title: IMR90_200_CASRC_replicate_3

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v2 gene expression microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 5 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray data were log transformed to yield z-scores. The z-ratio was calculated as the difference between the observed gene z-scores for the experimental and the control comparisons, and dividing by the standard deviation associated with the distribution of these differences. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a 5% false discovery rate (FDR) threshold. The complete set was tested for gene set enrichment using parametric analysis of gene set enrichment. For each pathway z-score, a p-value was computed using JMP 6.0 software to test for the statistical significance.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low-Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were evaluated with the NanoDrop ND-1000 Spectrophotometer (Wilmington, DE).

growth_protocol: Human IMR-90 (ATCC) were cultured in Dulbecco's modified Eagle's medium (DMEM, Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco), Penn/Strep (Gibco), Sodium Pyruvate (Gibco), and non-essential amino acids (Gibco) in a 5% CO2 incubator.  Cells were maintained at low population doubling levels (PDL) ranging between PDL15 and PDL25.  Every control condition included equivalent concentrations of vehicle (DMSO).  Doxycycline (1 µg/ml) for the induction of lentiviral constructs was refreshed every 24 h.  Lentiviral constructs were commercially produced by Cellecta.  Either constitutively active SRC (CA-SRC, human SRC Y530F) or dominant-negative SRC (DN-SRC, human SRC K298M/Y530F) were cloned into Cellecta-pTMONRB-TRE-MCS-I2-TagRFP-EFS-rtTA-2A-Blast lentiviral plasmid with a C-terminal MYC-tag.  The mutations generated were based on extensive literature on SRC structure and function (Miyazaki et al., 2004, Cai et al., 2011).  Lentiviral constructs were also packaged by Cellecta and transduced at a 3 MOI with polybrene (Millipore).

extract_protocol: RNA was isolated with RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer's instructions. RNA concentration and quality was assayed on an RNA6000 Bioanalyzer chip (Agilent).

treatment_protocol: RNA was extracted by lyzing cells in RLT buffer (Qiagen),  and purified using the QIAcube system (Qiagen), following the manufacturers protocol.  RNA quality and quantity were determined using the Agilent Bioanalyzer RNA6000 Chip (Agilent, Santa Clara, CA).

value: Fibroblast

tag: cell line

value: Etoposide 200 μM & constitutively active SRC lentiviral transfection

tag: treatment duration

value: 48 hours


title: tagcounts_WGREST_SKNSH

status: Public on Feb 17 2022

type: SRA

city: Bar Harbor

first: Kousuke

last: Mouri

state: ME

address: 600 Main Street

country: USA

institute: The Jackson Laboratory

library_source: transcriptomic

data_processing:
Library strategy: MPRA
Sequences were processed through MPRAduo pipeline (https://github.com/tewhey-lab/MPRAduo).
Supplementary_files_format_and_content: Processed data files contain raw count tables for barcode tag.

molecule: total RNA

organism: Homo sapiens

source_name: SK-N-SH

growth_protocol: 37C with 5% CO2 supplementation

extract_protocol:
Total RNA was purified by using Maxi RNeasy (QIAGEN) from homogenized cells. Then GFP mRNA was isolated by using biotinilated primers and magnetic beads followd by cDNA synthesis.
Libraries were initially amplified from cDNA or plasmid, and then secondarily amplified and added P5 and P7 tag sequences.

treatment_protocol: Cells were electroporated by using NEON transfection system and recovered in culture medium for 24 hours.

value: SK-N-SH

tag: library

value: WGREST

tag: molecule

value: GFP mRNA


title: 686_2

type: RNA

city: Linköping

first: Johannes

middle: Artiaga

last: Gubat

address: Ing. 68 Campus US. Linköpings Universitet

department: Biomedical and Clinical Sciences

country: Sweden

institute: Linköping university

hyb_protocol: 500nM if RBA was processed for microarray analysis using GeneChip WT PLUS reagent according to manufacturer instructions. The prepared RNA was hybridized to GeneChip HuGene 2.0 ST chips for 16 h using the GeneChip Hybridization Oven 645, washed and stained using the GeneChip Fluidics Station 450 using the FS450_0002 protocol

scan_protocol: The chip was scanned with a GeneChip Scanner 3000 7G

data_processing:
The affymetrix arrays were analyzed using the R packages oligo, affycoretools, ggplot2 and limma. For the annotation, the pd.hugene.2.0.st chip annotation package was used. Background correction, normalization, and summarization was done using a deconvolution method for background correction, quantile normalization and the RMA algorithm for summarization.
HuGene-2_0-st.pgf
HuGene-2_0-st.mps

source_name: MCF7 cells

growth_protocol: Cells were cultured in Minimum Essential Medium Eagle with 1mM sodium pyruvate supplemented with 10% fetal calf serum. Cells were maintained in a humidified incubator at 37C and 5% CO2

extract_protocol: Cells were lysed and the RNA was extracted using Rneasy Plus Mini Kit

treatment_protocol: Cells were treated with either DMSO or one of the treatment compounds for 6 hours at 37C at a concentration of 2x IC50 as determined by an MTT assay

tag: tissue type

value: ER + breast cancer

tag: agent

value: CB686 10microM


title: IMR90_200_CASRC_replicate_2

tag: cell type

tag: treatment


title: BCM3392Vs001

city: Vitry-sur-Seine

first: Emmanuel

last: Spanakis

address: 1 Imp. des Ateliers

department: Oncology

country: France

institute: Sanofi

description:
5% glucose till ~300mm3 and sampling
BCM3392 AN1469 MSTO211H shYAP1 processed.txt

data_processing:
STAR aligner
Cufflink
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with FPKM values for every gene and every sample

source_name: Malignant pleural mesothelioma

growth_protocol: Human malignant mesothelioma MSTO-211H cells transfected with a doxycycline-dependent sh-YAP1 construct were inoculated subcutaneously at a 3 × 106 cells dose mixed with Matrigel. Implanted tumors were allowed to growth up to 300 mm3 under glucose supplementation and were sampled just before doxycycline supplementation (time 0, n=5), or after 24 (n=5), 96 (n=5) or 216 hours (n=4) of doxycycline supplementation (time points 1 to 3, respectively). Tumor perpendicular diameters were measured twice a week with a caliper, and tumor volume (V) was calculated according to the following equation: V (mm3) = (d2 (mm2) x D (mm))/2, where d is the smallest, and D the largest perpendicular tumor diameters.

extract_protocol:
Fresh tumors were preserved in RNAlater and frozen at -200°C. Copurification of miRNA and total RNA was performed using a miRNeasy Mini Kit (QIAGEN, 217004). The RNA concentration and purity were evaluated with an ND-1000 spectrophotometer (NanoDrop, Thermo Fisher Scientific, Wilmington, DE, USA). Quality metrics were the RNA Integrity Number (RIN) and DV200 value (% of RNA fragments with a length ≥200nt). 100 ng total RNA per sample was used as input material for the library preparation.
100 ng total RNA per sample was used as input material for the library preparation. The libraries were prepared with the KAPA RNA HyperPrep Kit (Kapa Biosystems, KK8541) and KAPA Target Enrichment using the Kapa HyperCap V3.0 kit for Illumina following the manufacturer’s recommendations.
Second-strand sequencing of the libraries was performed using the NuGEN (San Carlos, CA, USA) RNA-Seq System

treatment_protocol: Mice were divided into groups. Each group received drinking water supplemented with either doxycycline (0.5mg/ml) and 5% glucose or with 5% glucose only.

value: sh-YAP1 transfected cell line in SCID mouse

tag: compound

value: glucose

value: MSTO-211H [sh-YAP1]

tag: time point


title: HFF cells, Ser5P DFF ChIP-Seq Rep1 (Sample 19)

city: Iowa City

first: David

last: Price

state: IA

address: 500 Newton Road, 260 EMRB

department: Biochemistry

institute: University of Iowa

library_source: genomic

data_processing:
Adapter trimming using trim_galore 0.6.
Alignment of trimmed reads to hg38, and HCMV (TB40e KF297339.1, Towne FJ616285.1) using bowtie 1.2.2.
Deduplication of fragments based on their unique molecular index tags using awk and bash.
Conversion of deduped bed files into bedGraph and bigwig using bedtools genomecov and kentUtils bedGraphToBigWig programs.
Genome_build: hg38, KF297339.1, FJ616285.1
Supplementary_files_format_and_content: bigwig files containing pileup of DFF ChIP-Seq fragments across whole genomes.

molecule: genomic DNA

source_name: Primary human foreskin fibroblast (HFF)

growth_protocol: HeLa cells were grown in T150 flasks in 25 ml DMEM (Gibco 11965-092), HFF cells were grown in MEM (Gibco 11095-080), and MRC5 cells were grown in a 1:1 mixture of Ham’s F-10 (Gibco 11550-043) and DMEM and all were supplemented with 5% fetal bovine serum (FBS, Gibco 26140-079)

extract_protocol:
Rapid nuclei isolation steps were performed on wet ice using ice-cold buffers as previously described (Nilson et al. 2017; Ball et al. 2019). Following DFF digestion, nuclei were lightly sonicated for 20s and the soluble material was immunoprecipitated with 2.5 µg of antibodies.
Library construction is detailed in the manuscript.

treatment_protocol: Treatment Protocol: 1 hour prior to harvest, when cell were at 80-90% confluence, 5 ml of media was removed and either 25 µl of DMSO or 1 mM flavopiridol in DMSO was added before the mixture was returned to the flask (final concentrations 0.1% DMSO or 1 µM flavopiridol and 0.1% DMSO). Nuclei isolated from these cells were digested with ~15 µg of DFF per T150. (~25 µg for excess digestion experiments)

value: HFF

tag: infection (duration and strain)

value: 48 hrs Towne BAC

tag: chip antibody

value: untreated

tag: condition

value: Low Salt

tag: exp


title: 686_1


title: 383_1

value: CB383 2.5microM


title: IMR90_200_CASRC_replicate_1


title: SKNAS WT KIF5A RIP2

city: Worcester

first: John

last: Landers

state: MA

address: 55 N Lake Ave

institute: UMass Chan Medical School

description: SKNAS cells transfected with V5-WT KIF5A construct

data_processing:
The sequence reads were mapped with Gencode "GRCh38.primary_assembly.genome.fa" reference.
Strandedness was calculated with rseqc tool using infer_experiment.py module
HTSeq was used to extract the numbers of reads per transcript using stranded parameter and further analysis was done with DESeq2
Genome_build: GRch38
Supplementary_files_format_and_content: tab-delimited test file inclue HTSeq raw counts for each transcript in different samples
Supplementary_files_format_and_content: DESeq2 results in matrix format

source_name: SKNAS cells

growth_protocol: SKNAS cells were maintained at 37C with 5% CO2 in Dulbecco’s modified Eagle’s medium supplemented with 10% (v/v) heat-inactivated FBS, 2 mm L-glutamine and 1% (v/v) penicillin and streptomycin solution.

extract_protocol:
RNA was extracted from immunoprecipitation elution samples using Trizol reagent. For the IP, conjugated beads were used, the Anti-V5 Tagged Magnetic Beads (MBL International Corp, Cat# M167-11).
RNA transcripts are enriched by selectively depleting ribosomal RNA molecules using the Ribogone Low-input-Mammalian kit (Clontech Cat. Nos. 634846 & 634847 ), which allows for the specific removal of rRNA sequences (5S, 5.8S, 18S, and 28S), as well as mitochondrial rRNA sequences (12S), from human, mouse, or rat total RNA. Fragmentation times are adjusted based on the RIN value for each sample so that an insert size of 150-200 bp can be achieved.  The SMARTer Stranded RNA-Seq Kit (Cat. Nos. 634836) is then used to generate a cDNA library.  The cDNA library is then amplified and indexed adapters are added.  Libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the Perkin Elmer LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: SKNAS cells were grown to 75% confluency then media was removed and replaced with fresh media. After an 1hr incubation at 37°C, the cells were transfected with Lipofectamine 2000 using a DNA:Lipo ratio of 3ug:8ul per 6 well according to the manufacturer’s instructions. Experment was started twenty-four hours after transfection.

value: SKNAS

value: V5-WT KIF5A RIP2


title: HFF cells, Pol II DFF ChIP-Seq Rep1 (Sample 17)

value: Pol II


title: HFF cells, Pol II DFF ChIP-Seq Rep2 (Sample 18)


title: tagcounts_WGREST_HepG2


title: HFF cells, UL87 DFF ChIP-Seq (Sample 15)


title: HFF cells, Ser5P DFF ChIP-Seq (Sample 14)

value: 48 hrs Towne TB40e


title: 113_2

value: CB113 10microM


title: IMR90_50_DNSRC_replicate_2

value: Fibroblast

value: Etoposide 50 μM & dominant-negative SRC lentiviral transfection

value: 48 hours


title: Gm12878_benchmark_run1

value: benchmark

value: GFP mRNA


title: HFF cells, Pol II DFF ChIP-Seq (Sample 12)

value: Triptolide


title: HFF cells, Pol II DFF ChIP-Seq (Sample 11)


title: HFF cells, Pol II DFF ChIP-Seq (Sample 10)


title: Gm12878_benchmark_run2


title: SKNAS d27 KIF5A RIP1

description: SKNAS cells transfected with V5-d27 KIF5A construct

value: V5-d27 KIF5A RIP1


title: HFF cells, Pol II DFF ChIP-Seq (Sample 8)

value: HFF

value: uninfected


title: HFF cells, TBP DFF ChIP-Seq (Sample 13)

value: TBP

value: untreated


title: HFF cells, H3K4me3 DFF ChIP-Seq (Sample 9)

value: Low Salt


title: 113_1

value: ER + breast cancer


title: IMR90_200_ETOP_replicate_3

value: Etoposide 200 μM


title: 113_3


title: IMR90_50_DNSRC_replicate_1


title: Resected tumor mouse #5

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

description:
Resected_5
SxTumExp2_20

data_processing:
RNA-seq processing:
Eightyfive-base-pair single-end sequenced reads followed adapter and polyA tail removal as indicated by Lexogen. The resulting reads were fed to Xenome to separate the xenograft-derived human and mouse reads. Human reads were analysed with the nextpresso pipeline (http://www.eurekaselect.com/154865/article) as follows: sequencing quality was checked with FastQC v0.11.0 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the human genome (GRCh38) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.19, allowing 3 mismatches and 20 multihits. The Gencode v29 gene annotation for GRCh38 was used. Read counts were obtained with HTSeq. Differential expression and normalization was performed with DESeq2, filtering out those genes where the normalized count value was lower than 2 in more than 50% of the samples. From the remaining genes, those that had an adjusted p-value below 0.05 FDR were selected. GSEAPreranked was used to perform gene set enrichment analysis for several gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered. A single sample gene set enrichment analysis (ssGSEA) test was performed with the GSVA R package. Heatmaps showing pathway enrichment were plot with Morpheus (https://software.broadinstitute.org/morpheus).
Genome_build: GRCh38
Supplementary_files_format_and_content: Normalized counts obtained with DESeq2

source_name: Brain tumor

extract_protocol:
Whole RNA was isolated using the RNAeasy Mini Kit (Qiagen) according to manufacturer’s instructions
500ng of total RNA samples were used. Sample RNA Integrity numbers were 8.6 on average (range 5.9-9.5) when assayed on an Agilent 2100 Bioanalyzer. Sequencing libraries were prepared with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) by following manufacturer instructions. Library generation is initiated by reverse transcription with oligodT priming, and a second strand synthesis is performed from random primers by a DNA polymerase. Primers from both steps contain Illumina-compatible sequences. Libraries are completed by PCR {This kit generates directional libraries stranded in the sense orientation: the read1, the only read in single read format, has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq)}. cDNA libraries are purified, applied to an Illumina flow cell for cluster generation and sequenced on an Illumina NextSeq 550 (with v2.5 reagent kits) by following manufacturer's protocols.

value: Neurosurgery


title: 383_2

value: CB383 2.5microM


title: Resected tumor mouse #6

description:
Resected_6
SxTumExp2_50


title: HFF cells, H3K4me3 DFF ChIP-Seq (Sample 16)

value: 48 hrs Towne TB40e


title: IMR90_200_ETOP_replicate_1

value: Fibroblast


title: IMR90_200_ETOP_replicate_2


title: IMR90_50_ETOP_replicate_3

value: Etoposide 50 μM


title: sj_wt_2_ChIP_Seq_H3K9me2

city: Edinburgh

first: Elizabeth

middle: H

last: Bayne

address: Alexander Crum Brown Road

department: Institute of Cell Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
Raw reads were filtered for quality and adapter using Trim Galore! (v0.4.3.1), reads that became shorter than 20nt were discarded
Trimmed reads were aligned to the S. japonicus reference genome (SJ5) using Bowtie2 (v2.3.4.3)
Coverage bigWig files were generated for each sample using bamCoverage (v3.3.2.0.0). RPKM was used for normalisation with a bin size of 50bp.
Ratios IP/Input were calculated using bigwigCompare (v3.3.2.0.0)
Ratios [H3K9/Input]/[H3/Input] were calculated using bigwigCompare (v3.3.2.0.0)
Genome_build: GCA_000149845.2
Supplementary_files_format_and_content: bedgraph files plotting the ratio of [H3K9me2/Input]/[H3/Input] for each sample

organism: Schizosaccharomyces japonicus

source_name: S. japonicus cell culture

growth_protocol: Cells were grown in YES at 32C

extract_protocol:
Cells were lysed using a bead beater (Biospec products) for 4 x 2min, and lysates were sonciated using a Bioruptor twin (Diagenode) for 7 x 4min cycles (30 secs on/30 secs off on 'high' power). Samples were pre-cleared with Protein-G Agarose for 1 hour, then incubated with fresh Protein-G agarose and antibody overnight.  Beads were washed, then crosslinks were reveresed at 65°C, before contaminating RNA was removed using RNaseA. Proteins were digested with Proteinase K and immuniprecipatated genomic DNA was recovered using PCR purifcation columns (Qiagen).
Libraries were constructed using the NEBNext Library Prep Master Mix Set (NEB) according to manufacturer's instructions

treatment_protocol: Cells were fixed with 1% formaldehyde for 15 min at room temperature

tag: strain

tag: genotype

value: h- mat-P2028 ura4-D3 ade6(sj)-domE


title: Resected tumor mouse #4

description:
Resected_4
SxTumExp2_3


title: Resected tumor mouse #3

description:
Resected_3
SxTumExp2_2


title: HC39

city: Xian

first: chengsheng

last: zhang

state: Shaanxi

address: 277 West Yanta Road, Xi'an, Shaanxi, P.R.China

department: precision medicine center

country: China

institute: First Affiliated Hospital of Xi 'an Jiaotong University

data_processing:
Illumina bcl2fastq software used for for basecalling.
we further reduced the dimensionality of all 207,718 cells by Seurat and used t-Distributed Stochastic Neighbor Embedding (t-SNE) to project the cells into 2D space. The steps included:1.Using the LogNormalize method of the "Normalization" function of the Seurat software to calculated the expression value of genes; 2.PCA (Principal component analysis) analysis was performed using the normalized expression value, Within all the PCs, the top 10 PCs were used to do clustering and t-SNE analysis; 3.To find clusters, selecting weighted Shared Nearest Neighbor (SNN) graph-based clustering method. Marker genes for each cluster were identified with the "bimod"(Likelihood-ratio test)with default parameters via the FindAllMarkers function in Seurat. This selects markers genes which were expressed in more than 10% of the cells in a cluster and average log (Fold Change) of greater than 0.26. To further avoid interference of putative multiplets (where more than one cell may have loaded into a given well on an array), cells in defined cluster had high expression of more than one cell type canonical marker gene (Figure 1, Supplementary Figure 1 ) so that were considered low quality were filtered out. Finally, 119,799 cells were kept in this experiment.  Next, the nine cell types were integrated for further subclustering. After integration, genes were scaled to unit variance. Scaling, principal component analysis and clustering were performed as described above.
using "bimod" with default parameters in Seurat. DEGs were filtered using a minimum log2 (fold change) of 0.26, a P value < 0.05 and detection in > 10% of cells in at least one group. To further understand the associations and function of the DEGs, we performed a GO annotation analysis and a KEGG analysis. DEGs with a log2 mean expression difference ≥ 0.26 enriched in GO or KEGG pathways were considered as candidate biomarkers or pathway for the pathogenesis.
Genome_build: GRCh38_v96

source_name: Peripheral blood

extract_protocol:
Retrieving the PBMC-containing cryo-tubes from the -196℃ liquid nitrogen storage tank and placing them in a 37℃ water bath for rapid thawing. PBMCs were mixed with 10 mL washing medium (90% DMEM+10% FBS) in a 15-mL polypropylene tube and centrifuged at 500g for 20 min. The supernatant was then aspirated (repeat twice). The cell pellets were resuspended with 500 μl× PBS (0.04% BSA) in the sterile RNase-free vacutainer tubes and added with 5 ml 1× red blood cell lysis buffer (MACS 130-094-183, 10×) and incubated at room temperature for 10 min to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 500g for 20 min at room temperature. The suspension was resuspended in 100 μl Dead Cell Removal MicroBeads (MACS 130-090-101) and remove dead cells using Miltenyi ® Dead Cell Removal Kit (MACS 130-090-101). Then the suspension was resuspended in 1× PBS (0.04% BSA) and centrifuged at 300 g for 3 min at 4 °C (repeat twice). The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion, which needed to be above 85%, single cell suspensions were counted using a Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Health control

tag: tissue

value: Peripheral blood

value: peripheral blood mono-nuclear cells

tag: age

tag: gender

value: female

tag: disease symptom

tag: disease severity


title: HC31

value: male


title: HC58


title: HC60


title: Resected tumor mouse #2

description:
Resected_2
SxTumExp1_2


title: IMR90_50_ETOP_replicate_1

tag: cell line

tag: treatment duration

value: 48 hours


title: HC36

tag: cell type


title: Resected tumor mouse #1

description:
Resected_1
SxTumExp1_2

tag: treatment


title: HC21


title: IMR90_50_ETOP_replicate_2


title: HC05


title: IMR90_CTR_replicate_3

value: DMSO (vehicle)


title: HC23


title: HC07


title: 72 hpi PRO-Cap

data_processing:
Library strategy: PRO-Seq
Adapter trimming using trim_galore 0.6.
Alignment of trimmed reads to hg38, and HCMV (TB40e KF297339.1) using bowtie 1.2.2.
Deduplication of fragments based on their unique molecular index tags using awk and bash.
Conversion of deduped bed files into bedGraph and bigwig using bedtools genomecov and kentUtils bedGraphToBigWig programs.
Genome_build: hg38, KF297339.1
Supplementary_files_format_and_content: bigwig files containing pileup of DFF ChIP-Seq fragments across whole genomes.

growth_protocol: HFF were isolated and cultured as described in the manuscript. Cells were maintained in Minimum Essential Medium (Gibco 11095-080) supplemented with 5% fetal bovine serum (FBS, Gibco 26140-079and grown to confluence for at least one week before infection.

extract_protocol:
Rapid nuclei isolation steps were performed on wet ice using ice-cold buffers as previously described (Nilson et al. 2017; Ball et al. 2019).
Library construction is detailed in the manuscript.

treatment_protocol: Treatment Protocol: Infection details are in the manuscript. As indicated, 1 µM Flavopiridol or 0.1% DMSO were added to media 1 h before harvest.

value: HFF

value: 72 hrs TB40/E

value: DMSO


title: Relapsed tumor mouse #5

description:
Relapse_5
RelapTumExp2_20


title: HC01


title: Relapsed tumor mouse #6

description:
Relapse_6
RelapTumExp2_50


title: COV166

value: symptomatic

value: Severe Recovery

tag: disease duration

value: long term

tag: patient comorbidity

value: Yes


title: COV165

value: No


title: HC20


title: IMR90_CTR_replicate_1

value: Fibroblast


title: COV164


title: Relapsed tumor mouse #3

description:
Relapse_3
RelapTumExp2_2

value: Neurosurgery


title: ND_08_1

city: Chongqing

first: Ma

last: Huan

address: Daping Street

institute: Daping Hospital,Army Medical University

data_processing:
Sub-pixel Registration software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
We used RSEM v.1.2.8 to calculate the gene expression level of each sample with parameters -p 8 --forward-prob 0.5 --paired-end
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts and fpkm for every gene and every sample

organism: Mus musculus

source_name: central amygdala

extract_protocol:
Central amygdala was removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmentedinto small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA wasgenerated using random hexamer-primed reverse transcription, followed by a second-strand cDNAsynthesis. afterwards, A-Tailing Mix and RNA Index Adapters were addedby incubating to endrepair. The cDNA fragments obtained from previous step were amplified by PCR, and productswere purified by Ampure XP Beads, then dissolved in EB solution. The product was validated onthe Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR productsfrom previous step were heated denatured and circularized by the splint oligo sequence to get thefinal library. The single strand circle DNA (ssCir DNA) was formatted as the final library. Thefinal library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300copies of one molecular, DNBs were loaded into the patterned nanoarray andsingleend50basesreads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: central amygdala

value: post natal month 7

value: post normal chow diet weeks 20


title: HFF cells, H3K4me3 DFF ChIP-Seq (Sample 7)

tag: infection (duration and strain)

value: uninfected

tag: chip antibody

value: untreated

value: Low Salt


title: IMR90_CTR_replicate_2

value: DMSO (vehicle)

value: 48 hours


title: Relapsed tumor mouse #4

description:
Relapse_4
RelapTumExp2_3


title: Relapsed tumor mouse #2

description:
Relapse_2
RelapTumExp1_3


title: ND_05_1


title: COV163

value: Peripheral blood

value: peripheral blood mono-nuclear cells

value: female


title: SKNAS WT KIF5A RIP1

value: SKNAS

value: V5-WT KIF5A RIP1


title: COV161

value: male

value: symptomatic

value: Severe Recovery

value: long term


title: HFF cells, H3K4me3 DFF ChIP-Seq Rep 1 (Sample 23)

value: HFF

value: 48 hrs Towne BAC

tag: condition

tag: exp


title: ND_02_1

tag: strain

value: central amygdala

value: post natal month 7

value: post normal chow diet weeks 20


title: 72 hpi Flavo PRO-Seq

value: 72 hrs TB40/E

value: Flavo


title: 48 hpi DMSO PRO-Seq

value: 48 hrs TB40/E

value: DMSO


title: COV158

tag: disease state

value: Peripheral blood

value: peripheral blood mono-nuclear cells

value: Yes


title: Relapsed tumor mouse #1

description:
Relapse_1
RelapTumExp1_2

value: Neurosurgery


title: COV159

tag: tissue

value: female


title: 24 hpi Flavo PRO-Seq

value: 24 hrs TB40/E


title: 24 hpi DMSO PRO-Seq


title: 48 hpi Flavo PRO-Seq


title: 72 hpi DMSO PRO-Seq


title: COV126

tag: age

value: male

value: symptomatic

value: Severe Recovery

value: short term


title: HFD_08_1

value: central amygdala

value: post high fat diet weeks 20


title: ND_01_1

value: post natal month 7

value: post normal chow diet weeks 20


title: MED1-/- macrophage B

city: Xi'an

first: Liang

last: Bai

address: Yanta West Road No.76

institute: Xi'an Jiaotong University

data_processing:
Base calling and quality scoring were performed by an updated implementation of Real-Time Analysis (RTA), termed RTA v2, on the NextSeq 500 system. bcl2fastq Conversion Software v1.8.4 was used to demultiplex data and convert BCL files to FASTQ file formats.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mm9 whole genome using tophat v2.0.14 with parameters -p -G -o
Reads per kilobase of exon per megabase of library size (RPKM) were calculated using cufflinks v2.2.1, which assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: peritoneal macrophages

extract_protocol:
Total RNA was exracted and purified using the mirVana mRNA isolation kit according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PMs from 8-week-old MED1fl/fl and MED1ΔMac mice were treated without or with lipopolysaccharide (LPS; 50 ng/mL) for 6 hours.

value: peritoneal macrophages

tag: genotype


title: 12 hpi Flavo PRO-Seq

value: HFF

value: 12 hrs TB40/E

value: Flavo


title: WT-macrophage B

value: WT


title: COV119

value: Peripheral blood

value: peripheral blood mono-nuclear cells

tag: gender

tag: disease symptom

value: No


title: MED1-/- macrophage+LPS B

value: LPS


title: COV055

value: male

tag: disease severity

value: long term

value: Yes


title: 12 hpi DMSO PRO-Seq

value: DMSO


title: HFD_05_1

value: central amygdala


title: HFD_02_1

value: post high fat diet weeks 20


title: WT-macrophage+LPS B


title: 4 hpi Flavo PRO-Seq

value: 4 hrs TB40/E


title: MED1-/- macrophage+LPS A


title: HFD_01_1

value: post natal month 7


title: COV037

value: female

value: symptomatic

value: Severe Recovery

value: short term


title: MED1-/- macrophage A

value: peritoneal macrophages


title: 4 hpi DMSO PRO-Seq

value: HFF


title: Mnase-seq_H2A.Z_KO_MEF_rep2

city: Lyon

first: Kiran

last: Padmanabhan

address: 32-34 avenue Tony Garnier

department: IGFL

institute: ENS-Lyon

data_processing:
Sequenced reads were mapped to mm10 whole genome using bowtie
Read were elongated to 150 bp using danpos2 to generate wig file
Genome_build: mm10

source_name: MEF cells

extract_protocol:
Nuclei were digested in light Mnase conditions and DNA purified
Libraries were sequenced on BGI plateform in single-end method

value: embryonic-fibroblast

value: H2A.Z flox/flox


title: Mock Flavo PRO-Seq

value: Flavo


title: WT-macrophage+LPS A

value: WT

value: LPS


title: Mnase-seq_H2A.Z_KO_MEF_rep1


title: COV057

value: Peripheral blood

value: peripheral blood mono-nuclear cells

value: male

value: Severe

value: Yes


title: WT-macrophage A


title: Mnase-seq_PerTKO_MEF_rep2

value: PerTKO


title: Mnase-seq_PerTKO_MEF_rep1


title: MRC5 cells, Pol II DFF ChIP-Seq (Sample 6)

source_name: Medical Research Council cell strain 5 (MRC5)

tag: cell line

value: uninfected

value: GFP

value: High Salt


title: High_Mnase-seq_H2A.Z_KO_MEF_rep2

data_processing:
Sequenced reads were mapped to mm10 whole genome using bowtie
Read were elongated to 150 bp using danpos2 to generate wig file
Genome_build: mm10
Supplementary_files_format_and_content: bw

extract_protocol:
Nuclei were digested in high Mnase conditions and DNA purified
Libraries were sequenced on NextSeq plateform in single-end method

tag: cell type

value: embryonic-fibrobalst


title: COV047

value: symptomatic

value: short term


title: High_Mnase-seq_H2A.Z_KO_MEF_rep1


title: Mnase-seq_WT_MEF_rep2

value: embryonic-fibroblast


title: Mnase-seq_WT_MEF_rep1


title: MRC5 cells, H3K4me3 DFF ChIP-Seq (Sample 3)

tag: treatment

value: untreated

value: Low Salt


title: MRC5 cells, H3K4me3 DFF ChIP-Seq (Sample 4)

value: Flavo


title: COV045

value: female

value: Severe Recovery

tag: disease duration

value: No


title: High_Mnase-seq_PerTKO_MEF_rep1


title: HeLa cells, H3K4me3 DFF ChIP-Seq (Sample 2)

source_name: HeLa cells

value: HeLa


title: COV021

value: Peripheral blood

value: peripheral blood mono-nuclear cells

value: Severe

tag: patient comorbidity


title: High_Mnase-seq_WT_MEF_rep2

value: WT


title: Mock DMSO PRO-Seq

value: HFF

tag: infection (duration and strain)

value: DMSO


title: COV007

value: male


title: MRC5 cells, Pol II DFF ChIP-Seq (Sample 5)

value: uninfected

tag: chip antibody

value: GFP

value: High Salt


title: COV029

value: symptomatic

value: short term

value: Yes


title: MRC5 cells, Pol II DFF ChIP-Seq (Sample 1)

value: Flavo

tag: condition

value: Low Salt


title: High_Mnase-seq_WT_MEF_rep1

value: embryonic-fibrobalst


title: Testicular Microenvironment_B04_Lep 1

city: Miami

first: Derek

last: Van Booven

state: FL

address: 1501 NW 10th Ave

institute: University of Miami

data_processing:
Adapters trimmed with Trim_galore
Alignment and Quantification with STAR
Genome_build: hg19
Supplementary_files_format_and_content: matrix.txt (Gene Raw Counts in tab delimited text format)

source_name: Human Testis Biopsy

extract_protocol:
The protocol for LSC isolation has been described previously (12). Briefly, interstitial cells from the testes were dissociated from the seminiferous tubules by treatment with 1 mg/ml trypsin followed by collagenase (collagenase D; Roche Molecular Biochemicals) treatment in DMEM for 10 min at 34°C with shaking.  The separated cells were filtered through two layers of 70-μm pore-size nylon mesh, centrifuged at 250 × g, and re-suspended in DMEM. The cells were washed with PBS, centrifuged at 250 × g, re-suspended in phenol red-free 1:1 DMEM: F12 and plated for cell culture.
Truseq standard Total RNA Library Prep
Libraries were prepared according to Illumina's instructions accompanying the Sample Kit (Truseq standard Total RNA Library Prep).

treatment_protocol: Cells were extracted from LSCs that were exposed to increasing concentrations of leptin ranging from 0, 0.25, 1, and 10ng/ml. Post treatment, RNA was extracted and RNA library was generated.

value: Testicular Microenvironment

value: Leydig cells+Sertoli cells+PMC

value: Leptin 1ng/ml


title: COV077

value: Peripheral blood

value: peripheral blood mono-nuclear cells

value: Severe


title: TacT3

city: Moscow

first: Dmitry

middle: Vadimovich

last: Bikmetov

state: Moscow

address: Vavilova, 34/5

country: Russia

institute: Center for Precision Genome Editing and Genetic Technologies for Biomedicine, IGB RAS

data_processing:
library strategy: Ribosome-profiling
The raw reads were trimmed and quality filtered with Skewer 0.2.2
Reads mapped to rRNA and tRNA sequences were discarded. Mapping was performed using Bowtie 1.2.2, allowing no more than two mismatches.
Remaining reads were uniquely mapped to the E. coli MG1655 genome with the same program and parameters.
Reads shorter than 15 nt or longer than 40 nt were excluded.
Ribosome density (occupancy) was calculated as the number of 3’-ends of footprints normalized by the total number of uniquely mapped reads (in millions).
Genome_build: NC_000913.2
Supplementary_files_format_and_content: Separate wig files for each strand containing ribosome density (occupancy).

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

source_name: Cell culture

growth_protocol: The overnight cultures of E. coli BW25113 cells transformed with pBAD33 bearing a toxin gene or an empty pBAD33 vector were diluted 200-fold into 200 ml of MOPS medium supplemented with 33 μg/ml chloramphenicol and 1% glucose and were grown at 37°C with vigorous shaking to an OD600 of 0.2.

extract_protocol:
The cells were harvested and lyzed as described in Becker et al. 2013. The cellular lysates were clarified by centrifugation at 20,000 x g at 4°C for 10 min. The lysates were diluted with the lysis buffer  to adjust the OD260 to 0.1 in the final volume of 220 μl and treated with ~450 U of MNase (Roche) at 25°C for 1 hr. The reaction was quenched by the addition of EGTA to the final concertation of 5 mM. The monosomal material was purified by sucrose gradient centrifugation. RNA was purified as described in Becker et al. 2013.
Libraries were constructed as described in Becker et al. 2013

treatment_protocol: The cells were pelleted and resuspended in fresh MOPS medium supplemented with 33 μg/ml chloramphenicol without glucose and grown at 37°C for 30 min, followed by 15 min induction with 1 mM arabinose.

tag: strain background

tag: genotype/variation

tag: time point

value: 15 min after induction


title: Testicular Microenvironment_B04_Lep 10

tag: tissue

value: Leptin 10ng/ml


title: Testicular Microenvironment_B04_Lep 0.25

value: Leptin 0.25ng/ml


title: COV016

tag: disease state

tag: age

value: male

value: No


title: High_Mnase-seq_PerTKO_MEF_rep2

tag: strain

tag: genotype

value: PerTKO


title: Pten pc-/-; Timp1-/-_rep2

city: Bellinzona

first: Andrea

last: Alimonti

address: Via vela 6

department: Molecular Oncology

country: Switzerland

institute: Institute of oncology research

data_processing:
Sequencing data were processed by CellRanger (version 3.1.0) and reads were aligned to mouse genome (mm10 v3.0.0) with STAR (v.2.5.1b).
To reduce the ‘dropout’ phenomenon, RMagic package was used on gene-counts. Single cell sequencing analysis was performed in epithelial cells purified from both Ptenpc-/- and Ptenpc-/- ; Timp1-/- tumors. For each cell, we calculated different quality measures: percent of mitochondrial genes, number of genes and gene biotype. We removed cells that had more than 25% expression on mitochondrial genes, fewer than 100 total genes expressed and we considered only protein coding genes defined using getBM (biomaRt package)
All the samples were integrated using Seurat package (FindIntegrationAnchors and IntegrateData function after library-size normalization of each cell using NormalizeData function with default parameters).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Rmagic counts
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Epcam+ sorted cells

extract_protocol:
Prostate tumors were isolated, minced and processed for single cell suspension. Tissues were digested in 2 ml of Digestion Buffer composed by RPMI 10% FBS + 1% P/S, 500 mL of Collagenase D (1 mg/mL), 50mL of DNAse (100 U/mL) and 125mL of HEPES (25 mM). The cell suspension was incubated for 50 minutes at 37°C on a rocker. Then, the digestion was stopped adding 1 mL of RPMI 10% FBS + 1% P/S. The cells suspension was filtered through a 100 mm cell strainer and kept on ice for 4 minutes. Then cells suspension was filtered again through a 40 mm cell strainer and spun down at 1500 rpm for 5 min at 4°C. FACS staining was performed using EPCAM-FITC (anti-Mo CD326, eBioscience, clone G8.8 #11-5791-82) for the murine prostate tumors.
Single-cell transcriptomes was performed using 10X Chromium single cell platform (10X Genomics, Pleasanton, CA. USA). FACS-sorted Epcam+ prostate cells were used as the input source for the scRNA-seq. Cells were suspended in a phosphate buffer solution containing 0.04% weight/volume bovine serum albumin (BSA). The recommended volume of single cell suspension was loaded on a Chromium Single Cell Controller (10x Genomics) targeting ~10000 cells per murine prostate samples while for xenografts tumors we used a target cell recovery between 5000 and 10000 cells per sample. Bar- coded single-cell gel beads in emulsion (GEMs) were created by 10x Genomics! Chromium TM and then reverse transcribed to generate single-cell RNA-seq libraries using Chromium Single Cell 3’ Library and Gel Bead Kit v2 (10X Genomics) according to manufacturer’s instructions. Resulting short fragment libraries were checked for quality and quantity using an Agilent 2100 Bioanalyzer and Invitrogen Qubit Fluorometer. Unique molecular identifiers (UMIs), which were incorporated into the 5’ end of cDNA during reverse transcription, were used to quantify the exact number of transcripts in a cell.

value: prostate

value: Pten pc-/-; Timp1 -/-


title: COV013

tag: gender

tag: disease symptom

value: symptomatic

tag: disease severity

value: short term


title: Pten pc-/-; Timp1-/-_rep1


title: tagcounts_WGREST_plasmid

molecule: other

organism: synthetic construct

source_name: plasmid vector

tag: cell line

tag: library

value: benchmark

tag: molecule

value: plasmid


title: ItaT


title: COV012

tag: cell type

tag: disease duration

tag: patient comorbidity

value: Yes


title: COV078


title: IMR90_50_DNSRC_replicate_3

data_processing: Raw microarray data were log transformed to yield z-scores. The z-ratio was calculated as the difference between the observed gene z-scores for the experimental and the control comparisons, and dividing by the standard deviation associated with the distribution of these differences. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a 5% false discovery rate (FDR) threshold. The complete set was tested for gene set enrichment using parametric analysis of gene set enrichment. For each pathway z-score, a p-value was computed using JMP 6.0 software to test for the statistical significance.

extract_protocol: RNA was isolated with RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer's instructions. RNA concentration and quality was assayed on an RNA6000 Bioanalyzer chip (Agilent).

value: Fibroblast

tag: treatment

value: Etoposide 50 μM & dominant-negative SRC lentiviral transfection

tag: treatment duration

value: 48 hours


title: Pten pc-/-_rep2

value: Pten pc-/-


title: COV011

value: Peripheral blood

value: peripheral blood mono-nuclear cells

value: Severe


title: COV009

value: male


title: INV455

city: London

first: Suzanne

last: Hocking

address: Keppel Street

institute: London School of Hygiene and Tropical Medicine

data_processing:
Samples were demultiplexed using Illumina BaseSpace
Short reads were trimmed of low quality bases with Trimmomatic v0.3.2 using default parameters, which will drop reads if they are less than 36 bases in length, remove leading and trailing bases with low quality (less than 3), and move along the read in a 4-base sliding window, cutting the read when the average quality of the window drops below 15 (Bolger Lohse 2014)
Whole transcriptome short read sequence data were assembled by alignment to the P. falciparum 3D7 v3 reference genome using HISAT2 (Kim et al. 2015) with default parameters
Raw gene counts for each sample were made using the summarizeOverlaps function of the GenomicAlignments package (Lawrence, Huber et al., 2013) in R using a custom made GFF reference file which had been prepared previously in which P. falciparum sub-telomeric, polymorphic gene families (var, rifin, stevor) and regions of the genome which showed allelic diversity between the P. falciparum 3D7 version 3 reference genome and ten schizont stage (40 h.p.i.) clinical isolate transcriptomes was used for generating read counts per gene (Tarr et al., 2018)
Differential expression analysis was carried out in R using the package DESeq2 (Love et al. 2014).
Genome_build: Plasmodium falciparum 3D7 v3
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Plasmodium falciparum

source_name: Plasmodium falciparum clinical isolate blood stage

growth_protocol: Clinical isolates were introduced into culture ex vivo at 2.5% haematocrit in complete media. Parasites were cultured with washed whole blood (various blood types) incubated with 5% O2, 5% CO2, and 90% N2, at 37 ̊C while shaking at 60 R.P.M.

extract_protocol:
Parasite schizont-enriched material from individual isolates was stored in either TRIzol® or RNAlater™ (Thermo Fisher Scientific, MA, USA), and RNA was extracted by phenol-chloroform and cleaned up using the NucleoSpin® RNA XS extraction kit (Macherey-Nagel, Germany).
RNA was reverse transcribed and cDNA amplified using the SmartSeq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio. Inc., Shiga Prefecture, Japan). Successfully amplified samples were prepared for paired end short-read sequencing using the Nextera XT Library Prep kit (Illumina, California, USA), according to manufacturer instructions

treatment_protocol: Magnetic MACS® seperation was used to enrich the cultures for schizonts on the second day in culture. Schizonts were then matured in the presence of E64 to prevent schizont rupture for 4 hours prior to harvesting

tag: culture

value: ex vivo

tag: Stage

value: schizont

value: clinical isolate

tag: proportion of mspdbl2-positive schizonts by ifa


title: Pten pc-/-_rep1

tag: tissue

value: prostate

tag: age


title: hSOD1-G93A ACM rep 5

first: Helene

last: Tran

address: 55 Lake Street

institute: Umass Medical School

description: Sample 19

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
clean reads were mapped to reference genome using Hisat with the following parameters: -p 8 --phred64 --sensitive -I 1 -X 1000  \end
Gene expression was calculated using the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) method;Li B and Dewey C N. (2011)
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample ...

organism: Rattus norvegicus

growth_protocol: Spinal cord cultures: Pregnant Sprague-Dawley rats were deeply anesthetized with CO2 and primary spinal cultures were prepared from E14 pups. Cultures of ventral spinal cords were prepared and maintained in neuronal growth media: 70% MEM (Gibco, Cat. # 11090-073), 25% Neurobasal media (Gibco, Cat. # 21103-049), 1% N2 supplement (Gibco, Cat. # 17502-048), 1% L-glutamine (Gibco, Cat. # 25030-081), 1% penicillin-streptomycin (Gibco, Cat. # 15140-122), 2% horse serum (Gibco, Cat. # 15060-114; lot 1517711) and 1% sodium pyruvate (Gibco, Cat. # 11360-070). Cultures were maintained for 7-9 DIV at 37oC under 5% CO2 and supplemented with 45 μg/ml E18 chick leg extract; media was renewed every 3 days.   ACM: Primary astrocyte cultures and ACM were prepared from P1-2 mutSOD1 spinal cords derived from neonatal SOD1G93A transgenic mice (mutSOD1). Non-transgenic astrocytes from littermates (Ctrl) and astrocytes expressing wtSOD1 (wtSOD1) were used as controls. Cells were maintained in DMEM (Hyclone, Cat. # SH30081.01) containing 10% FBS (Gibco, Cat. # 16000-044), 1% L-glutamine (Gibco, Cat. # 25030-081) and 1% penicillin–streptomycin (Gibco, Cat. # 15140-122) at 37°C, 5% CO2. Cultures reached confluence after ~3 weeks. Next, media was replaced by neuronal growth media: 70% MEM (Gibco, Cat. # 11090-073), 25% Neurobasal media (Gibco, Cat. # 21103-049), 1% N2 supplement (Gibco, Cat. # 17502-048), 1% L-glutamine (Gibco, Cat. # 25030-081), 1% penicillin-streptomycin (Gibco, Cat. # 15140-122), 2% horse serum (Gibco, Cat. # 15060-114; lot 1517711) and 1% sodium pyruvate (Gibco, Cat. # 11360-070). After 7 days, ACM was collected, supplemented with 4.5 mg ml/L D-glucose (final concentration), filtered and stored at -80°C.

extract_protocol:
Total RNA was extracted from 4-5 independent cultures/condition using RNeasy kit (Qiagen). RNA quality was verified on a bioanalyzer before library preparation
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq polyA enriched mRNA)

treatment_protocol: Spinal cord cultures (4 DIV) were treated for 90 min with polyPL (100 μM), mutSOD1-ACM or wtSOD1-ACM.

tag: strain

value: Sprague-Dawley

value: cultures (7 DIV) from W14 spinal cord tissue

tag: genotype

value: wild type

value: hSOD1-G93A ACM (90 min)


title: hSOD1-G93A ACM rep 4

description: Sample 18


title: INV450


title: COV157

tag: disease state

tag: gender

tag: disease symptom

value: symptomatic

value: Moderate

value: long term

value: No


title: Testicular Microenvironment_B04_CTL

value: Testicular Microenvironment

value: Leydig cells+Sertoli cells+PMC

value: untreated


title: KO_Rep3

city: New York

first: Zhaoning

last: Wang

state: New York

address: 701 West 168th Street Hammer 14 - 1410

department: Genetics and Development

institute: Columbia University

description: biological replicate 3

data_processing:
Quality control of RNA-Seq data was performed using FastQC Tool (Version 0.11.4).
Sequencing reads were aligned to mouse GRCm38 (mm10) reference genome using HiSTAT2 (Version 2.0.4) with default settings and --rna-strandness FR.
Aligned reads were counted using featurecount (Version 1.6.0) per gene ID.
Differential gene expression analysis was performed with the R package edgeR (Version 3.30.1) using the GLM approach. For each comparison, genes with more than 1 CPM (Count Per Million) in at least three samples were considered as expressed and were used for calculating normalization factor. Cutoff values of absolute fold change greater than 2.0 and false discovery rate less than 0.01 were used to select differentially expressed genes between sample group comparisons. Normalized gene CPM values were used to calculate RPKM (Reads Per Kilobase per Million mapped reads) values, which were then used for heatmap plotting.
Alternative splicing events were analyzed using rMATS (v4.0.2), and events with |IncLevelDifference| > 0.1 and FDR < 0.05 were considered as significant.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw count values and RPKM values for each sample, and differential expression analysis results from edgeR.

molecule: polyA RNA

source_name: KO_Heart (Ventricle)

growth_protocol: Animals were housed in a 12 h light/dark cycle in a temperature-controlled room in the Animal Research Center of UT Southwestern, with ad libitum access to water and food.

extract_protocol:
Mice were euthanized and heart ventricles from WT and Rbpms KO mice were dissected. RNA was extracted using the RNeasy mini kit (QIAGEN, 74104) according to the manufacturer's protocol.
Stranded mRNA-Seq libraries were generated using the KAPA mRNA HyperPrep Kit (Roche, KK8580) following manufacturer’s protocol.

tag: strain background

tag: genotype/variation

value: Rbpms KO

value: Heart (Ventricle)


title: hSOD1-G93A ACM rep 3

description: Sample 17


title: INV449

value: ex vivo


title: COV156

value: Peripheral blood

tag: cell type

value: peripheral blood mono-nuclear cells

value: female

tag: disease severity

value: Yes


title: INV459

value: schizont

value: clinical isolate


title: KO_Rep2

description: biological replicate 2


title: COV102

tag: disease duration

tag: patient comorbidity


title: INV448


title: hSOD1-G93A ACM rep 2

description: Sample 16

value: Sprague-Dawley

value: cultures (7 DIV) from W14 spinal cord tissue

value: wild type

tag: treatment

value: hSOD1-G93A ACM (90 min)


title: INV446

tag: culture


title: WT_Rep3

description: biological replicate 3

source_name: WT_Heart (Ventricle)

value: WT


title: KO_Rep1

description: biological replicate 1


title: hSOD1-G93A ACM rep 1

description: Sample 15


title: hSOD1-WT ACM rep 4

description: Sample 14

value: hSOD1-WT ACM (90 min)


title: COV101

value: symptomatic

value: Moderate

value: short term


title: WT_Rep2

description: biological replicate 2

value: Heart (Ventricle)


title: INV445

value: ex vivo

tag: Stage


title: INV440

tag: proportion of mspdbl2-positive schizonts by ifa


title: hSOD1-WT ACM rep 3

description: Sample 13

tag: tissue


title: INV425


title: COV098

value: Peripheral blood

tag: age

value: No


title: hSOD1-WT ACM rep 2

description: Sample 12

tag: strain


title: COV089

value: peripheral blood mono-nuclear cells

value: female

value: long term


title: RNAseq_H2A.Z_KO_MEF_rep4

description: total RNA (ribo depleted)

data_processing:
Sequenced reads were mapped to mm10 whole genome using STAR
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was purified using Trizol reagent and treated with Dnase
Illumina TruSeq Stranded Total RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. After adapter ligation DNA was PCR amplified with Illumina primers for 13 cycles. Libraries were sequenced on the Illumina NextSeq 500 following the manufacturer's protocols.

value: embryonic-fibroblast

tag: genotype

value: H2A.Z flox/flox


title: INV419

value: schizont

value: clinical isolate


title: hSOD1-WT ACM rep 1

description: Sample 11

value: Sprague-Dawley

value: cultures (7 DIV) from W14 spinal cord tissue

value: wild type


title: RNAseq_H2A.Z_KO_MEF_rep3

description: total RNA (ribo depleted)


title: INV410


title: COV087

tag: disease state

value: male

value: symptomatic

value: Yes


title: PolyP rep 5

description: Sample 10

source_name: polyP

value: polyPL (100 μM; 90 min)


title: COV086

tag: gender

value: Moderate

value: short term


title: RNAseq_H2A.Z_KO_MEF_rep2

description: total RNA (ribo depleted)


title: RNAseq_H2A.Z_KO_MEF_rep1

description: total RNA (ribo depleted)


title: INV406

value: ex vivo


title: PolyP rep 3

description: Sample 8


title: INV396


title: RNAseq_PerTKO_MEF_rep4

description: total RNA (ribo depleted)

value: perTKO


title: COV074

value: Peripheral blood

value: peripheral blood mono-nuclear cells

tag: disease symptom

value: No


title: PolyP rep 4

description: Sample 9


title: WT_Rep1

description: biological replicate 1

tag: strain background

value: WT

value: Heart (Ventricle)


title: INV395

value: schizont

value: clinical isolate


title: INV401


title: RNAseq_PerTKO_MEF_rep3

description: total RNA (ribo depleted)

value: embryonic-fibroblast


title: PolyP rep 2

description: Sample 7

value: Sprague-Dawley

value: cultures (7 DIV) from W14 spinal cord tissue

value: wild type


title: COV048

value: female

value: symptomatic

value: Yes


title: INV374


title: PolyP rep 1

description: Sample 6

value: polyPL (100 μM; 90 min)


title: RNAseq_PerTKO_MEF_rep2

description: total RNA (ribo depleted)


title: control WT rep 5

description: Sample 5

source_name: control


title: COV091

value: male

value: Moderate

value: short term


title: COV155

value: Peripheral blood

value: peripheral blood mono-nuclear cells

value: asymptomatic


title: INV236

value: ex vivo


title: RNAseq_PerTKO_MEF_rep1

description: total RNA (ribo depleted)

value: perTKO


title: control WT rep 4

description: Sample 4


title: RNAseq_WT_MEF_rep4

description: total RNA (ribo depleted)

value: WT


title: COV154


title: COV076


title: RAW 264.7 cell- miR-146a over expressed Exp2

city: Kolkata

first: Ishita

last: Mukherjee

state: West Bengal

address: IICB-Translational Research Unit of Excellence, CN - 6, Sector V, Salt Lake City

country: India

institute: CSIR-Indian Institute of Chemical Biology

data_processing:
Real-time base calling was performed by the built-in software RTA to produce binary bcl data
Demultiplexing performed by Illumina software bcl2fastq (v2.17).
Data quality was assessed with FastQC and data was trimmed for adapter content and lower quality bases using Cutadapt (v2.8).
Cleaned and filtered reads greater were aligned to the ncRNA pool of Mus Musculus using Bowtie1 (v1.1.2)
Novel microRNAs are predicted from mature, star and loop sequence according to the RNAfold algorithm using miRDeep2(v2.0.0.8).
TMM was used for normalizing the read count value, and the edgeR (v3.24.3) was used for differential expression analysis (microRNA).
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: raw counts, fold-change

source_name: Macrophage Cell Line (RAW 264.7 cells)

growth_protocol: RAW 264.7 cells were cultured in RPMI 1640 medium (Gibco) supplemented with 2 mM L‐glutamine, 0.5% β‐mercaptoethanol and 10% heat‐inactivated fetal calf serum.

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

treatment_protocol: 400 ng/ml of Doxycycline has been added to induce the expression of miR-146a on Tet-ON responsive RAW264.7 cells.

value: BALB/c

tag: cell line

value: Abelson murine leukemia virus transformed macrophage cells

tag: genotype/variation

value: miR-146a over expressed


title: COV147

tag: cell type

tag: disease severity

value: No


title: RNAseq_WT_MEF_rep3

description: total RNA (ribo depleted)

value: embryonic-fibroblast


title: RAW 264.7 cell- miR-146a over expressed Exp1


title: COV072

value: female

value: symptomatic

tag: disease duration

value: long term

tag: patient comorbidity


title: COV146

value: male


title: RNAseq_WT_MEF_rep2

description: total RNA (ribo depleted)


title: control WT rep 1

description: Sample 1

value: Sprague-Dawley

value: cultures (7 DIV) from W14 spinal cord tissue

value: wild type

tag: treatment


title: COV144

value: Peripheral blood

value: peripheral blood mono-nuclear cells

value: short term


title: control WT rep 2

description: Sample 2


title: RAW 264.7 cell- control 2

value: control


title: RAW 264.7 cell- control 1


title: RNAseq_WT_MEF_rep1

description: total RNA (ribo depleted)

value: WT


title: 229-20

status: Public on Feb 16 2022

city: Frederiksberg

first: Xiaoyu

last: Pan

address: Dyrlægevej 68

department: Department of Veterinary and Animal Sciences

country: Denmark

institute: University of Copenhagen

data_processing:
Quality and adapter trimming of raw reads were performed using TrimGalore (Babraham Binoinformatics).
The remaining clean reads were aligned to the porcine genome (Sscrofa11.1) using HISAT2
The annotated gene information of porcine genome was downloaded from Ensembl (release 99).
The script htseq-count was used to generate gene count matrix.
The gene count was normalized using DESeq2.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Raw counts of sequencing reads for each gene (Ensembl gene IDs) generated from htseq-count.

organism: Sus scrofa

source_name: cerebellum

extract_protocol:
Total RNA was isolated with RNeasy Lipid Tissue Mini Kit  (Qiagen).
RNA libraries were prepared by Novogene Europe (Cambridge, UK) and sequenced on the Illumina NovaSeq platform with paired-end 150-bp reads production.

tag: weight

value: NORM

tag: Sex

value: F

tag: diet

value: VEG


title: 235-20

value: IUGR

value: MILK


title: 230-20

value: M


title: 232-20


title: 226-20


title: 234-20


title: 225-20


title: control WT rep 3

description: Sample 3

tag: tissue

tag: age


title: 228-20


title: 227-20


title: 219-20


title: 221-20


title: 217-20


title: 222-20


title: 218-20


title: 220-20


title: 216-20


title: 215-20


title: 233-20


title: 214-20


title: 213-20


title: 212-20


title: 210-20


title: 207-20


title: 211-20


title: 224-20


title: 206-20


title: 231-20


title: 205-20


title: 204-20


title: 201-20


title: 202-20


title: BM MPC Lama-KO rep3

city: Stockholm

first: Hong

last: Qian

address: Hälsovägen 7C (lastkaj), 14157 Huddinge/Stockholm

department: Department of Medicine

institute: Karolinska Institute

data_processing:
The data were geenerated on Illumina Nextseq 550 via a 75-cycle v2 sequencing run
Sample quality was assessed using FastQC (v0.11.8) and MultiQC (v1.7). Reads were aligned to a reference built from Ensembl GRCm38 genome sequences using STAR (v2.6.1d).
All mapped counts to each gene were further calculated by FeatureCounts function from Subread package 5 installed in R. Genes with Reads Per Kilobase of transcript per Million mapped reads (RPKM) values more than 0.1 were considered as being actively transcribed and proceeded to the analysis of Differential Gene Expression (DGE).6
The normalized read counts assigned to each sample were generated by Deseq2 and used for unsupervised clustering.
The differentially expressed genes between the MSC subsets were identified by adjusted P value (padj < 0.05) using Benjamini-Hochberg correction for multiple testing, together with thresholds at log2fold changes >1 (up-regulated) or <-1 (down-regulated).
Genome_build: mm10
Supplementary_files_format_and_content: csv file; Matrix table with raw and normarized gene counts for every gene and every sample, together with multiple testing results with Benjamini-Hochberg correction

source_name: Bone Marrow

extract_protocol:
RNA from BM MPCs that were sorted from Lama4-/- and age-matched wild type mice at 6 weeks post sublethal irradiation (7Gy) was extracted using RNeasy Microkit (Qiagen, USA) according to the manufacturer’s recommendations. cDNA was prepared using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio. Cat. No. 634898).  The cDNA quality was examined on Agilent TapeStation system using a High Sensitivity D5000 ScreenTape (Agilent, Cat. No. 5067-5592). One ng cDNA was used for library preparation using Nextera XT DNA Library Preparation Kit (Illumina, Cat. Nos. FC-131-1024 & FC-131-1096).
cDNA was prepared using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio. Cat. No. 634898).
The cDNA quality was examined on Agilent TapeStation system using a High Sensitivity D5000 ScreenTape (Agilent, Cat. No. 5067-5592). One ng cDNA was used for library preparation using Nextera XT DNA Library Preparation Kit (Illumina, Cat. Nos. FC-131-1024 & FC-131-1096). ). The yield and quality of the amplified libraries were analyzed using Qubit by Thermo Fisher and the Agilent Tapestation System. The indexed cDNA libraries were sequenced on the Illumina 2000 or Nextseq 550 (Illumina, San Diego, CA).  for a 75-cycle v2 sequencing run generating 75 bp single-end reads.

tag: strain

value: Bone Marrow

value: 14 weeks

tag: genotype

value: Mesenchymal Progenitor Cell (MPC)


title: BM MPC Lama-KO rep2


title: BM MPC Lama-KO rep1


title: BM MPC WT rep3


title: BM MPC WT rep1


title: BM MPC WT rep2


title: 223-20


title: Col10a1-Cre;R26-tdTomato Bone marrow cells [NonTomato 3]

city: Durham

first: Matthew

middle: J.

last: Hilton

state: NC

address: 450 Research Drive, LSRC B321C

institute: DUKE UNIVERSITY SCHOOL OF MEDICINE

data_processing:
RNA-seq data processed TrimGalore toolkit
Gene counts were compiled using the HTSeq tool
Normalization and differential gene expression was carried out using the DESeq2 Bioconductor package with the R statistical programming environment.
 The false discovery rate was calculated to control for multiple hypothesis testing. Biological thresholds were determined by taking the log2 expression value plotted on a histogram. A bimodal distribution is observed for low expressed genes followed by a larger Guassian distribution. The split point between these was used as a value cutoff for biological relevance (this dataset cutoff = 16).
Non-coding genes were removed
Genes with a p-value >0.05 and log2 < 1 were removed
Gene ontology analysis was performed using geneontology.org Analysis Type: PANTHER Overrepresentation test released 02-24-2021. Annotation version and release date: release date 01-01-2021 and version 10.5281/zenodo.4437524 for biological processes using Mus musculus as the reference.
Genome_build: GRCm38v73
Supplementary_files_format_and_content: Colony Bulk RNAseq contains raw reads of each sample for each gene and is then processed by coding, p-value <0.05, and Tomato or Nontomato genes log2 fold >1. Gene ontology analysis terms are also included based on the gene set enrichment of each colony type.

source_name: Bone marrow cells

growth_protocol: Animals were bred in accordance to Duke University IACUC protocols and aged to 2 months.

extract_protocol:
Animals were euthanized according to IACUC protocol and hind limbs were isolated. Surrounding tissues were dissected off and bones were washed with PBS. Bones were bissected and centrifuged to 10000xG. Red blood cells were lysed and remaining cells were counted and plated at clonal density. Plates were washed 3 hours post-plating. Media was changed every 3 days and cells were isolated using a Corning cloning cylinder at 10 days post-plating for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tag

value: Bone marrow

tag: group

value: NonTomato


title: Col10a1-Cre;R26-tdTomato Bone marrow cells [Tomato 3]

value: Tomato


title: Col10a1-Cre;R26-tdTomato Bone marrow cells [Tomato 2]


title: 209-20


title: Col10a1-Cre;R26-tdTomato Bone marrow cells [NonTomato 1]


title: 208-20


title: Col10a1-Cre;R26-tdTomato Bone marrow cells [Tomato 1]


title: 203-20


title: SAAXIG

city: Chapel Hill

first: Federico

last: Innocenti

state: North Carolina

address: 120 Mason Farm  Road, CB7361

department: Eshelman School of Pharmacy

institute: University of North Carolina at Chapel Hill

data_processing:
RNA-seq reads were aligned to ribosomal RNA sequences to remove ribosomal reads
Remaining reads were aligned to the human reference genome using GSNAP4,5 version '2013-10-10' allowing maximum of two mismatches per 75 base sequence
To quantify gene expression levels, the number of reads mapped to the exons of each RefSeq gene was calculated in a strand-specific manner using the functionality provided by the R package GenomicAlignments13
Genome_build: NCBI Build 38
Supplementary_files_format_and_content: CALGB 80405 RNAseq Processed data.csv - gene read counts

source_name: metastatic tumor

extract_protocol: Illumina TruSeq RNA Access

tag: tumor type

value: metastatic colorectal cancer

value: Male

tag: race

value: White

tag: treatment group

value: Cetuximab


title: SABELL

value: Bevacizumab


title: SABEFB

source_name: unknown primary or metastatic tumor


title: SAARVH


title: 200-20

value: NORM


title: SAASIM


title: SAARZA

value: Bevacizumab/Cetuximab


title: SABEEY


title: SAAVZI

value: Female


title: SABCZU


title: SAAPMV


title: SAANZF


title: SAAKHP


title: SAANJI

source_name: tumor adjacent normal


title: SAANSE


title: SAAKGV

value: Asian


title: SAANDA


title: SAAHEU


title: SAAEMW


title: SAAELZ


title: SAAEVF


title: SAAAZS


title: SAAFBW


title: SAASMW

source_name: primary tumor


title: SAASKX


title: SAARPM


title: SAAPGV


title: SAAPPX


title: SAARMW


title: SAARIX

value: Black or African American


title: SAARDE

value: American Indian or Alaska Native


title: SAAPPA


title: SAAPHR


title: SAANIX


title: SACHDB


title: SACHCL


title: SACHCN


title: SACHBZ


title: SACGZA


title: SACWDM


title: SAAELV


title: SABZXI


title: SACHCZ


title: SACGZV


title: SABMKA


title: SACEZD


title: SABMHM

value: More then one race


title: SABMFE


title: SABMGX


title: SABLZH


title: SABLHT


title: SABKBA


title: SABJCT


title: SABKUN


title: SABEYW


title: SABLHS


title: SABEYY


title: SABEYN


title: SABFAH


title: SABEYK


title: SABEYI


title: SABMZT


title: SABEXT


title: SABYUI


title: SABEVV


title: SABEVY


title: SABEXR


title: SABEWM


title: SABEUJ


title: SABETK


title: SABEVP


title: SABERY


title: SABESH


title: SABMDE


title: SABERU


title: SABERR


title: SABERT


title: SABEPW


title: SABEPE


title: SABEYR


title: SABEMY


title: SABERB


title: SABENW


title: SABEMI


title: SABEML


title: SABELS


title: SABEYJ


title: SABELY


title: SABEUT


title: SABELN


title: SABEKR


title: SABELK


title: SABEKK


title: SABELH


title: SABEKL


title: SABELC


title: SABEJV


title: SABEJX


title: SABEJS


title: SABEJF


title: SABEIP


title: SABEKH


title: SABEKJ


title: SABEHX


title: SABEGF


title: SABEFY


title: SABEHJ


title: SABEHT


title: SABEDT


title: SABEDZ


title: SABEFS


title: SABEES


title: SABECX


title: SABEDC


title: SABECT


title: SABEFR


title: SABEAF


title: SABDZH


title: SABEAA


title: SABEAN


title: SABDZF


title: SABEIM


title: SABDYS


title: SABDXS


title: SABDYH


title: SABDXC


title: SABDXJ


title: SABDYP


title: SABDWF


title: SABDWC


title: SABDWP


title: SABDVL


title: SABDVI


title: SABDUP


title: SABDTM


title: SABDRF


title: SABDRA


title: SABDRE


title: SABDRY


title: SABDSR


title: SABDLM


title: SABDMS


title: SABDJR


title: SAAXIH


title: SABACB


title: SABCXC


title: SAAWIX


title: SAAWIW


title: SAAWHH


title: SABDXV


title: SABDWU


title: SAAWFJ


title: SAAWAN


title: SAAWAC


title: SAAUNR


title: SAATSF


title: SAAWAY


title: SAATDS


title: SAASTC


title: SAASTA


title: SAASSI


title: SAASRZ


title: SAASRX


title: SAASRS


title: SAASNW


title: SAASPY


title: Col10a1-Cre;R26-tdTomato Bone marrow cells [NonTomato 2]


title: SAAWCB


title: SAASLG


title: SAASMY


title: SAASKK


title: SAASLT


title: SAASMT


title: SAASMB


title: SAASLU


title: SAASJN


title: SAASJJ


title: SAASMA


title: SAASJP


title: SAASJA


title: WT_AML_REP3

data_processing:
The data were geenerated on Illumina Nextseq 2000 via a 100-cycle p2 sequencing run
Sample quality was assessed using FastQC (v0.11.8) and MultiQC (v1.7). Reads were aligned to a reference built from Ensembl GRCm38 genome sequences using STAR (v2.6.1d).
All mapped counts to each gene were further calculated by FeatureCounts function from Subread package 5 installed in R. Genes with Reads Per Kilobase of transcript per Million mapped reads (RPKM) values more than 0.1 were considered as being actively transcribed and proceeded to the analysis of Differential Gene Expression (DGE).6
The normalized read counts assigned to each sample were generated by Deseq2 and used for unsupervised clustering.
The differentially expressed genes between the MSC subsets were identified by adjusted P value (padj < 0.05) using Benjamini-Hochberg correction for multiple testing, together with thresholds at log2fold changes >1 (up-regulated) or <-1 (down-regulated).
Genome_build: mm10
Supplementary_files_format_and_content: excel file; Matrix table with raw and normarized gene counts for every gene and every sample, together with multiple testing results with Benjamini-Hochberg correction

source_name: Bone marrow

growth_protocol: Lama4-/- MSC or WT MSC were plated onto 12-well plate at 30,000/well, 24h before seeding culture-expanded MLL-AF9 AML cells at 30,000/well. 48h post co-culture, cells from the co-cultures were dissociated by trypsin and MSC (CD45-CD44-Sca1+) and MLL-AF9 cells (CD45.1+) were isolated into RLT buffer via FACs-sorting.

extract_protocol:
FACS-sorted MSC or MLL-AF9 cells from co-culture system were used for RNA extraction using RNeasy Microkit (Qiagen, USA) according to the manufacturer’s recommendations. cDNA was prepared using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio. Cat. No. 634898).  The cDNA quality was examined on
cDNA was prepared using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio. Cat. No. 634898).
The cDNA quality was examined on Agilent TapeStation system using a High Sensitivity D5000 ScreenTape (Agilent, Cat. No. 5067-5592). One ng cDNA was used for library preparation using Nextera XT DNA Library Preparation Kit (Illumina, Cat. Nos. FC-131-1024 & FC-131-1096). ). The yield and quality of the amplified libraries were analyzed using Qubit by Thermo Fisher and the Agilent Tapestation System. The indexed cDNA libraries were sequenced on the Illumina 2000 or Nextseq 550 (Illumina, San Diego, CA).  for a 75-cycle v2 sequencing run generating 75 bp single-end reads.

value: Bone Marrow

value: 10-12 weeks

value: wild type

tag: cell type

value: MLL-AF9 AML Cells

tag: cell subtype

value: bone marrow Lineage-KIT+ cells were retrovirally transduced with human MLL-AF9 gene


title: KO_AML_REP2


title: KO_AML_REP1


title: SAASJI

value: metastatic colorectal cancer


title: SAASIP

value: Male


title: SAASPF

value: White


title: SAASMX


title: SAASNJ


title: SAASIW


title: KO_AML_REP3


title: WT_AML_REP2


title: WT_AML_REP1


title: SAASIE

value: Cetuximab


title: SAASHX


title: KO_MSC_AML_REP3

value: 10-14 weeks


title: SAASMF

value: Bevacizumab


title: SAASHR


title: KO_MSC_AML_REP2

value: Mesenchymal Stem Cell (MSC)

value: expaned from FACS-sorted lineage-CD45-CD31-CD44-SCA1+CD51+ cells


title: KO_MSC_AML_REP1


title: SAASHW


title: SAASHP


title: SAASHS


title: WT_MSC_AML_REP5


title: WT_MSC_AML_REP4


title: SAASHL

value: Female


title: SAASJC

value: Bevacizumab/Cetuximab


title: SAASGT


title: WT_MSC_AML_REP3


title: WT_MSC_AML_REP1


title: SAASGV


title: SAASGJ


title: WT_MSC_AML_REP2


title: SAASFZ


title: SAASGN


title: KO_MSC_REP4


title: KO_MSC_REP3


title: KO_MSC_REP1


title: KO_MSC_REP2


title: SAASGI


title: SAASFY

value: Black or African American


title: WT_MSC_REP4


title: SAASHH


title: WT_MSC_REP3


title: SAASFW


title: SAASFV


title: WT_MSC_REP2


title: SAASER


title: SAASFA


title: SAASEA


title: SAASEG


title: SAASDV


title: SAASDR


title: SAASDP

value: Asian


title: SAASDM


title: V. cholerae hapR+ ravAviA+ non treated_replicate 2

city: Paris

first: Zeynep

last: Baharoglu

address: 28 Rue du Docteur Roux

department: Génomes et Génétique

institute: Institut Pasteur

data_processing:
The RNA-seq analysis was performed with Sequana 0.9.2. In particular, we used the RNA-seq pipeline 0.9.6 built on top of Snakemake 5.31.1.
Briefly, reads were trimmed from adapters using cutadapt 2.10 then mapped to the Vibrio cholerae reference genome GCF_000006745.1 from NCBI using Bowtie 2.3.5.1.
Clustering of transcriptomic profiles were assessed using a Principal Component Analysis (PCA).
Differential expression testing was conducted using DESeq2 library 1.24.0 scripts indicating the significance (Benjamini-Hochberg adjusted p-values, false discovery rate FDR < 0.05) and the effect size (fold-change) for each comparison.
Genome_build: V. cholerae N16961 accession numbers AE003852 and AE003853
Supplementary_files_format_and_content: excel files containing number of reads and differencial expression values

organism: Vibrio cholerae O1 biovar El Tor str. N16961

source_name: bacterial culture

growth_protocol: growth in liquid MH supplemented or not up to OD 0.3

extract_protocol:
Cultures were centrifuged, and RNA was harvested using Trizol reagent. Illumina TruSeq mRNA Sample Prep Kit (20020595) was used with 7 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols (Krin et al., 2018, PMID: 29783948)

treatment_protocol: no treatment or supplemented with glucose 0.4% or maltose 0.4%

value: hapR+ ravAviA+

tag: growth phase

value: exponential phase OD 0.3

value: untreated


title: V. cholerae hapR+ ravAviA+ non treated_replicate 3


title: V. cholerae hapR+ ΔravAviA non treated_replicate 3

value: hapR+ delta ravAviA


title: V. cholerae hapR+ ravAviA+ maltose 0.4_replicate 2

value: maltose 0,4%


title: V. cholerae hapR+ ΔravAviA non treated_replicate 2


title: V. cholerae hapR+ ravAviA+ glucose 0.4_replicate 3

value: glucose 0,4%


title: V. cholerae hapR+ ravAviA+ glucose 0.4_replicate 2


title: V. cholerae hapR+ ravAviA+ maltose 0.4_replicate 3


title: V. cholerae hapR+ ravAviA+ non treated_replicate 1


title: V. cholerae hapR+ ravAviA+ maltose 0.4_replicate 1


title: WT_MSC_REP1

value: Bone Marrow

value: wild type


title: SAASDC

value: metastatic colorectal cancer

value: Male

value: White

value: Cetuximab


title: SAASDF


title: SAASDD

value: Bevacizumab


title: SAASEH


title: SAASCZ


title: SAASDA


title: V. cholerae hapR+ ΔravAviA maltose 0.4_replicate 3


title: SAASCT


title: V. cholerae hapR+ ΔravAviA maltose 0.4_replicate 1


title: V. cholerae hapR+ ΔravAviA non treated_replicate 1


title: V. cholerae hapR+ ΔravAviA maltose 0.4_replicate 2


title: V. cholerae hapR+ ΔravAviA glucose 0.4_replicate 3


title: SAASCS

value: Female


title: V. cholerae hapR+ ΔravAviA glucose 0.4_replicate 2


title: SAASDN


title: V. cholerae hapR+ ravAviA+ glucose 0.4_replicate 1


title: V. cholerae hapR+ ΔravAviA glucose 0.4_replicate 1


title: SAASCF


title: V. cholerae hapR+ non treated_replicate 1

value: hapR+


title: V. cholerae hapR+ non treated_replicate 2


title: SAASBX


title: SAASCE


title: SAASBR


title: SAASBV


title: V. cholerae hapR+ maltose 0.4_replicate 3


title: V. cholerae hapR+ non treated_replicate 3


title: V. cholerae hapR+ maltose 0.4_replicate 2


title: SAASBK

value: Black or African American


title: V. cholerae hapR+ glucose 0.4_replicate 3


title: SAASBM


title: V. cholerae hapR+ maltose 0.4_replicate 1


title: V. cholerae Δcrp non treated_replicate3

value: delta crp


title: SAASBG


title: SAASBF


title: SAASBE


title: V. cholerae hapR+ glucose 0.4_replicate 1


title: V. cholerae Δcrp non treated_replicate2


title: V. cholerae hapR+ glucose 0.4_replicate 2


title: SAASCH


title: V. cholerae Δcrp non treated_replicate1


title: SAASBD


title: V. cholerae Δcrp maltose 0.4_replicate 2


title: SAASBA


title: SAASBC


title: SAASAV

value: More then one race


title: SAASBT


title: SAASAS

value: Asian

value: Bevacizumab/Cetuximab


title: V. cholerae Δcrp glucose 0.4_replicate 3

value: exponential phase OD 0.3


title: V. cholerae Δcrp glucose 0.4_replicate 2


title: V. cholerae non treated_replicate 3

value: WT

value: untreated


title: SAASAJ


title: V. cholerae Δcrp glucose 0.4_replicate 1

value: glucose 0,4%


title: SAASAK


title: SAASAH


title: V. cholerae non treated_replicate 1


title: SAASAE


title: V. cholerae Δcrp maltose 0.4_replicate 3

value: maltose 0,4%


title: SAARZR

value: metastatic colorectal cancer


title: SAARZZ

value: Male


title: SAASAG

value: White


title: V. cholerae glucose 0.4_replicate3


title: V. cholerae maltose 0.4_replicate2


title: SAARWJ

value: Cetuximab


title: V. cholerae maltose 0.4_replicate 1


title: SAARWD

value: Bevacizumab


title: V. cholerae maltose 0.4_replicate3


title: Aorta Col3a1+/G182R rep3

first: Anne

last: Legrand

address: 56 rue Leblanc

institute: Inserm

data_processing:
STAR 2.7.6a & RSEM v1.3.1
STAR --runThreadN 25 --runMode genomeGenerate --genomeDir [/path/to/index/directory/newly/created] --genomeFastaFiles [/path/to/reference/fasta] --sjdbGTFfile [/path/to/reference/gtf] --sjdbOverhang 74
STAR --genomeDir [/path/to/STAR/index] --sjdbGTFfile [/path/to/gtf] --runThreadN 20 --readFilesIn [/path/to/R1/fastq] [/path/to/R2/fastq] --outFileNamePrefix [sample-name] --twopassMode Basic --sjdbOverhang 74 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMunmapped Within --outFilterType BySJout --quantMode TranscriptomeSAM
rsem-prepare-reference --num-threads 20 --gtf [/path/to/reference/gtf] [/path/to/reference/fasta] [RSEM-index-name]
rsem-calculate-expression -p 40 --paired-end --bam --no-bam-output [/path/to/alignedToTransciptomFile/from/STAR] [/path/to/RSEM/index] [sample-name]
Genome_build: Mus_musculus GRCm38 from Ensembl database, release 101
Supplementary_files_format_and_content: RSEM expression count file

source_name: Aorta

extract_protocol:
Aortas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Aorta

value: post natal 7 weeks

value: knock-in Col3a1+/G182R


title: V. cholerae glucose 0.4_replicate2


title: SAARVW

value: Female


title: V. cholerae glucose 0.4_replicate 1


title: Aorta Col3a1+/G182R rep2


title: V. cholerae Δcrp maltose 0.4_replicate 1

value: delta crp


title: SAASAI


title: SAARVM


title: V. cholerae non treated_replicate 2


title: SAARVE


title: SAARVI


title: SAARVT


title: Aorta WT rep4

value: wild type


title: Aorta WT rep3


title: SAARVC

value: Black or African American


title: Aorta WT rep2


title: SAARZL


title: Aorta WT rep1


title: SAARVA


title: SAARUG


title: SAARUE


title: SAARUA


title: Tet2 KO ILC3 hmC rep2

city: St. Louis

first: Vincent

last: Peng

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine in St. Louis

data_processing:
library strategy: hmC-seal
The reads for MeDIP-seq, MRE-seq, and hmC-Seal were trimmed using cutAdapt and aligned to the mm10 reference genome with BWA and then processed by methylQA. The signal for MeDIP-seq, MRE-seq, and hmC-Seal at each CpG was the number of reads aligned to that location divided by total reads (million). The average signal for MeDIP-seq, MRE-seq, and hmC-Seal in each window was the mean of signal at all bases in that window.
After processing by methylQA, de-duplicated reads from hmC-seal samples were used to call broad peaks using MACS2 with a FDR threshold of 0.01. hmC peaks were then used for differential enrichment analysis with DiffBind and DHMRs were called using a q value of 1e-15 and an absolute log2FoldChange cutoff >= 194. De-duplicated reads from MeDIP-seq and MRE-seq samples were then used to identify 500bp differentially methylated regions using MethylM&M35. Briefly, M&M computes a probability score for a given genomic window based on observed MeDIP-Seq and MRE-seq measurements using the null hypothesis that there is an equal amount of methylation between two samples for the given region. An empirical FDR was estimated using intrareplicate comparisons and a q threshold for NK vs. ILC2 and NK vs. ILC3 DMRs were called using a cutoff of q = 1e-5 whereas ILC2 vs. ILC3 DMRs were called using q = 0.05. ENCODE blacklisted regions, chrM, chrX, and chrY regions were removed from our DHMR and DMR sets.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files containing RPKM for MeDIP, MRE, and hmC-Seal

source_name: Tet2 KO ILC3 hmC

extract_protocol:
For sorting, spleens were dissociated and washed through 70um cell strainers and enriched with DX5+ MACS positive selection columns. For immune phenotyping and cell stimulation, spleens were dissociated and washed through 70um cell strainers. Lysates were lysed for red blood cells and resuspended in medium. Small intestinal ILC2 and ILC3 were isolated as previously described. Briefly, small intestines were dissected and washed with Peyer’s patches and mesenteric fat removed. Intestines were opened lengthwise; gently agitated for 20 min in Hanks’ balanced salt solution (HBSS) containing HEPES, bovine calf serum, and EDTA; and then vortexed. Small intestines were subjected to a second round of gentle agitation and vortexing in EDTA. The tissue was then rinsed with HBSS before digestion with collagenase IV (Sigma-Aldrich) in complete RPMI 1640 for 40 min at 37°C under agitation. Digests were filtered through 100-um mesh and subjected to density gradient centrifugation using 40 and 70% Percoll solutions.
MeDIP-seq libraries were generated as previously described with few modifications. One hundred nanograms of sheared DNA was ligated with Illumina adapters, and methylation-enriched adapter-ligated DNA fragments were immunoprecipitated with 0.1 ug of anti-methylcytidine antibody (Eurogentec, BI-MECY-0100). MeDIP DNA fragments were amplified with Illumina barcodes with NEBNext High-Fidelity 2× PCR Master Mix (polymerase chain reaction) master mix (NEB, M0541). MeDIP-seq libraries were sequenced on Illumina NextSeq 500 platform. MRE-seq libraries were generated as previously described with few modifications. In brief, 20 ng of genomic DNA was digested by four restriction enzymes (HpaII, HinP1I, AciI, and HpyCH4IV) that generate a CG overhang. Adapter ligation was performed with custom Illumina adapters (5'-ACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3' and 5'-P-CGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3'). Adapter-ligated DNA fragments were amplified with Illumina barcodes with NEBNext High-Fidelity 2× PCR Master Mix master mix (NEB, M0541) and sequenced on Illumina NextSeq 500 platform. To identify 5hmC-enriched regions, we performed hmC-Seal on cell samples. In brief, 275 ng of sheared DNA was ligated with Illumina adapters. Hydroxymethylation-enriched adapter-ligated DNA fragments were glucosylated by incubating in a 50-ul solution containing 1× glucosylation buffer, 200 uM UDP-azide-glucose (Active Motif, 55020), and 5 U of T4 B-glucosyltransferase (Thermo Fisher Scientific, EO0831) at 37°C for 1 hour. After glucosylation, the DBCO-PEG4-biotin reaction and streptavidin C1 bead pull-down were same as the Nano-hmC-Seal. The beads were washed 10 times with 1× binding-washing buffer and twice with double-distilled water (ddH2O) and were resuspended in 15 ul of ddH2O. The captured DNA fragments were amplified and barcoded with Illumina barcodes with the NEBNext High-Fidelity 2× PCR Master Mix (NEB, M0541). hmC-Seal libraries were sequenced on Illumina NextSeq 500 platform.

value: small intestine lamina propria

tag: cell type/genotype

value: Tet2 WT ILC3


title: SAARUB


title: SAARUL


title: SAARUT


title: SAARTZ

value: Asian


title: Tet2 WT ILC3 hmC rep1

source_name: Tet2 WT ILC3 hmC


title: ILC3 hmC rep1

source_name: ILC3 hmC


title: ILC3 hmC rep2


title: SAARTW


title: Aorta Col3a1+/G182R rep1


title: ILC3 MeDIP rep2

data_processing:
The reads for MeDIP-seq, MRE-seq, and hmC-Seal were trimmed using cutAdapt and aligned to the mm10 reference genome with BWA and then processed by methylQA. The signal for MeDIP-seq, MRE-seq, and hmC-Seal at each CpG was the number of reads aligned to that location divided by total reads (million). The average signal for MeDIP-seq, MRE-seq, and hmC-Seal in each window was the mean of signal at all bases in that window.
After processing by methylQA, de-duplicated reads from hmC-seal samples were used to call broad peaks using MACS2 with a FDR threshold of 0.01. hmC peaks were then used for differential enrichment analysis with DiffBind and DHMRs were called using a q value of 1e-15 and an absolute log2FoldChange cutoff >= 194. De-duplicated reads from MeDIP-seq and MRE-seq samples were then used to identify 500bp differentially methylated regions using MethylM&M35. Briefly, M&M computes a probability score for a given genomic window based on observed MeDIP-Seq and MRE-seq measurements using the null hypothesis that there is an equal amount of methylation between two samples for the given region. An empirical FDR was estimated using intrareplicate comparisons and a q threshold for NK vs. ILC2 and NK vs. ILC3 DMRs were called using a cutoff of q = 1e-5 whereas ILC2 vs. ILC3 DMRs were called using q = 0.05. ENCODE blacklisted regions, chrM, chrX, and chrY regions were removed from our DHMR and DMR sets.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files containing RPKM for MeDIP, MRE, and hmC-Seal

source_name: ILC3 MeDIP


title: ILC3 MeDIP rep1


title: ILC3 MRE rep1

source_name: ILC3 MRE


title: SAARUD


title: ILC2 hmC rep2

source_name: ILC2 hmC


title: SAARUS


title: SAARTS


title: ILC2 hmC rep1


title: Tet2 WT ILC3 hmC rep2


title: Tet2 KO ILC3 hmC rep1


title: SAARTH


title: SAARTJ


title: ILC2 MRE rep1

source_name: ILC2 MRE


title: SAARTF


title: SAARTG


title: SAARTD


title: SAARTM


title: ILC2 MeDIP rep1

source_name: ILC2 MeDIP


title: NK hmC rep1

source_name: NK hmC

value: spleen

value: NK


title: NK hmC rep2


title: SAARTB

value: metastatic colorectal cancer


title: ILC2 MeDIP rep2


title: SAARSV

value: Male


title: SAARST

value: White


title: SAARSI

value: Cetuximab


title: Col10a1-Cre;R26-tdTomato total bone cells e16.5 post-FACS

data_processing:
Raw base call demultiplex into Fastq Files
Matrix generation 10X cell ranger software 3.0.1
PCA analysis, clustering, and gene expression analysis Seurat version 4
Monocle trajectory analysis Monocle3
Genome_build: mm10
Supplementary_files_format_and_content: RDS file provided after PCA and clustering, from which gene expression was taken and monocle3 was performed

source_name: Bone cells

extract_protocol:
Animals were euthanized according to IACUC protocol and hind limbs were isolated. Surrounding tissues were dissected off and bones were washed with PBS. Bones were mechanically digested and placed in collagenase II in complete media with constant agitation for 2 hours. Red blood cell lysis was performed. Cells were FACS sorted on tomato expression and submitted for 10X Genomics single cell isolation and barcoding.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: developmental stage

value: Total bone


title: NK MRE rep1

source_name: NK MRE


title: SAARSM

tag: Sex

value: More then one race


title: NK MeDIP rep2

source_name: NK MeDIP


title: E18-RightHb-2

city: Utrecht

first: Lieke

last: van de Haar

address: Universiteitsweg 100

department: Translational Neuroscience

country: Netherlands

institute: UMC Utrecht

data_processing:
Alignment of the Celseq2 reads was performed using the mapandgo. Following merging of the reads generated in multiple lanes and removal of the reads that lack Celseq2 barcodes, the data was trimmed using Trimgalore (version 0.4.3107) that employs cutadapt108 to remove the Illumina library adapters and fastQC109 reads with low quality base-calls at the end of the reads.
Alignment of the reads to the mm10 reference genome was done STAR (version 2.5.3a), and single-cell libraries were de-multiplexed using the barcoded present in preloaded primer sequences.
Following UMI correction, reads were adjusted for the possibility of false assignment of reads from different mRNAs as duplicates due to the low chance of having the same UMI on different mRNA molecules. This was the final count file used for the analysis.
count files were merged into .tsv files containing all samples per experiment (Dev Hb series file and E18 file). Each experiment countains a file containing the spliced, unspliced and total counts.
Genome_build: mm10
Supplementary_files_format_and_content: *.tsv: Tab separated data file merged for all sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. The first column lists the official gene symbol followed by the functional annotation of hte gene and the chromosome name, separated by a double underscore. Cells are labeled according to their ID as listed under "sample name". E18 data and DevHb (series) are in separated .tsv files

source_name: E18 mouse habenula

extract_protocol:
RNA was extracted by 2x heat lysis (65C) in 384 well, which were immediately used for downstream single cell RNA sequencing reactions (Celseq2)
Single-cell RNA sequencing was performed with Cel-seq2 at the Single Cell Discoveries (Utrecht, NL), as described by Hashimshony et al., 2016 and Muraro et al., 201625,106. Plates contained preloaded barcoded poly-T primers that specifically amplify the mRNA and introduce a 6bp unique molecular identifier (UMI), an 8bp cell barcode and a T7 RNA polymerase binding site. In addition, plates were pre-loaded with ERCC spike-ins that allowed quality control of reactions in individual wells. Cells were lysed by heating at 65C for 5 min followed by rapid chilling on ice for 2 min (twice). mRNA was reversed transcribed using Superscript II (ThermoFisher Scientific) and converted into second stranded DNA by DNA polymerase I (ThermoFisher Scientific). Material from each plate was then pooled, cleaned up using Ampure beads (Beckman Coulter, #A63881) and amplified by in vitro transcription overnight using the MEGAscript T7 transcription kit (ThermoFisher Scientific, # AMB1334). Following a second round of clean up, amplified RNA was measured using the Agilent RNA 6000 pico chips (Agilent # 5067-1513), reverse-transcribed using random hexamer primers that introduce Truseq Small RNA kit RP1 primer binding sites (Illumina) and finally converted into DNA libraries using custom rpi primers (RNA PCR Primer Index) adapted from the Truseq Small RNA kit (Illumina)106. Following two rounds of Ampure bead clean up and quality control using the Agilent High Sensitivity DNA Kit (5067-4626), libraries were sent for sequencing at the Utrecht Sequencing Facility (USEQ, Life Sciences faculty, Utrecht University) for paired end sequencing (26bp for read 1 and 50bp for read 2) by Nextseq500. 5 plates were combined for a full sequencing run, which yielded ~300M assigned to the libraries.

tag: mouse line

value: right hemisphere habenula


title: E1-LeftRightHb

tag: tissue

value: left and right hemisphere habenula


title: E18-LeftHb-1

value: left hemisphere habenula


title: ILC2 MRE rep2


title: SAARRY

source_name: primary tumor

tag: age


title: SAARRU


title: SAARRZ

value: Bevacizumab


title: SAARSB

value: Female


title: E12-1

source_name: mouse habenula

value: habenula


title: SAARRV


title: SAARRS


title: E18-RightHb-1


title: P7-2


title: P4-2


title: NK MeDIP rep1


title: P4-1


title: SAARRI


title: SAARRC


title: SAARRM


title: SAARRF


title: SAARPY


title: E18-LeftHb-2


title: SAARPS


title: P7-1


title: NK MRE rep2


title: SAARPW


title: adult-1

value: adult


title: SAARPN


title: SAARRK


title: SAARPL


title: SAARPI


title: SAARPJ


title: SAARPF


title: E11-1


title: E11-2


title: E13-2


title: E15-2


title: E18-1


title: adult-2


title: SAARPC


title: E13-1


title: SAARNX


title: Col10a1-Cre;R26-tdTomato Bone marrow cells post-FACS

data_processing:
Raw base call demultiplex into Fastq Files
Matrix generation 10X cell ranger software 3.0.1
PCA analysis, clustering, and gene expression analysis Seurat version 3
Monocle trajectory analysis Monocle3
Genome_build: mm10
Supplementary_files_format_and_content: RDS file provided after PCA and clustering, from which gene expression was taken and monocle3 was performed

source_name: Bone marrow cells

extract_protocol:
Animals were euthanized according to IACUC protocol and hind limbs were isolated. Surrounding tissues were dissected off and bones were washed with PBS. Bones were bissected and centrifuged to 5000xG from 0, two times. Bone marrow isolate and bones were subjected to 30 minutes of Collagenase II digestion in complete media. Bone pieces were removed and red blood cell lysis was performed. Cells were FACS sorted on tomato expression and submitted for 10X Genomics single cell isolation and barcoding.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: mouse strain

value: Bone marrow


title: SAARNV


title: SAARMX


title: E15-1


title: SAARMY


title: Restimulate-1.5h-FP-4

first: Thomas

last: Malek

state: Florida

address: 1600 N.W. 10th Avenue

department: Department of Microbiology and Immunology

institute: University of Miami Miller School of Medicine

description: rawdata.Malak_Restimulate_mouse.filtrcpms.csv

data_processing:
Reads from RNA-seq were mapped to the Mus musculus genome GRCm38 using STAR (ver.2.5.0) aligner. Raw counts were generated on Ensembl gene (GENCODE M13) with featureCounts (ver.1.5.0). Differential expressed genes in Tregs between the mIL-2 or mIL-2/CD25 and PBS injected mice were identified using DESeq2, and determined according to threshold of false discovery rate (FDR) <0.01
Genome_build: GRCm38

source_name: regulatory T cells

extract_protocol:
RNA was isolated from sorted Tregs using TRIzol Reagent (Thermo Fisher) and column purified using miRNeasy Micro Kit (Qiagen). RNA quality was assessed using an Agilent 2100 BioAnalyzer and was quantified using Qubit RNA assay
RNA-seq libraries were prepared from 25 ng of total RNA using the KAPA’s RNA Hyperprep with RiboErase protocol and quantified using Qubit DNA and  Kapa qPCR Library Quantification kit for Illumina (KapaBiosystems).

treatment_protocol: RFP-FoxP3+ BL6 mice were injected with 20 ug of FP or 100 uL of control PBS. 1.5 hr post injection splenic Tregs were sorted out.

tag: strain

value: Spleen

tag: injected molecule

value: mIL-2/CD25 and 2nd mIL-2/CD25

tag: treatment

tag: sample id


title: Restimulate-1.5h-FP-3


title: SAARMU

tag: tumor type

tag: race


title: Restimulate-1.5h-single-3

value: control PBS and single mIL-2/CD25


title: SAARMT

value: metastatic colorectal cancer

tag: treatment group


title: SAARMP

value: Male

value: Black or African American


title: SAARMN

value: White


title: Restimulate-1.5h-single-1


title: Restimulate-1.5h-PBS-3

value: control PBS and PBS


title: E18-2


title: SAARMK

value: Cetuximab


title: Restimulate-1.5h-single-2


title: SAARMI


title: Restimulate-1.5h-PBS-2


title: SAARLX

value: Bevacizumab/Cetuximab


title: Restimulate-1.5h-PBS-1


title: SAARLV


title: Restimulate-1.5h-FP-1


title: SAARLY


title: High-Dose-IL2-3

description: rawdata.Malek.high-dose.filtrcpms.csv


title: SAARMR


title: SAARLS


title: High-Dose-IL2-2

description: rawdata.Malek.high-dose.filtrcpms.csv