title: scRNAseq_post_transplant_BM_WT_1

description: 10x Genomics


title: HiC_HPC5-1

status: Public on Aug 24 2023

type: SRA

city: Memphis

first: Kim

last: Nichols

state: TN

address: 262 Danny Thomas Pl

department: Oncology

country: USA

institute: St. Jude Children's Research Hospital

library_source: genomic

data_processing:
Hi-C analysis was performed using the HemTools pipeline hicpro as described previously11. HiC-Pro (v2.11.1) was used with default parameters; for global read mapping: --very-sensitive --L 30 --score-min L,−0.6,−0.2 --end-to-end --reorder; for local read mapping: --very-sensitive --L 20 --score-min L,−0.6,−0.2 --end-to-end --reorder; cutoffs for minimal and maximal values were not defined for FRAG_SIZE, INSERT_SIZE and CIS_DIST; for read pair filtering: RM_SINGLETON = 1, RM_MULTI = 1 and RM_DUP = 1. Then, all Hi-C data were downsampled to 200 million valid read pairs based on.allValidPairs files. HiC-Pro was used for iced matrix generation with default parameters of BIN_SIZE = 10,000, MAX_ITER = 100, FILTER_LOW_COUNT_PERC = 0.02, FILTER_HIGH_COUNT_PERC = 0 and EPS = 0.1. HicFindTADs from HiCExplorer (v3.5.1) was used for topologically associating domain (TAD) calling with default parameters after converting HiC-Pro iced matrix to H5 format (hicConvertFormat).
Assembly: mm10
Supplementary files format and content: bedj files- TAD boundaries, chromatin loops (medium and high confidence)
Supplementary files format and content: bigwig files- AB compartments (50K and 250K)

molecule: genomic DNA

organism: Mus musculus

source_name: Bone Marrow

extract_protocol: Hi-C was performed using 5 million HPC5 according to the manufacturer’s instructions (Arima Hi-C kit(#A410030). Cells were crosslinked with 2% formaldehyde for 10 min at room temperature, followed by quenching using Arima Stop solution. After washing with PBS, the cell pellet was collected and stored at -80C until use. Nuclei were permeabilized using Arima lysis buffer and crosslinked chromatin was digested using the Arima restriction enzyme (RE) cocktail. The ends of restriction fragments were labeled with biotinylated nucleotides and ligated using a Arima enzymes A1, A2, B, C, and D. After reversal of crosslinks using Arima conditioning solution, the ligated DNA was purified with AMPure® XP Beads (#A63880) and sheared to a size of ∼400 bp with a Covaris M220 ultrasonicator (500295).  After enrichment using Arima enrichment beads, DNA fragments were used for constructing a sequencing library using NEBNext® Ultra II DNA library prep kit (#E7103) which was then subjected to Illumina sequencing.

tag: tissue

value: Bone Marrow

tag: cell line

tag: cell type

value: BM-derived HPC

tag: genotype

tag: treatment

value: Hi-C


title: CUT_HPC5_WT_ETV6_rep2

data_processing:
FASTQ files were mapped to mm10 by using BWA-MEM (version 0.7.16a). Reads that could not be uniquely mapped to the mouse genome were removed by SAMtools (version 0.17). Peaks were called using MACS2 (version 2.1.1). bigWig files were generated using DeepTools (version 3.2.0). Footprint analysis was performed by using CUT&RUNTools. Downstream analysis for binding site distribution and peak annotation were performed using R Bioconductor packages DiffBind7, ChIPseeker8, and clusterProflier9,10.
Assembly: mm10, hg38
Supplementary files format and content: bigwig tracks to be loaded in a genome browser
Library strategy: CUT&RUN

extract_protocol: CUT&RUN was performed as previously described3,4. 1x10^6 HPC5 cells were harvested from culture and 50-100,00 LSK  cells were isolated from mouse bone marrow as previously described. After three rinses each with 1-ml wash buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM spermidine, and protease inhibitors) followed by 3 min 600 g spin at RT, cells in 1 ml wash buffer were captured by Concanavalin A-coated magnetic beads (10 µl per million cells; Bangs laboratories, Inc.) at RT for 10 min with constant rotation. Upon three more washes, captured cells were permeabilized in 100 to 300 µl of the same wash buffer plus 0.05% digitonin and 2 mM EDTA with simultaneous antibody binding (purified anti-ETV6 antibody and corresponding amounts of IgG control) at 4°C overnight. Permeabilized cells/nuclei retained on the beads were washed 3 times with the same digitonin-wash buffer before incubation with 150 µl of Protein A-fused Micrococcal Nuclease (pA-MNase; 700 ng/ml) at 4°C for 1 h. After washing away unbound pA-MNase, antibody-associated protein-DNA complex was released from chromatin by adding CaCl2 to digitonin-wash buffer for a final 2 mM CaCl2 concentration and incubated at 0°C (i.e., ice-water bath) for 30 min. Equal volume of 2x stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% digitonin, 100 µg/ml RNase A, 50 µg/ml glycogen) containing spike-in yeast DNA (20 pg/ml) was then added to the reaction with an additional 30-min incubation at 37°C. The released DNA was isolated by proteinase K treatment and phenol/chloroform extraction and ethanol precipitation4. NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) was used to prepare CUT&RUN libraries. Barcoded libraries were sequenced using NextSeq 500 High Output.

value: Cut&Run antibody


title: HiC_HPC5-2


title: CUT_HPC5_WT_ETV6_rep1


title: CUT_LSK_MUT_ETV6_rep2

value: LSK


title: CUT_HPC5_IgG


title: ATAC_HPC5-1

data_processing:
FASTQ files were mapped to mm10 by using BWA-MEM (version 0.7.16a). Reads that could not be uniquely mapped to the mouse genome were removed by SAMtools (version 0.17). Peaks were called using MACS2 (version 2.1.1). bigWig files were generated using DeepTools (version 3.2.0). Footprint analysis was performed by using CUT&RUNTools. Downstream analysis for binding site distribution and peak annotation were performed using R Bioconductor packages DiffBind7, ChIPseeker8, and clusterProflier9,10.
Assembly: mm10
Supplementary files format and content: bigwig tracks to be loaded in a genome browser

extract_protocol: ATAC-seq was performed following the Fast-ATAC protocol5. Briefly, 10,000 of HPC5 cells were treated with transposition mix: 1) 22 uL nuclease-free water; 2) 25 uL 2 × TD Buffer; 3) 2.5 uL TDE1 transposase; 4) 0.5 uL 1% Digitonin (added right before removing supernatant from cell pellets), followed by incubation at 37°C on thermomixter at 300 rpm for 30 minutes. DNA was purified by using the MinElute Reaction Cleanup kit (Qiagen, 28204), and amplified for 5 cycles with the following mix: 10 uL transposed DNA, 2.2 uL nuclease-free water; 6.25 uL 10 uM barcoded Nextera primer-F; 6.25 uL 10 uM barcoded Nextera primer-R; 0.3 uL 100 × SYBR Green I (Invitrogen, S-7563); 25 uL NEBNext® High-Fidelity 2X PCR Master Mix (NEB, M0541). PCR products were subsequently re-amplified for 6 additional PCR cycles and subjected to purification using SPRIselect beads (Beckman Coulter, B23317).

value: ATAC-seq


title: CUT_LSK_IgG


title: CUT_LSK_MUT_ETV6_rep1


title: RNAseq_LSK_3month_MUT_3

library_source: transcriptomic

data_processing:
Total stranded RNA sequencing data were processed by the internal AutoMapper pipeline. The raw reads were firs trimmed (Trim-Galore version 0.60), mapped to mouse genome assembly (mm10) (STAR v2.7). The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (M22 [mm10]).
Assembly: mm10
Supplementary files format and content: coutns matrix, RSEM counts

molecule: total RNA

growth_protocol: cKit+ cells were isolated by magnetic enrichment using anti-CD117 microbeads (Miltenyi Biotec, Carlsbad, CA) and an autoMACs magnetic cell separator (Miltenyi Biotec, Carlsbad, CA). For LSK (Lineage- Sca-1+ cKit+) cells isolation, cells were stained with Lineage-BV650 cocktail described in the flow cytometry section, Sca-1-FITC (D7) and cKit-APC (2B8). For LT-HSCs (Lineage-Sca-1+ c-Kit+CD48-CD150+) and ST-HSC (Lineage-Sca-1+ c-Kit+CD48-CD150-) isolation, cells were stained with Lineage-BV650 cocktail, Sca1-PerCP-Cy5.5 (D7), cKit-APCeF780 (B2B8), CD48-Alexa700 (cHM48-1) and CD150-APC (W19132B). DAPI (Sigma-Aldrich, St. Louis, MO) was used for dead cell exclusion. All cell isolation was performed using cell sorting on FACSAria III (BD Biosciences, San Jose, CA).

extract_protocol:
RNA was extracted from sorted cell populations using the RNeasy Micro Kit (Qiagen, Germantown, Maryland). The quality and quantity of the initial RNA was determined by using the Agilent 2100 Bioanalyzer with the Eukaryote Total RNA Pico kit.
For each good quality sample, 2.5-25 nanograms of total RNA was used in the Tecan Ovation RNA sequencing system v2 protocol as written to create SPIA (single primer isothermal amplification)-cDNA. Once the cDNA was purified, five hundred nanograms of each sample was sheared using the Covaris LE220 focused ultra sonicator. The shearing plate used was the 96 microtube-50 AFA fiber plate and the target base pair size was 300. The settings for the shearing were the following: Peak incident Power (W) of 450, duty factor of 15%, cycles per burst 1000 with a 100 second treatment time. Once the cDNA was sheared, libraries were created using the KAPA Hyper-Prep kit from Roche.
Based on the starting cDNA input amount, the Kapa Hyper protocol recommended four pcr cycles for the amplification step while the rest of the protocol was followed as described. The indexes used were the UDI DNA indexes from Illumina. Eukaryote Total RNA Pico kit (catalog: 5067-1513) Tecan (formally NuGen) Ovation RNA sequencing system v2 (catalog: 7102-32) Covaris 96 tube plate (catalog:520168) KAPA Hyper-Prep (catalog: KK8504) UDI DNA Indexes from Illumina (catalog: 20022370)

tag: strain

tag: age

value: 3 Months


title: ATAC_HPC5-2


title: RNAseq_LSK_3month_MUT_1


title: RNAseq_LSK_3month_MUT_2


title: RNAseq_LSK_3month_WT_2


title: scRNAseq_post_transplant_BM_RX_1

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing reads from 10X experiment were mapped to mouse reference genome (mm10) using cellranger-7.1.0 (transcriptome version: mm10-2020-A). Single cell counts matrices were then processed using Scanpy as described in the best practices workflow previously (https://www.sc-best-practices.org). For quality control, doublet cells were filtered out, and low-quality cells with excess outliers calculated as 3 MADs (Median absolute deviations) for no. of counts per barcode, no. of genes per barcode, and fraction of counts from mitochondrial genes. We performed SCRAN normalization followed by dimensionality reduction with top 40 PCs selected using elbow plot using UMAP and tSNE algorithms. We used the Leiden algorithm for finding clusters at resolution of 0.25,0.5, and 1 and selected 0.25 as final resolution with optimal number of clusters preserving distinct cell populations.
For cell type identification across 22 clusters, we used a combination of known gene markers for cell populations or top gene markers that distinguished each cluster from other clusters identified using rank_genes_groups function in Scanpy. We used two determine hematopoietic sub populations of cells, bloodspot (https://servers.binf.ku.dk/bloodspot) and mouse cell atlas (https://bis.zju.edu.cn/MCA/atlas2.html; accessed April 2023) along with literature mining for known cell markers. We also used hscScore and scCATCH tools to aid cell identification. Finally, two authors (MB, NO) independently identified these clusters and finalized annotations.
We next performed integration of all 6 replicates, 3 each for wild-type and mutant genotypes, using Harmony algorithm, re-clustered the populations and annotated using the iterative process described above. Integrated anndata file was used to preform cell composition analysis within each cluster using scCODA Bayesian model for labeled clusters and Milo algorithm for unlabeled clusters. We used edgeR algorithm to identify significant differentially expressed genes within each cluster. We performed gene set enrichment analysis using MSigDb v.7.5.1 Hallmark genesets using python package GSEApy.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol: For each mouse, sort-purified CD45.1+ and CD45.2+ LSK and BM cells were washed three times with 1X Phosphate-Buffered Saline (PBS-, calcium-, and magnesium-free) containing 0.04% weight/volume BSA (Thermo Fisher Scientific, Waltham, Massachusetts) and manually counted. LSK and BM cells were mixed at a ratio 1:1 to have a total desired recovery target of 8,000-10,000 total cells and loaded onto a Chromium Next GEM Chip K (10X Genomics, Pleasanton, California) with Master Mix from Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index; 10X Genomics, Pleasanton, California), Single Cell VDJ 5' Gel Beads (10X Genomics, Pleasanton, California) and Partitioning Oil (10X Genomics, Pleasanton, California) following the manufacturer's protocol. Briefly, gel beads-in-emulsion (GEMs) were generated, lysed and 10x barcoded, and full-length cDNA from polyadenylated mRNA was produced. Next, GEMs were broken, pooled fractions were recovered, and cDNA was purified by Dynabeads MyOne SILANE (10X Genomics, Pleasanton, California). Barcoded, full-length cDNA was amplified via PCR, purified by SPRIselect Reagent (Beckman Coulter, Brea, California), and quantified using High Sensitivity D5000 ScreenTape with High Sensitivity D5000 Reagents at the Agilent 2200 TapeStation system and used for library preparation (10X Genomics, Pleasanton, California; Library Construction Kit, Dual Index Kit TT Set A). The High Sensitivity D1000 ScreenTape and the High Sensitivity D1000 Reagents were used to assess library’s quality at the Agilent 2200 TapeStation system. Libraries were sequenced on the NovaSeq 6000 (Illumina, San Diego, California) according to the manufacturer's recommendations.


title: CUT_CD34_WT_ETV6_rep1

organism: Homo sapiens


title: RNAseq_LSK_3month_WT_1


title: CUT_CD34_WT_ETV6_rep2


title: Gastirc Organoid, HTO-derived cDNA

status: Public on Jul 24 2023

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
The file B6_gastric_organoid_Library_408495_1_feature_ref.csv contains HTO barcodes for each cell type and condition.

library_source: other

data_processing:
scRNA reads were aligned by STARsolo using the genome build GENCODE GRCm39 Release M26.
QC, normalization, clustering and downstream analysis were performed by scater, scran and Seurat packages.
Integration of datasets was performed using Harmony package.
Mapping analysis and gene enrichment analysis were performed using SingleR and fgsea packages respectively.
Hashtag demultiplexing was performed by cellranger.
Assembly: GRCm39
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz.

molecule: other

source_name: HTO

growth_protocol: Stomachs of 8-10 week-old mice were harvested, opened along the greater curvature and washed in ice-cold DPBS . Mucus and muscle/serosa layer were removed under a stereomicroscope using forceps; antrum and corpus were separated with a large safety margin, and both tissues were cut into 2-5 mm² sized pieces. Pieces were dissociated in 43.4 mM sucrose, 54.9 mM d-sorbitol in DPBS by 5-10 rounds of vigorous pipetting and washing, followed by incubation in 10 mM EDTA at 4°C for 1h 20 min (rolling shaker). After one more washing step in 43.4 mM sucrose, 54.9 mM d-sorbitol, glands were extracted by placing tissue pieces under a glass slide and applying enough pressure to release individual glands; glands were collected in DMEM, pushed through a 40 um filter, counted, collected by centrifuging and mixed with Matrigel, seeded into 24 well plates (50 l per well) and cultivated at 37°C in ADMEM medium (Advanced DMEM/F12 + 10mM Pen/strep) supplemented with wnt-conditioned medium, R-spondin1, N-acetylcysteine, EGF, FGF, Noggin, [Leu15]-Gastrin I, N2, B27, HEPES, Glutamax, Y27632 (10uM; only on the seeding day; exclude thereafter).

extract_protocol:
RNA was extracted using the Quiagen RNeasy Mini Kit following manufacturer’s protocol.
TotalSeq-B with 10x Feature Barcoding Reagent Kits User Guide.

treatment_protocol: For seeding in 2D, 7-day-old 3D organoids were dissociated in cold DMEM by vigorous pipetting. Organoid fragments were resuspended in TrypLE and incubated at 37°C for 10 min. Single cell suspensions were washed, centrifuged, counted and seeded at 15’000 cells/well into rat tail collagen-coated wells in 2D culture medium (which is identical to 3D medium, but lacks Wnt-conditioned medium, R-spondin, Pen/Strep, FGF, Noggin and N-acetylcysteine; contains 10% FCS, and 1 M TGF- inhibitor); cells receive fresh medium after 2 days in culture, and are infected with H. pylori after 3 days in culture. Bacterial numbers were determined by measuring the optical density at 600 nm, and bacteria were added to cells at an MOI of 50 for 6 h, unless otherwise specified. The H. pylori strains used in this study were G27, PMSS1  and PMSS1RFP. Organoid cells were treated with the NF-B inhibitor BAY 11-7082, and the Cdck1 inhibitor XL413 at 0.2 M final concentration. -ADP-heptose was added at 0.5M final concentration for six hours.

value: Stomach

value: Epithelial cells

tag: antibodies/tags

value: MHC Class I/CD45


title: CUT_CD34_IgG


title: scRNAseq_post_transplant_BM_WT_2

description: 10x Genomics


title: CUT_LSK_WT_ETV6_rep1


title: CAGE-seq.C13_JQ1_5 uM_24h_R2

status: Public on Jul 23 2023

city: Yokohama

first: Nando

middle: Dulal

last: Das

state: -- Choose State --

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

data_processing:
Mapping of ChIP-seq data was performed by aligning to hg19 of the human genome using bowtie2
ChIP-seq peaks were called over cell-specific input controls using MACS2. For CAGE-seq, FANTOM CAT was used to annotate the CAGE reads at 5' ends. Count table was genereated by FANTOM CAT using custom script and expression counts were saved in 5th column of each CAGE bed file.
Genome_build: hg19
Supplementary_files_format_and_content: bam files were generated and mapped to the hg19 human genome
Supplementary_files_format_and_content: BigWig (bw) files were generated using UCSC bedGraphToBigWig. bedGraph files were generated at log likelihood option using MACS2 peak calling from untreated, DMSO- and JQ1-treated ChIP-seq samples.

source_name: Microglia cell line

growth_protocol: Human glioblastoma stem cell line (GSC316) was cultured and maintained in the neurobasal medium (Life Technologies, Carlsbad, CA) containing N2, B27 (Life Technologies), human recombinant basic fibroblast growth factor (233-FB-025, R&D Systems, Minneapolis, MN, USA), and epidermal growth factor (20 ng/ml; 236-EG-200, R&D Systems). The U-87 MG (U87) cell line (ATCC® HTB-14TM) was maintained using Eagle’s minimum essential medium (MEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 10 μg/ml streptomycin. The human microglia cell line, C13NJ was cultured in DMEM supplemented with 10% FBS and 50 μg/ml gentamicin.

extract_protocol:
[Epigenomic profiling]  GSC316 cells were treated with 0.5% formaldehyde for 6 min at room temperature to crosslink histone to DNA, which was followed by the addition of 1.25 M glycine to quench the crosslinking reaction. Cells were subsequently washed by ice-cold PBS with BSA (5 mg/ml), only ice-cold PBS, and PBS with protease inhibitors. After aspiration of supernatant, cell pellets were flash-frozen in liquid nitrogen. Flash-frozen cell pellets were stored at -80 °C. Cell pellets were lysed with lysis buffer (50 mM Tris-HCl pH 8.1 containing 1% SDS, 10 mM EDTA, and protease inhibitors-4693116001, Roche) by incubation on ice for 10 min, followed to sonication by Covaris (Duty Cycle: 5%, Cycles per Burst: 200, Volume 130 μl) for 8 min at low cell chromatin shearing mode. Sizes of sheared chromatin were examined by Agilent Bioanalyzer. The sheared chromatin was diluted in the dilution buffer (20 mM Tris-HCl pH 8.1 containing 150 mM NaCl, 1% Triton, and 2 mM EDTA). A fraction of sheared chromatin was prepared for input control by treating with RNase A and Proteinase K and heated for de-crosslinking. After clearing, the sheared chromatin was incubated for 10 to 12 hrs at 4 °C with antibody bounded magnetic beads (40 μl of DynabeadsTM sheep anti-mouse IgG, Cat. no. 11201D or sheep anti-rabbit IgG, Cat. no. 11203D for each ChIP. A total of 2.5 to 10 μg of each antibody per 2.5 – 8 × 106 cells was used. Specifically, anti-H4K5acK8ac (3 μg for 4 × 106 cells), anti-H3K4me3 (3 μg for 3 × 106 cells), anti-H3K27ac (2.5 μg for 3 × 106 cells), anti-H3K4me1 (4 μg for 4 × 106 cells), and anti-BRD4 (10 μg for 8 × 106 cells) antibodies were used for each ChIP. The antibody-bead conjugated chromatin was subsequently washed two times with low-salt wash buffer (20 mM Tris-HCl pH 8.1 containing 150 mM NaCl, 0.1% SDS, 2 mM EDTA, and 1% Triton X-100), two times with high-salt wash buffer (20 mM Tris-HCl pH 8.1 containing 500 mM NaCl, 0.1% SDS, 2 mM EDTA, and 1% Triton X-100), two times with LiCl wash buffer (10 mM Tris-HCl pH 8.1 containing 0.25 M LiCl, 1% IGEPAL-CA630, 1% deoxycholic acid, and 1 mM EDTA) and twice with Tris-EDTA wash buffer (10 mM Tris-HCl pH 8.1 containing 1 mM EDTA). For BRD4-ChIP, single washes for each of low-salt, high-salt, LiCl wash buffer and twice for Tris-EDTA wash buffer were used. The chromatin was eluted in elution buffer (100 mM NaHCO3 containing 1% SDS) and de-crosslinked at 65 °C for 5 to 6 hrs. RNA and protein were digested using 1 μl of RNase A and 1.5 μl of Proteinase K (20 mg/ml). The DNA was then isolated using Qiagen MinElute column purification for U87 and C13NJ cell lines. The Agencourt AMPure XP (A63880, Beckman Coulter) was used for DNA purification in GSC316. DNA was then subjected to qPCR with locus-specific primers. The ChIP-qPCR results were normalized to the input DNA.
[Transcriptomic profiling]  RNA samples from cells (DMSO-treated, JQ1-treated, and untreated) of GSC316, U87, and C13NJ were subjected for cap-analysis of gene expression (CAGE) transcriptome profiling. RNA was isolated from the nuclear fractions of three biological replicates of each treatment group.
[ChIP-seq]  For ChIP-seq library preparation, Mondrian (2 ng of ChIP DNA and 11 PCR-cycles) was used and each ChIP-seq library was subjected to 50-bp sequencing using HiSeq 2500.
[CAGE-seq]  The RNA integrity value of the above nine samples was confirmed through Agilent Bioanalyzer and RNA (at least 3 μg of each sample) samples were subjected for CAGE library preparation. Each CAGE library was sequenced at least 15 million reads.
Illumina HiSeq2500 High output run mode

treatment_protocol: For the drug treatment, JQ1 (2070-1, BioVision), which was dissolved in DMSO, was used. GSC316, U87, and C13NJ cells were first cultured on a 100 mm plate at the number of 2.5 × 106, 2 × 106, and 2 × 106 cells/plate, respectively, 24 hrs before the drug treatment. All cell types were treated with 5 μM JQ1 and DMSO for 24 hrs. The medium containing JQ1 and an equivalent volume/percentage of DMSO for each cell type was freshly prepared on the day of treatment.

value: Microglia cell line C13NJ

value: JQ1-treated for 24h


title: CAGE-seq.C13_JQ1_5 uM_24h_R3


title: CAGE-seq.C13_DMSO_24h_ R1

value: DMSO-treated


title: CAGE-seq.C13_JQ1_5 uM_24h_R1


title: CAGE-seq.C13_DMSO_24h_ R2


title: CAGE-seq.C13_No Treatment_R1

value: Untreated


title: RNAseq_LSK_3month_WT_3


title: CAGE-seq.C13_No Treatment_R2


title: CAGE-seq.C13_No Treatment_R3


title: CAGE-seq.U87_JQ1_5 uM_24h_R3

source_name: Glioblastoma cell line

value: Glioblastoma cell line U87


title: CUT_LSK_WT_ETV6_rep2


title: CAGE-seq.U87_JQ1_5 uM_24h_R2


title: CAGE-seq.U87_JQ1_5 uM_24h_R1


title: CAGE-seq.U87_DMSO_ R2


title: CAGE-seq.U87_No Treatment_R2


title: Gastric Organoid, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
The file B6_gastric_organoid_Library_408495_1_feature_ref.csv contains HTO barcodes for each cell type and condition.

molecule: polyA RNA

source_name: mRNA


title: CAGE-seq.U87_DMSO_ R1


title: CAGE-seq.U87_No Treatment_R1


title: CAGE-seq.GSC_316_JQ1_5uM_R3

value: Patient derived glioblastoma stem cell line GSC316


title: CAGE-seq.GSC_316_DMSO_R1

source_name: Patient derived glioblastoma stem cell line


title: CAGE-seq.GSC_316_DMSO_R2


title: CAGE-seq.GSC_316_no treatment_R3


title: CAGE-seq.GSC_316_JQ1_5uM_R1


title: ChIP-seq.C13.Input

tag: chip antibody


title: CAGE-seq.GSC_316_no treatment_R2


title: ChIP-seq.C13.BRD4.JQ1.R2

value: BRD4 (Bethyl Laboratories, A301-985A100)


title: CAGE-seq.GSC_316_JQ1_5uM_R2


title: ChIP-seq.C13.BRD4.DMSO.R2


title: CAGE-seq.GSC_316_no treatment_R1


title: ChIP-seq.C13.H3K4me3.untreated.R2

value: H3K4me3 (Millipore, 17-614)


title: ChIP-seq.C13.BRD4.DMSO.R1


title: ChIP-seq.C13.BRD4.JQ1.R1


title: ChIP-seq.C13.H3K27ac.JQ1.R2

value: H3K27ac (Abcam, ab4729)


title: ChIP-seq.C13.H3K27ac.untreated.R1


title: ChIP-seq.C13.H3K4me1.untreated.R1

value: H3K4me1(Diagenode, C15410194)


title: ChIP-seq.C13.H3K27ac.JQ1.R1


title: ChIP-seq.C13.H3K4me3.untreated.R1


title: CAGE-seq.U87_No Treatment_R3


title: ChIP-seq.C13.H3K27ac.untreated.R2


title: ChIP-seq.C13.H3K27ac.DMSO.R1


title: ChIP-seq.C13.H4K5acK8ac.JQ1.R2

value: H4K5acK8ac (Mouse Monoclonal, Handoko, L. et. al. Epigenetics 13(4):410, 2018)


title: ChIP-seq.C13.H4K5acK8ac.untreated.R2


title: ChIP-seq.C13.H4K5acK8ac.untreated.R3


title: ChIP-seq.U87.Input


title: ChIP-seq.C13.H4K5acK8ac.DMSO.R1


title: ChIP-seq.U87.BRD4.JQ1.R3


title: ChIP-seq.C13.H3K27ac.DMSO.R2


title: ChIP-seq.C13.H4K5acK8ac.JQ1.R1


title: ChIP-seq.U87.BRD4.DMSO.R2


title: ChIP-seq.U87.BRD4.JQ1.R2


title: ChIP-seq.U87.H3K4me3.untreated.R1


title: ChIP-seq.U87.H3K4me1.untreated.R2


title: ChIP-seq.U87.H3K4me1.untreated.R1


title: ChIP-seq.U87.H3K27ac.untreated.R1


title: ChIP-seq.U87.H3K4me3.untreated.R2


title: ChIP-seq.C13.H3K4me1.untreated.R2


title: ChIP-seq.U87.H3K27ac.untreated.R2


title: ChIP-seq.U87.H3K27ac.JQ1.R1


title: ChIP-seq.U87.H3K27ac.DMSO.R1


title: ChIP-seq.U87.H4K5acK8ac.untreated.R2


title: ChIP-seq.U87.H3K27ac.DMSO.R2


title: ChIP-seq.U87.H4K5acK8ac.JQ1.R2


title: ChIP-seq.C13.H4K5acK8ac.DMSO.R3


title: ChIP-seq.U87.H4K5acK8ac.DMSO.R2


title: ChIP-seq.U87.H4K5acK8ac.JQ1.R1


title: ChIP-seq.U87.BRD4.DMSO.R1


title: ChIP-seq.GSC316.BRD4.JQ1.R2


title: ChIP-seq.GSC316.BRD4.DMSO.R3


title: ChIP-seq.GSC316.BRD4.JQ1.R1


title: ChIP-seq.GSC316.BRD4.DMSO.R1


title: ChIP-seq.GSC316.H3K4me3.untreated.R2


title: ChIP-seq.GSC316.H3K4me3.untreated.R1


title: ChIP-seq.GSC316.H3K4me1.untreated.R4


title: ChIP-seq.GSC316.H3K4me1.untreated.R3


title: ChIP-seq.GSC316.H3K27ac.untreated.R2


title: ChIP-seq.U87.H3K27ac.JQ1.R2


title: ChIP-seq.U87.H4K5acK8ac.DMSO.R4


title: ChIP-seq.GSC316.H3K27ac.DMSO.R2


title: ChIP-seq.GSC316.H3K27ac.JQ1.R2


title: ChIP-seq.U87.H4K5acK8ac.untreated.R1


title: ChIP-seq.GSC316.H4K5acK8ac.JQ1.R3


title: ChIP-seq.GSC316.H4K5acK8ac.untreated.R2


title: ChIP-seq.GSC316.H3K27ac.JQ1.R3


title: ChIP-seq.GSC316.H4K5acK8ac.JQ1.R1


title: ChIP-seq.GSC316.H3K27ac.DMSO.R1


title: ChIP-seq.GSC316.H4K5acK8ac.untreated.R1


title: ChIP-seq.GSC316.H4K5acK8ac.DMSO.R1


title: ChIP-seq.GSC316.Input


title: ChIP-seq.GSC316.H4K5acK8ac.DMSO.R3


title: CD b_CD colon

status: Public on Jun 13 2023

type: RNA

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

description: CD b

hyb_protocol: NanoString® ISH probes were prepared by incubation at 95°C for 2 min and placed on ice, and the ISH probe mix (1nM 980 plex ISH probe, 10nM Attenuation probes, 1nM SMI-0006 custom, 1X Buffer R, 0.1 U/μL SUPERase•In™ [Thermo Fisher Scientific] in DEPC H2O) was pipetted into the hybridization chamber. The chamber was sealed to prevent evaporation, and hybridization was performed at 37°C overnight. Tissue sections were washed twice in 50% formamide (VWR) in 2X SSC at 37°C for 25 min, washed twice with 2X SSC for 2 min at room temperature, and blocked with 100 mM NHS-acetate in the dark for 15 min. In preparation for loading onto the CosMx SMI instrument, a custom-made flow cell was affixed to the slide.

scan_protocol: RNA target readout on the CosMx SMI instrument was performed. Briefly, the assembled flow cell was loaded onto the instrument and Reporter Wash Buffer was flowed to remove air bubbles. A preview scan of the entire flow cell was taken, and 15-25 fields of view (FoVs) were placed on the tissue to match regions of interest identified by H&E staining of an adjacent serial section. RNA readout began by flowing 100 μl of Reporter Pool 1 into the flow cell and incubation for 15 min. Reporter Wash Buffer (1 mL) was flowed to wash unbound reporter probes, and Imaging Buffer was added to the flow cell for imaging. Nine Z-stack images (0.8 μm step size) for each FoV were acquired, and photocleavable linkers on the fluorophores of the reporter probes were released by UV illumination and washed with Strip Wash buffer. The fluidic and imaging procedure was repeated for the 16 reporter pools, and the 16 rounds of reporter hybridization-imaging were repeated multiple times to increase RNA detection sensitivity. After RNA readout, the tissue samples were incubated with a 4-fluorophore-conjugated antibody cocktail against CD298/B2M (488 nm), PanCK (532 nm), CD45 (594 nm), and CD3 (647 nm) proteins and DAPI stain in the CosMxTM SMI instrument for 2 h. After unbound antibodies and DAPI stain were washed with Reporter Wash Buffer, Imaging Buffer was added to the flow cell and nine Z-stack images for the 5 channels (4 antibodies and DAPI) were captured.

data_processing:
Images were segmented to obtain cell boundaries, assign transcripts at the cell-level, and obtain a transcript by cell count matrix. Cells with an average negative control count greater than 0.5 and less than 20 detected features were filtered out. After quality control, a mean of 95,3% of cells across samples and FoVs was retained, corresponding to ~46,160 cells per sample on average.
CosMx_normalized_matrix.txt: Counts of molecules for each gene in each segmented cell.

label: SMI imaging barcodes

source_name: CD colon

label_protocol: After HIER, tissue sections were digested with 3 µg/ml Proteinase K diluted in ACD Protease Plus at 40°C for 30 minutes. Tissue sections were then washed twice with diethyl pyrocarbonate (DEPC)-treated water (DEPC H2O) and incubated in 0.00075% fiducials (Bangs Laboratory) in 2X saline sodium citrate, 0.001% Tween-20 (SSCT solution) for 5 min at room temperature in the dark. Excess fiducials were rinsed from the slides with 1X PBS, then tissue sections were fixed with 10% neutral buffered formalin (NBF) for 5 min at room temperature. Fixed samples were rinsed twice with Tris-glycine buffer (0.1M glycine, 0.1M Tris-base in DEPC H2O) and once with 1X PBS for 5 min each before blocking with 100 mM N-succinimidyl (acetylthio) acetate (NHS-acetate, Thermo Fisher Scientific) in NHS-acetate buffer (0.1M NaP, 0.1% Tween pH 8 in DEPC H2O) for 15 min at room temperature. The sections were then rinsed with 2X saline sodium citrate (SSC) for 5 min and an Adhesive SecureSeal Hybridization Chamber (Grace Bio-Labs) was placed over the tissue.

extract_protocol: FFPE tissue sections were prepared for CosMxTM SMI profiling. Briefly, five-micron tissue sections mounted on VWR Superfrost Plus Micro slides (cat# 48311-703) were baked overnight at 60°C, followed by preparation for in-situ hybridization (ISH) on the Leica Bond RXm system by deparaffinization and heat-induced epitope retrieval (HIER) at 100°C for 15 minutes using ER2 epitope retrieval buffer (Leica Biosystems product, Tris/EDTA-based, pH 9.0).

treatment_protocol: Surgical samples were fixed in formalin and paraffin embedded (FFPE) for CosMxTM SMI and tissue staining (IHC IF, ISH).

value: colon

tag: gender

value: female

tag: biopsy

value: transverse colon

tag: disease

value: Crohn's disease (CD)


title: CD c_CD colon

description: CD c


title: CD a_CD colon

description: CD a

value: male

value: sigmoid colon


title: UC c_UC colon

description: UC c

source_name: UC colon

value: ulcerative colitis (UC)


title: UC a_UC colon

description: UC a


title: HC c_non-IBD colon

description: HC c

source_name: non-IBD colon

value: healthy (non-IBD)


title: UC b_UC colon

description: UC b


title: Oocyte_IVO-MII_10 scRNAseq

status: Public on May 27 2023

first: Sara

last: Pietroforte

address: Balmes 236

institute: Eugin Group

description: Processed data file column: 48_2020

data_processing:
Sequencing of libraries was carried out using a HiSeq 2500 (Illumina) with 2x150 bp paired-end reads, with 30 million reads per sample.
FastQC (Babraham Bioinformatics) was used to perform the quality control of the sequencing.
After quality control of raw reads, the remaining clean reads for each sample were aligned to the GRch38 human reference genome. Subsequently, reads belonging to whole genes or single exons were counted using the function SummarizeOverlaps of the Bioconductor/R package Genomic Features. DESeq2 was then used to detect differentially expressed genes between experimental groups.
Assembly: hg38

source_name: oocyte

extract_protocol:
10 freshly collected oocytes were included in the study as GV immediately after ovum pick-up, 10 as MII after in vitro maturation in 30 µL of G2-plus media (Vitrolife, Sweden) covered by Ovoil (Vitrolife, Sweden) in a humidified atmosphere of 6% CO2 at 37°C for 32 hours (IVM-MII), 10 as GV that failed to mature after IVM in the same previously described conditions (FTM-GV) and 10 MII were collected in vivo (IVO-MII) and included in the study after vitrification/warming according to the Cryotop method of vitrification using the Cryotop vitrification open system (Kitazato BioPharma Co., Ltd, Fuji, Japan).
Single oocyte cDNA libraries were constructed using the Ovation SoLo RNA-Seq System (NuGEN) according to the manufacter's instructions.

value: oocyte

tag: developmental stage

value: IVO-MII


title: Oocyte_IVO-MII_9 scRNAseq

description: Processed data file column: 47_2020


title: Oocyte_IVO-MII_6 scRNAseq

description: Processed data file column: 44_2020


title: Oocyte_IVO-MII_8 scRNAseq

description: Processed data file column: 46_2020


title: ChIP-seq.GSC316.H3K27ac.untreated.R1

value: Untreated


title: Oocyte_IVO-MII_4 scRNAseq

description: Processed data file column: 27_2020


title: Oocyte_IVO-MII_3 scRNAseq

description: Processed data file column: 26_2020


title: Oocyte_IVO-MII_5 scRNAseq

description: Processed data file column: 28_2020


title: Oocyte_IVO-MII_2 scRNAseq

description: Processed data file column: 25_2020


title: Oocyte_IVO-MII_1 scRNAseq

description: Processed data file column: 24_2020


title: Oocyte_IVM-MII_10 scRNAseq

description: Processed data file column: 41_2020

value: IVM-MII


title: Oocyte_IVM-MII_8 scRNAseq

description: Processed data file column: 39_2020


title: Oocyte_IVM-MII_9 scRNAseq

description: Processed data file column: 40_2020


title: Oocyte_IVM-MII_7 scRNAseq

description: Processed data file column: 37_2020


title: Oocyte_IVM-MII_6 scRNAseq

description: Processed data file column: 35_2020


title: Oocyte_IVM-MII_3 scRNAseq

description: Processed data file column: 14_2020


title: Oocyte_IVM-MII_2 scRNAseq

description: Processed data file column: 13_2020


title: Oocyte_IVM-MII_4 scRNAseq

description: Processed data file column: 16_2020


title: Oocyte_FTM-GV_10 scRNAseq

description: Processed data file column: 34_2020

value: FTM-GV


title: Oocyte_FTM-GV_9 scRNAseq

description: Processed data file column: 33_2020


title: Oocyte_FTM-GV_7 scRNAseq

description: Processed data file column: 31_2020


title: Oocyte_FTM-GV_8 scRNAseq

description: Processed data file column: 32_2020


title: HC a_non-IBD colon

description: HC a


title: Oocyte_FTM-GV_4 scRNAseq

description: Processed data file column: 22_2020


title: Oocyte_FTM-GV_3 scRNAseq

description: Processed data file column: 21_2020


title: Oocyte_IVO-MII_7 scRNAseq

description: Processed data file column: 45_2020


title: Oocyte_FTM-GV_6 scRNAseq

description: Processed data file column: 29_2020


title: Oocyte_GV_9 scRNAseq

description: Processed data file column: 42_2020

value: GV


title: HC b_non-IBD colon

description: HC b

value: descending colon


title: Oocyte_FTM-GV_2 scRNAseq

description: Processed data file column: 20_2020


title: Oocyte_GV_6 scRNAseq

description: Processed data file column: 30_2020


title: Oocyte_IVM-MII_5 scRNAseq

description: Processed data file column: 17_2020


title: Oocyte_GV_10 scRNAseq

description: Processed data file column: 43_2020


title: Oocyte_FTM-GV_1 scRNAseq

description: Processed data file column: 19_2020


title: Oocyte_GV_8 scRNAseq

description: Processed data file column: 38_2020


title: Oocyte_GV_5 scRNAseq

description: Processed data file column: 18_2020


title: Oocyte_IVM-MII_1 scRNAseq

description: Processed data file column: 12_2020


title: Oocyte_GV_7 scRNAseq

description: Processed data file column: 36_2020


title: Oocyte_GV_4 scRNAseq

description: Processed data file column: 15_2020


title: Oocyte_GV_2 scRNAseq

description: Processed data file column: 10_2020


title: Oocyte_GV_3 scRNAseq

description: Processed data file column: 11_2020


title: Oocyte_FTM-GV_5 scRNAseq

description: Processed data file column: 23_2020


title: RCMV_UV_3

status: Public on May 15 2023

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description: polyA enrichment

data_processing:
Sequencing reads were aligned to the rn6 version of the rat genome using hisat2 (Kim et al, 2015) with standard parameters.
Reads were then quantified using quasR (Gaidatzis et al, 2015).
Assembly: rn6
Supplementary files format and content: tab-separated values

organism:
Rattus norvegicus
Murid betaherpesvirus 8

source_name: spleen

growth_protocol: Sprague Dawley rats were bred at the animal facility of the Robert Koch Institute and sacrificed by an isoflurane overdose.

extract_protocol:
Cells were resuspended in Trizol LS (Thermo Fisher) and RNA isolated using the Zymo Clean and Concetrator Kit (Zymo).
PolyA enriched RNA-sequencing library were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: DCs were enriched from spleen homogenates using OX-62 (CD103) microbeads (Miltenyi Biotec), and RNA was either directly extracted after enrichment or 24h hours later following infection with wt/∆vXLC1/UV-irradiated rat CMV at an MOI of 3 or mock infection, as indicated.

value: Sprague Dawley rats

value: spleen

value: Dendritic cells

value: UV-irradiated RCMV wt

tag: timepoint


title: RCMV_UV_2

description: polyA enrichment


title: RCMV_dXCL1_3

description: polyA enrichment

value: RCMV deltavXCL1 infection


title: RCMV_Wt_3

description: polyA enrichment

value: RCMV wt infection


title: RCMV_dXCL1_2

description: polyA enrichment


title: RCMV_UV_1

description: polyA enrichment


title: RCMV_Wt_1

description: polyA enrichment


title: RCMV_Wt_2

description: polyA enrichment


title: CD8_Prf1_Ruxo_3

status: Public on Apr 24 2023

description:
CD8_Prf1_Ruxo_3
2355255_14_CD8

data_processing:
Total stranded RNA sequencing data were processed by the internal AutoMapper pipeline. The raw reads were firs trimmed (Trim-Galore version 0.60), mapped to mouse genome assembly (mm10) (STAR v2.7). The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (M22 [mm10]).
Assembly: mm10
Supplementary files format and content: counts matrix, RSEM counts

source_name: Blood

treatment_protocol: Prf1-/- mice were infected intraperitoneally with 2x105 plaque-forming units (PFU) of LCMV Armstrong (kindly provided by John Wherry, University of Pennsylvania, Philadelphia, PA). Mice were treated orally twice a day with 90 mg/kg ruxolitinib (kindly provided by Ross Levine, Memorial Sloan Kettering Cancer Center, New York, NY or from Incyte Corporation) starting day 4 post-infection.  Ruxolitinib was dissolved in citrate buffer (0.1M, pH 3.5) with captisol (20% w/v).  Anti-IFNg (aIFNg) neutralizing antibody (clone XMG1.2) (BioXCell) was administered peritoneally at 0.5 mg per mouse on days 4 and 7 post-infection (p.i.) or combined with ruxolitinib. Mice were euthanized and multiple HLH parameters were evaluated on day 9 p.i.

value: C57BL/6 Prftm1Sdz/J

value: Blood

value: CD8+ T cells

value: LCMV + Ruxolitinib

value: Day 9


title: CD8_Prf1_combo_3

description:
CD8_Prf1_combo_3
2355256_15_CD8

value: LCMV + aIFNG + Ruxolitinib


title: CD8_Prf1_UnRx_3

description:
CD8_Prf1_UnRx_3
2355253_12_CD8

value: LCMV untreated


title: CD8_Prf1_combo_2

description:
CD8_Prf1_combo_2
2355251_10_CD8


title: CD8_Prf1_aIFNg_3

description:
CD8_Prf1_aIFNg_3
2355254_13_CD8

value: LCMV + aIFNg


title: CD8_Prf1_Naive_3

description:
CD8_Prf1_Naive_3
2355252_11_CD8

value: naive


title: CD8_Prf1_Naive_2

description:
CD8_Prf1_Naive_2
2355247_6_CD8


title: CD8_Prf1_combo_1

description:
CD8_Prf1_combo_1
2355246_5_CD8


title: Oocyte_GV_1 scRNAseq

description: Processed data file column:  9_2020

value: oocyte

value: GV


title: CD8_Prf1_aIFNg_2

description:
CD8_Prf1_aIFNg_2
2355249_8_CD8


title: CD8_Prf1_UnRx_2

description:
CD8_Prf1_UnRx_2
2355248_7_CD8


title: CD8_Prf1_Naive_1

description:
CD8_Prf1_Naive_1
2355242_1_CD8


title: CD8_Prf1_Ruxo_2

description:
CD8_Prf1_Ruxo_2
2355250_9_CD8


title: CD8_Prf1_UnRx_1

description:
CD8_Prf1_UnRx_1
2355243_2_CD8


title: CD8_Prf1_Ruxo_1

description:
CD8_Prf1_Ruxo_1
2355245_4_CD8


title: TU0078_Neg

status: Public on Mar 29 2023

city: La Jolla

first: Cecilia

middle: Sofie

last: Lindestam

state: CA

address: 9420 Athena Circle

department: Sette

institute: La Jolla Institute for Immunology

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were against the GRCh38 reference genome and Gencode v27 annotations using STAR v2.6.1 (default options)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Assembly: GRCh38.gencode.v27B
Supplementary files format and content: read count matrix with rows as genes and columns as cells

source_name: blood - PBMC

growth_protocol: PBMC were thawed and added at a density of 1 million cells per well to a round-bottom 96-well plate.

extract_protocol:
After 24 hrs, cells were resuspended in PBS with 10% (v/v) FBS and incubated at 4C for 10 min. Cells were then stained with fixable viability dye eFluor506 (eBioscience) and an antibody mixture containing anti-human CD3-AF700 (UCHT1; ThermoFisher), CD4-APCeFluor780 (RPA-T4; eBioscience), CD8-BV650 (RPA-T8; BioLegend), CCR7-PerCPCy5.5 (G043H7, Biolegend) CD14-V500 (M5E2; BD Bioscience), CD19-V500 (HIB19; BD Bioscience), CD25-FITC (M-A251; BD Bioscience), CD45RA-eFluor450 (HI100, eBiosciences), CD137-APC (4B4-1; BioLegend), OX40-PECy7 (Ber-ACT35; BioLegend), and PD-L1-PE (29E.2A3; BioLegend) for 20 min at room temperature. Cells were washed and resuspended in PBS before being transferred into a 5 ml polypropylene FACS tube (BD Bioscience). PBMCs were sorted, based on forward and side scatter excluding debris and doublets, on a FACSAria into TRIzol LS (Thermo Fisher). Acquisition files were analyzed using FlowJo. Total RNA was extracted from ~100,000 cells in TRIzol LS using the miRNeasy Micro Kit (Qiagen) on a QIAcube (Qiagen). Total RNA was amplified according to Smart Seq protocol (2). cDNA was purified using AMPure XP beads. cDNA was used to prepare a standard barcoded sequencing library (Illumina). Samples were sequenced using an Illumina HiSeq2500 to obtain 50-bp single end reads. Samples that failed to be sequenced due to limited sample availability or failed the quality control were eliminated from further sequencing and analysis. The full protocol can be found at protocols.io (http://dx.doi.org/10.17504/protocols.io.bxr6pm9e).
Sequencing was performed according to a paired-end strategy using the NovaSeq sequencer (Illumina). Samples that failed quality control standards were eliminated from further analysis21.

treatment_protocol: PBMCs were stimulated for 24hrs at 37 degree C with MTB300, Mtb whole cell lysate, as well as left unstimulated as a negative control. After 24hrs cells were stained for sorting

tag: with susceptibiliy allele

value: yes

tag: stimulation

value: Unstim

value: PBMC


title: TU0075_Neg


title: CD8_Prf1_aIFNg_1

description:
CD8_Prf1_aIFNg_1
2355244_3_CD8


title: TU0064_Neg


title: TU0063_Neg


title: TU0133_Neg


title: 1152_GA_Neg


title: TU0024_Neg


title: RCMV_dXCL1_1

description: polyA enrichment

value: Sprague Dawley rats

value: spleen

value: Dendritic cells


title: 1042_GA_Neg


title: 2055_GA_Neg


title: 1307_GA_Neg


title: 1304_GA_Neg


title: 1303_GA_Neg


title: 1153_GA_Neg


title: 1142_GA_Neg


title: 1046_GA_Neg


title: TU0137_Neg

value: no


title: 1045_GA_Neg


title: TU0081_Neg


title: TU0025_Neg


title: TU0070_Neg


title: TU0055_Neg


title: TU0013_Neg


title: 2047_GA_Neg


title: TU0033_Neg


title: 2053_GA_Neg


title: 2051_GA_Neg


title: 2054_GA_Neg


title: TU0005_Neg


title: 1312_GA_Neg


title: 1306_GA_Neg


title: 1311_GA_Neg


title: 1156_GA_Neg


title: 1147_GA_Neg


title: 1151_GA_Neg


title: 1309_GA_Neg


title: 1141_GA_Neg


title: 1302_GA_Neg


title: TU0133_MTB300


title: TU0064_MTB300


title: TU0078_MTB300


title: 1149_GA_Neg


title: TU0024_MTB300


title: 1037_GA_Neg


title: TU0010_MTB300


title: TU0063_MTB300


title: TU0046_Neg


title: 2066_GA_MTB300


title: 1152_GA_MTB300


title: 1042_GA_MTB300


title: 1313_GA_Neg


title: 1303_GA_MTB300


title: 1153_GA_MTB300


title: 1307_GA_MTB300


title: 1154_GA_MTB300


title: TU0137_MTB300


title: 1299_GA_Neg


title: 1142_GA_MTB300


title: TU0070_MTB300


title: 1045_GA_MTB300


title: TU0055_MTB300


title: TU0046_MTB300


title: 2054_GA_MTB300


title: TU0033_MTB300


title: TU0013_MTB300


title: 2047_GA_MTB300


title: 1314_GA_MTB300


title: 1317_GA_MTB300


title: 1311_GA_MTB300


title: 1312_GA_MTB300


title: 1309_GA_MTB300


title: 2053_GA_MTB300


title: 2051_GA_MTB300


title: 1141_GA_MTB300


title: 1043_GA_MTB300


title: 1302_GA_MTB300


title: 1147_GA_MTB300


title: 1306_GA_MTB300


title: 1299_GA_MTB300


title: 1157_GA_MTB300


title: 1149_GA_MTB300


title: TU0133_Lysate

value: Lysate


title: 1144_GA_MTB300


title: 1037_GA_MTB300


title: TU0078_Lysate


title: TU0075_Lysate


title: TU0005_MTB300


title: TU0064_Lysate


title: TU0024_Lysate


title: TU0010_Lysate


title: 1042_GA_Lysate


title: 1152_GA_Lysate


title: 2066_GA_Lysate


title: 1310_GA_MTB300


title: 1156_GA_MTB300


title: 1307_GA_Lysate


title: 1304_GA_Lysate


title: 1154_GA_Lysate


title: 1157_GA_Lysate


title: 1317_GA_Lysate


title: 1046_GA_Lysate


title: 1153_GA_Lysate


title: 1045_GA_Lysate


title: TU0070_Lysate


title: TU0033_Lysate


title: TU0013_Lysate


title: 2054_GA_Lysate


title: TU0046_Lysate


title: 2051_GA_Lysate


title: 2053_GA_Lysate


title: 2047_GA_Lysate


title: 1312_GA_Lysate


title: 1311_GA_Lysate


title: 1306_GA_Lysate


title: 1314_GA_Lysate


title: 1302_GA_Lysate


title: 1151_GA_Lysate


title: 2055_GA_Lysate


title: 1147_GA_Lysate


title: 1141_GA_Lysate


title: 1043_GA_Lysate


title: 1037_GA_Lysate


title: YC_1070

status: Public on Mar 06 2023

city: Pamplona

first: SERGIO

last: ROA

address: Irunlarrea, 1

department: Biochemistry and Genetics

institute: University of Navarra

description: SE50 sequencing of oligo dT-based mRNA enrichment (polyA RNA)

data_processing:
QC control of sample sequencing was verified using FastQC software.
Fastq files were mapped to mm10 mouse assembly using STAR 2.5.2b with default parameters.
Gene expression quantification was carried out with featureCounts v1.6.0 using read counts of exonic gene regions.
The gene annotation reference was Gencode vM25.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are tab-delimited text files including raw counts values for each annotated gene.

source_name: FACS-sorted B220+YFP+ cells from spleen

extract_protocol:
Murine spleens were submitted to cellular disggregation, followed by lysis of erythrocytes using ACK buffer. Then, single-cell preparations were stained with B220 and submitted to fresh cellular sorting in a FACSAria Ilu sorter (BD) after exclusion of dead cells with 7AAD. Total RNA was extracted from sorted cells using TRIzol (Invitrogen) as described in manufacturer´s protocol and quality control of extracted RNA was measured using Agilent 2100 Bioanalyzer.
DNBseq SE50 20M reads

treatment_protocol: Fresh murine spleens were collected from moribund or control mice.

tag: murine model

value: normal control

value: YC controls (YFPstopF/+Cg1Cre/+)

tag: cell type/tissue

value: splenic GC B cells (B220+YFP+)


title: YC_1671


title: YC_1669


title: YC_1067


title: TU0025_Lysate


title: pBIC_1766

source_name: FACS-sorted B220+GFP+ cells from spleen

value: ABC-DLBCL lymphoma (pBIC)

value: splenic lymphoma B cells (B220+GFP+)


title: pBIC_1521


title: P931

status: Public on Jan 10 2023

first: Mariko

last: Horii

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

data_processing:
Quality control was performed using FastQC (v. 0.11.3). Reads were mapped to GRCh38.89 (Ensembl) using STAR (v. 2.5.3a) (Dobin et al., 2013). The STAR parameters used were: --runThreadN 24 --sjdbOverhang 99 --genomeDir ref_ensembl_GRCh38_89/star_index --sjdbGTFtagExonParentGene gene_id --sjdbGTFfile ref_ensembl_GRCh38_89/Homo_sapiens.GRCh38.89.gtf --outSAMtype BAM Unsorted SortedByCoordinate --outReadsUnmapped Fastx --quantMode GeneCounts. Ensembl genes with at least 10 counts in 25% of samples were filtered for the analysis. Normalization and differential expression analysis were performed using R (v. 4.0.3) package DESeq2 (v. 1.30.1) (Love 2014). BiomaRt (v. 2.42.1) was used to convert Ensembl gene ID to HUGO gene names (Durinck 2009), and gene set enrichment analysis was done using R (v. 4.0.3) package FGSEA (v. 1.16.0).
Genome_build: GRCh38.89(Ensembl)
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample post filtering

source_name: Placental tissue

extract_protocol:
Total RNA was isolated using mirVana RNA Isolation Kit (ThermoFisher). RNA concentration was measured using Qubit RNA BR assay kit (ThermoFisher). RNA integrity was checked using RNA 6000 Nano chip read by Aligent 2100 bioanalyzer. All samples had a RIN above 7.0.
RNAseq libraries were prepared using the TruSeq Stranded Total RNA Sample preparation kit with Ribo-Zero Gold (Illumina).

value: Severe preeclampsia

value: Male

tag: sga


title: P824


title: P1932

value: Female


title: P1912

value: Non-hypertensive Control


title: P1787

value: yes


title: P753


title: P1745


title: P1831


title: Developing_Biolrep_3

status: Public on Dec 24 2022

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

data_processing:
Raw counts were obtained with kallisto.
Assembly: GCA_028583425.1
Supplementary files format and content: Raw counts in a tab delineated matrix.

organism: Eublepharis macularius

source_name: developing teeth

extract_protocol:
Each  sample contained 3 teeth and the teeth . Tubes were snap frozen in liquid nitrogen. Each sample was disrupted using a glass tissue grinder and a Qiagen Shredder column (ID:79656). Total RNA was extracted using a Qiagen RNeasy micro kit (ID: 74004).
Qualifying samples were prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs) at Biomedical research Center sequencing Core at University of British Columbia. Sequencing was performed on the Illumina NextSeq2000 with Paired End 59bp × 59bp reads. Sequencing data was demultiplexed using Illumina's bcl2fastq2. The output was 20 million paired end reads

tag: tissue

value: developing teeth

tag: Sex

value: female

value: adult

tag: rin number

tag: number of_teeth_per_sample


title: P1257


title: Developing_Biolrep_2


title: 1149_GA_Lysate

tag: cell type

value: PBMC


title: P1434


title: Functional_Biolrep_3

source_name: functional teeth

value: functional teeth


title: Functional_Biolrep_2


title: Developing_Biolrep_1


title: Functional_Biolrep_1


title: PINT shRNA1+LPS 2 [RNA-190404-6-2]

status: Public on Oct 01 2022

city: Wuhan

first: RUI

last: Zhou

address: Donghu Road 185

country: China

institute: Wuhan University

data_processing:
The cleandata were obtained using a fastp（v 0.19.7）fastq database. The main parameters are (-w 5-m 20-3-l 20-w 10)
Map the cleandata with the reference genome (grch37) using the HiSat2 software (2.1.0), with default parameters.
The presented results of FPKM (i.e. Genes.FPKM.Symbol.xls) was calculated using StringTie software (v1.3.4d) and annotation database (Ensembl: GRCh37.87)
Genome_build: hg19
Supplementary_files_format_and_content: abundances

source_name: SW480_PINT shRNA1+LPS

growth_protocol: SW480 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) (Gibco, USA), with 10% Fetal Bovine Serum (Gibco, USA).

extract_protocol:
mRNA was isolated using Trizol (Life Technologist, Carlsbad, CA)
Sequencing was carried out on Illumina Hiseq Xten platform following the manufacturers instruction.

treatment_protocol: Inhibit the expression of PINT and EZH2 by lentiviral vectors encoding short hairpin RNA in SW480 cells following exposed to PBS or LPS (1 μg/ml) for 4h.

tag: cell line

value: Intestinal epithelial cells

tag: treatment

value: short hairpin RNA (PINT)+lipopolysaccharide


title: PINT shRNA1+LPS 1 [RNA-190404-6-1]


title: PINT shRNA1 3-1 [RNA-190404-5-3]

source_name: SW480_PINT shRNA1

value: short hairpin RNA (PINT)


title: PINT shRNA1+LPS 3 [RNA-190404-6-3]


title: pBIC_1761

tag: strain

tag: genotype


title: PINT shRNA1 2 [RNA-190404-5-2]


title: PINT shRNA1 3 [RNA-190404-5-3]


title: LPS 3 [RNA-190404-2-3]

value: lipopolysaccharide (LPS)


title: PINT shRNA1 1-1 [RNA-190404-5-1]


title: Control 3 [RNA-190404-1-3]


title: Control 1 [RNA-190404-1-1]


title: Control 2 [RNA-190404-1-2]


title: LPS 2 [RNA-190404-2-2]


title: LPS 1 [RNA-190404-2-1]


title: APAP2

status: Public on Sep 16 2022

city: Kansas City

first: David

middle: S

last: Umbaugh

email: dumbaug@gmail.com, hjaeschke@kumc.edu

state: KS

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, mapped to mm39 genome using Hisat2.
Read counts were generated using subread with parameters -t exon - g gene_id.
Assembly: mm39 (GRCm39)
Supplementary files format and content: *.txt: Matrix tables with raw or normalized (DESeq2) gene counts for every gene and every sample.

source_name: Hepatocytes

extract_protocol:
Piece of whole liver, RNA extracted using TRIZOL.
RNA libraries were prepared for sequencing using standard Illumina protocols.
Tecan universal plus mRNA-seq.

treatment_protocol: n=3, APAP 300mgkg i.p. in saline, APAP+HDF (500,000 i.v. in saline), APAP+MSCs (500,000 i.v. in saline).

value: Liver

value: Hepatocytes

tag: age

value: 8 wk

value: APAP


title: APAP3


title: APAP1


title: APAP_HDF3

value: APAP+HDF


title: APAP_MSC2

value: APAP+MSC


title: APAP_HDF2


title: GS3-PDX-P4_4 weeks

status: Public on Sep 05 2022

city: Duarte

first: Shiuan

last: Chen

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

description:
processed data file:
E2_P4_interval_read_counts.txt

data_processing:
The reads were aligned back to human genome (hg19) using STAR software (2.6.0.a)
Htseq software was applied to generate the count matrix, with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Tab separated values; MatrixMarket

source_name: breast cancer patient-derived xenograft model

growth_protocol: Surgically resected brain metastasis tumor pieces were implanted into the 4th mammary fat pat of female NOD-scid/IL2Rγ-/- (NSG) mice, that were 6-8 weeks old, to establish PDX lines.

extract_protocol:
Total  RNA was extracted with Qiagen RNAeasy Mini kit (Cat 74101);
RNA libraries were prepared for sequencing using Kapa mRNA HyperPrep kit (Cat:KK8581) with 200ng of total RNA

treatment_protocol: After tumor volume reached approximately 200mm3, mice were randomized and implanted with Placebo,  E2 (estradiol, 1 mg), P4 (progesteron, 10 mg), E2+P4 (estradiol, 1 mg + progesteron, 10 mg) pellets on their backside. These treatments lasted  4 weeks. For intermittent E2 treatment, mice were implanted with the E2 (1 mg)) pellet which remained in the mice 28 days, and then the pellet was removed on day 28. After 28 days interval with no treatment, the mice were again implanted with the E2 (1 mg) pellet for another 28 days. This intermittent E2 treatment was repeated three rounds.

value: breast cancer PDX

value: progesterone (P4, 10mg pellet) for 4 weeks


title: APAP_HDF1


title: 1309_GA_Lysate

value: no

value: Lysate


title: GS3-PDX-E2-plus-P4_4 weeks

value: estradiol (E2, 1mg pellet) and progesterone (P4, 10mg pellet) for 4 weeks


title: APAP_MSC3


title: GS3-PDX-E2_4 weeks

value: estradiol (E2, 1mg pellet) for 4 weeks


title: APAP_MSC1


title: PINT shRNA1 2-1 [RNA-190404-5-2]


title: GS3-PDX-control

value: placebo


title: PINT shRNA1 1 [RNA-190404-5-1]

value: Intestinal epithelial cells


title: GS3-PDX-interval

value: Intermittent E2 treatment (E2, 1mg pellet, on/off every 4 weeks, 3 rounds)


title: GS3-PDX641

description:
ribosome-depleted,stranded
RNA-Seq data, Treat3, PDX model, replicate 1

data_processing:
Real Time Analysis (RTA, v1.18.64) was used for base calling, and bcl2fastq was used to generate FASTQ files (v1.8.4 for samples 1-6 in run 1, and v2.18 for samples 7-8 in run 2)
Reads aligned using TopHat2 (v2.0.14), with --no-coverage-search --library-type fr-firststrand
Unique reads quantified using htseq-count (version 0.6.0), with database generated from TxDb.Hsapiens.UCSC.hg19.knownGene (Bioconductor annotations, downloaded 6/8/2016).
Genome_build: hg19
Supplementary_files_format_and_content: RPKM normalized expression (using quantified reads and TxDb annotations in R) and read counts (calculated using htseq-count)

source_name: breast cancer PDX model, Treat3, replicate 1

extract_protocol:
Total RNA from GS3 tumors were extracted using the RNeasy Plus Mini Kit (Qiagen)
RiboZero Stranded mRNA-Seq Kit; stranded ribosome-depletion RNA-Seq

treatment_protocol: After tumor volume reached approximately 200mm3, mice were randomized and implanted with an Placebo or E2 (1mg) pellet on their backside. These treatments lasted 5/10/53 days for experiments on RNA sequencing analysis.

value: Treat3 (E2, 53 days)

tag: run

value: run 2


title: GS3-PDX085

description:
ribosome-depleted,stranded
RNA-Seq data, Control, PDX model, replicate 2

source_name: breast cancer PDX model, Control, replicate 2

value: Control

value: run 1


title: GS3-PDX089

description:
ribosome-depleted,stranded
RNA-Seq data, Treat1, PDX model, replicate 2

source_name: breast cancer PDX model, Treat1, replicate 2

value: Treat1 (E2, 5 days)


title: GS3-PDX080

description:
ribosome-depleted,stranded
RNA-Seq data, Control, PDX model, replicate 1

source_name: breast cancer PDX model, Control, replicate 1


title: GS3-PDX090

description:
ribosome-depleted,stranded
RNA-Seq data, Treat1, PDX model, replicate 1

source_name: breast cancer PDX model, Treat1, replicate 1


title: Cxcr4+ macrophages_3

status: Public on May 31 2022

description:
MC_558
Tecan universal plus mRNA-seq

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, mapped to mm39 genome using Hisat2.
Read counts were generated using subread with parameters -t exon - g gene_id.
Assembly: mm39
Supplementary files format and content: RNAseq_rawcounts.csv: Matrix table with raw counts for every gene and every sample.

source_name: Macrophages

extract_protocol:
Flow sorted cells, RNA extracted using TRIZOL.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: APAP 300mgkg i.p. in saline, sacrifice at 72h post APAP or control macrophages.

value: liver

value: macrophages

value: 8 wk

value: APAP


title: GS3-PDX644

description:
ribosome-depleted,stranded
RNA-Seq data, Treat3, PDX model, replicate 2

source_name: breast cancer PDX model, Treat3, replicate 2

value: breast cancer PDX


title: Control_macrophages

description:
MC_Ct
Tecan universal plus mRNA-seq


title: GS3-PDX323

description:
ribosome-depleted,stranded
RNA-Seq data, Treat2, PDX model, replicate 2

source_name: breast cancer PDX model, Treat2, replicate 2

value: Treat2 (E2, 10 days)


title: APAP2h 2

status: Public on Apr 13 2022

description: 10x Genomics Chromium Single Cell Gene Expression data

data_processing:
Data was analyzed using the 10x Genomics Chromium Single cell software suite
The demultiplexing and conversion of Illumina base call files (BCL) to raw FASTQ files was done using "cellranger mkfastq" with default parameters.
The sequencing reads were aligned to the mouse reference (GRCm38: refdata-cellranger-GRCm38-3.0.0) and analyzed using "cellranger count".
Assembly: mm10
Supplementary files format and content: cellranger generated unfilterted feature-barcode matrix file; Hierarchical Data Format (H5)

extract_protocol:
Single cell suspension was generated using collagenase perfusion method. Cell viability and concentration were measured by Countess II FL Automated cell counter
The RT reaction to generate 10X barcoded single stranded cDNA, in the single cell containing GEMs, is performed using an Eppendorf MasterCycler Pro thermal cycler. Post GEM-RT Cleanup is conducted by breaking the GEMS with 10X Recovery Agent to separate the aqueous phase from the Recovery Agent and Partitioning oil. A cleanup of the sscDNA containing aqueous phase is completed using Dynabeads MyOne Silane beads (Life Technologies 37002D). The second strand cDNA amplification is performed using the cDNA Amplification Mix on the Eppendorf MasterCycler Pro. The 3’ gene expression library construction is initiated with fragmentation, end repair and A-tailing of the dscDNA followed by adapter ligation and a sample index PCR using the Illumina compatible indexed adapters in the Chromium i7 Multiplex kit (10X Genomics 120262). Validation of the single cell library is conducted using the Agilent Tapestation 4200 ScreenTape assay (Agilent 5067-5576).

treatment_protocol: APAP 300mgkg i.p. in saline or control (saline treated)

value: Hepatocytes


title: APAP2h 1


title: Cxcr4+ macrophages_1

description:
MC_556
Tecan universal plus mRNA-seq


title: Vehicle control 3

source_name: Vehicle control


title: Cxcr4+ macrophages_2

description:
MC_557
Tecan universal plus mRNA-seq


title: GS3-PDX092

description:
ribosome-depleted,stranded
RNA-Seq data, Treat2, PDX model, replicate 1

source_name: breast cancer PDX model, Treat2, replicate 1


title: Vehicle control 2


title: Vehicle control 1


title: VUB06_MT

status: Public on Mar 31 2022

city: Brussels

first: Claudia

last: Spits

address: Laarbeeklaan 103

department: Research Group of Reproduction and Genetics

country: Belgium

institute: Vrije Universiteit Brussel

data_processing:
mapping sequences:  STAR 2.7.3, STAR --runThreadN 8 --runMode alignReads \  --quantMode  TranscriptomeSAM \ --twopassMode Basic \  --outSAMtype BAM SortedByCoordinate
count tables :  RSEM 1.3.2, rsem-calculate-expression -p 8 \ --alignments Aligned.toTranscriptome.out.ba
RNA seq analysis:  edgeR and DESeq2
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Count_table.txt

source_name: myotubes non-DM1

extract_protocol:
Total RNA was extracted using the QIAGEN Rneasy Mini kit, following manufacturers instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human embryonic stem cells derived myotubes


title: VUB19_MT

source_name: myotubes DM1


title: VUB01_MT


title: VUB03_3MT


title: VUB24_MT


title: VUB03_2MT


title: VUB03_1MT


title: VUB06_MB

source_name: myoblasts non-DM1

value: human embryonic stem cells derived myoblasts


title: VUB02_MB


title: VUB01_MB


title: VUB19_MB

source_name: myoblasts DM1


title: VUB24_MB


title: APAP2h 3


title: VUB03_1MB


title: VUB03_2MB


title: VUB19_SC

source_name: human embryonic stem cells DM1

value: human embryonic stem cells


title: VUB03_3MB


title: VUB01_SC

source_name: human embryonic stem cells non-DM1


title: VUB24_SC


title: VUB03_2SC


title: VUB02_MT


title: VUB02_SC


title: 2900

status: Public on Jan 01 2022

city: Boston

first: Gayani

last: Perera

state: MA

address: 800 Washington Street

department: MCRI

institute: Tufts Medical Center

data_processing:
Demultiplexing, read alignment, and read counting, and nuclei calls were done with Cellranger 3.0
Quality control (QC) filtering, clustering, dimensionality reduction, visualization, and differential gene expression was performed using the development version of the R package Seurat in R 3.5.0
Genome_build: GRCh38-1.2.0
Supplementary_files_format_and_content: tab separated values files with barcode sequences corresponding to column indices, features corresponding to row indices.  For each feature, its feature ID and names are stored in the first and second column of the features.tsv file.  The third column of this file indentifies that it is a gene expression feature.  The actual gene cell matrix, .mtx file, is stored in the Market Exchange Format (MEX) for sparse matrices.

molecule: nuclear RNA

source_name: Adult human septal tissue

extract_protocol:
Nuclei were released from the tissue via dounce homogenization and then nuclei were processed using 10x genomics Chromium Single Cell 3' reagent V2 kit
10x Genomics Chromium Single Cell 3' reagent v2 kit
single nuclei RNA-seq

value: adult heart IVS

tag: gender

value: Male

tag: disease status

value: Normal


title: VUB03_1SC


title: 2891

value: Non-Obstructive HCM


title: 5171

value: Female


title: 2890


title: MPP_pIC

status: Public on Dec 22 2021

city: Cambridge

first: Eva

last: Fast

address: 1 Portland st

institute: Pfizer

description: stimulation scRNAseq experiment

data_processing:
scRNA-Seq: For HSC_Repl1 cellranger (v2.1.0) was used for demultiplexing and count matrix generation. For stimulation scRNA-Seq experiment Cellranger (v3.0.1) command ‘mkfastq’ was used to demutliplex raw base call (BCL) files into individual samples and separate cDNA fastq files and HTO surface fastq files. The cellranger ‘count’ command was used with default options to generate count matrices from cDNA fastq files.
scRNA-Seq: For HTO surface libraries, fastq files split into different lanes but from the same read (e.g. L001_R2, L002_R2) were combined using 'cat'. Reads shorter than 26bp were filtered using 'cutadapt'. CITE-Seq 'count' (version 1.4.3) was used to generate surface count by cell matrices from the HTO surface fastq libraries using the following barcodes: MPP0 - GGTCGAGAGCATTCA, MPP1 - ACCCACCAGTAAGAC, MPP2 - CTTGCCGCATGTCAT, MPP3/4 - AAAGCATTCTTCACG and expected cell numbers per conditions: control - 5064 cells, dmPGE2 - 6497 cells, GCSF - 5297 cells, indo - 4665 cells and pIC - 5035 cells. Final pooled HTO/cDNA dataset including all stimulated HSC and MPP conditions is available here: https://mouse-hsc.cells.ucsc.edu.
scATAC-Seq: For scATAC-seq cellranger-atac mkfastq and count (1.2.0) was used for demultiplexing, alignment and generation of the fragment file. To generate the count matrix MACS2 was run with default parameters (keeping duplicates) on the aligned reads. Resulting peak summits were extended to 300 bp and this peak file was used to extract a count matrix from the fragment file via a custom script (see https://github.com/evafast/scrnaseq_paper).
Genome_build: mm10
Supplementary_files_format_and_content: scRNA-Seq matrixes are defined by barcode, features (both .tsv) and count matrix (.mtx)
Supplementary_files_format_and_content: scATAC-Seq count matrixes can be generated with peak (.bed) and fragments file (.tsv). Barcode file (.tsv) indicates cell identities and .csv file provides metadata.

source_name: FACS sorted bone marrow

growth_protocol: All cells were isolated from 9-12 week old male and female mice pooled at equal ratios. For treatment with niche stimulants and for scATAC-seq mice were ordered from Jackson Laboratories (C57BL/6J, #00664). Mice were kept for at least one week in the animal facility before initiating experiments. Control HSC replicate 1 (HSC_Repl1) is derived from the following mouse strain (Jackson Laboratories #016617) which carries a GFP transgene and was bred in house.

extract_protocol:
Whole Bone marrow was isolated from femur, tibia, hip and vertebrae via gentle crushing using a mortar and pestle. Stem and progenitor cells were enriched via lineage depletions (Miltenyi Biotech, 130-090-858). For treatment with niche stimulants cells were FAC-sorted  into the following populations: HSCs (Lin-, c-Kit+, Sca1+, CD48-, CD150+, CD34-), MPP1s (Lin-, c-Kit+, Sca1+, CD48-, CD150+, CD34+), MPPs (Lin-, c-Kit+, Sca1+, CD48-, CD150-), MPP2s (Lin-, c-Kit+, Sca1+, CD48+, CD150+), and MPP3/4s (Lin-, c-Kit+, Sca1+, CD48+, CD150-). Sorted MPPs were each labeled with different hashtag oligonucleotide (HTO) conjugated antibodies (Biolegend, TotalSeq™-A Cell Hashing). After 30min incubation cells were washed and the four MPP samples were pooled at equal ratios into a single MPP sample per condition (control, dmPGE2, pIC, GCSF, indo) for library preparation.
scRNA-Seq: Library for HSC_Repl1 were processed according to manufacturer’s recommendations (10X Genomics V2, CG00052 Rev B). Libraries were sequenced on a Next-seq 500 using a 75 cycle kit. Libraries for stimulated HSC and MPP scRNA-Seq samples were processed according to manufacturer’s recommendations (10X Genomics V3, CG000185 Rev B) through Post Gem-RT Cleanup – Dynabeads (step 2.1). At the cDNA amplification step (Step 2.2) an HTO additive primer was added to the amplification mix and steps 2.3A and 2.3B (using 70 µL of SPRI beads) were followed exactly to separate HTOs from cDNAs. cDNA library preparation was finished according to 10x Genomics recommendations. Purified HTO fraction was amplified using SI PCR primer and TruSeq D70x_s indexes according to HTO antibody manufacturer instructions (Biolegend).
scATAC-Seq: For ATAC-seq nuclei were isolated from HSCs and MPPs (pooled MPP, MPP1, MPP2 and MPP3/4) according to manufacturer's recommendations (CG000169 Rev D - Low Cell Input Nuclei Isolation). ScATAC-Seq libraries were prepared using manufacturers recommendations (10x Chromium Single Cell ATAC , CG000168 Rev B). ScRNA-Seq libraries form niche stimulation experiment and scATAC-Seq libraries were sequenced on a NOVAseq 6000 using a 100 cycle kit.

treatment_protocol: For the niche stimulation scRNA-Seq experiment the following treatments were used: Indomethacin (Sigma, 6mg/l) was administered for 7 days in acidified drinking water to maintain stability. Mice were injected with the following drugs and euthanized after 2 hours: Poly(I:C) HMW (Invivogen), IP injection 10mg/kg. G-CSF Recombinant Human Protein (Thermo fisher), IP injection, 0.25mg/kg. DmPGE2 (Cayman), SC injection, 2mg/kg.

value: MPP


title: MPP_dmPGE2

description: stimulation scRNAseq experiment


title: MPP_indo

description: stimulation scRNAseq experiment

value: indomethacin


title: 2815

source_name: Adult human myectomy tissue

value: Obstructive HCM


title: MPP_GCSF

description: stimulation scRNAseq experiment

value: G-CSF


title: 3045


title: VUB06_SC


title: 2930


title: MPP_ct

description: stimulation scRNAseq experiment

value: control


title: Cortex_5

status: Public on Nov 08 2021

city: Solna

first: Thomas

last: Perlmann

address: Solnavägen 1

country: Sweden

institute: Karolinska Institutet

data_processing:
All reads were aligned to the human (hg19) genome using STAR v2.3.0e (Dobin et al. 2013)
Non-uniquely mapped reads were removed using Samtools
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE. Gene annotations used were transcripts in Ensembl ( June 2015)
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression values are provided as rpkms and counts (comma separated text files)

source_name: Human post mortem tissue

extract_protocol:
Neuromelanin-positive dopamine neurons were isolated by laser capture microdissection from post mortem human substantia nigra from Control, PD and ILBD cases. cDNA was generated using Smart-seq2 protocol (Picelli et al. Nature Methods 2013).
Nextera XT DNA sample preparation index kit, 96 indices (Illumina)

value: cortical neuron


title: Cortex_7


title: wild-type neonate scRNA-seq

status: Public on Nov 24 2021

city: Pullman

first: Sean

last: Thompson

state: WA

address: BLS 240

department: School of Molecular Biosciences

institute: Washington State University

description:
WT1 to WT4
Isolated cells were pooled from each sample prior to library construction; both scRNA-seq and scATAC-seq were run in parallel from the same pool of cells.

data_processing:
CellRanger 5.0.0's cellranger function to align Fastq files to mm10 for scRNA-seq.
cellranger-atac 1.2.0 function to align Fastq files to mm10 for scATAC-seq.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Cell Ranger 1.2.0 processing of FASTQ to standard scATAC-seq and scRNA-seq outputs.
Supplementary_files_format_and_content: peaks.bed: peak coordinates for scATAC from the P0 WT mice; default cell ranger output in filtered_peak_bc_matrix folder.
Supplementary_files_format_and_content: barcodes.tsv: single-cell barcodes for P0 WT scATAC; default cell ranger output in filtered_peak_bc_matrix folder.
Supplementary_files_format_and_content: matrix.mtx: filtered peak reads for P0 WT scATAC; default cell ranger output in filtered_peak_bc_matrix folder.
Supplementary_files_format_and_content: unpublished_peaks.bed: peak coordinates for scATAC from a currently unpublished dataset and experiment. This unpublished_peaks.bed is used to create a common set of peak coordinates in order to allow two scATAC-seq dataset Seurat objects to be merged into one Seurat object. The peak coordinates between the two Seurat objects must be the same, so we use these unpublished peak coordinates to create a common set of peak coordinates in order to allow direct merging of these unpublished samples with the P0 WT dataset that is analyzed in this study as part of a manuscript that is currently in progress. The peaks.bed file is genomic coordinates and does not affect the P0 WT sequencing data in any way.
Supplementary_files_format_and_content: singlecell.csv: metadata for P0 WT scATAC.
Supplementary_files_format_and_content: fragments.tsv.gz: peak reads for P0 WT scATAC.
Supplementary_files_format_and_content: fragments.tsv.gz.tbi: indices to quickly call P0 WT scATAC fragments.tsv data into R w/o reading the entire fragments.tsv.gz file into memory.
Supplementary_files_format_and_content: WT_filtered_feature_bc_matrix.h5: P0 WT scRNA reads, barcodes, metadata.

source_name: trunk skin

growth_protocol: Cells were freshly isolated.

extract_protocol:
Cells were isolated from mouse skin samples as in Jensen & Driskell et al. Nature Protocols (2010). Nuclei for scATAC-seq were isolated using an optimized version of 10x Genomics protocol CG000169 Rev D.
10x Genomics Chromium Single Cell 3' Kit V3.

treatment_protocol: No treatment or cell sorting were utilized.

value: trunk skin

value: wild-type

value: postnatal day 0 (P0)


title: 2833


title: Cortex_19


title: 2918


title: Cortex_4


title: Cortex_14


title: Cortex_18


title: Cortex_3


title: Cortex_16


title: Cortex_2


title: Cortex_9


title: Cortex_20


title: Cortex_15


title: Cortex_13


title: DA-I-11-41-6-C

value: neuromelanin-positive dopamine neuron


title: DA-I-11-41-6-B


title: DA-I-11-41-6-A


title: VUB03_3SC


title: Cortex_17


title: DA-I-11-41-5-A


title: Cortex_12


title: Cortex_1


title: DA-I-11-41-5-C


title: DA-I-11-41-2-C


title: Cortex_10


title: DA-I-11-41-2-A


title: DA-I-11-41-1-B


title: DA-I-11-41-1-A


title: Cortex_11


title: DA-I-07-26-2-C


title: DA-I-05-33-5-C


title: DA-I-05-61-6-B


title: DA-I-05-33-5-B


title: DA-I-07-26-6-B


title: DA-I-05-61-5-B


title: DA-I-05-61-1-B


title: DA-I-05-33-6-A


title: DA-I-07-26-5-B


title: DA-I-07-26-6-A


title: DA-I-05-61-5-C


title: DA-I-07-26-6-C


title: DA-I-05-33-2-B


title: DA-I-07-26-5-C


title: DA-I-05-18-6-C


title: DA-I-05-61-6-A


title: DA-I-05-33-5-A


title: DA-I-11-41-1-C


title: DA-I-05-33-6-B


title: DA-I-05-33-2-A


title: DA-I-05-18-6-A


title: DA-I-05-33-1-A


title: DA-I-05-18-6-B


title: TU0081_Lysate

source_name: blood - PBMC

tag: with susceptibiliy allele

value: no

tag: stimulation

value: Lysate

value: PBMC


title: DA-I-05-61-5-A


title: DA-I-05-33-6-C


title: DA-I-05-61-1-C


title: DA-I-05-61-1-A


title: DA-I-05-33-1-B


title: DA-I-05-18-5-B


title: DA-I-05-18-1-B


title: DA-I-05-18-1-A


title: DA-I-05-18-2-A


title: DA-I-04-64-6-A


title: DA-I-04-64-5-C


title: DA-I-04-64-5-B


title: DA-I-05-18-2-B


title: DA-I-04-15-4-B


title: DA-I-04-15-3-B


title: DA-I-04-64-5-A


title: DA-I-05-18-5-C


title: DA-I-05-18-5-A


title: DA-I-04-15-3-A


title: DA-I-04-64-1-B


title: DA-I-04-15-1-B


title: DA-I-04-15-2-B


title: DA-I-05-18-1-C


title: DA-I-04-15-1-A


title: DA-PD-96-36-4-B


title: DA-I-04-64-6-B


title: DA-PD-96-36-4-A


title: DA-PD-96-36-3-B


title: DA-PD-96-36-2-B


title: DA-PD-96-36-2-A


title: DA-PD-96-36-3-A


title: DA-PD-96-36-1-B


title: DA-I-04-64-6-C


title: DA-PD-96-36-1-A


title: DA-I-04-15-4-A


title: DA-PD-95-19-4-B


title: DA-PD-95-19-3-B


title: DA-I-04-15-2-A


title: DA-PD-95-19-3-A


title: DA-PD-95-19-1-A


title: DA-PD-13-29-1-A


title: DA-PD-13-29-3-A


title: DA-PD-12-55-8-A


title: DA-PD-95-19-2-A


title: DA-PD-13-29-4-A


title: DA-PD-95-19-4-A


title: DA-PD-13-29-1-B


title: DA-PD-13-29-2-A


title: DA-PD-95-19-5-A


title: DA-PD-95-19-5-B


title: DA-PD-13-29-4-B


title: DA-PD-13-29-3-B


title: DA-PD-12-55-6-A


title: DA-PD-12-55-5-A


title: DA-PD-13-29-2-B


title: DA-PD-12-55-1-A


title: DA-PD-12-55-3-A


title: DA-PD-12-33-4-A


title: DA-PD-12-33-3-B


title: DA-PD-12-33-4-B


title: DA-PD-12-33-3-A


title: DA-PD-12-33-1-C


title: DA-PD-12-33-2-B


title: DA-PD-12-33-1-B


title: DA-PD-12-22-6-C


title: DA-PD-12-22-6-B


title: DA-PD-12-22-6-A


title: DA-PD-12-55-2-A


title: DA-PD-11-110-6-B


title: DA-PD-12-22-5-B


title: DA-PD-12-22-5-A


title: DA-PD-12-22-2-B


title: DA-PD-12-22-5-C


title: DA-PD-12-22-2-C


title: DA-PD-12-22-2-A


title: DA-PD-11-110-5-A


title: DA-PD-12-22-1-A


title: DA-PD-11-110-5-C


title: DA-PD-11-110-6-A


title: DA-PD-11-110-6-C


title: DA-PD-11-110-2-C


title: DA-PD-11-110-5-B


title: DA-PD-11-110-2-B


title: DA-PD-11-110-2-A


title: DA-PD-11-110-1-C


title: DA-PD-11-110-1-B


title: DA-PD-12-33-2-A


title: DA-PD-11-110-1-A


title: DA-PD-10-83-6-C


title: DA-PD-12-33-1-A


title: DA-PD-10-83-6-B


title: DA-PD-10-83-6-A


title: DA-PD-10-83-5-B


title: DA-PD-12-22-2-B.b


title: DA-PD-12-22-1-B


title: DA-PD-10-83-5-A


title: DA-PD-10-83-2-B


title: DA-PD-10-83-1-B


title: DA-PD-10-27-6-B


title: DA-PD-10-27-5-A


title: DA-PD-10-27-2-B


title: DA-PD-10-27-2-A


title: DA-PD-10-27-1-C


title: DA-PD-10-27-6-A


title: DA-PD-10-27-1-B


title: DA-PD-10-27-5-C


title: DA-PD-10-27-1-A


title: DA-PD-06-44-4-A


title: DA-PD-06-44-5-A


title: DA-PD-06-44-5-B


title: DA-PD-06-44-2-B


title: DA-PD-06-44-2-A


title: DA-PD-06-44-3-A


title: DA-PD-06-44-1-B


title: DA-PD-06-44-1-A


title: DA-PD-03-45-6-B


title: DA-PD-10-83-2-C


title: DA-PD-03-45-6-A


title: DA-PD-03-45-4-A


title: DA-PD-03-45-3-A


title: DA-PD-03-45-5-A


title: DA-PD-10-83-1-C


title: DA-PD-03-45-2-A


title: DA-PD-10-27-6-C


title: DA-PD-03-45-1-A


title: DA-PD-03-43-7-B


title: DA-PD-03-43-7-A


title: DA-PD-03-43-1-B


title: DA-PD-03-43-6-B


title: DA-PD-03-43-5-A


title: DA-C-15-78-3-B


title: DA-C-15-78-4-A


title: DA-C-15-78-2-A


title: DA-C-15-78-2-B


title: DA-PD-03-43-1-A


title: DA-PD-03-43-2-A


title: DA-C-15-78-1-A


title: DA-C-15-60-4-B


title: DA-C-15-60-4-A


title: DA-C-15-78-3-A


title: DA-C-15-60-3-B


title: DA-PD-10-27-5-B


title: DA-C-15-78-4-B


title: DA-C-15-60-3-A


title: DA-C-15-60-1-B


title: DA-C-15-78-1-B


title: DA-C-15-60-2-B


title: DA-C-15-60-1-C


title: DA-C-15-46-4-C


title: DA-C-15-60-1-A


title: DA-C-15-46-4-B


title: DA-PD-03-43-2-B


title: DA-C-15-60-2-A


title: DA-C-15-46-4-A


title: DA-C-15-46-2-B


title: DA-C-15-46-3-B


title: DA-C-15-46-3-A


title: DA-C-15-46-1-B


title: DA-C-15-46-2-A


title: DA-C-15-46-1-A


title: DA-C-14-42-4-B


title: DA-C-14-42-3-B


title: DA-C-14-42-4-A


title: DA-C-14-42-2-A


title: DA-C-14-42-2-B


title: DA-C-12-44-6-C


title: DA-C-14-42-1-B


title: DA-C-14-42-1-A


title: DA-C-12-44-6-B


title: DA-C-12-44-6-A


title: DA-C-12-44-5-C


title: DA-C-12-44-5-A


title: DA-C-12-44-2-C


title: DA-C-12-44-2-A


title: DA-C-12-44-2-B


title: DA-C-12-44-1-A


title: DA-C-10-39-7-A


title: DA-C-12-44-1-C


title: DA-C-10-39-6-B


title: DA-C-10-39-6-A


title: DA-C-10-39-3-A


title: DA-C-09-50-6-C


title: DA-C-09-50-6-B


title: DA-C-10-39-2-A


title: DA-C-09-50-6-A


title: DA-C-09-50-5-C


title: DA-C-14-42-3-A


title: DA-C-09-50-5-A


title: DA-C-09-50-5-B


title: DA-C-09-50-2-C


title: DA-C-09-50-2-B


title: DA-C-09-50-1-A


title: DA-C-12-44-5-B


title: DA-C-07-28-2-B


title: DA-C-07-28-2-A


title: DA-C-07-28-1-B


title: DA-C-07-28-1-A


title: DA-C-06-57-6-A


title: DA-C-06-57-6-C


title: DA-C-06-57-5-B


title: DA-C-06-57-6-B


title: DA-C-06-57-2-A


title: DA-C-06-57-2-B


title: DA-C-06-57-5-C


title: DA-C-06-57-1-B


title: DA-C-06-57-1-A


title: DA-C-04-52-5-C


title: DA-C-04-52-6-A


title: DA-C-04-52-5-A


title: DA-C-04-52-6-C


title: DA-C-04-52-5-B


title: DA-C-06-57-5-A


title: DA-C-09-50-2-A


title: DA-C-04-52-2-B


title: DA-C-04-52-6-B


title: DA-C-04-52-2-C


title: DA-C-04-52-1-B


title: DA-C-04-52-1-A


title: DA-C-09-50-1-B


title: HL7702 shTTP-2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using hisat2 v2.1.0.
The count of per reads were calculated using featureCounts v1.6.2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files.
Supplementary_files_format_and_content: counts.txt

source_name: HL7702 cell line

extract_protocol:
Total RNA was homogenized from tissues or cells with 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.
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: HL7702 shNC-3


title: HL7702 shTTP-1


title: HL7702 shNC-1


title: HL7702 shNC-2


title: Sample_CTRL

status: Public on Nov 02 2021

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, mapped to mm39 genome using Hisat2
Read counts were generated using subread with parameters -t exon - g gene_id
Genome_build: mm39
Supplementary_files_format_and_content: Normalized counts
Supplementary_files_format_and_content: Raw counts

source_name: Hepatocytes

extract_protocol:
Collagenase liver perfusion, FACs sorting removing Cd31 positive cells (endothelial) and cd45 cells (immune cells), followed by sorting for Cxcr2hi hepatocytes (20,000 cells), RNA extracted using TRIZOL
RNA libraries were prepared for sequencing using standard Illumina protocols
Tecan universal plus mRNA-seq

treatment_protocol: one sample was treated with 300 mg/kg acetaminophen, i.p, in saline

value: liver

value: 8 wk

tag: agent


title: Sample_AP-24hr

value: 300 mg/kg acetaminophen


title: Vehicle control treatment, replicate 4

status: Public on Sep 07 2021

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

data_processing:
Raw sequencing reads were filtered by Illumina HiSeq Control Software, only the Pass-Filter (PF) reads were de-multiplexed allowing 1 mismatch and used for further analysis.
The de-multiplexed dataset was processed using Galaxy platform. Specifically, RNA sequence reads are mapped to the mouse genome (Mus musculus GRCm38 genome with NCBI annotation) using RNAstar (v2.6.0b-1).
The transcript is assembled and counted using Cufflinks transcript assembly and FPKM (RPKM) estimates (Galaxy Version 2.2.1.2)
Genome_build: GRCm38_NCBI
Supplementary_files_format_and_content: Tabular file of FPKM estimates

source_name: Mouse mammary tumor treated w/ mock vehicle (corn oil + saline)

extract_protocol:
Mice were euthanized two days after the last treatment. Mammary tumors were collected and snap frozen in liquid nitrogen and store in -80C. The total RNA were prepared using RNAeasy kit from Qiagen.
The poly-A containing RNA transcripts were enriched from one microgram of total RNA for each sample using oligo-dT bead, further fragmented and converted to cDNA and Illumina sequencing library using PrepX RNA-seq library kit on the automated Apollo 324TM NGS Library Prep System (Clontech, CA).
Different DNA barcodes were attached to each library.  The RNA-seq libraries were examined on Agilent Bioanalyzer DNA High Sensitivity chips for size distribution, quantified by Qubit fluorometer (Invitrogen, CA), and pooled at equal molar amount.
The library pools were denatured and sequenced on Illumina HiSeq 2500 Rapid flowcells as single-end 75 nt reads according to manufacturer’s protocol.

treatment_protocol:
Tumor model: Age matched female FVB/N-Tg(MMTV-PyVT);UBC-CreERT+/-;Mtdhfl/fl mice with comparable tumor burden were radonmized to three groups receiving different treatments.
TMX group of mice received 60mg/kg Tamoxifen (reconstituted in corn oil) daily for consecutive 5 days. Tamoxifen activates the CreERT and cleave the flox sites in Mtdh loci, leads to acute Mtdh KO.
C26A6 group of mice received 15mg/kg C26A6, a novel small molecular compound identified to disrupt Mtdh-Snd1 interaction. C26A6 was dosed daily for 5 consecutive days.
Ctrl group of mice received equal volume of mixture of corn oil and saline, daily for 5 days.

value: mammary tumor

value: Female

value: Vehicle control (Corn oil + saline)

tag: time of sampling

value: 2 days after last treatment


title: DA-C-09-50-1-C


title: Vehicle control treatment, replicate 1

tag: tissue


title: Vehicle control treatment, replicate 2

tag: Sex


title: Vehicle control treatment, replicate 3


title: Tamoxifen treatment, replicate 3

source_name: Mouse mammary tumor treated w/ Tamoxifen to induce Mtdh KO

value: Tamoxifen, 60mg/kg, daily x 5 days


title: Tamoxifen treatment, replicate 1


title: C26A6 treatment, replicate 2

source_name: Mouse mammary tumor treated w/ C26A6

value: C26A6, 15mg/kg, daily x 5 days


title: C26A6 treatment, replicate 4


title: C26A6 treatment, replicate 1


title: Normal mammosphere with C26A6 treatment, replicate 2

data_processing:
Raw sequencing reads were filtered by Illumina HiSeq Control Software, only the Pass-Filter (PF) reads were de-multiplexed allowing 1 mismatch and used for further analysis.
The de-multiplexed dataset was processed using Galaxy platform (v2.2.1.2). Specifically, RNA sequence reads are mapped to the mouse genome (Mus musculus GRCm38 genome with NCBI annotation) using RNAstar (v2.7.6a).
The transcript is assembled and counted using Cufflinks transcript assembly and FPKM (RPKM) estimates (v2.0.1).
Genome_build: GRCm38_NCBI
Supplementary_files_format_and_content: Tabular file of FPKM estimates

source_name: Mouse normal mammary epithelial cell

growth_protocol:
Mouse mammary tumor cells were isolated from primary tumor in PyMT mice carrying inducible Mtdh KO (FVB/N-Tg(MMTV-PyVT);UBC-CreERT+/-;Mtdhfl/fl). Mouse normal epithelia cells were isolated from mammary gland from virgin FVB/N mice.
Cells were cultured in serum free media containing mammary epithelia supplements in ultra-low attachement plate. Spheriod structure were developed within 5-14 days.

extract_protocol:
Cells from 3D culture were spin down and the total RNA were prepared using RNAeasy kit from Qiagen.
The poly-A containing RNA transcripts were enriched from one microgram of total RNA for each sample using oligo-dT bead, further fragmented and converted to cDNA and Illumina sequencing library using PrepX RNA-seq library kit on the automated Apollo 324TM NGS Library Prep System (Clontech, CA).
Different DNA barcodes were attached to each library.  The RNA-seq libraries were examined on Agilent Bioanalyzer DNA High Sensitivity chips for size distribution, quantified by Qubit fluorometer (Invitrogen, CA), and pooled at equal molar amount.
The library pools were denatured and sequenced on Illumina HiSeq 6000 SP 100nt Lane v1.5 as paired-end according to manufacturer’s protocol.

treatment_protocol:
Tmx group of cells were treated with 0.02ug/ml 4OH-Tamoxifen for 5 days to induce Mtdh KO
C26A6 group of cells were treated with 200uM C26A6 for 5 days. C26A6 is a novel small molecular compound identified to disrupt Mtdh-Snd1 interaction.
Ctrl group of cells were treated with equal volume of mixture of corn oil and saline for 5 days.

value: Mouse normal mammary epithelial cell

tag: strain/genotype

value: FVB/N-;UBC-CreERT+/-;Mtdhfl/fl

value: C26A6, 200uM x 5days


title: C26A6 treatment, replicate 3


title: Normal mammosphere with ctrl mock treatment, replicate 2


title: Normal mammosphere with C26A6 treatment, replicate 1


title: PyMT tumorsphere with Mtdh KO, replicate 1

source_name: Mouse mammary tumor cell

value: Mouse mammary tumor cell

value: Tamoxifen, 0.02ug/ml x 5days


title: Normal mammosphere with ctrl mock treatment, replicate 1


title: PyMT tumorsphere with wild type Mtdh, replicate 2


title: HL7702 shTTP-3


title: PyMT tumorsphere with wild type Mtdh, replicate 1


title: MD01-005_W4_9

status: Public on Jul 21 2021

city: Baltimore

first: Kellie

middle: Nicole

last: Smith

state: MD

address: 1650 Orleans Street, CRB1, 4M

institute: Johns Hopkins University

data_processing:
Cell Ranger v3.1.0 was used to demultiplex the FASTQ reads, align them to the GRCh38 human transcriptome, and extract their “cell” and “UMI” barcodes. The output of this pipeline is a digital gene expression (DGE) matrix for each sample, which records the number of UMIs for each gene that are associated with each cell barcode.
Supplementary_files_format_and_content: Cell ranger output
Supplementary_files_format_and_content: RDS files include metadata with cell type annotations

source_name: blood

extract_protocol:
Cryobanked T cells were thawed and washed twice with pre-warmed RPMI with 20% FBS and gentamicin. Cells were resuspended in PBS and stained with a viability marker (LIVE/DEAD™ Fixable Near-IR; ThermoFisher) for 15mins at RT in the dark. Cells were the incubated with FC block for 15 mins on ice and stained with antibody against CD3 (BV421, clone SK7) for 30mins on ice. After staining, highly viable CD3+ T cells were sorted into 0.04% BSA in PBS using a BD FACSAria II Cell Sorter. Sorted cells were manually counted using a hemocytometer and prepared at the desired cell concentration (1000 cells/ul), when possible
The Single Cell 5’ V(D)J and 5’ DGE kits (10X Genomics) were used to capture immune repertoire information and gene expression from the same cell in an emulsion-based protocol at the single cell level. Cells and barcoded gel beads were partitioned into nanoliter scale droplets using the 10X Genomics Chromium platform to partition up to 10,000 cells per sample followed by RNA capture and cell-barcoded cDNA synthesis using the manufacturer’s standard protocols. Libraries were generated and sequenced on an Illumina NovaSeq instrument using 2x150bp paired end sequencing. 5’ VDJ libraries were sequenced to a depth of ~5,000 reads per cell, for a total of 5 million to 25 million reads. The 5’ DGE libraries were sequenced to a target depth of ~50,000 reads per cell

tag: patientid

value: lymphocytes

tag: response status

value: MPR


title: MD01-005_W4_6

tag: cell type


title: MD01-005_W4_7


title: MD01-005_W4_5


title: MD01-005_W4_8


title: Tamoxifen treatment, replicate 4

tag: treatment


title: MD01-005_W2_3


title: MD01-005_W2_4


title: MD01-005_M3_14


title: MD01-005_M3_13


title: MD01-005_W2_2


title: MD01-005_M3_11


title: MD01-005_M3_12


title: MD01-005_W4_10


title: MD01-005_W2_1


title: MD01-004_MANA0_4

source_name: tumor

value: Non-MPR


title: PyMT tumorsphere with Mtdh KO, replicate 2


title: MD01-004_Flu0_4


title: MD01-004_MANA10_2


title: MD01-004_MANA0.1_1


title: MD01-004_Flu10_2


title: MD01-004_Flu0.1_1


title: MD043-006_normal_1

source_name: adjacent normal lung


title: MD043-006_tumor_1


title: MD01-005_LN_3

source_name: LN


title: MD01-005_LN_1


title: MD01-005_tumor_8


title: MD01-005_LN_2


title: MD01-005_LN_4


title: MD01-005_tumor_9


title: MD01-005_tumor_4


title: MD01-005_tumor_6


title: MD01-005_normal_3


title: MD01-005_tumor_7


title: MD01-005_tumor_5


title: MD01-005_normal_1


title: MD01-005_normal_5


title: MD01-005_tumor_3


title: MD01-005_normal_2


title: MD01-005_normal_4


title: MD01-005_tumor_2


title: MD043-003_tumor_5


title: MD01-004_Flu1_3


title: MD043-003_tumor_1


title: MD043-003_tumor_2


title: MD01-004_MANA1_3


title: MD043-003_tumor_4


title: MD043-003_normal_2


title: MD043-003_tumor_3


title: Tamoxifen treatment, replicate 2


title: MD043-008_tumor_1


title: NY016-025_tumor_3


title: MD043-008_normal_1


title: NY016-025_normal_1


title: NY016-025_tumor_2


title: NY016-022_tumor_2


title: NY016-022_tumor_1


title: NY016-025_tumor_1


title: NY016-021_tumor_1


title: NY016-015_tumor_2


title: NY016-015_tumor_4


title: NY016-014_tumor_3


title: NY016-014_tumor_2


title: NY016-014_tumor_1


title: NY016-015_normal_1


title: NY016-007_tumor_3


title: NY016-007_tumor_1


title: NY016-025_tumor_4


title: NY016-007_tumor_2


title: MD01-019_normal_2


title: MD01-019_tumor_25


title: MD01-019_tumor_7


title: NY016-022_tumor_4


title: NY016-022_tumor_3


title: MD01-019_tumor_8


title: MD01-019_tumor_6


title: MD01-019_tumor_15


title: MD01-019_tumor_3


title: MD01-019_tumor_17


title: NY016-022_normal_1


title: MD01-019_tumor_10


title: MD01-019_tumor_11


title: NY016-015_tumor_1


title: NY016-015_tumor_3


title: MD01-019_normal_1


title: MD01-019_tumor_13


title: NY016-016_normal_1


title: MD01-019_tumor_1


title: MD043-011_LN_3


title: MD043-011_LN_2


title: MD043-011_normal_5


title: MD043-011_normal_2


title: NY016-007_normal_1


title: MD043-011_normal_4


title: MD043-011_tumor_5


title: MD043-011_tumor_4


title: MD043-011_mettumor_5

source_name: brain metastases


title: MD043-011_tumor_2


title: MD043-011_mettumor_4


title: MD043-011_normal_1


title: MD043-011_mettumor_2


title: MD043-011_mettumor_1


title: MD01-004_LN_3


title: MD01-004_LN_2


title: MD01-010_tumor_1


title: MD01-024_tumor_1


title: MD043-011_normal_3


title: MD043-011_mettumor_3


title: MD01-004_LN_1


title: MD01-004_tumor_1


title: MD01-010_normal_1


title: MD043-011_LN_1


title: MD043-011_tumor_3


title: Bleomycin Nintedanib 7 r3

status: Public on May 05 2021

city: Biberach an der Riss

first: Fidel

last: Ramírez

state: BW

address: Birkendorfer Str. 65

department: Computational Biology

institute: Boehringer Ingelheim Pharma GmbH & Co KG

data_processing:
CellRanger v2 was used to obtain cell matrices per sample. Seurat was used to process matrices.
Supplementary_files_format_and_content: .h5 cell ranger unfiltered count matrices

source_name: lung

extract_protocol:
Lungs were dissociated using the gentleMACS protocol; flushed through a 70 μm cell strainer and washed twice with HBSS/0.5% FCS/0.4% EDTA buffer, Lung immune cells were then isolated according to the Lymphocyte Separation Medium protocol  and cell pellets were washed to prepare cells for single cell RNA-seq.
Handling of the Chromium Controller and library preparation using the Single Cell 3’ Reagent Kits v2 (10x Genomics, Pleasanton, CA) were performed; The Single Cell 3’ Chip was loaded aiming to capture 5,000 cells. cDNA from captured immune cells was amplified during cDNA amplification (13 PCR cycles) and libraries were prepared from 110 ng of cDNA. 13 amplification cycles were performed during the final index PCR reaction. An additional and final cleanup step with 1 volume of SPRISelect Beads (Beckman Coulter, Brea, CA) was performed to remove any left-over primers and primer dimers.
Libraries were on average 450 bp in length and sequencing was performed on a HiSeq 4000 using a HiSeq 3000/4000 PE Cluster Kit and two 50-cycle SBS kits (Illumina, San Diego, CA). Paired-end sequencing included a 26 bp read 1 (16 bp cell barcode and 10 bp UMI), 8 bp index read and 98 bp read 2 (transcript sequence read).

tag: weight

tag: mouse train

value: C57BL/6J males

tag: days after treatment

tag: ntb [50 mg/kg]


title: Control None 7 r3