title: MVV vector in CPT3-LHKO1 cells

data_processing:
Paired-end reads were cropped to remove linker and virus LTR sequences.
Cropped paired reads were aligned to sheep genome OviAri4 using BWA MEM.
High-quality alignemnts were selected with samtools view -F 4 -F 256 -q 1.
The remaining alignements were parsed to select unique integration sites and extract coordinates of the central base pair step for each site.
Genome_build: OviAri4
Supplementary_files_format_and_content: bed

organism: Ovis aries

source_name: CPT3-LHKO1 cells infected with MVV vector

tag: infection protocol

value: Cells were infected with MVV vector and processed for linker-mediated PCR 5 days post infection.

value: CPT3-LHKO1 was generated by co-transfection of CPT3 with CRISPR-Cas9 RNPs targeting sheep PSIP1 and HDGFL2 genes.


title: shGPR56weak_A

status: Public on Feb 06 2022

type: SRA

city: Heidelberg

first: Christian

last: Arnold

state: Baden-Württemberg

address: Meyerhofstraße 1

country: Germany

institute: EMBL

library_source: transcriptomic

data_processing:
Adaptor trimming with cutadapt v1.18 (parameters: -m 30)
Alignment with STAR v2.6.1a_08-27 (parameters: --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignMatesGapMax 1000000 --alignIntronMin 20 --alignIntronMax 1000000 --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04. For gene annotation, we used the Gencode  v28 annotation. )
Gene counts with featureCounts v1.6.3 (parameters: -p -B -C -Q 10 -O -s 2 -t exon -g gene_id)
Differential gene expression DESeq2 v1.24.0 with the design formula ‘‘condition,’’ and size factor normalization to compare both the weak and the strong KD versus control. We computed and subsequently used the shrunken log2 fold-changes via lfcShrink from DESeq2 with the apeglm method.
Genome_build: hg38
Supplementary_files_format_and_content: We provide raw gene counts for each sample as well as the results of the DESEq2 analysis as described above. In addition, the final results from DESEq2 are provided, with base mean, shrunken log2 fold-change estimates, p-values, normalized read counts per sample, gene names & synonyms & Ensembl IDs

molecule: total RNA

organism: Homo sapiens

source_name: Cord Blood CD34+

growth_protocol: CD34+ cells were enriched from umbilical cord blood mononucleated cells (MNCs) through magnetic ultrabeads and grown and transduced in cytokine supplemented culture media.

extract_protocol:
RNA was isolated with Trizol reagent plus an additional purification step with RNAeasy Mini columns.
Ovation Human FFPE RNA-Seq Library Systems (Nugen)

treatment_protocol: GFP+ cells were sorted 72 hours post transduction and resuspended in Trizol.

tag: fluorescence

value: GFP

tag: individual

value: pooled

tag: cell type

value: Cord Blood CD34+

tag: knockdown


title: DAAO LV 7138

city: Boston

first: Fotios

last: Spyropoulos

state: USA

address: 75 Francis Street Thorn 1005

department: Pediatric Newborn Medicine

country: USA

institute: Brigham and Women's Hospital/Harvard Medical School

data_processing:
Reads (Fastq files) obtained from paired-end sequencing were aligned were to the rat genome (Rnor 6.0) using STAR (v2.7.0a)
Quality control was performed on raw reads and alignment results using fastQC and Qualimap, respectively. Sample clustering was visualized using principal component analysis.
Differential expression analysis was performed using DESeq2 (v1.26.0) using standard parameters, comparing DAAO rats with their controls
Genome_build: Rnor 6.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Heart

extract_protocol:
Hearts were removed, snap frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. RNA quantification and sample integrity were then analyzed using a Nanodrop spectrophotometer and an Agilent 2100 bioanalyzer, respectively.
Library preparation and sequencing were performed by Novogene (Sacramento, CA) using an Illumina Platform PE150.

tag: strain

value: WI

tag: tissue

value: Left ventricle + septum tissue


title: DAAO LV 7142


title: 23207

library_source: genomic

data_processing:
Adaptor trimming with Trimmomatic v0.38 (parameters: ILLUMINACLIP::1:30:4:1:true TRAILING:3 MINLEN:20)
Alignment with Bowtie2 v2.3.4.3 (parameters: -X2000 --very-sensitive -t)
Post-alignment processing (using samtools v1.9, Picard tools v2.18.16-SNAPSHOT): (0) cleaning the BAM file with Picard CleanSam, FixMateInformation, AddOrReplaceReadGroups and ReorderSam,  (1) removing mitochondrial reads and reads from non-assembled contigs or alternative haplotypes, (2) marking and removing duplicate reads with MarkDuplicates, (3) filtering reads with a mapping quality below 10 (-F 4 -q 10), (4) adjusting read start sites as described previously by 4 and -5 base pairs, and (5) removing reads with insertions or deletions using samtools, followed by final cleaning and sorting using Picard SortSam, CleanSam, and FixMateInformation
Peak calling with MACS2 (parameters: -q 0.01 -g hg19 --nomodel --keep-dup all) followed by filtering using bedtools subtract v2.27.1 against the publicly available blacklist regions
Genome_build: hg19
Supplementary_files_format_and_content: We provide the individual peak files as well as the main consensus peak set along with raw read counts for each sample

molecule: genomic DNA

source_name: AML cells

extract_protocol:
Briefly 50,000 cells from frozen samples were collected, then placed into lysis buffer (10 mM Tris·Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween 20), followed by Tn5 transposase-mediated tagmentation and adaptor incorporation at sites of accessible chromatin carried out using the Nextera DNA Library Prep kit (FC-121-1030, Illumina) at 37°C for 30 min.
Library amplification was performed using NEB Nex High-Fidelity 2x PCR Master Mix (M0541L, NEB) and primer combinations provided in Nextera DNA Library Prep kit.  The library was optimized for enrichment for 100-1000 bps fragments using SPRI beads based size-selection and the quality of the purified DNA library was analyzed on a Bioanalyzer (2100 Expert software, Agilent Technologies) using High Sensitivity DNA Chips (5067-4626; Agilent Technologies Inc.). The appropriate concentration of sample was determined using the Qubit Fluorometer (Molecular Probes). Ten 40nM samples were pooled and run on a NextSeq 500/550 High Output Kit (20024907; Illumina, Inc. San Diego, CA) and the NextSeq 500 Illumina Sequencer to obtain paired end reads of 75 bp.

value: primary AML cells


title: 14SE436_iBAT_Cold_miRNA

type: RNA

city: Bellaterra

first: Jordi

last: Rodo

state: Barcelona

address: Carrer de la Vall Moronta, edifici H

country: Spain

institute: CBATEG, UAB

hyb_protocol: The kit GeneAtlasTM Hybridization, Wash, and Stain Kit for miRNA Array Strips was used following the protocol by Progenika Biopharma (Progenika Biopharma, Grifols, Barcelona, CAT, ES).

scan_protocol: This procedure was performed by Progenika Biopharma (Progenika Biopharma, Grifols, Barcelona, CAT, ES).

data_processing: The Transcriptome Analysis Console (TAC) software version 4.0.2.15 was used to perform quality control, data normalization (using RMA+DABG) and statistical tests. Data were annotated using the “miRNA-4_1-st-v1 Transcript Cluster Annotations” from the 22/9/2016.

label: biotin

organism: Mus musculus

source_name: Interscapular Brown Adipose Tissue_4ºC

label_protocol: From 500ng of each sample, a Poly(A)-tail was first bound to the total RNA with a PolyA Polymerase, and then 3DNA dendrimers were biotin-labeled, following the Affymetrix FlashTagBiotin HSR (Affymetrix) protocol. Then a mix of RNA Spike controls included in the kit was added to the starting RNA to verify that the processing had proceeded as expected.

extract_protocol: Mice were anesthetized by inhalation anesthesia and euthanized by decapitation. Tissue samples were obtained in the morning and were immediately frozen in liquid nitrogen (N2) and then stored at -80 ºC. Tissues were homogenize using the lysis/binding buffer provided in the mirVana miRNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA, USA). Then miRNAs were extracted using this mirVana kit.

treatment_protocol: Male mice of the strain C57Bl/6JOlaHsd of 8 weeks of age were divided into two groups that were either exposed during 4 days to 4ºC in a humidity and temperature-controlled refrigerator room or housed at 22 ºC. Each mouse was housed individually, and the bedding of the cage was removed to keep mice from nesting to help regulate body temperature. Day and night cycles were maintained with 12 hours of light and 12 hours of darkness.

tag: age(weeks)

tag: gender

value: Male

tag: stimulus

value: Cold

tag: temperature(degree celsius)


title: CTL LV_7005


title: Plasmid library

city: New York

first: Danny

last: Reinberg

state: New York

address: 522 First Avenue, 2nd floor, Room 211

department: Biochemistry

institute: New York University School of Medicine

description:
lentiviral plasmid library
libAB_screen12.count.txt

data_processing:
Overall processing by using MaGeCK tools (Li et al., 2014 and Li et al., 2015)
Alignment to CRISPR library and counts were obtained by using "count" function within the MaGeCK tools
Relevant comparisons were made by using "test" function within the MaGeCK tools
Supplementary_files_format_and_content: Count files in "txt" format

organism: synthetic construct

source_name: lentiviral plasmid library

growth_protocol: ESCs were cultured in standard medium supplemented with LIF and 2i conditions (1 mM MEK1/2 inhibitor (PD0325901, Stemgent) and 3 mM GSK3 inhibitor (CHIR99021, Stemgent)). For motor neuron (MN) differentiation, the previously described protocol in Narendra et. al. (2015) was applied. Briefly, ESCs were differentiated into embryoid bodies in 2 days, and further patterning was induced with addition of 1 μM all-trans-retinoic acid (RA, Sigma) and 0.5 μM smoothened agonist (SAG, Calbiochem).

extract_protocol:
Cells were harvested, and genomic DNA was isolated as described before (Sanjana et al., 2014 and Shalem et al., 2014).
CRISPR libraries were prepared at each time point, and/or sorted population according to previously described protocol mainly consisting of two-step PCRs (Sanjana et al., 2014 and Shalem et al., 2014)
CRISPR knock-out

value: lentiviral plasmid library

tag: genotype

value: GeCKO v2 library expressing

tag: developmental stage


title: DAAO LV 7137


title: SK-N-BE(2) xenograft - 4SC-205_rep2

city: Barcelona

first: Marc

last: Masanas

state: - None -

address: Pg Vall d’Hebron 119 129, Mediterranean Building

institute: Vall Hebron Research Institute

description: SEGURAMIG_07_SKNBE2_treated_vs_vehicle_norm_counts

data_processing:
Base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA v3.4.4)
RNA-seq reads were mapped against human reference genome (GRCh38) using STAR software version 2.5.3a (A. Dobin et al., Bioinformatics, 2013) with ENCODE parameters.
Genes were quantified using RSEM version 1.3.0 (B. Li and C. N. Dewey., Bioinformatics, 2011) with default parameters and annotation file from GENCODE version 34.
Differential expression analysis was performed with DESeq2 v1.26.0 R package (M. I. Love, et al., Genome Biol., 2014) using a Wald test to compare vehicle and treated samples.
Genome_build: Genome Reference Consortium Human Build 38
Supplementary_files_format_and_content: Comma and space-delimited text files include basemean values for each sample

source_name: Tumor

growth_protocol: SK-N-BE(2) (5,000,000 cells/flank) were subcutaneously injected into the right flank of 6-week old female Fox Chase SCID mice (Charles River) in  300 µL of PBS:Matrigel.

extract_protocol:
Tumors were excised and total RNA was isolated using the miRNeasy mini kit (Qiagen). Qubit® RNA HS Assay (Life Technologies) and RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent) were used to determine the total RNA quality and quantity.
The RNASeq libraries were prepared following the TruSeq® Stranded mRNA LT Sample Prep Kit protocol (Illumina). Total RNA (500ng) was enriched for the polyA mRNA fraction and fragmented by divalent metal cations at high temperature. In order to achieve the directionality, the second strand cDNA synthesis was performed in the presence of dUTP. The blunt-ended double stranded cDNA was 3´adenylated and Illumina platform compatible adaptors with unique dual indexes and unique molecular identifiers (Integrated DNA Technologies) were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay (Agilent).The libraries were sequenced on NovaSeq 6000 (Illumina) with a read length of 2x51bp.

treatment_protocol: When tumors size was 200 mm3, mice were randomized in two groups and treated by oral gavage with vehicle (5% Polyethylene glycol 400 (PEG400, Fisher Scientific, 11449467), 0.9% NaCl, pH 3-4) or with 40 mg/kg 4SC-205 for 24 h.

tag: tumor type

value: High-risk neuroblastoma

tag: treatment

value: Treated with 4SC-205 for 24 hours


title: BT12_K27ac

city: Chicago

first: Yongzhan

last: zhang

state: Illinois

address: 303 East Superior Street

department: Department of Pediatrics, Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
TrimGalore-2 were used to remove the adaptor sequence and applied Bowtie 2 to align reads of the ChIP-seq samples to the UCSC hg19 reference genome
MACS2 were used to call the binding peaks.
P-values of differentially enriched ChIP-seq peaks between conditions were calculated using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated by deeptools

source_name: AT/RT cell

extract_protocol:
Chromatin was sonicated with the Covaris E220 for 4 minutes with 10% duty cycle, 140 peak intensity power, and 200 cycles per burst. Immunoprecipitations were carried out with rabbit monoclonal antibody directed against H3K27me3 (C36B11, #9733) and H3K27ac (D5E49, #8173) from Cell Signaling Technologies and Dynabeads Protein G (Invitrogen, Carlsbad, CA).
DNA libraries were prepared with KAPA HTP Library Preparation Kit (Roche, Basal, Switzerland)

value: 0.3 μM JQ1

tag: cell line

tag: chip antibody


title: 22412


title: SK-N-BE(2) xenograft - 4SC-205_rep1


title: shGPR56strong_A


title: 14SE429_iWAT_Cold_miRNA

source_name: Inguinal White Adipose Tissue_4ºC


title: 14SE428_iWAT_Cold_miRNA


title: wt_240J_60min

status: Public on Feb 05 2022

first: Evgeny

last: Nudler

state: NY

address: 450 E 29th St

institute: NYU Medical Center

data_processing:
Library strategy: CPD-Seq
Reads aligned using Bowtie, parameters: -S -m1 –seed 123.
Samtools was used to split reads based on fwd or rev orientation.
Custom scripts were used to produce TT-counts per gene.
Genome_build: U00096.3
Supplementary_files_format_and_content: *_TTcounts.csv: TT-counts normalized to seq depth and TT per gene.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli cells

extract_protocol:
Samples were lysed with lysozyme and DNA extraction was performed using Monarch Genomic DNA Purification Kit (NEB).
Libraries were prepared with sonication and the CPD-Seq protocol (Mao et. al).

value: WT

tag: time point

value: 60 min


title: BT12_H3K27me3

value: 6 μM GSK126


title: Rho-D210G

data_processing:
Reads aligned using Bowtie2, parameters: –quiet, -p 2, -x
Samtools was used to split reads based on fwd or rev orientation.
HTSeq used to produce gene feature count txt files.
Genome_build: U00096.3
Supplementary_files_format_and_content: *genes.txt: Gene feature raw counts (not normalized).

extract_protocol:
Samples were lysed with lysozyme and RNA extraction was performed using Mastpure DNA and RNA extraction kit (lucigen), treated with Turbo DNA Free and rRNA was removed using Ribominus (Thermo Fisher).
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit.


title: SK-N-BE(2) xenograft - 4SC-205_rep3


title: 14SE427_iWAT_Cold_miRNA


title: MVV vector in CPT3-LHKO2 cells

city: London

first: Peter

middle: P

last: Cherepanov

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

source_name: CPT3-LHKO2 cells infected with MVV vector

growth_protocol: Cells were cultured at 37°C in 5% CO2 atmosphere in Dulbecco's modified Eagle medium (DMEM, Life Technologies) supplemented with 10% heat-inactivated fetal bovine serum (FBS) and antibiotic/antimycotic solution (Sigma-Aldrich).

extract_protocol: Genomic DNA isolated from cells 5 days post-infection with MVV vector was processed for linker-mediated PCR, and the amplified viral LTR-chromosome junctions were sequenced. To this end, genomic DNA, digested with MseI overnight at 37°C, was ligated to a double-stranded DNA linker containing 5'-TA overhang overnight at 12°C. Customized DNA linkers were used in conjunction with barcoded primers to aid in multiplexing and prevent crosstalk between samples. The first round and the nested MVV U5 primers were 5'-CTAATTCCGTGCAACACCG and 5'-AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TNN NNN NCA ACA CCG GAG CGG ATC, respectively (underlined sequence represents the 6 nucleotides barcode specific to LTR primer for multiplexing). The nested PCR primers contained Illumina adaptor sequences appended at the 5' ends. The PCR products, multiplexed on a single lane of a flow cell, were subjected to 150-bp paired-end sequencing on a HiSeq-4000 Illumina instrument.

tag: infection protocol

value: Cells were infected with MVV vector and processed for linker-mediated PCR 5 days post infection.

value: CPT3-LHKO2 was generated by co-transfection of CPT3 with CRISPR-Cas9 RNPs targeting sheep PSIP1 and HDGFL2 genes.


title: mfd_plus_UV_rep2

value: mfd(-)


title: shLuc_ctrl_A

tag: fluorescence

value: GFP

tag: individual

value: pooled

value: Cord Blood CD34+


title: mfd_plus_UV_rep1


title: CTL LV_7118

value: WI

value: Left ventricle + septum tissue


title: shGPR56weak_B

tag: cell type

tag: knockdown


title: SK-N-BE(2) xenograft - Vehicle_rep3

value: Untreated


title: 14SE426_iWAT_Cold_miRNA

tag: strain

value: Male

value: Cold


title: MVV vector in CPT3-LKO1 cells

source_name: CPT3-LKO1 cells infected with MVV vector

value: CPT3-LKO1 was generated by transfection of CPT3 with CRISPR-Cas9 RNPs targeting sheep PSIP1 gene.


title: SK-N-BE(2) xenograft - Vehicle_rep2

value: High-risk neuroblastoma


title: shGPR56strong_B


title: CTL LV_7000

tag: tissue


title: WT_minus_UV_rep1


title: WT_plus_UV_rep2


title: MVV vector in CPT3 cells

source_name: CPT3 cells infected with MVV vector

value: CPT3 is a subclone of CPT-Tert, an ovine choroid plexus cell line immortalized by co-expression of simian virus 40 large T antigen and human telomerase.


title: L187R_60J_0min


title: D210G_60J_0min


title: wt_5_60J_20min

value: WT


title: D210G_60J_20min


title: SK-N-BE(2) xenograft - Vehicle_rep1


title: Rho-L187R


title: mfd_rif_60J_0min


title: wt_5_60J_NT

value: NT


title: WT


title: mfd_rif_60J_20min


title: L187R_60J_20min


title: L187R_60J_NT


title: WT_plus_UV_rep1


title: WT_minus_UV_rep2


title: mfd_minus_UV_rep2


title: D210G_60J_NT


title: MSK74711 PDX sample

city: Cambridge

first: Qian

last: Qin

state: MA

address: 24 Peabody Terrace, Unit 2002

department: Molecular Pathology Unit

institute: Massachusetts General Hospital

description: 10X sequencing, add more detailed information

data_processing:
Cellranger (v3.1.0) mkfastq was used to convert BCL into demultiplexed FASTQ
Cellranger (v3.1.0) count was used to perform sequence alignment, basic read quality filtering, cell barcode and unique molecular identifier (UMI) counting with the corresponding species reference genomes and transcriptome annotations.
scrublet (v0.2.1) was used to identify doublets within the single cell RNA-seq
Seurat (v3.2.2) was used for downstream quality control, normalization, dimensional reduction, differential gene expression analysis and visualization
The differentially expressed genes were analyzed by GSEAsig (https://www.gsea-msigdb.org/gsea/msigdb/annotate.jsp) and ClusterProfiler (v3.19)  based on the annotated gene sets from the Molecular Signature Database (MSigDB)
Cellassign was used to classify the tumor cells and non-tumor cells
Downstream analysis scripts were uploaded to https://github.com/qinqian/rms_analysis
Genome_build: hg19
Supplementary_files_format_and_content: tsv.gz, mtx.gz, csv files contain cellranger output
Supplementary_files_format_and_content: rds files contain the Seurat output R objects

source_name: Rhabdomyosarcoma

growth_protocol: PDX/SC PDX samples were maintained in the NSG (NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ) mice before collecting for the single-cell profiling. RD cells were grown either in DMEM/10%FBS supplemented with penicilim/strepmycin, or differentiating medium with DMEM/F12/2%Horse Serum/PenStrep.

extract_protocol:
PDX/SC PDX samples were harvested by necropsy. Dead cells were removed using a dead cell removal kit (Miltenyi Biotec, cat No. 130-090-101) and mouse cells were removed by mouse cell depletion kit (Miltenyi Biotec, cat No. 130-104-694). RD cells were dissociated by 0.05% Trypsin/EDTA for single-cell suspension. For primary tumors in frozen OCT block, cells were thawed and nuclei were extracted by TST extraction buffer described in Slyper et al. 2020, Nature Medicine. Then dissociated cells from all these three types of samples were loaded with 10X Genomics GEM-RT kit for barcoded RNA extraction, cDNA amplification and library construction.
10X Genomics v2 or v3 kits were used for library construction of the samples mentioned above, with slight modification of Larry barcoding system, by added a PCR step to grab the barcoding 3'UTR together with unique barcode for individual cells.
Single cells were emulsed in droplet with unique barcodes, within the droplet, Reverse-Transcription occurred. Then the cDNA from Reverse transcription were extracted by phase separation. This was followed by cDNA amplification, library construction, which is compatible with Illumina NextGeneration Sequencing kit.

treatment_protocol: PDXs or RD cells receive no special treatment, expect that RD cells were cultured under two different medium conditions.

value: mouse PDX sample

value: Mutation?


title: Urine_Control_7

city: Minato-ku

first: Fumihiko

last: Urabe

state: Tokyo

department: Urology

country: Japan

institute: The Jikei University School of Medicine

hyb_protocol: Hybridized for 16 h at 32.7 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was in accordance with the manufacturer’s instruction (TORAY Industries, Inc., Tokyo, Japan).

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified by the software Extraction (Toray Industries Inc., Tokyo, Japan).

data_processing: Background (BG) signals were subtracted from the raw signals by statistically inferring the true signal based upon the assumption of normal distribution for the BG signal and exponential distribution for the true signal (Irizarry RA et al., 2003). miRNAs with (BG-subtracted signal) > 2^6 with at least 50% of the samples were selected, and the other miRNAs were removed from the down-stream analyses. Quantile normalization was applied after BG subtraction and low-expression miRNAs removal. Log2 transformation was applied after quantile normalization.

source_name: Urine, Control

label_protocol: Extracted RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries, Inc., Tokyo, Japan) following the manufacture’s instruction.

extract_protocol: We extracted microRNAs (miRNA) from 500 μL urine sample using a nanowire-microfluidic device (1) (2). We fabricated the nanowire device by assembling ZnO nanowire scaffolds, COP resin microfluidic substrate, COP resin substrate, two stainless steel holders, and PEEK tubes. After assembling the device, the inlet PEEK tube was connected to a syringe pump (KDS-200, KD Scientific Inc.) to introduce urine and lysis buffer. On the other hand, the outlet PEEK tube was put in an RNase-free microfuge tube (Eppendorf AG.) to collect the flow-through urine and miRNA-containing solution. The miRNA-containing solution extracted with lysis buffer was purified using Wako microRNA Extractor SP Kit (FUJIFILM Wako Chemical Corporation) according to the manufacturer’s instructions.

tag: gender

value: Female

tag: age


title: wt_5_60J_0min


title: mfd_rif_60J_NT

value: mfd(-)


title: mfd_minus_UV_rep1


title: MSK82489 PDX sample

value: Wild type


title: Urine_Control_10


title: mfd_60J_0min


title: MSK72117 PDX sample


title: Urine_Control_8


title: Urine_Control_6


title: mfd_60J_20min


title: mfd_60J_NT


title: MAST85-r2-SC PDX sample


title: Urine_Control_9


title: MAST95 PDX sample


title: Urine_Control_5


title: wt_4_60J_30min


title: MSK72117-SC PDX sample


title: MAST85-r1 PDX sample


title: Urine_Control_3


title: MAST85-r2 PDX sample


title: MAST39 PDX sample


title: MAST139-SC PDX sample


title: Urine_Control_1


title: Urine_Control_4


title: Urine_BPS_2

source_name: Urine, BPS


title: Urine_Cystitis_8

source_name: Urine, Cystitis


title: wt_4_60J_0min


title: Urine_Cystitis_7


title: Urine_BPS_1


title: Urine_Cystitis_5


title: wt_4_60J_10min


title: Urine_Cystitis_3


title: Urine_Control_2


title: male 5th instar larval head [LM3_S6]

city: Buffalo

first: Dahong

last: Chen

state: Other

address: 955 Main Street

institute: SUNY Buffalo

data_processing:
Adapter sequences were trimmed from reads with cutadapt (v2.3; -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA --minimum-length 18)
Reads were aligned to Flybase release dm6 reference with bowtie2 (v2.3.5; --very-sensitive, pair-end mode)
Reads were depleted for those aligned to mitochondria (egrep -v chrM) and for multi-mapped reads with samtools (v1.9)
Uniquely mapped reads were further depleted for PCR duplicates with picard (MarkDuplicates REMOVE_DUPLICATES=true)
ATAC-seq peak calling was performed with macs2 (v2.2.6; pair-end mode -f BAMPE)
differential accessibility was called with the R package DiffBind (edgeR, p<0.05)
Genome_build: ASM15162v1
Supplementary_files_format_and_content: bw files that are used for ATAC-seq quantification and visulization

organism: Bombyx mori

source_name: male 5th instar larval head

growth_protocol: Embryos were kept in diapause at 4˚C for 3 mo to 1 y. For rearing, embryos were transferred to 28˚C, and larvae were fed fresh mulberry leaves or powdered mulberry chow (Carolina Biological).

extract_protocol: Active Motif ATAC-seq Kit (cat#53150)

tag: tissue/cell type

value: larval head

tag: Sex

value: male

value: commercial (Carolina Biological, Coastal Silkworms, Mulberry Farms)


title: male 5th instar larval head [LM2_S5]


title: Urine_Cystitis_4


title: Urine_Cystitis_1


title: Urine_Cystitis_2


title: wt_4_60J_NT

tag: genotype


title: male 5th instar larval head [LM1_S4]


title: MAST118 PDX sample


title: lexa_60J_20min


title: lexa_60J_0min


title: Urine_Cystitis_6


title: MAST111 PDX sample


title: lexa_60J_NT


title: female 5th instar larval head [LF3_S3]

source_name: female 5th instar larval head

value: female


title: male embryos [eM4_S14]

source_name: male embryos

value: embryonic (total)


title: RD cell line with LARRY barcodes after washing out Differentiation medium at third time point

description: 10X sequencing, second time point

value: RD cell line


title: wt_3_60J_20min


title: MAST139 PDX sample


title: female 5th instar larval head [LF2_S2]


title: RD cell line with LARRY barcodes with Regular medium at second time point

description: 10X sequencing, second time point


title: female 5th instar larval head [LF1_S1]


title: male embryos [eM1_S11]


title: wt_3_60J_NT


title: wt_3_60J_0min


title: male embryos [eM3_S13]


title: RD cell line with LARRY barcodes with Regular medium at first time point

description: 10X sequencing, first time point


title: female embryos [eF4_S10]

source_name: female embryos


title: RD cell line with LARRY barcodes with Differentiation medium at second time point

description: 10X sequencing, second time point


title: uvrd_60J_0min

value: uvrd(-)


title: siControl_1

city: Xinxiang

first: Zhongbo

last: li

state: Henan

country: China

institute: Xinxiang medical university

data_processing:
Using BGISEQ-500 sequencing platform
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: xlsx files include FPKM values for each Sample

source_name: human breast cancer cell line MDA-MB-231

growth_protocol: MDA-MB-231 cells were plated in 12-well plates at 30% fusion per well

extract_protocol:
Lysis of cells with Trizol reagent and harvesting of RNA
RNA libraries were prepared for sequencing using BGISEQ-500 protocols

treatment_protocol: MDA-MB-231 cells were transfected with siControl or siRBCK1.

tag: condition

value: breast cancer

value: siControl


title: siControl_3

tag: treatment


title: 20696 rhabdomyosarcoma primary patient sample

value: Primary cell


title: Cornea wounded_RNase rep2

city: Shanghai

first: Lan

last: Xihong

state: Shanghai

address: 2005 Songhu Road

department: school of life sciences

institute: Fudan University

data_processing:
STAR software was used to align the RNA-Seq reads to the mouse mm10 reference genome.
For RNA-Seq data, the RSEM tool was used to calculate the TPM values.
Differentially expressed genes were identified using the DESeq2 R package, with a log2 fold-change value of ≥ 1 and a false-discovery rate of < 0.05.
Genome_build: mm10

source_name: cornea

extract_protocol:
Corneas were removed and total RNAs were extracted using RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In cornea wound healing model, half of the limbus, corneal epithelium, and part of the stroma were surgically removed. RNase III was were applied to eye by subconjunctival injection.

tag: group

value: Cornea wounded_RNase

value: cornea

value: 6 weeks


title: siControl_2

tag: cell line


title: female embryos [eF3_S9]


title: wt_4_60J_20min

value: WT

tag: time point


title: uvrd_60J_20min


title: 29806 rhabdomyosarcoma primary patient sample


title: 21202 rhabdomyosarcoma primary patient sample


title: siRBCK1_3


title: female embryos [eF2_S8]


title: siRBCK1_1


title: Cornea unwounded rep2

value: Cornea unwounded


title: Cornea wounded rep1

value: Cornea wounded


title: Cornea unwounded rep1

value: Wild type


title: Cornea wounded_RNase rep1


title: uvrd_60J_NT

value: NT


title: 20082 rhabdomyosarcoma primary patient sample


title: uvra_60J_20min

value: uvra(-)


title: RD cell line


title: Cornea wounded rep2


title: wt_2_rif_60J_NT


title: siRBCK1_2


title: Control Sample 80min

city: Rochester

first: Xiaojia

last: Tang

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file including the raw read counts  for each sample

growth_protocol: The immortalized human cerebral microvascular endothelial cell line (hCMEC/D3) was kindly provided by P-O Couraud, Institut Cochin, France. The cells were cultured in EBM-2 endothelial basal media (Lonza, Walkersville, MD) containing 5% v/v fetal bovine serum (Atlanta biologicals, Flowery Branch, GA), 1% v/v penicillin-streptomycin (Corning, Walkersville, MD), 1.4µM hydrocortisone (Sigma-Aldrich, St Louis, MO), 5µg/ml ascorbic acid (Sigma-Aldrich, St Louis, MO), 1% v/v chemically defined lipid concentrate (Life Technologies, Grand Island, NY), 10 mM HEPES, 1 ng/ml bFGF (Peprotech, Rocky Hill, NJ). The hCMEC/D3 cells were seeded on collagencoated Transwell® filters and cultured) at 37 ° C under 5% CO2 in a humidified chamber.

extract_protocol:
poly-A mRNA was purified from total RNA using oligo dT magnetic beads.
RNA libraries from hCMEC/D3 cells were prepared according  to the manufacturer’s instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego CA)

treatment_protocol: The experiments were conducted as outlined in our previous publication [8], where we presented a comprehensive analysis of deep transcriptomics data (>900 million reads) from hCMEC/D3 monolayers with no treatment. In this study, the same BBB model was treated with 100 nm insulin at various time points (t=10, 20, 40, 80, and 300 minutes). We also harvested synchronized control hCMEC/D3 cell monolayers without insulin treatment at the respective time points

value: control

value: 80 min


title: Control Sample 20min

source_name: immortalized human cerebral microvascular endothelial cell line (hCMEC/D3)

value: 20 min


title: Control Sample 40min

value: 40 min


title: Control Sample 300min

value: 300 min


title: wt_2_60J_20min


title: wt_2_rif_60J_0min


title: wt_2_rif_60J_20min


title: uvra_60J_NT


title: wt_2_60J_0min


title: wt_240J_0min


title: Insulin Treated Sample 300min

value: insulin


title: wt_2_60J_NT


title: wt_240J_NT


title: uvra_60J_0min


title: Insulin Treated Sample 40min


title: Control Sample 10min

value: 10 min


title: Insulin Treated Sample 20min


title: Insulin Treated Sample 10min


title: Insulin Treated Sample 80min


title: si-ALYREF

city: Guangzhou

first: weibo

last: zhong

address: 1023-1063 shatai South Road, Baiyun District, Guangzhou

institute: southern medical university

description: siALYREFseq.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: C42 cell

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: C42 cell

tag: rip anti-body

value: si-ALYREF


title: rho15_0min


title: wt_240J_20min


title: rho15_NT


title: rho15_20min


title: RIP-input

value: IgG

value: untreated


title: wild-type trNK_Il21/iSTAT3 for bulk RNA-seq_2

city: Beijing

first: Chao

last: Zhong

address: 38 Xueyuan Rd , Haidian District

department: Institute of Systems Biomedicine

institute: Peking University

description:
bulk RNA-Seq
trNK_Il21_iSTAT3_2

data_processing:
Illumina Casava1.8 software used for basecalling.
For bulk RNA-Seq, sequence reads were mapped to the mouse (mm10) genome with hisat2 (2.1.0) with default settings and we kept one hit if multiple reads were mapped to the same position for each RNA-Seq library.For each RNA-Seq sample, gene expression was quantified using featureCounts function in Subread package.
For single-cell RNA-Seq, the sequencing data were aligned and quantified using the BD Rhapsody WTA Local bioinformatics pipeline (version 1.9.1, BD) against the mouse mm10 reference genome.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample

source_name: mouse uterine trNK in vitro

growth_protocol: Wild-typre males co-habited with virgin females overnight and the detection time of a copulation plug was thought as gd0.5. Then the males and females were separated into different cages.

extract_protocol:
Single cell suspension were obtained from the uterus in virgin mice or gd8.5 mice. For cell sorting, cells were stained with relative antibodies followed by sorting on a BD Aria III cell sorter for  "live CD45+NK1.1+NKp46+"
The viability of sorted cells was assessed as >90%. Single cell capture and cDNA synthesis were performed on the BD Rhapsody Single-Cell Analysis System (BD), according to the manufacturer’s instruction. Then, the single-cell library was generated and sent to sequencing on Illumina platform.

treatment_protocol: gd8.5-Il21r-/-+iCasp3: Caspase3 inhibitor was applied by intravenous injection at gd6.5 for 2 days

tag: strain/genotype

tag: isolate

value: live NK1.1+ lymphocytes in vitro

tag: in vivo treatment

tag: in vitro treatment

value: 20ng/mL IL-21 plus 1μM Stattic added for 3 days


title: wild-type trNK_Il21 for bulk RNA-seq_1

description:
bulk RNA-Seq
trNK_Il21_1

value: 20ng/mL IL-21 added for 3 days


title: wild-type trNK_Il21 for bulk RNA-seq_2

description:
bulk RNA-Seq
trNK_Il21_2


title: si-NC

description: siALYREFseq.xlsx

tag: cell type

value: si-NC


title: wild-type trNK_Il21/iSTAT3 for bulk RNA-seq_1

description:
bulk RNA-Seq
trNK_Il21_iSTAT3_1


title: wild-type trNK_ctrl for bulk RNA-seq_1

description:
bulk RNA-Seq
trNK_ctrl_1


title: RIP-ALYREF

value: ALYREF

value: Lv-ALYREF


title: wt_1_60J_20min

source_name: E. coli cells

value: WT


title: wild-type trNK_ctrl for bulk RNA-seq_2

description:
bulk RNA-Seq
trNK_ctrl_2


title: wild-type CB_hi at gd8.5 for bulk RNA-seq_1

description:
bulk RNA-Seq
trNK_CB_hi_1

source_name: mouse uterine trNK at gd8.5

value: uterine CD45+NK1.1+NKp46+CD49a+CXCR6-CD55high4-1BBhigh lymphocytes at gd8.5


title: wt_1_60J_30min


title: wt_1_60J_0min


title: wt_1_60J_NT

value: NT


title: wild-type CB_hi at gd8.5 for bulk RNA-seq_2

description:
bulk RNA-Seq
trNK_CB_hi_2


title: los2-5 mutant Rep2

city: Ithaca

first: Leiyun

last: Yang

address: 360 Tower road

department: Plant Biology

institute: Cornell University

description: los2 Rep2

data_processing:
The files have been generated by the Illumina pipeline software v2.18; The raw reads obtained from the sequencing facility were analyzed
raw reads were aligned to TAIR 10 transcriptome using STAR
Differentially expressed genes were identified in R with edgeR pakage
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file include raw read values for each sample was generated

organism: Arabidopsis thaliana

source_name: two-week-old shoot

growth_protocol: All plants were grown on soil (LM111) and put in 4C for two days before moving to the growth chamber (22C, 100 µmol m-2 s-1 constant light, 60% humidity). Plants were sampled when they were two-week-old after germination.

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen, 15596026) and purified by RNA clean and concentrator-5 (ZYMO RESEARCH, R1014). Then RNA libraries were prepared for sequencing using standard Illumina protocols.
3' RNA-seq

treatment_protocol: Three plants were pooled together as one biological replicate and each genotype had three biological replicates (from different pots).

tag: tissue

value: whole shoot

value: los2-5 mutant


title: wild-type CB_int at gd8.5 for bulk RNA-seq_2

description:
bulk RNA-Seq
trNK_CB_int_2

value: uterine CD45+NK1.1+NKp46+CD49a+CXCR6-CD55int4-1BBint lymphocytes at gd8.5


title: los2-5 mutant Rep3

description: los2 Rep3


title: wild-type CB_int at gd8.5 for bulk RNA-seq_1

description:
bulk RNA-Seq
trNK_CB_int_1


title: SH-SY5Y_SAPE_Rep2

city: Melbourne

first: Janith

last: Seneviratne

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description:
SAPE_2
TdT

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneChip Human Gene 2.0 ST Array according to manufacturer's instruction.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GC3000.

data_processing: Affymetrix CEL files were RMA normalised using the rma function as implemented in the oligo (version 1.48.0) R package. Probes were annotated using the AnnotationDbi (version 1.46.1) and hugene20sttranscriptcluster.db (8.7.0) R packages. Data processing were conducted on R version 3.6.1.

source_name: SH-SY5Y neuroblastoma cells, treated with 1µM SAHA and 1.5µM PENAO for 8 hours

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

growth_protocol: SH-SY5Y cells were seeded at 1 million cells per T25 flask and allowed to adhere overnight at 37C/5% CO2 in 5ml DMEM + 10% FBS cell culture medium.

extract_protocol: Following 8 hours incubation, the cells were harvested by trypsinisation and total RNA was extracted for microarray analysis using the PureLink mini RNA extraction kit (ThermoFisher Scientific) according to manufacturer's instructions.

treatment_protocol: Cell culture medium was aspirated and replaced with 5ml DMEM + 10% FBS containing either; 0.1% DMSO, 1µM SAHA, 1.5µM PENAO or 1µM SAHA + 1.5µM PENAO. Flasks were incubated at 37C/5% CO2 for 8 hours prior to RNA extraction.

value: Neuroblastoma cells

value: 1uM SAHA and 1.5uM PENAO

tag: timepoint

value: 8 hours

tag: replicate


title: wild-type CB_low at gd8.5 for bulk RNA-seq_2

description:
bulk RNA-Seq
trNK_CB_low_2

value: uterine CD45+NK1.1+NKp46+CD49a+CXCR6-CD55low4-1BBlow lymphocytes at gd8.5


title: los2-5 mutant Rep1

description: los2 Rep1


title: wild-type CB_low at gd8.5 for bulk RNA-seq_1

description:
bulk RNA-Seq
trNK_CB_low_1


title: Alcohol_and_losartan_treatment_repeat2

first: Yuanxiu

last: Song

address: 49 Huayuanbei Road, Haidian District, Beijing, China,100191

institute: Peking University Third Hospital

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by Removing reads containing sequencing adapter;
Removing reads whose low-quality base ratio base  quality less than or equal to 5) is more than 20%
Removing reads whose unknown  base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
Genome_build: hg38

source_name: human induced pluripotent stem cell-derived cardiomyocytes

growth_protocol: The cell line was routinely maintained in the presence of PSCeasy iPSC medium modified essential 8 medium on six-well plates coated with a 1:200 dilution of Matrigel.

extract_protocol:
Total RNA was extracted from the tissues using Trizol according . About 60 mg of cells were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The  mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HiPSC-CMs were treated with 100-mM alcohol or co-treated with 1 μM losartan

value: treated with 100-mM alcohol fand 1 μM losartan for 24h


title: WT Col-0 Rep3

description: Col-0 Rep3

value: WT (Col-0)


title: PAXF_2045_PDX

type: genomic

city: Freiburg

first: Hagen

last: Klett

address: Am Flughafen 12

department: Discovery Services Freiburg

institute: Charles River Laboratories

description: PICNIC value

hyb_protocol: Tumors were digested with proteinase K at 55°C overnight and the lysate was digested with DNase-free RNase (Qiagen). DNA was extracted with a mix of phenol:chloroform:isoamylalcohol and precipitated with ethanol. DNA pellets were washed and resuspended in TElow. The integrity of each DNA preparation was checked on a 1.3% agarose gel and the purity analyzed using NanoDrop 2000 (Thermo Scientific).

scan_protocol: Standard

data_processing:
Copy number variations were calculated using Affymetrix GTC v4.1 and PICNIC software provided by the Cancer Genome Project from the Welcome Trust Sanger Institute. Copy numbers were then matched to gene locations.
Copy_Number_PICNIC_Scores.txt: Copy Number PICNIC Score per Gene and Sample.

label: Biotin

source_name: pancreatic cancer model 2045

label_protocol: As per manufacturer (Affymetrix).

growth_protocol: Samples were grown in vivo.

extract_protocol: DNA was extracted from snap frozen tumor xenografts.

value: pancreatic cancer


title: SH-SY5Y_SAPE_Rep1

description:
SAPE_1
TdT


title: Alcohol_and_losartan_treatment_repeat1

value: human induced pluripotent stem cell-derived cardiomyocytes


title: Alcohol_treatment_repeat2

value: treated with 100-mM alcohol for 24h


title: wild-type trNK at gd11.5 for bulk RNA-seq_2

description:
bulk RNA-Seq
trNK_gd11.5_2

source_name: mouse uterine trNK at gd11.5

value: uterine CD45+NK1.1+NKp46+CD49a+CXCR6- lymphocytes at gd11.5


title: PAXF_1994_PDX

description: PICNIC value

source_name: pancreatic cancer model 1994


title: WT Col-0 Rep2

description: Col-0 Rep2


title: wild-type trNK at gd11.5 for bulk RNA-seq_1

description:
bulk RNA-Seq
trNK_gd11.5_1


title: Alcohol_treatment_repeat1


title: WT Col-0 Rep1

description: Col-0 Rep1


title: SH-SY5Y_SAHA_Rep2

description:
SAHA_2
TdT

source_name: SH-SY5Y neuroblastoma cells, treated with 1µM SAHA for 8 hours

value: 1uM SAHA


title: PAXF_2094_PDX

description: PICNIC value

source_name: pancreatic cancer model 2094


title: SH-SY5Y_SAHA_Rep1

description:
SAHA_1
TdT


title: SH-SY5Y_PENAO_Rep2

description:
PENAO_2
TdT

source_name: SH-SY5Y neuroblastoma cells, treated with 1.5µM PENAO for 8 hours

value: 1.5uM PENAO


title: PAXF_2108_PDX

description: PICNIC value

source_name: pancreatic cancer model 2108


title: wild-type trNK at gd8.5 for bulk RNA-seq_2

description:
bulk RNA-Seq
trNK_gd8.5_2

value: uterine CD45+NK1.1+NKp46+CD49a+CXCR6- lymphocytes at gd8.5


title: SH-SY5Y_PENAO_Rep1

description:
PENAO_1
TdT


title: SH-SY5Y_DMSO_Rep2

description:
DMSO_2
TdT

source_name: SH-SY5Y neuroblastoma cells, treated with DMSO for 8 hours

value: DMSO


title: HeLaA30ko_2m for mRNA-seq

city: guangzhou

first: xie

last: guoyou

address: 大学城中山大学

institute: 中山大学

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
For RNA-seq: The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0). For Ribo-seq: The 75bp single-end reads were aligned to rRNA and tRNA sequences so as to remove rRNA and tRNA reads using bowtie (v1.2.2) software, remaining reads were used to align to reference genome and transcriptome (Ensembl Version 91) using hisat2 (v2.1.0) and bowtie software separately.
The reads mapped the genome were calculated using featureCounts (v1.6.3).
Genome_build: hg38

source_name: cervical cancer

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
VAHTSTM Stranded mRNA-seq Library Prep Kit for Illumina v2 was used for library construction.

value: HeLa

value: knock-out the ALKBH3 by CRISPS CAS10


title: lfYap-4_S50_R1_001 and lfYap-4_S50_R2_001

first: Andrew

last: Cox

state: Victoria

address: 305 Grattan St

institute: PeterMacCallum Cancer Centre

description: Pool of 10 dissected 7 day old lf:Yap livers (with Yap hyperactivation)

data_processing:
Sequencing files were convereted to FastQ files using Galaxy
Reads were trimmed using Cutadapt (v1.16)
Reads were mapped to zebrafish genome (Ensembl danrer10) using HISAT (v2.1.0)
Counting was performed using featurecounts (v1.6.0)
Differentially expressed genes were identified using Degust (Limma-Voom v3.40.6)
Genome_build: Reads were mapped to zebrafish genome (Ensembl danrer10)
Supplementary_files_format_and_content: csv file containing the counts for all samples in the study (WT 1,2,3,4 and lf:YAP 1,2,3,4 )

organism: Danio rerio

source_name: larval zebrafish liver (pool of 10)

growth_protocol: Zebrafish larvae were raised from 3-7 days in a 6 well plate, before liver dissection at 7 day post fertilization

extract_protocol:
Larval zebrafish livers were dissected and transferred into TRIzol solution. RNA was extracted using an Direct-zol RNA miniPREP kit. RNA quality was confirmed a Tapestation system before sequencing
Libraries were prepared in accordance to SMARTer Stranded Total RNA-seq Kit V2 Pico Input
Libraries were sequeced using an Illumina  NextSeq 500, with paired end 75bp reads to a depth of 15M per sample

treatment_protocol: No treatment involved

tag: strain

value: lf:YAP (YAP activation specific to hepatocytes)


title: PAXF_2146_PDX

description: PICNIC value

source_name: pancreatic cancer model 2146


title: control_repeat1

value: no treatment


title: SH-SY5Y_DMSO_Rep1

description:
DMSO_1
TdT

value: Neuroblastoma cells


title: PAXF_1881_PDX

description: PICNIC value

source_name: pancreatic cancer model 1881


title: lfYap-3_S49_R1_001 and lfYap-3_S49_R2_001


title: HeLaA30ko_1m for mRNA-seq

value: knock-out the ALKBH3 by CRISPS CAS9


title: wild-type trNK at gd8.5 for bulk RNA-seq_1

description:
bulk RNA-Seq
trNK_gd8.5_1


title: wild-type trNK at gd6.5 for bulk RNA-seq_2

description:
bulk RNA-Seq
trNK_gd6.5_2

source_name: mouse uterine trNK at gd6.5

value: uterine CD45+NK1.1+NKp46+CD49a+CXCR6- lymphocytes at gd6.5


title: MEHP_415-553

city: Providence

first: Daniel

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

data_processing:
The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.
Sequence reads were trimmed using Trimmomatic v0.36 and mapped using STAR aligner v.2.5.2b.
Strand-specific read counts were generated using featureCounts from the Subread package v.1.5.2 to count unique reads within exon regions for each gene_id feature in the annotation file.
Differential expression analysis was performed using the Wald test in DESeq2. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes.
Genome_build: mm38
Supplementary_files_format_and_content: tab-delimited text files with read counts

source_name: testis

growth_protocol: Testes were obtained from timed pregnant C57BL/6 mice on GD 14.

extract_protocol:
Total RNA was extracted using Trizol (ThermoFisher Scientific) and purified from the aqueous phase of the extract using the Arcturus PicoPure kit (ThermoFisher).
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles.

treatment_protocol: Fetal testes were isolated from all male fetuses on GD 14 and dissected cleanly from the mesonephros. They were cultured on 480 uL of DMEM/F12, supplemented with pen/strep, gentamicin, ITS, BSA, Albumax, and ascorbic acid, on a millicell-CM cell culture insert. Treatment compounds were dissolved in cell culture media in DMSO vehicle (final DMSO dilution in all samples was 1:4000). Samples were isolated after 24 hours of culture and snap-frozen.

value: testis

value: MEHP


title: wild-type trNK at gd6.5 for bulk RNA-seq_1

description:
bulk RNA-Seq
trNK_gd6.5_1


title: MEHP_414-598


title: lfYap-2_S48_R1_001 and lfYap-2_S48_R2_001


title: PAXF_2131_PDX

description: PICNIC value

source_name: pancreatic cancer model 2131

value: pancreatic cancer


title: control_repeat2

value: human induced pluripotent stem cell-derived cardiomyocytes


title: HeLaA3KO_1R for Ribo-seq

data_processing:
Library strategy: Ribo-seq
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
For RNA-seq: The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0). For Ribo-seq: The 75bp single-end reads were aligned to rRNA and tRNA sequences so as to remove rRNA and tRNA reads using bowtie (v1.2.2) software, remaining reads were used to align to reference genome and transcriptome (Ensembl Version 91) using hisat2 (v2.1.0) and bowtie software separately.
The reads mapped the genome were calculated using featureCounts (v1.6.3).
Genome_build: hg38


title: PAXF_1657_PDX

description: PICNIC value

source_name: pancreatic cancer model 1657


title: PAXF_2051_PDX

description: PICNIC value

source_name: pancreatic cancer model 2051


title: WT-3_S45_R1_001 and WT-3_S45_R2_001

description: Pool of 10 dissected 7 day old WT livers

value: WT


title: PAXF_1965_PDX

description: PICNIC value

source_name: pancreatic cancer model 1965


title: vehicle_415-419

value: vehicle


title: wild-type trNK at virgin for bulk RNA-seq_2

description:
bulk RNA-Seq
trNK_virgin_2

source_name: mouse uterine trNK at virgin

value: uterine CD45+NK1.1+NKp46+CD49a+CXCR6- lymphocytes at virgin


title: PAXF_1982_PDX

description: PICNIC value

source_name: pancreatic cancer model 1982


title: WT-2_S44_R1_001 and WT-2_S44_R2_001


title: HeLaA3KO_2R for Ribo-seq


title: WT-4_S46_R1_001 and WT-4_S46_R2_001


title: HeLa1014_1m for mRNA-seq


title: MEHP_413-554


title: PAXF_2082_PDX

description: PICNIC value

source_name: pancreatic cancer model 2082


title: ATRA_411-434

value: ATRA


title: HeLa1014_2R for Ribo-seq


title: PAXF_2033_PDX

description: PICNIC value

source_name: pancreatic cancer model 2033


title: Il21r-/- uterine NK cells at gd8.5 treated with caspase3 inhibitor for single cell RNA-seq

description:
Sc-RNA-Seq
gd8.5-Il21r-/-+iCasp3

source_name: mouse uterine natural killer cells at gd8.5

value: uterine CD45+NK1.1+NKp46+ lymphocytes at gd8.5

value: Caspase3 inhibitor applied at gd6.5 for 2 days


title: PAXF_2011_PDX

description: PICNIC value

source_name: pancreatic cancer model 2011


title: WT-1_S43_R1_001 and WT-1_S43_R2_001


title: lfYap-1_S47_R1_001 and lfYap-1_S47_R2_001


title: PAXF_546_PDX

description: PICNIC value

source_name: pancreatic cancer model 546


title: PAXF_1887_PDX

description: PICNIC value

source_name: pancreatic cancer model 1887


title: PAXF_1998_PDX

description: PICNIC value

source_name: pancreatic cancer model 1998


title: MEHP + ATRA_413-463

value: MEHP + ATRA


title: wild-type uterine NK cells at gd8.5 for single cell RNA-seq

description:
Sc-RNA-Seq
gd8.5-WT


title: vehicle_415-528


title: PAXF_2196_PDX

description: PICNIC value

source_name: pancreatic cancer model 2196


title: HeLa1014_2m for mRNA-seq

source_name: cervical cancer

value: HeLa


title: wild-type trNK at virgin for bulk RNA-seq_1

description:
bulk RNA-Seq
trNK_virgin_1


title: vehicle_415-416


title: PAXF_1869_PDX

description: PICNIC value

source_name: pancreatic cancer model 1869


title: sc-Dorsal_Skin-ILC_Day10

description: sc-RNA-Seq

molecule: polyA RNA

source_name: SKIN

extract_protocol:
For bulk RNA-seq in skin ILC, single cell suspension were obtained from the skin of  RORγt-fm and RORγt-fmΔGata3 mice, C57BL/6 and Gata3fl/flCreERT2 mice. Cells were sorted by a BD Aria III cell sorter for live Lineage-γδTCR-CD90+. For scRNA-seq, skin ILC were sorted from ear and dorsal skin on Day 0 and Day 10 after depilation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C57BL/6  (WT) and Gata3fl/flCreERT2 mice were injected by 5 mg tamoxifen in 150 ml corn oil per mouse per injection intraperitoneally every other day for 3 times in total

tag: strain background

value: SKIN

tag: celltype

value: ILC


title: wild-type uterine NK cells at virgin for single cell RNA-seq

description:
Sc-RNA-Seq
virgin-WT

source_name: mouse uterine natural killer cells at virgin

value: uterine CD45+NK1.1+NKp46+ lymphocytes at virgin


title: vehicle_412-457

source_name: testis


title: vehicle_414-589


title: Differentiation IPC cell 4_d13

city: Pathumwan

first: QUYNH

middle: Dang

last: LE

state: Bangkok

address: Phayathai

country: Thailand

institute: FALCUTY OF VETERIANARY, CHULALONGKORN UNIVERSITY

description:
Differentiation IPC cell 4_d13
SAMPLE 24

data_processing:
For the normalization it uses the average of housekeeping gene:  GAPDH
Target gene signals were normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
normalized file reports normalized signal (against housekeeping genes).
Fold Change file reports differentiated/control ratios.

label: SYBR Green

organism: Canis lupus familiaris

source_name: cAD-MSC-derived IPC line 4_d13

label_protocol: The cDNA was obtained from RNA using ImProm-IITM Reverse Transcription System (Promega, USA). Targeted genes were amplified and detected by FastStart Essential DNA Green Master (Roche Diagnostics, USA) and CF96TM real-time PCR detection system (BioRad) with 45 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

growth_protocol: Normal undifferentiated cAD-MSCs were culture in DMEM

extract_protocol: The total cellular RNA was extracted using TRIzolTM reagent (Thermo Fisher Scientific) and Direct-zolTM RNA Miniprep kit (Zymo Research, USA)

treatment_protocol: IPCs were induced from cAD-MSCs with the three-stepwise protocol. For the first stage, cAD-MSCs was induced to definitive endoderm (DE) with the cooperation of Chir99021 and Activin A for 3 days. For the second stage, pancreatic endocrine (PE) progenitor was induced from DE after treatment with taurine, retinoic acid, FGF2 EGF, TGFβ inhibitor, dorsomorphin, nicotinamide, and DAPT for the next 5 days. In the last stage, the combination of taurine, nicotinamide, Glp-1, forskolin, PI3K inhibitor, and TGFβ inhibitor was used to yield efficiently functional IPCs from PE precursors for 5 days.


title: Differentiation IPC cell 2_d13

description:
Differentiation IPC cell 2_d13
SAMPLE 22

source_name: cAD-MSC-derived IPC line 2_d13


title: Differentiation IPC cell 3_d13

description:
Differentiation IPC cell 3_d13
SAMPLE 23

source_name: cAD-MSC-derived IPC line 3_d13


title: Monocytes_LPS (0.5 ug/ml)_F2

city: Houston

first: JEHAN

last: ALAM

state: TEXAS

address: Baylor One Plaza

institute: Baylor College of Medicine

data_processing:
bcl2fastq2 (v2.20) (processing of Illumina base-call data and demultiplexing)
Samtools (v0.1.19) (processing of BAM files)
BEDtools (v2.25.0) (processing of BED files)
wigToBigWig (v4) (generation of bigWIG files)
Subread (v1.5.2) (counting of reads in BAM files for DESeq2)

source_name: Monocytes

growth_protocol: Cultured bone marrow derived monocytes were purified using a purification kit

extract_protocol:
cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).  Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).
Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).

treatment_protocol: Monocytes were either treated with LPS or LPS plus 9CisRA

value: Monocytes

value: Treated with LPS


title: sc-Dorsal_Skin-ILC_Day0

description: sc-RNA-Seq


title: Monocytes_LPS (0.5 ug/ml)_9CisRA_100nM_F2

value: Treated with LPS plus 9CisRA


title: sc-Skin-ILC

description: sc-RNA-Seq


title: Differentiation IPC cell 1_d13

description:
Differentiation IPC cell 1_d13
SAMPLE 21

source_name: cAD-MSC-derived IPC line 1_d13


title: PAXF_1986_PDX

description: PICNIC value

source_name: pancreatic cancer model 1986


title: Monocytes_LPS (0.5 ug/ml)_9CisRA_100nM_F1


title: vehicle_410-525

value: testis


title: Monocytes_Control_F2

value: Vehicle


title: Gata3KO_2

description: RNA-Seq

tag: genotype/variation


title: Control Undifferentiation Cell 4_d13

description:
Control cell line 4_d13
SAMPLE 20

source_name: cAD-MSC line 4

tag: treatment


title: vehicle_413-453


title: MEHP_410-552

value: MEHP


title: HeLa1014_1R for Ribo-seq

value: no treatment


title: Monocytes_LPS (0.5 ug/ml)_F1


title: Control Undifferentiation Cell 3_d13

description:
Control cell line 3_d13
SAMPLE 19

source_name: cAD-MSC line 3


title: Adult Bone marrow cells

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

data_processing:
FASTQ files were processed by BD Rhapsody Targeted Analysis Pipeline (v1.0) supported by SevenBridges web-platform (igor.sbgenomics.com)
Genome_build: mm10
Supplementary_files_format_and_content: st files include UMI counts for each cell barcode and genes

source_name: Bone marrow

extract_protocol:
Bone marrow were dissected and digested to obtain single cell suspension solution. Fluorescence or magnetic beads conjugated antibodies were used to stain cells for unused cell seperation.
Standard commercial protocol for targeted scRNA-seq from BD
targeted single cell RNA-seq

value: Bone marrow

tag: developmental stage

value: Adult

tag: wt or mutant

value: WT

value: bone marrow cells


title: WT_2

description: RNA-Seq


title: E18.5 Bone marrow cells

value: Embryonic


title: ATRA_414-433

value: ATRA


title: WT_1

description: RNA-Seq


title: Control Undifferentiation Cell 2_d13

description:
Control cell line 2_d13
SAMPLE 18

source_name: cAD-MSC line 2


title: vehicle_411-428

value: vehicle


title: vehicle_411-456


title: E18.5 EC

value: endothelial cells


title: RORgt-fm_neg_Gata3flox_2

description: RNA-Seq

value: SKIN

value: ILC


title: RORgt-fm_neg_Gata3flox_3

description: RNA-Seq


title: Differentiation PE cell 3_d8

description:
Differentiation PE cell 3_d8
SAMPLE 15

source_name: cAD-MSC-derived PE line 3_d8


title: Differentiation PE cell 4_d8

description:
Differentiation PE cell 4_d8
SAMPLE 16

source_name: cAD-MSC-derived PE line 4_d8


title: vehicle_415-542


title: Differentiation PE cell 2_d8

description:
Differentiation PE cell 2_d8
SAMPLE 14

source_name: cAD-MSC-derived PE line 2_d8


title: RORgt-fm_neg_Gata3flox_1

description: RNA-Seq


title: Gata3KO_1

description: RNA-Seq


title: HT29 Atglistatin-3

city: New Orleans

first: Suzana

last: Savkovic

state: LA

address: 1324 Tulane Ave

department: Pathology

institute: Tulane Univeristy

description: Human colon cancer cell line - HT29 colonosphere atglistatin treated rep3

data_processing:
For HCT116  shATGL -/+ doxy samples, paired-end reads aligned to hg38 transcriptome and expression levels calculated using Bowtie(v1.1.1) with RSEM(v1.2.31). Differential expression testing was performed using EBSeq.
For HT29 samples paired-end reads were aligned to hg38 transcriptome using STAR(v.2.6.1d).  Abundance levels were calculated using Kallisto(v.0.46.0) and differential expression testing performed using DESeq2.
For HCT116  shATGL -/+ doxy samples, expression levels (read counts) were collated for each sample across both all conditions.
For HT29 samples abundance levels (read counts) were collated for each sample across all conditions.
Genome_build: hg38
Supplementary_files_format_and_content: text files of read counts

source_name: Colorectal adenocarcinoma cells

growth_protocol: Human colon cancer cells HT29 and HCT116  were obtained from the American Type Culture Collection (ATCC, Manassas, VA). HT29 and HCT116 cells were propagated in complete McCoy’s 5A media (Sigma, St. Louis, MO) containing 10% fetal bovine serum (FBS) (Peak Serum, Wellington, CO)

extract_protocol:
Isolation of total RNA was accomplished using the miRNeasy kit (Zymo Research, Irvine, CA) according to manufacturer’s instructions. RNA quality was determined by an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA) and samples with RNA integrity numbers (RIN) > 7 were used.
paired-end sequencing of 75bp reads on Iillumina NextSeq

treatment_protocol: 3 replicates of HT29 colonospheres treated with atglistatin (40 μM) (Cayman, Ann Arbor, MI) for 24 hours; 3 replicates of shATGL treated with doxycycline (2ug/mL)

value: epithelial-derived colorectal cancer cells

value: HT29 Colonopsheres  treated with Atglistatin ((40 μM)) 24 hrs

tag: growth media

value: HT29 cells  grown with cancer stem cell media:DMEM with L-glutamine, F12 Ham and 15 mM Hepes (Sigma), 20ng/ml bFGF (thermofisher), 20 ng/ml EGF (thermofisher), 4mg/ml BSA


title: Control Undifferentiation Cell 1_d13

description:
Control cell line 1_d13
SAMPLE 17

source_name: cAD-MSC line 1


title: HT29 Atglistatin-2

description: Human colon cancer cell line - HT29 colonosphere atglistatin treated rep2


title: Monocytes_Control_F1

value: Monocytes


title: HT29 Atglistatin-1

description: Human colon cancer cell line - HT29 colonosphere atglistatin treated rep1


title: MEHP + ATRA_413-464

value: testis

value: MEHP + ATRA


title: vehicle_414-424


title: Differentiation PE cell 1_d8

description:
Differentiation PE cell 1_d8
SAMPLE 13

source_name: cAD-MSC-derived PE line 1_d8


title: RORgt-fm_pos_Gata3flox_3

description: RNA-Seq

source_name: SKIN


title: HT29 Colonosphere Control-3

description: Human colon cancer cell line - HT29 colonosphere rep3

value: HT29 colonospheres untreated


title: RORgt-fm_pos_Gata3flox_2

description: RNA-Seq


title: MEHP + ATRA_412-436

source_name: testis


title: Control Undifferentiation Cell 4_d8

description:
Control cell line 4_d8
SAMPLE 12


title: MEHP + ATRA_411-465


title: RORgt-fm_pos_Gata3flox_1

description: RNA-Seq


title: HT29 Colonosphere Control-2

description: Human colon cancer cell line - HT29 colonosphere rep2


title: Control Undifferentiation Cell 2_d8

description:
Control cell line 2_d8
SAMPLE 10


title: Control Undifferentiation Cell 3_d8

description:
Control cell line 3_d8
SAMPLE 11


title: vehicle_413-596


title: RORgt-fm_neg_1

description: RNA-Seq


title: vehicle_413-533


title: HT29 adherent-Con-2

description: Human colon cancer cell line - HT29 adherent rep2

value: HT29 adherent untreated


title: Control Undifferentiation Cell 1_d8

description:
Control cell line 1_d8
SAMPLE 9


title: RORgt-fm_pos_2

description: RNA-Seq


title: ATRA_415-431


title: RORgt-fm_pos_1

description: RNA-Seq


title: ATRA_415-432


title: Differentiation DE cell 4_d3

description:
Differentiation DE cell 4_d3
SAMPLE 8

source_name: cAD-MSC-derived DE line 4_d3


title: Differentiation DE cell 3_d3

description:
Differentiation DE cell 3_d3
SAMPLE 7

source_name: cAD-MSC-derived DE line 3_d3


title: HT29 adherent-Con-1

description: Human colon cancer cell line - HT29 adherent rep1


title: Liver, untreated - CCI4 - rep3

city: Mainz

first: Federico

last: Marini

address: Obere Zahlbacher Strasse 69

department: Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)

institute: University Medical Center - Mainz

data_processing:
Sequenced reads were mapped to the mouse genome reference sequence with STAR (version 2.6.1a)
The ENSEMBL Mus_musculus.GRCm38 was chosen as reference genome, alignments were processed with the featureCounts function of the Rsubread package. The corresponding gtf annotation for the reference (ENSEMBL v76) was used.
Exploratory data analysis was performed with the pcaExplorer package (version version 2.12.0, Marini et al., 2019)
Differential expression analysis was performed with DESeq2 (version 1.26.0), setting the False Discovery Rate to 0.05
Accurate estimation of the effect sizes (in terms of log fold change) is performed using the apeglm shrinkage estimator (version 1.8.0)
Further analyses included Gene Ontology pathway enrichment of DEG using topGO (v2.38.0) and goseq (v1.38.0) (with all expressed genes set as background) were performed using the ideal package (version 1.10.0) [Marini et al. 2020].
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes raw counts as input matrix to DESeq2

source_name: Tissue from each liver lobe

growth_protocol: Five weeks CCl4 liver fibrosis induction

extract_protocol:
Total RNA was extracted from fresh frozen pieces of mouse liver using Qiagens RNeasy Mini Kit.
Quantity and quality was assessed using the Qubit 3 fluorometer with the RNA BR AssayKit (Invitrogen) and the Agilent Bioanalyzer 2100 system using the RNA Pico kit. mRNA-focused RNA libraries were prepared using Illumina’s TruSeq stranded RNA library prep kit with an input amount of 1000ng total RNA. Poly(A)-positive mRNA transcripts were isolated from total RNA by binding to magnetic oligo(d)T beads and subsequently fragmented and reverse transcribed during first and second strand synthesis to yield double-stranded cDNA. The ends of the cDNA molecules were end repaired and an adenosine overhang was added to all 3’ ends (A-tailing step) to facilitate the ligation of the adapter molecules. These adapters have individual dedicated index sequences and add the Illumina specific sequences that are needed for amplification, flow cell hybridization and sequencing. 8 bp single-index NEXTflex DNA barcodes (Perkin Elmer) were used. The final ligation product was amplified via PCR. Intermediate and final library purification steps were done using AMPure XP beads (Beckman Coulter). Final library quantity and quality was done using the Qubit 3 fluorometer with the dsDNA HS AssayKit (Invitrogen) and the Agilent Bioanalyzer 2100 system using the High Sensitivity DNA kit. All mRNA libraries were sequenced in paired-end mode (2 x 50 nt) on an Illumina NovaSeq 6000 instrument resulting in around 30 million distinct sequencing read pairs per library.

treatment_protocol: In the last two weeks of the fibrosis injection, mice received two injection per week with nanoparticular bisphosphonate (Alendronat 4 mg/kg)

value: BALB/c

value: Fibrotic control

value: liver

tag: selection

value: Liver fibrosis


title: HCT116 shATGL + doxy 2

description: Human colon cancer cell line - HCT116 shATGL+Doxy Rep2

value: HCT116 shATGL  treated with doxycycline (2ug/mL) for 48h


title: HCT116 shATGL + doxy 3

description: Human colon cancer cell line - HCT116 shATGL+Doxy Rep3


title: ATRA_412-462

value: ATRA


title: Differentiation DE cell 2_d3

description:
Differentiation DE cell 2_d3
SAMPLE 6

source_name: cAD-MSC-derived DE line 2_d3


title: Differentiation DE cell 1_d3

description:
Differentiation DE cell 1_d3
SAMPLE 5

source_name: cAD-MSC-derived DE line 1_d3


title: HT29 Colonosphere Control-1

description: Human colon cancer cell line - HT29 colonosphere rep1


title: RORgt-fm_neg_2

description: RNA-Seq


title: vehicle_413-448

value: vehicle


title: HCT116 shATGL + doxy 1

description: Human colon cancer cell line - HCT116 shATGL+Doxy Rep1


title: HCT116 shATGL - doxy 3

description: Human colon cancer cell line - HCT116 shATGL-Doxy Rep3

value: HCT116 adherent untreated


title: HT29 adherent-Con-3

description: Human colon cancer cell line - HT29 adherent rep3


title: Liver, untreated - CCI4 - rep2


title: Control Undifferentiation Cell 4_d3

description:
Control cell line 4_d3
SAMPLE 4

source_name: cAD-MSC line 4


title: Liver, treated Al/NP high - rep3

value: Bisphosphonate Nanoparticles


title: Control Undifferentiation Cell 3_d3

description:
Control cell line 3_d3
SAMPLE 3

source_name: cAD-MSC line 3


title: Il21r-/- uterine NK cells at gd8.5 for single cell RNA-seq

description:
Sc-RNA-Seq
gd8.5-Il21r-/-

source_name: mouse uterine natural killer cells at gd8.5

tag: strain/genotype

value: uterine CD45+NK1.1+NKp46+ lymphocytes at gd8.5


title: HCT116 shATGL - doxy 2

description: Human colon cancer cell line - HCT116 shATGL-Doxy Rep2

value: epithelial-derived colorectal cancer cells


title: Control Undifferentiation Cell 2_d3

description:
Control cell line 2_d3
SAMPLE 2

source_name: cAD-MSC line 2


title: MEHP_415-568

value: MEHP


title: Control Undifferentiation Cell 1_d3

description:
Control cell line 1_d3
SAMPLE 1


title: Liver, untreated - CCI4 - rep1


title: MEHP_413-599


title: HiC1_28719_wildtype

status: Public on Feb 04 2022

city: Edinburgh

last: Robertson

state: Midlothian

address: 2.28 Michael Swann Building, Kings Buildings, Mayfield Road

department: Discovery Research Platform for Hidden Cell Biology

institute: University of Edinburgh

description: RPL13A-2xFKBP12 fpr1Δ tor1-1 ndt80Δ

data_processing:
Fastq reads aligned to S.cerevisiae SK1 using HiC-Pro v2.11.4 , bowtie2 v2.3.4.1 (--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder), removing singleton, multi hit, MAPQ<10 and duplicated reads.
Valid interaction pairs were converted into the .cool contact matrix format using cooler v0.7.11 (1 kb resolution)
Matrixes balanced using Iterative correction
Genome_build: S.cerevisiae SK1
Supplementary_files_format_and_content: Cooler .cool matrix 1kb binned, balanced with iterative correction

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae

growth_protocol: Cells were grown to saturation in YPDA media before transfer to pre-sporulation media (BYTA). Cells were grown to for approx. 16 hours to OD(600) of approx. 4. Cells were diluted to OD(600) = 1.8 and sporulated for 6 hours in SPO media (0.3% Kac) to arrest in prophase I.

extract_protocol:
Lysates were prepared by grinding the frozen pellet in a chilled mortar with a pestle for 15 minutes and 1/10th of the initial pellet weight (~0.5 g) was taken for further processing. Restriction enzyme digestion (DpnII), filling-in, ligation, crosslink reversal, DNA concentration and purification and biotin removal were carried out as described in Schalbetter et al. (2018) doi: https://doi.org/10.1101/442038. DNA was then fragmented on a Bioruptor Plus sonication device (Diagenode) for a total of 2x 30 cycles 30 seconds on/off at High setting.
DNA end repair and A-tailing using T4 DNA polymerase, T4 Polynucleotide Kinase and Klenow fragment DNA polymerase I were carried out as in Schalbetter et al., 2018. Hi-C libraries were fractionated using Ampure XP beads as previously described in Belton et al. (2015) DOI: 10.1101/pdb.prot085209. Biotin pull-down, adapter ligation (NextFlex, Bioo Scientific) and sequencing (EMBL Core Genomics Facility, Heidelberg, Germany) were carried as in Schalbetter et al. (2018) doi: https://doi.org/10.1101/442038.

treatment_protocol: Cells were fixed and lysed as in Belton & Dekker (2015) DOI: 10.1101/pdb.prot085209. Briefly, 50 ml of cells at OD~1.8 carrying ndt80 deletion were arrested in meiotic prophase I, fixed with 3% formaldehyde for 20 minutes at 25 ˚C at 250 rpm and the reaction was quenched for 5 minutes by the addition of 0.35 M glycine (final concentration). Cells were washed with cold water, resuspended in 5 ml 1x NEBuffer 2 and frozen in liquid nitrogen.

tag: ploidy

value: Diploid

tag: cell cycle stage

value: Meiotic prophase I

tag: genotype

value: RPL13A-2xFKBP12 fpr1delta tor1-1 ndt80delta


title: cdc6-mn

description: RPL13A-2xFKBP12 fpr1∆ tor1-1 ndt80∆ pSCC1::3HA-CDC6

value: RPL13A-2xFKBP12 fpr1delta tor1-1 ndt80delta pSCC1::3HA-CDC6


title: eco1-aa cdc6-mn

description: RPL13A-2xFKBP12 fpr1∆ tor1-1 ndt80∆ Eco1-FRB-GFP pSCC1::3HA-CDC6

value: RPL13A-2xFKBP12 fpr1delta tor1-1 ndt80delta Eco1-FRB-GFP pSCC1::3HA-CDC6


title: clb5 clb6

description: pCUP-IME1 pCUP-IME4  clb5delta clb6delta

growth_protocol: Cells were grown to saturation in YPDA media before transfer to pre-sporulation media (BYTA). Cells were grown to for approx. 16 hours to OD(600) of approx. 4. Cells were diluted to OD(600) = 1.8 and sporulated for 2 hours in SPO media (0.3% Kac) to arrest prior to meiotic S phase

value: Prior to meiotic S phase

value: pCUP-IME1 pCUP-IME4  clb5delta clb6delta


title: HiC1_29781_eco1-aa_wpl1

source_name: eco1-aa wpl1Δ

tag: background strain

value: SK

value: RPL13A-2xFKBP12 fpr1-delta tor1-1 ndt80-delta Eco1-FRB-GFP wpl1-delta


title: HiC1_29750_wpl1

value: RPL13A-2xFKBP12 fpr1-delta tor1-1 ndt80-delta wpl1-delta


title: HiC1_28720_eco1-aa

value: RPL13A-2xFKBP12 fpr1-delta tor1-1 ndt80-delta Eco1-FRB-GFP


title: HiC2_11633_wt

source_name: wild type


title: Liver, treated Al/NP high - rep2

value: BALB/c

tag: tissue

value: liver

value: Liver fibrosis


title: HiC2_28841_clb5_clb6

source_name: clb5 clb6

value: ndt80-delta clb5-delta clb6-delta


title: bulk RNA data for NK1.1+ ILTCk rep1 dataset in Ext. Fig

city: New York

first: Christina

last: Leslie

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Cell Ranger v3.0.2 (10x genomics) was used for pre-processing of scRNA-seq data
Additional gene/cell filters were applied as described in the methods of the manuscript
Seurat v2.3.4 was used for analysis of all scRNA-seq data.   DESeq was used for analysis of bulk RNA-sequencing data.
Genome_build: mm10
Supplementary_files_format_and_content: Seurat object RDS files containing raw and normalized count matrices, UMAP coordinates

source_name: NK1.1+ ILTCk rep1

extract_protocol:
Tumor tissues were minced with a razor blade then digested in 280 U/mL Collagenase Type 3 (Worthington Biochemical) and 4 μg/mL DNase I (Sigma) in HBSS at 37°C for one hour and 15 minutes with periodic vortex every 20 minutes. Digested tissues were passed through 70 μm filters and pelleted. Cells were resuspended in 40% Percoll (Sigma) and layered above 60% Percoll. Sample was centrifuged at 1,900 g at 4°C for 30 minutes without brake. Cells at interface were collected, stained and analyzed by flow cytometry or sorting. Isolation of small intestinal intraepithelial lymphocytes has been previously described53. Briefly, small intestine between distal duodenum and proximal ileum was opened longitudinally and intestinal content was cleaned by washing in ice-cold PBS, followed by incubation in PBS/10 mM EDTA/1 mM Dithiothreitol solution at 37°C for 15 minutes with vigorous shaking. Tissues were passed through 100 m filters and pelleted. Cells were resuspended in 40% Percoll and centrifuged at 1,200 g at room temperature for 20 minutes. Cell pellets were collected, stained and analyzed by flow cytometry.  For flow cytometry experiments, cells were incubated with 2.4G2 mAb to block FcγR binding, DAPI (4, 6-diamidino-2-phenylindole; Sigma) or Aqua Live/Dead (Thermo Fisher Scientific) for the exclusion of dead cells and were stained with panels of antibodies for 30 minutes on ice. Granzyme B staining was carried out using the intracellular transcription factor buffer set from BD Pharmingen. All samples were acquired with an LSRII (BD) or LSR Fortessa (BD), and analyzed with FlowJo software version 9.6.2 (Tree Star). Cell sorting was performed with a FACSAria II (BD) using a 100 m nozzle. Tumor-infiltrating NK1.1+ abILTCks and PD-1+ T cells were sorted as CD45+TCRgd–TCRbeta+CD4–CD8alpha+PD-1–NK1.1+ and CD45+TCRgd–TCRbeta+CD4–CD8alpha+PD-1+NK1.1–, respectively. Thymic abILTCk/IEL progenitors and CD8 single positive cells were sorted as CD4–/dullCD8alpha–/dullCD1d/PBS-57–CD25–TCRbeta+CD122+CD5hiPD-1+NK1.1– and TCRbeta+CD4–CD8alpha+, respectively. For sorting of LSK cells, total bone marrow cells were incubated with CD117 MicroBeads (Miltenyi Biotec) according to the manufacturer’s instruction, followed by positive selection with an LS column (Miltenyi Biotec) prior to staining with monoclonal antibodies. LSK cells were sorted as Lineage– (CD3epsilon–B220–Gr1–CD11b–Ter119–) CD117+Sca1+.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: type

value: bulkRNA

tag: model

value: retrogenic

tag: cell type

value: NK1.1+ ILTCkP


title: bulk RNA data for PD1+ Tconv rep2 dataset in Ext. Fig

source_name: PD1+ Tconv rep2

value: PD1+ Tconv


title: bulk RNA data for PD1+ Tconv rep1 dataset in Ext. Fig

source_name: PD1+ Tconv rep1


title: Liver, treated Al/NP high - rep1

tag: strain

value: Bisphosphonate Nanoparticles


title: vehicle_412-420

source_name: testis

value: testis

value: vehicle


title: bulk RNA data for NK1.1- ILTCk rep2 dataset in Ext. Fig

source_name: NK1.1- ILTCk rep2

value: NK1.1- ILTCkP


title: bulk RNA data for NK1.1- ILTCk rep1 dataset in Ext. Fig

source_name: NK1.1- ILTCk rep1


title: bulk RNA data for NK1.1+ ILTCk rep2 dataset in Ext. Fig

source_name: NK1.1+ ILTCk rep2


title: scRNA data for mouse prostate rep1 dataset in Ext. Fig

source_name: prostate

value: scRNA

value: TRAMP

value: CD8 TILs


title: bulk RNA data for ILTCkP rep1 dataset in Ext. Fig

source_name: ILTCkP rep1

value: ILTCkP


title: bulk RNA data for CD8SP rep1 dataset in Ext. Fig

source_name: CD8SP rep1

value: CD8 SP


title: bulk RNA data for CD8SP rep2 dataset in Ext. Fig

source_name: CD8SP rep2


title: scRNA data for mouse prostate rep2 dataset in Ext. Fig


title: bulk RNA data for ILTCkP rep2 dataset in Ext. Fig

source_name: ILTCkP rep2


title: 99565 RNA-Seq Pro-B

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description: RNA-Seq Pro-B

data_processing:
ChIP-Seq: After sequencing, all reads that passed the Illumina quality filtering were considered for alignment. mm10: The ChIP-seq samples, which were used for generating the data shown in Fig. 5 B and Fig. S5, C, D and I, were aligned to the mouse genome assembly version of December 2011 (GRCm38/mm10) using the bwa program version 0.7.17. The read coverages, displayed in Fig. 5B and Fig. S5 I, were calculated with the bedtools program version 2.27.1, normalized to reads per millions (RPM) using the SAMtools version 1.9 and Kent tools version 20190507. Peaks were called with the MACS program version 2.2.5, using only one of the two read sequences in case of paired-end read samples, with the input sample 35327 as a control, except for the B-ALL samples 138002 and 138003, where the associated input sample 138001 was used. mm9: The ChIP-seq samples, which were used for generating the data shown in Fig. 7, H, I and L, Fig. S2 A, Fig. S5 A and Fig. S7, F and G, were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9), using the Bowtie program version 1.0.0. Peaks were called with the MACS program version 1.3.6.1. Peaks of samples 29936 and 29938, 38870 and 40031 and 40030 and 46051 were called by using the pro-B cell input GSM2461724 as control.
After sequencing, reads that passed the Illumina quality filtering were considered for alignment. Reads corresponding to mouse ribosomal RNAs (BK000964.1 and NR046144.1) or human ribosomal RNAs (U13369.1) were removed.  RNA-seq samples for experiment 2&3 which were used to define the gene expression changes between ex vivo sorted Pax5–/– and Pax5+/+ pro-B cells  (Fig. S2A) as well as ex vivo sorted pro-B cells from Vav-Bcl2 Rag1-Cre Stat5fl/fl and control Vav-Bcl2 Rag1-Cre Stat5fl/+ (Fig. S7D), were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Tophat program version 1.4.1a. The number of reads per gene was counted using featureCounts version 1.5.0 with the default settings and the modified refGene gene annotation described in (Schwickert et al. 2019, PMID: 31591571). TPM values were calculated as described (Wagner et al., 2012).  RNA-seq samples for experiments 1 & 4, which were used to define the gene expression changes between Pax5Jak2/+ and Pax5+/+ pro-B cells (Fig. 2A) as well as Pax5Jak2/+ and control Pax5+/– Cdkn2ab+/– B-ALL tumors (Fig. 2C), were aligned to the mouse genome assembly version of December 2011 (GRCm38/mm10) using the STAR program version 2.4.2a [PMID: 23104886] with the parameters ‘–outSAMStrandField intronMotif’ and ‘–removeNonCannonical RemoveNonCannonicalUnannotated’ in paired-end mode. The number of reads per gene was counted using featureCounts version 1.5.0 with the setting -p and the refGene gene annotation of mm10 downloaded from UCSC on Dec 6th 2018 expanded by Immunoglobulin and T cell receptor gene annotation from Gencode version 29. TPM values were calculated as described (Wagner et al., 2012).
Genome_build: NCBI37/mm9; GRCm38/mm10;
Supplementary_files_format_and_content: bigwig = read coverage (reads per million) in bigWIG format; txt = ASCII text format.

source_name: Pro-B cells

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

value: Pax5(JAK2/+) Meox2-cre

tag: cell preparation

value: Ex-vivo, FACS sorted, pooled


title: 99564 RNA-Seq Pro-B

description: RNA-Seq Pro-B


title: 99563 RNA-Seq Pro-B

description: RNA-Seq Pro-B


title: 99561 RNA-Seq Pro-B

description: RNA-Seq Pro-B

value: Pax5(+/+) Meox2-cre


title: 99562 RNA-Seq Pro-B

description: RNA-Seq Pro-B


title: scRNA data for mouse breast dataset in Fig. 1

source_name: breast

value: MMTV-PyMT


title: 38497 RNA-Seq Pro-B

description: RNA-Seq Pro-B

value: wild-type

value: Ex-vivo, FACS sorted


title: HiC1_28719_wt

value: Diploid

value: Meiotic prophase I

value: SK

value: RPL13A-2xFKBP12 fpr1-delta tor1-1 ndt80-delta


title: 38494 RNA-Seq Pro-B

description: RNA-Seq Pro-B


title: 38493 RNA-Seq Pro-B

description: RNA-Seq Pro-B


title: 38496 RNA-Seq Pro-B

description: RNA-Seq Pro-B


title: 38492 RNA-Seq Pro-B

description: RNA-Seq Pro-B


title: eco1-aa

description: RPL13A-2xFKBP12 fpr1∆ tor1-1 ndt80∆ Eco1-FRB-GFP

source_name: S. cerevisiae

value: RPL13A-2xFKBP12 fpr1delta tor1-1 ndt80delta Eco1-FRB-GFP


title: 24395 RNA-Seq Pro-B

description: RNA-Seq Pro-B

value: mixed C57BL/6 x 129/Sv

value: Stat5(F/+) Vav-Bcl2 Rag1-cre


title: 24396 RNA-Seq Pro-B

description: RNA-Seq Pro-B

value: Stat5(F/F) Vav-Bcl2 Rag1-cre


title: 24394 RNA-Seq Pro-B

description: RNA-Seq Pro-B


title: 24397 RNA-Seq Pro-B

description: RNA-Seq Pro-B


title: 36348 RNA-Seq Pax5-Jak2 B-ALL

description: RNA-Seq Pax5-Jak2 B-ALL

source_name: B-ALL cells

value: Ex-vivo


title: scRNA data for mouse breast dataset in Ext. Fig

value: scRNA

value: CD8 TILs


title: 36345 RNA-Seq Pax5-Jak2 B-ALL

description: RNA-Seq Pax5-Jak2 B-ALL


title: 36328 RNA-Seq control B-ALL

description: RNA-Seq control B-ALL


title: 138001 ChIP-Seq input B-ALL

description: ChIP-Seq input B-ALL

extract_protocol: ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols

value: B-ALL cell line

tag: chip antibody


title: 36329 RNA-Seq control B-ALL

description: RNA-Seq control B-ALL


title: 35327 ChIP-Seq input Pro-B

description: ChIP-Seq input Pro-B

value: Ex-vivo, FACS sorted, pooled


title: 99560 RNA-Seq Pro-B

description: RNA-Seq Pro-B

value: Pax5(+/+) Meox2-cre


title: 138003 ChIP-Seq Pax5 B-ALL

description: ChIP-Seq Pax5 B-ALL

value: anti-Pax5 A1 (Adams et al., 1992)


title: 36346 RNA-Seq Pax5-Jak2 B-ALL

description: RNA-Seq Pax5-Jak2 B-ALL


title: 138002 ChIP-Seq Pax5 B-ALL

description: ChIP-Seq Pax5 B-ALL


title: 35061 ChIP-Seq Pax5 Pro-B

description: ChIP-Seq Pax5 Pro-B

value: wild-type C57BL/6J


title: 100881 ChIP-Seq H3K4me3 Pro-B

description: ChIP-Seq H3K4me3 Pro-B

value: Progenitor culture


title: 35059 ChIP-Seq Pax5 Pro-B

description: ChIP-Seq Pax5 Pro-B


title: HCT116 shATGL - doxy 1

description: Human colon cancer cell line - HCT116 shATGL-Doxy Rep1

source_name: Colorectal adenocarcinoma cells

value: epithelial-derived colorectal cancer cells

tag: treatment

value: HCT116 adherent untreated


title: 36347 RNA-Seq Pax5-Jak2 B-ALL

description: RNA-Seq Pax5-Jak2 B-ALL


title: 100895 ChIP-Seq H3K27me3 Pro-B

description: ChIP-Seq H3K27me3 Pro-B

value: H3K27me3 Art.Nr:CST9733 clone C36B11


title: 100892 ChIP-Seq H3K27me3 Pro-B

description: ChIP-Seq H3K27me3 Pro-B


title: 100884 ChIP-Seq H3K27ac Pro-B

description: ChIP-Seq H3K27ac Pro-B

value: H3K27Ac Art.Nr:ab4729


title: 100882 ChIP-Seq H3K4me3 Pro-B

description: ChIP-Seq H3K4me3 Pro-B


title: 100886 ChIP-Seq H3K27ac Pro-B

description: ChIP-Seq H3K27ac Pro-B


title: 100887 ChIP-Seq H3K27ac Pro-B

description: ChIP-Seq H3K27ac Pro-B


title: 38870 Bio-ChIP-Seq Pro-B

description: Bio-ChIP-Seq Pro-B

value: Pax5(Jak2/+) Meox2(Cre/+)

value: Pro-B culture

value: Streptavidin


title: 100894 ChIP-Seq H3K27me3 Pro-B

description: ChIP-Seq H3K27me3 Pro-B


title: 46051 Bio-ChIP-Seq B-ALL

description: Bio-ChIP-Seq B-ALL


title: 40031 Bio-ChIP-Seq Pro-B

description: Bio-ChIP-Seq Pro-B


title: 100885 ChIP-Seq H3K27ac Pro-B

description: ChIP-Seq H3K27ac Pro-B


title: 100880 ChIP-Seq H3K4me3 Pro-B

description: ChIP-Seq H3K4me3 Pro-B


title: 40030 Bio-ChIP-Seq B-ALL

description: Bio-ChIP-Seq B-ALL


title: 29936 Bio-ChIP-Seq Pro-B

description: Bio-ChIP-Seq Pro-B

value: Pax5(Bio/Bio) Rag1(cre/cre)


title: 29938 Bio-ChIP-Seq Pro-B

description: Bio-ChIP-Seq Pro-B

value: Ex-vivo


title: X512 day 2 after CHMI [X7172519]

city: Seattle

first: Raphael

last: Gottardo

state: WA

address: 1100 Fairview Ave N

department: VIDD

institute: Fred Hutch

description:
512_G3_V06A
BSPZV1-34-074

data_processing:
Reads were aligned to the human hg19 genome using STAR.
htseq-count using the intersection-strict option was used to convert mapped reads into a gene count table.
Genes were filtered to retain only genes with >10 read counts in at least 5% of samples.
Counts were then normalized using the R limma and voom packages to account for sequencing depth and log2 transformed for all downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Whole Blood

extract_protocol:
Whole blood samples taken from participants via venipuncture and collected into PaxGene tubes. Total RNA was extracted using PAXgene Blood Kit (PreAnalytiX) and globin mRNA removed using GLOBINclear Human Kit (Ambion).
RNA libraries were generated using standard manufacturers’ protocols for Illumina’s HiSeq 4000

tag: visit

tag: day

tag: protection

value: NP

tag: immunization

value: YES

tag: group

tag: sample id

value: Whole Blood


title: X512 before CHMI [X7172492]

description:
512_G3_V05C
BSPZV1-34-074


title: X512 day 9 after CHMI [X9172026]

description:
512_G3_V07T0
BSPZV1-34-074


title: 100883 ChIP-Seq H3K4me3 Pro-B

description: ChIP-Seq H3K4me3 Pro-B


title: X512 day 7 after 2nd vac [X5170573]

description:
512_G3_V02B
BSPZV1-34-074


title: X512 day 7 after 1st vac [X7170422]

description:
512_G3_V01B
BSPZV1-34-074


title: X512 day 2 after 1st vac [X3169995]

description:
512_G3_V01A
BSPZV1-34-074


title: 100893 ChIP-Seq H3K27me3 Pro-B

description: ChIP-Seq H3K27me3 Pro-B


title: X512 day 0 [X2170282]

description:
512_G3_PreVAC
BSPZV1-34-074

value: Screen 3


title: X489 day 9 after CHMI [X5172022]

description:
489_G3_V07T0
BSPZV1-34-066


title: X489 before CHMI [X5172535]

description:
489_G3_V05C
BSPZV1-34-066


title: X489 day 2 after CHMI [X6172572]

description:
489_G3_V06A
BSPZV1-34-066


title: X489 day 7 after 1st vac [X7170413]

description:
489_G3_V01B
BSPZV1-34-066


title: X489 day 7 after 2nd vac [X5170555]

description:
489_G3_V02B
BSPZV1-34-066


title: X489 day 2 after 1st vac [X6170475]

description:
489_G3_V01A
BSPZV1-34-066


title: X473 before CHMI [X6172536]

description:
473_G3_V05C
BSPZV1-34-065


title: X473 day 7 after 1st vac [X5170420]

description:
473_G3_V01B
BSPZV1-34-065


title: X473 day 2 after 1st vac [X5170474]

description:
473_G3_V01A
BSPZV1-34-065


title: X473 day 2 after CHMI [X2172532]

description:
473_G3_V06A
BSPZV1-34-065


title: X473 day 7 after 2nd vac [X7170566]

description:
473_G3_V02B
BSPZV1-34-065


title: X473 day 9 after CHMI [X7172024]

description:
473_G3_V07T0
BSPZV1-34-065


title: X473 day 0 [X6170286]

description:
473_G3_PreVAC
BSPZV1-34-065


title: X453 day 9 after CHMI [X6172032]

description:
453_G3_V07T0
BSPZV1-34-049

value: P


title: X453 day 2 after CHMI [X4172516]

description:
453_G3_V06A
BSPZV1-34-049


title: X489 day 0 [X6169980]

description:
489_G3_PreVAC
BSPZV1-34-066


title: X453 before CHMI [X8172538]

description:
453_G3_V05C
BSPZV1-34-049


title: X453 day 7 after 1st vac [X8170423]

description:
453_G3_V01B
BSPZV1-34-049


title: X453 day 0 [X6169989]

description:
453_G3_PreVAC
BSPZV1-34-049


title: X453 day 2 after 1st vac [X3170472]

description:
453_G3_V01A
BSPZV1-34-049


title: X453 day 7 after 2nd vac [X6170565]

description:
453_G3_V02B
BSPZV1-34-049


title: X445 before CHMI [X9172539]

description:
445_G3_V05C
BSPZV1-34-043


title: X445 day 7 after 2nd vac [X5170564]

description:
445_G3_V02B
BSPZV1-34-043


title: X445 day 2 after CHMI [X5172517]

description:
445_G3_V06A
BSPZV1-34-043


title: X445 day 7 after 1st vac [X4170419]

description:
445_G3_V01B
BSPZV1-34-043


title: X445 day 0 [X8169964]

description:
445_G3_PreVAC
BSPZV1-34-043


title: X445 day 2 after 1st vac [X4169996]

description:
445_G3_V01A
BSPZV1-34-043


title: Infected (Wild Type) - 4dpi - Rep3 [W4D RNA-seq]

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

data_processing:
Raw 100nt strand-specific single-end reads were quality checked with FASTQC. As many samples presented undetermined nucleotides (“N”) and decreased quality after 76th position, all reads from all samples were truncated to the first 75 nucleotides.
Truncated (75nt) reads were aligned against mouse genome sequence (GRCm38) with TopHat2 (Kim et al. 2013) allowing intron sizes up to 100.000 nt and using default settings for single-end alignments.
Htseq-count function of HTSeq package (Anders et al., 2014) was used for assigning reads to each mouse gene and lncRNA. Genomic feature coordinates were obtained from mouse annotation version GRCm38.76 (ENSEMBL).
To evaluate differential expression of features between SARS-CoV-∆E (2dpi) and WildType (2dpi) samples, DESeq2 (Love et al., 2014) was used. Default parameters were used except detection of outlier counts by Cook’s distance that was not applied (cooksCutoff=FALSE). Three biological replicates per sample were included in the analysis and p.values obtained were adjusted by FDR (Benjamini and Hochberg, 1995).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include raw read count values for all samples

source_name: Infected (Wild Type)_4dpi_lung

growth_protocol: Specific-pathogen-free 8 week-old BALB/c OlaHsd female mice were purchased from Harlan. Mice were maintained for 8 additional weeks in the animal care facility at the National Center of Biotechnology (CNB-CSIC, Madrid).

extract_protocol:
To isolate long and small RNAs separately, one-half of the right lung was homogenized in 2 mL of Lysis/Binding Solution (mirVana miRNA Isolation Kit, Ambion) using a MACS homogenizer (Miltenyi Biotec), according to manufacturer’s protocols. Small and long RNAs were extracted separately from total RNA samples using mirVana miRNA Isolation protocol.
.6 µg of the long RNA fraction were treated to eliminate ribosomal RNA (RiboZero rRNA Removal Kit, Epicentre) and libraries were constructed (NEBNext Ultra directional Library prep A, Illumina) and subjected to 100SE sequencing on a Hiseq 2000 sequencer (Illumina, Parque Científico de Madrid, PCM), resulting in 20 million reads per sample.

treatment_protocol: 16-week-old mice were inoculated with rSARS-CoV wt or rSARS-CoV-ΔE in 50 μl of DMEM containing 2% fetal bovine serum (FBS, Biowhittaker). Mice were sacrificed at days 2 and 4 post infection and lung and serum samples were collected.

value: BALB/c OlaHsd

tag: age

tag: infected with

value: rSARS-CoV wild type

tag: time point

value: lung


title: X420 day 2 after CHMI [X4172570]

description:
420_G3_V06A
BSPZV1-34-037

tag: tissue


title: X420 before CHMI [X9172503]

description:
420_G3_V05C
BSPZV1-34-037


title: Infected (Wild Type) - 4dpi - Rep1 [W4A RNA-seq]


title: Infected (Wild Type) - 4dpi - Rep2 [W4C RNA-seq]


title: X420 day 7 after 2nd vac [X3170571]

description:
420_G3_V02B
BSPZV1-34-037


title: X420 day 7 after 1st vac [X3170418]

description:
420_G3_V01B
BSPZV1-34-037


title: Infected (Wild Type) - 2dpi - Rep3 [W2E RNA-seq]

source_name: Infected (Wild Type)_2dpi_lung


title: X420 day 2 after 1st vac [X6169998]

description:
420_G3_V01A
BSPZV1-34-037


title: Infected (Wild Type) - 2dpi - Rep2 [W2C RNA-seq]


title: X420 day 0 [X7170287]

description:
420_G3_PreVAC
BSPZV1-34-037


title: Infected (Wild Type) - 2dpi - Rep1 [W2B RNA-seq]


title: X445 day 9 after CHMI [X4172021]

description:
445_G3_V07T0
BSPZV1-34-043


title: X420 day 9 after CHMI [X5172031]

description:
420_G3_V07T0
BSPZV1-34-037


title: Mock - 4dpi - Rep1 [M4A RNA-seq]

value: mock


title: X411 day 9 after CHMI [X4172012]

description:
411_G3_V07T0
BSPZV1-34-081


title: X411 before CHMI [X6172482]

description:
411_G3_V05C
BSPZV1-34-081