title: CIA synovial cells scRNA-seq

description: Synovial cells pooled from 3 CIA mice

data_processing:
Single-cell RNA-seq was performed on knee joint synovial cells (3 CIA mice and 9 healthy control mice) on Day 21 after 2nd immunization with a target output of 3,000 cells, then captured with the 10x Genomics Chromium system.  The sequencing library was generated using the 10x Genomics Single Cell 3′ Solution (version 3) kit and subjected to Illumina sequencing (HiSeq 4000).  Alignment, quantitation and aggregation of sample count matrices (CIA + control) were performed using the 10x Genomics Cell Ranger pipeline as the manufacturer’s protocol (GENEWIZ JAPAN Corp.).
Genome_build: mm10
Supplementary_files_format_and_content: Aggregation data of CIA + Control mice synovial cells, the processed data files include barcodes, tsv; features, tsv; matrix, mtx

source_name: Synovial cells

extract_protocol:
Fresh synovial tissue was dissociated in type II collagenase solution (Worthington, 4 mg/mL) at 37 °C for 1 hour with frequent shaking. After the first 30-min incubation, cell suspensions were carefully homogenized by a series of 18G, 21G and 25G needles until the cell suspension passed through the needles smoothly. After digestion, cells were collected by centrifugation and the cell pellet was then treated with ACK buffer (Sigma) to lyse the red blood cells, and then filtered using 100-μm cell strainers to remove the tissue debris to get the single-cell suspensions.
Sequencing libraries were generated using a 10x Genomics Single-cell 3′ Solution (v.3) kit and then subjected to Illumina sequencing (HiSeq 4000)

treatment_protocol: Male DBA/1J mice were first immunized with an emulsion containing 50 μL of chicken type II collagen (Sigma-Aldrich, 4 mg/mL) and 50 μL incomplete Freund’s adjuvant (Difco Laboratories) containing heat-killed Mycobacterium tuberculosis H37Ra (3.3 mg/mL) delivered intradermally at the base of the tail. On day 21, mice were re-challenged with the same emulsion as used in the primary immunization. On day 42, synovial cells were isolated from the knee joints and were subjected to scRNA-seq.

tag: strain

value: arthritic synovium

value: Knee synovial cells of CIA mice (3 weeks after 2nd immunization)


title: ss11_213156, scRNAseq

status: Public on Jul 06 2022

type: SRA

city: London

first: Andrea

last: Streit

address: Guys Hospital, Great Maze Pond

department: Centre for Craniofacial & Regenerative Biology

country: United Kingdom

institute: Kings College London

library_source: transcriptomic

data_processing:
All data was processed using a custom Nextflow pipeline available at https://github.com/alexthiery/otic-reprogramming. All packages and versions are containerised in Docker images called by the pipeline. Full documentation of pipeline parameters and how to reproduce the analysis is available at https://alexthiery.github.io/otic-reprogramming/
Adaptor sequences were trimmed using cutadapt v2.10, aligned using hisat2 v2.2.1, sorted using samtools v1.10, and read counts obtained using htseq v0.12.4.
RNA velocity counts were obtained using Velocyto v0.17.17.
Genome_build: galgal6
Supplementary_files_format_and_content: assayData.csv (raw counts)
phenoData.csv (sample metadata)
gfpData.csv (raw gfp counts)
onefilepercell_ss8-TSS_P2_C10_75_and_others_TVIUH.loom (raw velocyto counts)

molecule: total RNA

organism: Gallus gallus

source_name: Pax2+ cells

growth_protocol: Chick embryos were electroporated and grown at 38°C until reaching the desired stage.

extract_protocol:
EGFP+ single cells were individually collected by FACS into 96 well plates.
Libraries were prepared following SmartSeq2 NexteraXT indications.
single cell RNA seq

treatment_protocol: Chick embryos were electroporated at head fold stage with pTK-Pax2E1-EGFP plasmids.

tag: cell type

value: Pax2+ cells

tag: Stage


title: ss11_212144, scRNAseq


title: E16.5_Dlx5/6-CIE; Rosa-Sp9-OE/+_LGE 2

city: Shanghai

first: Zhenmeiyu

last: Li

address: 138 Yi Xue Yuan Road

country: China

institute: Fudan University

data_processing:
Levels of gene expression were reported in fragments per kilobase of exon per million fragments mapped (FPKM).
Significantly differentially expressed genes were defined on the basis of a false detection rate (FDR) < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: LGE

extract_protocol:
Total RNA was purified with a Mini RNA isolation kit (Zymo)
according to the manufacturer’s protocol (Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Mouse).

value: LGE

tag: genotype

value: Dlx5/6-CIE; Rosa-Sp9-OE/+

tag: age


title: ss11_209108, scRNAseq


title: ss11_207179, scRNAseq


title: Control synovial cells scRNA-seq

city: Tokyo

first: Hiroshi

last: Takayanagi

address: 7-3-1, Hongo, Bunkyo-ku, Tokyo

department: Department of Immunology

country: Japan

institute: The University of Tokyo

description: Synovial cells pooled from 9 healthy control mice

tag: tissue

value: control synovium

value: Knee synovial cells of healthy mice


title: ss11_210120, scRNAseq


title: 111737: RNA-seq Pro-B cell Pax5(+/-)

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description: mRNA-Seq Pro-B cell Pax5(+/-)

data_processing:
ChIP-Seq Sequence Alignment: After sequencing, all reads that passed the Illumina quality filtering were considered for alignment. All samples were aligned to the mouse genome assembly version of December 2011 (GRCm38/mm10) using the Bowtie 2 program version 2.3.5.1 (Langmead, 2012). Read coverages (as displayed in Fig. 3 and Extended Data Fig. 4) were calculated with the BEDTool program version 2.27.1 (Quinlan, 2010), were normalized to reads per millions (RPM) using the SAMTools version 1.9 (Li, 2009) as well as the KentTools version 20190507 [Kuhn, 2013] and were visualized with the UCSC genome browser[Kuhn, 2013].
ChIP-Seq peak calling: Where necessary (e.g. for the comparisons of peak regions), reads were down-sampled to the lowest read number in the samples to be compared, using the Picard tool version 2.18.27 (McKenna, 2010). Peaks were called with the MACS program version 2.2.5 (Zhang, 2008 ), using only the reads of one DNA strand in the case of paired-end read samples, and a Rag2–/– pro-B cell input sample (GSM1145867, GSM1296537) as a control. We filtered all peaks for significance (P value < 10-10) and subsequently assigned them to genes as described[Revilla-i-Domingo, 2012), based on the RefSeq database, which was processed as described below. Peak overlap analyses were performed with the MULTOVL program[Aszódi, 2012]. Read density profiles were drawn with customized R scripts, based on genome-wide peak-centred read coverages.
RNA-Seq sequence alignment: For each sample, the reads of three sequencing runs were concatenated. Only reads that passed the Illumina quality filtering were further processed. Reads were subsequently filtered against rDNA with the Bowtie 2 program[Langmead, 2012]. The remaining reads were aligned with the STAR program version 2.4.2 (Dobin, 2013) to the Mus musculus genome version of December 2011 (GRCm38/mm10). Only uniquely mapping reads were used for gene expression analysis.
RNA-Seq gene annotation: Sequence alignment as well as the database generation of the RefSeq-annotated genes was performed as previously described[Wöhner, 2016]. To refine the annotation of immunoglobulin genes, the immunoglobulin l light-chain segments were replaced with their corresponding converted GRCm38.p3 annotations (Ensembl version 79)[Yates, 2016]. The resulting number of genes was 25,579.
Genome_build: mm10
Supplementary_files_format_and_content: bed = MACS peak coordinates in BED format; bigwig = read coverage (reads per million) in bigWIG format; txt = normalized count values, such as TPMs, in ASCII text format tab delimited.

molecule: polyA RNA

source_name: bone marrow

extract_protocol:
Rneasy Plus Mini Kit, Dynabeads mRNA purification kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pro-B cell

tag: cell preparation

value: Ex-vivo FACS sorted from bone marrow


title: 111738: RNA-seq Pro-B cell Pax5(+/-)

description: mRNA-Seq Pro-B cell Pax5(+/-)


title: ss11_203131, scRNAseq


title: ss11_201107, scRNAseq


title: ss11_206167, scRNAseq


title: ss11_204143, scRNAseq


title: ss11_205155, scRNAseq


title: ss11_202119, scRNAseq


title: 65449: in vitro Pro-B Pax5 Ab ChIP-Seq

description: ChIP-Seq in vitro Pro-B cell Rag2(R31Q/-)

library_source: genomic

molecule: genomic DNA

extract_protocol:
ChIP DNA Clean and Concentrator kit (Zymo Research)
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols

tag: chip antibody

value: anti-Pax5 (rabbit polyclonal Ab, detecting the paired domain (amino acids 17-145) (16); Busslinger laboratory)

value: in vitro Pro-B cell


title: ss11_211132, scRNAseq


title: 111741: RNA-seq Progenitor cell Pax5(fl/fl) Vav-Cre

description: mRNA-Seq Progeninor cell Pax5(fl/fl) Vav-Cre

value: Progenitor cell

value: Pax5(fl/fl) Vav-Cre


title: ss11_296189, scRNAseq


title: ss11_214168, scRNAseq


title: 111726: RNA-seq Progenitor cell Pax5(fl/fl) Vav-Cre


title: ss11_295120, scRNAseq


title: ss11_296108, scRNAseq


title: ss11_208191, scRNAseq


title: ss11_295177, scRNAseq


title: ss11_293153, scRNAseq


title: ss11_293144, scRNAseq


title: ss11_292156, scRNAseq


title: ss11_291168, scRNAseq


title: ss11_292141, scRNAseq


title: 111736: RNA-seq Pro-B cell Pax5(+/+)

description: mRNA-Seq Pro-B cell Pax5(+/+)


title: ss11_290117, scRNAseq


title: 111735: RNA-seq Pro-B cell Pax5(+/+)

description: mRNA-Seq Pro-B cell Pax5(+/+)


title: 111740: RNA-seq Pro-B cell Pax5(R31Q/-)

description: mRNA-Seq Pro-B cell Pax5(R31Q/-)


title: ss11_291129, scRNAseq


title: ss11_290180, scRNAseq


title: ss11_294132, scRNAseq


title: 65448: in vitro Pro-B Pax5 Ab ChIP-Seq

description: ChIP-Seq in vitro Pro-B cell Rag2(-/-)


title: ss11_288109, scRNAseq


title: WT_mESC_2

city: Illkirch CEDEX

first: Veronique

last: Fischer

address: 1 Rue Laurent Fries

country: France

institute: IGBMC

description:
Very similar material as project S19062: The material is nascent, 4sU-labelled RNA purified using a biotinylation procedure from a mixture of 90X mouse embryonic stem cells and 10X yeast cells. The yeast RNA serves as a spike-in control. Prior to the purification of the nascent RNA, the RNA was fragmented using Covaris to an average RNA size of ~1 kb. No Ribozero required.
VQFR26

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed using CUTADAPT 1.10 in order to remove adaptors and low-quality sequences and reads shorter than 40 bp were removed for further analysis. rRNA sequences were removed for further analysis. For samples VQFR25, VQFR26, VQFR29, VQFR30, remaining reads were aligned to a hybrid genome composed of mm10 and ASM294v2 assemblies of M. musculus and S. pombe genomes respectively with STAR 2.5.3a. For samples VQFR188, VQFR189, VQFR191, VQFR192, the hybrid genome was composed of hg38 and ASM294v2 assemblies of H. sapiens and S. pombe genomes respectively. Gene quantification was performed with htseq-count 0.6.1p1, using “union” mode and Ensembl 93 annotations for all organisms except for S. pombe where Ensembl Fungi 41 annotations were used. For 4sU-seq data, “type” option was set to “gene” in order to take also into account reads aligned onto introns. Differential gene expression analysis was performed using DESeq2 1.16.1 Bioconductor R package on H. sapiens or M. musculus counts normalized with size factors computed by the median-of-ratios method proposed by Anders and Huber based on the spike-in counts (using the following options: cooksCutoff=TRUE, independentFiltering=TRUE, alpha=0.05). P-values were adjusted for multiple testing using the Benjamini and Hochberg method.
Genome_build: hg38 for human data, mm10 for mouse data
Supplementary_files_format_and_content: alldata*txt: raw counts, norm. counts, DESeq2 results
Supplementary_files_format_and_content: spike*txt: raw counts of spike-in RNA from S. pombe

growth_protocol: Mouse ES E14 cells were cultured on plates coated with 0.1% gelatine solution in 1x PBS using DMEM medium supplemented with 15% foetal calf serum ES-tested, 2 mM ʟ-glutamine, 0.1% β-mercaptoethanol, 100 UI/ml penicillin and 100 μg/ml streptomycin, 0.1 mM non-essential amino acids, 1500 U/ml leukaemia inhibitory factor, 3 μM CHIR99021 and 1 μM PD0325901. Cells were grown at 37°C with 5% CO2 levels. S. pombe cells were grown in autoclaved YES medium (yeast extract, adenine, histidine, uracil, leucine, lysine, 3% glucose) at 32°C.

extract_protocol:
We purify newly transcribed RNA by adding 4sU (4-thiouridine), a metabolic analogue of uridine, to the cell culture medium for 15 minutes before collecting the cells. The cells readily take up 4sU and incorporate it into RNA transcribed during the time period of 15 minutes. This protocol is used to label newly transcribed RNA in both, human U2OS cells and mouse embryonic stem cells. 4tU was used to label newly synthesized RNA from S. pombe cells which served as a external spike-in for normalization. The incorporation of 4sU (with its specific thiol group) into newly transcribed RNA allows to separate the 4sU-containing RNA from the total RNA using biotinylation and Streptavidin-coated beads. The total RNA, used for the purification of the 4sU-containing RNA, was fragmented prior to purification (into on average ~700 bp fragments).
For mESC, 4sU RNA-seq libraries were generated from 15 ng of purified, newly synthesized RNA using TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo-Zero Gold (Illumina, San Diego, CA, Cat# RS-122-2301) according to the Illumina protocol with the following modifications. 4sU-labelled RNA was cleaned up using 1.8X RNAClean XP beads and fragmented using divalent cations at 94°C for 1 minutes without depletion of rRNA. While, double stranded cDNA synthesis and adapter ligation were performed according to manufacturer instructions, the number of PCR cycles for library amplification was reduced to 10 cycles. After purification using SPRIselect beads (Beckman-Coulter, Villepinte, France, Cat# B23319), the libraries were sequenced with 1x 50 base pairs on a HiSeq4000 machine (Illumina).

value: WT mESC

value: embryonic stem cells

tag: molecule subtype

value: 4sU RNA (newly synthesized RNA)


title: ss11_287121, scRNAseq


title: 111739: RNA-seq Pro-B cell Pax5(R31Q/-)

description: mRNA-Seq Pro-B cell Pax5(R31Q/-)


title: ss11_286164, scRNAseq


title: Supt3hKO_mESC_2

description:
Very similar material as project S19062: The material is nascent, 4sU-labelled RNA purified using a biotinylation procedure from a mixture of 90X mouse embryonic stem cells and 10X yeast cells. The yeast RNA serves as a spike-in control. Prior to the purification of the nascent RNA, the RNA was fragmented using Covaris to an average RNA size of ~1 kb. No Ribozero required.
VQFR30

value: Supt3h KO mESC


title: ss11_289192, scRNAseq


title: ss11_289105, scRNAseq


title: ss11_294165, scRNAseq


title: ss11_288188, scRNAseq


title: WT_mESC_1

description:
Very similar material as project S19062: The material is nascent, 4sU-labelled RNA purified using a biotinylation procedure from a mixture of 90X mouse embryonic stem cells and 10X yeast cells. The yeast RNA serves as a spike-in control. Prior to the purification of the nascent RNA, the RNA was fragmented using Covaris to an average RNA size of ~1 kb. No Ribozero required.
VQFR25


title: ss11_287176, scRNAseq


title: ss11_286133, scRNAseq


title: Supt3hKO_mESC_1

description:
Very similar material as project S19062: The material is nascent, 4sU-labelled RNA purified using a biotinylation procedure from a mixture of 90X mouse embryonic stem cells and 10X yeast cells. The yeast RNA serves as a spike-in control. Prior to the purification of the nascent RNA, the RNA was fragmented using Covaris to an average RNA size of ~1 kb. No Ribozero required.
VQFR29


title: mm_rna_spreB.5

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

country: USA

institute: University of Illinois at Chicago

description:
Ex Vivo Sorted WT small pre B cells
rna_counts.txt
mm9_plus_ig.gtf

data_processing:
RNA-seq: Raw reads were aligned to reference genome mm9 in a splice aware manner using STAR (Dobin et al., 2013; Dobin and Gingeras, 2015). Gene expression was quantified using featureCounts within the RSubread R package (Liao et al., 2019) against UCSC genes with Ensembl Ig genes from mm10 converted to mm9 coordinates with UCSC liftOver. GTF file is included in the submission.
ATAC-seq: Raw reads were aligned to the reference genome using BWA MEM, and apparent PCR duplicates removed using Picard MarkDuplicates. Read alignments were first adjusted to account for TAC transposon binding: +4 bp for +strand alignments, −5 bp for −strand alignments. The open chromatin enrichment track was generated by first creating a bedGraph from the raw reads using bedtools genomcov, then converted to bigWig using UCSC tool bedGraphToBigWig; tracks were normalized by the sum of alignment lengths over 1 billion. Open chromatin peaks were called using Macs2 (Zhang et al., 2008) with no model set and no background provided; peaks with a score of >5 were retained.
Genome_build: mm9
Supplementary_files_format_and_content: GTF formatted file: gene annotations used for RNA-seq. UCSC genes for mm9 + Ig genes from Ensembl mm10, lifted over to mm9
Supplementary_files_format_and_content: BED formatted file: peak calls for ATAC-seq
Supplementary_files_format_and_content: BigWig formatted file: normalized enrichment of open chromatin for ATAC-seq
Supplementary_files_format_and_content: Tab-delimited text formatted file: unnormalized counts per gene

growth_protocol: B cell progenitors (B220+IgM−) from WT, Igkdel , k-mac mice were isolated from BM with a MACS separation column (Miltenyi Biotec) and cultured in complete Opti-MEM containing 10% (v/v) FBS and IL-7 (16 ng ml−1) for 5 d.

extract_protocol:
RNA-seq: FACS sorted cells from small pre-B and immature B cells isolated from WT, Igkdel k-mac, k-mac CXCR4fl/fl and k-mac CXCR4fl/fl mb1-cre+ mice and total RNA isolated using Trizol (15596026, Invitrogen) following the protocol described by the Immunological Genome Project (Immgen.org).
RNA-seq: Libraries were generated TruSeq® Stranded mRNA Sample Prep” kit from Illumina and the associated user manual
ATAC-seq: 1.2x105 small pre-B and immature B cells sorted from WT, Igkdel k-mac, k-mac CXCR4fl/fl and k-mac CXCR4fl/fl mb1-cre+ mice were used for ATAC-seq. Cells were centrifuged at 500g at 4°C for 5 minutes, washed with 1X PBS, and centrifuged again. Cells were resuspended in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g at 4°C for 10 minutes. Pellet was resuspended in transposition reaction buffer (25ml 2x Tagment Buffer (FC-121-1030, Illumina), 2.5ml Tagment DNA Enzyme, 22.5ml nuclease free H2O) for 30 minutes at 37°C.
ATAC-seq: DNA was purified with a Qiagen MinElute Kit and amplified with Nextera PCR Primers (Illumina Nextera Index Kit) and NEBNext PCR Master Mix (M0541, New England BioLabs) for 11 cycles. Amplified DNA was purified with a Qiagen PCR cleanup kit. Libraries were sequenced on a NextSeq 550 sequencer at University of Chicago Genomics Facility.

treatment_protocol: After growth phase cells were cultured for 72 hours with 16 ng ml−1 IL-7 (+IL-7), 0.2 ng ml−1 IL-7 (−IL-7) or 0.2 ng ml−1 IL-7 with 100 ng CXCL12 (−IL-7+CXCL12).

tag: sample group

value: small Pre-B


title: mm_rna_spreB.6


title: ss11_285145, scRNAseq


title: KP4-T100-MYC-rep-2

city: San Francisco

first: Mirunalini

last: Ravichandran

state: CA

address: 513 Parnassus Avenue, HSW 1301

department: Anatomy

institute: University of California, San Francisco

data_processing:
ChIP-seq FASTQ’s were mapped and peak-called using ENCODE’s chip-seq-pipeline2 (https://github.com/ENCODE-DCC/chip-seq-pipeline2) from 2 biological replicate and their replicates.
IDR-Optimal peak set at a threshold of 5% was used for ChIP-experiment specific analysis.
Using GencodeV38’s ‘All’ Comprehensive Gene Annotation for GrCh38.p13 and the lysosomal geneset and MYC target geneset, promoter regions were designated as +/- 1kb from each TSS.
Using deepTools bamCompare, ChIP-input normalized bigwig files were generated with options: --binSize 50 –scaleFactorsMethod None –normalizeUsing CPM –smoothLength 1000 –extendReads 275 –centerReads.
Profile plots were generated using deepTools computeMatrix with options: --referencePoint center -a 2000 -b 2000 –skipZeros. The original MACS2 narrowpeak peaksets were also sorted by signalValue score for unique gene promoters from highest to lowest for further analysis of the top scoring genes.
Assembly: hg38
Supplementary files format and content: bigwig files

organism: Homo sapiens

growth_protocol: Cells were cultured in DMEM media supplemented with 10% FBS, 1% Pencillin/Streptomycin and 15mM HEPES.

extract_protocol:
ChIP lysates were prepared from 2X10^7 cells. Cells were fixed in 1% formaldehyde for 10min and lysed for 10min. The lysed cells were sonicated using Covaris Focused Sonicator at 4°C. Chromatin was subjected to ChIP using 3µg of antibody and incubated overnight at 4°C. Protein A Dynabeads was added to the chromatin and incubated for 2 hours, followed by sequential washing with ice-cold RIPA buffer containing 150 mM salt (50mM Tris-HCl pH 8, 0.15M NaCl, 1mM EDTA pH 8, 0.1% SDS, 1%  Triton X-100, 0.1% sodium deoxycholate), 500 mM salt (50mM Tris-HCl pH 8, 0.5M NaCl, 1mM EDTA pH 8, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate), twice with lithium chloride buffer (50mM Tris-HCl pH 8, 1mM EDTA pH 8, 1% Nonidet P-40, 0.7% sodium deoxycholate, 0.5M LiCl2) and 1xTE buffer (10mM Tris-HCl pH 8, 1mM EDTA pH 8). DNA was eluted for 4h at 55°C and reverse crosslinked overnight with Proteinase K at 65°C followed by phenol/chloroform extraction and ethanol precipitation. Eluted DNA was used for library preparation.
Libraries were prepared using Illumina DNA Flex library preparation method following the manufacturer’s protocol.

treatment_protocol: Cells were treated with DMSO or 100nM Trametinib for 48h.

tag: cell line

value: Human pancreatic ductal adenocarcinoma cells

tag: treatment

value: 100nM Trametinib (48h)


title: KP4-T100-TFE3-rep-1

value: TFE3 (Sigma, HPA023881)


title: KP4-T100-TFE3-rep-2


title: ss11_283128, scRNAseq

value: Pax2+ cells


title: ss11_280110, scRNAseq


title: ss11_283169, scRNAseq


title: ss11_282116, scRNAseq


title: ss11_282181, scRNAseq


title: ss11_284157, scRNAseq


title: ss11_281104, scRNAseq


title: ss11_279175, scRNAseq


title: ss11_284140, scRNAseq


title: KP4-T100-MYC-rep-1


title: KP4-T100-Input-rep-1


title: ss11_281193, scRNAseq


title: ss11_277151, scRNAseq


title: ss11_278134, scRNAseq


title: ss11_280187, scRNAseq


title: ss11_278163, scRNAseq


title: ss11_277146, scRNAseq


title: KP4-DMSO-TFE3-rep-2

value: DMSO (48h)


title: KP4-DMSO-TFE3-rep-1


title: ss11_275170, scRNAseq


title: ss11_276139, scRNAseq


title: ss11_275127, scRNAseq


title: ss11_279122, scRNAseq


title: KP4-DMSO-MYC-rep-1


title: ss11_274182, scRNAseq


title: KP4-T100-Input-rep-2


title: ss11_274115, scRNAseq


title: ss11_272111, scRNAseq


title: ss11_271123, scRNAseq


title: ss11_272186, scRNAseq


title: ss11_270162, scRNAseq


title: ss11_285152, scRNAseq


title: ss11_273194, scRNAseq


title: ss11_269147, scRNAseq


title: Mia cells-T100-rep.2

data_processing:
Sequencing reads were aligned to the human reference genome (GRCh38) and reads per gene matrix were counted using the latest Ensemble annotation build using STAR
Read counts per gene were used as input to DESeq2 to test for differential gene expression between conditions using a Wald test, while correcting for possible covariates.
Genes passing a multiple testing correct p-value of 0.1 (FDR method) were considered significant.
Assembly: hg38
Supplementary files format and content: tab-delimited text file of raw read counts

extract_protocol:
Total RNA was extracted using PureLink RNA Mini Kit.
Illumina compatible RNA-sequencing libraries were created from purified RNA using the Tecan Universal mRNA Plus kit


title: ss11_269150, scRNAseq


title: Mia cells-T100-rep.1


title: ss11_276158, scRNAseq


title: ss11_270135, scRNAseq


title: ss11_273103, scRNAseq


title: ss11_268159, scRNAseq


title: Mia cells-T100-rep.3


title: Mia cells-DMSO-rep.3


title: ss11_267171, scRNAseq


title: ss11_268138, scRNAseq


title: KP4-DMSO-MYC-rep-2


title: KP4-DMSO-Input-rep-1


title: ss11_265195, scRNAseq


title: KP4-DMSO-Input-rep-2


title: Mia cells-DMSO-rep.2


title: KP4 cells-T100-rep.3


title: Mia cells-DMSO-rep.1


title: KP4 cells-T100-rep.2


title: ss11_264185, scRNAseq


title: ss11_266183, scRNAseq


title: ss11_263173, scRNAseq


title: KP4 cells-T100-rep.1


title: KP4 cells-DMSO-rep.3


title: ss11_265102, scRNAseq


title: ss11_261149, scRNAseq


title: KP4 cells-DMSO-rep.2


title: KP4 cells-DMSO-rep.1


title: ss11_262136, scRNAseq


title: ss11_267126, scRNAseq


title: ss11_264112, scRNAseq


title: Treated peritoneal metastasis patient 3 [22_T_PER_PT3]

city: Zwijnaarde

first: Jordy

last: De Coninck

address: Technologiepark 71

department: Department of Biomedical Molecular Biology

country: Belgium

institute: University Gent

data_processing:
Data was processed using the Cell Ranger count pipeline (version 2.0.2 or 2.1.1)
Assembly: hg19 (Human)
Supplementary files format and content: h5 file containing raw gene counts (output from Cell Ranger count)

source_name: metastasis

extract_protocol: All methods are listed in Loret et al. Distinct transcriptional programs of ascitic and solid cancer cells induce a different response to chemotherapy in high-grade serous ovarian cancer. 2022

tag: patient

value: Patient 3

tag: disease state

value: High-grade serous ovarian cancer (HGSOC)

value: peritoneal metastasis

value: chemotreated

tag: platform

value: 10x Genomics - v2

tag: number of cells


title: ss11_259172, scRNAseq


title: ss11_262161, scRNAseq


title: ss11_263124, scRNAseq


title: ss11_266114, scRNAseq


title: ss11_261148, scRNAseq


title: ss11_260160, scRNAseq


title: ss11_260137, scRNAseq


title: Treated omental metastasis patient 3 [21_T_OM_PT3]

treatment_protocol: All methods are listed in Loret et al. Distinct transcriptional programs of ascitic and solid cancer cells induce a different response to chemotherapy in high-grade serous ovarian cancer. 2022

value: omental metastasis


title: ss11_258184, scRNAseq


title: ss11_259125, scRNAseq


title: ss11_257196, scRNAseq


title: ss11_258113, scRNAseq


title: ss11_257101, scRNAseq


title: Treated ascites patient 3 [20_T_A_PT3]

source_name: ascites

value: ascites


title: ss11_256196, scRNAseq


title: Treated ovarian tumor patient 3 [19_T_OT_PT3]

source_name: ovarian tumor

value: ovarian tumor


title: ss11_256101, scRNAseq


title: ss11_271174, scRNAseq


title: Naive peritoneal metastasis patient 3 [18_N_PER_PT3]

value: naive


title: Naive ascites patient 3 [17_N_A_PT3]


title: ss11_254125, scRNAseq


title: ss11_254172, scRNAseq


title: ss11_255184, scRNAseq


title: Naive ovarian tumor patient 3 [16_N_OT_PT3]


title: ss11_253160, scRNAseq


title: Treated peritoneal metastasis patient 2 [15_T_PER_PT2]

value: Patient 2


title: ss11_252149, scRNAseq


title: ss11_251161, scRNAseq


title: Treated ovarian tumor patient 2 [13_T_OT_PT2]


title: ss11_250173, scRNAseq


title: ss11_251136, scRNAseq


title: Treated omental metastasis patient 2 [14_T_OM_PT2]


title: Naive omental metastasis patient 2 [12_N_OM_PT2]


title: ss11_250124, scRNAseq


title: ss11_249185, scRNAseq


title: ss11_249112, scRNAseq


title: Naive ascites patient 2 [11_N_A_PT2]


title: ss11_253137, scRNAseq


title: ss11_255113, scRNAseq


title: ss11_247183, scRNAseq


title: Treated ascites patient 1 [9_T_A_PT1]

value: Patient 1


title: ss11_247114, scRNAseq


title: Naive ovarian tumor patient 2 [10_N_OT_PT2]


title: ss11_246171, scRNAseq


title: Treated peritoneal metastasis patient 1 [7_T_PER_PT1]


title: ss11_252148, scRNAseq


title: ss11_248102, scRNAseq


title: ss11_246126, scRNAseq


title: ss11_245138, scRNAseq


title: Treated omental metastasis patient 1 [8_T_OM_PT1]


title: ss11_244147, scRNAseq


title: ss11_245159, scRNAseq


title: ss11_244150, scRNAseq


title: ss11_243135, scRNAseq


title: ss11_243162, scRNAseq


title: Naive urinary bladder metastasis patient 1 [5_N_BL_PT1]

value: urinary bladder metastasis


title: ss11_241111, scRNAseq


title: ss11_242174, scRNAseq


title: Naive omental metastasis patient 1 [4_N_OM_PT1]


title: ss11_240194, scRNAseq


title: ss11_240103, scRNAseq


title: ss11_241186, scRNAseq


title: Naive peritoneal metastasis patient 1 [3_N_PER_PT1]


title: Naive ascites patient 1 [2_N_A_PT1]


title: Treated ovarian tumor patient 1 [6_T_OT_PT1]


title: ss11_239182, scRNAseq


title: Naive ovarian tumor patient 1 [1_N_OT_PT1]


title: ss11_248195, scRNAseq


title: ss11_237158, scRNAseq


title: ss11_239115, scRNAseq


title: ss11_238170, scRNAseq


title: ss11_236151, scRNAseq


title: ss11_234175, scRNAseq


title: ss11_238127, scRNAseq


title: ss11_235134, scRNAseq


title: ss11_234122, scRNAseq


title: ss11_237139, scRNAseq


title: ss11_242123, scRNAseq


title: ss11_235163, scRNAseq


title: ss11_236146, scRNAseq


title: ss11_231181, scRNAseq


title: ss11_233187, scRNAseq


title: ss11_231116, scRNAseq


title: ss11_233110, scRNAseq


title: ss11_232193, scRNAseq


title: ss11_230169, scRNAseq


title: ss11_228152, scRNAseq


title: ss11_230128, scRNAseq


title: ss11_227133, scRNAseq


title: ss11_227164, scRNAseq


title: ss11_224192, scRNAseq


title: ss11_225188, scRNAseq


title: C 3

city: Hefei

first: Dongyao

last: Wang

state: Anhui

address: Department of Hematology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

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

value: Blood

value: sepsis

tag: Sex

value: Female


title: A

institute: University of Science and Technology of China

value: Healthy

value: Male


title: ss11_229140, scRNAseq

value: Pax2+ cells


title: ss11_229157, scRNAseq


title: ss11_226121, scRNAseq


title: ss11_223180, scRNAseq


title: ss11_222168, scRNAseq


title: C 5


title: ss11_232104, scRNAseq


title: C


title: ss11_221141, scRNAseq


title: B


title: ss11_228145, scRNAseq


title: ss11_220153, scRNAseq


title: ss11_226176, scRNAseq


title: ss11_223117, scRNAseq


title: C 1


title: H3K36me3-1mM

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

institute: University of Rochester

data_processing:
alignment: bowtie2
peak calling: MACS
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph or bed files for the output by MACS

source_name: Hela

growth_protocol: Hela cells were cultured on uncoated plate in DMEM medium with 10% fetal bovine serum.

extract_protocol:
Histone-DNA complexes were isolated with antibody from sonicated whole cell lysate.
Libraries were prepared according to NEBNext Ultra II DNA Library Prep kit.

treatment_protocol: Cells were treated with 1mM H2O2 for 30min.

value: treat with 1mM H2O2 for 30min

value: Hela cell

value: H3K36me3 (Abcam, Ab9050)


title: ss11_225109, scRNAseq


title: ss11_221156, scRNAseq


title: ss11_224105, scRNAseq


title: ss11_222129, scRNAseq


title: input

value: untreat


title: ss11_220144, scRNAseq


title: ss11_219132, scRNAseq


title: ss11_219165, scRNAseq


title: ss11_218120, scRNAseq


title: ss11_217189, scRNAseq


title: ss11_218177, scRNAseq


title: MSH6-0mM


title: MSH6-1mM


title: ss11_217108, scRNAseq


title: ss11_216191, scRNAseq


title: H3K36me3-0mM


title: ss11_214167, scRNAseq


title: ss11_213155, scRNAseq


title: SETD2-0mM

value: Hela cell with a flag tag KI in SETD2 protein

value: Flag (Sigma, F7425)


title: ss11_215179, scRNAseq


title: ss11_214130, scRNAseq


title: ss11_216106, scRNAseq


title: ss11_215118, scRNAseq


title: ss11_213142, scRNAseq


title: OVM4 (miRNA-seq)

first: Jie

last: Yu

address: No. 639, Zhizaoju road, Huangpu district

department: Department of Ophthalmology

institute: Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology

data_processing:
We generated bw files using Deeptools, which can convert Bam file to bw files.
Genome_build: Hg38
Supplementary_files_format_and_content: bw

source_name: orbital venous malformation

extract_protocol:
Small RNA Sample Prep kit (Illumina) was employed to construct libraries according to the manufacturer’s instructions. Library quality control was validated by Agilent 2100 Bioanalyzer (Agilent Technologies) and sequencing was conducted on Hiseq X Ten.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: vascular tissues

tag: diagnosis

value: orbital venous malformation


title: ss11_212143, scRNAseq

tag: cell type


title: OVM2 (miRNA-seq)


title: ss11_212154, scRNAseq

tag: Stage


title: ss11_211166, scRNAseq


title: OVM3 (miRNA-seq)


title: ss11_211131, scRNAseq


title: ss11_210178, scRNAseq


title: OVM1 (miRNA-seq)


title: Control4 (miRNA-seq)

source_name: normal orbital vascular tissues

value: normal orbital vascular tissues


title: Control3 (miRNA-seq)


title: ss11_210119, scRNAseq


title: ss11_209190, scRNAseq


title: SETD2-1mM


title: ss11_206166, scRNAseq


title: ss11_208107, scRNAseq


title: Control2 (miRNA-seq)


title: ss11_207178, scRNAseq


title: ss11_207119, scRNAseq


title: ss11_208190, scRNAseq


title: ss11_204155, scRNAseq


title: ss11_205143, scRNAseq


title: Control1 (miRNA-seq)


title: OVM2 (RNA-Seq)

data_processing:
Illumina Casava1.7 software used for basecalling.
We generated bw files using Deeptools, which can convert Bam file to bw files.
Genome_build: Hg38
Supplementary_files_format_and_content: bw

extract_protocol:
Total RNA was isolated from OVM samples of four patients and four control individuals using a mirVana miRNA Isolation Kit (Ambion) according to the manufacturer’s protocol. Then, cDNA libraries were built by TruSeq stranded total RNA kit with Ribo‐Zero Gold (Illumina) following the manufacturerʼs instructions. A quality validation of the libraries was performed using Agilent 2100 Bioanalyzer (Agilent Technologies) and high-throughput RNA-seq of these libraries was performed on the Illumina sequencing platform (HiSeqTM2500).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: OVM4 (RNA-Seq)


title: ss11_206131, scRNAseq


title: Control4 (RNA-Seq)


title: ss11_201191, scRNAseq


title: ss11_205154, scRNAseq


title: ss11_202179, scRNAseq


title: OVM3 (RNA-Seq)


title: ss11_209107, scRNAseq


title: Control2 (RNA-Seq)


title: ss11_203167, scRNAseq


title: ss11_204142, scRNAseq


title: ss8_P3H5, scRNAseq


title: ss8_P3H7, scRNAseq


title: OVM1 (RNA-Seq)


title: Control3 (RNA-Seq)


title: ss11_203130, scRNAseq


title: ss11_202118, scRNAseq


title: Drug3_Liver

city: New York City

first: Nathaniel

last: Kastan

address: 1305 York Ave

institute: Tri-institutional MD-PHD program, Weill Cornell

data_processing:
Transcript Quantification with Salmon (version 0.8.2)
Normalization and rlog transformation of raw read counts in genes were performed using DESeq2 (version 1.20.0)
Geneset enrichment analysis was conducted using clusterProfiler (version 3.18.1)
Genome_build: Bsgenome.Mmusculus.UCSC.mm10 (version 1.4.0) and TxDb.Mmusculus.UCSC.mm10.knownGene (version 3.4.0)
Supplementary_files_format_and_content: quant.sf Salmon quantification files

extract_protocol:
Rneasy QIAGEN kits
TruSeq stranded mRNA kit

treatment_protocol: IP injection 200mg/kg of LKI-2

tag: strain

value: Swiss Webster

value: 6-8 weeks

value: Liver tissue hemogenates

tag: agent

value: 200mg/kg of LKI-2


title: ss11_201106, scRNAseq


title: ss8_P3H2, scRNAseq


title: ss8_P3H12, scRNAseq


title: Drug2_Liver

tag: age

tag: tissue


title: ss8_P3H8, scRNAseq


title: ss8_P3H11, scRNAseq


title: Drug1_Liver


title: ss8_P3H9, scRNAseq


title: ss8_P3H6, scRNAseq


title: Control1 (RNA-Seq)


title: ss8_P3H4, scRNAseq


title: Drug1_Heart

value: Heart tissue hemogenates


title: ss8_P3H3, scRNAseq


title: ss8_P3H1, scRNAseq


title: Drug3_Heart


title: Ctrl3_Liver


title: ss8_P3G6, scRNAseq


title: ss8_P3G5, scRNAseq


title: Drug2_Heart


title: ss8_P3H10, scRNAseq


title: ss8_P3G9, scRNAseq


title: ss8_P3G11, scRNAseq


title: MBM05_sc [TCR-Seq]

city: New York

first: Jana

last: Biermann

state: New York

address: 622 W168th Street

institute: Columbia University

description: Single-cell RNA sequencing; TCR-seq

data_processing:
Fastq files were analyzed using vdj in Cell Ranger (v6.1.1, 10x Genomics). Transcripts were aligned to the human GRCh38 reference genome.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger vdj output files (csv)
Library strategy: TCR-seq

source_name: Melanoma brain metastasis

extract_protocol:
Melanoma brain metastases from surgical resections were dissociated using the human tumor dissociation kit from Miltenyi and viable CD45+/CD15-/CD66b- populations were sorted. Of each sorting population 15,000 cells were loaded for droplet-based RNA capture and reverse transcription using 10x Genomics 5’ reagents and a Chromium controller.
Single-cell TCR sequencing libraries were generated using Chromium 5’ VDJ reagents and T cell enrichment kit according to the manufacturer protocol.

tag: metastatic site

value: MBM

tag: patient id

tag: mutation status

tag: sequencing technique

value: scRNA-seq

tag: tcr-seq

value: yes


title: ss8_P3G7, scRNAseq

value: Pax2+ cells


title: ss8_P3G10, scRNAseq


title: ss8_P3G4, scRNAseq


title: MBM04_sc [TCR-Seq]

description: Single-cell RNA sequencing; TCR-seq


title: ss8_P3G8, scRNAseq


title: Ctrl1_Liver


title: ss8_P3F9, scRNAseq


title: ss8_P3G2, scRNAseq


title: ss8_P3F7, scRNAseq


title: ss8_P3F8, scRNAseq


title: ss8_P3G1, scRNAseq


title: Ctrl2_Liver


title: Ctrl1_Heart


title: ss8_P3G3, scRNAseq


title: Ctrl3_Heart


title: MBM03_sc [TCR-Seq]

description: Single-cell RNA sequencing; TCR-seq


title: Ctrl2_Heart


title: ss8_P3F5, scRNAseq


title: ss8_P3F6, scRNAseq


title: MBM01_sc [TCR-Seq]

description: Single-cell RNA sequencing; TCR-seq


title: ss8_P3G12, scRNAseq


title: ss8_P3F2, scRNAseq


title: ss8_P3F4, scRNAseq


title: ss8_P3F12, scRNAseq


title: F2 HCC 1M 015

city: Dallas

first: Lianghao

last: Ding

state: TX

address: 2201 Inwood Rd

department: Radiation Oncology

institute: University of Texas Southwestern Medical Center

data_processing:
Trimming: FastQC
UMI correction: Qiagen
Mapping: Bowtie2
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text

source_name: Plasma

extract_protocol:
Total RNA from was isolated using 50µl of mouse plasma. The sample volumes were brought up to 200 µl with water and then processed for RNA purification using the miRNeasy Serum/Plasma Advanced Kit from Qiagen. Synthetic miRNA mimics, UniSP2, UniSP4 were added to each sample before isolation
A QIAseq miRNA Library Kit was used to build molecular-barcoding-enabled sequencing libraries

tag: mouse no.

tag: histology

value: HCC

tag: months after radiation

value: Male

tag: days before tumor detection


title: F2 HCC 6M 015

tag: Sex


title: ss8_P3F1, scRNAseq


title: U2OS_Fl-SUPT3H_2

source_name: U2OS cells

growth_protocol: Human U2OS osteosarcoma cells (HTB-96; ATCC) were cultured using DMEM medium supplemented with 10% foetal calf serum (Sigma Aldrich, Cat# F7524) and 40 µg/ml gentamycin (KALYS, Cat# G0124-25). Cells were grown at 37°C with 5% CO2 levels.

extract_protocol:
We purify newly transcribed RNA by adding 4sU (4-thiouridine), a metabolic analogue of uridine, to the cell culture medium for 15 minutes before collecting the cells. The cells readily take up 4sU and incorporate it into RNA transcribed during the time period of 15 minutes. This protocol is used to label newly transcribed RNA in both, human U2OS cells and mouse embryonic stem cells. 4tU was used to label newly synthesized RNA from S. pombe cells which served as a external spike-in for normalization. The incorporation of 4sU (with its specific thiol group) into newly transcribed RNA allows to separate the 4sU-containing RNA from the total RNA using biotinylation and Streptavidin-coated beads. The total RNA, used for the purification of the 4sU-containing RNA, was fragmented prior to purification (into on average ~700 bp fragments).
For U2OS cells, 4sU RNA-Seq libraries were generated from 15ng of purified, newly synthesized RNA using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit and IDT for Illumina RNA UD Indexes, Ligation (Illumina, San Diego, USA, Cat# 20040525 and 20040553/4, respectively), according to manufacturer's instructions. Briefly, abundant ribosomal RNAs were depleted by hybridization to specific DNA probes and enzymatic digestion. The depleted RNAs were purified and fragmented using divalent cations at 94°C for 2 minutes. After random hexamers annealing, fragmented RNAs were then reverse transcribed into first strand complementary DNA (cDNA). Second strand cDNA synthesis further generated blunt-ended double-stranded cDNA and incorporated dTTP in place of dUTP to achieve strand specificity by quenching the second strand during amplification. Following A-tailing of DNA fragments and ligation of pre-index anchors, PCR amplification was used to add indexes and primer sequences and to enrich DNA libraries (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C). Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France, Cat# B23319) and the final libraries were checked for quality and quantified using capillary electrophoresis.

tag: genotype

value: U2OS overexpressing SUPT3H

tag: cell line

tag: molecule subtype

value: 4sU RNA (newly synthesized RNA)


title: ss8_P3F11, scRNAseq

extract_protocol:
EGFP+ single cells were individually collected by FACS into 96 well plates.
Libraries were prepared following SmartSeq2 NexteraXT indications.
single cell RNA seq

tag: cell type

tag: Stage


title: U2OS_Fl-SUPT3H_1


title: ss8_P3F10, scRNAseq


title: ss8_P3E8, scRNAseq


title: F2 HCC 18M 010

tag: strain


title: F2 HCC 6M 014


title: U2OS_2

value: U2OS parental


title: MBM02_sc [TCR-Seq]

description: Single-cell RNA sequencing; TCR-seq

value: HRAS T58I


title: F2 HCC 1M 014


title: ss8_P3E6, scRNAseq


title: ss8_P3E7, scRNAseq


title: F2 HCC 18M 009


title: ss8_P3E4, scRNAseq


title: ss8_P3F3, scRNAseq


title: U2OS_1


title: ss8_P3E5, scRNAseq


title: ss8_P3E3, scRNAseq


title: F2 HCC 12M 012


title: ss8_P3E1, scRNAseq


title: ss8_P3E2, scRNAseq


title: F2 HCC 12M 013


title: B2_RNA

city: Bronx

first: Kamini

last: Singh

address: 1300 Morris Park Ave, Golding 203

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

description:
B2-Total
B2-Total

data_processing:
Sequence Alignment  First, ribosome footprint (RF) reads were filtered based on the quality score, which kept reads that have a minimum quality score of 25 for at least 75 percent of the nucleotides. Second, the linker sequence (5’- CTGTAGGCACCATCAAT-3’) was trimmed from the 3’ end of the reads. Next, we filtered out the reads shorter than 15nt after the linker-trimming step. All these aforementioned steps were done by using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html). The ribosome footprint reads were first aligned to the virus genome using Bowtie2 (Langmead and Salzberg, 2012). Specifically, the reads were first mapped to ZIKV and DENV genome. The unmapped reads were used for downstream analysis for human genome. To remove ribosomal RNA, the footprint reads were then aligned to the ribosome RNA sequences of GRCh37 downloaded from UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables). After removing the reads aligned to the ribosome RNAs, RF reads were mapped to the human genome sequence GRCh37 downloaded from Ensembl public database: http:// www.ensembl.org using HISAT2 with default parameters. We only used the uniquely aligned reads for further analysis.  Total mRNA sequencing reads were first aligned to the virus genome as done for the ribosome footprint reads. Then the unmapped reads were aligned to the GRCh37 reference using HISAT2. Similarly, as RF reads alignment, we performed the splice alignment for the paired-end mRNA-seq datasets with the default parameters. We only kept the uniquely aligned reads for the downstream analysis. The virus genome alignment quantification was done using featureCounts with the virus annotation (for both RF and mRNA sequencing in both ZIKV and DENV genome). The human genome alignment quantification for both RF and mRNA sequencing was done using featureCounts with the annotations of the protein coding genes of GRCh37 as input. Only reads aligned to the exonic regions of the protein coding genes were used for the downstream analysis.
Footprint Profile Analysis using Ribo-diff  We used Ribo-diff to analyse the translation efficiency based on the ribosome footprinting and mRNA sequencing data. Genes with at least 10 normalized read counts as the sum of RF and RNA sequencing data were used as input, which resulted in 19,821 protein coding mRNA. Genes with significantly changed translation efficiency were defined by the q-value cut-off equal to 0.05.
Motif analysis   The longest transcript was selected to represent each corresponding gene. The 5’UTR sequences of the transcripts were collected for predicting motifs. Both the significant genes with increased or decreased TE and the corresponding background gene sets were used to predict motifs by DREME (Grant et al., 2011). The occurrences of the significant motifs (E < 0.05 and P < 110-8 from DREME) were called using FIMO (Grant et al., 2011) with default parameters for strand specific prediction of all the 5’UTR sequences.
Assembly: GRCh37

source_name: primary hNPC

growth_protocol: We used primary hNPCs obtained from two different human donors (clone A and clone B).  NPCs were seeded onto matrigel-coated tissue culture plates at 300k cells per well of a 6-well plate in NPC medium (DMEM/F12 (Life Technologies, #10565) supplemented with 1 × N2 (Life Technologies, #17502-048), 1 × B27-RA (Life Technologies, #12587-010), 20 ng/ml FGF2 (R&D, #233-FB-10), 1 mg/ml Natural Mouse Laminin (Life Technologies, #23017-015). NPCs were fed every second day and split once per week using Accutase .

extract_protocol:
ZIKV IbH 30656 NR-50066 was isolated from the blood of a human in Ibadan, Nigeria and was obtained by M.K. through BEI Resources, NIAID, NIH, as part of the WRCEVA program. DENV-2 strain 16681 was obtained by M.K. from the World Arbovirus Reference Center, University of Texas Medical Branch, Galveston, TX. 6-well plates were coated with poly-L-Ornithine (PLO) and laminin before seeding hNPCs ( 8x105 cells per well) (Topol et al., 2015). 24h post-plating the cells were infected with ZIKV or DENV at a multiplicity of infection of 1 and incubated at 37°C. Viral inocula were removed at 3 hours post infection (hpi). Cells were collected and processed for ribosome footprinting at 72 hpi.
Human neuronal progenitor cells (hNPCs) (n=2) were infected with ZIKV-Ibh and DV-2 16681 (72 hr) followed by cycloheximide treatment for 10 minutes. Total RNA and ribosome-protected fragments were isolated following published protocol (Ingolia et al., 2012). Small RNA libraries were generated using SMARTer smRNA kit from Illumina. Deep sequencing libraries were generated from these fragments and sequenced on the HiSeq 2500 platform. Genome annotation was from the human genome sequence GRCh37 downloaded from Ensembl public database: http:// www.ensembl.org. For virus genome we used the reference genomes for ZIKV-Ibh and DV-2 16681 downloaded from the NCBI database (Coordinators, 2016).

value: primary hNPC

tag: donor

value: B

tag: infection status

value: ZIKV infected

value: RNA


title: B3_RNA

description:
B3-Total
B3-Total

value: DENV infected


title: A3_RNA

description:
A3-Total
A3-Total

value: A


title: ss8_P3E12, scRNAseq


title: ss8_P3E9, scRNAseq


title: F2 HCC 6M 013


title: F2 HCC 1M 013


title: B1_RNA

description:
B1-Total
B1-Total

value: uninfected


title: A2_RNA

description:
A2-Total
A2-Total


title: ss8_P3D9, scRNAseq


title: A1_RNA

description:
A1-Total
A1-Total


title: ss8_P3D7, scRNAseq


title: ss8_P3D8, scRNAseq


title: F2 HCC 12M 011


title: F2 HCC 18M 008


title: ss8_P3D5, scRNAseq


title: B3_ribo

description:
B3-RF
B3-RF

data_processing:
Sequence Alignment  First, ribosome footprint (RF) reads were filtered based on the quality score, which kept reads that have a minimum quality score of 25 for at least 75 percent of the nucleotides. Second, the linker sequence (5’- CTGTAGGCACCATCAAT-3’) was trimmed from the 3’ end of the reads. Next, we filtered out the reads shorter than 15nt after the linker-trimming step. All these aforementioned steps were done by using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html). The ribosome footprint reads were first aligned to the virus genome using Bowtie2 (Langmead and Salzberg, 2012). Specifically, the reads were first mapped to ZIKV and DENV genome. The unmapped reads were used for downstream analysis for human genome. To remove ribosomal RNA, the footprint reads were then aligned to the ribosome RNA sequences of GRCh37 downloaded from UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables). After removing the reads aligned to the ribosome RNAs, RF reads were mapped to the human genome sequence GRCh37 downloaded from Ensembl public database: http:// www.ensembl.org using HISAT2 with default parameters. We only used the uniquely aligned reads for further analysis.  Total mRNA sequencing reads were first aligned to the virus genome as done for the ribosome footprint reads. Then the unmapped reads were aligned to the GRCh37 reference using HISAT2. Similarly, as RF reads alignment, we performed the splice alignment for the paired-end mRNA-seq datasets with the default parameters. We only kept the uniquely aligned reads for the downstream analysis. The virus genome alignment quantification was done using featureCounts with the virus annotation (for both RF and mRNA sequencing in both ZIKV and DENV genome). The human genome alignment quantification for both RF and mRNA sequencing was done using featureCounts with the annotations of the protein coding genes of GRCh37 as input. Only reads aligned to the exonic regions of the protein coding genes were used for the downstream analysis.
Footprint Profile Analysis using Ribo-diff  We used Ribo-diff to analyse the translation efficiency based on the ribosome footprinting and mRNA sequencing data. Genes with at least 10 normalized read counts as the sum of RF and RNA sequencing data were used as input, which resulted in 19,821 protein coding mRNA. Genes with significantly changed translation efficiency were defined by the q-value cut-off equal to 0.05.
Motif analysis   The longest transcript was selected to represent each corresponding gene. The 5’UTR sequences of the transcripts were collected for predicting motifs. Both the significant genes with increased or decreased TE and the corresponding background gene sets were used to predict motifs by DREME (Grant et al., 2011). The occurrences of the significant motifs (E < 0.05 and P < 110-8 from DREME) were called using FIMO (Grant et al., 2011) with default parameters for strand specific prediction of all the 5’UTR sequences.
Assembly: GRCh37
Library strategy: Ribosome profiling

value: Ribosome protected RNA


title: ss8_P3D6, scRNAseq

data_processing:
All data was processed using a custom Nextflow pipeline available at https://github.com/alexthiery/otic-reprogramming. All packages and versions are containerised in Docker images called by the pipeline. Full documentation of pipeline parameters and how to reproduce the analysis is available at https://alexthiery.github.io/otic-reprogramming/
Adaptor sequences were trimmed using cutadapt v2.10, aligned using hisat2 v2.2.1, sorted using samtools v1.10, and read counts obtained using htseq v0.12.4.
RNA velocity counts were obtained using Velocyto v0.17.17.
Genome_build: galgal6
Supplementary_files_format_and_content: assayData.csv (raw counts)
phenoData.csv (sample metadata)
gfpData.csv (raw gfp counts)
onefilepercell_ss8-TSS_P2_C10_75_and_others_TVIUH.loom (raw velocyto counts)


title: F2 HCC 6M 012


title: ss8_P3D4, scRNAseq


title: ss8_P3D2, scRNAseq


title: ss8_P3D3, scRNAseq


title: A3_ribo

description:
A3-RF
A3-RF


title: ss8_P3E11, scRNAseq


title: ss8_P3E10, scRNAseq


title: ss8_P3D1, scRNAseq


title: ss8_P3D12, scRNAseq


title: F2 HCC 18M 007


title: ss8_P3D10, scRNAseq


title: ss8_P3C9, scRNAseq


title: A2_ribo

description:
A2-RF
A2-RF


title: B1_ribo

description:
B1-RF
B1-RF


title: F2 HCC 6M 011

value: Female


title: F2 HCC 12M 010


title: ss8_P3C6, scRNAseq


title: ss8_P3C7, scRNAseq


title: F2 HCC 6M 010


title: F2 HCC 1M 011


title: F2 HCC 1M 012


title: T2D_119_post [P7401_226]

city: Stockholm

first: Carolina

last: Nylén

address: Karolinska University Hospital

country: Sweden

institute: Karolinska Institutet

description: Human skeletal muscle biopsy from individuals with type 2 diabetes or healthy control before and after an acute bout of cycling exercise at 80% heart rate reserve for 35 min

data_processing:
Adapters trimming with Trim Galore! v0.6.4
Mapping using STAR v2.6.1d
Assembly: GRCh38
Supplementary files format and content: raw counts

source_name: Vastus Lateralis

extract_protocol:
mRNA was extracted by mirVana miRNA Isolation Kit (ThermoFisher Scientific AM1560).
Libraries were generated with TruSeq Stranded total RNA kit (Illumina 20020597) and ribosomal RNA removed with Ribo-Zero Plus rRNA depletion kit (Illumina 20037135)

treatment_protocol: Biopsies were obtained using a a Weil-Blakesley conchotome, washed with PBS and snap frozen in liquid nitrogen.

tag: diagnosis

tag: timepoint

value: Post

tag: age

tag: bmi

tag: tissue

value: Vastus Lateralis


title: ss8_P3D11, scRNAseq

value: Pax2+ cells


title: ss8_P3C5, scRNAseq


title: T2D_119_basal [P7401_225]

value: Basal

value: Male


title: T2D_119_rec [P7401_227]

value: Recovery


title: ss8_P3C3, scRNAseq


title: F2 HCC 1M 010

tag: mouse no.

tag: histology

value: HCC


title: B2_ribo

description:
B2-RF
B2-RF


title: ss8_P3C2, scRNAseq


title: F2 HCC 12M 009

tag: months after radiation

tag: days before tumor detection


title: ss8_P3C1, scRNAseq


title: ss8_P3C8, scRNAseq


title: ss8_P3B9, scRNAseq


title: ss8_P3C12, scRNAseq


title: ss8_P3B8, scRNAseq


title: ss8_P3C11, scRNAseq


title: F2 HCC 6M 009

tag: Sex


title: NGT_129_rec [P7401_224]

value: NGT


title: A1_ribo

description:
A1-RF
A1-RF

value: primary hNPC


title: NGT_129_post [P7401_223]


title: ss8_P3C10, scRNAseq


title: F2 HCC 1M 009


title: ss8_P3B7, scRNAseq


title: ss8_P3C4, scRNAseq


title: T2D_112_post [P7401_220]


title: F2 HCC 18M 006


title: ss8_P3B5, scRNAseq


title: F2 HCC 12M 008


title: ss8_P3B3, scRNAseq


title: ss8_P3B6, scRNAseq


title: T2D_109_rec [P7401_215]


title: F2 HCC 6M 008


title: T2D_109_post [P7401_214]


title: F2 HCC 1M 008


title: ss8_P3B4, scRNAseq


title: T2D_112_basal [P7401_219]


title: F2 HCC 18M 005


title: ss8_P3B11, scRNAseq


title: ss8_P3B12, scRNAseq


title: ss8_P3B10, scRNAseq


title: NGT_129_basal [P7401_222]


title: T2D_109_basal [P7401_213]


title: NGT_127_rec [P7401_212]


title: ss8_P3A7, scRNAseq


title: ss8_P3A9, scRNAseq


title: F2 HCC 12M 007


title: ss8_P3A8, scRNAseq


title: ss8_P3A6, scRNAseq


title: NGT_127_post [P7401_211]


title: F2 HCC 6M 007


title: ss8_P3B2, scRNAseq


title: F2 HCC 18M 004


title: ss8_P3A4, scRNAseq


title: F2 HCC 1M 007


title: ss8_P3A5, scRNAseq


title: T2D_108_rec [P7401_209]


title: ss8_P3B1, scRNAseq


title: ss8_P3A3, scRNAseq


title: ss8_P3A2, scRNAseq


title: ss8_P3A12, scRNAseq


title: ss8_P3A1, scRNAseq


title: T2D_108_basal [P7401_207]


title: T2D_108_post [P7401_208]


title: ss8_P3A10, scRNAseq


title: F2 HCC 12M 006


title: ss8_P2H9, scRNAseq


title: ss8_P3A11, scRNAseq


title: F2 HCC 1M 006


title: ss8_P2H8, scRNAseq


title: F2 HCC 6M 006


title: NGT_127_basal [P7401_210]


title: T2D_107_rec [P7401_203]


title: F2 HCC 6M 005


title: F2 HCC 1M 005


title: ss8_P2H6, scRNAseq


title: ss8_P2H5, scRNAseq


title: ss8_P2H7, scRNAseq


title: ss8_P2H4, scRNAseq


title: F2 HCC 12M 005


title: ss8_P2H3, scRNAseq


title: T2D_107_basal [P7401_201]


title: F2 HCC 18M 003


title: F2 HCC 6M 004


title: ss8_P2H2, scRNAseq


title: NGT_124_rec [P7401_194]


title: ss8_P2H12, scRNAseq


title: ss8_P2H11, scRNAseq


title: ss8_P2H10, scRNAseq


title: ss8_P2G9, scRNAseq


title: NGT_124_basal [P7401_193]


title: T2D_104_post [P7401_191]


title: T2D_104_rec [P7401_192]


title: T2D_107_post [P7401_202]


title: F2 HCC 1M 004


title: ss8_P2G8, scRNAseq


title: F2 HCC 12M 004


title: T2D_104_basal [P7401_190]


title: ss8_P2G6, scRNAseq


title: ss8_P2H1, scRNAseq


title: ss8_P2G5, scRNAseq


title: F2 HCC 6M 003


title: ss8_P2G3, scRNAseq


title: ss8_P2G2, scRNAseq


title: ss8_P2G4, scRNAseq


title: NGT_123_post [P7401_188]


title: NGT_123_rec [P7401_189]


title: ss8_P2G1, scRNAseq


title: F2 HCC 1M 003


title: NGT_123_basal [P7401_187]


title: F2 HCC 12M 003


title: ss8_P2G11, scRNAseq


title: ss8_P2G10, scRNAseq


title: ss8_P2G7, scRNAseq


title: F2 HCC 6M 002


title: ss8_P2G12, scRNAseq


title: ss8_P2F9, scRNAseq


title: T2D_101_post [P7401_185]


title: F2 HCC 18M 002


title: F2 HCC 1M 002


title: T2D_101_rec [P7401_186]


title: ss8_P2F8, scRNAseq


title: T2D_101_basal [P7401_184]


title: F2 HCC 12M 002


title: ss8_P2F5, scRNAseq


title: ss8_P2F6, scRNAseq


title: ss8_P2F3, scRNAseq


title: NGT_052_rec [P7401_183]


title: ss8_P2F2, scRNAseq


title: ss8_P2F1, scRNAseq


title: F2 HCC 6M 001


title: NGT_052_post [P7401_182]


title: F2 HCC 1M 001


title: NGT_052_basal [P7401_181]


title: ss8_P2F11, scRNAseq


title: ss8_P2E9, scRNAseq


title: F2 HCC 12M 001


title: T2D_035_rec [P7401_180]


title: F2 HCC 18M 001


title: ss8_P2F10, scRNAseq


title: ss8_P2F7, scRNAseq


title: ss8_P2E8, scRNAseq


title: T2D_035_post [P7401_179]


title: T2D_035_basal [P7401_178]


title: ss8_P2F4, scRNAseq


title: C3H non-HCC 005

value: non-HCC


title: C3H HCC 008


title: Skeletal muscle cells, GAC022

city: Lund

first: Nikolay

last: Oskolkov

address: Sölvegatan 35

institute: Lund University

description: 10x libraries from mixed muscle nuclei, chimp Storer + human sample 3

data_processing:
Post-processing pipeline Cell Ranger (https://support.10xgenomics.com/single-cell-gene-expression/software/) provided by 10X Genomics was used for demultiplexing, alignment, filtering, barcode and Unique Molecular Identifier (UMI) counting. The pipeline produced files in FASTQ and BAM formats, as well as the matrix of UMI counts.
We used Seurat workflow https://satijalab.org/seurat/ for further quality control and downstream analysis of the snRNAseq gene expression data.
We normalized the gene expression data with LogNormalize method of Seurat and standardized the count values prior for performing the Principal Component Analysis. JackStraw procedure38 was applied as a denoising step in order to select an optimal number of Principal Components (PCs), indicating that 3 PCs to keep for further downstream analysis, which can be viewed as identifying the true intrinsic dimensionality of the snRNAseq data.
Genome_build: HG38 and PanTro5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell in tab-delimited format

molecule: nuclear RNA

organism:
Pan troglodytes
Homo sapiens

source_name: Vastus lateralis muscle

growth_protocol: not applicable

extract_protocol:
For nuclei isolation from frozen tissue, all following steps were performed on ice with precooled buffers and centrifugation steps were performed at 4 °C. Tissue was disrupted and nuclei liberated through dounce homogenization in ice-cold homogenization buffer [0.32 M sucrose, 3 mM CaCl2, 2 mM magnesium acetate, 0.1 mM EDTA, 1 mM DTT, 10 mg/ml BSA, 10 mM Tris-HCL, protease inhibitors (Sigma-Aldrich)] in the presence of 0.1% NP40. The nuclei suspensions were sequentially passed through 40, 30 and 20-μm cell filters (Miltenyi Biotec) and centrifuged at 1000g for 10 min. The pellet was resuspended in 1% RNase-free BSA in PBS, and stained using DAPI (1:1,000, BD Pharmingen). Intact single nuclei were sorted in bulk using the DAPI-positive event population, at single cell sort precision and using a 100 µm nozzle (BD FACS AriaIII) into PBS / 1% BSA.
Nuclei were counted and loaded on a 10x Chromium microfluidic chip, aiming for the maximum possible number of nuclei to be targeted obtained from the sorting. Single-nucleus experiments were performed using the 10x Genomics Single Cell 3′ kit v.2 to encapsulate nuclei along with barcode tagged beads, generate and amplify cDNA and to generate sequencing libraries. Each pooled library was barcoded using i7 barcodes provided by 10x Genomics. cDNA and sequencing library quality and quantity were determined using Agilent’s High Sensitivity DNA Assay. Libraries were pooled and sequenced in 150-bp paired-end mode on Illumina’s HiSeq platform.

treatment_protocol: untreated

value: Skeletal muscle fibers

tag: library


title: Skeletal muscle cells, GAC021


title: NGT_050_post [P7401_176]


title: ss8_P2E4, scRNAseq

first: Andrea

last: Streit

address: Guys Hospital, Great Maze Pond

institute: Kings College London


title: ss8_P2E5, scRNAseq


title: ss8_P2E3, scRNAseq


title: ss8_P2F12, scRNAseq


title: C3H HCC 007


title: C3H HCC 006


title: T2D_031_rec [P7401_174]


title: C3H HCC 005


title: NGT_050_rec [P7401_177]


title: C3H non-HCC 004


title: ss15_296107, scRNAseq


title: NGT_050_basal [P7401_175]


title: ss15_295119, scRNAseq


title: ss15_293143, scRNAseq


title: T2D_031_post [P7401_173]


title: ss8_P2E7, scRNAseq


title: C3H non-HCC 003


title: ss8_P2E6, scRNAseq


title: C3H HCC 004


title: T2D_031_basal [P7401_172]


title: C3H HCC 003


title: NGT_033_rec [P7401_171]


title: ss15_291167, scRNAseq


title: NGT_033_post [P7401_170]


title: ss15_292155, scRNAseq


title: C3H HCC 002


title: C3H non-HCC 002


title: ss15_290179, scRNAseq


title: T2D_030_rec [P7401_168]


title: NGT_033_basal [P7401_169]


title: T2D_030_post [P7401_167]


title: ss15_287120, scRNAseq


title: ss15_289191, scRNAseq


title: T2D_030_basal [P7401_166]


title: DRUGseq-72hr-2

first: Isabella

last: Kong

address: 1300 York Ave

institute: Weill Cornell Medicine

description:
DRUGseq_raw_count.txt
DRUGseq_ID.txt
DRUGseq_metadata.txt

data_processing:
Library strategy: DRUG-seq
The paired-end 75bp reads were demultiplexed using bcl2fastq (v2.17.1.14) and Cutadapt (v2.1) was used for R2 read trimming.
The R2 trimmed reads were demultiplexed according to well barcodes and filtered for PCR duplicates using unique molecular identifiers (UMIs) both present in R1 reads, using the scruff R package (v4.0.2).
The R2 reads were subsequently mapped to the mouse reference genome (mm10) and ERCC sequences and counted across exon genomic intervals using the scruff R package (v4.0.2).
Count processing was perfromed using RUVseq (v1.24.1) and Seurat (v3.2.1) R packages.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes raw counts for each sample

source_name: Purified Primary B cells

growth_protocol: B cells were purified from C57Bl/6

extract_protocol:
Lysates were generated by incubating cell pellets in DRUG-seq lysis buffer and incubation at room termperatue with agitation for 15 minutes.
Cell lysate was transferred into each well of a new 96-well plate previously prepared with 1µl of 10 nM well-specific RT DRUG-seq primer and 7.5µl RT mix; the RT mix contains a TSO primer and external ERCC RNAs for normalization. The mixture was incubated for 2hr at 42C to create well-barcoded full-length cDNA, and then all the wells of a plate were combined into a single tube. Concentration and clean-up were done with DNA Clean & ConcentratorTM-100 (Zymo Research), and RNAClean XP (Beckman Coulter) and each plate were eluted in 22µl nuclease-free water. The purified cDNA was pre-amplified with KAPA HiFi HotStart ReadyMix (Roche), and DRUG-seq PreAmp PCR primer and the quality checked on a D5000 Screentape (TapeStation, Agilent). One barcoded library was prepared per plate using TD buffer and TDE1 enzyme (Illumina) for tagmentation and KAPA HiFi HotStart Ready Mix (Roche) and custom primers (DRUG-seq P5 PCR and DRUG-seq Indexing Mix) for amplification. Libraries were purified with DNA AMPure XP (Beckman Coulter), quality checked on a DNA1000 tape (TapeStation, Agilent) and quantity verified by qPCR. Two indexed libraries were sequenced on a NextSeq 500 instrument (Illumina) using a custom sequencing primer (DRUG-seq Read primer) and a High Output Kit v2.5 75 Cycles (Illumina) with paired-end configuration (25 base pairs for read 1 and 50 base pairs for read 2).

treatment_protocol: Cells were cultured with LPS (15ug/mL) and were either untreated or treated with 1uM of indicated compound. Samples were harvested at 24hr and 72hr.

value: B cell

tag: stimulation

value: LPS

tag: treatment


title: ss15_288108, scRNAseq

tag: cell type

tag: Stage


title: ss15_286132, scRNAseq


title: C3H HCC 001

tag: strain


title: ss15_294131, scRNAseq


title: NGT_028_rec [P7401_165]


title: ss15_285144, scRNAseq


title: DRUGseq-72hr-1


title: DRUGseq-24hr-2


title: NGT_028_post [P7401_164]


title: DRUGseq-24hr-1


title: NGT_028_basal [P7401_163]


title: ss15_284156, scRNAseq


title: T2D_026_rec [P7401_162]


title: T2D_026_post [P7401_161]


title: ChIP-Input-2

data_processing:
20 million single-end 75bp reads were generated per sample. CASAVA (v1.8.2) was used for demultiplexing.
The FASTQ files generated were aligned to the mouse reference genome (mm10) using bowtie (v2.2.3).
Samtools (v1.3) was used for manipulation of SAM and BAM files and MACS (V2.0.10) was used for peak calling.
BigWig file generated using deepTools 2.0
Genome_build: mm10
Supplementary_files_format_and_content: BigWig file generated using deepTools 2.0

extract_protocol:
Lysates were clarified from sonicated nuclei and H3K27me3-DNA complexes were isolated with antibody. DNA product was purified using Zymo ChIP DNA Clean and Concentrator Kit.
ChIP-enriched DNA was processed and sequenced using NEBnext Ultra II kit according to manufacturer’s instructions on Nextseq500 (Illumina).

treatment_protocol: Cells were cultured with LPS (15ug/mL) and were either untreated or treated with indicated concentrations of GSK126. Samples were harvested at indicated hours (0hr, 6hr, 71hr and 95hr for RNA; 0hr, 48hr and 72hr for ChIP)

tag: chip antibody

value: Input


title: ss15_282180, scRNAseq


title: C3H non-HCC 001


title: ChIP-Input-1


title: T2D_026_basal [P7401_160]

tag: diagnosis


title: NGT_027_rec [P7401_159]

tag: timepoint


title: ChIP-72hr-8uM-2

value: Abcam H3K27me3 (ab6002)

value: 72hr 8uM GSK126


title: ss15_281192, scRNAseq


title: ChIP-72hr-8uM-1


title: NGT_027_post [P7401_158]

tag: age


title: ss15_279121, scRNAseq


title: ChIP-72hr-4uM-2

value: 72hr 4uM GSK126


title: NGT_027_basal [P7401_157]

tag: bmi


title: T2D_024_rec [P7401_156]

tag: tissue


title: ss15_278133, scRNAseq


title: ChIP-72hr-4uM-1


title: ChIP-72hr-0uM-2

value: 72hr Untreated


title: T2D_024_post [P7401_155]

value: Post

value: Vastus Lateralis


title: ss15_277145, scRNAseq

value: Pax2+ cells


title: ss15_283168, scRNAseq


title: ss15_276157, scRNAseq


title: T2D_024_basal [P7401_154]

value: Basal

value: Male


title: ss15_275169, scRNAseq


title: NGT_023_rec [P7401_153]

value: Recovery


title: ss15_274181, scRNAseq


title: ChIP-72hr-0uM-1


title: NGT_023_post [P7401_152]

value: NGT


title: ChIP-48hr-8uM-1

value: 48hr 8uM GSK126


title: ChIP-48hr-4uM-2

value: 48hr 4uM GSK126


title: ss15_280109, scRNAseq


title: NGT_023_basal [P7401_151]


title: T2D_019_post [P7401_149]


title: ChIP-48hr-4uM-1


title: ss15_271122, scRNAseq


title: ss15_272110, scRNAseq


title: ss15_273193, scRNAseq


title: ChIP-48hr-0uM-2

value: 48hr Untreated


title: T2D_019_rec [P7401_150]


title: ChIP-0hr-0uM-2

value: B cell

value: 0hr Untreated


title: ChIP-48hr-0uM-1

value: LPS


title: ss15_270134, scRNAseq


title: ss8_P2E2, scRNAseq


title: NGT_022_rec [P7401_147]


title: ChIP-0hr-0uM-1

value: Abcam H3K27me3 (ab6002)


title: T2D_019_basal [P7401_148]


title: ChIP-48hr-8uM-2


title: ss8_P2E1, scRNAseq


title: NGT_022_basal [P7401_145]


title: ss8_P2E12, scRNAseq


title: T2D_017_rec [P7401_144]


title: RNA-95hr-8uM-3

data_processing:
The single-end 75bp were demultiplexed using CASAVAv1.8.2 and Cutadapt (v1.9) was used for read trimming.
The trimmed reads were subsequently mapped to the mouse genome (mm10) using HISAT2.
FeatureCounts was used for read counting after which differential gene expression analysis was performed using Voom-LIMMA packages.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was extracted using Qiagen Rneasy kit.
3’mRNA-sequencing libraries were prepared using 100 ng of total RNA using the QuantSeq 3’mRNA-Seq Library Prep (Lexogen) according to the manufacturer’s instructions and sequenced on the NextSeq 500 (Illumina).

value: 95hr 8uM GSK126


title: RNA-95hr-8uM-2


title: ss8_P2E11, scRNAseq


title: RNA-95hr-8uM-1


title: RNA-95hr-4uM-3

value: 95hr 4uM GSK126


title: T2D_017_post [P7401_143]


title: ss8_P2D9, scRNAseq


title: T2D_017_basal [P7401_142]


title: RNA-95hr-4uM-2


title: ss8_P2D8, scRNAseq


title: RNA-95hr-4uM-1


title: ss8_P2D7, scRNAseq


title: NGT_021_post [P7401_140]


title: ss8_P2D6, scRNAseq


title: RNA-95hr-0uM-3

value: 95hr Untreated


title: RNA-95hr-0uM-2


title: NGT_022_post [P7401_146]

value: Post


title: T2D_012_rec [P7401_138]

value: Vastus Lateralis


title: NGT_021_basal [P7401_139]


title: ss8_P2D3, scRNAseq

value: Pax2+ cells


title: ss8_P2D4, scRNAseq


title: RNA-95hr-0uM-1


title: T2D_012_post [P7401_137]


title: RNA-71hr-8uM-3

value: 71hr 8uM GSK126


title: NGT_020_rec [P7401_135]

value: Male


title: ss8_P2D2, scRNAseq


title: H3K27me3, OEPs, ChIPseq

data_processing:
Data was processed and aligned using the NF-core ChIPseq v1.2.0 pipeline (doi: 10.5281/zenodo.2634132).
Reads were trimmed using Trim Galore! Reads were aligned using BWA. Broad peaks were called using MACS2 with an effective genome size of 1.05e9.
Genome_build: galgal6
Supplementary_files_format_and_content: broadPeak

source_name: otic epibranchial progenitors (OEPs)

growth_protocol: Embryos were grown in ovo at 38°C until reaching the desired stage.

extract_protocol:
200 pieces of OEP tissue per sample were manually dissected. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared following standard protocols. Briefly, tissue was dissociated in nuclei expulsion buffer, cells were then pelleted, washed in PBS and snap-frozen. Crosslinked chromatin was fragmented by sonication and immunoprecipitated following Nano-ChIP protocol using antibodies for H3K27ac, H3K27me3, H3K4me3. Adaptors and primers for NEBNext library preparation kit (Illumina, E6040S) were used to prepare library following NanoChIP protocol.

value: OEPs

value: anti-H3K27me3 (Millipore, 07449)


title: RNA-71hr-8uM-2


title: RNA-71hr-8uM-1


title: ss8_P2E10, scRNAseq

source_name: Pax2+ cells


title: ss8_P2D1, scRNAseq


title: NGT_020_post [P7401_134]

value: NGT


title: H3K4me3, OEPs, ChIPseq

value: anti-H3K4me3 (Diagenode, A5051-001P)


title: RNA-71hr-4uM-3

value: 71hr 4uM GSK126


title: NGT_021_rec [P7401_141]

value: Recovery


title: NGT_020_basal [P7401_133]

value: Basal


title: H3K27Ac, OEPs, ChIPseq

value: anti-H3K27Ac (Abcam, ab4729)


title: ss8_P2D12, scRNAseq


title: ss8_P2D5, scRNAseq


title: ss8_P2D11, scRNAseq


title: RNA-71hr-4uM-1

value: B cell

value: LPS


title: Input, OEPs, ChIPseq


title: T2D_011_rec [P7401_132]


title: T2D_012_basal [P7401_136]


title: T2D_011_post [P7401_131]


title: RNA-71hr-0uM-3

value: 71hr Untreated


title: ss8_P2D10, scRNAseq


title: ss8_P2C9, scRNAseq


title: T2D_011_basal [P7401_130]


title: ss8_P2C8, scRNAseq


title: NGT_018_rec [P7401_129]


title: RNA-71hr-0uM-1


title: NGT_018_post [P7401_128]


title: RNA-71hr-0uM-2


title: MSC, TGF-b2, Horse L

city: Raleigh

first: Alix

middle: Kay

last: Berglund

state: NC

address: 1060 William Moore Dr

department: Clinical Sciences

institute: North Carolina State University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36.
The trimmed reads were mapped to the EquCab 3.0 using the STAR aligner v.2.5.2b.
Unique hit counts were calculated using featureCounts from the Subread package v.1.5.2.
Read count extraction and normalization were performed using DESeq2.
Assembly: EquCab 3.0
Supplementary files format and content: tab-deliniated text file containing normalized gene expression data

organism: Equus caballus

source_name: mesenchymal stem cell

growth_protocol: Primary equine bone marrow-derived mesenchymal cells were maintained in low glucose DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
PolyA selection

treatment_protocol: Half of the bone marrow from each horse was treated with 1 ng/ml human recombinant transforming growth factor-beta2 (TGF-b2) from initial isolation through passage 3 or 4

value: mesenchymal stem cell


title: MSC, control, Horse L

value: Control


title: NGT_018_basal [P7401_127]

value: Vastus Lateralis


title: RNA-71hr-4uM-2


title: ss8_P2C7, scRNAseq

city: London

value: Pax2+ cells


title: MSC, TGF-b2, Horse J


title: T2D_009_rec [P7401_126]


title: MSC, control, Horse W


title: RNA-6hr-8uM-2

value: 6hr 8uM GSK126


title: RNA-6hr-8uM-1


title: ss8_P2C4, scRNAseq


title: ss8_P2C6, scRNAseq


title: ss8_P2C5, scRNAseq


title: MSC, control, Horse J


title: T2D_009_post [P7401_125]

value: Post

value: Male


title: RNA-6hr-4uM-3

value: 6hr 4uM GSK126


title: MSC, TGF-b2, Horse W


title: T2D_009_basal [P7401_124]


title: ss8_P2C3, scRNAseq


title: RNA-6hr-4uM-2


title: MSC, TGF-b2, Horse D


title: NGT_016_rec [P7401_123]

value: NGT


title: RNA-6hr-8uM-3


title: RNA-6hr-4uM-1


title: ss8_P2C12, scRNAseq


title: RNA-6hr-0uM-3

value: 6hr Untreated


title: NGT_016_basal [P7401_121]


title: ss8_P2C1, scRNAseq


title: T2D_007_rec [P7401_120]


title: RNA-6hr-0uM-2


title: ss8_P2C11, scRNAseq


title: RNA-6hr-0uM-1


title: Saline_NC12

type: RNA

city: Bethesda

first: Nicolas

last: Cuburu

state: MD

address: 37 convent drive

department: CCR

institute: NIH/NCI

description: nCounter Mouse PanCancer Immune Profiling Panel

hyb_protocol: Set up a hybridization reaction at room temperature for each sample with the following components: 3 μL of Reporter CodeSet, 5 μL of hybridization buffer, up to 5 μL (25–100 ng) of sample RNA, and 2 μL of Capture ProbeSet

scan_protocol: nCounter XT CodeSet

data_processing: nSolver

source_name: 48h, third injection, TC-1 tumor

growth_protocol: injected subcutaneously 2.5x10^5 cells (TC-1)

extract_protocol: Frozen tumors were pulverized in 1mL Trizol (Thermo Fisher) using ceramic beads in reinforced tubes and a Precellys24 Homogenizer (Bertin Instruments). A volume of 0.2mL of chloroform was added to the tumor lysate and mixed thoroughly before centrifugation at 12,000rpm for 15min at 4 ̊C. Aqueous phase was further processed using the RNeasy Mini QIAcube Kit (Qiagen). Purified RNA was analyzed and quantified using Nanodrop device (Nanodrop Products). A total of 200ng of RNA was used for gene expression analysis using the mouse nCounter PanCancer Immune Profiling Panel (Nanostring Technologies). Sample preparation and hybridization was done following manufacturer’s instruction. The gene expression data were normalized using the nSolver Analysis Software 4.0 (Nanostring Technologies) before further analysis.

treatment_protocol: Tumor tissues were collected 48hrs after the last of three i.t. injections and flash-frozen in liquid nitrogen.

value: TC-1 tumor

tag: gender

value: female

tag: infection

value: MCMV

value: Saline

tag: injection

value: intratumoral


title: T2D_007_post [P7401_119]


title: Saline_NC09


title: ss8_P2C10, scRNAseq


title: MSC, control, Horse D


title: ss8_P2B9, scRNAseq


title: ss8_P2C2, scRNAseq


title: RNA-0hr-0uM-3

value: B cell

value: LPS

value: 0hr Untreated


title: pIC_NC04


title: T2D_006_rec [P7401_114]

value: Recovery


title: NGT_016_post [P7401_122]

value: Vastus Lateralis


title: ss8_P2B8, scRNAseq

value: Pax2+ cells


title: ss8_P2B7, scRNAseq


title: RNA-0hr-0uM-1


title: T2D_006_post [P7401_113]


title: pIC_NC03


title: RNA-0hr-0uM-2


title: Saline_NC08


title: D_LV10_2

city: Klosterneuburg

first: Sandra

last: Siegert

state: Lower Austria

address: Am Campus 1

institute: Institute of Science and Technology Austria

data_processing:
Trimmed fastq files are used for alignment to genome and transcriptome. The pipeline used the iGenomes as resource and created the transcript file using RSEM from genome.fasta and gtf. Alignment to the transcriptome is then used as input for Salmon.
Transcript abundance was quantified with Salmon and we used the resulting “quant.sf” files as input for downstream analysis with the DESeq2 package in R. The “quant.sf” files were imported with the tximport package with the “countsFromAbundance” argument set to “no”. This generates count data and omits correction for transcript length which is not necessary for 3’-mRNA sequencing data. Count data were then imported into DESeq2 with the “DESeqDataSetFromMatrix” command, using “Experiment_ID” and “Experimental_condition” as predictor variables for the design formula.
Genome_build: iGenomes
Supplementary_files_format_and_content: quant.sf files are the output of Salmon.
Supplementary_files_format_and_content: Counts from Salmon.txt provides a matrix of counts derived from quant.sf files that were imported through the tximport package
Supplementary_files_format_and_content: Normalized counts from DESeq2.txt provides a matrix of normalized counts extracted from the DESeq2 model for all genes (rows) and samples titles (columns)
Supplementary_files_format_and_content: salmon_tx2gene.tsv provides gene symbols corresponding to transcript accession numbers.

source_name: HMC3 cell line

extract_protocol: 3'-mRNA sequencing; Library preparation and sequencing was carried out by the Vienna BioCenter Core Facility. In brief, libraries were generated with the QuantSeq 3’ mRNA kit (Lexogen) and sequenced on an Illumina NextSeq550 SR75 High platform.

treatment_protocol: Non-transduced HMC3 cells or HMC3 cells stably expressing DREADD-based GPCR chimeras were seeded in 6-well plates at a density of 32,000 cells per well in a total volume of 2ml. Assays were performed three days after seeding when cells were approximately 80% confluent. Cells were then treated by applying fresh EMEM-complete medium containing the respective compounds. Concentrations of levalbuterol (LB) and CNO were always 10µM. IFNγ/IL1β was added at 10ng/ml each. Untreated control conditions only received fresh EMEM-complete medium. Every experimental repetition included one well per condition. After 6 hours incubation (37°C and 5% CO2), wells were briefly washed with DPBS before proceeding with total RNA isolation. RNA samples were immediately snap frozen on dry ice and then stored at -80°C. In total, 30 samples were collected on four different days, resulting in four batches (Experiment_ID). Together, this amounts to three replicates for each experimental condition.

tag: cell line background

tag: treatment 1

tag: treatment 2

tag: experimental condition

value: Batch 4


title: T2D_007_basal [P7401_118]

value: Basal

tag: Sex


title: pIC_NC01

tag: treatment


title: pIC_NC02


title: ss8_P2B6, scRNAseq

tag: cell type

tag: Stage


title: T2D_006_basal [P7401_112]

value: Male


title: Saline_NC11

tag: strain


title: D_LV8_1


title: NGT_010_post [P7401_110]

tag: diagnosis

value: Post


title: CD8pIC_NC12

value: MHC-1 MCMV peptide + polyI:C


title: CD8pIC_NC11


title: D_WT_4

value: Non-transduced


title: ss8_P2B5, scRNAseq


title: D_LV2_2


title: ss8_P2B3, scRNAseq


title: CD8pIC_NC10

value: TC-1 tumor


title: ss8_P2B4, scRNAseq


title: NGT_010_basal [P7401_109]

value: NGT

tag: timepoint


title: T2D_002_rec [P7401_108]

tag: age


title: T2D_002_basal [P7401_107]

tag: bmi


title: NGT_003_rec [P7401_106]

tag: tissue


title: CD8pIC_NC09

tag: gender

value: female

value: MCMV


title: ss8_P2B2, scRNAseq


title: NGT_010_rec [P7401_111]


title: NGT_003_post [P7401_105]


title: ss8_P2B11, scRNAseq


title: D_WT_2


title: CD8_NC10

tag: infection

value: MHC-1 MCMV

value: intratumoral


title: ss8_P2B1, scRNAseq


title: C_LV10_2

value: Batch 3


title: C_LV10_1


title: CD8_NC07

tag: injection


title: C_LV8_2

tag: cell line background


title: CD8_NC05


title: C_LV8_1

tag: treatment 1


title: ss8_P2A9, scRNAseq


title: NGT_003_basal [P7401_104]


title: T2D_001_rec [P7401_103]


title: D_WT_1

tag: treatment 2

value: Untreated


title: T2D_001_post [P7401_102]


title: ss8_P2A8, scRNAseq


title: C_LV2_1

tag: experimental condition


title: ss8_P2B12, scRNAseq


title: CD4pIC_NC08

value: MHC-2 MCMV peptide + pI:C


title: CD4pIC_NC07


title: C_WT_4


title: ss8_P2A7, scRNAseq


title: T2D_001_basal [P7401_101]

tag: Sex

value: Vastus Lateralis


title: CD4pIC_NC06

tag: treatment


title: ss8_P2B10, scRNAseq

tag: cell type

value: Pax2+ cells


title: C_WT_3


title: CD8_NC06


title: ss8_P2A6, scRNAseq

tag: Stage


title: MC-MO-RS8-MC8

first: Mark

last: Maienschein-Cline

address: 900 S Ashland Ave, Rm 1058, M/C 937

institute: University of Illinois at Chicago

description:
Ex Vivo Sorted IgKappa deleted immature B cells
rna_counts.txt
mm9_plus_ig.gtf

data_processing:
RNA-seq: Raw reads were aligned to reference genome mm9 in a splice aware manner using STAR (Dobin et al., 2013; Dobin and Gingeras, 2015). Gene expression was quantified using featureCounts within the RSubread R package (Liao et al., 2019) against UCSC genes with Ensembl Ig genes from mm10 converted to mm9 coordinates with UCSC liftOver. GTF file is included in the submission.
ATAC-seq: Raw reads were aligned to the reference genome using BWA MEM, and apparent PCR duplicates removed using Picard MarkDuplicates. Read alignments were first adjusted to account for TAC transposon binding: +4 bp for +strand alignments, −5 bp for −strand alignments. The open chromatin enrichment track was generated by first creating a bedGraph from the raw reads using bedtools genomcov, then converted to bigWig using UCSC tool bedGraphToBigWig; tracks were normalized by the sum of alignment lengths over 1 billion. Open chromatin peaks were called using Macs2 (Zhang et al., 2008) with no model set and no background provided; peaks with a score of >5 were retained.
Genome_build: mm9
Supplementary_files_format_and_content: GTF formatted file: gene annotations used for RNA-seq. UCSC genes for mm9 + Ig genes from Ensembl mm10, lifted over to mm9
Supplementary_files_format_and_content: BED formatted file: peak calls for ATAC-seq
Supplementary_files_format_and_content: BigWig formatted file: normalized enrichment of open chromatin for ATAC-seq
Supplementary_files_format_and_content: Tab-delimited text formatted file: unnormalized counts per gene

extract_protocol:
RNA-seq: FACS sorted cells from small pre-B and immature B cells isolated from WT, Igkdel k-mac, k-mac CXCR4fl/fl and k-mac CXCR4fl/fl mb1-cre+ mice and total RNA isolated using Trizol (15596026, Invitrogen) following the protocol described by the Immunological Genome Project (Immgen.org).
RNA-seq: Libraries were generated TruSeq® Stranded mRNA Sample Prep” kit from Illumina and the associated user manual
ATAC-seq: 1.2x105 small pre-B and immature B cells sorted from WT, Igkdel k-mac, k-mac CXCR4fl/fl and k-mac CXCR4fl/fl mb1-cre+ mice were used for ATAC-seq. Cells were centrifuged at 500g at 4°C for 5 minutes, washed with 1X PBS, and centrifuged again. Cells were resuspended in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g at 4°C for 10 minutes. Pellet was resuspended in transposition reaction buffer (25ml 2x Tagment Buffer (FC-121-1030, Illumina), 2.5ml Tagment DNA Enzyme, 22.5ml nuclease free H2O) for 30 minutes at 37°C.
ATAC-seq: DNA was purified with a Qiagen MinElute Kit and amplified with Nextera PCR Primers (Illumina Nextera Index Kit) and NEBNext PCR Master Mix (M0541, New England BioLabs) for 11 cycles. Amplified DNA was purified with a Qiagen PCR cleanup kit. Libraries were sequenced on a NextSeq 550 sequencer at University of Chicago Genomics Facility.

tag: sample group


title: C_WT_2


title: CD4pIC_NC05

tag: strain


title: ss8_P2A5, scRNAseq


title: CD4_NC04

value: MHC-2 MCMV peptide


title: ss8_P2A3, scRNAseq


title: C_WT_1


title: B_LV10_1

value: Batch 2


title: CD4_NC03


title: ss8_P2A4, scRNAseq


title: MC-RMO-3

description:
Ex Vivo Sorted IgKappa deleted small pre B cells
rna_counts.txt
mm9_plus_ig.gtf


title: CD4_NC01


title: B_LV8_1


title: MC-MO-RS8-MC5

description:
Ex Vivo Sorted Kappa-macroself immature B cells
rna_counts.txt
mm9_plus_ig.gtf


title: MC-MO-RS8-MC6


title: ss8_P2A1, scRNAseq


title: ss8_P2A12, scRNAseq


title: MC-MO-RS8-MC4


title: MC-MO-RS8-MC3


title: CD32Flox.Yaa;  Gr-CD11b+

city: Yokohama

first: Hidehiro

last: FUKUYAMA

state: Kanagawa

address: 1-7-22, Suehirocho, Tsurumi-ku

department: IMS

institute: RIKEN

data_processing:
Read alignment: TopHat2 v2.0.8 with default settings
expression level: Cufflinks v2.1.1 with default settings
FPKM (Fragments per Kirobase per Million reads) were calculated.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Gr-Monocytes from peripheral blood

extract_protocol:
RNA from ~1 x 10^5 sorted and collected cells was harvested using Trizol reagent. cDNA  libraries were generated using SMART-Seq v4 Ultra Low Input RNA kit for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: peripheral blood

value: Gr-Monocytes from peripheral blood

value: 8 months

tag: genotype

value: Fcgr2 fl/fl.Yaa


title: CD32null.Yaa;  Gr-CD11b+ #1

tag: age


title: CD32null.Yaa; Gr+CD11b+ #1

source_name: Gr+Monocytes from peripheral blood

value: Gr+Monocytes from peripheral blood


title: B_LV2_2


title: CD11cCreCD32Flox.Yaa;  Gr-CD11b+

value: CD11cCre;Fcgr2 fl/fl.Yaa


title: B_LV2_1


title: MC-MO-RS8-MC7


title: B_WT_4

value: Non-transduced


title: ss8_P2A10, scRNAseq


title: MC-MO-RS8-MC2

description:
Ex Vivo Sorted Kappa-macroself small pre B cells
rna_counts.txt
mm9_plus_ig.gtf


title: ss8_P2A11, scRNAseq


title: MC-RMO-1


title: CEBPaCreCD32Flox.Yaa;  Gr-CD11b+

value: CEBPaCre;Fcgr2 fl/fl.Yaa


title: ss8_P2A2, scRNAseq


title: ss8_P1H9, scRNAseq


title: B_WT_1


title: B_WT_3


title: CEBPaCreCD32Flox.Yaa; Gr+CD11b+


title: MC-MO-RS8-MC1


title: CD4_NC02

value: TC-1 tumor

value: female

value: MCMV


title: MC-RS11-low-KMO-5

description:
Ex Vivo Sorted Kappa-macroself Cxcr4fl/fl Mb1-cre - small pre B cells
rna_counts.txt
mm9_plus_ig.gtf


title: ss8_P1H8, scRNAseq


title: CD19CreCD32Flox.Yaa;  Gr-CD11b+

value: CD19Cre;Fcgr2 fl/fl.Yaa


title: CD19CreCD32Flox.Yaa; Gr+CD11b+


title: ss8_P1H7, scRNAseq


title: A_LV10_2

value: Batch 1


title: mm_atac_spreb_Cxcr4KOKmac.4

description: Ex Vivo Sorted Kappa-macroself Cxcr4fl/fl Mb1-cre + small pre B cells

value: spreB Cxcr4 KO Kmac


title: ss8_P1H6, scRNAseq

value: Pax2+ cells


title: A_LV2_1


title: A_LV10_1


title: A_WT_3


title: MC-RS11-low-KMO-3

description:
Ex Vivo Sorted Kappa-macroself Cxcr4fl/fl Mb1-cre + small pre B cells
rna_counts.txt
mm9_plus_ig.gtf


title: CD32null.Yaa; Gr+CD11b+ #2


title: A_WT_2


title: A_LV8_2


title: B_LV8_2


title: A_LV2_2


title: mm_atac_spreb_Cxcr4KOKmac.2


title: ss8_P1H5, scRNAseq


title: MC-RS11-low-KMO-1


title: ss8_P1H4, scRNAseq


title: SKOV3 cells, sipvt1, rep3

city: Birmingham

first: Ryan

last: Miller

state: AL

address: 1824 Sixth Ave S

department: Pathology

institute: UAB

data_processing:
Basecall to fastq file generation (bcl2fastq2/2.20.0-foss-2016b-Python-2.7.12)
Fragments aligned to the human genome using Star (STAR/2.7.3a-GCC-6.4.0-2.28)
Aligned fragments counted using Salmon (Salmon/0.14.1-foss-2018b)
DESeq2 analysis performed (variables for modeling: replicate, genotype, treatment) to obtain differential gene expression data, raw counts, and normalized counts (DESeq2_1.28.1)
Data was filtered to exclude genes where there were less than 3 samples with normalized read counts less than or equal to 5
Genome_build: GENCODE v32 (GRCh38.p13)
Supplementary_files_format_and_content: raw_counts.csv file is a matrix of raw read counts (every gene for every sample) obtained from R package DESeq2

source_name: ovarian cancer

extract_protocol:
RNA from cultured cells was extracted with Trizol
Library prep was performed using a KAPA mRNA HyperPrep Kit (KK8581) and prepared for sequencing using standard Illumina protocol (final loading concentration 1.65pM)

tag: cell line

value: Human ovarian cancer

value: wildtype


title: MC-RS11-low-KMO-2

city: Chicago


title: SKOV3 cells, sipvt1, rep1


title: mm_atac_spreb_Cxcr4floxKmac.3

description: Ex Vivo Sorted Kappa-macroself Cxcr4fl/fl Mb1-cre - small pre B cells

value: spreB Cxcr4 flox Kmac


title: ss8_P1H3, scRNAseq


title: mm_atac_spreb_Cxcr4KOKmac.3


title: MC-RS11-low-KMO-4


title: ss8_P1H11, scRNAseq


title: SKOV3 cells, sicontrol, rep3

value: control siRNA


title: mm_atac_spreb_Cxcr4KOKmac.1


title: SKOV3 cells, sipvt1, rep2


title: ss8_P1H12, scRNAseq


title: ss8_P1G9, scRNAseq


title: mm_atac_spreb_Cxcr4floxKmac.1


title: ss8_P1H1, scRNAseq


title: ss8_P1H10, scRNAseq


title: SKOV3 cells, sicontrol, rep1


title: mm_atac_spreb_Cxcr4floxKmac.2


title: ss8_P1G6, scRNAseq


title: mm_atac_spreb_kdel.2

description: Ex Vivo Sorted IgKappa deleted small pre B cells

value: Small Pre B K-del


title: ss8_P1H2, scRNAseq


title: mm_atac_spreb_kmac.1

description: Ex Vivo Sorted Kappa-macroself small pre B cells

value: Small Pre B K-Macroself


title: mm_atac_spreb_kmac.2


title: SKOV3 cells, sicontrol, rep2


title: ss8_P1G8, scRNAseq


title: Csspt 3

city: Beijing

first: zhongyi

last: wang

state: Beijing

address: No.2 Yuanmingyuan Xi Lu

institute: CAU(China Agricultural University)

data_processing:
Analyses of the transcriptome data were performed on the BMKCloud platform  (www.biocloud.net).
HISAT2 software used to compare the sequenced Reads to the reference genome (Kim D, Langmead B, Salzberg S L. HISAT: a fast spliced aligner with low memory requirements[J]. Nature methods, 2015, 12(4): 357-360.).
Differentially expressed genes (DEGs) were calculated using DESeq2 (Love MI, Huber W and Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, pp. 550. doi:10.1186/s13059-014-0550-8.). The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. The false discovery rate (FDR) less than 0.05 and the fold change larger than 2 as were set as the threshold.
Genome_build: ChineseLong_v2
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

organism: Cucumis sativus

source_name: stigma at anthesis

extract_protocol:
The RNA of the sample was harvested using Trizol reagent. Illumina NEBNext® Ultra™ RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: at anthesis

value: Csspt-/-

tag: tissue

value: cucumber stigma and style


title: mm_atac_spreb_kdel.1


title: ss8_P1G3, scRNAseq


title: ss8_P1G2, scRNAseq


title: CssptCsalc 3

value: CssptCsalc-/-


title: CssptCsalc 2


title: Csspt 1


title: ss8_P1G1, scRNAseq


title: CssptCsalc 1


title: WT 3

value: wild type


title: ss8_P1G7, scRNAseq


title: WT 2


title: ss8_P1G4, scRNAseq


title: mm_atac_immatureb_kdel.2

description: Ex Vivo Sorted IgKappa deleted immature B cells

value: ImmatureB K-del


title: mm_atac_spreb_kmac.3


title: Csspt 2


title: mm_atac_immatureb_kmac.2

description: Ex Vivo Sorted Kappa-macroself immature B cells

value: ImmatureB K-Macroself


title: mm_atac_immatureb_kdel.1


title: Replicate 2: HTO-derived cDNA

city: Houston

first: Jlenia

last: Guarnerio

address: 6767 Bertner Ave

department: Genetics

institute: MD Anderson Cancer Center

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

library_source: other

data_processing:
The Cell Ranger pipeline from 10X Genomics was used to align, filter, and count reads from FASTQ data, generating count matrices for both gene expression and HTO barcodes.
Seurat package (v4) for R was used to demultiplex sample identity based on oligo hashtags, and to filter for doublets and dead cells. Following preprocessing, Seurat was used to perform dimensionality reduction, clustering, and differential expression analysis.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix_sarc001__ccne1-REP1.h5: Feature count data as sparse matrix (ouput from 10x Genomics "cellranger count" pipeline)
Supplementary files format and content: Sarcoma1_hash_idents.csv: original sample ID of each single-cell barcode corresponding to a high-quality cell.
Supplementary files format and content: filtered_feature_bc_matrix_sarc002__ccne1-REP2.h5: Feature count data as sparse matrix (ouput from 10x Genomics "cellranger count" pipeline)
Supplementary files format and content: Sarcoma2_hash_idents.csv: original sample ID of each single-cell barcode corresponding to a high-quality cell.
Library strategy: CITE-Seq

molecule: protein

source_name: Whole tumor (sarcoma)

growth_protocol: Soft-tissue sarcoma cells were generated as transformed mesenchymal stem cells (bearing p53 KO and Ccne1 overexpression, allowed to form subcutaneous tumors in primary recipient mice).

extract_protocol:
Mouse tumors were digested into single-cell suspensions using the Mouse Tumor Dissociation Kit and gentleMACS dissociator (Miltenyi). CD45+ cells were enriched from each sample with magnetic beads. Enriched samples were individually hashtagged with a unique oligonucleotide barcodes (TotalSeq-A, Biolegend) and then pooled together in equal proportions at a concentration of 1000 cells/uL. Single cells were partitioned for RNA capture using 10X Chromium Controller.
mRNA and TotalSeq HTO libraries were prepared with the 10X Genomics Single Cell 3' Gene Expression kit v3 using standard manufacturer protocols, pooled together (5% for HTO library), and sequenced on the NovaSeq 6000 as 400M paired-end reads.

value: Whole tumor (sarcoma)

value: Tumor and immune cells

value: Mouse sarcoma p53-/- Ccne1+

tag: library type

value: HTO

tag: antibodies/tags

value: Biolegend TotalSeqA mouse hashtags 2, 3, 4, 6, 11, 12


title: mm_atac_immatureb_kappa.2

description: Ex Vivo Sorted immature B Kappa + cells

value: ImmatureB WT Kappa pos


title: ss8_P1G5, scRNAseq

value: Pax2+ cells


title: Csalc 3

value: Csalc-/-


title: ss8_P1G12, scRNAseq


title: mm_atac_immatureb_kappa.1

description: Ex Vivo Sorted immature B Kappa + cells


title: Replicate 1: HTO-derived cDNA


title: ss8_P1G11, scRNAseq


title: Replicate 1: mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: mRNA


title: WT 1


title: ss8_P1F7, scRNAseq


title: ss8_P1G10, scRNAseq


title: shSCR-2, Mif-WT

data_processing:
FASTQ files were trimmed with Trimmomatic.
Transcript abundances were quantified using salmon quant with the --gcBias flag set.
Assembly: mm10
Supplementary files format and content: Transcript abundance matrix (output from salmon)

source_name: Whole mouse tumor (sarcoma)

growth_protocol: Soft-tissue sarcoma cells were generated as transformed mesenchymal stem cells (bearing p53 KO and Ccne1 overexpression, allowed to form subcutaneous tumors in primary recipient mice). Then, transformed cells were additionally transduced with an sg- or shRNA against Mif or non-targeting control. sgRNA samples were transduced with Cas9. These cells were transplanted subcutaneously and allowed to grow tumors in secondary recipients.

extract_protocol: Total RNA was extracted from FACS-purified tumor cells using TRIzol (Invitrogen) according to the manufacturer's instructions.

value: Whole mouse tumor (sarcoma)

value: tumor cells ex vivo

value: Mif-wildtype