title: ChIP-seq CTCF DE-24h biol rep 1

extract_protocol:
ChIP-seq: Cells were crosslinked with 1% formaldehyde and then lysed and sonicated. Clear supernatant was collected for chromatin immunoprecipitation, decrosslinking and DNA purification. Sequencing library was generated by using the NEBNext® Ultra II DNA Library Prep Kit (New England Biolabs; E7103S) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs Index Primers Set 1; NEB, E7335S).
ChIP-seq: Samples were pooled and sequenced on Illumina HiSeq 4000 platform.


title: T47D 4uM MI503 24h BioRep 1

status: Public on Oct 01 2022

type: SRA

city: Atlanta

first: Jennifer

middle: Marie

last: Spangle

state: Georgia

address: 1365C Clifton Rd NE

country: USA

institute: Emory University

library_source: transcriptomic

data_processing:
Illumina Dragen 3.7.5 was used to map align and perform quantification (salmon) of transcript expression
Quantification was mapped to hg38 (GrCh38p13/gencode.v36)
Assembly: GrCh38p13
Supplementary files format and content: quant.sf file containing read counts

molecule: total RNA

organism: Homo sapiens

source_name: not applicable

growth_protocol: T47D were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was isolated using the Qiagen RNeasy kit with on-column DNaseI digestion. 1.5ug total RNA was used to construct sequencing libraries
Libraries were constructed by Novogene

treatment_protocol: T47D were treated with 4uM MI503 or DMSO for 24h

tag: tissue

value: not applicable

tag: cell line

tag: cell type

value: Hormone receptor + breast cancer

tag: genotype

value: WT

tag: treatment


title: ChIP-seq CTCF ESC-0h biol rep 2

city: Baltimore

first: Michael

middle: A

last: Beer

state: MD

address: 733 N. Broadway

department: Biomedical Engineering and Genetic Medicine

institute: Johns Hopkins University

library_source: genomic

data_processing:
ChIP-seq: Paired-end reads were mapped to hg38 with bowtie2 using default parameters, and peaks were called using macs2 using default parameters.
Assembly: hg38
Supplementary files format and content: bigwig, hic, barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, expr_table.tsv.gz, gRNA_table.tsv.gz

molecule: genomic DNA

value: hESC

value: idCas9-KRAB SOX17eGFP/+

value: ESC-DE differentiaion


title: Bone Marrow, T-ALL Control, rep1 [sample.315_aavs1]

city: St Louis

first: Grant

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

data_processing:
Partek Flow 10.0.22.0524
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek flow
Trimmed raw RNA-seq reads were aligned to the Ensembl release hg38 (Human) using STAR version 2.7.3a
Read count extraction and normalization were performed using Partek flow
Assembly: Ensembl release hg38 (Human)
Supplementary files format and content: Excel files include CPM values for each Sample

source_name: Bone Marrow

extract_protocol:
RNA was harvested using NucleoSpin RNA XS kit (Macherey-Nagel)
RNA libraries for RNA-seq were prepared using SMARTer Ultra Low RNA kit (Clontech) following manufacturer's protocols.

value: Bone Marrow

value: T-ALL blast

value: KDM6B wild type


title: ChIP-seq CTCF ESC-0h biol rep 1


title: T47D DMSO 24h BioRep 1

value: DMSO 24h


title: T47D DMSO 24h H3K4me3 C&R BioRep 2

data_processing:
Reads were trimmed from 3' end until the PHRED quality score was >33 using Trim Galore version 0.6.7. All read with PHRED quality score <20 were discarded.
Reads were aligned to the GRCh38.p14 genome using Bowtie2 version 2.2.5. All reads that did not have concordant alignment overlap between both paired end sequences were removed
Aligned sequences were sorted using samtools version 1.6 and duplicate reads were removed using the Picard Tools version 2.27.4.
To generate coverage plots, deeptools was used to normalize the bam files using the e. coli abundance which produced bigwig and bedGraph files.
Library strategy: CUT&RUN

extract_protocol:
Cells were detatched using accutase
Libraries were constructed following the manufacturer's protocol (Epicypher). 5ng of DNA was used as starting material for library preparation. Following the Epicypher protocol, libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were confirmed to be 200-500bp in length via bioanalyzer.


title: T47D DMSO 24h H3K4me3 C&R BioRep 1


title: T47D 4 uM MI503 24h MLL1 C&R


title: Huh-7 cells-2

city: Shanghai

first: xin

last: zhang

address: 415 Fengyang Road

country: China

institute: Changzheng hospital

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Clean reads were mapped to reference sequences and/or reference gene set using SOAPaligner/SOAP2. No more than 2 mismatches were allowed in the alignment.
The expression level for each gene is determined by the numbers of reads uniquely mapped to the specific gene and the total number of uniquely mapped reads in the sample
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads).
We use "FDR ≤0.001 and the absolute value of log2Ratio ≥1" as the threshold to judge the significance of gene expression difference.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count and normalized RPKM values for each Sample

source_name: Huh-7 cells

growth_protocol: Huh-7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA)
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads (foreukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using random.  hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End  reparation and 3'-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR  amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library.

treatment_protocol: SOX9 knockout (SOX9KO)Huh-7 cells were established by crisper-cas9 system. Then 1✖106 Huh-7 and SOX9KO Huh-7 cells  were seeded in 35mm dish and cultured for 48 hours.

value: Huh-7 cells

value: Hapatocarcinoma cells


title: Huh-7 cells-3


title: ChIP-seq CTCF DE-24h biol rep 2


title: ChIP-seq SOX17 DE-48h biol rep 1


title: adult T-cell lymphoblastic lymphoma specimens (344877)

type: RNA

city: Guangzhou

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

institute: Sun Yat-sen University Cancer Center

hyb_protocol: The labeled RNAs were then hybridized to Affymetrix Human Gene 2.0 ST GeneChips (Affymetrix, Santa Clara, CA, USA) under the support of Hybridization Oven 645 (Affymetrix) and Fluidics Station 450 (Affymetrix) following the manufacturer’s instructions.

scan_protocol: All slides were scanned with a GeneChip Scanner 3000 (Affymetrix) and Command Console Software 3.1(Affymetrix).

data_processing:
The signal value which was normalized by gene level parameters in Console software was transformed to log2 formation.
Significant analysis of microarray (SAM) was performed to identify differentially expressed mRNAs between progressive and progression-free tissues, with fold-change > 2.5 and associated p < 0.05 indicating significant differences.

label: Biotin

source_name: lymph node biopsy or puncture, formalin fixed paraffin-embedded (FFPE) tissues

label_protocol: Encore Biotin Module (NuGEN) was used for fragmentation and labeling

extract_protocol: Total cellular RNA was extracted from 50 FFPE samples using the QIAGEN FFPE RNeasy kit (QIAGEN GmbH, Hilden, Germany) and amplified with the Ovation FFPE WTA system (NuGEN, San Carlos, CA, USA).

tag: disease

value: T-cell lymphoblastic lymphoma

tag: disease status

value: relapse-free

tag: Sex

value: male

tag: age


title: adult T-cell lymphoblastic lymphoma specimens (303485)

value: female


title: adult T-cell lymphoblastic lymphoma specimens (321503)


title: adult T-cell lymphoblastic lymphoma specimens (298285)


title: adult T-cell lymphoblastic lymphoma specimens (329300)


title: adult T-cell lymphoblastic lymphoma specimens (352973)


title: ChIP-seq EOMES DE-48h biol rep 2


title: adult T-cell lymphoblastic lymphoma specimens (379217)


title: adult T-cell lymphoblastic lymphoma specimens (344257)


title: T47D 4uM MI503 24h H3K4me3 C&R BioRep 2


title: adult T-cell lymphoblastic lymphoma specimens (394891)


title: T47D 4uM MI503 24h BioRep 2


title: LRK

city: Dalian

first: Jinsong

last: Yan

state: Liaoning

address: 467 Zhongshan Road, Dalian 116027, Liaoning, P. R. China

department: Department of Hematology

institute: the Second Hospital of Dalian Medical University

data_processing:
We mapped the sequencing data to reference genome (hg38) using STAR, and STAR-Fusion (https://github.com/STAR-Fusion/STAR-Fusion/wiki) was used to detect the fusion transcripts.
Assembly: hg38
Supplementary files format and content: tsv file include fusion results for patient …

source_name: Bone marrow

extract_protocol:
Mononuclear cell layer from BM sample was separated by Ficoll Hypaque (1114547, Axis-Shield) density gradient separation. Total RNA of the mononuclear cells were extracted using the QIAamp AllPrep RNA Mini Kit (Cat# 80204, QIAGEN), according to the manufacturer's specifications.
Libraries were constructed using the TruSeq RNA Sample Preparation Kits (Illumina), and the quality of the library was assessed using Bioanalyzer 2100 (Agilent Technologies).

value: Bone marrow

value: Mononuclear cells


title: scRNA DE-60h

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
scRNA-seq: Chromium v3 analysis software Cell Ranger (Version 3.1.0) was run using “cellranger count –expect-cells 1000”.
Assembly: hg38
Supplementary files format and content: bigwig, hic, barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, expr_table.tsv.gz, gRNA_table.tsv.gz

extract_protocol:
scRNA-seq: Cells were harvested every 12h during DE differentiation for scRNA-seq experiments targeting a 3000-6000 cell range collection. Single-cell 3′ RNA-seq libraries were generated with 10x Genomics Chromium Single Cell 3′ Reagent Kit v.3 following the manufacturer’s guidelines.
scRNA-seq: Libraries were sequenced on NovaSeq 6000 platform following the manufacturer’s guidelines.


title: ChIP-seq SOX17 DE-48h biol rep 2


title: ChIP-seq EOMES DE-48h biol rep 1


title: T47D 4 uM MI503 24h H3K4me3 C&R BioRep 1

value: not applicable

value: Hormone receptor + breast cancer


title: scRNA DE-72h

description: 10x Genomics

value: hESC


title: scRNA DE-24h

description: 10x Genomics

value: idCas9-KRAB SOX17eGFP/+


title: scRNA DE-36h

description: 10x Genomics

value: ESC-DE differentiaion


title: adult T-cell lymphoblastic lymphoma specimens (435936)


title: adult T-cell lymphoblastic lymphoma specimens (402669)


title: scRNA DE-12h

description: 10x Genomics


title: T47D DMSO 24h MLL1 C&R

value: WT


title: ChIP-seq EOMES DE-24h biol rep 1


title: scRNA ESC-0h

description: 10x Genomics


title: adult T-cell lymphoblastic lymphoma specimens (437347)


title: Hi-C DE biol rep 3

data_processing:
Hi-C: Hi-C Pro 2.11.4 was used to fragment, with GATC and GANTC as the restriction enzymes.  Reads were aligned with default settings for Bowtie 2.4.1 in Hi-C Pro. Reads with a MAPQ of at least 30 were retained and duplicates were removed. Sample level Hi
Assembly: hg38
Supplementary files format and content: bigwig, hic, barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, expr_table.tsv.gz, gRNA_table.tsv.gz

extract_protocol:
Hi-C: 2 million cells were collected and fixed with 1% formaldehyde. The subsequent steps of Hi-C were then performed using the Arima-HiC kit (Arima; A510008).
Hi-C: Libraries for sequencing were prepared with the KAPA Hyper Prep Kit (KAPA; KK8502) following the manufacturer’s guidelines. Samples were pooled and sequenced on Illumina HiSeq 4000 platform.


title: adult T-cell lymphoblastic lymphoma specimens (442157)


title: Hi-C DE biol rep 2

data_processing:
Hi-C: Hi-C Pro 2.11.4 was used to fragment, with GATC and GANTC as the restriction enzymes.  Reads were aligned with default settings for Bowtie 2.4.1 in Hi-C Pro. Reads with a MAPQ of at least 30 were retained and duplicates were removed. Sample level Hi-C maps were converted to .hic file format with JuicerTools 1.22.01.
Assembly: hg38
Supplementary files format and content: bigwig, hic, barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, expr_table.tsv.gz, gRNA_table.tsv.gz


title: Spt5(1-820)CTR1_TA7minusTMPplusDoxy_mRNA_3

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

description: mRNAseq

data_processing:
Adapters were trimmed using cutadapt version 2.3
Reads were aligned using Salmon v1.3.0
Differential expression analysis was performed using DEBrowser v1.24.1
Assembly: hg19
Supplementary files format and content: tsv files containing counts from Salmon v1.3.0

growth_protocol: McCoy's 10% FCS, +200 ug/ml hygromycin, +1mg/ml G418+15 ug/ml blasticidin

extract_protocol:
Trizol extraction, oligodT selection
1ug of RNA was used with Tecan/Nugen ultra-low kit (9149-A01)

treatment_protocol: Avi-Spt5(1-820) CTR1_TA7 expression was induced with 2ug/ml doxycycline for 24 hrs

tag: growth conditions

value: McCoy's 10% FCS, +hygromycin, +G418, +blasticidin, +doxycycline


title: Spt5(1-820)CTR1_TE7minusTMPplusDoxy_mRNA_1

description: mRNAseq

treatment_protocol: Avi-Spt5(1-820) CTR1_TE7 expression was induced with 2ug/ml doxycycline for 24 hrs


title: Spt5(1-820)CTR1_TA7minusTMPplusDoxy_mRNA_2

description: mRNAseq


title: Spt5(1-820)CTR1_TE7minusTMPplusDoxy_mRNA_2

description: mRNAseq


title: Spt5(1-820)CTR1_TE7minusTMPplusDoxy_mRNA_3

description: mRNAseq


title: scRNA DE-48h

description: 10x Genomics


title: Hi-C DE biol rep 1


title: ChIP-seq EOMES DE-24h biol rep 2


title: Hi-C ESC biol rep 3


title: Spt5(1-820)CTR1_WTminusTMPplusDoxy_mRNA_1

description: mRNAseq

source_name: HCT116 Spt5-HA-dhfr pCW57AviSpt5(1-820)

treatment_protocol: Avi-Spt5(1-820) expression was induced with 2ug/ml doxycycline for 24 hrs


title: Spt5(1-820)CTR1_WTminusTMPplusDoxy_mRNA_3

description: mRNAseq


title: adult T-cell lymphoblastic lymphoma specimens (463991)


title: adult T-cell lymphoblastic lymphoma specimens (444563)


title: Spt5(1-820)CTR1_TA7minusTMPplusDoxy_mRNA_1

description: mRNAseq


title: Spt5(1-820)CTR1_WTminusTMPplusDoxy_mRNA_2

description: mRNAseq


title: Hi-C ESC biol rep 2


title: adult T-cell lymphoblastic lymphoma specimens (473425)


title: adult T-cell lymphoblastic lymphoma specimens (469390)


title: Hi-C ESC biol rep 1


title: CdLS-TO, scRNAseq

city: Rotterdam

first: Olivier

last: Schäffers

address: Dr. Molenwaterplein 40

country: Netherlands

institute: Erasmus Medical Center

description:
10x Genomics
OS_5017

data_processing:
Raw FASTQ files were quantified and aligned to the GRCh38 human reference genome using the Cell Ranger software pipeline (10x Genomics, version 4.0.0).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: TOs derived from chorionic villi with SMC1A c.532A>C mutation

extract_protocol:
Single cells were processed on the 10X Genomics Chromium Platform using the Chromium Next GEM Single Cell 3′ Reagent kit v3.1 with Dual Index Kit (10X Genomics) following the manufacturer’s protocol.
Library was performed according to the manufacter’s instructions (Single Cell 3’ v3.1 protocol, 10x Genomics). Briefly, 15,000 cells were loaded in each channel of a chip to be partitioned into gel beads in emulsion (GEMs). Within GEMs, cells were lysed followed by barcoded reverse tran-scription of RNA. Breaking of the GEMs was followed by amplification, fragmentation and addition of adapter and sample index. Libraries were pooled and sequenced on an Illumina NovaSeq 6000 instrument (minimum coverage of 25,000 raw reads per cell).

value: Trophoblast

value: Day 14 of culture


title: DS-TO, scRNAseq

description:
10x Genomics
OS_705

source_name: TOs derived from chorionic villi with trisomy 21


title: Control CVS-TO, scRNAseq

description:
10x Genomics
OS_940

source_name: TOs derived from chorionic villi

value: TOs derived from chorionic villi


title: 914, purkinje cells, control

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

data_processing:
Trimming of Illumina adapters from FASTQ via TrimGalore v0.6.1
Alignment of FASTQ to GRCh38 with STAR aligner v2.5.0a
Gene quantification using the GeneCounts function in STAR against the human GENCODE v35 gtf
Assembly: GRCh38
Supplementary files format and content: text tab delimited file containing raw read counts for each gene feature in GENCODE v35

source_name: cerebellar Purkinje cells

extract_protocol:
Qiagen RNeasy Micro Kit was used to extract RNA from laser capture microdissection captured Purkinje cells from human postmortem brain sections.
100ng of total RNA prepared with the Nugen Ovation SoLo RNA-Seq Library Preparation Kit and sequenced in single end 100bp reactions

value: cerebellar Purkinje cells

tag: brain region

value: crus II

tag: condition

value: control


title: ATAC DE 72h rep 3

data_processing:
ATAC-seq:  Paired-end reads were mapped to hg38 with bowtie2 using default parameters, duplicate reads were removed with picard, and peaks were called using macs2 using default parameters.
Assembly: hg38
Supplementary files format and content: bigwig, hic, barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, expr_table.tsv.gz, gRNA_table.tsv.gz

extract_protocol:
ATAC-seq: 50K cryopreserved cells were washed in cold PBS and lysed. The transposition reaction containing TDE1 Tagment DNA Enzyme (Illumina; 20034198) was incubated at 37°C for 30 minutes. The DNA was purified with the MinElute PCR Purification Kit (QIAGEN; 28004) and  amplified for 5 cycles using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs; 529 M0541L). After evaluation by real-time PCR, 3-14 additional PCR cycles were done. Final product was cleaned by AMPure XP beads (Beckman Coulter; A63882) at a 1X ratio, and size selection was performed at a 0.5X ratio.
ATAC-seq: Libraries were sequenced on a HiSeq 4000 or NovaSeq 6000 platform in a PE50 run, using the HiSeq 3000/4000 SBS Kit or NovaSeq 6000 S1 Reagent Kit (100 Cycles) (Illumina).


title: adult T-cell lymphoblastic lymphoma specimens (470455)

value: T-cell lymphoblastic lymphoma

value: relapse-free


title: 5926, purkinje cells, control


title: 5922, purkinje cells, control


title: ATAC DE 72h rep 2


title: 5889, purkinje cells, control


title: 5813, purkinje cells, control


title: ATAC DE 72h rep 1


title: 5566, purkinje cells, control


title: ATAC DE 60h rep 2


title: 5419, purkinje cells, autism

value: autism


title: ATAC DE 60h rep 3


title: 5391, purkinje cells, control


title: adult T-cell lymphoblastic lymphoma specimens (487653)

value: male


title: adult T-cell lymphoblastic lymphoma specimens (473646)


title: adult T-cell lymphoblastic lymphoma specimens (474242)


title: 5403, purkinje cells, autism


title: ATAC DE 60h rep 1


title: 5308, purkinje cells, autism


title: 5297, purkinje cells, autism


title: C LmjF_PP1_Flox_+rapamycin

city: Athens

first: Haidong

address: 220 Mark Twain Cir Apt D

institute: University of Georgia

data_processing:
Raw reads were trimmed with the default settings of fastp (v0.19.5)
alignment: Bowtie2 v2.3.4.1 using sensitive local alignment mode
sorting: Samtools v1.2 using default parameters
expression levels: DESeq2 variance stabilized counts
Assembly: L. major Friedlin strain genome version 9.0  (from TriTrypDB.org)
Supplementary files format and content: tab-delimited text file, see metafile for column headers

organism: Leishmania major

source_name: PP1 DiCre  parasite

growth_protocol: Leishmania major Friedlin V1 cells were  grown at 26°C in M199 medium supplemented with 40 mM 4-(2-hydroxyethyl)-1-piperazineethanesuphonic acid (HEPES) pH 7.4, 100 uM adenine , 1 µg mL-1 biotin, 10 µg mL-1 hemin , 2 µg mL-1 biopterin, 50 units/mL penicillin, 50 µg/mL streptomycin, and 10% (v/v) heat inactivated fetal calf serum. Cell density was determined by using a hemocytometer.

extract_protocol:
Total RNA was isolated from L. major cultures using TriPure, according to the manufacturer’s instructions. 5x107 cells were used for each prep.
For mRNA-seq, total RNA was isolated from wild-type and PP1-8e KO L. major cultures using TriPure. Six mRNA-seq libraries were constructed (triplicate samples for WT and PP1-8eKO) using Illumina TruSeq Stranded RNA LT Kit following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 µg, and all volumes were reduced to a third of the described quantity. High throughput sequencing was performed at the Georgia Genomics and Bioinformatics Core (GGBC) on a Novaseq 6000 (Illumina).

treatment_protocol: DiCre mediated PP1 KO was induced by supplementing media with 300 nM Rapamycin for 14 days

tag: strain, lifestage

value: Friedlin V1, promastigotes

tag: genotype/variation


title: ATAC DE 48h rep 3


title: B LmjF_PP1_Flox_+rapamycin


title: 5294, purkinje cells, autism


title: ATAC DE 48h rep 2


title: 5878, purkinje cells, autism


title: adult T-cell lymphoblastic lymphoma specimens (509543)


title: A LmjF_PP1_Flox_+rapamycin


title: 5278, purkinje cells, autism


title: adult T-cell lymphoblastic lymphoma specimens (576255)


title: adult T-cell lymphoblastic lymphoma specimens (534867)


title: adult T-cell lymphoblastic lymphoma specimens (550982)


title: adult T-cell lymphoblastic lymphoma specimens (574198)

value: female


title: C LmjF_PP1_Flox_-rapamycin

value: KO


title: 5176, purkinje cells, autism


title: 5170, purkinje cells, control


title: ATAC DE 36h rep 3

value: hESC

value: idCas9-KRAB SOX17eGFP/+


title: B LmjF_PP1_Flox_-rapamycin


title: ATAC DE 36h rep 2

value: ESC-DE differentiaion


title: ATAC DE 36h rep 1


title: ATAC DE 48h rep 1


title: 5163, purkinje cells, control


title: 5144, purkinje cells, autism


title: ATAC DE 24h rep 3


title: Input_rep2

city: Paris

first: Cosmin

last: Saveanu

address: 25 rue Docteur Roux

country: France

institute: Pasteur Institute

data_processing:
The raw data are fastq sequences already reverse complemented.
Sequences were trimmed with associated index using Cutadapt (version 1.16) using : -a –o –m 20.
Index files are annotated with : "adapt_name_of_the_sample.fa"
Sequences were mapped on the Saccharomyces cerevisiae S288c genome. For the mapping, we use the software STAR (version STAR_2.7), it allows to map reads on intron notably. We use the default parameters except for these three: --alignIntronMax 1500 --alignMatesGapMax 1500 --alignSJoverhangMin 25 . The outfile is in BAM format.
For the reads counting per features, we have used the function featureCounts of the subread package (version Subread-1.6.2). Annotation file is specific to our study, it contains pervasive transcript, dubious ORF, intron, etc.
For convenient analysis, tables were cut using the parameters : sed '2d' | cut -f 1,7 -d $'\t' >
Genome_build: Saccharomyces cerevisiae S288c genome was indexed and prepared by STAR genomeGenerate.
Supplementary_files_format_and_content: The processed data files are tables with gene ID for the first column and feature counts for the second column.

organism: Saccharomyces cerevisiae S288C

source_name: exponential state cells

growth_protocol: Yeast cells growed until exponential phase DO 0.6 in YPD media at 30°C.

extract_protocol:
After collection, RNA are extracted by hot acid phenol/chloroform method, precipitated with ammonium acetate and ethanol.
Samples were treated by RiboZero or Ribominus and libraries were prepared using TruSeq Stranded mRNA kit (Illumina). We strictly followed the protocol except that we started directly at the fragmentation step after the ribozero and we adjusted the number of cycle required to amplified libraries.

treatment_protocol: TAP‐tagged proteins were purified using a one‐step purification method. Frozen cell pellets of 4 L culture were resuspended in lysis buffer (20 mM HEPES K pH 7.4, 100 mM KOAc, 0.5% Triton X100, 5mM MgCl2, Protease inhibitor, 1X Vanadyl‐Ribonucleoside Complex, 40 units ml−1 RNasin) and lysed using a MagNA Lyser (two passages 90s at 4000 rpm). The lysate was cleared at 4°C for 20 min at 14000 rpm. Magnetic beads (Dynabeads M‐270 epoxy) coupled to IgG were added to the protein extract and incubated for 1,5 h at 4°C (Oeffinger et al, 2007). Beads were collected with a magnet and extensively washed five times with a washing buffer (20 mM HEPES K pH 7.4, 100 mM KOAc 0.5% Triton X100, 5mM MgCl2). After washing, proteins were eluted by incubation in elution buffer (SDS 2% in Tris-EDTA pH 7.5) 10 minutes at 65°C.

tag: epitope tag for bait protein

value: TAP (CBP-TeV-Protein A)

tag: bait protein

value: just before the purification, an aliquot of the total extract was taken for RNA extraction

tag: sample type

value: total RNAs


title: Input_rep3


title: ATAC DE 24h rep 2


title: 5113, purkinje cells, control


title: Input_rep1


title: adult T-cell lymphoblastic lymphoma specimens (584047)


title: adult T-cell lymphoblastic lymphoma specimens (337988)

value: relapse


title: adult T-cell lymphoblastic lymphoma specimens (314519)


title: ATAC DE 24h rep 1


title: 5079, purkinje cells, control

value: cerebellar Purkinje cells


title: adult T-cell lymphoblastic lymphoma specimens (337506)


title: 5027, purkinje cells, autism

value: crus II


title: A LmjF_PP1_Flox_-rapamycin


title: ATAC DE 12h rep 3


title: adult T-cell lymphoblastic lymphoma specimens (589033)


title: Lsm1_rep2

value: TAP‐tagged Lsm1

value: associated RNAs of Lsm1 (ribosomic depleted)


title: 4999, purkinje cells, autism


title: ATAC DE 12h rep 2


title: adult T-cell lymphoblastic lymphoma specimens (345948)

value: T-cell lymphoblastic lymphoma


title: Lsm1_rep1


title: 4599, purkinje cells, control

value: control


title: Pab1_rep3

value: TAP‐tagged Pab1

value: associated RNAs of Pab1 (ribosomic depleted)


title: ATAC DE 12h rep 1


title: 4334, purkinje cells, autism

value: autism


title: ATAC ESC 0h rep 4


title: adult T-cell lymphoblastic lymphoma specimens (397816)

value: male


title: Lsm1_rep3


title: adult T-cell lymphoblastic lymphoma specimens (382837)

value: no response


title: 1158, purkinje cells, control


title: adult T-cell lymphoblastic lymphoma specimens (395556)


title: ATAC ESC 0h rep 3

value: hESC

value: idCas9-KRAB SOX17eGFP/+


title: adult T-cell lymphoblastic lymphoma specimens (399350)


title: 6033, purkinje cells, autism


title: ATAC ESC 0h rep 2

value: ESC-DE differentiaion


title: adult T-cell lymphoblastic lymphoma specimens (400490)


title: Pab1_rep1

value: TAP (CBP-TeV-Protein A)


title: Rpl16a_rep3

value: TAP‐tagged Rpl16a

value: associated RNAs of Rpl16a (ribosomic depleted)


title: Pab1_rep2


title: adult T-cell lymphoblastic lymphoma specimens (395446)

value: relapse


title: 5978, purkinje cells, autism

value: cerebellar Purkinje cells

value: crus II


title: ATAC ESC 0h rep 1


title: 5945, purkinje cells, autism


title: Rpl16a_rep1


title: Rpl16a_rep2


title: adult T-cell lymphoblastic lymphoma specimens (436233)


title: adult T-cell lymphoblastic lymphoma specimens (453291)


title: 5940, purkinje cells, autism


title: Upf1_rep3

value: TAP‐tagged Upf1

value: associated RNAs of Upf1 (ribosomic depleted)


title: 5893, purkinje cells, control

value: control


title: RNA-seq DE 72h biol rep 1

data_processing:
RNA-seq: We alignned reads to hg38 with STAR_2.5.1b and quantified transcripts with RSEM v1.2.23.
Assembly: hg38
Supplementary files format and content: bigwig, hic, barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, expr_table.tsv.gz, gRNA_table.tsv.gz

extract_protocol:
RNA-seq:  Total RNA was extracted using Quick-RNA MiniPrep kits (ZYMO research; R1055).  cDNA was produced by using High Capacity cDNA Reverse Transcription Kit (AppliedBiosystems; 4368817)
RNA-seq: 500ng of total RNA underwent polyA selection and TruSeq library preparation following Illumina (TruSeq Stranded mRNA LT Kit; RS-122-2102), with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 or NovaSeq 6000 platform in a PE50 run, using the HiSeq 3000/4000 SBS Kit or NovaSeq 6000 SP or S2 Reagent Kit (100 Cycles) (Illumina).

value: ESC-DE differentiation


title: Upf1_rep2


title: adult T-cell lymphoblastic lymphoma specimens (453650)

value: T-cell lymphoblastic lymphoma


title: Upf1_rep1


title: adult T-cell lymphoblastic lymphoma specimens (412160)

value: female


title: adult T-cell lymphoblastic lymphoma specimens (473795)

value: male


title: adult T-cell lymphoblastic lymphoma specimens (460665)


title: 5705, purkinje cells, control


title: 5841, purkinje cells, autism

value: autism


title: BY4741_rep2

value: Control. There is no tagged protein in these purifications, we wanted to check the background, so the bound RNAs in the experiment independently of the tag. Purifications have been done with the same process as for the tagged strains.

value: background RNAs


title: RNA-seq DE 60h biol rep 2

value: hESC

value: idCas9-KRAB SOX17eGFP/+


title: RNA-seq DE 60h biol rep 1


title: 5669, purkinje cells, control


title: RNA-seq DE 60h biol rep 3


title: BY4741_rep3


title: RNA-seq DE 72h biol rep 3


title: 5646, purkinje cells, control


title: 5565, purkinje cells, autism


title: BY4741_rep1


title: RNA-seq DE 72h biol rep 2


title: RNA-seq DE 48h biol rep 3


title: RNA-seq DE 48h biol rep 2


title: adult T-cell lymphoblastic lymphoma specimens (477495)


title: 5387, purkinje cells, control


title: adult T-cell lymphoblastic lymphoma specimens (478126)


title: RNA-seq DE 48h biol rep 1


title: adult T-cell lymphoblastic lymphoma specimens (477944)


title: adult T-cell lymphoblastic lymphoma specimens (478958)


title: adult T-cell lymphoblastic lymphoma specimens (509675)


title: RNA-seq DE 36h biol rep 3


title: 5334, purkinje cells, control


title: 5115, purkinje cells, autism


title: 4849, purkinje cells, autism


title: RNA-seq DE 36h biol rep 2


title: RNA-seq DE 36h biol rep 1


title: Sample 11_697 cell line_PRDM1-β rep 2 [exp1]

city: Newcastle Upon Tyne

first: Paul

middle: B

last: Sinclair

state: Tyne and Wear

address: Level 6, Herschel Building, Newcstle university

department: Translational and Clinical Research Institute

country: United Kingdom

institute: Newcastle University

data_processing:
Base-calling by standard, illumina sequencing
BAM files generated and reads alligned to hg19 using STAR v2.6
Reads quantified and mapped to transcripts (Genecode v.17) using DEXseq v.1.4.
Read counts normalised and VST transformed using DESeq 2.
Genome_build: Hg19
Supplementary_files_format_and_content: Matrix of RAW gene read counts, Matrix of normalised VST transformed read counts (abundance measurments).

molecule: polyA RNA

source_name: 697 cell line_PRDM1-β

growth_protocol: culture in RPMI with 10% FCS

extract_protocol:
RNA extraction with Qiagen RNeasy mini kits
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: lentiviral transduction cDNA expression constructs / FACS sort for EGFP positive cells

value: pre-B cell

tag: sub-type

value: leukaemia

value: transduced with PRDM1β expression construct


title: 6-Tg_A2_3

city: Tokyo

first: Yasutaka

last: Hayashi

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Cellular Therapy, Advanced Clinical Research Center

country: Japan

institute: Institute of Medical Science, The University of Tokyo

hyb_protocol: Cy3-pCp-labeled RNA was hybridized on Agilent SurePrint G3 Mouse miRNA 8x60K Rel.21 (design ID: 070155) array at 55°C for 20 hours.

scan_protocol: After washing, microarray were scanned using an Agilent SureScan Microarray Scanner System (G4900DA).

data_processing: Intensity values of each scanned feature were quantified using Agilent Feature Extraction software version 12.1.1.1 or 11.5.1.1 which performs background subtractions.

organism: Mus musculus

source_name: EVs derived from Tg_A2 bone marrow cells

label_protocol: RNA was labeled with cyanine 3 (Cy3) using miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Inc.) following the manufacturer’s instructions. Briefly, 100 ng of RNA was dephosphorylated using Calf Intestinal Alkaline Phosphatase (CIP) Master Mix incubated at 37°C for 30 min. Dephosphorylated RNA was denatured with DMSO incubated at 100°C for 5 min and then immediately transfers to on ice for 2 min. These products were mixed with a Ligation master mix for T4 RNA Ligase and Cy3-pCp (Cyanine 3-Cytidine biphosphate) and incubated at 16°C for 2 hours. Labeled RNA was dried using vacuum concentrator at 55°C for 1.5 hours up using vacuum concentrator at 55°C for 1.5 hours.

extract_protocol: The supernatant was collected from cells that were cultured in media containing 10% EV-depleted FBS, 50 ng/mL SCF, 20 ng/mL TPO, 40 ng/mL FLT3L and 20 ng/mL IL-3 for 72 h and subsequently subjected to sequential centrifugation at 800×g for 5 min and 2,000×g for 10 min. The resulting supernatant was then filtered using 0.22-μm filters, and a pellet was recovered at 100,000×g in a SW32 Ti rotor after 1 h and 10 min of ultracentrifugation (Beckman). The supernatant was aspirated, and the pellet was resuspended in PBS and subsequently ultracentrifuged at 100,000×g for another 1 h and 10 min. The pellet collected from the supernatant of 5x106 cells was resuspended in 200 μL PBS.

tag: strain

value: NUP98-HOXD13 transgenic


title: 11-Tg_B2_2

source_name: EVs derived from Tg_B2 bone marrow cells


title: 12-Tg_B2_3


title: Sample 12_697 cell line_PRDM1-β rep 3 [exp1]

tag: cell line

tag: cell type


title: 5-Tg_A2_2


title: RNA-seq DE 24h biol rep 3

tag: genotype

tag: treatment


title: 9-WT_B1_3

source_name: EVs derived from WT_B1 bone marrow cells

value: wild type


title: CS19-3

city: Uppsala

first: Mohamad

middle: Moustafa

last: Ali

state: Uppsala län

address: husargatan 3, Biomedical Center

department: IMBIM

country: Sweden

institute: Uppsala University

description: Replicate 3 of SNAI1 KO derived from single cell clone#19

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic tool v0.36
Trimmed reads were aligned against the reference human genome (GRCh38) using STAR aligner v2.7.2b with two-pass mode
Aligned reads were annotated and quantified against the gencode comprehensive gene annotation release 38 (GRCh38.p13) using featureCounts of subread package v2.0.0
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include quantified reads from Subread package

growth_protocol: MDA-MB-231 WT and KO cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using ReliaPrep RNA Cell miniprep system (Promega). 600 ng of total RNA was used for the construction of sequencing libraries.
Library preparation was constructed using the TruSeq stranded total RNA Gold library preparation kit with RiboZero Gold treatment and unique dual indexes according to the manufacturer’s instructions

treatment_protocol: No treatment were done

value: triple-negative breast cancer cells


title: 3-WT_A1_3

source_name: EVs derived from WT_A1 bone marrow cells


title: Sample 10_697 cell line_PRDM1-β rep 1 [exp1]

tag: disease


title: CS19-2

description: Replicate 2 of SNAI1 KO derived from single cell clone#19


title: CS19-1

description: Replicate 1 of SNAI1 KO derived from single cell clone#19


title: 8-WT_B1_2


title: RNA-seq DE 24h biol rep 1


title: Sample 9_697 cell line_PRDM1-⍺ rep 3 [exp1]

source_name: 697 cell line_PRDM1-⍺

value: transduced with PRDM1⍺ expression construct


title: RNA-seq DE 12h biol rep 3


title: adult T-cell lymphoblastic lymphoma specimens (534235)

tag: disease status

value: relapse

tag: Sex


title: KO verus WT SOL Replicate 2

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 270 S Russell St

department: Animal Science

institute: Purdue University

description: Biological replicate 2 of 3.

hyb_protocol: 300 ng of cRNA from the control and test samples were combined and fragmented at 60°C for 30 minutes in a reaction volume of 25 uL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 uL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized on an Agilent SurePrint G3 mouse 8x60K microarray (028005) 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent SureScan Microarray scanner following manufacturer's protocol

data_processing: Array image data was extracted using Agilent Feature Extraction Software 11.5 (Agilent Technologies, Santa Clara, CA). Array image data was then uploaded to GeneSpring 12.5 (Agilent Technologies, Santa Clara, CA) for statistical analysis. Microarray analysis was completed with an ANOVA and a Tukey's post-hoc test when a significant ANOVA was observed. In addition, a mean absolute log2 expression ratio of at least 0.585 (50% increase or decrease in expression) must be satisfied.

source_name: SOL muscle from WT mice

label_protocol: Cy3 (WT) and Cy5 (KO) labeled cRNA was prepared using the Agilent LowInput QuickAmp Labeling Kit according to manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice were all fed on regular chow diet

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: age

value: wildtype

tag: gender

value: Male

source_name: SOL muscle from KO mice


title: 2-WT_A1_2


title: CS16-3

description: Replicate 3 of SNAI1 KO derived from single cell clone#16


title: KO verus WT SOL Replicate 3

description: Biological replicate 3 of 3.


title: CS16-2

description: Replicate 2 of SNAI1 KO derived from single cell clone#16


title: RNA-seq DE 24h biol rep 2

value: ESC-DE differentiation


title: RNA-seq DE 12h biol rep 2


title: 18-Abcg2_cKit_6

source_name: EVs derived from cKit+ Abcg2 MDS/AML cells


title: Sample 7_697 cell line_PRDM1-⍺ rep 1 [exp1]


title: Sample 6_697 cell line_FOXO3 rep 3 [exp1]

source_name: 697 cell line_FOXO3

value: transduced with FOXO3 expression construct


title: WT-2

description: Replicate 2 of WT cells

value: WT


title: WT-3

description: Replicate 3 of WT cells


title: 17-Abcg2_cKit_5


title: RNA-seq DE 12h biol rep 1


title: Sample 5_697 cell line_FOXO3 rep 2 [exp1]


title: 15-Control_cKit_3

source_name: EVs derived from cKit+ Control bone marrow cells

value: Control


title: 16-Abcg2_cKit_4


title: WT-1

description: Replicate 1 of WT cells


title: Sample 4_697 cell line_FOXO3 rep 1 [exp1]


title: KO verus WT SOL Replicate 1

description: Biological replicate 1 of 3.


title: GCTB2_2

city: Stanford

first: Matt

last: van de Rijn

state: California

address: 300 Pasteur Drive

institute: Stanford University

description:
10x Genomics
GCTB2_2

data_processing:
scRNA-Seq: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.
IsoSeq: alignment using pbmm2.
IsoSeq: Other than the aligned Bam files there is no processed data. The paper contains some text and a screen capture regarding the aligned reads.
Assembly: GRCh38
Supplementary files format and content: scRNA-Seq: Raw feature bc matrix for downstream analysis.

source_name: Giant Cell Tumor of Bone

extract_protocol:
scRNA-seq: dissociation with Miltenyi tumor dissociation kit. IsoSeq: Qiagen Rnease Kit RNA extraction.
scRNA-seq: 10x v3.1 3' library according to protocol. IsoSeq: PacBio IsoSeq protocol.

value: Tumor

tag: tissue

value: Giant Cell Tumor of Bone


title: ATL29

city: Chicago

first: Rebecca

last: Luchtel

state: IL

address: 303 E Superior St

institute: Northwestern University

data_processing:
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 using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Comparison of gene expression between sample groups was performed using DESeq2
Assembly: hg38
Supplementary files format and content: normalized read counts

extract_protocol: RNA sequencing libraries were prepared using Stranded mRNA kit (Illumina).

value: adult T-cell leukemia/lymphoma (ATLL)


title: 14-Control_cKit_2


title: Sample 2_697 cell line_SIN-SIEW rep 2 [exp1]

source_name: 697 cell line_SIN-SIEW

value: pre-B cell

value: transduced with control vector


title: Sample 8_697 cell line_PRDM1-⍺ rep 2 [exp1]

value: leukaemia


title: 13-Control_cKit_1


title: Sample 1_697 cell line_SIN-SIEW rep 1 [exp1]


title: ATL18


title: GCTB1

description:
10x Genomics
GCTB1


title: CS16-1

description: Replicate 1 of SNAI1 KO derived from single cell clone#16


title: ATL13


title: GCTB2_1

description:
10x Genomics
GCTB2_1


title: LAEC_4

city: Perth

first: Patricia

last: Agudelo-Romero

state: WA

address: Northern Entrance, Perth Children's Hospital, 15 Hospital Ave, Nedlands

department: Chronic and Severe Diseases

country: Australia

institute: Telethon Kids Institute

data_processing:
Briefly, FASTQ files from the same sample were concatenated and quality control was carried out using FastQC software. Reads were trimmed and adapters removed with Trimmomatic. High-quality reads were then mapped to human reference genome (GRCh37) using Spliced Transcripts Alignment to a Reference (STAR). Gene-level quantification of raw counts was performed using High-Throughput Sequencing (HTSeq).
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample

source_name: Distal lung biopsies

extract_protocol:
Total RNA was extracted using the PureLink® RNA kit (Life Technologies) following their instructions and treated with RNase Inhibitor (Applied Biosystems™) and DNase I (Invitrogen™). RNA concentration and integrity were then determined using a NanoDrop system and an Agilent Bioanalyser, respectively.
Libraries were generated using TruSeq Stranded mRNA (Illumina) kit and Poly(A) enrichment. Sequencing was performed using 100 bp single-end configuration (SE; 100 bp; 20 M).

value: Distal lung biopsies

tag: patient diagnosis

value: Cystic fibrosis


title: TGCT3

description:
10x Genomics
TGCT3

source_name: Tenosynovial Giant Cell Tumor

value: Tenosynovial Giant Cell Tumor


title: Sample 3_697 cell line_SIN-SIEW rep 3 [exp1]


title: 3-Abcg2_3

source_name: EVs derived from Abcg2 MDS/AML cells

tag: genotype/variation


title: 2-Abcg2_2


title: 1-Abcg2_1


title: LAEC_3

value: Female


title: P0260EPR00

first: Marie-Pier

last: Tetreault

address: 300 East Superior Street

department: Medicine/GI&Hep division

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Assembly: hg38
Supplementary files format and content: raw counts

source_name: human esophageal mucosa

extract_protocol:
Esophageal mucosal biopsies were collected. Tissue was stored in RNA later. RNA was isolated using Qiagen RNeasy Micro Kit (#74104).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Esophageal mucosa

tag: disease state

value: Achalasia


title: P0264EPR00


title: P0243EPR00


title: TGCT2_1

description:
10x Genomics
TGCT2_1


title: SAEC_3


title: 5 mg EE2/kg body weight, rep5 [QA1-H6]

city: Sainte-Anne-de-bellevue

first: Yeon-Seon

last: Jeon

state: Quebec

address: 21111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

data_processing:
Processed using the Kallisto workflow on Galaxy.ecotoxxplorer.ca and manually formatted to be used for NetworkAnalyst.ca
Assembly: Coturnix japonica 2.0 genome from Ensemble (GCA_001577835.1)
Supplementary files format and content: Count table in a tab-delimited text file format with Entrez IDs in rows and samples in columns

organism: Coturnix japonica

source_name: Left-lobe liver

growth_protocol: The housing and husbandry practices for quail adhered to the guidelines established by the National Research Council (2011). The photoperiod was constant 8-hour light and 16-hour dark. The birds were acclimated to the facility for 12 weeks, which included 9-week cage acclimation prior to test initiation. They were fasted for 16 hours prior to dosing.

extract_protocol:
Liver tissue was homogenized in buffer RLT using a TissueLyser II (Qiagen, Toronto, ON, CA), and RNA was extracted using the RNeasy® Mini QIAcube Kit (Qiagen) following the manufacturer’s protocol. An extra DNase I digestion step was included to eliminate genomic DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A single dose (4 mL per kilogram of bodyweight) of corn oil or EE2 solution was orally administered by gavage into the crop of each bird following US EPA guideline OCSPP 850.2100 (US EPA, 2012).

value: Left-lobe liver

value: 12-week old

value: 5 mg EE2/kg body weight


title: P0234EPR00


title: TGCT1_2

description:
10x Genomics
TGCT1_2


title: LAEC_2

source_name: Proximall lung biopsies

value: Proximall lung biopsies

value: Congenital heart disease


title: 6-Control3

source_name: EVs derived from Control bone marrow cells

value: Control


title: P0228EPR00


title: TGCT1_1

description:
10x Genomics
TGCT1_1

value: Tumor


title: 5-Control2


title: SAEC_2


title: 5 mg EE2/kg body weight, rep4 [QA1-H5]


title: 4-Control1


title: LAEC_1


title: P0188EPR00


title: 5 mg EE2/kg body weight, rep3 [QA1-H3]


title: SAEC_4

value: Male


title: TGCT2_2

description:
10x Genomics
TGCT2_2


title: 5 mg EE2/kg body weight, rep2 [QA1-H2]


title: P0172EPR00


title: 5 mg EE2/kg body weight, rep1 [QA1-H1]


title: P0151EPR00


title: SAEC_1


title: human renal proximal tubule epithelial cells p8

city: Firenze

first: Roberto

last: Semeraro

address: Viale Pieraccini, 6

department: Medicina Sperimentale e Clinica

country: Italy

institute: Università degli studi di Firenze

data_processing:
Basecall performed with cellranger mkfastq v3.0.1.
Single cell feature counts performed with cellranger count v.3.0.1.
Assembly: GRCh38
Supplementary files format and content: matrix.mtx (filtered count matrix), barcodes.tsv, and features.tsv files generated through cellranger count.

source_name: kidney

growth_protocol: Primary hPTC cultures (ATCC-PCS-400-010) at passage 3 were put in culture and maintained in REGM (Lonza, CC-3190).

extract_protocol:
The single cell suspension with over 97% viability was run on a 10x Chromium Single Cell instrument (10x Genomics, Pleasanton, CA) following Manufacturer’s instructions
3’ gene expression libraries were constructed following 10x Genomics's instructions

treatment_protocol: hPTC were seeded at a density of 100,000 cells/6-well. 48h after plating the cells were harvested. A full 6-well plate was employed for each experiment.

tag: cell

value: primary cell culture

tag: developmental stage

value: adult

tag: passage


title: P0142EPR00


title: 0.5 mg EE2/kg body weight, rep5 [QA1-M5]

value: 0.5 mg EE2/kg body weight


title: COVID_PV12376

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

data_processing:
Libraries were sequenced on Illumina Nova-seq platform. First, paired end reads were split by barcode sequence using Je demultiplex with options BPOS=BOTH BM=READ_1 LEN=4:6 FORCE=true C=false 6. BM and LEN options were adjusted for samples with a 3 nt barcode instead of 4, and for samples where the barcode is located in read 2
Next read 2 files were used to map with bowtie2 with the following parameters: -q -p 10 --local —no-unal. Reads were mapped to curated list of non-redundant tRNA genes with tRNAScane score >40; mRNA was mapped to hg38 transcriptome
Bowtie2 output sam files were converted to bam files, then sorted using samtools. Next IGV was used to collapse reads into 1 nt window. IGV output .wig files were reformatted using custom python scripts (available on GitHub at https://github.com/ckatanski/MSRR-seq).
The bowtie2 output Sam files were also used as input for a custom python script using PySam, a python wrapper for SAMTools ( https://github.com/pysam-developers/pysam) to sum all reads that mapped to each gene
Data was visualized with custom R scripts (available on GitHub at https://github.com/ckatanski/CovidNasalSwabs_2022)
Assembly: Hg19
Library strategy: MSR-seq

source_name: Nasal swab RNA extracted from patients with SARS-CoV2

extract_protocol:
Total RNA was extracted using miRvana MagMax RNA extraction kit from ThermoFisher (A27828)
Libraries were constructed as described in Watkins et. al 2022. First bar-code ligation: Sampes were input to one-pot deacylation and β-elimination. Up to 100 ng of total RNA input was used in a ligation reaction of 50 µL with the following components: 1 U/µL T4 RNA ligase I (NEB), 1x NEB T4 RNA ligase I buffer, 15% PEG 8000, 50 µM ATP, 1 mM hexaamine cobalt chloride, and 5% DMSO. After adding the ligation mix to the sample, the capture hairpin oligo was added to a final concentration of 1 µM and the samples were incubated at 16 °C overnight (12+ hours). Binding to Dynabeads: The ligation mixture was diluted by adding an equal volume of water to reduce the viscosity of the solution. Next, streptavidin-coated MyOne C1 Dynabeads (ThermoFisher) were added to each sample in a 1.2:1 excess over CHO (for example, a 50 µL reaction had 50 pmol capture hairpin oligo; beads were supplied at 10 mg/ml and had binding capacity of 500 pmol biotinylated oligo per mg, so use 12 µL beads). The bead-sample mixture was incubated at room temperature for 15 minutes. After binding, supernatants were removed, and the beads washed once with high salt wash buffer (1 M NaCl, 20 mM Tris-HCl, pH 7.4) and once with low salt wash buffer (100 mM NaCl, 20 mM Tris-HCl, pH 7.4). After washing, multiple individually barcoded samples can be combined for downstream steps. Dephosphorylation: A 50 µL dephosphorylation mix containing the following was added to the multiplexed sample on bead: 0.04 U/µL calf intestine phosphatase (Roche), 10 mM MgCl2, 0.5 mM ZnCl2, 20 mM HEPES, pH 7.3. The sample was incubated at 37 °C for 30 minutes. The sample was then washed once with high salt wash buffer and once with low salt wash buffer, then resuspended in 20 µL water. Reverse transcription: 5 µL of SuperScript IV VILO 5x master mix (ThermoFisher) was added to the dephosphorylated sample (final volume of 25 µL) and then incubated at 55 °C for 10 minutes. The sample was then washed once with high salt wash buffer and once with low salt wash buffer. Identical results were obtained upon extending the reaction time to 60 minutes. For overnight reverse transcription, after the initial 10 min incubation at 55 °C, the samples are further incubated at 35 °C overnight. RNase H digestion: Beads were then resuspended into 50 µL of RNase H master mix containing 0.4 U/uL RNase H (NEB) and 1x NEB RNase H buffer and incubated at 37 °C for 15 minutes. The sample was then washed once with high salt wash buffer and once with low salt wash buffer. The sample was then resuspended in 40 µL water. Periodate oxidation: 10 µL of 250 mM freshly prepared sodium periodate, 0.5 M sodium acetate, pH 5 were added to the RNase H digested sample and incubated at room temperature for 30 minutes. Afterwards, ribose was added to a final concentration of 167 mM to quench excess periodate at room temperature for 5 minutes. The sample was then washed once with high salt wash buffer and once with low salt wash buffer. Second ligation: Beads were resuspended into 50 µL of a ligation master mix with the following components: 2U/µL T4 RNA ligase I (NEB), 1x NEB T4 RNA ligase I buffer, 2 µM second ligation oligo (Table S5), 25% PEG 8000, 50 µM ATP, 7.5% DMSO, and 1 mM hexaamine cobalt chloride. After incubation at room temperature overnight (12+ hours), the reaction was diluted with 50 µL water to reduce viscosity, washed once with high salt wash buffer and once with low salt wash buffer, and then resuspended in water. The amount of water was 6 µL per sample in the first ligation reaction, before pooling the barcoded samples. For example, if the second ligation mixture contains a pool of 6 samples, the amount of water used for resuspension would be 36 µL. Samples can be stored at 4 °C or frozen at -20 °C; both can be used for the next PCR step. PCR: A 50 µL PCR reaction was run using 5-10% of the bead slurry products from the second ligation reaction using Q5 DNA polymerase (NEB) and following the manufacturer’s instructions: 0.02 U/µL Q5 DNA polymerase, 1x Q5 reaction buffer, 0.2 mM dNTPs, 0.5 µM Illumina index primer, and 0.5 µM Illumina multiplex primer. Typical PCR cycles were 9-15 cycles at 10 seconds at 98 °C, 15 seconds at 55 °C, and 72 °C for 20 seconds. PCR reactions were then processed through the DNA Clean and Concentrate kit (Zymo Research). TBE-PAGE gel extraction: Following desalting, PCR products were run on 10% non-denaturing TBE gel with dsDNA size markers; lanes were cut according to the desired product size, mashed by pipette tip, and then resuspended in crush-and-soak buffer (500 mM sodium acetate, pH 5.0). The gel fragments were extracted overnight and then ethanol precipitated.

tag: condition


title: COVID_PV12408


title: COVID_PV09423


title: COVID_PV12414


title: human renal proximal tubule epithelial cells p7


title: 0.5 mg EE2/kg body weight, rep4 [QA1-M4]


title: 0.5 mg EE2/kg body weight, rep3 [QA1-M3]


title: P0125EPR00


title: COVID_PV12358


title: human renal proximal tubule epithelial cells p6


title: P0134EPR00


title: COVID_PV12362


title: COVID_PV12349


title: Assay_RNAseq_1

city: New York

first: Oded

last: Regev

address: 215 Mercer St

institute: New York University

data_processing:
Sequences were cleaned and processed using a custom pipeline.
Our pipeline reads the raw DNA reads, filters out those that don't look like barcode reads, and sorts by barcode.
Next, it takes cDNA reads, and produces splicing statistics per barcode.
Assembly: hg38
Supplementary files format and content: The files whose names end in "_splicing_analysis.csv" contain splicing statistics per barcode for each replicate.

source_name: HeLa

growth_protocol: HeLa cells were originally purchased from the ATCC (ATCC CCL-2). Cell cultures were assayed for mycoplasma roughly every six months using a standard PCR protocol and consistently tested negative. Cells were cultured in DMEM (Corning 10-013-CV) medium supplemented with 10% Fetal Bovine Serum (Sigma-Aldrich F0926) and penicillin and streptomycin (Thermo Fisher 10378016) in standard conditions (37°C with 5% CO2).

extract_protocol:
Briefly, after detachment following Accutase treatment, cells were pelleted and RNA extracted according to manufacturer’s instructions including DNase treatment (Cytiva illustra™ RNAspin Mini Isolation Kit, Fisher Scientific 45-001) using an automated QIAcube platform.
DNA: UMIs were introduced with first and second strand synthesis (NEB 2X Hot Start HotFlex Phusion). Amplicons were further amplified using sequences upstream and downstream of the UMIs. Enzymes were removed after every reaction (QIAGEN Qiaquick PCR Purification). RNA: RNA was reverse transcribed using specific primers with UMIs following manufacturer’s instructions in a 20µL reaction including RNase H treatment (SuperScript™ IV Reverse Transcriptase, ThermoFisher 180900). Second strand synthesis was generated using a single round of amplification (NEB 2X HotStart HotFlex Phusion) using specific primers with UMIs. Amplicons were further amplified using sequences upstream and downstream of the UMIs. Enzymes were removed after every reaction (QIAGEN Qiaquick PCR Purification).

treatment_protocol: The massively parallel reporter assay was transfected in a 10cm dish. Cells were seeded the day before transfection as 2.0 × 10^6 cells in 12mL media on 10cm dishes. Transfection followed a 1:3 ratio of plasmid DNA to transfection reagent following manufacturer’s protocol (FuGENE® HD, Promega E2311) with OptiMEM (OptiMEM I™, ThermoFisher 31985062) to final 100µL volume. For a 10cm dish, 3µg plasmid DNA was mixed with 9µL transfection reagent. Each DNA/transfection reagent mixture was vortexed briefly, incubated at room temperature for 10min, then added to cells and incubated at 37°C. RNA was extracted from cells 24h after transfection

value: HeLa

tag: sample id

tag: lib strategy

value: amplicon RNA

tag: lib selection

tag: replicate number


title: DNA_exon_barcode

tag: cell type

value: amplicon DNA


title: 0.5 mg EE2/kg body weight, rep2 [QA1-M2]

tag: treatment


title: P0025EPR00


title: Assay_RNAseq_2


title: 0.5 mg EE2/kg body weight, rep1 [QA1-M1]


title: P0063EPR00


title: P0016EPR00


title: COVID_PV09493


title: Solvent, rep6 [QA1-S6]

value: Corn oil (solvent)


title: HCE042EPR00

value: Esophageal mucosa

value: Healthy control


title: Assay_RNAseq_3


title: Solvent, rep5 [QA1-S5]

value: Left-lobe liver


title: COVID_PV09486


title: Sample 9_697 cell line_FOXO1 rep 3 [exp2]

data_processing:
base calling by standard illumina sequencing
Reads alighned  (to GENECODE v34) and counted using SALMON 1.6.0.
Counts normalised using DESeq 2
Genome_build: CRCh38
Supplementary_files_format_and_content: Matrix of RAW gene read counts, Matrix of normalised gene read counts.

source_name: 697 cell line

treatment_protocol: lentiviral transduction cDNA expression constructs and FACS enrichment for EGFP positive cells

value: pre-B cell

tag: sub-type

tag: disease

value: leukaemia

value: transduced with FOXO1 expression construct


title: HCE040EPR00


title: HCE038EPR00


title: Sample 8_697 cell line_FOXO1 rep 2 [exp2]


title: Solvent, rep4 [QA1-S4]

tag: age

value: 12-week old


title: Sample 7_697 cell line_FOXO1 rep 1 [exp2]


title: HCE037EPR00

tag: tissue


title: Solvent, rep2 [QA1-S2]


title: Sample 6_697 cell line_FOXO3 rep 3 [exp2]

value: transduced with FOXO3 expression construct


title: COVID_PV09495


title: COVID_PV09482


title: COVID_PV09481


title: Sample 5_697 cell line_FOXO3 rep 2 [exp2]


title: HCE035EPR00


title: COVID_PV09480


title: Solvent, rep1 [QA1-S1]


title: COVID_PV09471


title: HCE036EPR00


title: HCE034EPR00


title: Thp1-M.tb-sciDLOHiC

city: Wuhan

first: Ping

last: Hong

state: Hubei

address: No.1,Shizishan Street

department: college of informatics

institute: Huazhong Agricultural University

description:
Single cell indexed DLO Hi-C
MGISEQ-2000
THP-1 cells after differentiation and activated by M.tb H37Ra

data_processing:
PETs extraction step using the expet tool from sciDLO package, the parameter “--fq1 [R1_file] --fq2 [R2-file] –linker GTCGGANNNNNNNNGCTAGCNNNNNNNNTCCGAC --enzyme T^TA^A -b” were used.
Mapping, pairing, and result filtering using DLO-HiC-Tools pipeline with default parameters.
Cell split using the spcell tool from sciDLO package, the default parameters were used: 1, 2, 4 hamming distance difference is allowed for the compare between “read barcode VS library barcode”, “barcode1 VS barcode2(within same reads)”, “barcode R1 VS barcode R2 (barcode within R1 and R2).”
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.tar: The tar archives include the pairs files of all cells. The pairs files contain the chromosome contacts of each cell.

source_name: Peripheral blood

growth_protocol: THP-1 (ATCC, TIB-202) cells were grown in RPMI-1640 supplemented with 10% FBS.

extract_protocol:
DNA was precipitated at room temperature with 10 µl of Dr. GenTLE Precipitation Carrier (Takara), 100 µl of 3M sodium acetate (pH 5.2), and an equal volume of isopropanol.
For sciDLO Hi-C library construction, the cells were firstly pooled for fixation, in situ digestion and then aliquoted to 96 wells to added the first barcode through ligation of barcoded MmeI half linker. The intact nucleus was pooled again for proximity ligation and then aliquoted to about 30 nucleus per tube for multiple displacement amplification (MDA). The amplification products were digested by MmeI digestion which released a specific 80-bp barcoded chromatin interaction DNA fragment. As we only recycled these DNA fragments containing chromatin interaction pairs, it can greatly reduce the sequencing noise caused by MDA, which is an advantage of this method. Moreover, the number of barcode indexes (96) in each tube exceeds the number of nuclei (30), the vast majority of single nuclei are tagged by a unique barcode.

treatment_protocol: To differentiate the monocytes to macrophages, cells were treated with PMA (phorbol 12-myristate 13-acetate) (final concentration = 40 ng/µl) for 48 h at 37 °C in a 5% CO2 atmosphere, and then washed with pre-warmed PBS and incubated with fresh culture medium for another 24 h. For M.tb infection experiment, H37Ra was pelleted (4,000 rpm, RT, 10 min), washed twice with RPMI-1640, resuspended in 1 ml THP-1 culture medium, and dispersed using BD insulin syringes (BD, 328421). Monocyte derived macrophages (Thp1-macro) were infected with H37Ra at MOI (multiplicity of infection) 20. Four hours later the infected cells were washed twice with pre-warmed PBS and incubated with fresh culture medium for another 8 h.

tag: cell line

value: Differentiation and activated by M.tb H37Ra


title: Sample 4_697 cell line_FOXO3 rep 1 [exp2]


title: Thp1-macro-sciDLOHiC

description:
Single cell indexed DLO Hi-C
MGISEQ-2000
THP-1 cells after differentiation

value: Differentiation


title: HCE032EPR00


title: COVID_PV09467


title: Sample 3_697 cell line_SIN-SIEW rep 3 [exp2]

value: transduced with control vector


title: Solvent, rep3 [QA1-S3]


title: COVID_PV09466


title: Sample 1_697 cell line_SIN-SIEW rep 1 [exp2]


title: P0260EDR00

value: Achalasia


title: COVID_PV09472


title: COVID_PV09459


title: MV411 PGP KO ironomycin 24hrs rep3

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

institute: Peter MacCallum Cancer Centre

data_processing:
bcl2fastq v2.20.0.422 was used to generate fastq files.
Reads were aligned with HiSAT2 to G1k V37
Reads were assigned to genes using htseq-count
Genome_build: hg19
Supplementary_files_format_and_content: Text file of the counts matrix of all samples generated by htseq-count

source_name: Biphenotypic B Myelomonocytic Leukemia

growth_protocol: All cells were maintained in RPMI-1640 + glutamine supplemented with 10% FCS, 100 IU ml-1penicillin, 100 ug ml-1 streptomycin under standard culture conditions (5% CO2, 37°C).

extract_protocol:
RNA from cells was prepared using the Qiagen RNeasy kit.
Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit

treatment_protocol: Cells were treated with either DMSO or Ironomycin (AM5) for 6 or 24 hrs.

value: ironomycin

tag: genotype

value: PGP CRISPR KO


title: CT26 cells, radiation+MEKi, rep3

city: jinan

first: yawen

last: zheng

address: jiefang road,No105

institute: jinan central hospital

data_processing:
In this project, we sequence 12 samples used DNBSEQ platform, averagely generating about 1.15G Gb bases per sample. The average mapping ratio with reference genome is 85.55%, the average mapping ratio with gene is 78.44%; 18351 genes were identified.
Supplementary files format and content: matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: matrix table with RPKM values for  every gene and every sample

source_name: colon cancer

growth_protocol: Freshly isolated tumor tissues were cleaned using PBS. Tissue blocks (50 mm3) were cut to avoid the necrotic site, and three tumor tissues from different mice were analyzed for each group. Tissues were placed in TRIzol, stored at −80 °C, and transported to BGI for gene sequencing using dry ice. Sequencing was started after samples passed quality control.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: In total, 3 × 105 CT26 or LLC cells were subcutaneously injected into the right flank of BALB/c or C57BL/6 mice. When the tumor volume reached 50–75 cm3, the mice were randomly assigned to the following four groups: Control, drug (MEK inhibitor or AMG510), RT, and drug + RT. Each group contained six or seven mice. Mice in the MEKi and MEKi + RT groups were administered trametinib (1 mg/kg) via oral gavage daily, mice in the AMG510 and AMG510 + RT groups were administered sotorasib (3 mg/kg) via oral gavage daily, and the others were administered the solvent (corn oil) via oral gavage at the same time. After 2 days of oral gavage, the mice in the RT and combined therapy groups received radiation (8 Gy/1F).

value: colon cancer

value: colon cancer cell

value: WT

value: trametinib 1mg/Kg+8Gy/1f


title: CT26 cells, radiation+MEKi, rep2


title: CT26 cells, radiation+MEKi, rep1


title: P0243EDR00

value: Esophageal mucosa

tag: disease state


title: MV411 PGP KO ironomycin 24hrs rep2


title: P0234EDR00


title: CT26 cells, radiation, rep3


title: COVID_PV09454


title: Sample 2_697 cell line_SIN-SIEW rep 2 [exp2]


title: P0188EDR00


title: MV411 PGP KO ironomycin 24hrs rep1


title: Thp1-mono-sciDLOHiC

description:
Single cell indexed DLO Hi-C
MGISEQ-2000
THP-1 cells before differentiation

value: Before differentiation


title: CT26 cells, radiation, rep2


title: P0264EDR00


title: COVID_PV09460


title: CT26 cells, radiation, rep1


title: COVID_PV09453


title: MV411 PGP KO dmso rep2

value: dmso


title: MV411 PGP KO dmso rep3


title: COVID_PV09452


title: P0172EDR00


title: COVID_PV09451


title: CT26 cells, control, rep3

value: control


title: COVID_PV09455


title: MV411 HK2 KO ironomycin 24hrs rep3

value: HK2 CRISPR KO


title: P0151EDR00


title: COVID_PV09450


title: MV411 HK2 KO ironomycin 24hrs rep2


title: P0142EDR00


title: COVID_PV09449


title: P0228EDR00


title: CT26 cells, control, rep1


title: COVID_PV09433


title: MV411 HK2 KO ironomycin 24hrs rep1


title: CT26 cells, MEKi, rep3

value: trametinib 1mg/Kg


title: CT26 cells, MEKi, rep2


title: P0063EDR00


title: P0125EDR00


title: COVID_PV09432


title: MV411 HK2 KO dmso rep3


title: COVID_PV09430


title: CT26 cells, MEKi, rep1


title: COVID_PV09427


title: MV411 HK2 KO dmso rep1


title: COVID_PV09429


title: MV411 HK2 KO dmso rep2


title: MV411 PGP KO dmso rep1


title: CT26 cells, control, rep2


title: P0025EDR00


title: COVID_PV09425


title: MV411 wildtype ironomycin 24hrs rep2

value: wildtype


title: HCE040EDR00

value: Healthy control


title: COVID_PV09412


title: HCE042EDR00


title: MV411 wildtype ironomycin 24hrs rep3


title: MV411 wildtype ironomycin 24hrs rep1


title: COVID_PV09411


title: P0134EDR00


title: HCE038EDR00


title: MV411 wildtype ironomycin 6hrs rep3


title: HCE037EDR00


title: P0016EDR00


title: COVID_PV09464


title: COVID_PV09504


title: HCE036EDR00


title: MV411 wildtype ironomycin 6hrs rep2


title: HCE035EDR00


title: COVID_PV13343


title: MV411 wildtype ironomycin 6hrs rep1


title: MV411 wildtype dmso rep3


title: COVID_PV12420


title: MV411 wildtype dmso rep2


title: HCE032EDR00


title: HCE034EDR00


title: COVID_PV12413


title: OCC_Case4_TeEVs_rep2

city: Takatsuki

first: Hiroshi

last: Maruoka

state: Osaka

address: 2-7 Daigakumachi

institute: Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceu-tical University

description: OCC:ocvarian clear cell carcinoma

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000(Affymetrix).

data_processing: Image analysis was performed using Affymetrix GeneChip Command Console Software ver. 3.2.4. Data analysis was performed using Expression ConsoleTM Software ver. 1.4.1.46 (Affymetrix). The algorithms were RMA and DABG.

label: biotin

source_name: normal region,Te-EVs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 130 ng total RNA (User Manual, 2012, Affymetrix).

growth_protocol: Following excision, tissue samples were immediately immersed in 9 ml serum-free medium (Wako) with 1 ml exosome-depleted FBS (SBI) and stored in a CO2 incubator at 37 °C for 3 h. The tissue-immersed medium was filtered using a 0.22 μm filter (Merck Millipore, Bedford, MA, USA) to remove cell debris and centrifuged at 2,000×g for 30 min at 16,000×g for 30 min.

extract_protocol: Total RNA extractions from EVs were performed using the miRNeasy Mini Kit, according to the manufacturer's protocol (Qiagen GmbH, Hilden, Germany).

treatment_protocol: To pellet EVs from the collected supernatant, ultracentrifugation was performed using an Optima XE-100 (Beckman Coulter, Brea, CA, USA), SW41 T1 (Beckman Coulter), and Ultra-Clear tube (Beckman Coulter) at 100,000 g for 70 min.

tag: gender

value: female

value: ovary

tag: tumor stage


title: OCC_Case2_TeEVs_rep1

description: OCC:ocvarian clear cell carcinoma

source_name: cancer region,Te-EVs


title: OCC_Case2_TeEVs_rep2

description: OCC:ocvarian clear cell carcinoma


title: OCC_Case3_TeEVs_rep2

description: OCC:ocvarian clear cell carcinoma

value: ⅢB


title: OCC_Case1_TeEVs_rep2

description: OCC:ocvarian clear cell carcinoma


title: MV411 wildtype dmso rep1


title: DLD1-treatment-2

city: Harbin

first: Haopeng

last: Zhang

state: Heilongjiang

address: No. 37 Yiyuan Street

department: Department of General Surgery & Bio-Bank of General Surgery

institute: The Fourth Aﬃliated Hospital of Harbin Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using TopHat v2.1.0 with default parameters
Transcript assembly and FPKM (RPKM) estimated for RNA-Seq data using Cufflinks v2.2.1.0 with default parameters
Genome_build: hg38
Supplementary_files_format_and_content: Excel file includes RPKM values for each Sample ...

source_name: colorectal carcinoma

growth_protocol: DLD-1 cells were cultured in DMEM medium supplemented with 10% Fetal Bovine Serum, 100 U/mL penicillin and 0.1 mg/mL streptomycin at in a 37 °C humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted using Total RNA Miniprep Kit (Axygen, Hangzhou, China) according to the supplier’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We chose the concentration of 400 μg/mL RK for 72 h to study

value: epithelial cells

value: treatment with RK


title: COVID_PV12401


title: DLD1-treatment-3


title: OCC_Case1_TeEVs_rep1

description: OCC:ocvarian clear cell carcinoma


title: OCC_Case4_TeEVs_rep1

description: OCC:ocvarian clear cell carcinoma


title: OCC_Case3_TeEVs_rep1

description: OCC:ocvarian clear cell carcinoma


title: Non-mineralized aortic valves-newNor09

city: Beijing

first: Long

last: Chen

address: No. 167 North Lishi Road, Xich

institute: Fuwai hospital

data_processing:
Quality control: Raw data of fastq format were firstly processed through in-house pel script. In this step, clean data were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20,Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome websitr directly. Index of reference genome was built using bowtie2 v2.2.8 and paired-end clean reads were aligned to the reference genome using HISAT2 v2.0.4. HISAT2 was run with '--rna-strandness RF', other parameters were set as default.
Transcriptome assmbly: The mapped reads of each sample were assembled by StringTie uses a nevol network folw algorithm as well as an optional de nov assembly step to assemble and quantitate full length transcript s representing multiple splice variants for each gene locus.
Quantification of gene expression level : Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample. Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Differential expression anlysis: The Ballgown suit includes functions for interactive exploration of the transcript structures and feature-specific abundances for each locus, and post-hoc annotation of assembled features to annotated features. Transcripts with an P-adjust <0.05 wre assigned as differentially expressed. Cuffdiff PROVIDES statistical routines for determining differential expression in digital transcript or gene expression data using a model based on the negative binomial distribution. Transcript with an P-adjust<0.05 were assigned as differentially expressed.
Assembly: homo sapiens GRCh38.p12
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: aortic valve

extract_protocol:
Total RNA was extracted from aortic valves. First, ribosomal RNA (rRNA) was removed by Ribo-Zero TM rRNA Removal Kit (Epicentre)
Sequencing libraries were prepared from the rRNA-depleted RNA by NEBNext® Ultra TM Directional RNA library Prep Kit for Illumina® (New England Biolabs) following manufacturer’s recommendations, and then sequenced on the Illumine HiSeq 2500 platform by Novogene (China) and 100 bp paired end reads were generated.

value: male

value: non-mineralized aortic valves


title: COVID_PV12399


title: Input DNA, SUPT1 with overexpression of STAT5B_N642H mutant, treated

city: Utrecht

first: Rico

last: Hagelaar

address: Heidelberglaan 25

institute: Princess Maxima Center

data_processing:
Raw reads were aligned to Hg38 using BWA, default settings
MACS2 was used for peakcalling. Narrow peak calling was used for transcription factors. Remainder of settings were left at default
Normalised BigWig files (bw) were created using BamCoverage of the Deeptools package, using the reads per genome coverage (RPCG) scaling factor
Genome_build: CRCh38
Supplementary_files_format_and_content: peak text files
Supplementary_files_format_and_content: BigWig files; containing RPGC normalised values

source_name: SUPT-1 cell line

growth_protocol: SUPT-1 cells were cultured in RPMI-1640 medium (Gibco) supplemented with 1x Glutamax, 10% heat-inactivated fetal bovine serum (Gibco), 2% pencillin/streptomycin (Gibco) and 0,4% Fungizone (Gibco). Media for SUPT-1 cells was supplemented with 1-2 μg/mL puromycin for purification of doxycycline-inducible cells

extract_protocol:
20x10^6 cells were fixed and chromatin-immunoprecipitation (ChIP) was performed according to the manufacturer’s instructions (Simple ChIP Enzymatic Chromatin IP Kit, #9003, CST). Water bath sonification was performed for seven cycles (30 seconds on 30 seconds off), and DNA fragment size was validated by electrophoresis.
DNA library preparation was performed using the NEBNext Ultra II DNA Library Prep kit (New England Biolabs #E7103) with an additional 0,52X beads purification step.

treatment_protocol: Doxycycline-induced STAT5WT and STAT5BN642H SUPT-1 cells were cultured with or without 250µg/ml prednisolone for 16 hours

tag: overexpression

value: 250ug/ml prednisolone for 16 hours


title: Non-mineralized aortic valves-newNor10


title: DLD1-control-2


title: Non-mineralized aortic valves-newNor08


title: Input DNA, SUPT1 with overexpression of STAT5B_N642H mutant, untreated

value: untreated


title: COVID_PV12397

tag: condition


title: COVID_PV12382


title: DLD1-control-1


title: Non-mineralized aortic valves-newNor07


title: KP Arid1a Chip-Seq (Cut & Tag)

city: Shanghai

first: Xiaoyu

last: Liu

state: Shanghai

address: 180 Yue-yang road

department: Department of Interventional Radiology

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2 or hisat2
The potential PCR duplicates were removed using sambamba (sambamba 0.7.1) with the option: sambamba markdup --overflow-list-size 600000 --tmpdir='./' -r.
The mitochondrial DNA (mtDNA) were also estimated and removed using a custom script.
For peak calling, the parameters of MACS2 were setting as : macs2 callpeak -t file -g hs/mm --keep-dup all -p 0.05 -n file_name.Deeptools 3.3.0 were used to generated RPKM-normalized  Bigwig files and heatmap of the open-chromatin or protein binding regions
Genome_build: mm10
Supplementary_files_format_and_content: htseq-counts for RNA-seq;wig files for ATAC and ChIP-seq;

source_name: genetically engineered mouse models

growth_protocol: KRAS driven lung tumors

extract_protocol: Standered protocal for library preparation of RNA-seq and ATAC-seq. Cut & Tag method for ChIP-seq.

treatment_protocol: AAV/lenti induction

value: Lung

value: tumor

value: KP


title: COVID_PV12381


title: Non-mineralized aortic valves-newNor03


title: DLD1-treatment-1


title: STAT5B pull down SUPT1 with overexpression of STAT5B wild type (WT), treated with prednisolone

value: Wild type (WT)


title: Non-mineralized aortic valves-newNor02


title: Non-mineralized aortic valves-newNor01


title: KPA ATAC-seq rep1

value: KPA


title: STAT5B pull down SUPT1 with overexpression of STAT5B wild type (WT), untreated


title: NR3C1 pull down SUPT1 with overexpression of STAT5B wild type (WT), treated with prednisolone


title: COVID_PV12372


title: COVID_PV12364


title: KPA ATAC-seq rep2


title: COVID_PV12357


title: KP ATAC-seq rep2


title: NR3C1 pull down SUPT1 with overexpression of STAT5B wild type (WT), untreated


title: KP ATAC-seq rep1


title: Non-mineralized aortic valves-Nor04


title: KPA RNA-seq rep2


title: KP Arid1a Chip-Seq IgG


title: COVID_PV12355


title: COVID_PV12337


title: Non-mineralized aortic valves-Nor06


title: Input DNA, SUPT1 with overexpression of STAT5B wild type (WT), untreated


title: Non-mineralized aortic valves-Nor02


title: STAT5B pull down SUPT1 with overexpression of STAT5B_N642H mutant, untreated


title: NR3C1 pull down SUPT1 with overexpression of STAT5B_N642H mutant, treated with prednisolone


title: COVID_PV12369


title: COVID_PV09492


title: KP RNA-seq rep2


title: Non-mineralized aortic valves-Nor01


title: Calcific aortic valves-newcal07

value: calcific aortic valve disease


title: KP RNA-seq rep1


title: MA9-FF-3

city: Tokyo

first: Susumu

last: Goyama

address: 4-6-1 Shirokanedai, Minato-ku

department: Graduate School of Frontier Sciences

institute: The University of Tokyo

data_processing:
Sequence reads were processed using cutadapt (1.8.1) and fastx-toolkit (0.0.13) to remove Illumina adaptor sequence and to trim low-quality bases.
Processed reads were aligned to GRCm38 reference transcripts using TopHat(2.1.1)-Cufflinks(2.2.1) pipeline (60-62) to derive gene FPKM values.
Assembly: GRCm38
Supplementary files format and content: text files include FPKM values for each Sample

source_name: MLL-AF9-transduce mouse bone marrow cells

growth_protocol: MLL-AF9 cells were transplanted into C57BL/6 mice.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen), and the quality and quantity of RNA were checked using Agilent High Sensitivity RNA Screen Tape and Qubit.  RNA libraries were prepared using 1000 ng total RNA with SureSelect Strand-Specific RNA Preparation Kit (Agilent) according to the manufacturer’s protocol.
RNA libraries were prepared using 500 ng total RNA with SureSelect Strand-Specific RNA Preparation Kit (Agilent) according to the manufacturer’s protocol.

treatment_protocol: MLL-AF9-bearing mice were treated with 160 mg/kg FF-10501-01, or vehicle in 2 consecutive days. Bone marrow cells were then harvested from the mice 48 hours after the first administration of the drugs.

tag: strain


title: NR3C1 pull down SUPT1 with overexpression of STAT5B_N642H mutant, untreated


title: Calcific aortic valves-newcal05


title: Non-mineralized aortic valves-Nor05


title: COVID_PV09468


title: MA9-FF-2

value: MLL-AF9-transduce mouse bone marrow cells


title: Peripheral blood, T-ALL KO, rep3 [ko_6d]

city: St Louis

first: Grant

last: Challen

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

data_processing:
Partek Flow 10.0.22.0524
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek flow
Trimmed raw RNA-seq reads were aligned to the Ensembl release mm10 (Mouse) using STAR version 2.7.3a
Read count extraction and normalization were performed using Partek flow
Assembly: Ensembl release mm10 (Mouse)
Supplementary files format and content: Excel files include CPM values for each Sample

extract_protocol:
RNA was harvested using NucleoSpin RNA XS kit (Macherey-Nagel)
RNA libraries for RNA-seq were prepared using SMARTer Ultra Low RNA kit (Clontech) following manufacturer's protocols.

value: Peripheral blood

value: T-ALL blast

value: Kdm6b homozygous mutant


title: MA9-FF-1


title: COVID_PV09470


title: STAT5B pull down SUPT1 with overexpression of STAT5B_N642H mutant, treated with prednisolone


title: COVID_PV09463


title: Calcific aortic valves-newcal03


title: Peripheral blood, T-ALL KO, rep2 [ko_6c]


title: Peripheral blood, T-ALL KO, rep4 [ko_6e]


title: Peripheral blood, T-ALL KO, rep1 [ko_6b]


title: Calcific aortic valves-newcal04


title: MA9-vehicle-3

value: vehicle


title: COVID_PV09457


title: COVID_PV09461


title: KPA RNA-seq rep1


title: Calcific aortic valves-newcal02


title: MA9-vehicle-2


title: MA9-vehicle-1


title: Calcific aortic valves-cal05


title: Peripheral blood, T-ALL Control, rep4 [control_2d]

value: Kdm6b wild type


title: COVID_PV12416


title: Calcific aortic valves-cal04


title: Influenxa_4

source_name: Nasal swab RNA extracted from patients with influenza

value: Influenza


title: Peripheral blood, T-ALL Control, rep3 [control_2c]


title: Peripheral blood, T-ALL Control, rep2 [control_2b]


title: Calcific aortic valves-cal03

value: male


title: Caicific aortic valves-cal02


title: mESC, TKO-tamoxifenTreatment_acute, 1

city: SAN DIEGO

first: Anjana

last: Rao

state: CALIFORNIA

address: 9420 Athena CIRCLE, LA JOLLA

institute: LA JOLLA INSTITUTE

description:
WGS_LowCov-Bulk_TetiTKO-TamoxifenTreated_Acute_r1
Whole Genome Sequencing (WGS) Low Coverage

data_processing:
WGS bulk low-coverage data was mapped to mm10 reference genome, using BSmap 2.74v allowing for maximum four mismatches (-v 4) and removing low-quality 3’ reads (-q 10).
Optical duplicate reads were removed Picard MarkDuplicates tool.
CNVkit (Talevich et. al 2016) was employed to detect copy number alterations (.cnn), in WGS, correcting for CG content and mappability bias. employing 500kb bins (or as indicated).
Assembly: mm10
Supplementary files format and content: .cnn.txt, sample genome coverage.

source_name: mouse Embryonic Stem Cell

growth_protocol: mESC were cultured under 2i-conditions (CHIR99021 and PD0325901) using Mouse Embryonic Fibroblasts (MEFs) as feeders.

extract_protocol:
Samples were generated after sorting by CD326+/GFP+/Live/Thy1.2-/LiveDead dye- for Ctrl and TetiTKO mESCs and by CD326+/Live/Thy1.2-/LiveDead dye- for Dnmt TKO mESCs. Genomic DNA was extracted using PureLinkTM genomic DNA mini kit.
TruSeq DNA PCR-Free Sample Preparation kit (Illumina, 20015963).

treatment_protocol: mESCs were treated with tamoxifen (1µM) for 2.5 days, cultured for 4 additional days and then collected for the acute-deletion comparison. Monoclonal populations from TetiTKO and Ctrl mESC were maintained for 30 days in culture for long-term comparisons. DnmtTKO (germline Knock-out [non-inducible]) mESC samples were included as part of the long-term comparison.

value: Tet1,2,3 fl/fl; Cre/ERT2; Rosa26-LSL-H2b-Egfp

value: mouse Embryonic Stem Cell

value: tamoxifen treatment, acute


title: Healthy_5

source_name: Nasal swab RNA extracted from healthy volunteers

value: Healthy


title: Peripheral blood, T-ALL Control, rep1 [control_2a]

state: MO


title: Influenza_3


title: Influenza_2


title: Influenza_1


title: Male SERTPyramid∆ 2

city: Bronx

first: Ji

middle: Ying

last: Sze

state: NY

address: 1300 Morris Park Ave

department: Molecular Pharamcology

institute: Albert Einstein College of Medicine

data_processing:
Adaptor trimming
Alignment to genome
Remove duplicate reads
Create and compile counts matrix file
Assembly: mm10
Supplementary files format and content: txt file with raw counts matrix containing all samples

source_name: Dorsal hippocampus tissue pooled from four mice

extract_protocol:
RNA extraction was performed using Trizol (Thermo Fisher, 15596026)-chloroform, followed by cleanup and elution into RNAse-free water using the RNeasy Minelute Cleanup kit (Qiagen, 74204) per manufacturer instructions.
mRNA libraries were prepared using the Illumina Truseq RNA Library Prep Kit V2 (#RS-122-2001) per manufacturer instructions on 250 ng total RNA.

tag: Sex

value: Male

value: SERTPyramid


title: mESC, Dnmt TKO-LongTerm, 1

description:
WGS_LowCov-Bulk_DnmtTKO-LongTerm_r1
Whole Genome Sequencing (WGS) Low Coverage

value: Dnmt1,3a,3b TKO

value: long-term


title: Male SERTPyramid∆ 1

value: Dorsal hippocampus tissue pooled from four mice


title: K562_control

city: Leiden

first: Daniel

middle: M.

last: Borras

address: Einthovenweg 20

department: CI

institute: LUMC

data_processing:
All samples were quality controlled and processed identically using the available ATAC-seq peak calling pipeline published by ENCODE, version 0.3.0 (DOI: 10.5281/zenodo.156534).
Alginment performed against the GRCh37 reference genome
Peaks were annotated with epigenomic signatures of K562, downloaded from ENCODE Project (Pazin, 2015).
Contrasts of peaks called to the untreated (Ctr) samples was performed with the R package DiffBind (Caryn et al 2012).
Genome_build: GRCh37
Supplementary_files_format_and_content: Processed files in BED-like format contain upregulated peaks contrasted to untreated (Ctr) samples.

source_name: cells

extract_protocol:
Extraction performed as described in Corces MR et al., 2017 (Nat.Meth.)
Sequencing libraries produced using the ATAC-seq protocol as described in Corces MR et al., 2017 (Nat.Meth.), and sequenced with a HiSeq4000.

treatment_protocol: 5 x 10^7 K562 cells per sample were treated with 10 µM Doxo, 20 µM Acla, 10 µM diMe-Doxo, for 4 hours

value: none (untreated control)


title: mESC, TKO-tamoxifenTreatment_LongTerm, 3

description:
WGS_LowCov-Bulk_TetiTKO-TamoxifenTreated_LongTerm_r3
Whole Genome Sequencing (WGS) Low Coverage

value: tamoxifen treatment, long-term


title: Calcific aortic valves-cal01

value: calcific aortic valve disease


title: Male SERTPyramid∆ 3


title: K562_Doxo

value: 10 µM Doxo for 4 hours


title: mESC, TKO-tamoxifenTreatment_LongTerm, 2

description:
WGS_LowCov-Bulk_TetiTKO-TamoxifenTreated_LongTerm_r2
Whole Genome Sequencing (WGS) Low Coverage


title: Healthy_2

city: Chicago


title: mESC, Ctrl-tamoxifenTreatment_LongTerm, 2

description:
WGS_LowCov-Bulk_WT-TamoxifenTreated_LongTerm_r2
Whole Genome Sequencing (WGS) Low Coverage

value: Cre/ERT2; Rosa26-LSL-H2b-Egfp


title: Healthy_4


title: K562_Acla

value: 20 µM Acla for 4 hours


title: mESC, Ctrl-tamoxifenTreatment_acute, 1

description:
WGS_LowCov-Bulk_WT-TamoxifenTreated_Acute_r1
Whole Genome Sequencing (WGS) Low Coverage


title: Male SERTfl/fll 3

value: SERTfl/fl


title: Healthy_3


title: Male SERTfl/fll 2


title: Male SERTfl/fll 1


title: mESC, TKO-tamoxifenTreatment_LongTerm, 1

description:
WGS_LowCov-Bulk_TetiTKO-TamoxifenTreated_LongTerm_r1
Whole Genome Sequencing (WGS) Low Coverage


title: Healthy_1


title: mESC, Ctrl-tamoxifenTreatment_LongTerm, 1

description:
WGS_LowCov-Bulk_WT-TamoxifenTreated_LongTerm_r1
Whole Genome Sequencing (WGS) Low Coverage


title: DRG neurons, sc-RNA seq batch 35

first: Xi-Yin

address: College Road

department: Neuroscience Research Institute

institute: Peking University

data_processing:
Illumina Casava1.7 software used for basecalling.
Extract Barcode and UMI: umi_tools extract.
Trim TSO and PolyA: trim_TSO_polyA.pl, seqtk trimfq.
Mapping With STAR, add feature using featureCounts of subread
Sort and index bam file using Samtools
Assembly: Rnor_6.0.102
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell-id

organism: Rattus norvegicus

source_name: Dorsal root ganglia

growth_protocol: Specific pathogen-free (SPF) male Sprague-Dawley (SD) rats weighing 200 g were supplied by the Animal Center of Peking University Health Science Center. The animals were housed in an SPF laboratory in ventilated cages (IVC) (3-5 rats per cage) on a 12-hour light-dark cycle (lights on at 8:00 AM) with free access to food and water. All experiments were performed according to the guidelines of the Animal Care and Use Committee of Peking University, and efforts were made to minimize the discomfort of the animals.

extract_protocol:
A modified Smart-seq2 protocol developed by the Tang laboratory was used for single-cell RNA-seq. Briefly, acutely dissociated DRG neurons were plated on dishes as described previously. After 15 min, the DMEM was replaced with PBS, and a mouth pipette was then used to place each individual fluorescently labeled single DRG neuron into a volume of lysis buffer under a fluorescence microscope. Harvesting of the single DRG neurons from one rat was completed in 4 h, and the L4-5 DRG of at least 5 rats were harvested at each time point.
The reverse transcription reaction was performed with a TSO primer added at the 5’ end and with 25 nt oligo (dT) primer anchored with an 8 nt cell-specific barcode and 8 nt unique molecular identifiers (UMIs) added at the 3’ end. After reverse transcription, cDNAs were amplified by 15 cycles of PCR, during which the IS primer and the 3’P2 primer were added to the 5’ and 3’ ends of the cDNAs, respectively. The amplified cDNAs from single cells were pooled, purified using a DNA Clean & concentration-5 kit (Zymo Research, D4014) and AMPure XP beads (Beckman Coulter, A63882), and quantified using a Qubit dsDNA HS Assay Kit (Invitrogen, Q32854). To add biotin tags to the 3’ ends of the amplified cDNAs, biotinylated preindexed primers and IS primer were used to further amplify the PCR product through an additional 4 cycles of PCR. The biotinylated cDNAs were then sheared to approximately 300 bp using Covaris S2, and the 3’ termini of the cDNAs were captured using C1 beads (Dynabeads® Myone™ Streptavidin C1, Invitrogen, 65001). The RNA-seq library was constructed using a Kapa Hyper Prep Kit (KAPA Biosystems, KK8505), and short universal primers and QP2 primers were used in the last amplification. Finally, the genome and transcriptome libraries were subjected to 150 bp paired-end sequencing on an Illumina HiSeq 4000 platform (sequenced by Novogene).

treatment_protocol: Adult naïve rats were deeply anesthetized with 10% chloral hydrate and their bilateral L4-L5 DRGs were quickly dissected. Acute-dissociated DRG neurons were collected and resuspended in plating medium (DMEM containing 10% FBS) and then plated onto a 3.5-cm dish coated with poly-D-lysine. After 3 hours, the medium was replaced with Neurobasal medium supplemented with 2% B27 and 2 mM GlutaMAX-I. After 72 hours, the Neurobasal medium was replaced with PBS, and a mouth pipette was then used to place each single DRG neuron with neurites into a volume of lysis buffer under a microscope.

value: Dorsal root ganglia

value: Neurons

value: SD

value: male

tag: numbers of_cells


title: Wildtype biol rep 3

city: East Melbourne

first: Raymond

middle: CB

last: Wong

state: VIC

address: 32 Gisborne St

institute: Centre for Eye Research Australia

description:
100bp
ARPE_WT_3

data_processing:
Salmon v1.8
Salmon v1.8 was used for abundance estimates of transcripts
The Salmon pseudocounts were mapped to the GRCh38 genome assembly using the tximport v1.22.0 package
The gene count matrix was inputted to DESeq2 v1.34.0 for normalisation to make fair gene expression comparisons between samples
Assembly: GrCh38

extract_protocol:
Total RNA of ARPE-19 cell lines was extracted using the Illustra RNAspin Mini Kit (GE Healthcare Life Sciences) according to manufacturer’s instructions
RNA quality was checked by bioanalyzer and the TruSeq Stranded mRNA kit (Illumina) was used to prepare transcriptome libraries according to manufacturer's instructions.

value: retinal pigment epithelial cells

value: wildtype

value: Regular maintenance

tag: time

value: Day 3


title: Wildtype biol rep 2

description:
100bp
ARPE_WT_2

tag: cell type


title: DRG neurons, sc-RNA seq batch 34


title: Female SERTPyramid∆ 1

value: Female

value: SERTPyramid


title: mESC, TKO-preTreatment_noactivated, 1

description:
WGS_LowCov-Bulk_TetiTKO_preTAM-noActivated_r1
Whole Genome Sequencing (WGS) Low Coverage

value: Tet1,2,3 fl/fl; Cre/ERT2; Rosa26-LSL-H2b-Egfp

value: mouse Embryonic Stem Cell

tag: treatment

value: pre-treatment, not activated


title: Female SERTPyramid∆ 2

value: Dorsal hippocampus tissue pooled from four mice


title: DRG neurons, sc-RNA seq batch 32


title: DRG neurons, sc-RNA seq batch 33


title: K562_diMe-Doxo

value: 10 µM diMe-Doxo for 4 hours


title: mESC, Ctrl-tamoxifenTreatment_LongTerm, 3

description:
WGS_LowCov-Bulk_WT-TamoxifenTreated_LongTerm_r3
Whole Genome Sequencing (WGS) Low Coverage

value: Cre/ERT2; Rosa26-LSL-H2b-Egfp

value: tamoxifen treatment, long-term


title: POLDIP2 KO biol rep 3

description:
100bp
ARPE_KO_3

value: POLDIP knockout