title: single_cell RNA seq data of CSF from patient SMA1_7_untreated

city: Muenster

first: I-Na

last: Lu

state: NRW

address: Domagkstraße 20

department: Department of Pediatric Hematology and Oncology

institute: University Children's Hospital Münster

library_source: transcriptomic single cell

data_processing:
Processing of sequencing data was performed with the cellranger pipeline v6.1.0 (10X Genomics), according to the manufacturer’s instructions. Briefly, raw BCL files were de_multiplexed using the CellRanger mkfastq pipeline. Subsequent read alignments and transcript counting was done individually for each sample using the CellRanger count and CellRanger vdj pipelines with standard parameters.
Assembly: GRCh38
Supplementary files format and content: Standard cellranger output format
Supplementary files format and content: gene expression matrix h5
Supplementary files format and content: contig annotations

source_name: CSF

extract_protocol:
CSF cells were processed within 2 hours post lumbar puncture to ensure optimal sample quality. For processing, CSF was collected into round bottom polypropylene tubes and then centrifuged for 10 min at 300x g. CSF cell pellets were resuspended in 5 ml of X_Vivo15 media (Lonza) and stored on crushed ice. The samples were then transported with same day shipping on crushed ice to the laboratory. Cell suspensions were then centrifuged again for 5 min at 400 x g and resuspended in 50 μl of X_Vivo15 media. Out of this volume, 6 μl were used for cell counting and the remaining volume was entirely used for scRNA_seq.
Single cell suspensions were loaded onto the Chromium Controller (10X Genomics) using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kits v3 and v3.1 (10X Genomics). For TCR sequencing, we applied a previously described technique to sequence antigen receptor information from the 3’ scRNA_seq libraries. In short, the method involves self_circulating the cDNA library, enriching the VDJ region and re_linearizing to remove the constant region of antigen receptors during enrichment, while maintaining their cell barcode and unique molecular identifier (UMI) information attached to the 3' of the cDNA molecules. Library preparation was performed according to manufacturer's instructions using AMPure beads (Beckman Coulter). Sequencing was carried out on a local Illumina Nextseq 500/2000 and Novaseq6000 with a 28_8_0_91 read setup.

treatment_protocol: Nusinersen was administered to SMA patients by lumbar puncture on days 1, 14, 28, and 63 followed by a repetitive application every 4 months according to the treatment guideline. Treatment was performed between the years 2017 - 2021 in the center in Essen. Before each nusinersen injection, the same amount (5 mL) of CSF was withdrawn to prevent excessive intra_CSF pressure.

value: CSF leukocytes

tag: diagnosis

value: SMA

value: untreated


title: Colon, 24 Months, Rep7

status: Public on Mar 27 2024

type: SRA

city: Kiel

first: Lena

last: Best

address: Michaelis-Straße 5

department: Institute of Experimental Medicine

country: Germany

institute: Christian-Albrechts-University Kiel

description:
24M.N7
Colon_24M_N7
colon_RNA_gene_counts.tsv.gz

library_source: transcriptomic

data_processing:
Illumina TruSeq adapter sequences were trimmed from forward and reverse reads using Cutadapt (1.12) with minimum sequence overlap of 3 bp, at most 10% mismatches allowed and minimum read length filter for 20 bp, as well as a 3’-end quality trimming for a phred-score >=30.
An additional quality filter was applied with Prinseq lite (0.20.4) for at most 8 unknown nucleotides (‘N’) per read, an overall mean read quality of at least phred-score 15 and a minimum quality trim also from the 5’-end of the read for a minimum phred-score of 12.
Filtered reads were then mapped against Mus musculus reference genome (GRCm38.p6, mm10) via Hisat2 (2.1.0) with RNA strandedness set to FR, employing non-deterministic random seeds and suppressing the mixed alignments of read pairs. Only primary alignments for each read were kept, via a filtering step (-F 256) with Samtools (1.9).
Gene counts were extracted using HTSeq count (0.6.1) with reverse stranded information in union mode.
Assembly: GRCm38.p6 (mm10)
Supplementary files format and content: Tabular delimited matrix text files of read counts per GRCm38 gene (rows) and sample (columns).

molecule: polyA RNA

organism: Mus musculus

source_name: Colon

growth_protocol: All the mice were kept solely for aging in a controlled environment and  a controlled health status.

extract_protocol:
RNA was extracted from tissue samples of liver, colon and left brain hemisphere with the phenol-chloroform extraction method using for each tissue 1ml Qiazol Lysis Reagent (Qiagen, Hilden, Germany).
RNA was reverse transcripted into Illumina shotgun sequencing libraries at Competence Centre for Genomic Analysis (CCGA, Kiel Germany) with TruSeq RNA stranded kit (Illumina, San Diego, CA) with polyA enrichment according to the manufacturer’s instructions and sequenced for 2x75 cycles (2x100 for colon) in paired end mode with ~13 samples per lane on a HiSeq4000 machine. Demultiplexing was done with zero mismatches allowed in the barcodes.

tag: tissue

value: Colon

tag: strain

tag: Sex

value: Male

tag: age

value: 24 Months

tag: library batch

value: Run 3


title: 2chloroethyltrimethylammoniumchloride _C1 R1

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description:
count_table.tsv
S_2CTAC_326_C1_SP0250_P01_A04

library_source: other

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.23.2
Alignment was performed using STAR v2.7.10b
Gene counts were performed with qCount in the QuasR R package v1.38.0
Normalization was performed with DESeq2 v1.38.0
Assembly: Biospyder Human Human_S1500+Surrogate2.0 Gene Set
Supplementary files format and content: count_table.tsv is a genes by samples count matrix of raw counts from the TempO-Seq data alignments.
Library strategy: TempO-Seq

molecule: other

organism: Homo sapiens

source_name: liver tumor associated with chronic hepatitis C

growth_protocol: Cryopreserved differentiated HepaRGTM cells (Biopredic International, Saint-Grégoire, France) were cultivated according to the manufacturer’s protocol. Differentiated HepaRGTM cells were thawed and seeded into collagen-coated wells at a density of approximately 0.072 x 106 viable cells per well (i.e. 100 μL of the cell suspension per well) in 96-well plates, using HepaRGTM Thawing/Plating/General Purpose Medium 670 (ADD670C, Biopredic International, Saint-Grégoire, France). After 24h, the media were changed to HepaRGTM Maintenance Medium 620 (ADD620C, Biopredic International, Saint-Grégoire, France) for cell maintenance. Cells were incubated for 7 days at 37°C, 5% CO2 and saturating humidity.

extract_protocol:
Cell lysates were used directly for TempO-Seq library building
TempO-Seq® gene expression analysis was conducted on exposed and control HepaRGTM cell lysates. Libraries were prepared in a 96-well plate format using the TempO-Seq® Human Whole Transcriptome Panel reagent kit (BioSpyder Technologies, Carlsbad, CA, USA), following the manufacturer’s protocol. Human Brain Total RNA and qPCR Human Reference Total RNA (Takara Bio, CA, USA) were included as positive assay controls and a no-lysate control (1X TempO-Seq® R Lysis Buffer only) was included as a negative assay control (two replicates per control). In brief, 2 µl cell lysates were hybridized with the targeted detector oligo (DO) probe mix in 1X TempO-Seq® R Lysis Buffer for 10 min at 70oC followed by a temperature gradient with a ramp rate of 0.5oC/min to 45oC over a 50 min period, followed by a nuclease digestion at 37oC for 90 min to remove excess, unbound, or incorrectly bound DOs enzymatically. Ligation of the DO pairs bound to adjacent target sequences was then completed with a 60 min incubation at 37oC, immediately followed with a 15 min enzyme denaturation at 80oC to generate a pool of amplification templates. All amplification templates (i.e., 10 µl of ligated DOs) were transferred to its corresponding well of the 96-well PCR Pre-Mix and Primers plate. Amplification proceeded with a CFX96 Real-Time PCR Detection System (Bio-Rad, Mississauga, ON, Canada) to attach a unique sequence tag and the sequencing adaptors to each sample using the following PCR program settings: 37oC for 10 min, 95oC for 2 min; 6 cycles of 95oC for 30 sec, 54oC for 30 sec, 72oC for 120 sec; 16 cycles of 95oC for 30 sec; 72oC for 2 min; 72oC for 1 min. The TempO-Seq® libraries were pooled (5 µl of all 96 samples) and purified using the Macherey-Nagel NucleoSpin® Gel and PCR Clean-Up kit (Clontech Laboratories Inc., Bethlehem, PA, USA), according to the manufacturer’s instructions for PCR cleanup with three modifications outlined in the TempO-Seq® Assay User Guide. The pooled, purified TempO-Seq® libraries were sequenced using a NextSeq® 2000 High Output flow cell (v2 kit, 75 cycles) on an Illumina NextSeq® 2000 Sequencing platform (Illumina, San Diego, CA, USA).

treatment_protocol: At day 7, cells were exposed in triplicate to 4 concentrations of test chemical and refreshed with test chemical in HepaRGTM Induction Medium 640 (ADD640C, Biopredic International, Saint-Grégoire, France) daily for 72 hours (i.e., 3-day repeat exposures; 0 h, 24 h, 48 h). Cells were exposed to mitomycin C (0.17, 0.5, 1.5, 4.5 µM), 4-nitroquinoline-N-oxide (0.9, 2.7, 8, 12 µM), aflatoxin B1 (0.025, 0.1, 0.5, 1.5 µM), colchicine (0.1, 0.3, 1, 3 µM), cyclophosphamide (78, 233, 700, 2100 µM), eugenol (60, 170, 500, 1000 µM) and 2-chloroethyltrimethylammoniumchloride (370, 1100, 3300 and 10000 µM). After 72 h exposure, cells were used to generate cell lysates for gene expression analysis (n = 3 per treatment group per assay for TempO-Seq®).

tag: cell line

value: HepaRGTM

tag: cell type

value: liver progenitor cells

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

tag: solvent control

value: F

tag: reference rna

tag: technical control

tag: chemical type

value: test

tag: cas-nr


title: Colon, 24 Months, Rep6

description:
24M.N6
Colon_24M_N6
colon_RNA_gene_counts.tsv.gz

tag: tissue

tag: strain

tag: Sex

tag: age


title: iPSC2_1932_Naive_iPSC_2

city: La Jolla

first: Robert

middle: E

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

country: USA

institute: UCSD

description:
DESeq2_normalized_counts.csv
rawCounts_hgnc.csv

data_processing:
Reads were mapped to GRCh38.p10 (GENCODE release 26) using STAR (v. 2.7.3a) and annotated using featureCounts (subread v.1.6.3, GENCODE release 26 primary assembly annotation). The STAR parameters used were: --runMode alignReads --outSAMmode Full --outSAMattributes Standard --genomeLoad LoadAndKeep --clip3pAdapterSeq AGATCGGAAGAGC --clip3pAdapterMMp 1. The featureCounts parameters were: -s 2 -p -t exon -T 13 -g gene_id.
ENSEMBL genes without at least three samples with 10 or more reads were removed from analysis.
Normalization and differential expression analysis were performed using the R (v. 4.2.1) package DESeq2 (v. 1.36.0)89. BiomaRt (v. 2.42.1) was used to convert Ensembl gene ID’s to HUGO gene names90, and gene set enrichment analysis was done using the R(v. 4.2.1) package FGSEA (v. 1.22.0).
Assembly: GRCh38.p10
Supplementary files format and content: comma separated values text file contains raw counts for each sample
Supplementary files format and content: comma separated values text file contains DESeq2 normalized counts for each sample

molecule: total RNA

growth_protocol: Derivation of the TSC line from primed hPSC was performed under a protocol approved by the UCSD Institutional Review Board and Embryonic Stem Cell Research Oversight Committee (ESCRO Protocol number: 171648).  Previously established and characterized primed-iPSCs, which preeclampsia (PE) with severe features showed placental pathologic findings of MVM, and control (non-PE) cases show absence of maternal hypertensive disease or fetal growth restriction, with no evidence of MVM or other placental disc lesions, were used in the study. pTSC was derived using the previously published protocol. In brief, primed-iPSC were cultured on Geltrex- (ThermoFisher) coated plates (using 1:200 diluted Geltrex) in StemFlex (ThermoFisher) or mTeSR Plus (Stem Cell Technologies). The cells were differentiated to trophectoderm (TE)-like cells using the first step of a previously established protocol. In brief, hPSCs were dissociated using TrypLE Express (ThermoFisher) and plated for 1.0 x105 cells/well of the 6 well plate coated with Geltrex (ThermoFisher) in the presence of 5μM Y-27632 (Selleck Chemicals). The next day, media was changed to first-step differentiation media: DMEM/F12 (ThermoFisher), with 1x ITS (Millipore-Sigma), 64μg/ml L-ascorbic acid (Millipore-Sigma), 543μg/ml NaHCO3 (Fisher Scientific), 2% BSA (Gemini), 10 ng/mL BMP4 (ThermoFisher), and 2μM IWP2 (Selleck Chemicals). Media was changed every day for 4 days. Conversion into TE-like cells was confirmed based on surface EGFR expression of over 90% by flow cytometry. Subsequently, cells were replated on collagen IV (Millipore Sigma, 5 μg/mL) in iCTB media: Advanced DMEM/F12 (ThermoFisher), 1X N2 (ThermoFisher), 1X B27 (ThermoFisher), 1X Glutmax (ThermoFisher), 150 μM 1-thioglycerol (Millipore Sigma), 0.05% BSA (Gemini), 1% knockout serum replacement (KSR; ThermoFisher), 2 μM CHIR99021 (Millipore Sigma), 0.5 μM A83-01 (Tocris), 1 μM SB431542 (Millipore Sigma), 5 μM Y27632 (Selleck Chemicals), 130 μg/mL VPA sodium salt (Millipore Sigma), 100 ng/mL recombinant human FGF2 (BioPioneer), 50 ng/mL recombinant human EGF (R&D Systems), 50 ng/mL recombinant human HGF (Stem Cell Technologies), and 20 ng/mL Noggin (R&D System). Cells were passaged for 5 times to derive primed-PSC derived TSC (pTSC). Cell purity were checked for surface expression of CTB marker (EGFR) and EVT marker (HLA-G) to ensured that the cells over 90% EGFR+, and less then 20% HLA-G+ cells. Naïve-iPSC was derived using previously published protocol84,85. In brief, primed-iPSC were seeded on a MEF feeder layer in mTeSR Plus under 5% O2 and 5% CO2. Two days later, media was switched to 5i/L/A, then after 7 to 10 days, cells were passaged using TrypLE Express on a MEF feeder layer under 5% O2 and 5% CO2. Cells were passaged for 6-8 times to establish naïve iPSC. Subsequently, cells were single cell dissociated using TryPLE Express, and  0.5-1.0x106 cells/well were seeded in one well of a 6-well plate coated with 5μg/mL Collagen IV initially in hTSC media for 5 passages, then transitioned to iCTB media for an additional 3-4 passages to derive nTSC.

extract_protocol:
Total RNA was isolated using mirVana RNA Isolation Kit (Ambion). RNA concentration was measured using Qubit RNA BR assay kit (ThermoFisher). RNA integrity was checked using RNA 6000 Nano chip read by a 2100 bioanalyzer (Agilent). All samples had a RIN above 8.0.
Total RNA was isolated using mirVana RNA Isolation Kit (Ambion). RNA concentration was measured using Qubit RNA BR assay kit (ThermoFisher). RNA integrity was checked using RNA 6000 Nano chip read by a 2100 bioanalyzer (Agilent). All samples had a RIN above 8.0.

treatment_protocol: Differentiation of TSCs into EVT were followed by modified Okae protocol. Prior to differentiation, TSCs were tested for the purity to ensure the starting cells are over 90% EGFR+, and less then 20% HLA-G+ cells. TSC were dissociated using TrypLE Express, and seeded for 2.0x105 cells per well of 6 well plate on 20 μg/ml fibronectin coated plate in 2 mL EVT basal media [DMEM/F12 no HEPES (ThermoFisher) supplemented with 0.1 mM 2-mercaptoethanol (ThermoFisher), 0.3% BSA, 1% ITS-X (ThermoFisher), 7.5 mM A83-01 (Tocris), 2.5 mM Y27632(Selleck Chemicals)] supplemented with 4% KSR (ThermoFisher), 100 ng/mL NRG1 (Abcam), and 2% Matrigel (Corning). On day 3, the media were replaced with EVT basal medium supplemented with 4% KSR, and 0.5% Matrigel. On day 5, cells were collected for the flow cytometric analysis, RNA-seq, and WGBS.

tag: progenitor type

value: naive

tag: cell line

tag: cell type

value: iPSC

tag: disease state

value: preeclamptic

tag: fetal sex

value: Female


title: iPSC2_1932_Naive_iPSC_3


title: SAEC, DMSO, biological replicate 1, RNAseq

city: Hangzhou

first: Sida

last: Shao

state: Zhejiang

address: 18 Shilongshan Rd, Xihu District

country: China

institute: Westlake University

data_processing:
bcl2fastq software used for basecalling. Quantification of transcript abundance was obtained from sequenced reads using Salmon v.0.7.2. Abundance measurements in transcripts per million (TPM) units were calculated at the gene-level.
Assembly: GRCh38 release 25 (GENCODE)
Supplementary files format and content: tsv files include measure of abundance in TPM (transcripts per million) units

source_name: lung

growth_protocol: Small airway epithelial cells(SAECs) were maintained in Small Airway Epithelial Cell Growth Medium from LONZA. For the experiments comparing effects of treatment, SAECs were maintained in minimal media as described in manuscript.

extract_protocol:
After 4-day treatment with compounds, cells were washed once with PBS and then trypsinized with 500 µL of TrypLE Express dissociation reagent (Gibco) and neutralized with the addition of 1 mL of growth medium. After pelleting cells with centrifugation (300g) for 3 minutes in 1.5 mL microfuge tubes, total RNA was isolated using a RNeasy kit (Qiagen).
Three biological replicates were submitted for library preparation at BGI.

treatment_protocol: SAECs were treated with DMSO or indicated growth factors and small molecules for 4 days.

value: lung

value: SAEC

tag: treatment

value: DMSO


title: SAEC, donor5, biological replicate 3, RNAseq


title: SAEC, IGF1, biological replicate 3, RNAseq

value: IGF1, 5 ng/mL


title: iPSC2_1932_Prime_hTSC_2

value: prime

value: hTSC


title: iPSC2_1932_Naive_iPSC_1


title: Colon, 24 Months, Rep5

description:
24M.N5
Colon_24M_N5
colon_RNA_gene_counts.tsv.gz

value: Colon

value: Male

tag: library batch


title: SAEC, donor5, biological replicate 2, RNAseq


title: iPSC2_1932_Prime_EVT_3

value: EVT


title: iPSC2_1932_Naive_hTSC_3


title: Colon, 24 Months, Rep4

description:
24M.N4
Colon_24M_N4
colon_RNA_gene_counts.tsv.gz

value: 24 Months

value: Run 3


title: single_cell RNA seq data of CSF from patient SMA1_6_untreated

value: CSF leukocytes

tag: diagnosis

value: SMA

value: untreated


title: SAEC, donor5, biological replicate 1, RNAseq


title: single_cell RNA seq data of CSF from patient SMA1_5_nusinersen_10 months

value: nusinersen

tag: time point

value: 10 months


title: iPSC2_1932_Prime_EVT_2

value: preeclamptic

value: Female


title: Colon, 24 Months, Rep3

description:
24M.N3
Colon_24M_N3
colon_RNA_gene_counts.tsv.gz


title: single_cell RNA seq data of CSF from patient SMA1_5_nusinersen_2 months

value: 2 months


title: SAEC, donor4, biological replicate 3, RNAseq

value: lung

value: SAEC


title: Colon, 24 Months, Rep2

description:
24M.N2
Colon_24M_N2
colon_RNA_gene_counts.tsv.gz


title: iPSC2_1932_Naive_hTSC_2

value: naive


title: single_cell RNA seq data of CSF from patient SMA1_6_nusinersen_6 months

value: 6 months


title: SAEC, donor4, biological replicate 2, RNAseq


title: iPSC2_1932_Naive_hTSC_1

value: hTSC


title: Colon, 24 Months, Rep1

description:
24M.N1
Colon_24M_N1
colon_RNA_gene_counts.tsv.gz

value: Colon

value: Male


title: single_cell RNA seq data of CSF from patient SMA1_4_nusinersen_10 months


title: iPSC2_1932_Naive_EVT_2

value: EVT


title: SAEC, donor3, biological replicate 3, RNAseq


title: single_cell RNA seq data of CSF from patient SMA1_5_untreated


title: Colon, 15 Months, Rep9

description:
15M.N9
Colon_15M_N9
colon_RNA_gene_counts.tsv.gz

value: 15 Months

value: Run 3


title: iPSC2_1932_Naive_EVT_3


title: SAEC, donor4, biological replicate 1, RNAseq


title: iPSC2_1932_Naive_EVT_1


title: 2chloroethyltrimethylammoniumchloride _C2 R1

description:
count_table.tsv
S_2CTAC_326_C2_SP0250_P01_B04

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

value: liver progenitor cells

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

tag: solvent control

value: F

tag: reference rna

value: test


title: Colon, 15 Months, Rep10

description:
15M.N10
Colon_15M_N10
colon_RNA_gene_counts.tsv.gz

tag: tissue

tag: strain

tag: Sex

tag: age


title: SAEC, donor3, biological replicate 2, RNAseq

tag: cell type


title: MSC_1754_3

tag: progenitor type

value: primary

tag: cell line

value: MSC

tag: disease state

value: control

tag: fetal sex


title: single_cell RNA seq data of CSF from patient SMA1_4_nusinersen_6 months

value: CSF leukocytes

tag: diagnosis

value: SMA

tag: treatment

value: nusinersen

tag: time point


title: single_cell RNA seq data of CSF from patient SMA1_4_untreated

value: untreated


title: Colon, 15 Months, Rep7

description:
15M.N7
Colon_15M_N7
colon_RNA_gene_counts.tsv.gz

value: Colon

tag: library batch


title: SAEC, donor3, biological replicate 1, RNAseq

value: lung

value: SAEC


title: single_cell RNA seq data of CSF from patient SMA1_3_nusinersen_6 months

value: 6 months


title: Colon, 15 Months, Rep8

description:
15M.N8
Colon_15M_N8
colon_RNA_gene_counts.tsv.gz

value: Male

value: 15 Months

value: Run 3


title: MSC_1754_1


title: single_cell RNA seq data of CSF from patient SMA1_3_untreated


title: SAEC, donor2, biological replicate 3, RNAseq


title: SAEC, donor2, biological replicate 2, RNAseq


title: Colon, 15 Months, Rep6

description:
15M.N6
Colon_15M_N6
colon_RNA_gene_counts.tsv.gz


title: MSC_1754_2


title: single_cell RNA seq data of CSF from patient SMA1_2_nusinersen_10 months

value: 10 months


title: Colon, 15 Months, Rep5

description:
15M.N5
Colon_15M_N5
colon_RNA_gene_counts.tsv.gz


title: single_cell RNA seq data of CSF from patient SMA1_2_nusinersen_6 months


title: iPSC3_1754_Prime_iPSC_3

value: prime

value: iPSC


title: Colon, 15 Months, Rep4

description:
15M.N4
Colon_15M_N4
colon_RNA_gene_counts.tsv.gz


title: SAEC, donor1, biological replicate 3, RNAseq


title: Colon, 15 Months, Rep2

description:
15M.N2
Colon_15M_N2
colon_RNA_gene_counts.tsv.gz


title: SAEC, donor1, biological replicate 2, RNAseq


title: SAEC, donor2, biological replicate 1, RNAseq


title: Colon, 15 Months, Rep3

description:
15M.N3
Colon_15M_N3
colon_RNA_gene_counts.tsv.gz


title: single_cell RNA seq data of CSF from patient SMA1_1_nusinersen_10 months


title: iPSC3_1754_Prime_iPSC_1


title: Colon, 15 Months, Rep1

description:
15M.N1
Colon_15M_N1
colon_RNA_gene_counts.tsv.gz


title: iPSC3_1754_Prime_hTSC_3

description:
DESeq2_normalized_counts.csv
rawCounts_hgnc.csv

value: hTSC


title: single_cell RNA seq data of CSF from patient SMA1_2_untreated


title: iPSC3_1754_Prime_hTSC_2


title: NPC-TW01-EBV-eGFP_H3K27ac

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

library_source: genomic

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.3.3.1.
Duplication reads were removed from aligned file by using picard-tools-2.18..
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER makeUCSCfile command.  BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg19
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: EBV infected nasopharyngeal carcinoma cell lines

growth_protocol: NP69T was cultured in keratinocyte serum-free medium (Gibco, Carlsbad, CA). C666-1 was cultured in RPMI-1640 medium with 10% FBS (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO). NPC-TW01 and NPC-TW01-EBV-eGFP were cultured in minimal essential medium (Sigma-Aldrich, St. Louis, MO) supplemented with 10% FBS and penicillin/streptomycin. These cells were incubated in a humidified atmosphere containing 5% CO2 at 37 ℃.

extract_protocol:
For ChIP-seq, sonicated nuclear fraction was incubated with each antibody and histone-DNA complexes were isolated.
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit (KAPA Biosystems) following the manufacturer’s protocol.

tag: chip antibody

value: H3K27ac_ChIP (Active Motif, 91193)


title: 839 cells,sgRELB-2

city: Chapel Hill

first: Daqi

last: Li

address: 450 West Dr

institute: Univerity of North Carolina at Chapel Hill

data_processing:
RNA sequencing was performed using BGISEQ-500 platforms. FASTQ sequencing reads were trimmed using Trim Galore (RRID:SCR_011847), and transcript quantification was performed using Salmon with the quasi-mapping mode
Assembly: hg38
Supplementary files format and content: FPKM, tpm, readcounts
Supplementary files format and content: RELB_core_table_gene.xls.gz include FPKM values for 4 of total 8 Samples

source_name: glioblastoma

extract_protocol:
Total RNA was extracted with Trizol reagent (Takara) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: glioblastoma

value: glioma stem cells

tag: genotype

value: sgRELB


title: Colon, 9 Months, Rep10

description:
9M.N10
Colon_9M_N10
colon_RNA_gene_counts.tsv.gz

value: 9 Months


title: SAEC, donor1, biological replicate 1, RNAseq


title: single_cell RNA seq data of CSF from patient SMA1_1_nusinersen_6 months

value: CSF leukocytes

value: SMA

value: nusinersen


title: iPSC3_1754_Prime_hTSC_1

value: control


title: Colon, 9 Months, Rep9

description:
9M.N9
Colon_9M_N9
colon_RNA_gene_counts.tsv.gz

value: Colon


title: single_cell RNA seq data of CSF from patient SMA1_1_untreated

value: untreated


title: 839 cells,sgRELB-1


title: NPC-TW01-EBV-eGFP_H3K4me3

value: EBV infected nasopharyngeal carcinoma cell lines

value: H3K4me3_ChIP (Active Motif, 39159)


title: iPSC3_1754_Prime_EVT_2

value: EVT

value: Male


title: Colon, 9 Months, Rep8

description:
9M.N8
Colon_9M_N8
colon_RNA_gene_counts.tsv.gz

value: Run 3


title: iPSC3_1754_Prime_EVT_3

value: prime


title: NPC-TW01-EBV-eGFP_H3K4me1

value: H3K4me1_ChIP (CST, 5326S)


title: iPSC3_1754_Prime_iPSC_2

value: iPSC


title: 839 cells,sgRELBControl-1

value: glioblastoma

value: glioma stem cells

value: sgRELBControl


title: Colon, 9 Months, Rep7

description:
9M.N7
Colon_9M_N7
colon_RNA_gene_counts.tsv.gz

value: 9 Months


title: iPSC3_1754_Prime_EVT_1


title: NPC-TW01_H3K27ac

source_name: EBV(-) nasopharyngeal carcinoma cell lines

value: H3K27ac_ChIP (Active Motif, 91193)


title: iPSC3_1754_Naive_iPSC_3

value: naive


title: Colon, 9 Months, Rep6

description:
9M.N6
Colon_9M_N6
colon_RNA_gene_counts.tsv.gz


title: 839 cells,sgIFI35-2


title: 839 cells,sgIFI35-1


title: Colon, 9 Months, Rep5

description:
9M.N5
Colon_9M_N5
colon_RNA_gene_counts.tsv.gz


title: iPSC3_1754_Naive_iPSC_2

value: control


title: NPC-TW01_H3K4me1

value: EBV(-) nasopharyngeal carcinoma cell lines


title: Colon, 9 Months, Rep4

description:
9M.N4
Colon_9M_N4
colon_RNA_gene_counts.tsv.gz

value: Colon


title: iPSC3_1754_Naive_iPSC_1


title: C666-1_H3K27ac

source_name: EBV(+) nasopharyngeal carcinoma cell lines


title: Colon, 9 Months, Rep3

description:
9M.N3
Colon_9M_N3
colon_RNA_gene_counts.tsv.gz


title: iPSC3_1754_Naive_hTSC_3

value: hTSC


title: 839 cells,sgRELBControl-2


title: iPSC3_1754_Naive_hTSC_2


title: 839 cells,sgIFI35Control-2


title: C666-1_H3K4me3

value: EBV(+) nasopharyngeal carcinoma cell lines

value: H3K4me3_ChIP (Active Motif, 39159)


title: iPSC3_1754_Naive_hTSC_1

value: Male


title: SLC_Ngn2_2d_1

city: Stanford

first: Cheen Euong

last: Ang

address: 265 Campus Drive, G3145

institute: Stanford University

data_processing:
Sequences were mapped using STAR
CPM and TPM values were obtained using STAR or RSEM
Genome_build: hg19
Supplementary_files_format_and_content: txt file containing the TPM values for all the samples.

source_name: hES derived induced neurons

growth_protocol: Human neurons were generated by directed reprogramming of embryonic stem cells or neural progenitor cells using overexpression of Neurogenin-2. Cells were cultured in N3 and Neurobasal media, according to Zhang et al., Neuron, 2013.

extract_protocol:
Cells were dissociated, and isolated using fluorescence activated cell sorting. Cells were then resuspended directly in TRIzol reagent, and the RNA was extracted according to manufacturer's protocol.
The libraries were constructed by BGIseq

treatment_protocol: The starting populations were human ES cells or differentiated neural progenitor cells using drugs.

value: hES-iN


title: Colon, 9 Months, Rep1

description:
9M.N1
Colon_9M_N1
colon_RNA_gene_counts.tsv.gz

value: Run 3


title: NP69T_H3K27ac

source_name: nasopharyngeal epithelial cell lines

value: nasopharyngeal epithelial cell lines


title: Colon, 2 Months, Rep10

description:
2M.N10
Colon_2M_N10
colon_RNA_gene_counts.tsv.gz

value: 2 Months


title: iPSC3_1754_Naive_EVT_3

value: EVT


title: NPC-TW01_H3K4me3


title: C666-1_H3K4me1

value: H3K4me1_ChIP (CST, 5326S)


title: Colon, 2 Months, Rep9

description:
2M.N9
Colon_2M_N9
colon_RNA_gene_counts.tsv.gz


title: NP69T_H3K4me3


title: NP69T_H3K4me1


title: Colon, 9 Months, Rep2

description:
9M.N2
Colon_9M_N2
colon_RNA_gene_counts.tsv.gz


title: SLC_1


title: Colon, 2 Months, Rep7

description:
2M.N7
Colon_2M_N7
colon_RNA_gene_counts.tsv.gz


title: Colon, 2 Months, Rep8

description:
2M.N8
Colon_2M_N8
colon_RNA_gene_counts.tsv.gz


title: H9_Ngn2_2d_2


title: H9_Ngn2_2d_3


title: 839 cells,sgIFI35Control-1

value: glioblastoma

value: glioma stem cells


title: iPSC3_1754_Naive_EVT_1


title: Primary_1276C_hTSC_3

value: primary

value: Female


title: Colon, 2 Months, Rep5

description:
2M.N5
Colon_2M_N5
colon_RNA_gene_counts.tsv.gz


title: C666-1_4C_bait1_OriP

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
w4Cseq was used for demultiplexing, trimmning bait primer sequence, mapping to hg19 genome, and making bedgraph files from raw fastq files.
Assembly: hg19
Supplementary files format and content: bedgraph

growth_protocol: C666-1 was cultured in RPMI-1640 medium with 10% FBS (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO). NPC-TW01-EBV-eGFP was cultured in minimal essential medium (Sigma-Aldrich, St. Louis, MO) supplemented with 10% FBS and penicillin/streptomycin. NP69T was cultured in keratinocyte serum-free medium (Gibco, Carlsbad, CA). These cells were incubated in a humidified atmosphere containing 5% CO2 at 37 ℃.

extract_protocol:
Cells were lysed, and cross-linked DNA was digested with the primary restriction enzyme. Next, digested DNA was subjected to proximity ligation using T4 DNA ligase (EL0013, Thermo Scientific), followed by cross-link removal using Proteinase K (P8107S, New England Biolabs), which resulted in 3C libraries. The 3C libraries were then subjected to a second restriction enzyme digestion, followed by a circularization reaction using T4 DNA ligase.
For the viewpoint of bait1 and 2, the 4C template was used to perform a scaled-up inverse nested PCR. Inverse primers were designed including appropriate adaptors and index sequences. For the viewpoint at the TSS of PLA2G4A, two-step PCR was performed. The first PCR were performed with the primer designed including TSS of PLA2G4A and adaptors. The second PCR was performed to add indexes.

tag: restricion enzymes

value: NlaIII, DpnII


title: H9_2


title: H9_Ngn2_2d_1


title: NP69T_4C_PLA2G4A


title: SL_1


title: C666-1_4C_bait2_EBER


title: normal children, 2-4 years old [Sample C10]

city: Changsha

first: Sha

last: Zhao

address: No. 86, Ziyuan Road, Yuhua District

institute: Department of Child Healthcare, Hunan Children’s Hospital & University of South China

description: 5 ml peripheral whole blood

data_processing:
Exosomes were extracted from peripheral blood by supercentrifugation.200KV transmission electron microscope was used to observe and photograph.
Exosomes-associated markers (CD9, CD63 and CD81) were determined by Western blot analysis. The total protein concentration of exosomes was quantified by the bicinchoninic acid (BCA) assay,  the fluorescence signal was quantified by a western blot detection system.
TRIzol LS Reagent (Invitrogen life technologies: 10296028) was used for isolation of RNA from exosomes. The integrity of RNA was confirmed via a 2% agarose gel, and the concentration (OD 260) and protein contamination (Ratio OD260/OD280) of the total RNA samples were determined with NanoDrop ND-1000. The quality and concentration of the sequencing library were assessed with Agilent 2100 bioanalyzer. According the manufacturer’s protocol, sequencing was performed based on Illumina NextSeq 500.
Assembly: hg18
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: peripheral blood cells

value: peripheral blood cells

tag: disease

value: normal


title: Colon, 2 Months, Rep6

description:
2M.N6
Colon_2M_N6
colon_RNA_gene_counts.tsv.gz

tag: tissue

value: Colon


title: SL_Ngn2_2d_1


title: C666-1_4C_PLA2G4A


title: Primary_1276C_hTSC_2

description:
DESeq2_normalized_counts.csv
rawCounts_hgnc.csv

value: hTSC

value: control


title: Primary_1276C_EVT_2


title: Primary_1276C_hTSC_1


title: SL_Ngn2_2d_3


title: iPSC3_1754_Naive_EVT_2

value: naive

value: Male


title: Primary_1276C_EVT_1


title: normal children, 2-4 years old [Sample C8]

description: 5 ml peripheral whole blood

extract_protocol:
TRIzol LS Reagent (Invitrogen life technologies: 10296028) was used for isolation of RNA from exosomes. The integrity of RNA was confirmed via a 2% agarose gel, and the concentration (OD 260) and protein contamination (Ratio OD260/OD280) of the total RNA samples were determined with NanoDrop ND-1000.
The quality and concentration of the sequencing library were assessed with Agilent 2100 bioanalyzer. According the manufacturer’s protocol, sequencing was performed based on Illumina NextSeq 500.


title: Colon, 2 Months, Rep3

description:
2M.N3
Colon_2M_N3
colon_RNA_gene_counts.tsv.gz

tag: strain

value: Run 3


title: Primary_1276C_EVT_3


title: SLC_Ngn2_2d_3

value: hES-iN


title: normal children, 2-4 years old [Sample C9]

description: 5 ml peripheral whole blood


title: Primary_1049_hTSC_3


title: Colon, 2 Months, Rep2

description:
2M.N2
Colon_2M_N2
colon_RNA_gene_counts.tsv.gz

tag: Sex

value: 2 Months


title: H9_1


title: SLC_3


title: SL_3


title: Colon, 2 Months, Rep4

description:
2M.N4
Colon_2M_N4
colon_RNA_gene_counts.tsv.gz

tag: age


title: normal children, 2-4 years old [Sample C7]

description: 5 ml peripheral whole blood

tag: cell type


title: Primary_1049_hTSC_2

tag: progenitor type


title: SLC_Ngn2_2d_2


title: normal children, 2-4 years old [Sample C6]

description: 5 ml peripheral whole blood


title: Primary_1049_hTSC_1

tag: cell line


title: genetrap tumor rep 8

city: Bethesda

first: Kent

last: Hunter

state: MD

address: 37/4048 37 Convent Drive

department: Center for Cancer Research

institute: National Cancer Institute

data_processing:
Fastq files were imported into Partek Flow and end bases with Phred scores below 20 trimmed.  Data was aligned to the mm39 genome using STAR 2.7.8a
aligned sequences were quantified to the Partek E/M annotation model and normalized by the Median ratio
differentially expressed genes were determined by DESeq2, with a final FDR threshold of 0.05
Assembly: mm39
Supplementary files format and content: tab delimited text containing raw counts for all of the samples

source_name: mammary tumor

growth_protocol: Tumors were harvested from littermates from either wildtype MMTV-PyMT animals of MMTV-PyMT/Resf1 +/- compound animals

extract_protocol:
RNA was isolated from tissues using Trizol, following the manufacturers recommended protocol
Libraries were constructed using TruSeq Stranded Total RNA Library Prep, following the manufacturers protocol

value: mammary tumor

value: genetrap


title: normal children, 2-4 years old [Sample C5]

description: 5 ml peripheral whole blood


title: genetrap tumor rep 6


title: normal children, 2-4 years old [Sample C4]

description: 5 ml peripheral whole blood


title: Primary_1049_EVT_3

value: EVT

tag: disease state


title: Primary_1049_EVT_2

tag: fetal sex


title: SL_Ngn2_2d_2


title: control tumor rep 8

value: wildtype


title: normal children, 2-4 years old [Sample C3]

description: 5 ml peripheral whole blood


title: control tumor rep 7


title: Primary_1049_EVT_1

value: primary


title: normal children, 2-4 years old [Sample C2]

description: 5 ml peripheral whole blood


title: Colon, 2 Months, Rep1

description:
2M.N1
Colon_2M_N1
colon_RNA_gene_counts.tsv.gz


title: Primary_1048_hTSC_3

value: Female


title: normal children, 2-4 years old [Sample C1]

description: 5 ml peripheral whole blood


title: LPS induced, vehicle treated, day 8, biological replicate 1-4, scRNAseq

description: 10X Genomics

data_processing:
Computational analysis of scRNA-seq data was performed on an in house high performance computing cluster according to published methods (https://github.com/theislab/single-cell-tutorial). Raw BCL files were demultiplexed with Cell Ranger (v6.0, 10X Genomics) ‘mkfastq’ command to generate the combined FASTQ files for gene expression libraries and cell multiplexing libraries. Transcripts were aligned to the mouse GRCm38-mm10 reference genome. Subsequently, a count matrix was generated for individual sample by running the ‘cellranger multi’ pipeline with minimal assignment confidence set up as 0.75. This parameter was chosen based on investigation into tag calling per cell.
Assembly: mm10
Supplementary files format and content: processed data contain tsv files for features and barcodes, mtx files for expression matix, and loom files for trajectory inference of each sample.

extract_protocol:
For isolation of single cell suspensions from lung, mice were euthanized followed by whole body perfusion via the injection of 15 mL ice cold PBS through the right ventricle. Upon lung whitening at the end of the perfusion period, the trachea was then exposed, and a small nick was made on the ventral surface. 1 mL of 10 U/mL Dispase diluted in PBS was slowly injected into the lung via the trachea followed by 0.6 mL of lukewarm 1% low-melt agarose. Lung was then covered with ice for 2 min to allow the agarose to solidify. The lung was then excised and then transferred to media containing 5 U/mL Dispase, 1 mM EDTA (Gibco), and 0.1 mg/mL DNase1 in DMEM followed by incubation at room temperature for 45 minutes. The lung was then minced with a razor blade and the resulting cell suspension was filtered through a 70 µm cell strainer followed by a 40 µm cell strainer. Red blood cells were then lysed using RBC lysis buffer and the cells were again filtered through 40 µm cell strainer. After the last centrifugation step at 300 g for 5 minutes, single cells were triturated in 5 mL of PBS containing 10 µM EDTA, counted, and cellular separation and overall cell viability was assessed (overall above 90%). Final single cell suspensions containing 1,000 cells/μL were typically achieved and used immediately in single-cell RNA sequencing-based experiments.
Cells pooled from four samples were loaded on a 10X Chromium Controller using Chromium Next GEM Single Cell 3ʹ v3.1 reagents (10X Genomics) with a targeted cell recovery of 30,000 cells per reaction or 7,500 cells per sample. Single-cell RNAseq libraries were prepared per the manufacturer’s instructions. Single-cell RNA libraries were analyzed and quantified using a Bioanalyzer 2100 system (Agilent) and Qubit HS DNA quantification kit (ThermoFisher). Libraries were pooled equimolarly and quality-controlled under a 1 million-read sequencing using MiSeq system (Illumina). Single cell gene expression libraries and cell multiplexing libraries were then sequenced on a NovaSeq 6000 with S4 flow cell ((Illumina) using paired-end, dual indexing sequencing with 28 cycles for read 1 and 90 cycles for read 2. Single cell gene expression matrices were generated with an average of ~6,000 cells assigned per sample, and ~1,900 genes detected per cell.

value: lung

value: Mixed

value: Vehicle


title: LPS induced, sitagliptin treated, day 8, biological replicate 1-4, scRNAseq

description: 10X Genomics

value: Sitagliptin


title: genetrap tumor rep 5


title: Primary_1048_hTSC_2

value: hTSC


title: genetrap tumor rep 7


title: genetrap tumor rep 4


title: LPS induced, vehicle treated, day 4, biological replicate 1-4, scRNAseq

description: 10X Genomics


title: genetrap tumor rep 3


title: LPS induced, sitagliptin treated, day 3, biological replicate 1-4, scRNAseq

description: 10X Genomics


title: LPS induced, sitagliptin treated, day 4, biological replicate 1-4, scRNAseq

description: 10X Genomics


title: genetrap tumor rep 2


title: SLC_2


title: Primary_1048_EVT_3

value: control


title: LPS induced, vehicle treated, day 3, biological replicate 1-4, scRNAseq

description: 10X Genomics


title: ASD children, 2-4 years old [Sample A7]

description: 5 ml peripheral whole blood

value: peripheral blood cells

value: autism spectrum disorder


title: genetrap tumor rep 1


title: Primary_1048_EVT_2


title: Primary_1048_EVT_1


title: ASD children, 2-4 years old [Sample A8]

description: 5 ml peripheral whole blood


title: control tumor rep 6


title: LPS induced, sitagliptin treated, day 2, biological replicate 1-4, scRNAseq

description: 10X Genomics


title: ASD children, 2-4 years old [Sample A6]

description: 5 ml peripheral whole blood


title: control tumor rep 5


title: Primary_1048_hTSC_1


title: non-treated, biological replicate 3, scRNAseq

description: 10X Genomics


title: control tumor rep 4


title: LPS induced, vehicle treated, day 2, biological replicate 1-4, scRNAseq

description: 10X Genomics


title: ASD children, 2-4 years old [Sample A10]

description: 5 ml peripheral whole blood


title: ASD children, 2-4 years old [Sample A9]

description: 5 ml peripheral whole blood


title: Definitive_resequencing

city: Philadelphia

first: Giulia

last: Pavani

state: Pennsylvania

address: 3501 Civic Center Blvd, CTRB 10060-05

institute: Children's Hospital of Philadelphia

description: 10x Genomics

data_processing:
Cell Ranger (version 6.0.0) software from 10x Genomics was used to align and quantify the droplet-based sequencing raw data with default parameters.
Assembly: GRCh38
Supplementary files format and content: tab-separated values file and matrix files

source_name: iPSC

extract_protocol:
cells were harvested from cell culture plates, washed 3 times with PBS 0.1%BSA
Cells were immediately processed using the 10x Genomics Chromium Single Cell 3’ Reagent kit v3.1 per manufacturer’s instructions. 20,000 cells were loaded for each sample. Cells were partitioned into gel beads, lysed, and barcoded through reverse transcription. cDNA was purified and amplified using appropriate cycle number following the manufacturer’s protocol. Library quantification and quality control were performed using High sensitivity DNA ScreenTape kit(Agilent Technologies). Libraries were uniquely indexed using the Chromium dual Index Kit, pooled, and sequenced on an Illumina NovaSeq 6000 sequencer in a paired-end, dual indexing run (28:10:10:90)with a target of 20,000 mean reads per cell.

treatment_protocol: Cells were coltured for 6 day in erythroid expansion media

value: iPSC

value: erythroblasts


title: non-treated, biological replicate 2, scRNAseq

description: 10X Genomics


title: ASD children, 2-4 years old [Sample A5]

description: 5 ml peripheral whole blood


title: ASD children, 2-4 years old [Sample A3]

description: 5 ml peripheral whole blood


title: Fetal Liver_resequencing

description: 10x Genomics

source_name: Fetal Liver

value: Fetal Liver


title: ASD children, 2-4 years old [Sample A1]

description: 5 ml peripheral whole blood


title: control tumor rep 3

value: mammary tumor


title: non-treated, biological replicate 1, scRNAseq

description: 10X Genomics


title: Primitive_resequencing

description: 10x Genomics


title: control tumor rep 2


title: Colon, SiglecXII_4_S73

city: La Jolla, CA 92093

first: Pradipta

last: Ghosh

address: 9500 Gilman Drive (MC 0651)

department: Departments of Medicine and Cellular and Molecular Medicine

institute: University of California San Diego

data_processing:
RNASeq data was processed using kallisto (version 0.45.0). Gene-level TPM values and gene annotations were computed using a custom Perl Script.
Assembly: Mus_musculus genome build GRCm38.94
Supplementary files format and content: tab-delimited text file includes log2 of TPM values

extract_protocol:
RNA extraction was done  using a commertial kit as per manufacturer’s protocol
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

value: Colon


title: ASD children, 2-4 years old [Sample 34]

description: 5 ml peripheral whole blood


title: control tumor rep 1


title: Definitive

description: 10x Genomics


title: Fetal Liver

description: 10x Genomics


title: ASD children, 2-4 years old [Sample 30]

description: 5 ml peripheral whole blood


title: Colon, SiglecXII_2_S71


title: Heterozygous tumor rep4

value: Resf1 +/- heterozygous


title: Human Kidney

city: Birmingham

first: Rebecca

last: Asiimwe

state: Alabama

address: 1720 2nd Ave South

department: Surgery

institute: The University of Alabama at Birmingham

description:
D1_S1_L001
Fresh frozen Spatial transcriptome sequencing

data_processing:
library strategy: Spatial Transcriptomics
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to a hybrid human-pig reference genome to generate count matrices using Space Ranger’s default settings
Assembly: The human GRCh38 (GCA_000001405.28) or porcine Sus scrofa 11.1 (GCA_000003025.6)
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: high resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png: low resolution image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots

source_name: Kidney

extract_protocol:
Frozen biopsy OCT blocks were equilibrated to -10°C before use. Using a cryostat, a 10 μm section was placed onto a Visium Spatial Gene Expression Slide (10X Genomics) and processed according to the manufacturer’s protocol
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides and Reagent kit according to the manufacturer’s protocol

value: Kidney


title: Heterozygous tumor rep3


title: CMV infected organoid rep 3

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

country: Australia

institute: UNSW

data_processing:
Sequence reads were aligned to the human genome sequence (GRCh38) using Subread (version 1.6.3).
The featureCounts function of Subread was used to generate counts of reads uniquely mapped to annotated genes using the GRCh38.108 gtf file
Assembly: Ensembl homo sapiens genome (GRCh38)
Supplementary files format and content: Tab-delimited text file showing counts for each sample generated using featureCounts function of Subread.

source_name: Cerebral organoids generated from iPSC

growth_protocol: Cerebral organoids were generated from iPSC (Lancaster and Knoblich, 2014). Embryoid bodies were generated by seeding 9,000 live iPSCs in low-bFGF hESC medium in a low-attachment 96-well U-bottom plate. The embryoid bodies were cultured for 5-7 days, with half the medium was removed and replaced with fresh media every other day. ROCK inhibitor and bFGF were only included for the first four days. Primitive neuroepithelial cell clusters were generated by transferring the embryoid bodies to a low-attachment 24-well plate and cultured for 4-5 days in neural induction medium. Every 48 hours of culture, fresh neural induction medium was added to each well. After 4-5 days of culture, the neuroepithelial tissues were embedded in Matrigel droplets and transferred to Petri dishes containing cerebral organoid differentiation medium without vitamin A. Following 48 hours of culture, the medium was replaced with fresh cerebral organoid differentiation medium without vitamin A. After 4 days in culture, the Matrigel-embedded organoids were transferred to Petri dishes containing cerebral organoid differentiation medium containing vitamin A. The Petri dishes were transferred to an orbital shaker and the medium was replaced every 3-4 days with cerebral organoid differentiation medium containing vitamin A. The organoids were cultured for 55 days before undergoing mock or CMV infection and confirmation of cerebral differentiation of the organoid.

extract_protocol:
Total RNA extraction was performed using the RNeasy mini kit (RNeasy Mini Kit; Qiagen) as per manufacturer’s instructions.
mRNA libraries were prepared at the Ramaciotti Centre for Genomics (UNSW University of New South Wales, Australia) using the Illumina Stranded Total RNA with RiboZero Plus kit. The libraries were sequenced using the Illumina NextSeq 500 to produce 75 bp paired end reads. R1.fastq and R2.fastq files were produced for each sample.
RNA-Seq paired end

value: Cerebral organoids generated from iPSC

tag: experiment

value: Inoculated with CMV Merlin

tag: infection

value: CMV


title: Heterozygous tumor rep2


title: Colon, Control_4_S69

tag: treatment

value: Control


title: FTE cells, d3, rep4 (RNAseq)

city: New York

first: Tony

middle: T

last: Huang

state: NY

address: 450 East 29th St, Rm 807

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

data_processing:
Quality check of paired-end fastq files (FastQC)
Adaptor trimming (Trimmomatic)
Alignment to hg19 (STAR)
Generate normalized genome browser tracks
Determine the distribution of bases within the transcripts (Picard)
Generate genes-samples counts matrix (featureCounts)
Assembly: hg19
Supplementary files format and content: Txt file of counts matrix vs genes for four replicates per condition

growth_protocol: FT194 cells (FTEs) with doxycycline (DOX)-inducible shRNA against BRCA2 grown in DMEM-F12 media supplemented with 2% USG and 1% penicillin/streptomycin at 37˚C under 5% CO2

extract_protocol:
RNA isolated from cell pellets using Qiagen Rneasy Kit
PolyA unstranded TruSeq RNA Library Prep (Illumina)

treatment_protocol: d0=untreated FTEs, d3=3 days of doxycyline(DOX) treatment to media every 24 hours with cells passaged to maintain 50-70% confluency

value: Immortalized human fallopian tube epithelial cells

value: BRCA2 knockdown

tag: time


title: CMV infected organoid rep 2

treatment_protocol: The organoids were cultured for 55 days before undergoing mock or CMV infection and confirmation of cerebral differentiation of the organoid.


title: Colon, SiglecXII_4_S64


title: Colon, Control_1_S67


title: Wildtype tumor rep 4

value: wildtype


title: FTE cells, d3, rep3 (RNAseq)


title: Heterozygous tumor rep1


title: FTE cells, d3, rep2 (RNAseq)


title: Control organoid rep 4

value: Not treated


title: CMV infected organoid rep 1


title: Colon, SiglecXII_3_S63


title: Wildtype tumor rep 3


title: Control organoid rep 3


title: FTE cells, d3, rep1 (RNAseq)


title: CMV infected organoid rep 4


title: Colon, SiglecXII_3_S72


title: Colon, SiglecXII_2_S62


title: FTE cells, d0, rep4 (RNAseq)

value: control


title: Wildtype tumor rep 2


title: Control organoid rep 2


title: Colon, SiglecXII_1_S61


title: Wildtype tumor rep 1


title: Primitive

description: 10x Genomics


title: FTE cells, d0, rep3 (RNAseq)


title: Control organoid rep 1


title: Colon, Control_4_S60


title: 6DT1 shH6 rep3

source_name: Mammary

growth_protocol: DMEM plus 10% FBS and PS with 10 ug/ml puromycin

extract_protocol:
For RNA-seq, cells were seeded at equal density in triplicate per condition. After 24 hours, media was aspirated and TriPure isolation reagent was added to the dish to collect cells before centrifugation to separate RNA and organic phases. After separation, the RNA phase was transferred to a new tube and isopropanol was added to the RNA to precipitate. The RNA isopropanol precipitation sample mixture was added to a Qiagen RNeasy Spin column for purification using the Qiagen RNeasy kit. Samples were analyzed by the Agilent 2200 TapeStation electrophoresis system. All samples used for RNA-seq had an RNA integrity number (RIN) score greater than 7 and were sent to the Illumina Sequencing Core at the Frederick National Labs for sequencing.
Libraries were constructed using TruSeq Stranded Total RNA Library Prep, following the manufacturers protocol

treatment_protocol: TLC lentiviral shRNA constructs against Resf1 were obtained from Dharmacon. shRNAs targeting the mouse Resf1 gene, sh-Resf1 H4 (5’-TTTCGATTTGTAACATAGGTC-3') and sh-Resf1 H6 (5’-AAACAACCAAGTTACCTCAGG-3') were used for Resf1 knockdown in mouse cell lines.  For lentivirus production, 1ug of shRNA-containing plasmids and 1ug of viral packaging plasmids, pMD2.G (250ng) (Addgene plasmid #12259) and psPAX2 (750ng) (Addgene plasmid #12260) (both were obtained as a gift from the Trono lab) were transfected  into human 293T (Thermo Fisher Scientific) cell line using X-tremeGene 9 DNA transfection reagent (Roche). 48 hours post-transfection, virus-containing supernatant was then passed through a 45um filter to obtain viral particles, which were transferred to human or mouse breast cancer cell lines. 24 hours post-transduction, the viral media was replaced with fresh 10% DMEM. Finally, after 24 hours, the cells were selected with 10ug/ml puromycin- (Sigma)

value: Mammary

value: mammary cancer

value: Resf1 sh6 knockdown


title: Colon, Control_3_S59


title: 6DT1 shH6 rep2


title: FTE cells, d0, rep1 (RNAseq)


title: MCF7_rep4

city: Amsterdam

first: Wilbert

last: Zwart

state: Noord-Holland

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Raw fastq data were analyzed at 10kb resolution using the snHiC pipeline (v0.2.0) [Gregoricchio, S. and W. Zwart, snHiC: a complete and simplified snakemake pipeline for grouped Hi-C data analysis. Bioinformatics Advances, 2023. 3(1)] applying default parameters.
Assembly: Hg19/GRCh37
Supplementary files format and content: .cool, Hi-C contact matrices
Supplementary files format and content: .h5, Hi-C contact matrices

growth_protocol: MCF7 human breast cancer cell lines have been cultured in Dulbecco’s Modified Eagle Medium (DMEM, Gibco) supplemented with 10% Fetal Bovine Serum (FBS-12A, Capricorn Scientific) and penicillin/streptomycin (100μg/mL, Gibco). Cell lines were subjected to regular Mycoplasma testing, and underwent authentication by short tandem repeat profiling (Eurofins Genomics).

extract_protocol:
Hi-C single-index library preparation of MCF7 cells was performed as previously described [Donaldson-Collier, M.C., et al., EZH2 oncogenic mutations drive epigenetic, transcriptional, and structural changes within chromatin domains. Nature Genetics, 2019. 51(3): p. 517-528.] using MboI (New England Biolabs) restriction enzyme.
Single-indexing 75bp Paired-end

value: breast cancer


title: 6DT1 shH6 rep1


title: MCF7_rep3


title: FTE cells, d6, rep2 (Okseq)

data_processing:
Quality check of paired-end fastq files (FastQC)
Adaptor trimming (Trim Galore)
Alignment to hg19 (bowtie2)
Duplicate removal (Picard)
Split fragments mapped to each DNA strand with custom Python script
Convert each strand data to bedgraph in 1-kb bin sizes in a .txt file
Assembly: hg19
Supplementary files format and content: .txt files containing watson and crick strand reads binned to 1-kb
Library strategy: Ok-seq

extract_protocol:
EdU pulse-labeled Okazaki fragments were extracted from frozen and lysed cell pellets, isolated by ultracentrifugation on a 5-30% sucrose gradient, and purified by biotinylation-azide Click chemistry
Library was constructed with adapter ligation, PCR amplification, and purification with SPRI beads. Quality testing of DNA was performed using Qubit analysis.
replication origin mapping

treatment_protocol: d0=untreated FTEs, d3=3 days of doxycyline(DOX) treatment to media every 24 hours with cells passaged to maintain 50-70% confluency, d6=6 days of DOX treatment every 24 hours with cells passaged to maintain 50-70% confluency


title: MCF7_rep2


title: Colon, Control_1_S57


title: Colon, Control_2_S58


title: 6DT1 shH4 rep3

value: Resf1 sh4 knockdown


title: 6DT1 shH4 rep2


title: MCF7_rep1


title: RNAseq, Droshafl/fl_CreER_mESC, 4OHT, rep3

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

institute: St Vincent's Institute of Medical Research

description: Stranded mRNA seq

data_processing:
The raw reads were aligned to the mouse reference genome GRCm38 (mm10) using RNA STAR with default parameters (version 2.7.8a). Differential gene expression analysis between Drosha-deficient and control ESCs was conducted using the edgeR package (version 3.26.1).
Assembly: GRCm38 (mm10)
Supplementary files format and content: edgeR_drosha_de_withName.txt, contains the output of the edgeR analysis for differential gene expression.

source_name: embryonic stem cells

growth_protocol: All ESCs were cultured in KnockOut DMEM, supplemented with 10% heat-inactivated fetal bovine serum (FBS; GE Healthcare Life Sciences), 5% KnockOut Serum Replacement (Gibco), 1% sodium pyruvate (Gibco), 1% non-essential amino acids, 1% penicillin-streptomycin glutamine (PSQ; Gibco), 0.1 mM 2-mercaptoethanol and 103 U/mL LIF on a Mitomycin C-inactivated mouse embryonic fibroblasts.

extract_protocol:
Total RNA was harvested using TRIsure.
Libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit.

treatment_protocol: Deletion of the floxed Drosha allele was achieved by adding 100 nM 4-hydroxytamoxifen (Sigma-Aldrich) to the Drosha fl/fl Gt(ROSA)26SorCreERT2 ESCs for 72h. The medium was then replaced (without 4-hydroxytamoxifen) for a further 48h to completely deplete Drosha-dependent miRNAs before analysis. Deletion the floxed Dicer allele was achieved by transducing the Dicerfl/fl ESCs with Cre-expressing retrovirus. The virus also contained a GFP reporter that allowed for sorting of transduced cells. GFP+ ESCs were sorted 3 days after transduction, then cultured for a further 2 days before analysis.

value: embryonic stem cells

value: Drosha KO

value: 4-OH tamoxifen


title: 6DT1 shH4 rep1


title: RNAseq, Droshafl/fl_CreER_mESC, 4OHT, rep2

description: Stranded mRNA seq


title: FTE cells, d3, rep2 (Okseq)


title: NC-66-EV

city: Beijing

first: Zhi

middle: John

last: Lu

address: Shuangqing Road

department: School of Life Sciences

institute: Tsinghua University

description: RNA-seq of homo sapiens: healthy donor's EV RNA; Provided by Peking University First Affiliated Hospital;  Constructed by Detector-seq; Purpose: To explore novel plasma and extracellular RNA biomarkers for cancer diagnosis

data_processing:
Adaptors and low-quality sequences in the raw sequencing data were trimmed using cutadapt version 2.3. Remeined reads were mapped to ERCC's spike-in sequences, NCBI's UniVec sequences and human rRNA sequences sequentially. GC oligos introduced in reverse transcription were trimmed off, after which reads shorter than 30 nt were discarded.
STAR (version 2.5.4a) was used to map clean reads to the hg38 genome index built with the GENCODE v38 annotation
Duplicates in the aligned reads were removed using umi_tools(v1.1.2)
The count matrix was constructed using featureCounts11 v1.6.2 with the GENCODE v38 annotation, circular RNA annotation from circBase, intron, intergenic regions frm UCSC Genome Browser. Reads mapped to mitochondrial RNAs were excluded.
Assembly: hg38
Supplementary files format and content: Matrix table of raw gene counts for each gene and sample

source_name: plasma

extract_protocol:
Cell-free RNAs in plasma were extracted using QIAzol Lysis Reagent (Qiagen, 79306). Cell-free RNAs in plasma extracellular vesicles (EVs) were extracted using exoRNeasy Midi Kit (Qiagen, 77144).
Detector-seq

value: plasma

value: healthy donor

tag: gender

value: female

tag: Stage

value: No stage (healthy donor)


title: FTE cells, d3, rep1 (Okseq)

value: Immortalized human fallopian tube epithelial cells

tag: genotype


title: RNAseq, Droshafl/fl_CreER_mESC, 4OHT, rep1

description: Stranded mRNA seq


title: NC-57-EV

tag: disease


title: NC-56-EV

tag: tissue


title: FTE cells, d0, rep2 (RNAseq)


title: 6DT1 shControl rep3


title: FTE cells, d0, rep1 (Okseq)


title: RNAseq, Droshafl/fl_CreER_mESC, notreat, rep3

description: Stranded mRNA seq

value: WT

value: no treatment


title: 6DT1 shControl rep2

value: wildtype


title: NC-55-EV

value: male


title: FTE cells, d6, rep1 (Okseq)

value: BRCA2 knockdown


title: RNAseq, Droshafl/fl_CreER_mESC, notreat, rep2

description: Stranded mRNA seq


title: 6DT1 shControl rep1

value: Mammary

value: mammary cancer


title: NC-54-EV


title: hBM replicate 3 scHi-C

city: Pittsburgh

first: Jian

last: Ma

address: 5000 Forbes Ave

institute: Carnegie Mellon University

data_processing:
Demultiplexing using custom scripts
Alignment by BWA (version 0.7.17-r1188) for genomic DNA and by STAR (version 2.7.8a) for RNA
Deduplication using custom scripts
Contact calling by pairtools (version 0.3.1-dev.1)
RNA read count extraction by featureCounts (version 2.0.1)
Assembly: hg38; mm10
Supplementary files format and content: Tab-delimited text files include chromatin contact pairs for single cells
Supplementary files format and content: Tab-delimited text files include RNA reads and mapped genes for single cells

source_name: Human bone marrow

extract_protocol:
GAGE-seq protocol
Hi-C and scRNA-seq

value: Human bone marrow


title: RNAseq, Droshafl/fl_CreER_mESC, notreat, rep1

description: Stranded mRNA seq


title: hBM replicate 3 scRNA


title: NC-53-EV


title: Bai1KO_P7_Homo_Rep7

city: Paris

first: Fiorella

last: Grandi

address: 105 Bld d'Hopital

department: Centre de Recherche de Myologie

country: France

institute: Sorbonne Universite

description:
Bai1KO_P7_Homo_Rep7
salmon_counts_P7.csv

data_processing:
nf-core/rnaseq pipeline
alignment to mm10 with STAR
counts with salmon
differential expression Deseq2
Assembly: mm10
Supplementary files format and content: salmon_counts_P22.tsv; salmon counts P22
Supplementary files format and content: salmon_counts_P7.csv; salmon counts P7

source_name: cochlea

growth_protocol: The sensory epithelium and spiral ganglion neurons from 4 mice were micro dissected in DNase free ice-cold PBS 1X and immediately snap frozen in liquid nitrogen. Two batches of 3 and 4 replicates (P7) and one batch of 3 replicates (P22) from each genotype.

extract_protocol:
RNA was extracted using RNeasy Plus Micro Kit (Qiagen) according to manufacturer’s instructions. RNA quantity was established using a Nanodrop spectrophotometer and RNA integrity number (RIN) was calculating using a BioAnalyzer (Agilent Tapestation 4200). All samples had RIN score greater than 9.1.
mRNA library preparation was performed using poly A enrichment and sequenced on the Illumina NovaSeq sequencer using paired-end 150bp reads.

value: cochlea

value: Homo


title: 6DT1 sg3 rep3

data_processing:
Fastq files were imported into Partek Flow and end bases with Phred scores below 20 trimmed.  Data was aligned to the T2Tv2 genome using STAR 2.7.8a
aligned sequences were quantified to the Partek E/M annotation model and normalized by the Median ratio
differentially expressed genes were determined by DESeq2, with a final FDR threshold of 0.05
Assembly: T2Tv2
Supplementary files format and content: tab delimited text containing raw counts for all of the samples

treatment_protocol: TLC lentiviral shRNA constructs against Resf1 were obtained from Dharmacon. shRNAs targeting the human RESF1 gene, sh-RESF1 565 (5’-GAATACAAACTCTGTGGAAGA-3') and sh-RESF1 G5 (5’-GATGGATTTGAGATGCTACAA-3'). For lentivirus production, 1ug of shRNA-containing plasmids and 1ug of viral packaging plasmids, pMD2.G (250ng) (Addgene plasmid #12259) and psPAX2 (750ng) (Addgene plasmid #12260) (both were obtained as a gift from the Trono lab) were transfected  into human 293T (Thermo Fisher Scientific) cell line using X-tremeGene 9 DNA transfection reagent (Roche). 48 hours post-transfection, virus-containing supernatant was then passed through a 45um filter to obtain viral particles, which were transferred to human or mouse breast cancer cell lines. 24 hours post-transduction, the viral media was replaced with fresh 10% DMEM. Finally, after 24 hours, the cells were selected with 10ug/ml puromycin- (Sigma)

value: Resf1 KO

value: sgResf1 CRISPR KO


title: 6DT1 sg3 rep2


title: Bai1KO_P7_Homo_Rep6

description:
Bai1KO_P7_Homo_Rep6
salmon_counts_P7.csv


title: hBM replicate 2 scHi-C


title: 6DT1 sg3 rep1


title: hBM replicate 2 scRNA


title: FTE cells, d0, rep2 (Okseq)

value: control


title: NC-51-EV

value: plasma

value: healthy donor


title: 6DT1 sg2 rep3


title: Bai1KO_P7_Homo_Rep4

description:
Bai1KO_P7_Homo_Rep4
salmon_counts_P7.csv


title: 6DT1 sg2 rep2


title: NC-38-EV

value: No stage (healthy donor)


title: hBM replicate 1 scHi-C


title: MDSL scHi-C

source_name: MDS-L

value: MDS-L


title: Bai1KO_P7_Homo_Rep5

description:
Bai1KO_P7_Homo_Rep5
salmon_counts_P7.csv


title: NC-47-EV

value: female


title: 6DT1 sg2 rep1


title: hBM replicate 1 scRNA


title: Bai1KO_P7_Homo_Rep3

description:
Bai1KO_P7_Homo_Rep3
salmon_counts_P7.csv


title: NC-34-EV


title: 6DT1 sg1 rep3


title: Bai1KO_P7_Homo_Rep2

description:
Bai1KO_P7_Homo_Rep2
salmon_counts_P7.csv


title: NC-33-EV


title: MDSL scRNA


title: NC-52-EV


title: K562-GM12878 scHi-C


title: 6DT1 sg1 rep2


title: NC-32-EV


title: K562-GM12878 scRNA


title: NC-31-EV


title: Bai1KO_P7_Het_Rep6

description:
Bai1KO_P7_Het_Rep6
salmon_counts_P7.csv

value: Het


title: 6DT1 sgControl rep3

value: wild type

value: sgScranble control


title: 6DT1 sgControl rep2


title: HEK293 cells, REST-KO E6, replicate 2

city: Austin

first: Svetlana

last: Panina

state: TX

address: 101 East 21st St.

department: Molecular Biosciences

institute: The University of Texas at Austin

data_processing:
Quality of raw reads was assessed using FastQC read quality reports (Galaxy).
Adaptor trimming, deduplicating, and quality filtering were performed using a published pipeline (https://github.com/z0on/tag-based_RNAseq).
Next, trimmed reads were aligned to human reference genome, GRCh38 version, using HISAT2 fast aligner v.2.2.1 with default parameters, except Forward (F) --rna-strandedness. Gencode v38 gtf file was used as annotation gtf.
Lastly, mapped fragments were quantified by featureCounts v.2.0.1 in Galaxy.
Assembly: GRCh38
Supplementary files format and content: tabular files including FeatureCounts for each Sample
Library strategy: Tag-Seq

growth_protocol: Cells were routinely cultured in Dulbecco’s modified Eagle’s media, supplemented with 10% fetal bovine serum at 37 °C in humidified atmosphere with 5% CO2

extract_protocol:
Total RNA was isolated using DirectZol RNA Miniprep kit (Zymo Research).
Libraries were prepared at the University of Texas Genomic Sequencing and Analysis Facility (GSAF) based on the protocols from Lohman BK et al. [PMID 27037501] and Meyer E et al. [PMID 21801258]. Libraries were quantified using the Quant-it PicoGreen dsDNA assay (ThermoFisher) and pooled equally for subsequent size selection at 350-550 bp on a 2% gel using the Blue Pippin (Sage Science).  The final pools were checked for size and quality with the Bioanalyzer High Sensitivity DNA Kit (Agilent) and their concentrations were measured using the KAPA SYBR Fast qPCR kit (Roche).

treatment_protocol:
To express REST-KO sgRNAs, two pairs of DNA oligos were synthesized: REST-RY1F (caccgGTTATGGCCACCCAGGTAAT) and REST-RY1R (aaacATTACCTGGGTGGCCATAACC); REST-RG6F (caccgGTCTTCTGAGAACTTGAGTA) and REST-RG6R (aaacTACTCAAGTTCTCAGAAGACC). Annealed double-stranded sgRNAs were cloned into pX330 plasmid.
HEK293 and T98G cells were co-transfected with two sgRNA expression vectors (RY1, RG6) and Cas9-2A-GFP plasmid. As CRISPR-recombination control, we used cells co-transfected with empty pX330 vector and Cas9-2A-GFP plasmid. At 48 h post-transfection, single GFP-expressing cells were sorted into 96-well plates with complete DMEM media for clone expansion.

value: embryonic kidney cells

value: REST-KO

tag: clone

value: REST-KO E6


title: HEK293 cells, REST-KO E6, replicate 1


title: Bai1KO_P7_Het_Rep4

description:
Bai1KO_P7_Het_Rep4
salmon_counts_P7.csv


title: Bai1KO_P7_Het_Rep5

description:
Bai1KO_P7_Het_Rep5
salmon_counts_P7.csv


title: LC-41-EV

description: RNA-seq of homo sapiens: lung cancer patient's EV RNA; Provided by Peking University First Affiliated Hospital;  Constructed by Detector-seq; Purpose: To explore novel plasma and extracellular RNA biomarkers for cancer diagnosis

value: lung cancer

value: male

value: I


title: Bai1KO_P7_Het_Rep3

description:
Bai1KO_P7_Het_Rep3
salmon_counts_P7.csv

value: cochlea


title: HEK293 cells, REST-KO D10, replicate 2

value: REST-KO D10


title: LC-40-EV


title: MBA-MD-231 knockdown rep3

source_name: Breast

value: Breast

value: breast cancer

value: RESF1 shRNA knockdown


title: Bai1KO_P7_Homo_Rep1

description:
Bai1KO_P7_Homo_Rep1
salmon_counts_P7.csv

value: Homo


title: Bai1KO_P7_Het_Rep2

description:
Bai1KO_P7_Het_Rep2
salmon_counts_P7.csv


title: LC-37-EV

value: plasma


title: LC-42-EV

value: II


title: HEK293 cells, REST-KO D10, replicate 1


title: Bai1KO_P7_Het_Rep7

description:
Bai1KO_P7_Het_Rep7
salmon_counts_P7.csv

value: Het


title: Bai1KO_P22_Homo_Rep3

description:
Bai_P22_ko_R3
salmon_counts_P22.tsv


title: HEK293 cells, CRISPR Control, replicate 2

value: WT

value: CRISPR Control


title: MBA-MD-231 knockdown rep2


title: MBA-MD-231 knockdown rep1


title: LC-34-EV


title: T98G cells, REST-KO D4, replicate 2

value: glioblastoma (GBM)

value: REST-KO D4


title: MBA-MD-231 shControl rep2

value: wildtype


title: LC-32-EV

value: lung cancer


title: Bai1KO_P22_Homo_Rep1

description:
Bai_P22_ko_R1
salmon_counts_P22.tsv


title: MBA-MD-231 shControl rep3


title: Bai1KO_P22_Homo_Rep2

description:
Bai_P22_ko_R2
salmon_counts_P22.tsv


title: T98G cells, REST-KO D4, replicate 1

value: REST-KO


title: MBA-MD-231 shControl rep1


title: LC-31-EV

value: female

value: I


title: HEK293 cells, CRISPR Control, replicate 1

value: embryonic kidney cells


title: 6DT1 sgControl rep1

value: Mammary

value: mammary cancer

value: wild type

value: sgScranble control


title: Bai1KO_P22_Het_Rep3

description:
Bai_P22_het_R3
salmon_counts_P22.tsv

value: cochlea


title: T98G cells, REST-KO G2, replicate 2

value: REST-KO G2


title: Bai1KO_P7_Het_Rep1

description:
Bai1KO_P7_Het_Rep1
salmon_counts_P7.csv

value: Het


title: iHeps WT-3 day 13 (exp.5)

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

data_processing:
CLC Genomics Workbench v 11.0.1 / CLC Genomics Workbench v 12.0.3
Trimming. Quality trimming (quality limit: 0.01); Ambiguity trimming (ambigous limit: 2 nucleotides); Minimum number of nucleotides in reads: 30 nucleotides; Discard short reads
Trimmed sequence reads were mapped to the reference genome: Human (hg38). Parameters: Length fraction= 0.8; Similarity fraction= 0.8
The result of mapping served to determine the gene expression levels based on the TPM (Trancripts Per Kilobase Million per Million) and RPKM (Reads Per Kilobase MillionReads per Kilobase Million) methods
Differential gene expression analyses with TPM and RPKM values comparing human fibroblast starting samples with generated iHeps were performed using MultiExperimentViewer (MeV) (version 4.9.0) software. T-test (p<0.001) and LIMMA-test (p<0.001) were applied to both TPM and RPKM values of coding genes.
Gene set enrichment analyses were conducted with GSEA (version 4.1.0) software 74, using the TPM values of protein coding genes.
Assembly: hg38
Supplementary files format and content: "TPM_matrix.txt"
Supplementary files format and content: log2(TPM values), 0.0001 if value=0.
Supplementary files format and content: "RPKM_matrix.txt"
Supplementary files format and content: log2(RPKM values), 0.0001 if value=0.

source_name: Induced-hepatocytes

growth_protocol: Human fibroblasts were cultured in DMEM with GlutaMAX, 10% HyClone Research Grade Fetal Bovine Serum and 1% penicillin/streptomycin solution under normoxic conditions (37°C, 21% O2, 5% CO2 and 95% relative humidity).

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher) and purified with RNeasy MinElute Cleanup Kit (Qiagen).
cDNA library was constructed using Kapa Stranded mRNA Library Preparation Kit and sequenced in the IlluminaHiSeq 4000 or Illumina Novaseq platform, using 150bp paired-end sequencing reads.

treatment_protocol:
Primary fibroblasts were immortalized by lentiviral transduction with a vector coding for the telomerase reverse transcriptase hTERT, the catalytic subunit of the telomerase enzyme (pLOX-TERT-iresTK, Addgene plasmid #12245). Healthy donor fibroblasts were also transduced with the lentiviral vector pCCL-Enh1mTTR:eGFP-wpre coding for the green fluorescent protein (eGFP) under the control of a synthetic promoter (Enh1mTTR) that was shown to restrict transgene expression to hepatocytes.
Hepatic transdifferentiation: For induced-hepatocyte (iHeps) generation, fibroblasts were transduced with four lentiviral vectors coding for selected  human hepatic transcription factors (FOXA2, HNF1α, HNF4α and TBX3) and cultured in hepatic-specific culture media. Two defined culture media were employed sequentially. Three-five days in endoderm induction medium (cDMEM supplemented with 4.99mM nicotinamide, 10ng/ml recombinant human FGF-basic, 20ng/ml recombinant human HGF, 0.10% DMSO, 2μM A-83-01 and 3μM CHIR99021). Then, in hepatic maturation medium until day 13 (cDMEM supplemented with 0.1μM dexamethasone, ITS (insulin, transferrin, sodium selenite) liquid media supplement, 640μM N-nitro-L-arginine methyl ester hydrochloride (L-NAME), 20ng/ml recombinant human HGF, 20ng/ml recombinant human oncostatin M, 0.10% DMSO, 2μM A-83-01 and 3μM CHIR99021).

value: Induced-hepatocytes

value: control donor

value: Hepatic transdifferentiation (FOXA2, HNF1a, HNF4a and TBX3 lentiviral overexpression and hepatic-specific culture media).


title: LC-29-EV

value: plasma

value: male


title: Bai1KO_P22_Het_Rep1

description:
Bai_P22_het_R1
salmon_counts_P22.tsv


title: T98G cells, REST-KO G2, replicate 1

value: glioblastoma (GBM)


title: T98G cells, REST-KO F7, replicate 2

value: REST-KO

value: REST-KO F7


title: LC-35-EV

value: lung cancer

value: I


title: LC-30-EV

value: female


title: T98G cells, REST-KO F7, replicate 1


title: Gabbr1_KO

city: Chaoyang Distric

first: Nian

last: Liu

state: Beijing

address: Institute of Biophysics,#15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
Pools were sequenced on Illumina NovaSeq 6000 with 150 bp paired end reads. Raw reads were processed with fastQC and fastp to remove low quality reads. Poly-A tails and adaptor sequences were removed by cutadapt.
After quality control, reads were mapped to the reference genome mm10 using STAR. Gene counts and UMI counts were acquired by featureCounts software. Expression matrix files for subsequent analyses were generated based on gene counts and UMI counts.
ScRNA-seq data were further analyzed using R version 4.2.2, Seurat package version 4.3.0. CD45+CD127+ immune cells and CD45-EpCAM+ epithelial cells were discriminated by expression of marker genes (including Ptprc, Il7r and Epcam).
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: small intestine

extract_protocol:
Single-cell suspensions with 1×105 cells/mL in concentration in PBS were prepared. Single-cell suspensions were then loaded onto microfluidic devices.
ScRNA-seq libraries were constructed according to Singleron GEXSCOPE® protocol by GEXSCOPE® Single-Cell RNA Library Kit (Singleron Biotechnologies) . Individual libraries were diluted to 4nM and pooled for sequencing.

value: small intestine

value: mouse primary cells

value: CD127+ immune cells and EpCAM+ epithelial cells

value: Gabbr1 knockout

tag: strain


title: iHeps WT-3 day 8 (exp.5)


title: iHeps WT-3 day 8 (exp.1)


title: iHeps WT-3 day 13 (exp.1)


title: LC-28-EV

tag: age


title: T98G cells, REST-KO C10, replicate 2

tag: cell type

value: REST-KO C10


title: LC-27-EV


title: T98G cells, REST-KO C10, replicate 1


title: Gabbr1_WT

value: Gabbr1 wild-type


title: LC-26-EV


title: Medulloblastoma, Ptf1a-Cre/+; Ptch1fl/fl; Pgbd5-/-, ATAC, rep 3

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

institute: Lady Davis Institute for Medical Research

description:
ATAC part of a 10X Genomics scMultiome sample
medullo_Pgbd5minus_rep3.Rds

library_source: genomic single cell

data_processing:
Cell Ranger ARC v2.0.0 (10X Genomics) was used (‘count’ option with default parameters) to filter and align raw reads, identify transposase cut sites, detect accessible chromatin peaks, call cells and generate raw count matrices for scMultiome samples. Alignment was performed using the mm10 reference genome build coupled with the Ensembl 98 gene annotation. Reads that mapped to the intronic regions were excluded for the RNA modality
Quality control (QC) and data processing steps were performed using Signac v1.3.0 and Seurat v4.3.0. QC metrics for RNA and ATAC modalities were calculated independently but were jointly used to filter cells. In the RNA modality, cells were filtered on the number of genes, unique molecular identifiers (UMIs), and mitochondrial content. In the ATAC modality, cells were filtered on the number of peaks detected, transcription start site enrichment, and nucleosome signal.
Normalization and dimensionality reduction: For the RNA modality, libraries were scaled to 10,000 UMIs per-cell and log normalized. UMI counts and mitochondrial content were regressed out from normalized gene counts and the residuals z-scored gene-wise. Dimensionality reduction was performed using principal-component analysis (PCA) on the top 2,000 most variable features. For the ATAC modality, peaks were called using MACS2 (v2.2.7.1) using the CallPeaks function from Signac library with default parameters. ATAC reads were quantified in each peak per cell and a resulting count matrix was generated. Dimensionality reduction was performed using latent semantic indexing (LSI). A weighted nearest neighbor graph was constructed between all cells using the first 30 principal components from the RNA data and the top 6 dimensions of the LSI reduction from the ATAC data with the following default parameters: 20 multimodal neighbors, 200 approximate neighbors and L2 normalization enabled. This weighted nearest neighbor graph was used as input for projection into two dimensions using uniform manifold approximation and projection (UMAP) and for clustering using a shared nearest-neighbor (SNN) algorithm based on the Louvain algorithm on a k-nearest neighbor graph with k = 20 and resolution 0.2.
Cell type annotation in single nuclei RNA data: Annotation of cell types were performed using four different reference-based annotation tools: three machine learning-based prediction methods (SciBet, SingleCellNet, and SingleR) and a statistical model (Spearman correlation). A consensus label annotation was assigned when at least two methods agreed. Cell type annotation was performed using a murine cerebellar developmental atlas (9 developmental samples ranging from timepoints, E10 - P14; N = 62,040 cells) as the reference.
Malignant cell identification in single nuclei RNA data: Copy number variants (CNVs) were inferred on a sample basis using inferCNV (v1.10.1) with the following parameters: cutoff = 0.1, window_length = 101, analysis_mode = “samples”, cluster_by_groups = FALSE, sd_amplifier = 1.5, HMM = FALSE, and denoise = TRUE. The mitochondrial chromosome (defined as having gene symbols starting with ‘mt’-), ribosomal genes (defined as having gene symbols matching ‘Rps’, ‘Rpl’, ‘Mrps’, ‘Mrpl’), and MHC genes (defined as having gene symbols starting with ‘H2-‘) were excluded from the CNV inference. A normal reference was assembled selecting clusters composed of a single cell type and originating from multiple samples (immune and oligodendrocyte precursor cells clusters) in the integrated snRNA-seq space. Finally, hierarchical clustering of cells based on their CNV profiles was used to identify subtrees of malignant cells with prominent copy-number signal, distinguishing them from normal cells lacking copy-number variation signal.
Assembly: mm10
Supplementary files format and content: *.Rds: R Seurat object containing RNA data (assay RNA), ATAC data (assay ATAC) and metadata for each cell, including cell type annotation (Broad_CellClass_Prediction) and malignant cell identification (inferCNV_malignant_calls)

source_name: Cerebellum

extract_protocol:
Frozen pieces (~50 mg) of tumors from Ptf1a-Cre/+; Ptch1fl/fl; Pgbd5+/+ (n=3) and Pgbd5-/- (n=3) were used for nuclei isolation. Nuclei extraction was performed according to the protocol from Masilionis et al 2022 (doi:10.17504/protocols.io.j8nlkkmq6l5r/v1). Singlulator100 (S2 Genomics) was used for nuclei extraction. Extracted nuclei were stained with 7-Aminoactinomycin D (Invitrogen) and FACS-sorted for further nuclei purification.
Ten thousand nuclei were targeted for library construction using ChromiumNextGEM Multiome ATAC + Gene Expression kit (10xGenomics)
Other: Single cell multiome ATAC + Gene Expression

treatment_protocol: Snap-frozen tissue was stored at -80 prior to nuclei extraction

value: Cerebellum

value: Granule cells

value: medulloblastoma

value: Pgbd5 -/-

value: Conditional KO of Ptch1


title: Medulloblastoma, Ptf1a-Cre/+; Ptch1fl/fl; Pgbd5+/+, ATAC, rep 3

description:
ATAC part of a 10X Genomics scMultiome sample
medullo_Pgbd5plus_rep3.Rds

value: Pgbd5 +/+


title: LC-25-EV

value: plasma


title: iHeps WT-1 day 13 (exp.6)

value: Induced-hepatocytes

value: control donor

value: Hepatic transdifferentiation (FOXA2, HNF1a, HNF4a and TBX3 lentiviral overexpression and hepatic-specific culture media).


title: hFibros WT-3

source_name: Skin

value: Skin

value: Fibroblasts


title: Bai1KO_P22_Het_Rep2

description:
Bai_P22_het_R2
salmon_counts_P22.tsv

value: cochlea

value: Het


title: T98G cells, CRISPR Control, replicate 2

value: glioblastoma (GBM)

value: WT

value: CRISPR Control


title: T98G cells, CRISPR Control, replicate 1


title: Medulloblastoma, Ptf1a-Cre/+; Ptch1fl/fl; Pgbd5+/+, ATAC, rep 2

description:
ATAC part of a 10X Genomics scMultiome sample
medullo_Pgbd5plus_rep2.Rds

value: Cerebellum


title: iHeps WT-1 day 13 (exp.5)


title: LC-24-EV

value: lung cancer

value: female


title: iHeps WT-1 day 13 (exp.1)


title: LC-23-EV

value: I


title: Medulloblastoma, Ptf1a-Cre/+; Ptch1fl/fl; Pgbd5+/+, ATAC, rep 1

description:
ATAC part of a 10X Genomics scMultiome sample
medullo_Pgbd5plus_rep1.Rds

value: Granule cells

value: medulloblastoma

value: Conditional KO of Ptch1


title: single_cell TCR seq data of CSF from patient IIH91_untreated

city: Muenster

first: I-Na

address: Domagkstraße 20

institute: University Children's Hospital Münster

data_processing:
Processing of sequencing data was performed with the cellranger pipeline v6.1.0 (10X Genomics), according to the manufacturer’s instructions. Briefly, raw BCL files were de_multiplexed using the CellRanger mkfastq pipeline. Subsequent read alignments and transcript counting was done individually for each sample using the CellRanger count and CellRanger vdj pipelines with standard parameters.
Assembly: GRCh38
Supplementary files format and content: Standard cellranger output format
Supplementary files format and content: gene expression matrix h5
Supplementary files format and content: contig annotations

source_name: CSF

extract_protocol:
CSF cells were processed within 2 hours post lumbar puncture to ensure optimal sample quality. For processing, CSF was collected into round bottom polypropylene tubes and then centrifuged for 10 min at 300x g. CSF cell pellets were resuspended in 5 ml of X_Vivo15 media (Lonza) and stored on crushed ice. The samples were then transported with same day shipping on crushed ice to the laboratory. Cell suspensions were then centrifuged again for 5 min at 400 x g and resuspended in 50 μl of X_Vivo15 media. Out of this volume, 6 μl were used for cell counting and the remaining volume was entirely used for scRNA_seq.
Single cell suspensions were loaded onto the Chromium Controller (10X Genomics) using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kits v3 and v3.1 (10X Genomics). For TCR sequencing, we applied a previously described technique to sequence antigen receptor information from the 3’ scRNA_seq libraries. In short, the method involves self_circulating the cDNA library, enriching the VDJ region and re_linearizing to remove the constant region of antigen receptors during enrichment, while maintaining their cell barcode and unique molecular identifier (UMI) information attached to the 3' of the cDNA molecules. Library preparation was performed according to manufacturer's instructions using AMPure beads (Beckman Coulter). Sequencing was carried out on a local Illumina Nextseq 500/2000 and Novaseq6000 with a 28_8_0_91 read setup.

value: CSF leukocytes

tag: diagnosis

value: IIH

value: untreated


title: iHeps WT-1 day 8 (exp.5)_biol.rep.2

value: Induced-hepatocytes

value: control donor

value: Hepatic transdifferentiation (FOXA2, HNF1a, HNF4a and TBX3 lentiviral overexpression and hepatic-specific culture media).


title: single_cell TCR seq data of CSF from patient IIH53_untreated


title: single_cell TCR seq data of CSF from patient IIH10_untreated


title: iHeps WT-1 day 8 (exp.5)_biol.rep.1


title: LC-22-EV

value: plasma


title: Medulloblastoma, Ptf1a-Cre/+; Ptch1fl/fl; Pgbd5-/-, ATAC, rep 2

description:
ATAC part of a 10X Genomics scMultiome sample
medullo_Pgbd5minus_rep2.Rds

tag: cell line

value: Pgbd5 -/-


title: Medulloblastoma, Ptf1a-Cre/+; Ptch1fl/fl; Pgbd5-/-, ATAC, rep 1

description:
ATAC part of a 10X Genomics scMultiome sample
medullo_Pgbd5minus_rep1.Rds


title: hFibros WT-1_biol.rep.2

value: Skin

value: Fibroblasts


title: LC-21-EV

value: male


title: CRC-54-EV

description: RNA-seq of homo sapiens: colorectal cancer patient's EV RNA; Provided by Peking University First Affiliated Hospital;  Constructed by Detector-seq; Purpose: To explore novel plasma and extracellular RNA biomarkers for cancer diagnosis

value: colorectal cancer

value: IIIB


title: Medulloblastoma, Ptf1a-Cre/+; Ptch1fl/fl; Pgbd5+/+, RNA, rep 3

description:
RNA part of a 10X Genomics scMultiome sample
medullo_Pgbd5plus_rep3.Rds

value: Cerebellum

value: Pgbd5 +/+


title: single_cell TCR seq data of CSF from patient IIH68_untreated


title: hFibros WT-1_biol.rep.1


title: single_cell TCR seq data of CSF from patient SMA1_9_nusinersen_10 months

value: SMA

value: nusinersen

tag: time point

value: 10 months


title: PM154, DNMT3A knockout, rep3

city: Chiba

first: Yasutaka

last: Yamada

state: MA

address: 1-8-1 Inohana, chuo-ku

department: Urology

institute: Graduate School of Medicine, Chiba University

data_processing:
RNA quantity and integrity were determined using the Qubit® Fluorometer and the Fragment Analyzer system with the PROSize 3.0 software (Agilent Technologies, Palo Alto, California, USA).
The RQN were ranging from 8.8 to 10 for all samples, which was considered sufficient. Illumina TruSEQ RNA library prep and sequencing reagents were used following the manufacturer’s recommendations using polyA-selected transcripts (Illumina, San Diego, CA, USA).
The samples were sequenced on the Illumina NovaSeq platform (2 x 150 bp, single index) and generated ~20 million paired-end reads for each sample.
Assembly: GRCh38
Supplementary files format and content: Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Below are the statistics of mapping the reads to the reference genome.
Supplementary files format and content: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.

growth_protocol: The medium for this cell lines is prostate specific media using advanced DMEM.

extract_protocol:
 Total RNA was extracted from each tissue by using Qiagen's ‘RNeasy’ RNA extraction kit (Qiagen).
RNA-sequencing was performed by GENEWIZ (South Plainfield, NJ, USA). RNA quantity and integrity were determined using the Qubit® Fluorometer and the Fragment Analyzer system with the PROSize 3.0 software (Agilent Technologies, Palo Alto, California, USA). The RQN were ranging from 8.8 to 10 for all samples, which was considered sufficient. Illumina TruSEQ RNA library prep and sequencing reagents were used following the manufacturer’s recommendations using polyA-selected transcripts (Illumina, San Diego, CA, USA). The samples were sequenced on the Illumina NovaSeq platform (2 x 150 bp, single index) and generated ~20 million paired-end reads for each sample.

value: Prostate cancer cell line

value: DNMT3A knockout


title: PM154, DNMT3A knockout, rep2


title: CRC-53-EV

value: female

value: IIA


title: Medulloblastoma, Ptf1a-Cre/+; Ptch1fl/fl; Pgbd5-/-, RNA, rep 3

description:
RNA part of a 10X Genomics scMultiome sample
medullo_Pgbd5minus_rep3.Rds

value: Granule cells

value: medulloblastoma

value: Conditional KO of Ptch1


title: CRC-52-EV

value: plasma

value: I


title: Medulloblastoma, Ptf1a-Cre/+; Ptch1fl/fl; Pgbd5+/+, RNA, rep 1

description:
RNA part of a 10X Genomics scMultiome sample
medullo_Pgbd5plus_rep1.Rds


title: CRC-51-EV

value: male


title: PM154, DNMT3A knockout, rep1


title: single_cell TCR seq data of CSF from patient SMA1_7_nusinersen_6 months

department: Department of Pediatric Hematology and Oncology

value: CSF leukocytes

value: 6 months


title: CRC-49-EV

value: colorectal cancer


title: Medulloblastoma, Ptf1a-Cre/+; Ptch1fl/fl; Pgbd5-/-, RNA, rep 2

description:
RNA part of a 10X Genomics scMultiome sample
medullo_Pgbd5minus_rep2.Rds

value: Cerebellum

value: Pgbd5 -/-


title: single_cell TCR seq data of CSF from patient SMA1_7_nusinersen_2 months

value: SMA

value: nusinersen

value: 2 months


title: Medulloblastoma, Ptf1a-Cre/+; Ptch1fl/fl; Pgbd5-/-, RNA, rep 1

description:
RNA part of a 10X Genomics scMultiome sample
medullo_Pgbd5minus_rep1.Rds


title: PM154, DNMT1 knockout, rep3

value: Prostate cancer cell line

value: DNMT1 knockout


title: CRC-48-EV

value: IIA


title: PM154, DNMT1 knockout, rep2


title: CRC-47-EV


title: PM154, DNMT1 knockout, rep1


title: single_cell TCR seq data of CSF from patient SMA1_8_nusinersen_10 months

value: 10 months


title: single_cell TCR seq data of CSF from patient SMA1_7_untreated

value: untreated


title: single_cell TCR seq data of CSF from patient SMA1_6_nusinersen_10 months


title: Medulloblastoma, Ptf1a-Cre/+; Ptch1fl/fl; Pgbd5+/+, RNA, rep 2

description:
RNA part of a 10X Genomics scMultiome sample
medullo_Pgbd5plus_rep2.Rds

value: Granule cells

value: medulloblastoma

value: Pgbd5 +/+

value: Conditional KO of Ptch1


title: ovary, VCD affected for 30 days, rep 4

city: 兰州市

first: Yi

last: Li

state: 甘肃

address: 甘肃省兰州市城关区东岗西路1号兰州大学第一医院

institute: Lanzhou University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include readcount values for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: ovary

growth_protocol: Mice are kept in separate cages (Total six cages with five mice per cage) and have free to access food and water. The environment has a normal circadian rhythm and a constant temperature and humidity (24 ± 2°C/40%).

extract_protocol:
Ovarian tissues’ RNA extraction using TRLzol kit. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalentcationsunder elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: All the mice were treated intraperitoneally once a day for 15 days and starting the same day. The control group was injected with sesame oil and the experimental group had VCD dissolved in sesame oil at a concentration of 160 mg/kg.

value: ovary

tag: developmental stage

tag: Sex

value: female

value: Intraperitoneal Injection VCD

value: 15 days


title: CRC-45-EV

value: plasma

value: colorectal cancer

value: male


title: single_cell TCR seq data of CSF from patient SMA1_7_nusinersen_10 months

state: NRW

value: CSF leukocytes

value: SMA

value: nusinersen


title: ovary, VCD affected for 30 days, rep 5

address: 甘肃省兰州市城关区东岗西路1号兰州大学第一医院


title: single_cell TCR seq data of CSF from patient SMA1_6_nusinersen_6 months

value: 6 months


title: single_cell TCR seq data of CSF from patient SMA1_6_untreated


title: ovary, VCD affected for 30 days, rep 3

address: 甘肃省兰州市城关区东岗西路1号兰州大学第一医院


title: PM154, Control, rep2

value: Prostate cancer cell line

value: Wild Type


title: ovary, VCD affected for 30 days, rep 2

address: 甘肃省兰州市城关区东岗西路1号兰州大学第一医院


title: LC-36-EV

value: lung cancer

value: I


title: single_cell TCR seq data of CSF from patient SMA1_5_nusinersen_10 months

value: 10 months


title: ovary, VCD affected for 30 days, rep 1

address: 甘肃省兰州市城关区东岗西路1号兰州大学第一医院


title: CRC-42-EV

value: IV


title: CRC-41-EV

value: IIIC


title: single_cell TCR seq data of CSF from patient SMA1_5_untreated

value: untreated


title: 6DT1 sg1 rep1

city: Bethesda

first: Kent

last: Hunter

address: 37/4048 37 Convent Drive

institute: National Cancer Institute

value: Mammary

value: mammary cancer

value: Resf1 KO

value: sgResf1 CRISPR KO


title: ovary, VCD affected for 15 days, rep 5

address: 甘肃省兰州市城关区东岗西路1号兰州大学第一医院

value: ovary

value: female

value: Intraperitoneal Injection VCD

value: 15 days


title: CRC-46-EV

value: plasma

value: colorectal cancer

value: IIIB


title: CRC-40-EV


title: ovary, VCD affected for 15 days, rep 4

address: 甘肃省兰州市城关区东岗西路1号兰州大学第一医院


title: single_cell TCR seq data of CSF from patient SMA1_4_nusinersen_10 months

value: CSF leukocytes

value: SMA

value: nusinersen


title: ovary, VCD affected for 15 days, rep 2

address: 甘肃省兰州市城关区东岗西路1号兰州大学第一医院


title: single_cell TCR seq data of CSF from patient SMA1_4_untreated