title: INF2-CA-HSPC, rep2, RNAseq

city: wuhan

first: song

last: zemin

address: no.185 the road of eastlake

institute: wuhan university

data_processing:
single-cell RNA-seq reads were aligned to the mouse mm10 reference genome, and gene expression was quantified via the Cell Ranger count tool (10×Genomics, version 7.1.0). We excluded single cells with fewer than 800 detected genes, over 7500 detected genes, or more than 8% of reads aligned to mitochondrial genes. The Seurat package's IntegrateData function was employed for data combination, with a resolution value of 0.2 and 30 principal components for cell clustering analysis. For RNAseq, raw fastq reads underwent alignment to the mouse genome (mm10) utilizing HISAT2 version 2.1.0. The raw read counts were normalized to Reads per Million (RPM) per sample and were portrayed as bigWig-formatted coverage tracks in the UCSC genome browser. To quantify read counts within specific genomic regions, HTSeq-count15 (version 0.12.3) was employed, and these counts were subsequently utilized by DESeq216 (version 1.32.0) for differential gene expression analysis.
Assembly: mm10

source_name: Bone marrow

extract_protocol:
Bone marrow was extracted from leukemia and wildtype mice's femurs and tibias. Bone marrow cell suspension was obtained by flushing bones with ice-cold PBS using a 25-gauge needle and 5-mL syringe, followed by filtration through a 70-µm nylon mesh strainer to remove debris. Bone marrow cells were further treated with ACK buffer for 2 minutes at 4°C to lyse red blood cells.
Utilizing the 10xGenomics Chromium Next GEM Single-cell 3′ v3.1 kit, we constructed single-cell RNA sequencing libraries as per the manufacturer's instructions. For RNAseq, poly(A)-containing mRNA was selectively enriched from 1 μg of total RNA utilizing VAHTS mRNA capture beads (Vazyme, N401-02). To generate fragments of 200-500 nucleotides in length, the enriched mRNA was fragmented through treatment with 2× ProtoScript II buffer (NEB, M0368). Following fragmentation, the first- and second-strand cDNA were generated, and adaptor ligation was carried out, followed by 12-15 cycles of PCR amplification.

value: ckit+HSPC

value: wild type


title: 39_192

status: Public on Jan 01 2025

type: RNA

city: Salt Lake City

first: Robert

middle: B

last: Weiss

state: UT

department: Human Genetics

country: USA

institute: University of Utah

hyb_protocol: Hybridization was performed at 45°C for 16 h using 5 μg of biotinylated target with each GeneChip® Human Exon 1.0 ST array (HuEx-1_0-st-v2, Affymetrix). Following hybridization, non-specifically bound material was removed by washing and detection of specifically bound target was performed using the GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix) and raw data were extracted from the scanned images and analyzed with the Expression Console software package (Affymetrix). Expression Console was used to compute separate gene-level and exon-level signal estimates for the Exon 1.0 ST Array data.

data_processing:
Exon-level estimates were derived using the PLIER (pm-gcbg) method after quantile sketch normalization. Probes sets (exons) were filtered for a ‘detected above background’ (DABG) P-value less than 0.05, resulting in 313 707 filtered exons that were considered in this study. Exon-level probe sets annotations were derived from the Affymetrix NetAffx file HuEx-1_0-st-v2 Probeset Annotations, CSV Format, Release 31. Gene-level estimates were derived using the IterPLIER (pm-gcbg) method after quantile sketch normalization. Only genes with core annotation (22 012 genes) were considered in this study. Transcript annotations were derived from the Affymetrix NetAffx file HuEx-1_0-st-v2 Transcript Cluster Annotations, CSV, Release 31.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.na33.1.hg19.probeset.csv
Exon-level estimates were derived using the PLIER (pm-gcbg) method after quantile sketch normalization. Gene-level estimates were derived using the IterPLIER (pm-gcbg) method after quantile sketch normalization.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Typical Williams syndrome deletion, Male

label_protocol: Biotinylated target was prepared following the protocol described in Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling and Control Reagents (Affymetrix P/N 900652).

growth_protocol: The immortalized lymphoblastiod cells (LCLs) were grown in RMPI 1640 with 10% FBS, 5% pen/strep, 5% L-glutamine and 0.5% gentamycin.

extract_protocol: Total RNA was isolated using the QIAGEN RNeasy Kit. Ribosomal RNA was removed from total RNA (1 μg per sample) using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen).

tag: disease state

value: Williams syndrome patient


title: rtgill.per.1.D06

type: SRA

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description:
Library name: rtgill.per.1.D06
Cell lysate
per.counts.txt
per.lib15_S1.D06.expression.values

library_source: transcriptomic

data_processing:
RNA-seq Analysis Portal (RAP; Qiagen)
Raw RNA Sequencing fastq files were submitted to QIAGEN’s RNA-seq Analysis Portal (RAP) (QIAGEN). First, raw files were demultiplexed to yield individual reads files for each sample (well) and then mapped to the rainbow trout genome (Omyk_1.0.105) to yield raw counts.
The counts were submitted to ExpressAnalyst for differential expression analysis and benchmark dose response analysis
Assembly: Omyk_1.0.105
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Oncorhynchus mykiss

source_name: RTgill-W1 per rep 1 conc 5

growth_protocol: Cells were grown in Thermo Scientific™ BioLite™ Cell Culture Treated 100 mm Petri dishes containing 10 ml of complete culture medium (Leibovitz L-15 culture medium supplemented with 10% fetal bovine serum and 1% Penicillin-Streptomycin), at 21°C.

extract_protocol:
OECD Test Guideline 249 for RTgill-W1 cell exposures, and QIAseq UPXome RNA Library Kits (QIAGEN) for library preparation
QIAseq UPXome RNA Library Kits (QIAGEN) protocol  for library preparation

tag: cell line

tag: cell type

value: Rainbow trout gill

tag: treatment


title: rtgill.per.1.E06

description:
Library name: rtgill.per.1.E06
Cell lysate
per.counts.txt
per.lib15_S1.E06.expression.values

source_name: RTgill-W1 per rep 1 conc 4


title: 5hmC_Seal SEQ16691

city: Shanghai

first: Yixiang

last: Shi

address: Room 303, Building #1, 928 Shenhong Road

country: China

institute: Accrete Covenant (AC) (Shanghai) Medical Technology Co., Ltd.

library_source: genomic

data_processing:
raw sequencing reads were trimmed for adaptor sequences using Trimmomatic
Low quality bases were also trimmed , followed by alignment to the current human genome reference (hg19) using Bowtie2 with the end-to-end alignment mode,Read pairs were concordantly aligned with fragment length ≤ 500 bp and with average ≤ 1 ambiguous base and up to four mismatched bases per 100 bp length.
Alignments with Mapping Quality Score ≥ 10 were counted for gene bodies, according to the gene start and gene end annotations by the GENCODE Project(release 19), using featureCounts without strand information.
Assembly: hg19
Supplementary files format and content: 5hmC_Count_Matrix.csv
Library strategy: 5hmC-Seal

molecule: genomic DNA

source_name: Plasma

extract_protocol:
Blood samples were prospectively collected for analysis at before the first cycle of chemotherapy. Approximately ~5 mL blood was collected for each patient. Plasma was separated within 2 hrs after blood draw, followed by extraction of circulating cfDNA using the Qiagen Circulating DNA Isolation Kit. DNA quality and quantity was examined with standard molecular protocols. High-quality cfDNA samples were frozen at -80C before library construction for the 5hmC-Seal pull-down.
Tagmentation reactions were performed in a 50ml solution with 1X tagmentation buffer from Nextera DNA Sample Preparation Kit (FC-121-1031). The input DNA ranged from 5 ng to 50 ng. Reactions were performed and purified according to the manufacturer’s instruction. In brief, the fragmentation reaction was performed in 50 ml solutions containing 25 ml 23 tagmentation buffer, gDNA, and 0.5-5 X l Tagmentase, at 55℃ for 5 min. The fragmented DNA was eluted into 17.5 ml ddH2O. The glucosylation reactions were performed in a 20 ml solution containing 50 mM HEPES buffer (pH 8.0), 25 mM MgCl2, purified DNA, 100 mM N3-UDP-Glc, and 1 mM bGT, at 37℃ for 1 hr. After the reaction, 2 ml DBCO-PEG4-DBCO (Click Chemistry Tools, 20 mM stock in DMSO) was added to the reaction mixture, and the mixture was incubated at 37℃ for 2 hr. Next, the modified DNA was purified by a Micro Bio-Spin 30 Column (Bio-Rad). The purified DNA was incubated with 5 ml C1 Streptavidin beads (Life Technologies) in 23 buffer (13 buffer: 5 mM Tris [pH 7.5], 0.5 mM EDTA, and 1 M NaCl) for 15 min according to the manufacture’s instruction. The beads were subsequently undergone six 5 min washes with 1X buffer. All binding and washing were done at room temperature with gentle rotation. The captured DNA fragments were amplified with 12–17 cycles of PCR amplification using the enzyme mix supplied in the Nextera kit. The PCR products were purified using AMPure XP beads according to the manufacture’s instruction. Separate input libraries were made by direct PCR from fragmented DNA without labeling and capture according to the manufacture’s instruction in the Nextera kit.
Briefly, each cfDNA sample was first prepared and ligated with adaptors. Next, the T4 bacteriophage enzyme β-glucosyltransferase (β-GT) was used to transfer an engineered glucose moiety containing an azide-group to 5hmC in duplex DNA. A biotin tag was then installed onto the azide group using Huisgen cycloaddition (“Click”) chemistry, followed by capturing of 5hmC-containing DNA fragments using avidin beads. The 5hmC-Seal library for DNA sample was then constructed through PCR amplification, followed by paired-end sequencing (PE38) on the Illumina Next-Seq 500 platform at Shanghai Epican Genetech, Ltd. (Shanghai, China).

tag: population

value: Chinese

tag: patient id

tag: tissue

value: Plasma


title: HCT116 GART-OE cells

city: China

first: Mengying

last: Ke

state: Jiangsu

institute: Nanjing University of Chinese Medicine

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 (FPKM) 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.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Multiple Myeloma cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: GART-OE


title: INF2-CA-HSPC, rep1, RNAseq

molecule: polyA RNA

organism: Mus musculus

value: Bone marrow

tag: disease


title: rtgill.per.1.C06

description:
Library name: rtgill.per.1.C06
Cell lysate
per.counts.txt
per.lib15_S1.C06.expression.values

source_name: RTgill-W1 per rep 1 conc 6


title: 37_191

source_name: Typical Williams syndrome deletion, Female


title: 33_138


title: 31_120


title: 15_5831


title: Ex-vivo expanded BM-MSCs from donor HDPV5

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

data_processing:
Basecalling using blc2fastq and trimming using cutadapt
Alignment using STAR and gene abundance estimation using featurecounts
Differential gene expression computed using DESeq2
Assembly: GRCh38
Supplementary files format and content: Tab-separated raw count file of gene quantifications

extract_protocol:
Total RNA was purified from sorted and ex-vivo expanded MSCs using the RNeasy Micro Kit (QIAGEN). DNase treatment was performed using RNase-free DNAse Set (QIAGEN), according to the manufacturer’s instructions. RNA was quantified with Nanodrop (Thermo Fisher) and its quality assessed by a 2100 Agilent Bioanalyser (Agilent Tech-nologies).
Minimum quality was defined as RNA integrity number (RIN) > 8. 300 ng of total RNA were used for library preparation with TruSeq Stranded mRNA (Illumina)

value: Mesenchymal Stromal Cells

tag: condition

value: Ex-vivo

tag: donor


title: 5hmC_Seal SEQ16609


title: MYLK-HSPC, rep1, RNAseq


title: 5hmC_Seal SEQ16315


title: rtgill.per.1.B06

description:
Library name: rtgill.per.1.B06
Cell lysate
per.counts.txt
per.lib15_S1.B06.expression.values

source_name: RTgill-W1 per rep 1 conc 7


title: ROCK1-KD-HSPC, rep2, RNAseq


title: rtgill.per.1.A06

description:
Library name: rtgill.per.1.A06
Cell lysate
per.counts.txt
per.lib15_S1.A06.expression.values

source_name: RTgill-W1 per rep 1 conc 8


title: HCT116 wildtype cells

value: wildtype


title: 07_5081


title: lung, unchallenged, rep4

city: Heidelberg

first: Christoph

last: Plass

address: Im Neueneimer Feld 280

department: Division of Cancer Epigenomics

country: Germany

institute: DKFZ (German Cancer Research Center)

description:
barcodes.tsv
counts.mtx
genes.tsv
metadata.tsv
normalised_counts.mtx

library_source: transcriptomic single cell

data_processing:
Merged FASTQ files were processed using cellranger v6.1.1 with default parameters and aligned to the mouse GRCm38 assembly. Subsequent analyses were conducted using Seurat v3.2.2 [Stuart et al., 2019]
To ensure data quality, we employed quantile-based thresholds for individual cell assessment. Cells exceeding the upper quantile threshold (90%) for the percentage of ribosomal and mitochondrial gene counts were considered potential outliers and excluded from downstream analyses. Moreover, we evaluated the number of detected features in each cell. Cells falling below the lower quantile threshold (2.5%) or exceeding the upper quantile threshold (97.5%) were categorized as low-quality or outlier cells, respectively, and were removed from further analyses.
For dimensionality reduction, we applied the RunUMAP function using the first 17 principal components for the entire dataset and the first 12 dimensions for the fibroblast subsetted dataset. Clustering was performed using the FindNeighbors function with the first 17 principal components and the FindClusters function with a resolution of 0.5. Marker genes for the identified clusters were determined using the FindAllMarkers function, with criteria set at >25% of cells expressing the markers in the given cluster and a log fold change of >0.25. To visualize gene expression levels projected onto UMAP plots, we utilized the cellcuratoR package [Voigt et al., 2020]. Cluster annotation was performed using known cell type markers to assign biological identities to the identified cell clusters.
To analyze the cell cycle phase for each cell, we followed the approach described by Tirosh et al. [2016]. Specifically, we assessed the relative expression of a set of 43 G1/S and 55 G2/M genes for each cell to generate a cell cycle score. Based on this score, we assigned cells to their corresponding cell cycle phase.
Assembly: mm10
Supplementary files format and content: Barcodes.tsv : cell barcodes
Supplementary files format and content: counts.mtx: raw counts matrix in matrix market format
Supplementary files format and content: normalized_counts.mtx: normalized counts matrix in matrix market format
Supplementary files format and content: genes.tsv: gene names corresponding to the counts matrix
Supplementary files format and content: metadata.tsv: tab-delimited file containing cell metadata

source_name: lung

extract_protocol:
Tissues of primary tumors (n=6), lung metastases (n=5) and unchallenged lungs (n=4) were mechanically dissociated followed by incubation for 45 min, rotating in the cold room, in 4 ml per 200 mg tissue of an enzyme mix containing LiberaseTM (#05401127007 Roche, Switzerland; 0.25 U/ml), Collagenase D (#11088866001 Roche, Switzerland; 0.6 U/ml), Dispase II (#17105-041 Gibco/ Thermo Fisher Scientific, USA; 4.5 U/ml) and DNaseI (Sigma Aldrich, USA; 50 U/ml). Remaining tissue fragments were further dissociated by passing the suspension through a syringe with an 18G cannula. The enzymatic reaction was stopped by adding DMEM containing 1 % BSA and 2.5 mM EDTA. After lysis of red blood cells (ACK buffer: 150 mM NH4Cl, 10 mM KHCO3, 0.1 mM EDTA) cell suspensions were cryopreserved in 90 % FCS + 10 % DMSO until library preparation. The above described protocol for dissociation and cryopreservation was developed based on recommendations from 10x Genomics (CG00039 Rev D) and multiple protocols described in literature 38-41. Before library preparation, cells were rapidly thawed, washed in pre-warmed DMEM + 2 % BSA and FACsorted. Cells were either sorted for living tdTomato+ cells or for living tdTomato+ CD45-cells. For additional CD45+ cell depletion, cells were re-suspended in Fc-block (CD16/32; 1:100), incubated 10 min on ice in the dark. Next, CD45- APC/Cy7 antibody (30-F11, BioLegend 103115) was added to a final dilution of 1:100 and further incubated for 20 min on ice in the dark. After washing, the cell pellet was re-suspended in 500 µl FACS buffer. Immediately before the sort DAPI was added 1:1000 (DAPI stock 10 mg/ml). Cells were collected in DNA low binding tubes containing 200 µl PBS + 0.04 % BSA + 0.1 mM EDTA.
Library preparation was performed using the Chromium Next GEM single cell 3' GEM, Library and Gel Bead Kit v3.1 together with the Chromium Next GEM Chip G Single Cell Kit, following manufacturer's instructions. Sequencing of the libraries was performed by the next-generation sequencing (NGS) Core Facility at the German Cancer Research Centre on a NovaSeq 6000.

value: lung

value: unchallenged


title: 5hmC_Seal SEQ16097


title: rtgill.diq.3.H05

description:
Library name: rtgill.diq.3.H05
Cell lysate
diq.counts.txt
diq.lib23_S1.H05.expression.values

source_name: RTgill-W1 diq rep 3 conc 1


title: 14_5785


title: 5hmC_Seal SEQ13951


title: EV2-HSPC, rep2, RNAseq


title: MYLK-HSPC, rep2, RNAseq


title: 13_5724


title: rtgill.diq.3.G05

description:
Library name: rtgill.diq.3.G05
Cell lysate
diq.counts.txt
diq.lib23_S1.G05.expression.values

source_name: RTgill-W1 diq rep 3 conc 2


title: rtgill.diq.3.F05

description:
Library name: rtgill.diq.3.F05
Cell lysate
diq.counts.txt
diq.lib23_S1.F05.expression.values

source_name: RTgill-W1 diq rep 3 conc 3


title: EV2-HSPC, rep1, RNAseq


title: 12_5596


title: 5hmC_Seal SEQ14254


title: 5hmC_Seal SEQ14269


title: ΔACD-S-HSPC, rep2, RNAseq


title: 5hmC_Seal SEQ14683


title: 09_107


title: 08_5783


title: 5hmC_Seal SEQ16613


title: rtgill.diq.3.D05

description:
Library name: rtgill.diq.3.D05
Cell lysate
diq.counts.txt
diq.lib23_S1.D05.expression.values

source_name: RTgill-W1 diq rep 3 conc 5


title: rtgill.diq.3.E05

description:
Library name: rtgill.diq.3.E05
Cell lysate
diq.counts.txt
diq.lib23_S1.E05.expression.values

source_name: RTgill-W1 diq rep 3 conc 4


title: ΔRBD-S-HSPC, rep2, RNAseq


title: ROCK1-KD-HSPC, rep1, RNAseq


title: rtgill.diq.3.C05

description:
Library name: rtgill.diq.3.C05
Cell lysate
diq.counts.txt
diq.lib23_S1.C05.expression.values

source_name: RTgill-W1 diq rep 3 conc 6


title: 5hmC_Seal SEQ16288


title: ΔRBD-S-HSPC, rep1, RNAseq

source_name: Bone marrow


title: rtgill.diq.3.B05

description:
Library name: rtgill.diq.3.B05
Cell lysate
diq.counts.txt
diq.lib23_S1.B05.expression.values

source_name: RTgill-W1 diq rep 3 conc 7


title: 05_5073


title: CS-HSPC, rep2, RNAseq


title: 5hmC_Seal SEQ16289


title: rtgill.diq.3.A05

description:
Library name: rtgill.diq.3.A05
Cell lysate
diq.counts.txt
diq.lib23_S1.A05.expression.values

source_name: RTgill-W1 diq rep 3 conc 8


title: 5hmC_Seal SEQ14691


title: CS-HSPC, rep1, RNAseq


title: rtgill.diq.2.H05

description:
Library name: rtgill.diq.2.H05
Cell lysate
diq.counts.txt
diq.lib19_S1.H05.expression.values

source_name: RTgill-W1 diq rep 2 conc 1


title: EV-HSPC, rep2, RNAseq


title: 5hmC_Seal SEQ14356

source_name: Plasma


title: 01_166


title: ΔACD-S-HSPC, rep1, RNAseq


title: 06_5656


title: 11_5082


title: rtgill.diq.2.G05

description:
Library name: rtgill.diq.2.G05
Cell lysate
diq.counts.txt
diq.lib19_S1.G05.expression.values

source_name: RTgill-W1 diq rep 2 conc 2


title: 5hmC_Seal SEQ13071


title: EV-HSPC, rep1, RNAseq


title: rtgill.diq.2.F05

description:
Library name: rtgill.diq.2.F05
Cell lysate
diq.counts.txt
diq.lib19_S1.F05.expression.values

source_name: RTgill-W1 diq rep 2 conc 3


title: 5hmC_Seal SEQ14076


title: 07_5678

source_name: Typical Williams syndrome deletion, Female


title: MYL12B-2E, rep2, RNAseq

value: bone marrow cells

value: Acute myeloid leukemia


title: MYL12B-2E, rep3, RNAseq


title: rtgill.diq.2.E05

description:
Library name: rtgill.diq.2.E05
Cell lysate
diq.counts.txt
diq.lib19_S1.E05.expression.values

source_name: RTgill-W1 diq rep 2 conc 4


title: 04_5067

source_name: Typical Williams syndrome deletion, Male


title: 5hmC_Seal SEQ14239


title: 03_5025


title: 10_198


title: 02_5001


title: rtgill.diq.2.D05

description:
Library name: rtgill.diq.2.D05
Cell lysate
diq.counts.txt
diq.lib19_S1.D05.expression.values

source_name: RTgill-W1 diq rep 2 conc 5


title: MYL12B-2E, rep1, RNAseq


title: 5hmC_Seal SEQ14252


title: rtgill.diq.2.C05

description:
Library name: rtgill.diq.2.C05
Cell lysate
diq.counts.txt
diq.lib19_S1.C05.expression.values

source_name: RTgill-W1 diq rep 2 conc 6


title: 60_5025a

value: unaffected parental control


title: INF2-CA, rep3, RNAseq


title: rtgill.diq.2.A05

description:
Library name: rtgill.diq.2.A05
Cell lysate
diq.counts.txt
diq.lib19_S1.A05.expression.values

source_name: RTgill-W1 diq rep 2 conc 8


title: rtgill.diq.2.B05

description:
Library name: rtgill.diq.2.B05
Cell lysate
diq.counts.txt
diq.lib19_S1.B05.expression.values

source_name: RTgill-W1 diq rep 2 conc 7


title: INF2-CA, rep1, RNAseq


title: 5hmC_Seal SEQ13282


title: rtgill.diq.1.H05

description:
Library name: rtgill.diq.1.H05
Cell lysate
diq.counts.txt
diq.lib15_S1.H05.expression.values

source_name: RTgill-W1 diq rep 1 conc 1


title: INF2-CA, rep2, RNAseq


title: 5hmC_Seal SEQ19498


title: MYLK, rep3, RNAseq


title: rtgill.diq.1.G05

description:
Library name: rtgill.diq.1.G05
Cell lysate
diq.counts.txt
diq.lib15_S1.G05.expression.values

source_name: RTgill-W1 diq rep 1 conc 2


title: MYLK, rep2, RNAseq


title: 5hmC_Seal SEQ17063


title: rtgill.diq.1.F05

description:
Library name: rtgill.diq.1.F05
Cell lysate
diq.counts.txt
diq.lib15_S1.F05.expression.values

source_name: RTgill-W1 diq rep 1 conc 3


title: MYLK, rep1, RNAseq

source_name: Bone marrow


title: 5hmC_Seal SEQ17356


title: 19_5657a

source_name: Parental Control, Female


title: 5hmC_Seal SEQ19285


title: ROCK1-KD, rep3, RNAseq


title: 24_5656b

source_name: Parental Control, Male


title: rtgill.diq.1.D05

description:
Library name: rtgill.diq.1.D05
Cell lysate
diq.counts.txt
diq.lib15_S1.D05.expression.values

source_name: RTgill-W1 diq rep 1 conc 5


title: 5hmC_Seal SEQ19975

source_name: Plasma


title: 17_5623a


title: 22_5082a


title: 21_5884a


title: ROCK1-KD, rep2, RNAseq


title: 08_5081B


title: rtgill.diq.1.C05

description:
Library name: rtgill.diq.1.C05
Cell lysate
diq.counts.txt
diq.lib15_S1.C05.expression.values

source_name: RTgill-W1 diq rep 1 conc 6


title: 5hmC_Seal SEQ16470


title: ROCK1-KD, rep1, RNAseq


title: 10_5682A


title: rtgill.diq.1.B05

description:
Library name: rtgill.diq.1.B05
Cell lysate
diq.counts.txt
diq.lib15_S1.B05.expression.values

source_name: RTgill-W1 diq rep 1 conc 7


title: 5hmC_Seal SEQ14993


title: 48_5079a


title: 5hmC_Seal SEQ19919


title: rtgill.diq.1.A05

description:
Library name: rtgill.diq.1.A05
Cell lysate
diq.counts.txt
diq.lib15_S1.A05.expression.values

source_name: RTgill-W1 diq rep 1 conc 8


title: 5hmC_Seal SEQ12671


title: 46_5067a


title: 45_5065b


title: ΔRBD-L, rep3, RNAseq


title: rtgill.diq.1.E05

description:
Library name: rtgill.diq.1.E05
Cell lysate
diq.counts.txt
diq.lib15_S1.E05.expression.values

source_name: RTgill-W1 diq rep 1 conc 4


title: ΔRBD-L, rep2, RNAseq


title: 5hmC_Seal SEQ9542


title: rtgill.clp.3.H04

description:
Library name: rtgill.clp.3.H04
Cell lysate
clp.counts.txt
clp.lib23_S1.H04.expression.values

source_name: RTgill-W1 clp rep 3 conc 1


title: 5hmC_Seal SEQ16682


title: ΔRBD-L, rep1, RNAseq


title: 23_5001b


title: ΔRBD-S, rep3, RNAseq


title: rtgill.clp.3.F04

description:
Library name: rtgill.clp.3.F04
Cell lysate
clp.counts.txt
clp.lib23_S1.F04.expression.values

source_name: RTgill-W1 clp rep 3 conc 3


title: 5hmC_Seal SEQ9517


title: 5hmC_Seal SEQ13792


title: 42_566b


title: ΔRBD-S, rep1, RNAseq


title: rtgill.clp.3.E04

description:
Library name: rtgill.clp.3.E04
Cell lysate
clp.counts.txt
clp.lib23_S1.E04.expression.values

source_name: RTgill-W1 clp rep 3 conc 4


title: ΔRBD-S, rep2, RNAseq


title: 40_192a


title: 5hmC_Seal SEQ13771


title: rtgill.clp.3.D04

description:
Library name: rtgill.clp.3.D04
Cell lysate
clp.counts.txt
clp.lib23_S1.D04.expression.values

source_name: RTgill-W1 clp rep 3 conc 5


title: 5hmC_Seal SEQ19261


title: 38_191a


title: CS, rep3, RNAseq


title: 36_156a


title: rtgill.clp.3.B04

description:
Library name: rtgill.clp.3.B04
Cell lysate
clp.counts.txt
clp.lib23_S1.B04.expression.values

source_name: RTgill-W1 clp rep 3 conc 7


title: CS, rep2, RNAseq


title: rtgill.clp.3.G04

description:
Library name: rtgill.clp.3.G04
Cell lysate
clp.counts.txt
clp.lib23_S1.G04.expression.values

source_name: RTgill-W1 clp rep 3 conc 2


title: rtgill.clp.3.C04

description:
Library name: rtgill.clp.3.C04
Cell lysate
clp.counts.txt
clp.lib23_S1.C04.expression.values

source_name: RTgill-W1 clp rep 3 conc 6


title: 5hmC_Seal SEQ19359


title: CS, rep1, RNAseq


title: 34_138a


title: 5hmC_Seal SEQ16735


title: HSPC, rep3, RNAseq


title: rtgill.clp.3.A04

description:
Library name: rtgill.clp.3.A04
Cell lysate
clp.counts.txt
clp.lib23_S1.A04.expression.values

source_name: RTgill-W1 clp rep 3 conc 8


title: rtgill.clp.2.H04

description:
Library name: rtgill.clp.2.H04
Cell lysate
clp.counts.txt
clp.lib19_S1.H04.expression.values

source_name: RTgill-W1 clp rep 2 conc 1


title: 5hmC_Seal SEQ17170


title: HSPC, rep2, RNAseq

source_name: Bone marrow


title: 35_156

source_name: Typical Williams syndrome deletion, Female


title: 5hmC_Seal SEQ14238


title: 32_120a

source_name: Parental Control, Female


title: HSPC, rep1, RNAseq


title: CD3_transcripts-GVHD.Lungs-7

city: Boston

first: Kayleigh

last: Ingersoll Omdahl

address: 1 Blackfan st

institute: Boston Children's Hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degrees C on GeneChip Rhesus Macaque Genome Array.  GeneChip arrays were washed and stained in the Affymetrix Fluidics Station 450 using the Fluidics script FS450_0001.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 scanner with 7G upgrade.

data_processing: Data from .CEL files were uploaded to the Bioconductor for further analysis and normalized using RMA (‘affy’ package).  Resulting fluorescent intensities were normalized to account for batch effects using the Limma package.

organism: Macaca mulatta

source_name: CD3_transcripts, allogeneic transplant, lungs

label_protocol: Biotinylated cRNA were prepared using the Affymetrix 3’IVT Plus protocol from 70-85 ng total RNA.

extract_protocol: CD3 T cells were lysed in RLT Buffer and total RNA was isolated using the RNAEasy kit per manufacturers instructions.

treatment_protocol: Cohorts of rhesus macaques received either an allogeneic or autologous HCT.  Flow Cytometric sorting of CD3+CD20- T cells was performed using a FACSAria or FACSJazz Cell Sorters (BD). T cells were sorted on day +8 post-transplant or at the time of terminal analysis when the allogeneic transplant group animals met endpoint criteria.

tag: individual

tag: group

value: GVHD

value: Lungs

tag: batch

tag: day post hct

tag: gender

value: F


title: rtgill.clp.2.E04

description:
Library name: rtgill.clp.2.E04
Cell lysate
clp.counts.txt
clp.lib19_S1.E04.expression.values

source_name: RTgill-W1 clp rep 2 conc 4


title: rtgill.clp.2.G04

description:
Library name: rtgill.clp.2.G04
Cell lysate
clp.counts.txt
clp.lib19_S1.G04.expression.values

source_name: RTgill-W1 clp rep 2 conc 2


title: rtgill.clp.2.F04

description:
Library name: rtgill.clp.2.F04
Cell lysate
clp.counts.txt
clp.lib19_S1.F04.expression.values

source_name: RTgill-W1 clp rep 2 conc 3


title: 5hmC_Seal SEQ10909

source_name: Plasma


title: BM MNC, rep2, RNAseq

value: mononuclear cells

value: wild type


title: rtgill.clp.2.D04

description:
Library name: rtgill.clp.2.D04
Cell lysate
clp.counts.txt
clp.lib19_S1.D04.expression.values

source_name: RTgill-W1 clp rep 2 conc 5

value: Rainbow trout gill


title: 5hmC_Seal SEQ14440

value: Chinese

value: Plasma


title: CD3_transcripts-GVHD.Lungs-6


title: BM MNC, rep1, RNAseq

value: Bone marrow


title: rtgill.clp.2.C04

description:
Library name: rtgill.clp.2.C04
Cell lysate
clp.counts.txt
clp.lib19_S1.C04.expression.values

source_name: RTgill-W1 clp rep 2 conc 6


title: MP, rep3, RNAseq

value: lin-ckit+Sca-


title: 5hmC_Seal SEQ13844


title: CD3_transcripts-GVHD.Lungs-5


title: rtgill.clp.2.B04

description:
Library name: rtgill.clp.2.B04
Cell lysate
clp.counts.txt
clp.lib19_S1.B04.expression.values

source_name: RTgill-W1 clp rep 2 conc 7


title: CD3_transcripts-GVHD.Lungs-3

value: M


title: MP, rep2, RNAseq


title: CD3_transcripts-GVHD.Lungs-4


title: rtgill.clp.2.A04

description:
Library name: rtgill.clp.2.A04
Cell lysate
clp.counts.txt
clp.lib19_S1.A04.expression.values

source_name: RTgill-W1 clp rep 2 conc 8


title: CD3_transcripts-GVHD.Lungs-1


title: 5hmC_Seal SEQ13726


title: CD3_transcripts-GVHD.Liver-9

source_name: CD3_transcripts, allogeneic transplant, liver

value: Liver


title: CD3_transcripts-GVHD.Lungs-2


title: 5hmC_Seal SEQ17247


title: CD3_transcripts-GVHD.Liver-8


title: BM MNC, rep3, RNAseq


title: 5hmC_Seal SEQ16929


title: 5hmC_Seal SEQ13724


title: MP, rep1, RNAseq


title: MYL12B-2E, scRNAseq

description: 10x Genomics


title: rtgill.clp.1.H04

description:
Library name: rtgill.clp.1.H04
Cell lysate
clp.counts.txt
clp.lib15_S1.H04.expression.values

source_name: RTgill-W1 clp rep 1 conc 1


title: 5hmC_Seal SEQ17139


title: rtgill.clp.1.G04

description:
Library name: rtgill.clp.1.G04
Cell lysate
clp.counts.txt
clp.lib15_S1.G04.expression.values

source_name: RTgill-W1 clp rep 1 conc 2


title: rtgill.clp.1.F04

description:
Library name: rtgill.clp.1.F04
Cell lysate
clp.counts.txt
clp.lib15_S1.F04.expression.values

source_name: RTgill-W1 clp rep 1 conc 3


title: INF2-CA, scRNAseq

description: 10x Genomics


title: MYLK, scRNAseq

description: 10x Genomics


title: 5hmC_Seal SEQ13822


title: CD3_transcripts-GVHD.Liver-4


title: CD3_transcripts-GVHD.Liver-6


title: CD3_transcripts-GVHD.Liver-7


title: 5hmC_Seal SEQ14986


title: rtgill.clp.1.E04

description:
Library name: rtgill.clp.1.E04
Cell lysate
clp.counts.txt
clp.lib15_S1.E04.expression.values

source_name: RTgill-W1 clp rep 1 conc 4


title: ROCK1-KD, scRNAseq

description: 10x Genomics

source_name: Bone marrow


title: rtgill.clp.1.D04

description:
Library name: rtgill.clp.1.D04
Cell lysate
clp.counts.txt
clp.lib15_S1.D04.expression.values

source_name: RTgill-W1 clp rep 1 conc 5


title: 5hmC_Seal SEQ14442


title: 5hmC_Seal SEQ13801


title: CD3_transcripts-GVHD.Liver-3


title: ΔRBD-S, scRNAseq

description: 10x Genomics


title: rtgill.clp.1.B04

description:
Library name: rtgill.clp.1.B04
Cell lysate
clp.counts.txt
clp.lib15_S1.B04.expression.values

source_name: RTgill-W1 clp rep 1 conc 7


title: CD3_transcripts-GVHD.Liver-5


title: 5hmC_Seal SEQ10933


title: ΔRBD-L, scRNAseq

description: 10x Genomics


title: rtgill.clp.1.C04

description:
Library name: rtgill.clp.1.C04
Cell lysate
clp.counts.txt
clp.lib15_S1.C04.expression.values

source_name: RTgill-W1 clp rep 1 conc 6


title: rtgill.clp.1.A04

description:
Library name: rtgill.clp.1.A04
Cell lysate
clp.counts.txt
clp.lib15_S1.A04.expression.values

source_name: RTgill-W1 clp rep 1 conc 8


title: 5hmC_Seal SEQ16220


title: CD3_transcripts-GVHD.Liver-2


title: 5hmC_Seal SEQ13255


title: CS, scRNAseq

description: 10x Genomics


title: WT, scRNAseq

description: 10x Genomics


title: 5hmC_Seal SEQF4727


title: CD3_transcripts-GVHD.Liver-1


title: Chase

city: Chengdu

first: XUEYANG

last: LIAO

state: Sichuan

address: NO.14 3rd section of Renminnan Road

institute: Sichuan university

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow stromal cells

extract_protocol:
For isolation of stromal cells from endosteum niche, the femur and tibia bones were dissected out with the removal of muscle, connective tissue including periosteum, the epiphysis ends, the growth plates. 3mm length of the metaphysis ends of distal femur and proximal tibia were collected for future use. While the 3mm ends of proximal femur and distal tibia were removed and discarded. Bone marrow from the diaphysis was gently flushed out with 4ml flushing medium (M-199 supplemented with 10% FBS) for each bone with a 27-G needle at a fluid flow rate of 20ml/min. The rest of diaphysis middle shaft bones together with the 3mm metaphysis ends were cut into pieces (4-5 pieces for each bone), then were transferred into a 15ml centrifuge tube. The bone pieces were added with 5ml of freshly made digestion medium (1 mg/mL STEMxyme1 and 1 mg/mL Dispase II dissolved in M-199 with 2% FBS and filter sterilized with 0.45um filter) and digested on a shaker at a speed of 110rpm for 25min at 37℃. After the digestion, cell pellets were washed with 10ml cold washing buffer and passed through 70um cell strainer. Cells were then centrifuged at 300rpm for 5min, and were re-suspended in appropriate volume of cold sorting buffer (HBSS supplemented with 25mM HEPES pH7 and 2% FBS, filter sterilize using 0.2uM filter) to make the cell concentration at 0.8-1.2×107/ml. A MoFlo Astrios Sorter was used for sorting. Bright dTomato+ (0.01% of total in the pulse sample, 0.29% of total in the chase sample) cells were collected for single cell RNA-seq.
scRNA-seq libraries were constructed with bone marrow mesenchymal cells from endosteal niche of pulse versus chase sample with the Single Cell 3’ Reagent Kits v3.1 (10x Genomics).

treatment_protocol: Four Adipoq-CreERT2;Ai9 male mice were used for single-cell RNA sequencing. Mice were tamoxifen administrated at 8 weeks of age for 3 consecutive days and were harvested after 24hrs for the pulse dataset and 4wks for chase dataset.

value: bone marrow stromal cells

value: tdTomato+ bone marrow mesenchymal cells in endosteum niche of femur and tibia

value: Tamoxifen oral gavage at 8 weeks of age, harvested after 4 weeks.


title: CD3_transcripts-GVHD.Blood-9

source_name: CD3_transcripts, allogeneic transplant, blood

value: Blood


title: rtgill.diz.3.G02

description:
Library name: rtgill.diz.3.G02
Cell lysate
diz.counts.txt
diz.lib22_S1.G02.expression.values

source_name: RTgill-W1 diz rep 3 conc 2


title: CD3_transcripts-GVHD.Blood-8


title: Pulse

description: 10x Genomics

value: Tamoxifen oral gavage at 8 weeks of age, harvested after 24hrs


title: 5hmC_Seal SEQ10265

source_name: Plasma


title: rtgill.diz.3.F02

description:
Library name: rtgill.diz.3.F02
Cell lysate
diz.counts.txt
diz.lib22_S1.F02.expression.values

source_name: RTgill-W1 diz rep 3 conc 3


title: CD3_transcripts-GVHD.Blood-6

value: GVHD


title: 5hmC_Seal SEQ5582


title: CD4 T Cells, ORAI1/2 KO, Uninfected, rep2

city: New York

first: Maxwell

last: McDermott

state: NY

address: 550 1st Ave

department: Pathology

institute: NYU Langone Health

data_processing:
ATAC-seq reads were aligned to the mm10 genome using bowtie 2.2.2, guide by GTF
Calculating insert size and standard deviation performed using Picard tools
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Assembly: mm10
Supplementary files format and content: The BigWig files include RPKM values in 1bp bins for each ATAC-seq sample.

source_name: Spleen

extract_protocol:
Mediastinal LN were isolated at day 8 to prepare single-cell suspensions, and CD4+ T cells were isolated from single cell suspensions by negative separation using a mouse CD4+ T cell Enrichment kit (STEMCELL Technologies). ATAC-seq library purification was performed with the MinElute PCR Purification Kit (Zymo Research) and library size distribution was assessed using the Bioanalyzer High Sensitivity DNA Kit (Agilent).
ATAC-seq libraries were quantified before pooling and sequencing using the real-time library quantification kit (KAPA Biosystems). Paired-end sequencing was performed on a S1 100 Cycle Flow cells v 1.5 with 100 cycles for each read.

treatment_protocol: CD4+ T cells isolated from Orai1fl/fl Orai2-/- Cd4Cre OTII mice without influenza infection

value: Spleen

value: CD4+ T cells

value: Orai1 & Orai2 Knockout

tag: infection

value: Uninfected


title: CD3_transcripts-GVHD.Blood-7

value: F


title: rtgill.diz.3.D02

description:
Library name: rtgill.diz.3.D02
Cell lysate
diz.counts.txt
diz.lib22_S1.D02.expression.values

source_name: RTgill-W1 diz rep 3 conc 5

value: Rainbow trout gill


title: 5hmC_Seal SEQ19438

value: Chinese

value: Plasma


title: 5hmC_Seal SEQ19437


title: rtgill.diz.3.E02

description:
Library name: rtgill.diz.3.E02
Cell lysate
diz.counts.txt
diz.lib22_S1.E02.expression.values

source_name: RTgill-W1 diz rep 3 conc 4


title: rtgill.diz.3.C02

description:
Library name: rtgill.diz.3.C02
Cell lysate
diz.counts.txt
diz.lib22_S1.C02.expression.values

source_name: RTgill-W1 diz rep 3 conc 6


title: 5hmC_Seal SEQ19243


title: CD4 T Cells, ORAI1 KO, Uninfected, rep2

treatment_protocol: CD4+ T cells isolated from Orai1fl/fl Cd4Cre OTII mice without influenza infection

value: Orai1 Knockout


title: CD4 T Cells, ORAI1/2 KO, Uninfected, rep1


title: CD3_transcripts-GVHD.Blood-5

value: M


title: 5hmC_Seal SEQ17298


title: CD4 T Cells, ORAI1 KO, Uninfected, rep1


title: CD4 T Cells, Wildtype, Uninfected, rep2

treatment_protocol: Wildtype OTII CD4+ T cells isolated from mice without influenza infection

value: WT


title: rtgill.diz.3.H02

description:
Library name: rtgill.diz.3.H02
Cell lysate
diz.counts.txt
diz.lib22_S1.H02.expression.values

source_name: RTgill-W1 diz rep 3 conc 1


title: CD3_transcripts-GVHD.Blood-3


title: rtgill.diz.3.A02

description:
Library name: rtgill.diz.3.A02
Cell lysate
diz.counts.txt
diz.lib22_S1.A02.expression.values

source_name: RTgill-W1 diz rep 3 conc 8


title: 5hmC_Seal SEQ16760


title: 5hmC_Seal SEQ16762


title: CD4 T Cells, Wildtype, Uninfected, rep1


title: rtgill.diz.2.H03

description:
Library name: rtgill.diz.2.H03
Cell lysate
diz.counts.txt
diz.lib18_S1.H03.expression.values

source_name: RTgill-W1 diz rep 2 conc 1


title: CD4 T Cells, ORAI1/2 KO, 8 Day Infected, rep3

source_name: mediastinal lymph nodes

treatment_protocol: Orai1fl/fl Orai2-/- Cd4Cre OTII CD4+ T cells isolated from TCRA -/- mice after adoptive transfer and post 8 days infection with influenza virus strain PR8-OVA (200 VFU)

value: mediastinal lymph nodes

value: 8 Day Infected


title: rtgill.diz.2.G03

description:
Library name: rtgill.diz.2.G03
Cell lysate
diz.counts.txt
diz.lib18_S1.G03.expression.values

source_name: RTgill-W1 diz rep 2 conc 2


title: rtgill.diz.3.B02

description:
Library name: rtgill.diz.3.B02
Cell lysate
diz.counts.txt
diz.lib22_S1.B02.expression.values

source_name: RTgill-W1 diz rep 3 conc 7


title: CD3_transcripts-GVHD.Blood-1


title: 5hmC_Seal SEQ16763


title: CD3_transcripts-GVHD.Blood-2


title: CD4 T Cells, ORAI1/2 KO, 8 Day Infected, rep2


title: CD3_transcripts-GVHD.Blood-4


title: CD3_transcripts-Healthy.Control.Lungs-9

source_name: CD3_transcripts, healthy control, lungs

value: HC

value: Lungs


title: 5hmC_Seal SEQ14910


title: CD3_transcripts-Healthy.Control.Lungs-7


title: rtgill.diz.2.E03

description:
Library name: rtgill.diz.2.E03
Cell lysate
diz.counts.txt
diz.lib18_S1.E03.expression.values

source_name: RTgill-W1 diz rep 2 conc 4


title: CD3_transcripts-Healthy.Control.Lungs-6


title: 5hmC_Seal SEQ14487


title: 5hmC_Seal SEQ14163


title: CD4 T Cells, Wildtype, 8 Day Infected, rep2

treatment_protocol: Wildtype OTII CD4+ T cells isolated from TCRA -/- mice after adoptive transfer and post 8 days infection with influenza virus strain PR8-OVA (200 VFU)


title: CD4 T Cells, ORAI1 KO, 8 Day Infected, rep2

treatment_protocol: Orai1fl/fl Cd4Cre OTII CD4+ T cells isolated from TCRA -/- mice after adoptive transfer and post 8 days infection with influenza virus strain PR8-OVA (200 VFU)


title: rtgill.diz.2.D03

description:
Library name: rtgill.diz.2.D03
Cell lysate
diz.counts.txt
diz.lib18_S1.D03.expression.values

source_name: RTgill-W1 diz rep 2 conc 5


title: rtgill.diz.2.C03

description:
Library name: rtgill.diz.2.C03
Cell lysate
diz.counts.txt
diz.lib18_S1.C03.expression.values

source_name: RTgill-W1 diz rep 2 conc 6


title: CD4 T Cells, ORAI1/2 KO, 8 Day Infected, rep1


title: 5hmC_Seal SEQ14162


title: rtgill.diz.2.B03

description:
Library name: rtgill.diz.2.B03
Cell lysate
diz.counts.txt
diz.lib18_S1.B03.expression.values

source_name: RTgill-W1 diz rep 2 conc 7


title: CD4 T Cells, ORAI1 KO, 8 Day Infected, rep1


title: rtgill.diz.2.F03

description:
Library name: rtgill.diz.2.F03
Cell lysate
diz.counts.txt
diz.lib18_S1.F03.expression.values

source_name: RTgill-W1 diz rep 2 conc 3


title: CD3_transcripts-Healthy.Control.Lungs-5


title: CD3_transcripts-Healthy.Control.Lungs-8


title: E16.5 Urethra mesenchyme, male biol replicate 4

city: Bengaluru

first: Diya

last: Binoy Joseph

state: Karnataka

address: GKVK - Post, Bellary Rd

country: India

institute: Institute for Stem Cell Science and Regenerative Medicine

description:
Litter 0041
0041_M_UrSt_S8

data_processing:
Basecalling and demultiplexing was peformed using Illumina bcl2fastq.
Read mapping was peformed using hisat2-2.1.0 using reference grcm38.
.sam files obtained after read mapping were converted to unsorted.bam files using samtools1.12. Using samtools, .bam files were sorted and deduplicated.
Feature counts were extracted from deduplicated .bam files using subread-1.6.3 with Gencode evidence-based annotation of the mouse genome (GRCm38), version M23 (Ensembl 98).
Raw read counts were processed in R using DESeq2 to obtain normalized counts.
Assembly: grcm38
Supplementary files format and content: tab-delimited text file containing read counts for each sample.
Supplementary files format and content: tab-delimited text file containing read counts summary for each sample.
Supplementary files format and content: comma-separated values file containing normalized counts for each sample.

source_name: E16.5 urethra mesenchyme

growth_protocol: CD-1 wildtype females were maintained on standard chow and in specific-pathogen free housing. Timed breeding was performed with CD-1 wildtype males and noon of vaginal plug identification was considered to be embryonic day 0.5. Timed pregnant females were euthanized on embryonic day 16.5 and embryos were collected for the study.

extract_protocol:
Tissues were directly lysed in 350 ul of RLT plus buffer with beta-mercaptoethanol from the Qiagen Rneasy Microkit (#74004). Tissue samples were subject to vortexing and stored at -80 C. For RNA extraction, tissue samples were thawed and homogenized using Qiashredder columns before processing with the Qiagen RNeasy Microkit following manufacturer instructions. According to instructions, a genomic DNA removal step was performed using genomic DNA removal columns. RNA was eluted in 16 ul of nuclease free water and RNA amounts were quantified using Qubit RNA-high sensitivity kit.
250 ng of total RNA was used for library construction. NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490L) was used for mRNA isolation according to manufacturer instructions. NEBNext® Ultra™ II Directional RNA Library Prep kit with Sample Purification Beads (#E7765L) was used for library preparation according to manufacturer instructions. Samples were sequenced using NovaSeq 6000. 100 bp pair-ended reads were obtained.

treatment_protocol: Lower urinary tract including bladder and pelvic urethra were dissected from embryonic day 16.5 embryos. Tissues were treated with a 1% trypsin solution on ice for 90 minutes. Tissues were washed in HBSS solution and briefly treated with Dnase. Epithelial and mesenchymal layers of the bladder and urethra were mechanically separated using fine forceps. Male and female tissues from each litter were pooled separately to obtain 4 samples per litter: Female bladder mesenchyme, Female urethral mesenchyme, Male bladder mesenchyme, Male urethral mesenchyme. Tissues were collected from 4 independent litters for a total of 16 samples.

value: E16.5 urethra mesenchyme

tag: strain

tag: Sex

value: male

value: Wildtype


title: 5hmC_Seal SEQ19435

source_name: Plasma


title: 5hmC_Seal SEQ19236


title: CD3_transcripts-Healthy.Control.Lungs-3


title: CD4 T Cells, Wildtype, 8 Day Infected, rep1

tag: cell type

value: CD4+ T cells


title: CD3_transcripts-Healthy.Control.Lungs-2


title: 5hmC_Seal SEQ14073


title: E16.5 Urethra mesenchyme, male biol replicate 3

description:
Litter 0040
0040_M_UrSt_S6

tag: treatment


title: rtgill.diz.1.H03

description:
Library name: rtgill.diz.1.H03
Cell lysate
diz.counts.txt
diz.lib14_S1.H03.expression.values

source_name: RTgill-W1 diz rep 1 conc 1

tag: cell line


title: rtgill.diz.1.G03

description:
Library name: rtgill.diz.1.G03
Cell lysate
diz.counts.txt
diz.lib14_S1.G03.expression.values

source_name: RTgill-W1 diz rep 1 conc 2


title: CD3_transcripts-Healthy.Control.Lungs-4


title: E16.5 Urethra mesenchyme, male biol replicate 2

description:
Litter 0039
0039_M_UrSt_S4


title: CD3_transcripts-Healthy.Control.Lungs-1


title: rtgill.diz.1.F03

description:
Library name: rtgill.diz.1.F03
Cell lysate
diz.counts.txt
diz.lib14_S1.F03.expression.values

source_name: RTgill-W1 diz rep 1 conc 3


title: rtgill.diz.2.A03

description:
Library name: rtgill.diz.2.A03
Cell lysate
diz.counts.txt
diz.lib18_S1.A03.expression.values

source_name: RTgill-W1 diz rep 2 conc 8


title: 5hmC_Seal SEQ14472

tag: population

tag: patient id


title: E16.5 Urethra mesenchyme, male biol replicate 1

description:
Litter 0035
0035_M_UrSt_S2

tag: tissue

tag: genotype


title: rtgill.diz.1.E03

description:
Library name: rtgill.diz.1.E03
Cell lysate
diz.counts.txt
diz.lib14_S1.E03.expression.values

source_name: RTgill-W1 diz rep 1 conc 4


title: 5hmC_Seal SEQ19252


title: E16.5 Urethra mesenchyme, female biol replicate 4

description:
Litter 0041
0041_F_UrSt_S16

value: female


title: CD3_transcripts-Healthy.Control.Liver-9

source_name: CD3_transcripts, healthy control, liver

value: Liver


title: 5hmC_Seal SEQ14251


title: E16.5 Urethra mesenchyme, female biol replicate 3

description:
Litter 0040
0040_F_UrSt_S14


title: rtgill.diz.1.D03

description:
Library name: rtgill.diz.1.D03
Cell lysate
diz.counts.txt
diz.lib14_S1.D03.expression.values

source_name: RTgill-W1 diz rep 1 conc 5


title: rtgill.diz.1.C03

description:
Library name: rtgill.diz.1.C03
Cell lysate
diz.counts.txt
diz.lib14_S1.C03.expression.values

source_name: RTgill-W1 diz rep 1 conc 6


title: 5hmC_Seal SEQ14498


title: E16.5 Urethra mesenchyme, female biol replicate 2

description:
Litter 0039
0039_F_UrSt_S12


title: CD3_transcripts-Healthy.Control.Liver-10


title: CD3_transcripts-Healthy.Control.Liver-8


title: rtgill.diz.1.B03

description:
Library name: rtgill.diz.1.B03
Cell lysate
diz.counts.txt
diz.lib14_S1.B03.expression.values

source_name: RTgill-W1 diz rep 1 conc 7


title: E16.5 Urethra mesenchyme, female biol replicate 1

description:
Litter 0035
0035_F_UrSt_S10


title: 5hmC_Seal SEQ17290


title: CD3_transcripts-Healthy.Control.Liver-6

value: F


title: 5hmC_Seal SEQ14250


title: CD3_transcripts-Healthy.Control.Liver-7


title: E16.5 Bladder mesenchyme, male, biol replicate 4

description:
Litter 0041
0041_M_BlSt_S7

source_name: E16.5 bladder mesenchyme

value: E16.5 bladder mesenchyme


title: 5hmC_Seal SEQ17258

value: Chinese


title: 5hmC_Seal SEQ16751

value: Plasma


title: CD3_transcripts-Healthy.Control.Liver-5


title: rtgill.diz.1.A03

description:
Library name: rtgill.diz.1.A03
Cell lysate
diz.counts.txt
diz.lib14_S1.A03.expression.values

source_name: RTgill-W1 diz rep 1 conc 8

value: Rainbow trout gill


title: E16.5 Bladder mesenchyme, male, biol replicate 2

description:
Litter 0039
0039_M_BlSt_S3


title: rtgill.dca.6.E01

description:
Library name: rtgill.dca.6.E01
Cell lysate
dca.counts.combined.txt
dca.v2.lib22_S1.E01.expression.values

source_name: RTgill-W1 dca rep 6 conc 1


title: 5hmC_Seal SEQ13916


title: rtgill.dca.6.C01

description:
Library name: rtgill.dca.6.C01
Cell lysate
dca.counts.combined.txt
dca.v2.lib22_S1.C01.expression.values

source_name: RTgill-W1 dca rep 6 conc 3


title: rtgill.dca.6.B01

description:
Library name: rtgill.dca.6.B01
Cell lysate
dca.counts.combined.txt
dca.v2.lib22_S1.B01.expression.values

source_name: RTgill-W1 dca rep 6 conc 4


title: 5hmC_Seal SEQ14420


title: 5hmC_Seal SEQ13764


title: CD3_transcripts-Healthy.Control.Liver-3

value: M


title: CD3_transcripts-Healthy.Control.Liver-2


title: CD3_transcripts-Healthy.Control.Liver-4


title: CD3_transcripts-Healthy.Control.Liver-1


title: E16.5 Bladder mesenchyme, female, biol replicate 4

description:
Litter 0041
0041_F_BlSt_S15


title: CD3_transcripts-Healthy.Control.Blood-22

source_name: CD3_transcripts, healthy control, blood

value: Blood


title: E16.5 Bladder mesenchyme, male, biol replicate 3

description:
Litter 0040
0040_M_BlSt_S5


title: 5hmC_Seal SEQ13837


title: E16.5 Bladder mesenchyme, female, biol replicate 3

description:
Litter 0040
0040_F_BlSt_S13


title: 5hmC_Seal SEQ13718


title: rtgill.dca.5.E02

description:
Library name: rtgill.dca.5.E02
Cell lysate
dca.counts.combined.txt
dca.v2.lib18_S1.E02.expression.values

source_name: RTgill-W1 dca rep 5 conc 1


title: rtgill.dca.5.D02

description:
Library name: rtgill.dca.5.D02
Cell lysate
dca.counts.combined.txt
dca.v2.lib18_S1.D02.expression.values

source_name: RTgill-W1 dca rep 5 conc 2


title: rtgill.dca.5.C02

description:
Library name: rtgill.dca.5.C02
Cell lysate
dca.counts.combined.txt
dca.v2.lib18_S1.C02.expression.values

source_name: RTgill-W1 dca rep 5 conc 3


title: E16.5 Bladder mesenchyme, female, biol replicate 1

description:
Litter 0035
0035_F_BlSt_S9


title: 5hmC_Seal SEQ13821

source_name: Plasma


title: E16.5 Bladder mesenchyme, male, biol replicate 1

description:
Litter 0035
0035_M_BlSt_S1


title: E16.5 Urethra epithelium, male biol replicate 4

description:
Litter 0041
0041_M_UrEpi

data_processing:
Basecalling and demultiplexing was peformed using Illumina bcl2fastq.
Read mapping was peformed using hisat2-2.2.0 using reference grcm38.
.sam files obtained after read mapping were converted to unsorted.bam files using samtools-1.9. Using samtools, .bam files were sorted and deduplicated.
Feature counts were extracted from deduplicated .bam files using subread-2.0.6 with Gencode evidence-based annotation of the mouse genome (GRCm38), version M23 (Ensembl 98).
Raw read counts were processed in R using DESeq2 to obtain normalized counts.
Assembly: grcm38
Supplementary files format and content: tab-delimited text file containing read counts for each sample.
Supplementary files format and content: tab-delimited text file containing read counts summary for each sample.
Supplementary files format and content: comma-separated values file containing normalized counts for each sample.

source_name: E16.5 urethra epithelium

extract_protocol:
Tissues were directly lysed in 350 ul of RLT plus buffer with beta-mercaptoethanol from the Qiagen Rneasy Microkit (#74004). Tissue samples were subject to vortexing and stored at -80 C. For RNA extraction, tissue samples were thawed and homogenized using Qiashredder columns before processing with the Qiagen RNeasy Microkit following manufacturer instructions. According to instructions, a genomic DNA removal step was performed using genomic DNA removal columns. RNA was eluted in 16 ul of nuclease free water and RNA amounts were quantified using Qubit RNA-high sensitivity kit.
60 ng of total RNA was used for library construction. NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490L) was used for mRNA isolation according to manufacturer instructions. NEBNext® Ultra™ II Directional RNA Library Prep kit with Sample Purification Beads (#E7765L) was used for library preparation according to manufacturer instructions. Samples were sequenced using NovaSeq 6000. 100 bp pair-ended reads were obtained.

treatment_protocol: Lower urinary tract including bladder and pelvic urethra were dissected from embryonic day 16.5 embryos. Tissues were treated with a 1% trypsin solution on ice for 90 minutes. Tissues were washed in HBSS solution and briefly treated with Dnase. Epithelial and mesenchymal layers of the bladder and urethra were mechanically separated using fine forceps. Male and female tissues from each litter were pooled separately to obtain 4 samples per litter: Female bladder epithelium, Female urethral epithelium, Male bladder epithelium, Male urethral epithelium. Tissues were collected from 4 independent litters for a total of 16 samples.

value: E16.5 urethra epithelium


title: rtgill.dca.5.B02

description:
Library name: rtgill.dca.5.B02
Cell lysate
dca.counts.combined.txt
dca.v2.lib18_S1.B02.expression.values

source_name: RTgill-W1 dca rep 5 conc 4


title: E16.5 Bladder mesenchyme, female, biol replicate 2

description:
Litter 0039
0039_F_BlSt_S11


title: 5hmC_Seal SEQ14438


title: 5hmC_Seal SEQ14437


title: rtgill.dca.5.A02

description:
Library name: rtgill.dca.5.A02
Cell lysate
dca.counts.combined.txt
dca.v2.lib18_S1.A02.expression.values

source_name: RTgill-W1 dca rep 5 conc 5


title: E16.5 Urethra epithelium, male biol replicate 2

description:
Litter 0039
0039_M_UrEpi


title: E16.5 Urethra epithelium, male biol replicate 3

description:
Litter 0040
0040_M_UrEpi


title: rtgill.dca.6.A01

description:
Library name: rtgill.dca.6.A01
Cell lysate
dca.counts.combined.txt
dca.v2.lib22_S1.A01.expression.values

source_name: RTgill-W1 dca rep 6 conc 5


title: CD3_transcripts-Healthy.Control.Blood-21


title: CD3_transcripts-Healthy.Control.Blood-18


title: CD3_transcripts-Healthy.Control.Blood-17


title: CD3_transcripts-Healthy.Control.Blood-19


title: E16.5 Urethra epithelium, male biol replicate 1

description:
Litter 0035
0035_M_UrEpi


title: rtgill.dca.4.E01

description:
Library name: rtgill.dca.4.E01
Cell lysate
dca.counts.combined.txt
dca.v2.lib14_S1.E01.expression.values

source_name: RTgill-W1 dca rep 4 conc 1


title: 5hmC_Seal SEQ16998


title: CD3_transcripts-Healthy.Control.Blood-16


title: 5hmC_Seal SEQ16330


title: CD3_transcripts-Healthy.Control.Blood-15


title: rtgill.dca.4.D01

description:
Library name: rtgill.dca.4.D01
Cell lysate
dca.counts.combined.txt
dca.v2.lib14_S1.D01.expression.values

source_name: RTgill-W1 dca rep 4 conc 2


title: 5hmC_Seal SEQ13814


title: CD3_transcripts-Healthy.Control.Blood-23


title: CD3_transcripts-Healthy.Control.Blood-20


title: E16.5 Urethra epithelium, female biol replicate 4

description:
Litter 0041
0041_F_UrEpi


title: 5hmC_Seal SEQ14934


title: rtgill.dca.4.C01

description:
Library name: rtgill.dca.4.C01
Cell lysate
dca.counts.combined.txt
dca.v2.lib14_S1.C01.expression.values

source_name: RTgill-W1 dca rep 4 conc 3


title: E16.5 Urethra epithelium, female biol replicate 3

description:
Litter 0040
0040_F_UrEpi


title: CD3_transcripts-Healthy.Control.Blood-14


title: 5hmC_Seal SEQ12160


title: rtgill.dca.4.A01

description:
Library name: rtgill.dca.4.A01
Cell lysate
dca.counts.combined.txt
dca.v2.lib14_S1.A01.expression.values

source_name: RTgill-W1 dca rep 4 conc 5


title: E16.5 Urethra epithelium, female biol replicate 2

description:
Litter 0039
0039_F_UrEpi


title: 5hmC_Seal SEQ12169


title: 5hmC_Seal SEQ13079


title: CD3_transcripts-Healthy.Control.Blood-13


title: CD3_transcripts-Healthy.Control.Blood-12


title: rtgill.dca.3.E11

description:
Library name: rtgill.dca.3.E11
Cell lysate
dca.counts.combined.txt
batch.lib9_S1.E11.expression.values

source_name: RTgill-W1 dca rep 3 conc 1


title: E16.5 Bladder epithelium, male, biol replicate 4

description:
Litter 0041
0041_M_BlEpi

source_name: E16.5 bladder epithelium

value: E16.5 bladder epithelium


title: rtgill.dca.6.D01

description:
Library name: rtgill.dca.6.D01
Cell lysate
dca.counts.combined.txt
dca.v2.lib22_S1.D01.expression.values

source_name: RTgill-W1 dca rep 6 conc 2


title: E16.5 Urethra epithelium, female biol replicate 1

description:
Litter 0035
0035_F_UrEpi


title: 5hmC_Seal SEQ10837


title: E16.5 Bladder epithelium, male, biol replicate 3

description:
Litter 0040
0040_M_BlEpi


title: 5hmC_Seal SEQ10244


title: E16.5 Bladder epithelium, male, biol replicate 2

description:
Litter 0039
0039_M_BlEpi


title: rtgill.dca.4.B01

description:
Library name: rtgill.dca.4.B01
Cell lysate
dca.counts.combined.txt
dca.v2.lib14_S1.B01.expression.values

source_name: RTgill-W1 dca rep 4 conc 4


title: CD3_transcripts-Healthy.Control.Blood-10

source_name: CD3_transcripts, healthy control, blood

value: HC


title: rtgill.dca.3.B11

description:
Library name: rtgill.dca.3.B11
Cell lysate
dca.counts.combined.txt
batch.lib9_S1.B11.expression.values

source_name: RTgill-W1 dca rep 3 conc 4


title: E16.5 Bladder epithelium, male, biol replicate 1

description:
Litter 0035
0035_M_BlEpi


title: 5hmC_Seal SEQ10587


title: 5hmC_Seal SEQ9812


title: CD3_transcripts-Healthy.Control.Blood-11


title: rtgill.dca.3.A11

description:
Library name: rtgill.dca.3.A11
Cell lysate
dca.counts.combined.txt
batch.lib9_S1.A11.expression.values

source_name: RTgill-W1 dca rep 3 conc 5


title: CD3_transcripts-Healthy.Control.Blood-9


title: E16.5 Bladder epithelium, female, biol replicate 4

description:
Litter 0041
0041_F_BlEpi


title: CD3_transcripts-Healthy.Control.Blood-7


title: 5hmC_Seal SEQ9582


title: rtgill.dca.2.E10

description:
Library name: rtgill.dca.2.E10
Cell lysate
dca.counts.combined.txt
batch.lib4_S1.E10.expression.values

source_name: RTgill-W1 dca rep 2 conc 1


title: E16.5 Bladder epithelium, female, biol replicate 3

description:
Litter 0040
0040_F_BlEpi


title: CD3_transcripts-Healthy.Control.Blood-8


title: 5hmC_Seal SEQF2489

source_name: Plasma


title: rtgill.dca.3.D11

description:
Library name: rtgill.dca.3.D11
Cell lysate
dca.counts.combined.txt
batch.lib9_S1.D11.expression.values

source_name: RTgill-W1 dca rep 3 conc 2


title: E16.5 Bladder epithelium, female, biol replicate 2

description:
Litter 0039
0039_F_BlEpi


title: rtgill.dca.3.C11

description:
Library name: rtgill.dca.3.C11
Cell lysate
dca.counts.combined.txt
batch.lib9_S1.C11.expression.values

source_name: RTgill-W1 dca rep 3 conc 3


title: rtgill.dca.2.C10

description:
Library name: rtgill.dca.2.C10
Cell lysate
dca.counts.combined.txt
batch.lib4_S1.C10.expression.values

source_name: RTgill-W1 dca rep 2 conc 3


title: CD3_transcripts-Healthy.Control.Blood-5


title: E16.5 Bladder epithelium, female, biol replicate 1

description:
Litter 0035
0035_F_BlEpi


title: CD3_transcripts-Healthy.Control.Blood-4


title: Injury_12dpi_CR GFP -ve

city: Toronto

first: Akram

last: Hamed

department: Molecular Genetics

institute: University of Toronto

description: brain.injury.samples.RData

data_processing:
Raw sequencing data were aligned to the mm10 mouse reference using Cell Ranger (v3.1.0). Doublets and multiplets were identified by scDblFinder (v1.4.0), and low-quality cells (percent of mitochondrial > 12%; number of genes detected per cell < 800; number of Unique Molecular Identifier (UMI) per cell < 500) were removed as part of the QC process. Seurat (v4.5) was used to cluster data from all samples together and perform the downstream analyses.
Assembly: mm10
Supplementary files format and content: Seurat RData - tumourigenesis atlas samples
Supplementary files format and content: Seurat RData - malignant cells from the Sox2CEPPT and NestinCPPT mouse models samples (isolated from the tumourigenesis atlas)
Supplementary files format and content: Seurat RData - brain injury samples (Sox2eGFP mice)

source_name: Brain

extract_protocol:
1) Tumourigenesis atlas samples: fresh brain tissue was harvested from mutant mice at four MRI-defined stages: the “preneoplastic” stage at which the brain imaging shows no signs of neoplastic lesion development; the “early lesion” stage characterized by small abnormalities seen on T2/FLAIR MRI sequences; the “mid-lesion” stage when the lesion has reached a larger size as indicated by T2/FLAIR-bright mass in asymptomatic animals and occupies a significant fraction of the brain hemisphere; and, finally, the “endpoint” stage when mice develop symptoms of raised intracranial pressure or focal neurologic abnormalities, with the tumour extending over a large portion of the brain hemisphere(s), typically with midline shift. Each brain sample was dissociated followed by fluorescent activated cell sorting to separate the mutant (tdTomato+) cells from non-mutant (tdTomato-) cells. Following sorting, both populations were characterized by scRNA-seq using the 10X Genomics platform. 2) Brain injury samples: we removed the cannula on day 5 and collected brain samples at the 5-days post-implantation (5dpi) timepoint as well as 7 days following the removal of the cannula (12dpi timepoint). For each timepoint, we processed the ipsilateral (IP) and contralateral (CR) hemispheres separately so the latter could serve as an internal control. Each sample was dissociated into single cells followed by FACS sorting of the GFP+ and GFP- cells and then each processed for scRNA-seq using the 10X Genomics platform.
We used the 10X Genomics platform according to the manufacturer's protocols.

treatment_protocol: Brain injury samples: to create an injury phenotype, we implanted an intracranial cannula in the right hemisphere of 4-6 week old non-mutant Sox2eGFP mice at stereotactic coordinates that place the cannula near the subventricular zone. The cannula was connected to an osmotic pump to slowly infuse the brain with saline over a period of 5 days. This resulted in structural tissue damage on the ipsilateral hemisphere.

value: Brain

value: Brain inury


title: CD3_transcripts-Healthy.Control.Blood-3


title: rtgill.dca.2.A10

description:
Library name: rtgill.dca.2.A10
Cell lysate
dca.counts.combined.txt
batch.lib4_S1.A10.expression.values

source_name: RTgill-W1 dca rep 2 conc 5


title: rtgill.dca.2.D10

description:
Library name: rtgill.dca.2.D10
Cell lysate
dca.counts.combined.txt
batch.lib4_S1.D10.expression.values

source_name: RTgill-W1 dca rep 2 conc 2


title: Injury_12dpi_CR

description: brain.injury.samples.RData


title: control

city: South Bend

first: Murlidharan

middle: T

last: Nair

state: IN

address: 1700 Mishawaka Ave

department: Biology and CS/Informatics

institute: Indiana University South Bend

description: Arima-HiC kit

data_processing:
For .hic files the matrix for each sample was analyzed using the Juicer pipeline (version 1.6) on default parameters. The reads were aligned to the mm10 reference genome using BWA (Burrow-wheeler aligner). On average, it was generated around 800 million paired-end reads in each Hi-C library.
For .wig files the eigenvalues (for determining A/B compartments) were computed using the Eigenvector algorithm at 100kb resolution across the genome. These eigenvalues were then transformed and consolidated into a single .wig file that encompassed the final A/B compartment assignments.
For .h5 files the Fastq files obtained from the sequencing of the two samples were aligned to the mm10 reference genome using BWA. The resulting bam files in each case were used to construct matrices using hicBuildMatrix and saved as .h5 files. These files were subsequently merged using hicMergeMatrixBins to create matrices at various resolutions, including 5, 10, 50, 100, and 500 Kbps. Each of the merged files was then subjected to correction using hicCorrectMatrix, with a filter range of -1 to 3, resulting in corrected h5 files.   Each of the merged and corrected h5 files were analyzed using hicFindTADs and hicDifferentialTAD. To analyze the matrices using TAD compare, the merged and corrected h5 matrix files of different resolution were converted into hicpro format using hicConvertFormat. These were then analysed using TADCompare.
Assembly: mm10
Supplementary files format and content: .HiC is a binary format to store the HiC matrix for each sample with multiple bin sizes and corrections in a single file.
Supplementary files format and content: .wig Eigenvectors containing A/B compartments calls at 100kb resolution in wiggle format
Supplementary files format and content: .h5 matrice files output from hicBuildMatrix at 1kbp

source_name: liver

growth_protocol: males 16 weeks of age

extract_protocol:
The Arima-HiC kit (Part Number: A510008) was employed for the assays following the manufacturer’s protocols.
The methodology for generating Arima-HiC libraries from fresh frozen livers involves a series of precise steps to capture the spatial interactions within the genome. Initially, the livers were crosslinked and digested using a cocktail of restriction enzymes (RE). The resulting 5’-overhangs were then filled in, leading to the labeling of the digested ends with a biotinylated nucleotide. Subsequently, spatially proximal digested ends of DNA were ligated, enabling the capture of both the sequence and structure of the genome. The ligated DNA underwent a purification process, yielding pure proximally-ligated DNA. This DNA was then fragmented using the Bioruptor Pico from DiagenodeÒ. Biotinylated fragments were selectively enriched using Streptavidin beads. The enriched fragments underwent a custom library preparation protocol that utilized the Swift BiosciencesÒ Accel-NGSÒ 2S Plus DNA Library Kit (Cat # 21024 or 21096) and the Swift BiosciencesÒ Indexing Kit (Cat # 26148, 26248, 26396, 26596, 26696, 26796, 26896, or 269384). These kits collectively contributed to the creation of Arima-HiC libraries, which were then prepared for sequencing.

value: liver

tag: development stage

value: adult

value: male

value: Cre-ALB

value: not treated


title: ALB-D2KO

description: Arima-HiC kit


title: Injury_12dpi_IP GFP -ve

description: brain.injury.samples.RData


title: rtgill.dca.1.D12

description:
Library name: rtgill.dca.1.D12
Cell lysate
dca.counts.combined.txt
batch.lib13_S1.D12.expression.values

source_name: RTgill-W1 dca rep 1 conc 2


title: LAC/IsdB/aIL10 [BCR-seq]

city: San Diego

first: Nathan

middle: E.

last: Lewis

state: CA

address: 9500 Gilman Dr.

department: Pediatrics

institute: University of California, San Diego

library_source: other

data_processing:
Library strategy: BCR-seq
The BCR sequence data were processed using the Immcantation toolbox (v4.0.0) with default parameter values. Initial germline V(D)J gene annotation was performed using IgBLAST with IMGT germline sequence databases.The IgBLAST database was further used to assign V(D)J gene annotations to the BCR FASTA files for each sample using the Change-O package. The derived matrix contains sequence alignment information for each sample with both light and heavy chain sequences, and individualized genotypes were inferred using the TIgGER package and used to finalize V(D)J annotations.
The clonal groups were identified by the R package – scRepertoire (11) based on paired heavy and light chains. To determine clonal groups, we first used the filtered contig annotation obtained from the results performed using the Cell Ranger Single-Cell Software Suites (http://software.10xgenomics.com/single-cell/overview/welcome). Then, for the cells with high quality paired heavy and light chains were sequenced, clones were assigned based on strict definition of clonotype using the CTstrict() function that considers clonally related two sequences with identical V gene usage and > 85% normalized Levenshtein distance of the nucleotide sequence. The clonotype changes between samples were visualized by thecompareClonotypes()function with the clones called by amino acid sequence of the CDR3 region.
Assembly: Initial germline V(D)J gene annotation was performed using IgBLAST with IMGT germline sequence databases.The IgBLAST database was further used to assign V(D)J gene annotations to the BCR FASTA files for each sample using the Change-O package
Supplementary files format and content: clonotypes.csv, consensus.fasta, and filtered_contig_annotations.csv.gz

molecule: other

source_name: Spleen and kidneys

growth_protocol: Overnight S. aureus cultures were diluted 1:200 in Todd Hewitt broth (THB) and grown to an optical density of 0.8. Unless otherwise stated, 6-8 weeks old female mice were administered 2x107 LAC (USA 300) i.p. for each S. aureus challenge.

extract_protocol: protocol Splenocytes from IsdB immunized or LAC-experienced mice were incubated with phycoerythrin (PE)–labeled IsdB and allophycocyanin-conjugated anti-mouse CD45R/B220. IsdB+ B220+ cells were sorted by FACSAria II (BD) and subjected to single-cell preparation by using a Single Cell 5’ Library and Gel Bead kit and Chromium Single Cell A Chip kit, the cell suspension was loaded onto a Chromium single cell controller to generate single-cell gel beads in the emulsion (GEMs) according to the manufacturer’s protocol: (10X Genomics). scRNA-seq libraries were constructed using a Chromium Single Cell V(D)J Enrichment Kit, Mouse B Cell following instructions provided by the manufacturer (10X Genomics). The libraries were sequenced using an Illumina Novaseq6000 sequencer with a paired-end 150-bp (PE150) reading strategy (performed by Institute for Genomic Medicine, UCSD).

treatment_protocol: Mice were immunized i.p. three times with IsdB (75μg, 50μg and 50μg) plus aluminum hydroxide (alum, InvivoGen) (450 μg per dose) or with aluminum hydroxide alone at 7-day intervals. Mouse sera were screened for reactivity to IsdB by ELISA.

value: Spleen and kidneys

value: LAC-infected mice

value: vaccinated with IsdB and treated w/ αIL-10


title: Injury_12dpi_IP

description: brain.injury.samples.RData


title: LAC/IsdB [BCR-seq]

value: vaccinated with IsdB


title: rtgill.dca.1.E12

description:
Library name: rtgill.dca.1.E12
Cell lysate
dca.counts.combined.txt
batch.lib13_S1.E12.expression.values

source_name: RTgill-W1 dca rep 1 conc 1

value: Rainbow trout gill


title: 5hmC_Seal SEQ5607

value: Chinese

value: Plasma


title: Injury_5dpi_CR GFP -ve

description: brain.injury.samples.RData


title: CD3_transcripts-Healthy.Control.Blood-1

value: Blood

value: M


title: rtgill.dca.1.C12

description:
Library name: rtgill.dca.1.C12
Cell lysate
dca.counts.combined.txt
batch.lib13_S1.C12.expression.values

source_name: RTgill-W1 dca rep 1 conc 3


title: LAC [BCR-seq]

value: No IsdB vaccinated (given adjuvant alone)


title: rtgill.dca.1.B12

description:
Library name: rtgill.dca.1.B12
Cell lysate
dca.counts.combined.txt
batch.lib13_S1.B12.expression.values

source_name: RTgill-W1 dca rep 1 conc 4


title: CD3_transcripts-Auto.Lungs-3

source_name: CD3_transcripts, Autologous transplant, lungs

value: Auto

value: Lungs

value: F


title: CD3_transcripts-Healthy.Control.Blood-6

source_name: CD3_transcripts, healthy control, blood

value: HC


title: CD3_transcripts-Healthy.Control.Blood-2


title: rtgill.dca.2.B10

description:
Library name: rtgill.dca.2.B10
Cell lysate
dca.counts.combined.txt
batch.lib4_S1.B10.expression.values

source_name: RTgill-W1 dca rep 2 conc 4


title: HashTagLibrary

city: Braunschweig

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using CellRanger software (cellranger-7.0.0, 10x Genomics).
Assembly: mm10, refdata-cellranger-mm10-3.0.0
Supplementary files format and content: matrix file (h5, 10X Genomics)

source_name: HashTagOligo

extract_protocol:
Splenocytes from co-transplanted mice were harvested 12 days after transplantation. Ex vivo progenies were labeled with Hashtag-Abs (TotalSeq™-B0301-4 anti-mouse Hashtag 1-4 Antibody, BioLegend, catalog: 155831, 155833, 155835, 155837). Cells were sorted for Tom+/7AAD- (BioLegend; catalog 420404) with an Aria III fluorescence-activated cell sorter (BD). The single cell suspension was loaded onto a well on a 10X Chromium Controller (10x Genomics).
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 3'v3.1 + Cell Surface Protein (Dual Index), 10x Genomics). Cellular mRNA and hashtag oligos (HTO) were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were amplified by PCR according to the Chromium Single Cell 3’ v3.1 protocol.
scRNA-seq (gene expression with feature barcoding

value: HashTagOligo


title: CD3_transcripts-Auto.Lungs-2


title: CD3_transcripts-Auto.Lungs-4


title: CD3_transcripts-Auto.Lungs-1


title: Injury_5dpi_CR

description: brain.injury.samples.RData

value: Brain

value: Brain inury


title: rtgill.col.3.H09

description:
Library name: rtgill.col.3.H09
Cell lysate
col.counts.txt
col.lib8_S1.H09.expression.values

source_name: RTgill-W1 col rep 3 conc 1


title: Injury_5dpi_IP GFP -ve

description: brain.injury.samples.RData


title: V6.5 mTELSC-TO, WGBS

city: Beijing

first: Chunhui

last: Wang

state: Beijing

address: 5 Summer Palace Road, Haidian District, Beijing

department: School of Life Sciences

institute: Peking University

data_processing:
ATAC-seq data were firstly trimmed by Trimmomatic software. Bowtie2 was used to align the clean reads to mm10 reference genome “-X 1000 –mm -local”. Picard was used to remove duplicates and we only remained the high-quality reads. Then, after calling the peaks by MACS2, we used the merge and multicov commands in bedtools to extract the count of the peaks in all the samples and bdgdiff function in MACS2 was used to normalize the count matrix and calculate the differential peaks with parameters “-g 100 -l 50 -C 2”.
To analyze polyA(+) RNA-seq data, adapters of raw data were trimmed with Trimmomatic software. The quality of these data was evaluated by FastQC software. HISAT2 software with default parameters was used to align sequences to the mouse genome (mm10, UCSC). Output files after sequence alignment were used to obtain gene count matrix with featureCounts software using corresponding UCSC RefSeq as gene annotations. For further analyses, gene counts in each sample were normalized to the total reads of the library to calculate counts per million (CPM).
ATAC-seq data were firstly trimmed by Trimmomatic software (version 0.39). Bowtie2 (version 2.4.4) was used to align the clean reads to mm10 reference genome “-X 1000 –mm -local”. Picard was used to remove duplicates and we only remained the high-quality reads. Then, after calling the peaks by MACS2, we used the merge and multicov commands in bedtools to extract the count of the peaks in all the samples and bdgdiff function in MACS2 was used to normalize the count matrix and calculate the differential peaks with parameters “-g 100 -l 50 -C 2”.
ChIP-seq data were firstly trimmed by Trimmomatic software. Bowtie2 (version 2.4.4) was used to align the clean reads to mm10 reference genome with parameters “--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700”. We used MACS2 (version 2.1.4) to call peaks and differential peaks were detected by macs2 bdgdiff command.
WGBS reads were trimmed by Trimmomatic software with default parameters. The cleaned data were aligned to the mm10 reference with Bismark. Duplicate reads were removed by deduplicate_bismark command and the methylation calls were extracted from unique alignment using bismark_methylation_extractor with ‘‘–bedGraph’’ parameter. Bismark2 summary command was used to calculate the genome CpG methylation level.
Single-cell transcriptome data were first applied to Cell Ranger (version 3.6.0) against mm10 genome reference to generate count matrix, which of the column was cell name and the row was gene. The downstream analysis was performed in Seurat (version 3.1.0) R package.
Assembly: mm10
Supplementary files format and content: Big wig files for ATAC-seq and CUT&Tag samples, comma-separated value files include CPM values for RNA-seq samples, bedGraph files for Bisulfite-seq samples

extract_protocol:
DNA and RNA were extracted from mESCs, mTBLCs, mTELCs, mTELSCs, mTSCs and TOs for highthrough sequencing, including ATAC-seq, CHIP-seq, WGBS and scRNA-seq. TRIzol reagent (Invitrogen) was used to isolate total RNA according to the manufacturer’s instructions. 100 ng genomic DNA was used as input and was bisulfite-converted using the EpiArt DNA Methylation Bisulfite Kit (Vazyme). A total of 50, 000 viable cells were extracted using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme) for ATAC-seq.  A total of 50, 000 viable cells were extracted using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme).
RNA-seq libraries were conducted using VAHTS Stranded mRNA-seq Library Prep Kits (Vazyme) .To assess chromatin accessibility of TELCs and TELSCs, ATAC-seq were conducted using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme) according to the manufacturer’s instructions. Bisulfite-converted DNA was used to construct the library with the EpiArtTM DNA Methylation Library Kit V3 (Vazyme) according to the manufacturer’s instructions. A total of 50, 000 viable cells were used for CUT&Tag experiments with the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the manufacturer’s instructions.

value: mTELSC-TO cultured in TO medium


title: rtgill.col.3.G09

description:
Library name: rtgill.col.3.G09
Cell lysate
col.counts.txt
col.lib8_S1.G09.expression.values

source_name: RTgill-W1 col rep 3 conc 2


title: Injury_control

description: brain.injury.samples.RData


title: Splenocytes

description: 10X Genomics

source_name: Spleen

value: Spleen

value: Splenocytes


title: rtgill.col.3.F09

description:
Library name: rtgill.col.3.F09
Cell lysate
col.counts.txt
col.lib8_S1.F09.expression.values

source_name: RTgill-W1 col rep 3 conc 3


title: V6.5 mTELC, WGBS

value: mTELCs induced from mTBLCs


title: Injury_control GFP -ve

description: brain.injury.samples.RData

source_name: Brain


title: Injury_5dpi_IP

description: brain.injury.samples.RData


title: rtgill.col.3.E09

description:
Library name: rtgill.col.3.E09
Cell lysate
col.counts.txt
col.lib8_S1.E09.expression.values

source_name: RTgill-W1 col rep 3 conc 4

value: Rainbow trout gill


title: V6.5 mTELSC-TO, Day8, scRNA-seq

description: 10× Genomics

value: V6.5 mTELSC-TO cultured in TO medium


title: rtgill.col.3.D09

description:
Library name: rtgill.col.3.D09
Cell lysate
col.counts.txt
col.lib8_S1.D09.expression.values

source_name: RTgill-W1 col rep 3 conc 5


title: CD3_transcripts-Auto.Liver-2

source_name: CD3_transcripts, Autologous transplant, liver

value: Liver


title: mTSC-TO, Day9

source_name: ICR

value: ICR

value: mTSC-TO cultured in TO medium


title: CD3_transcripts-Auto.Liver-4

value: M


title: CD3_transcripts-Auto.Liver-3

value: Auto


title: Endpoint_rep_5

description: tumourigenesis.atlas.RData

value: Sox2CreER/+; p53f/f; R26td/td


title: CD3_transcripts-Auto.Blood-4

source_name: CD3_transcripts, Autologous transplant, blood

value: Blood


title: rtgill.dca.1.A12

description:
Library name: rtgill.dca.1.A12
Cell lysate
dca.counts.combined.txt
batch.lib13_S1.A12.expression.values

source_name: RTgill-W1 dca rep 1 conc 5


title: Endpoint_rep_4 td -ve

description: tumourigenesis.atlas.RData

value: NestinCre/+; p53f/f; Ptenf/+; R26td/+


title: mTSC-TO, Day7


title: V6.5 mTELSC, WGBS

value: mTELSC cultured in TX medium


title: CD3_transcripts-Auto.Liver-1

value: F


title: CD3_transcripts-Auto.Blood-2


title: mTSC-TO, Day5


title: rtgill.col.3.B09

description:
Library name: rtgill.col.3.B09
Cell lysate
col.counts.txt
col.lib8_S1.B09.expression.values

source_name: RTgill-W1 col rep 3 conc 7


title: Endpoint_rep_4

description:
tumourigenesis.atlas.RData
malignant.cells.Sox2CEPPT.and.NestinCPPT.models.RData

value: Brain


title: Endpoint_rep_3


title: Endpoint_rep_6

description: tumourigenesis.atlas.RData


title: CD3_transcripts-Auto.Blood-3


title: rtgill.col.3.A09

description:
Library name: rtgill.col.3.A09
Cell lysate
col.counts.txt
col.lib8_S1.A09.expression.values

source_name: RTgill-W1 col rep 3 conc 8


title: Ami-YGL1_Line 8_field10.00.A.M._treatment_leaf_totalRNA_4

city: shanghai

first: linxiong

last: mao

state: shanghai

address: NO.300 fenglin road

institute: CAS Center for Excellence in Molecular Plant Sciences / Institute of Plant Physiology and Ecology

description:
Y8_4
Ami-YGL1_Line 8_field10.00.A.M._treatment_leaf_totalRNA

data_processing:
none
none
none
none
none
Assembly: none
Supplementary files format and content: count

organism: Oryza sativa Japonica Group

source_name: leaf

extract_protocol:
Trizol reagent (15596018, Thermo Fisher Scientific, USA)
The p35s-Ami-YGL1 mutant plants were generated with RNAi technology as described earlier (Mao et al., 2023). We used three homozygote transgenic lines (line 1, 7 and 8) during this study.  Rice (Oryza sativa spp japonica cv Nipponbare) and p35s-Ami-YGL1 were grown in the experimental station of the Shanghai Institute of Plant Physiology and Ecology (121°8′1.33″E, 30°56′26.73″N). During the growth period in 2021 or 2022, the rice was transplanted into the well-fertilized field in a 7×7 layout (25cm ×25 cm) and for each line. To avoid boundary effects, plants belong to the boundary lines were excluded in the measurement. The experiments were done in two years at different field sites (2019, 2021).   At the same time, we also carried out relevant measurements in the plant greenhouse. The greenhouse was subjected to an alternating light/dark cycle (12 hours of light and 12 hours of darkness), with a light intensity of approximately 400 μmol m-2 s-1 and the temperature was set at around 28 oC.

value: leaf

tag: cultivar

value: Nipponbare

value: Ami-YGL1_Line 8

value: field treatment


title: Ami-YGL1_Line 8_field10.00.A.M._treatment_leaf_totalRNA_2

description:
Y8_2
Ami-YGL1_Line 8_field10.00.A.M._treatment_leaf_totalRNA


title: rtgill.col.2.H09

description:
Library name: rtgill.col.2.H09
Cell lysate
col.counts.txt
col.lib3_S1.H09.expression.values

source_name: RTgill-W1 col rep 2 conc 1

value: Rainbow trout gill


title: mTSC

value: mTSC cultured in TX medium


title: CD3_transcripts-Auto.Blood-1

tag: individual


title: Endpoint_rep_2

value: Sox2CreER/+; p53f/f; Ptenf/f; R26td/td


title: rtgill.col.2.G09

description:
Library name: rtgill.col.2.G09
Cell lysate
col.counts.txt
col.lib3_S1.G09.expression.values

source_name: RTgill-W1 col rep 2 conc 2


title: rtgill.col.3.C09

description:
Library name: rtgill.col.3.C09
Cell lysate
col.counts.txt
col.lib8_S1.C09.expression.values

source_name: RTgill-W1 col rep 3 conc 6


title: V6.5 mTELSC-TO, Day9

value: V6.5 mTELSC-TO cultured in TO medium


title: Endpoint_rep_1 td -ve

description: tumourigenesis.atlas.RData


title: rtgill.col.2.F09

description:
Library name: rtgill.col.2.F09
Cell lysate
col.counts.txt
col.lib3_S1.F09.expression.values

source_name: RTgill-W1 col rep 2 conc 3


title: V6.5 mTELSC-TO, Day7


title: Ami-YGL1_Line 7_field10.00.A.M._treatment_leaf_totalRNA_4

description:
Y7_4
Ami-YGL1_Line 7_field10.00.A.M._treatment_leaf_totalRNA

value: Ami-YGL1_Line 7


title: Endpoint_rep_1


title: rtgill.col.2.E09

description:
Library name: rtgill.col.2.E09
Cell lysate
col.counts.txt
col.lib3_S1.E09.expression.values

source_name: RTgill-W1 col rep 2 conc 4


title: Ami-YGL1_Line 7_field10.00.A.M._treatment_leaf_totalRNA_3

description:
Y7_3
Ami-YGL1_Line 7_field10.00.A.M._treatment_leaf_totalRNA


title: Ami-YGL1_Line 8_field10.00.A.M._treatment_leaf_totalRNA_1

description:
Y8_1
Ami-YGL1_Line 8_field10.00.A.M._treatment_leaf_totalRNA


title: Ami-YGL1_Line 7_field10.00.A.M._treatment_leaf_totalRNA_2

description:
Y7_2
Ami-YGL1_Line 7_field10.00.A.M._treatment_leaf_totalRNA


title: V6.5 mTELSC-TO, Day5


title: Ami-YGL1_Line 8_field10.00.A.M._treatment_leaf_totalRNA_3

description:
Y8_3
Ami-YGL1_Line 8_field10.00.A.M._treatment_leaf_totalRNA


title: Mid_lesion_rep_3

description: tumourigenesis.atlas.RData

value: Brain inury


title: V6.5 mTELSC-TO, Day3


title: V6.5 mTELSC, P10


title: Ami-YGL1_Line 7_field10.00.A.M._treatment_leaf_totalRNA_1

description:
Y7_1
Ami-YGL1_Line 7_field10.00.A.M._treatment_leaf_totalRNA


title: rtgill.col.2.B09

description:
Library name: rtgill.col.2.B09
Cell lysate
col.counts.txt
col.lib3_S1.B09.expression.values

source_name: RTgill-W1 col rep 2 conc 7


title: Mid_lesion_rep_2


title: Mid_lesion_rep_3 td -ve

description: tumourigenesis.atlas.RData


title: WT_field10.00.A.M._treatment_leaf_totalRNA_4

description:
WT_4
WT_field10.00.A.M._treatment_leaf_totalRNA

value: WT


title: Mid_lesion_rep_2 td -ve

description: tumourigenesis.atlas.RData


title: Mid_lesion_rep_1

description:
tumourigenesis.atlas.RData
malignant.cells.Sox2CEPPT.and.NestinCPPT.models.RData


title: V6.5 mTELSC, P6


title: rtgill.col.1.H09

description:
Library name: rtgill.col.1.H09
Cell lysate
col.counts.txt
col.lib12_S1.H09.expression.values

source_name: RTgill-W1 col rep 1 conc 1


title: mTSC-TO, Day3

value: ICR

value: mTSC-TO cultured in TO medium


title: Early_lesion_rep_5

source_name: Brain

value: NestinCre/+; p53f/f; Ptenf/+; R26td/+


title: rtgill.col.1.G09

description:
Library name: rtgill.col.1.G09
Cell lysate
col.counts.txt
col.lib12_S1.G09.expression.values

source_name: RTgill-W1 col rep 1 conc 2


title: V6.5 mTELSC, P8

value: mTELSC cultured in TX medium


title: WT_field10.00.A.M._treatment_leaf_totalRNA_3

description:
WT_3
WT_field10.00.A.M._treatment_leaf_totalRNA


title: Early_lesion_rep_4


title: V6.5 mTELSC, P4


title: WT_field10.00.A.M._treatment_leaf_totalRNA_2

description:
WT_2
WT_field10.00.A.M._treatment_leaf_totalRNA


title: V6.5 mTELSC, P3


title: rtgill.col.2.D09

description:
Library name: rtgill.col.2.D09
Cell lysate
col.counts.txt
col.lib3_S1.D09.expression.values

source_name: RTgill-W1 col rep 2 conc 5


title: rtgill.col.1.F09

description:
Library name: rtgill.col.1.F09
Cell lysate
col.counts.txt
col.lib12_S1.F09.expression.values

source_name: RTgill-W1 col rep 1 conc 3


title: rtgill.col.2.C09

description:
Library name: rtgill.col.2.C09
Cell lysate
col.counts.txt
col.lib3_S1.C09.expression.values

source_name: RTgill-W1 col rep 2 conc 6


title: Early_lesion_rep_3 td -ve

description: tumourigenesis.atlas.RData


title: WT_field10.00.A.M._treatment_leaf_totalRNA_1

description:
WT_1
WT_field10.00.A.M._treatment_leaf_totalRNA


title: Early_lesion_rep_3


title: V6.5 mTELSC, P2


title: V6.5 mTELC, Cdx2-tdTomato, FACS-purified, Day3

value: mTELC derived from Cdx2-tdTomato, cultured in TS medium


title: Pancreatic islets, Wfs1KO, replicate4

city: Ube

first: Katsuya

last: Tanabe

state: Yamaguchi

address: 1-1-1 Minamikogushi

country: Japan

institute: Yamaguchi University

data_processing:
The bcl2fastq conversion software version 2.19.1.403 was used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Alignment: Raw sequence reads were aligned to the UCSC mm10 reference genome and displayed using UCSC annotated genes using STAR version 2.6.0a with default parameters.
Alingment files were transformed into "Tag Directory" using Homer version 4.11.1  “makeTagDirectory", then differantial gene expression alaysis (DeSeq2) was perfomed using Homer　“getDiffExpression.pl"
TPM files were created using Homer "analyzeRepeats.pl" and specifying "-count exons -tpm" .
Assembly: mm10
Supplementary files format and content: DeSeq2 verson 1.8.2 analysis were performed using HOMER.
Supplementary files format and content: TPM files were generated using HOMER.

source_name: Pancreatic islets

growth_protocol: Pancreatic islets were isolated from 12-week-old male Wfs1KO and WT mice using ductal collagenase digestion followed by density gradient purification.

extract_protocol:
Total RNA was isolated from pancreatic islets using Direct-zol RNA MicroPrep Kit (Zymo Research). Polyadenylated mRNA was purified from 200 ng of total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
Sequencing libraries were prepared using NEBNext Ultra II RNA LibraryPrep Kit for Illumina (NEB) according to manufacturer's instructions. Library concentrations were quantified by a Bioanalyzer (Agilent).

value: Pancreatic islets

value: male

tag: age

value: 12 weeks old

value: Wfs1 knockout


title: Early_lesion_rep_2

value: Brain


title: rtgill.col.1.D09

description:
Library name: rtgill.col.1.D09
Cell lysate
col.counts.txt
col.lib12_S1.D09.expression.values

data_processing:
RNA-seq Analysis Portal (RAP; Qiagen)
Raw RNA Sequencing fastq files were submitted to QIAGEN’s RNA-seq Analysis Portal (RAP) (QIAGEN). First, raw files were demultiplexed to yield individual reads files for each sample (well) and then mapped to the rainbow trout genome (Omyk_1.0.105) to yield raw counts.
The counts were submitted to ExpressAnalyst for differential expression analysis and benchmark dose response analysis
Assembly: Omyk_1.0.105
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: RTgill-W1 col rep 1 conc 5

extract_protocol:
OECD Test Guideline 249 for RTgill-W1 cell exposures, and QIAseq UPXome RNA Library Kits (QIAGEN) for library preparation
QIAseq UPXome RNA Library Kits (QIAGEN) protocol  for library preparation

value: Rainbow trout gill


title: rtgill.col.1.E09

description:
Library name: rtgill.col.1.E09
Cell lysate
col.counts.txt
col.lib12_S1.E09.expression.values

source_name: RTgill-W1 col rep 1 conc 4


title: Pancreatic islets, Wfs1KO, replicate3


title: V6.5 mTELC, Day3

value: mTELC induced from mTBLC using TS medium


title: Early_lesion_rep_1

value: Sox2CreER/+; p53f/f; Ptenf/f; R26td/td


title: rtgill.col.2.A09

description:
Library name: rtgill.col.2.A09
Cell lysate
col.counts.txt
col.lib3_S1.A09.expression.values

source_name: RTgill-W1 col rep 2 conc 8


title: Pancreatic islets, Wfs1KO, replicate1


title: rtgill.col.1.C09

description:
Library name: rtgill.col.1.C09
Cell lysate
col.counts.txt
col.lib12_S1.C09.expression.values

source_name: RTgill-W1 col rep 1 conc 6


title: rtgill.col.1.B09

description:
Library name: rtgill.col.1.B09
Cell lysate
col.counts.txt
col.lib12_S1.B09.expression.values

source_name: RTgill-W1 col rep 1 conc 7


title: V6.5 mTELC, FACS-purified, Day3

value: mTELC cultured in TS medium


title: V6.5 mTBLC

value: mESC cultured in SLP medium


title: rtgill.col.1.A09

description:
Library name: rtgill.col.1.A09
Cell lysate
col.counts.txt
col.lib12_S1.A09.expression.values

source_name: RTgill-W1 col rep 1 conc 8


title: Preneoplastic_rep_4

description: tumourigenesis.atlas.RData

value: Sox2CreER/+; p53f/f; R26td/td


title: V6.5 mESCs

value: mESC cultured in serum/lif medium


title: Pancreatic islets, WT, replicate4

value: WT


title: Pancreatic islets, WT, replicate3


title: rtgill.cat.3.H08

description:
Library name: rtgill.cat.3.H08
Cell lysate
cat.counts.txt
cat.lib8_S1.H08.expression.values

source_name: RTgill-W1 cat rep 3 conc 1


title: Preneoplastic_rep_3


title: V6.5 mTELSC


title: Pancreatic islets, WT, replicate2


title: rtgill.cat.3.G08

description:
Library name: rtgill.cat.3.G08
Cell lysate
cat.counts.txt
cat.lib8_S1.G08.expression.values

source_name: RTgill-W1 cat rep 3 conc 2


title: Preneoplastic_rep_2 td -ve

description: tumourigenesis.atlas.RData


title: V6.5 mTELC, FACS-purified using CD40, Day3

value: mTELCs induced from mTBLCs


title: rtgill.cat.3.F08

description:
Library name: rtgill.cat.3.F08
Cell lysate
cat.counts.txt
cat.lib8_S1.F08.expression.values

source_name: RTgill-W1 cat rep 3 conc 3


title: Pancreatic islets, Wfs1KO, replicate2


title: Pancreatic islets, WT, replicate1


title: BAT, TxnipKO, 30C, replicate3

data_processing:
The bcl2fastq conversion software version 2.19.1.403 was used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Alignment: Raw sequence reads were aligned to the UCSC mm10 reference genome and displayed using UCSC annotated genes using STAR version 2.7.5a with default parameters.
Alingment files were transformed into "Tag Directory" using Homer version 4.11.1  “makeTagDirectory", then differantial gene expression alaysis (DeSeq2) was perfomed using Homer　“getDiffExpression.pl"
TPM files were created using Homer "analyzeRepeats.pl" and specifying "-count exons -tpm" .
Assembly: mm10
Supplementary files format and content: DeSeq2 analysis were performed using HOMER.
Supplementary files format and content: TPM files were generated using HOMER.

source_name: brown adipose tissue

growth_protocol: Txnip-deficient (TxnipKO) and wild-type (WT) mice were acclimated to room temperature (23°C) or thermoneutrality (30°C) for 1week

extract_protocol:
Total RNA was isolated from brown adipose tissue using Direct-zol RNA Miniprep Plus Kit (Zymo Research). Polyadenylated mRNA was purified from 500 ng of total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
Sequencing libraries were prepared using NEBNext Ultra II RNA LibraryPrep Kit for Illumina (NEB) according to manufacturer's instructions. Library concentrations were quantified by a Bioanalyzer (Agilent).

value: brown adipose tissue

value: 10 week old

value: Txnip knockout

value: 30 C (thermoneutrality)


title: sg-Mrpl9_Bl_biorep5

city: Rochester

first: Kirk

last: Wangensteen

state: MN

address: GU1034H, 222 3rd Ave SW

department: Gastroenterology & Hepatology

institute: Mayo Clinic

data_processing:
Base call (.bcl) files for each cycle of sequencing were generated by Illumina Real Time Analysis (RTA) software.
2 x 150bp FastQ paired-end reads for 30 samples (n=19.6 Million average reads per sample) were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.
Read mapping was performed via Hisat2 (v2.1.0) using the mouse genome (Mus musculus GRCm39.109) as a reference.
Gene quantification was done via Feature Counts for raw read counts.
Assembly: mm39
Supplementary files format and content: Compressed fastq files contain raw read1 and read2 data
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: liver tumor

extract_protocol:
Total RNA was extracted from approximately 25 mg of liver tumor tissue using the Qiagen RNeasy plus mini kit (Qiagen #74134).
Thirty unique dual-indexed libraries were created using the TruSeq stranded mRNA library preparation kit (Illumina #20020594).

value: liver tumor

value: dCas9+ Black


title: rtgill.cat.3.E08

city: Sainte-Anne-de-Bellevue

last: Basu

institute: McGill University

description:
Library name: rtgill.cat.3.E08
Cell lysate
cat.counts.txt
cat.lib8_S1.E08.expression.values

source_name: RTgill-W1 cat rep 3 conc 4


title: Preneoplastic_rep_1 td -ve

description: tumourigenesis.atlas.RData

source_name: Brain


title: Preneoplastic_rep_4 td -ve

description: tumourigenesis.atlas.RData


title: Preneoplastic_rep_1

description:
tumourigenesis.atlas.RData
malignant.cells.Sox2CEPPT.and.NestinCPPT.models.RData


title: BAT, TxnipKO, 30C, replicate2

value: male


title: sg-Mrpl9_Bl_biorep3


title: sg-Mrpl9_Bl_biorep4


title: BAT, TxnipKO, 30C, replicate1


title: Control_2 GFP -ve

description: tumourigenesis.atlas.RData

value: Brain


title: rtgill.cat.3.C08

description:
Library name: rtgill.cat.3.C08
Cell lysate
cat.counts.txt
cat.lib8_S1.C08.expression.values

source_name: RTgill-W1 cat rep 3 conc 6

value: Rainbow trout gill


title: sg-Mrpl9_Bl_biorep2


title: Preneoplastic_rep_2


title: rtgill.cat.3.D08

description:
Library name: rtgill.cat.3.D08
Cell lysate
cat.counts.txt
cat.lib8_S1.D08.expression.values

source_name: RTgill-W1 cat rep 3 conc 5


title: BAT, WT, 30C, replicate3