipeline.
Supplementary_files_format_and_content: frac_reads.txt: Number of reads aligned uniquely to host genes in the fractionation samples
Supplementary_files_format_and_content: slam_inf_params.txt: Output of the GRAND-SLAM pipeline on the Infected slam-seq samples. Includes, number of reads, NTR mean and MAP, and more.
Supplementary_files_format_and_content: slam_uninf_params.txt: Output of the GRAND-SLAM pipeline on the UnInfected slam-seq samples. Includes, number of reads, NTR mean and MAP, and more.
Supplementary_files_format_and_content: halflife.txt: Half-life values (calculated based on regression of the log old fraction, estimated by the GRAND-SLAN, as function of time)


title: frac_uninf_cyto_rep2


title: Jejunum - total RNA - JEJ-100


title: MV411_rep3

first: Kristen

last: Lynch

state: Pennsylvania

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Molecular Biophysics

data_processing:
fastq.gz reads trimmed with TrimGalore! to remove low-quality base calls and library adaptor sequences.
For expression analyses, reads mapped with Salmon were quantified for transcript level counts.
For splicing analyses, reads mapped with STAR were quantified for alternative splicing with MAJIQ algorithm
Genome_build: hg38
Supplementary_files_format_and_content: Salmon's quant.sf files are tab-separated with effective counts, effective gene lengths, and TPMs. See: salmon.readthedocs.io/en/latest/file_formats.html

source_name: cell culture

extract_protocol:
Total RNA isolated with Trizol/Qiagen protocol
RNA library preparation with polyA selection

treatment_protocol: No treatment

tag: sample type

value: MV411 cell line

tag: aml type

value: Cell line

tag: rin


title: 40_Virgin

tag: strain


title: slam_uninf_2h_4sU_rep2


title: MV411_rep2


title: 39_Virgin


title: Jejunum - total RNA - JEJ-99

data_processing:
FASTQ files were trimmed for quality and the removal of adaptors using the Cutadapt and FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) programs as implemented by Trim Galore! (V.0.61)
High-quality trimmed reads mapped to Mus musculus reference genome assembly GRCm38 using STAR RNA-seq aligner (V.2.6.1)
Gene differential expression identified with the Bioconductor R package DeSeq2 (V.1.24.0)
Genome_build: Mus musculus reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files describing sample subsetting
Supplementary_files_format_and_content: tab-delimited tables of raw gene counts for all genes and samples

tag: tissue

tag: treatment


title: slam_uninf_2h_4sU_rep1


title: Jejunum - total RNA - JEJ-103


title: Jejunum - total RNA - JEJ-98


title: MV411_rep1


title: 38_Virgin

tag: condition


title: slam_uninf_1h_4sU


title: Jejunum - total RNA - JEJ-97


title: 37_Virgin


title: slam_uninf_no4sU


title: CD34+_2

source_name: Bone marrow

value: Normal donor


title: HL-60

value: HL-60 cell line


title: Jejunum - total RNA - JEJ-96


title: 36_Virgin


title: HEMA-090

city: Taichung City

first: thh

last: lab

address: 1650 Taiwan Boulevard Sect. 4, Taichung, Taiwan 40705, ROC

country: Taiwan

institute: TCVGH

data_processing:
Low quality bases (< Q20) and adapters were removed by Trimmomatic v0.36.
Clean reads were aligned to the Ensembl GRCh38 human reference genome using HISAT 2 2.2.0.
We used the featureCounts v2.0.0 to count the mapped reads against Ensembl annotated genes (ENSG IDs).
Gene-level read counts were normalized and tested for differential expression between AML patients with and without CR by an R package DESeq2 1.26.0.
Genome_build: GRCh38
Supplementary_files_format_and_content: featureCounts raw read counts
Supplementary_files_format_and_content: DESeq2-normalized read counts

source_name: CR_bone marrow

extract_protocol:
Total RNA was extracted from these isolated mononuclear cells using TRIzol (Thermo Fisher Scientific, Inc., Wilmington, Delaware, USA) and purified RNA samples were obtained using a RNeasy Mini Kit and DNase I (Qiagen, Valencia, CA, USA).
The purified RNA was used for the preparation of the sequencing library by TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations.

treatment_protocol: All patients received and complete the “7+3” (cytarabine 100–200 mg/M2 for 7 days; idarubicin 12 mg/M2 for 3 days) regimen. Bone marrow samples were collected before treatment.

value: bone marrow

tag: response to standard induction chemotherapy

value: CR (complete remission)

tag: cell type

value: bone marrow mononuclear cells

tag: disease state

value: acute myeloid leukemia (AML) patient


title: P6348

value: Acute Myeloid Leukemia (AML)

value: De Novo


title: HEMA-080


title: P6344

source_name: PB-MNC


title: CD34+_1


title: HEMA-084


title: Jejunum - total RNA - JEJ-71


title: 34_Mated

value: Mated

value: ICRF


title: Jejunum - total RNA - JEJ-70


title: 33_Mated


title: HEMA-077


title: Jejunum - total RNA - JEJ-69


title: P6273

value: Relapsed


title: 32_Mated


title: 31_Mated


title: P6200

value: De Novo (prior MDS)


title: HEMA-068

source_name: Non-CR_bone marrow

value: Non-CR (non-complete remission)


title: P6133

source_name: Pheresis


title: Jejunum - total RNA - JEJ-67

source_name: Jejunum tissue

value: Jejunum


title: Jejunum - total RNA - JEJ-66


title: HEMA-076


title: 30_Mated


title: Jejunum - total RNA - JEJ-68


title: HEMA-067


title: Jejunum - total RNA - JEJ-65


title: P6110


title: 35_Mated


title: Jejunum - total RNA - JEJ-72


title: 29_Mated


title: HEMA-045


title: P5882

value: De Novo (secondary)


title: HEMA-050


title: HEMA-036


title: Jejunum - total RNA - JEJ-64


title: 28_Mated


title: 27_Mated


title: P5868

value: Refractory


title: Jejunum - total RNA - JEJ-63


title: 26_Mated


title: HEMA-035


title: Jejunum - total RNA - JEJ-62


title: 25_Mated


title: HEMA-030


title: P5851


title: Jejunum - total RNA - JEJ-61


title: P6129


title: 24_Mated


title: P5637


title: HEMA-029


title: 23_Mated


title: Jejunum - total RNA - JEJ-36


title: 22_Mated


title: HEMA-027


title: Jejunum - total RNA - JEJ-34


title: HEMA-025


title: Jejunum - total RNA - JEJ-33


title: P5575

value: Refractory (prior MDS)


title: P5503


title: P5498

value: Relapsed (11q23)


title: 21_Mated


title: HEMA-024


title: 20_Aged

value: Aged


title: Jejunum - total RNA - JEJ-31


title: Jejunum - total RNA - JEJ-32


title: P5854

value: De Novo (PTP53 deletion)


title: 19_Aged


title: Jejunum - total RNA - JEJ-30


title: HEMA-022

value: bone marrow


title: P4943

value: De Novo (11q23)


title: P5052


title: HEMA-020

value: bone marrow mononuclear cells

value: acute myeloid leukemia (AML) patient


title: 18_Aged


title: 17_Aged


title: Jejunum - total RNA - JEJ-29


title: HEMA-019

value: CR (complete remission)


title: P4851

value: Acute Myeloid Leukemia (AML)

value: De Novo


title: HEMA-013


title: 16_Aged


title: Jejunum - total RNA - JEJ-27


title: P3965


title: HEMA-009


title: P4393


title: HEMA-011


title: 15_Aged


title: P3875


title: Jejunum - total RNA - JEJ-26


title: Jejunum - total RNA - JEJ-25


title: HEMA-006


title: P2711


title: HEMA-001


title: P3568

value: Unknown


title: 11_Aged


title: 14_Aged


title: 12_Aged


title: Calu3_mrna_uninf_2_total

description: RNA-seq without polyA selection

data_processing:
The reads of the ribo-seq libraries was trimmed to remove the linker CTGTAGGCACCATCAAT by using cutadapt.
Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus.
Reads that failed to align to genome, were aligned to the host transcriptome and to the viral breaking points according to strong break point at Kim et. al, plus few breakpoints from  our STAR runs.
The alignments above was made with Bowtie1. In the ribo-seq libraries the p-site was calculated as an offset (adjusted to the read length) from the read start site.
The STAR alignment was made with the flags recommended by Kim et. al. to get all the breakpoints.
Genome_build: Host : hg19 genome and annotation from UCSC, besides the mitochendria genes which are from Ensembl. Virus Genebank NC_045512.2 with 3 changes to match the used strain, 241:C->T, 3037:C->T, 23403:A->G.
Supplementary_files_format_and_content: All processed files are tab delimited files with the number of reads on the transcripts, coding sequence, introns of the host genes, on the coding sequence of the virus, and also global number of reads aligned to the rRNA abd tRNA
Supplementary_files_format_and_content: global.txt: Global number of reads aligned to rRNA, host and Virus
Supplementary_files_format_and_content: transcript_host.txt: For each host gene, number of read aligned uniquely to the transcript
Supplementary_files_format_and_content: cds_host.txt: For each host gene, number of read aligned uniquely to the coding sequence
Supplementary_files_format_and_content: cds_virus.txt: For each viral gene, number of read aligned uniquely to the coding sequence
Supplementary_files_format_and_content: transcript_introns.txt: For each host gene, number of read aligned uniquely to the transcript

source_name: Homo Sapiens

extract_protocol:
For RNA-seq, cells were harvested with Tri-Reagent (Sigma-Aldrich), total RNA was extracted. poly-A selection was performed using Dynabeads mRNA DIRECT Purification Kit (Invitrogen). For ribosome profiling, medium was aspirated from dishes, which were immediately placed on ice and rinsed with 10 ml ice-cold PBS supplemented with drugs used in pretreatment of the cells. PBS was aspirated and 800 μl ice-cold lysis buffer (20 mM Tris, pH 7.4, 250 mM NaCl, 15 mM MgCl2, 1 mM dithiothreito, 0.5% Triton X-100 and 24 U / ml Turbo DNase (Ambion, AM2239), along with any drugs used for sample treatment) was dripped onto dishes. Cells were scraped and the lysate was removed and incubated 10 min on ice. The lysate was then clarified by centrifugation for 10 min at 20,000 × g, 4°C and ∼1.1 ml supernatant was recovered.
RNA-seq: mRNA samplewas subjected to DNAseI treatment and 3’ dephpsphorylation using FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific) and T4 PNK (NEB) followed by 3’ adaptor ligation using T4 ligase (NEB). The ligated products used for reverse transcription with SSIII (Invitrogen) for first strand cDNA synthesis. The cDNA products were 3’ ligated with a second adaptor using T4 ligase and amplified for 8 cycles in a PCR for final library products of 200-300bp. Ribo-seq:

treatment_protocol: Cells were infected for 3, 5 or 8 hours before treatment or left uninfected. For Ribo-seq libraries, samples were treated with 100μg/mL CHX for 1 minute. Cells were placed on ice immediately after treatment, washed twice with PBS containing 100μg/mL CHX.

tag: virus strain

value: Calu 3 cells, ATCC HTB-55

value: uninfected


title: Sorted CD3+ adipose tissue T cells from obese mice - rep1

city: Ann Arbor

first: Carey

middle: N

last: Lumeng

state: MI

address: 109 Zina Pitcher Place

department: Pediatrics

institute: University of Michigan

description: 10x Genomics

data_processing:
Libraries were sequenced on Novaseq.  bcl2fastq was used to demultiplex this data
Data was process using the CellRanger count pipeline from 10X Genomics.
Genome_build: mm10
Supplementary_files_format_and_content: Unfiltered feature-barcode matrices from cellranger count

source_name: Adipose tissue T cells

extract_protocol:
Stromal vascular cells were isolated from adipose tissue after collagenase digestion.  Live CD45+CD3+ cells were FACS sorted from stromal vascular fraction cells prior to library construction
10X Genomics Single Cell RNAseq Libraries V2

value: Epididymal adipose tissue

tag: diet

value: high fat diet


title: Sorted CD3+ adipose tissue T cells from lean mice - rep2

description: 10x Genomics

value: normal


title: Calu3_fp_uninf_1

description: Ribo-seq after treatment with Cycloheximide

data_processing:
Library strategy: Ribo-seq
The reads of the ribo-seq libraries was trimmed to remove the linker CTGTAGGCACCATCAAT by using cutadapt.
Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus.
Reads that failed to align to genome, were aligned to the host transcriptome and to the viral breaking points according to strong break point at Kim et. al, plus few breakpoints from  our STAR runs.
The alignments above was made with Bowtie1. In the ribo-seq libraries the p-site was calculated as an offset (adjusted to the read length) from the read start site.
The STAR alignment was made with the flags recommended by Kim et. al. to get all the breakpoints.
Genome_build: Host : hg19 genome and annotation from UCSC, besides the mitochendria genes which are from Ensembl. Virus Genebank NC_045512.2 with 3 changes to match the used strain, 241:C->T, 3037:C->T, 23403:A->G.
Supplementary_files_format_and_content: All processed files are tab delimited files with the number of reads on the transcripts, coding sequence, introns of the host genes, on the coding sequence of the virus, and also global number of reads aligned to the rRNA abd tRNA
Supplementary_files_format_and_content: global.txt: Global number of reads aligned to rRNA, host and Virus
Supplementary_files_format_and_content: transcript_host.txt: For each host gene, number of read aligned uniquely to the transcript
Supplementary_files_format_and_content: cds_host.txt: For each host gene, number of read aligned uniquely to the coding sequence
Supplementary_files_format_and_content: cds_virus.txt: For each viral gene, number of read aligned uniquely to the coding sequence
Supplementary_files_format_and_content: transcript_introns.txt: For each host gene, number of read aligned uniquely to the transcript


title: Calu3_fp_uninf_2


title: 10_Aged


title: P2698


title: 13_Aged


title: Sorted CD3+ adipose tissue T cells from lean mice - rep1

description: 10x Genomics


title: P2623

value: Relapsed


title: P2293


title: 9_Aged


title: P2323

value: De Novo (prior MDS)


title: Calu3_mrna_uninf_1_total

description: RNA-seq without polyA selection


title: RNA-seq1-cKO-1

city: wuhan

first: Haojian

last: Zhang

state: Hubei

address: Donghu Rd

department: Medical Research Institute

institute: Wuhan university

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low quality sequances, then pseudoaligned to GRCm38 whole transcriptome using hisat2(version 2.1.0) with default parameters
FeatureCounts were used to summary raw counts from bam files
rlog normalize  and  differential genes' expression  were performed by  DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include normalzied reads each Sample

source_name: Leukemia cells

extract_protocol:
leukemia cells were collect from bone marrow.Total RNA were extracted with Trizol and mRNA were isolated with Oligo dT beads.
Libraries were prepared according to VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (Part# NR601). Briefly, mRNA was interrupted with metal ions in interrupted buffer , cDNA synthesis using random primers for reverse transcription of mRNA. The cDNA strands in the hybrid double strands were digested by RNaseH to synthesize cDNA complementary strands for cDNA second strand synthesis. Repair sticky ends were repaired to blunt ends   add A-tail,and connection connector.After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: genotype


title: RNA-seq2-cKO-3


title: 8_Aged

value: Aged


title: P3261


title: RNA-seq1-WT-5

value: WT


title: Calu3_mrna_uninf_2

description: RNA-seq with polyA selection


title: Calu3_mrna_uninf_1

description: RNA-seq with polyA selection


title: P985


title: 7_Aged


title: RNA-seq1-WT-4

value: bone marrow


title: 6_Aged


title: Leukemia cells-YBX1-/-_24h

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to GRCh38 whole transcriptome using hisat v2.1.0 with default parameters
T>C conversion was calculated following slamdunk pipeline
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include T>C unnormalized conversion

extract_protocol:
Cell collected at indicated time points was extraction using TRIzol. NEBNext RNA Library Prep Kit (NEB, #E7760) was used for library preparation.
NEBNext RNA Library Prep Kit (NEB, #E7760) was used for library preparation.

treatment_protocol: Cells was labeled with 50μM 4sU (Sigma) for 24h and then washed twice with 1×PBS and incubated with standard medium supplemented with 10mM uridine (Sigma).

tag: time point


title: Jejunum - total RNA - JEJ-28

city: Fermoy

first: Kanishka

last: Nilaweera

address: Moorepark

institute: Teagasc Food Research Centre

extract_protocol:
Rneasy mini kit (Qiagen,74104)
Total RNA extracted using QIAGEN Rneasy Mini Kit (74104) following manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Jejunum


title: Leukemia cells-YBX1-/-_12h


title: 3_Aged


title: 4_Aged


title: RH4_sgSMARCB1_7D_rep2_T_UZH

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

data_processing:
adaptor trimming and QC: fastqc v0.11.7
reads alignment: Hisat2 v2.1.0 with options ?--rna-strandness RF --fr?
BAM generation and index: Samtools v1.9
Mapping QC: Qualimap v2.2.1
read fragment count at the gene level: featurecounts v1.6.3 with the options ?-p -B -O -M --fraction?
differential gene expression: DESeq2 v3.7
Genome_build: GRCH38
Supplementary_files_format_and_content: final expression level of genes in text file format

extract_protocol:
Total RNAs were extracted by RNeasy Plus Mini Kit (Qiagen).
Truseq Stranded Total RNA Library

treatment_protocol: Cas9 expressing RH4 cells were transduced with indicaed and scramble control sgRNAs. Cells were harvested for total RNA isolation after 7 days.

tag: cell line

tag: diagnosis

value: rhabdomyosarcoma

value: CRISPR targeting; sgRNA against SMARCB1 (BAF47); GACGGCGAGTTCTACATGAT, RNA collection 7 days post transduction

tag: antibody


title: RH4_sgscr_7D_rep3_T_UZH

value: CRISPR targeting; sgRNA neg crtl (scrambled); GTAGCGAACGTGTCCGGCGT, RNA collection 7 days post transduction


title: RH4_sgSMARCB1_7D_rep1_T_UZH


title: Leukemia cells-YBX1-/-_18h


title: Leukemia cells-YBX1-/-_3h


title: RH4_sgscr_7D_rep1_T_UZH


title: RH4_sgscr_7D_rep2_T_UZH


title: Leukemia cells-YBX1-/-_1h


title: 2_Aged


title: RH4_sgSMARCB1_7D_rep3_T_UZH


title: MECP2 Macrophage rep1

city: Madison

first: Deepika

last: Rajesh

state: WI

address: 525 Science Dr

department: Life Sciences

institute: Fujifilm Cellular Dynamics Inc.

data_processing:
Base calling was performed using RTA 3 on Illumina Novaseq 6000 platform
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using a splice-aware software Hisat2 v 2.1.0 with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cuffdiff v2.2.1 program with default parameters which includes geometric library normalization method and pooled dispersion method
Cuffdiff output was reformatted to tab-delimited tabular file using in-house perl script
Genome_build: HG38
Supplementary_files_format_and_content: MO_Experiment_FCDI.txt.gz  (tab-delimited text file includes FPKM values for each Sample)

source_name: iPSC

growth_protocol: iPSC were differentiated into Hematopoietic Progenitor Cells (HPC), expanded into Common Myeloid Progenitors (CMPs), and then further differentiatied into end stage Macrophages.

extract_protocol:
Pelleted end stage macrophages were lysed using RLT Lysis buffer and stored at -800C.  RNA extraction was preformed using Rneast Mini Kit according to the manufacturer's protocol.  Post extraction the sample was incubated with Turbo DNase at 37°C for 30 minutes and subsequently re-purified using RNeasy clean-up protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: End stage macrophages were harvested from the cell culture vessel and sample was centrifuged prior to addition of RLT lysis buffer

value: MECP2 HM

tag: engineering target

value: Methly CpG Binding domain

value: iPSC Derived Macrophages

value: Rett Syndrome Model


title: RH4_sgPAX3FOXO1_7D_rep3_T_UZH

value: CRISPR targeting; sgRNA against PAX3-FOXO1; CACGAATGAACTTGCTGTGT, RNA collection 7 days post transduction


title: Leukemia cells-YBX1-/-_0.5h


title: SNCA A53T Macrophage rep1

value: SNCA A53T HO

value: Alpha-synuclein gene

value: PD Disease Model


title: 5_Aged

data_processing:
Base calling was performed by VBCF NGS unit
Mapping: iterative mapping (see Imakaev et al, 2012) using bwa
Read filtering was performed as in Flyamer et al., 2017:
Summary of filtering: If two reads map to the same strand, and each side of the read is within 500 bp of any side of the other read, we retain only one copy of the read. We separate the genome into 500 bp bins. If any two bins are interacting more than once, only one interaction is counted. Since each region is only present in the single cell up to 4 times (in oocytes), we eliminated all 500 bp bins that form more than 8 unique interactions with other bins.
Filtered reads were then binned at different resolutions (we provide 4 resolutions) using read start as a read position and stored in the Cool file format. No normalization was applied to the data.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix of whole-genome locus interaction frequencies binned at 1kb, 10kb, 40kb, and 100kb resolutions stored in the Cool file format.

source_name: oocyte


title: RH4_sgPAX3FOXO1_7D_rep2_T_UZH


title: breast tumour 97C

city: Dunedin

first: Anita

last: Dunbier

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol of iScan

data_processing: The data was filtered to remove any non-expressed probes using the detection p-value from Illumina. Across all samples probes for which the intensity values were not significantly different (p>0.01) from the negative controls were removed from the analysis. Following filtering the data was transformed and normalized using variance-stabilizing transformation and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization.

source_name: breast tumour

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: mRNA from tumour biopsies taken 16 weeks after commencement of anastrazole treatement were extracted with an RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).

tag: Sex

value: female

tag: timepoint

value: 16 weeks

value: breast tumor

tag: patient

tag: age

tag: size

tag: grade

tag: nodal status

tag: her2 status

tag: pgr status pre_treatment

tag: response

value: Stable/No Response


title: breast tumour 31C

tag: tissue

value: Partial Response


title: breast tumour 211C


title: breast tumour 209C


title: breast tumour 133C

value: Partial/Complete Response


title: RH4_sgPAX3FOXO1_7D_rep1_T_UZH

value: rhabdomyosarcoma

tag: treatment

tag: genotype


title: Leukemia cells-YBX1-/-_0h

value: bone marrow

tag: strain

tag: time point


title: Leukemia cells-YBX1-/-_6h


title: Leukemia cells-WT_24h

value: WT


title: GRN R493X Macrophage rep2

value: GRN R493X HO

value: Progranulin gene

tag: cell type

tag: disease state

value: NCL Disease Model


title: RH4_sgBRG1_7D_rep3_T_UZH

tag: cell line

tag: diagnosis

value: CRISPR targeting; sgRNA against BRG1; GGGGCAGCAGCATTCGCCAT, RNA collection 7 days post transduction

tag: antibody


title: 1_Aged

tag: condition

value: Aged


title: 01279 AHN Macrophage rep3

value: Apparently Healthy Normal

tag: engineering target

value: iPSC Derived Macrophages

value: Parental line


title: RH4_sgBRG1_7D_rep1_T_UZH


title: Leukemia cells-WT_18h


title: RH4_sgBRG1_7D_rep2_T_UZH


title: Leukemia cells-WT_6h


title: GRN R493X Macrophage rep3


title: Leukemia cells-WT_3h


title: Leukemia cells-WT_12h


title: 01279 AHN Macrophage rep2


title: HepG2-M2MEHP-rep3

city: Beijing

first: Hui

last: Yang

address: 7 Panjiayuan Nanli, Room314

department: Department of Toxicology

institute: China National Center for Food Safety Risk Assessment (CFSA)

description:
gene_fpkm.xls
M2MP3

data_processing:
Illumina novaseq6000 sequencer and software used for sequencing and basecalling.
Sequenced reads were trimmed for adaptor sequence,reads containing ploy-N and low quality reads from raw data, then mapped to reference genome of hg38 using HISTA2. The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.  Differential expression analysis of two groups were performed using DESeq2.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected.
Genome_build: GRCh38(hg38)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: liver hepatocellular carcinoma

growth_protocol: HepG2 cells were routinely maintained in MEM complete medium with sodium pyruvate,non-essential amino acid and fetal bovine serum.

extract_protocol:
After treatment, cells were collected and flash frozen liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After attachment, cells were treated with MEHP (200μM) or combination of MEHP(200μM) and M1/M2 macrophages (30,000 cells/well) for 24h.

value: hepatocellular carcinoma cells

value: treated with combination of MEHP (200uM) and M2 macrophages (30,000 cells/well) for 24h


title: breast tumour 14C

tag: Sex

value: female

tag: timepoint

value: 16 weeks

value: breast tumor

tag: patient

tag: age

tag: size

tag: grade


title: breast tumour 204C

tag: tissue

tag: nodal status

tag: her2 status

tag: pgr status pre_treatment

tag: response

value: Stable/No Response


title: breast tumour 202C


title: breast tumour 208C

value: Partial Response


title: breast tumour 194C


title: HepG2-M2MEHP-rep2

description:
gene_fpkm.xls
M2MP2

tag: cell type

tag: treatment


title: Leukemia cells-WT_1h

value: bone marrow

tag: strain

tag: genotype

tag: time point


title: 01279 AHN Macrophage rep1

tag: engineering target

tag: disease state


title: Leukemia cells-WT_0.5h

value: WT


title: GRN R493X Macrophage rep1

value: GRN R493X HO


title: breast tumour 177C

tag: Sex

tag: timepoint


title: HepG2-M2MEHP-rep1

description:
gene_fpkm.xls
M2MP1


title: Leukemia cells-WT_0h


title: breast tumour 119C

tag: patient

tag: age


title: HepG2-M1MEHP-rep2

description:
gene_fpkm.xls
M1MP2

value: treated with combination of MEHP (200uM) and M1 macrophages (30,000 cells/well) for 24h


title: HepG2-M1MEHP-rep1

description:
gene_fpkm.xls
M1MP1


title: patient#3 post-Neosporin

city: Baltimore

first: Luis

last: Garza

state: Maryland

address: 1551 Orleans Street

department: Dermatology

institute: Johns Hopkins University

description:
Gene expression data from wounded human popliteal fossae with or without antibiotic treatment.
patient#3 post-Neosporin

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform. RMA normalization was used to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.
Clariom_S_Human.r1.pgf
Clariom_S_Human.na36.mm10.transcript.csv

source_name: Skin treated with Neosporin

label_protocol: Biotinylated cRNAs were prepared with the Affymetrix GeneChip 3' IVT Plus Kit per manufacturer's instructions.

growth_protocol: 4-mm punch biopsies, microbiome swabs, and clinical photographs of bilateral popliteal fossae (PF). were obtained from participants under the above IRB protocol. Participants were asked to avoid washing 24 hours prior to sample collection and to use scent-free, non-antibacterial soap for the duration of the study. Samples were collected at two visits spanning an average of 15 days, including at a baseline visit prior to intervention (Day 0) and at a follow-up visit following secondary intention to obtain post-treatment samples (Day 15). A total of 12 skin biopsies were obtained from 3 individuals at identical anatomical sites across 2 time points. For tissue collection, 1% lidocaine with epinephrine was administered, and 4mm full-thickness punch biopsies were obtained from the center PF.

extract_protocol: Total RNA was isolated from cells using the RNeasy kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: For the left PF, the wound was washed with Hibiclens (Molnlycke, 57516), and Neosporin was applied (Johnson & Johnson); for the right PF, Vaseline (Unilever) was applied. Both sites were occluded with bandages, and participants were asked to rebandage left and right PF daily with Neosporin and Vaseline, respectively, until wound closure to evaluate the changes in gene expressions.

tag: individual

value: Popliteal fossa

value: Neosporin


title: Nematostella_ACME_scRNAseq

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

data_processing:
Mapping, demultiplexing and UMI counting was performed using CellRanger v5.0.1 (10x genomics), using as a reference the Nematostella vectensis genome (https://mycocosm.jgi.doe.gov/Nemve1/Nemve1.home.html) with gene interval definitions as in the Nematostella reference single-cell atlas (Sebe-Pedros et al. 2018, doi.org/10.1016/j.cell.2018.05.019)
Genome_build: Nematostella vectensis genome (https://mycocosm.jgi.doe.gov/Nemve1/Nemve1.home.html)
Supplementary_files_format_and_content: RDS

organism: Nematostella vectensis

source_name: Juvenile polyps

extract_protocol:
ACME protocol (described in this paper)
10x genomics Single Cell 3' v3.1 chemistry

tag: stage/cell type

value: Juvenile polyps

value: Wild type


title: patient#3 post-vaseline

description:
Gene expression data from wounded human popliteal fossae with or without antibiotic treatment.
patient#3 post-vaseline

source_name: Skin treated with Vaseline

tag: tissue

value: Vaseline


title: HepG2-MEHP-rep3

description:
gene_fpkm.xls
MP3

value: treated with MEHP (200uM) for 24h


title: patient#2 post-Neosporin

description:
Gene expression data from wounded human popliteal fossae with or without antibiotic treatment.
patient#2 post-Neosporin


title: HepG2-M1MEHP-rep3

description:
gene_fpkm.xls
M1MP3

value: hepatocellular carcinoma cells


title: breast tumour 169C

tag: size

tag: grade

tag: nodal status

tag: her2 status


title: breast tumour 114C

tag: pgr status pre_treatment


title: breast tumour 116C

tag: response


title: a19: WT_Kidney_SD

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

country: Germany

institute: Martin Luther University - Halle-Wittenberg

data_processing:
Alignment (HISAT2 2.1.0)
Counting (featureCounts - 2.0.0)
Genome_build: mm10
Supplementary_files_format_and_content: txt files containing raw counts obtained after Counting with featureCounts

source_name: Kidney from mouse with endothelial cells-EGFR WT

growth_protocol: Mice were kept at constant temperature of 22±2°C, relative humidity of 30–60%, under a 12/12 h light-dark cycle with ad libitum access to water and standard chow. Recently, we generated and described an inducible knock out for EGFR in VSMC via the Cre/loxP system by mating EGFRflox/flox C57BL/6 mice (originally provided by Maria Sibilia, Vienna, Austria) with the B6.Cg-Tg(Tek-cre)1Ywa/J mouse (Cre-Recombinase under control of the Tie2-promotor, purchased from JAX, first described by Dr. Masashi Yanagisawa, Southwestern Medical School)

extract_protocol:
Total RNA was isolated with TriZol Reagent, following the manufacturer's instructions. Eventual gDNA contaminations were removed using Turbo DNAse (ambion, Life Technologies).
mRNA were enriched using oligo(dT) beads and then fragmented randomly by adding fragmentation buffer. cDNA synthesis is done with random hexamers primers and is followed by second strand synthesis after sequencing adaptor ligation. Double-stranded cDNA libraries are then subjected to size selection (250-300bp) and PCR enrichment. Libraries were pooled before clustering on flowcell for sequencing.

treatment_protocol: Mice received 1:1 HFD:SD for seven days at an everage age of 5 weeks, at 6 weeks of age chow was changed to HFD alone for 18 weeks. Afterwards mice were anaesthetized with isofluran, sacrificed in deep narcosis by cervical dislocation. Aortas were freed of adjacent fat and connective tissue, both organs were snap frozen in liquid nitrogen.

tag: organ

value: Kidney

tag: genotype

tag: treatment

value: SD


title: HepG2-MEHP-rep1

description:
gene_fpkm.xls
MP1

tag: cell type


title: HepG2-MEHP-rep2

description:
gene_fpkm.xls
MP2


title: patient#1 post-Neosporin

description:
Gene expression data from wounded human popliteal fossae with or without antibiotic treatment.
patient#1 post-Neosporin


title: patient#2 post-vaseline

description:
Gene expression data from wounded human popliteal fossae with or without antibiotic treatment.
patient#2 post-vaseline


title: a16: WT_Kidney_SD


title: a17: WT_Kidney_SD


title: HepG2-rep3

description:
gene_fpkm.xls
CT3

value: treated with 0.1% DMSO


title: a20: WT_Kidney_SD


title: breast tumour 89C

tag: Sex

value: female

value: 16 weeks

value: breast tumor


title: breast tumour 74C

tag: timepoint


title: patient#3 pre-Neosporin

description:
Gene expression data from unwounded human popliteal fossae.
patient#3 pre-Neosporin

source_name: Skin before treatment

value: Untreated


title: a15: WT_Kidney_HFD

value: WT

value: HFD


title: a18: WT_Kidney_SD


title: breast tumour 83C

tag: patient

value: Stable/No Response


title: breast tumour 165C

tag: age

value: Partial Response


title: HepG2-rep2

description:
gene_fpkm.xls
CT2


title: a14: WT_Kidney_HFD


title: breast tumour 101C


title: HepG2-rep1

description:
gene_fpkm.xls
CT1


title: breast tumour 33C


title: a13: WT_Kidney_HFD


title: LNCaP-95 [LN95_P24_290]

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: LNCaP-95 PDX tumor

data_processing:
PDX Sequencing reads were mapped to the hg38 human and mm10 mouse genomes using STAR.v2.7.3a. Sequences aligning to the mouse genome deriving from potential contamination with mouse tissue were removed from the analysis using XenofiltR . PrEC Cell line sequencing reads were mapped to the hg38 human genome only using STAR.v2.7.3a.
Gene level abundance was quantitated from the filtered human alignments in R using the Genomic Alignments Bioconductor package using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: LNCaP-95 PDX tumor

growth_protocol: Triple immune‐deficient NSG (i.e. NOD.Cg‐PrkdcScidIl2rgtm1Wji/Szj), adult (>8 week old) male mice obtained from the Sidney Kimmel Comprehensive Cancer Center (SKCCC) Animal Core Facility were used for xenografting. For each line tested, 100 μl of sterile saline containing 2 x 106 cancer cells was mixed at 4˚C with 100 μl of Matrigel obtained from BD Biosciences and then the mixture inoculated subcutaneously in the flank of 5 intact and 5 castrated adult male NSG mice.

extract_protocol:
Total RNA was extracted from flash-frozen xenograft tissue using the Qiagen RNeasy Kit, (Qiagen Inc.), according to the manufacturer's protocol. On-column DNase digestion was performed.
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.
Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 or NovaSeq generating 50 bp paired end reads.

tag: gender

value: male

value: prostate cancer


title: patient#3 pre-vaseline

description:
Gene expression data from unwounded human popliteal fossae.
patient#3 pre-vaseline

tag: individual

value: Popliteal fossa


title: patient#2 pre-Neosporin

description:
Gene expression data from unwounded human popliteal fossae.
patient#2 pre-Neosporin

tag: tissue


title: patient#1 post-vaseline

description:
Gene expression data from wounded human popliteal fossae with or without antibiotic treatment.
patient#1 post-vaseline

value: Vaseline


title: a11: WT_Kidney_HFD


title: a12: WT_Kidney_HFD


title: YBX1-Flag-IP-rep2

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to Hg19 whole transcriptome using hisat v2.1.0 with default parameters
bigWig files were generated using Deeptools v2.0 bamCoverage with parameters --binSize 10 --normalizeUsingRPKM
Peak were called from macs2(version 2.2.7.1) with q-value <= 0.05
Genome_build: Hg19
Supplementary_files_format_and_content: .bigWig files for each sample

growth_protocol: DMEM with 10% FBS, 100 IU ml−1 penicillin and 100μg ml−1 streptomycin.

extract_protocol:
RNA was harvested using Trizol reagent.mRNA are isolated，fragmented and Ybx1-specific antibodies are used to immunoprecipitate RNA. Ybx1 binding RNA is reverse-transcribed to cDNA through first strand synthesis and second strand synthesis
Illumina TruSeq DNA Sample Prep Kit (Cat#15026486) was used with DNA for the construction of sequencing libraries. Libraries were prepared for sequencing using Illumina protocols.

treatment_protocol: Flag-Ybx1 were overexpressed in 293T

tag: cell line

value: Flag-YBX1 overexpression

tag: rip antibody

value: FLAG (M2, F3165, Sigma-Aldrich)


title: PrEC [PrEC_4d]

description: PrEC (human prostate basal epithelial cells )

growth_protocol: Primary cultures of human prostate basal epithelial cells (i.e. PREC) were established and grown in low calcium-serum free defined media as described (PMID 24948876.)

extract_protocol:
Total RNA was extracted from frozen cell pellets using the Qiagen RNeasy Kit, (Qiagen Inc.), according to the manufacturer's protocol. On-column DNase digestion was performed.
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.
Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 or NovaSeq generating 50 bp paired end reads.

value: human prostate basal epithelial cells


title: patient#2 pre-vaseline

description:
Gene expression data from unwounded human popliteal fossae.
patient#2 pre-vaseline


title: breast tumour 18C

tag: size

tag: grade

tag: nodal status