title: 20220216_AOberst-20220215-02_21_09

city: Seattle

first: Andrew

last: Oberst

state: WA

address: 750 Republican street

institute: University of Washington

description: Gene Expression CodeSet profiling 254 genes; 248 inflammation-related mouse genes and 6 housekeeping genes.

hyb_protocol: NanoString nCounter XT gene expression assay protocol

data_processing: Data was normalized, quantified, and analyzed using the nSolver software (Nanostring Technologies Inc., Seattle, WA) with default parameters to noramlize data to housekeeping genes.

label: Capture probe-3'biotin, Reporter probe-5' barcode signal

source_name: mouse embryonic fibroblasts

growth_protocol: Cell were grown in complete DMEM medium in 12 well plates.

extract_protocol: Cell were collected in TRIzol reageatnt and total RNA was extracted by phenol-chloroform phase separation followed by RNA precipitation according to the manufacturer's protocol.

treatment_protocol: 5x10^5 cells were collected for each treatment

tag: genotype

value: mutADAR WT

tag: drug

value: Mock


title: leukemia cell-THP1-Bort

status: Public on Aug 10 2022

type: SRA

city: wenzou

first: zhou

last: bin

address: Xuefubei Street, Ouhai District, Wenzhou

country: China

institute: The First Afliated Hospital of Wenzhou Medical University

library_source: transcriptomic

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 the reference genome.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh37
Supplementary_files_format_and_content: counts and FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: leukemia cell

extract_protocol:
cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: blood

tag: cell line

value: THP-1 monocytic leukemia cell line

tag: treatment

value: treated with Bortezomib for 24 hours


title: S3

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

country: USA

institute: University of Wisconsin-Madison

data_processing:
The quality of the sequencing reads was evaluated using FastQC software (version 0.11.7). Read trimming was performed using Trim Galore software (version 0.4.4).
Reads were mapped to the bovine reference genome ARS-UCD1.2 using Hisat2 sofware (version 2.1.0).
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty).
Assembly: Bovine genome assembly: (ARS-UCD1.2)
Supplementary files format and content: Tab-delimited text files including ensembl gene id and number of mapped reads

organism: Bos taurus

source_name: peripheral white blood cells

extract_protocol:
Total RNA was isolated and purified using TRIzol™ LS Reagent. RNA quantiy and quality were determined using Nanodrop One and Agilent Bioanalyzer. All samples had RNA integrity number (RIN) values > 8.
All the RNA-sequencing procedures were performed by Macrogen (Korea). Libraries were sequenced using Illumina’s HiSeq 2000.

value: peripheral white blood cells

tag: breed

value: Holstein

value: pregnant


title: S2


title: 20220216_AOberst-20220215-02_20_08

type: RNA

organism: Mus musculus

label_protocol: NanoString nCounter XT gene expression assay protocol


title: 20220216_AOberst-20220215-02_19_07


title: S1


title: 20220216_AOberst-20220215-01_3_03

value: mutADAR ZBP1ko


title: 20220216_AOberst-20220215-01_1_01


title: 20210827_AOberst-20210826-01_12_12

treatment_protocol: 5x10^5 cells were transfected with siRNA using Dharmafect reagent for 24 hours.

tag: cell type

value: mouse embryonic fibroblasts

tag: sirna

value: siADAR


title: LT-HSC cells, FoxM1flPlus1

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

data_processing:
use STAR V2.7.2b for reads alignment and counts summary
GRCm38 (mm10)
raw counts data were summerized from STAR output ReadsPerGene
Normalization were performed using R package limma 'voom'
Assembly: GRCm38 (mm10)
Supplementary files format and content: normalized data and counts data in .txt format

source_name: CD150+CD48-LSK cells from Foxm1 heterozygous mice

extract_protocol:
orted LT-HSC cells (CD150+CD48-LSK)
Trizol (Invitrogen)
Total RNA was isolated using the AllPrep DNA/RNA Mini Kit (QIAGEN, Cat No. 8020). RNA quality was evaluated using Bioanalyzer (Agilent, Santa Clara, CA). All RNA samples displayed RNA Integrity Number (RIN) >7. RNAseq including cDNA library preparation was processed at the Genomics Core Facility of UCLA. Total RNA in the amount of 100-500μg per sample was depleted of ribosomal RNA using the Ribo-Zero kit (Epicentre, Madison, WI). The directional (first strand) cDNA libraries were prepared following the guide of TruSeq Stranded Total RNA Sample Preparation kit.

tag: strain

value: Bone marrow

value: sorted LT-HSC cells (CD150+CD48-LSK)

value: Foxm1 heterozygous


title: 20210827_AOberst-20210826-01_11_11


title: LT-HSC cells, FoxM1flPlus2


title: LT-HSC cells, FoxM1flPlus3


title: LT-HSC cells, Wild type2

source_name: CD150+CD48-LSK cells from wild type

value: WT


title: 20210827_AOberst-20210826-01_10_10


title: 20210827_AOberst-20210826-01_8_08

value: MLKLko


title: 20210827_AOberst-20210826-01_9_09


title: Experiment group

city: Changsha

first: Wen

last: Meng

state: Outside the United States or Canada

address: The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China.

institute: Central South University

description: library 1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2(version:2.0.4).
Hisat2（version:2.0.4） software used for basecalling.
Stringtie（version:1.3.0 were used to count the number of Fragments for each gene after Hisat2 alignment, and then normalized by TMM (trimmed mean of M values) method. Finally, the FPKM value of each gene was calculated.
Differentially expressed genes were identified using edgeR [8]. The p-value significance threshold in multiple tests was set by the false discovery rate (FDR).
The fold-changes were also estimated according to the FPKM in each sample. The differentially expressed genes were selected using the following filter criteria: FDR ≤0.05 and fold-change ≥2.
Assembly: hg38
Supplementary files format and content: Excel file include FPKM values for each Sample.

source_name: liver

extract_protocol:
Total RNA was extracted using RNAiso Plus Total RNA extraction reagent (#9109, TAKARA)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples were collected and stored at -80˚C until required for further use.

value: liver

value: miRNA-182 KO

value: two-thirds partial hepatectomy (PH)


title: NKT_mm_Thymus_St3_2: Mouse thymus stage 3 iNKT cell sample 2

city: Detroit

first: Indra

last: Adrianto

state: MI

address: 1 Ford Place

department: Public Health Sciences

institute: Henry Ford Health System

description: Stage 3 iNKT cells from mouse thymus (sample 2)

data_processing:
Sequencing read demultiplexing, aligning to the mm10 mouse reference genome, barcode processing, and UMI counting were performed using the 10X Genomics Cell Ranger (v2.0.1) pipeline.
Estimated number of cells captured per sample were between 1,296-3,290 with 34,258-95,264 mean reads per cell, 764-1,892 median genes per cell, and 1,266-6,412 median UMI counts per cell.
A filtered gene-barcode matrix for each sample containing only detected cellular barcodes was generated and subsequently analyzed using the R Seurat package.
Samples have 3 fastq files associated with them with a tag in the filename, namely I1, R1, and R2. The I1 contains the sample index. The R1 contains the 10x barcode (16 base pairs) followed by UMI (10 bp). The R2 contains the transcript reads.
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger filtered gene-barcode matrix outputs of cell barcode, gene name, and UMI count matrix files.

source_name: Thymus

extract_protocol:
Murine thymi were harvested from 5 weeks old C57BL/6 mice or Vα14 transgenic mice. The thymus iNKT cells were enriched by positive selection using biotinylated antibodies against PE. Stage 1(CD24-CD44-NK1.1-), stage 2(CD24-CD44+NK1.1-) and stage 3(CD24-CD44+NK1.1+) were sorted  from 5 weeks C57BL/6 mouse thymus, and Stage 0 iNKT cells (CD24+NK1.1-) were sorted from 5 weeks old Vα14 transgenic mouse thymus through BD FACS AriaII.
Single cell sequencing libraries were generated using the 10X Genomics Chromium Single Cell 3’ Reagent Kit (v2 Chemistry) and Chromium Single Cell Controller. Reverse transcription of the GEM (GEM-RT) was performed in a Thermocycler (Veriti™ 96-Well Fast Thermal Cycler, Applied Biosynthesis; 53 °C 45 min, 85 °C 5 min, 4 °C hold). cDNA amplification was performed after GEM-RT cleanup with Dynabeads MyOne Silane (Thermo Fisher Scientific) with the same Thermocycler (98 °C 3 min; 98 °C 15 sec, 67 °C 20 sec, 72 °C 1 min, repeat 12 cycles; 72 °C 1 min, 4 °C hold). Amplified cDNA is cleaned up with SPRIselect Reagent Kit (Beckman Coulter) and followed by library construction procedure, including fragmentation, end repaired, adaptor ligation, and library amplification. A Bioanalyzer (Agilent) was used for library quality control. Libraries were sequenced on an Illumina HiSeq4000 using paired-end flow cell: Read 1, 26 cycles, i7 index 8 cycles; Read 2: 110 cycles.

value: Thymus

tag: age

value: 5 weeks

value: Invariant natural killer T cells (iNKT) cells


title: Control group

description: library 2


title: 20210827_AOberst-20210826-01_4_04

value: siNT


title: 20220216_AOberst-20220215-01_2_02

value: Mock


title: 20210827_AOberst-20210826-01_7_07


title: 20210827_AOberst-20210826-01_6_06


title: NeuSes3

city: Milano

first: Luca

last: Massimino

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

description:
SES-transduced Cortical neurons; RNA-Seq
Mouse_Normalized_counts.tsv

data_processing:
ChIP-Seq/ATAC-Seq/Cut-n-Tag: Trimming and QC by Trimmomatic. Genome mapping by Bowtie2. Peak calling by MACS3. Coverage analysis by DeepTools.
RNA-Seq: Trimming and QC by Trimmomatic. Genome mapping and gene quantification by STAR. Differential analysis by DESeq2.
Assembly: hg38, mm10
Supplementary files format and content: DESeq2 normalized counts, MACS3 peaks

molecule: polyA RNA

source_name: Cortical neurons

growth_protocol: SNB19 (human glioblastoma cell lines) were cultured in plastic-adherence condition in DMEM medium (Dulbecco’s Modified Eagle’s Medium - high glucose, Sigma-Aldrich) containing 10% fetal bovine serum (FBS, Sigma-Aldrich), 1% Pen/Strept (Sigma-Aldrich), 2mM Glutamine (Sigma-Aldrich), 1% non-essential amino acids (MEM NEAA, ThermoFisher Scientific), 1% sodium pyruvate solution (Sigma-Aldrich) and passaged twice a week using Trypsin-EDTA solution (Sigma-Aldrich). Cortical neurons were coltured Neurobasal medium (Gibco), 2 % B27 (Thermo-fisher), 0.02 % Pen-strep and glutamin, 1.6 Glucose.

extract_protocol:
For RNA-seq RNA was extracted using the TRI Reagent isolation system (Sigma-Aldrich) according to the manufacturer’s instructions.RNA libraries were generated starting from 1 mg of total RNA (deriving from U87, SNB19 and murine hippocampi) which quality was assessed by using a TapeStation instrument (Agilent). ATAC-seq was performed using 50000 cells for each experimental condition (SNB19 infected with SOX2V5 or SESV5), 2 technical replicates each. Briefly, cells were detached, counted, collected, and then washed by performing a centrifuge at 500 rcf for 5’ at 4° in PBS. Subsequently cells were gently lysed by suspending them in 50 ul of ATAC-RSB (Corces et al., 2017) supplemented with 0.1% NP-40, 0.1% Tween-20 and 0.01% digitonin for 5’ on ice. After the lysis cells were washed using 1ml of ATAC-RSB with Tween-20, but no NP-40 or digitonin. Transposition was then performed using Tn5 trasposase and buffer from Illumina (cod. 20034197). for meDiP 1μg of purified genomic DNA (gDNA) was used with qiAMP DNA mini kit (Qiagen, cat. 51304). In brief, for methylated DNA immune precipitation and purification MagMeDIPseq kit was used (Diagenode, cod. C02010040). First, gDNA was sonicated to obtain a fragment size between 150- 300 bp, then, it was de-naturated to ssDNA and immune-precipitated using α-metyl-cytosine antibody provided by the kit. The next day, immunoprecipitated DNA and Input were purified and eluted. Chromatins were isolated from SNB19. Cells were plated in adherent condition using Matrigel coated 15mm plates at a density of 6x10^6 per plate. When the plates reached 90% of confluence, cells were fixed adding formaldehyde directly to the cell culture media to reach a final concentration of 1%, then were incubated for 10 min at RT. The reaction was quenched adding glycine to a final concentration of 125 mM and incubated 5 min at RT. Medium was then removed and cells were washed 3 times with cold, sterile PBS + protease inhibitors, then cells were gently scraped and collected for centrifugation at 4°C for 50 at 1200 rpm. ChIP experiments were performed as previously described (Sessa et al. 2019). Briefly, collected cell pellets were lysed in lysis buffer (50 mM Tris-HCl pH 8, 0.1% SDS, 10 mM EDTA pH 8, 1 mM phenylmethylsulfonyl fluoride (PMSF, Sigma # P7626), protease inhibitor cocktail (Roche #04693159001) and chromatin was sonicated with a Branson D250 sonifier (4 cycles of 30 s, 20% amplitude), to reach an average fragment size of 0.1–0.5 kb. Following quantification, 100 mg of sonicated chromatin were used in each immunoprecipitation and incubated O/N at 4° C with 4 mg of V5 antibody (mouse, 1:5, ThermoFisher Scientific, R96025).
RNA was processed according to the TruSeq Stranded mRNA Library Prep Kit protocol. ChIP-seq libraries were produced using 5 ng of each immunoprecipitated and purified DNA. End  repair of DNA fragments was achieved by sequential 15 min incubations at 12°C and 25°C with 0.15  U/ml T4 PNK (NEB #M0201L), 0.04 U/ml T4 POL (NEB #M0203L) and 0.1 mM dNTPs (NEB  #N0446S). A-base addition was performed by an incubation with 0.25 U/ml of Klenow fragment  (NEB # M0212L) and 167 mM dATP (NEB N0440S) for 30 min at 30°C. Adaptor ligation was  achieved by using the Quick ligation kit (NEB #M2200L) and performing an incubation of 15 min at  25°C. DNA fragments were finally amplified for 14 cycles, by using the PfuUltra II Fusion HS DNA  Pol kit (Agilent #600674). DNA purification steps after each enzymatic reaction were performed  using Agencourt AMPure XP SPRI beads (Beckman #A63882). MeDIP immunoprecipitated DNA and Input were purified and eluted. Library preparation was performed using NEBNext Ultra II kit for Illumina (cod. E7645), following  manufacturer instruction. ATAC-seq DNA After transposition was purified and libraries were amplified for the required amount of cycles  as previously described (Buenrostro et al., 2013).

treatment_protocol: Cells were infected with 10ul of mock (GFP), SOX2-V5 or SES-V5 in 6 well plate. Next day media was changed.

value: Cortical neurons

value: SES-transduced Cortical neurons


title: 20210827_AOberst-20210826-01_3_03

value: mouse embryonic fibroblasts


title: LT-HSC cells, Wild type1


title: NeuSes2


title: NeuSes1


title: NeuMock3

description:
Mock-transduced Cortical neurons; RNA-Seq
Mouse_Normalized_counts.tsv

value: Mock-transduced Cortical neurons


title: 20210827_AOberst-20210826-01_2_02


title: LT-HSC cells, Wild type3

value: Bone marrow


title: 20210827_AOberst-20210826-01_1_01


title: NeuMock2


title: NeuMock1


title: Neu-SES-2

description: SES-transduced Cortical neurons; SES-V5 ChIP-Seq

library_source: genomic

molecule: genomic DNA


title: Neu-SES-3


title: Neu-Input

description: SES-transduced Cortical neurons; Input


title: 20210827_AOberst-20210826-01_5_05


title: ko8-th17

city: Hangzhou

first: Yali

last: Chen

address: 66 Yuhangtang Road

department: School of Medicine

institute: Zhejiang University

description: Th17 cells were collected at 3 days under Th17 differentiation conditions

data_processing:
cDNA library construction and sequencing were performed by Beijing Genomics Institute using Illumina HiSeq platform.
High-quality reads were aligned to the mouse reference genome (GRCm38.p6) using Bowtie2
The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM) using RNA-Seq by Expectation Maximization (RSEM).

source_name: spleen CD4+ T cells

extract_protocol:
Th17 cells were collected at indicated times for RNA extraction, total RNA was extracted with TRIzol reagent.
cDNA library construction and sequencing were performed by Beijing Genomics Institute using Illumina HiSeq platform.

treatment_protocol: Naïve CD4+ T cells from  WT and lncRNA-GM-/- mice differentiated under Th17 polarizing condition for 3 d.

value: Th17 cell

value: lncRNA-GM-/-


title: wt-th17

value: wild type


title: BC2 sgAAVS1 Control BC2_Brunello_sgAAVS1

city: Chicago

first: Eva

middle: Henriette

last: Gottwein

state: IL

address: 320 E Superior St., Tarry building, Room 6-752

department: Microbiology-Immunology

institute: Northwestern University

description: BC2 sgAAVS1 Control

data_processing:
Concatenation of samples (BCBL1 shRNA) repeated on HiSeq4000 and NextSeq500
Adapter trimming with Cutadapt v4.1
Aligned to Brunello library reference guide sequences with Bowtie v1.1.2 9 allowing for 1 up to 1 mismatch per read
Guide-level counts were collected using MAGeCK v0.5.9
Further statistical analysis was performed using MAGeCK v0.5.9 (MAGeCK-RRA)
Assembly: Not Applicable
Supplementary files format and content: Tab-separated values containing guide-level read counts

source_name: BC-2/Cas9 Pool

growth_protocol: RPMI 1640 with L-glutamine (Corning, MT10040CM) supplemented with 10% (BCBL-1) or 20% (BC-2) Serum Plus-II (Sigma-Aldrich, catalog number 14009C, lots 15H243 and 21C421), 10 µg/mL gentamycin (ThermoFisher, 15710064) and 0.05 mM β-mercaptoethanol (Sigma-Aldrich, M3148-25ML).

extract_protocol:
Genomic DNA was extracted from frozen pellets following a salt-precipitation protocol outlined in Manzano et al, Nat Comm 2018.
For HiSeq4000 runs, a two-step PCR protocol was used for the amplification Brunello lentiGuide inserts before adding Illumina adapters and sample barcodes, as as outlined previously (Manzano et al., Nat Comm 2018). For NextSeq 500 runs, a single PCR was performed to simultaneously amplify lentiGuide inserts, add Illumina adapters, and barcode samples.
OTHER: CRISPR guide amplicon sequencing

value: BC-2/Cas9 Pool

value: primary effusion lymphoma


title: BC2 sgCFLIP Depletion BC2_Brunello_sgCFLIP

description: BC2 sgCFLIP Depletion

value: sgCFLIP


title: BCBL1 shM Depletion BCBL1_Brunello_shM-cFLIP_B

description: BCBL1 shM Depletion

source_name: BCBL-1/Cas9 Clone C2

value: BCBL-1/Cas9 Clone C2

value: shM-cFLIP


title: BCBL1 shN Depletion BCBL1_Brunelo_shN-cFLIP_B

description: BCBL1 shN Depletion

value: shN-cFLIP


title: BCBL1 sh1 Control BCBL1_Brunello_sh1-cFLIP_B

description: BCBL1 sh1 Control


title: BCBL1 shRen713 Control BCBL1_Brunello_shRen713_B

description: BCBL1 shRen713 Control


title: BCBL1 shRen308 Control BCBL1_Brunello_shRen308_B

description: BCBL1 shRen308 Control


title: TMAO stimulated HK-2 6 hours rep 4

city: örebro

first: isak

last: demirel

address: campus usö

country: Sweden

institute: örebro University

description: Gene expression after 6 hours of unstimulated human fibroblasts

hyb_protocol: Labelled samples were hybridised onto G4851C SurePrint G3 Human Gene Expression v3 8x60K Microarray glass slides (Agilent)

scan_protocol: Microarrays were scanned with a G2565 CA array laser scanner (Agilent) followed by image analysis and data extraction with Feature Extraction Software version 10.7.3.1 (Agilent).

data_processing: 75th percentile shift normalisation and baseline adjusted

source_name: TMAO stimulated HK-2 6 hours

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the low input quick amp labeling kit,one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The HK-2 cell line was cultured in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine and 1 mM non-essential amino acids (all from Thermo Fisher Scientific, Waltham, MA, USA) at 37 °C in 5% CO2 atmosphere.

extract_protocol: Total RNA was isolated from the HK-2 cells using the E.Z.N.A. Total RNA Kit I. RNA quality and integrity were evaluated using Agilent TapeS  tation 2200 platform (Agilent Technologies, Palo Alto, CA, USA) according to manufacturer in-structions. The RNA integrity number (RIN) was 10 for all RNA samples.

treatment_protocol: HK-2 cells were stimulated with TMAO (300 µM) for 6 h at 37 °C in 5% CO2.

value: human immortalized proximal tubule epithelial cell line HK-2

value: TMAO stimulated


title: Unstimulated HK-2 6 hours rep 4

source_name: Unstimulated HK-2 6 hours


title: TMAO stimulated HK-2 6 hours rep 2


title: TMAO stimulated HK-2 6 hours rep 1


title: Unstimulated HK-2 6 hours rep 3


title: Unstimulated HK-2 6 hours rep 1


title: TMAO stimulated HK-2 6 hours rep 3


title: 200130_Tn_CD8+Tfh_001_005

city: Sapporo

first: Ippei

last: Ikegami

state: Hokkaido

address: S1 W17, Chuo-ku

department: Department of Human Immunology

country: Japan

institute: Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine

description: Gene expression of CD4+CD8+ GC-Tfh in tonsil

hyb_protocol: Cy3-labeled cRNA was hybridized to SurePrint G3 Human 8x60K v3(Agilent Technologies) for 17 hours using Gene Expression Hybridizeation Kit(Agilent Technologies) following the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner using one color scan setting for 8x60k array slides ( Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software v.12.1.1.1 (Agilent Technologies) using default parameters (protocol GE1_1200_Jun14 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Tonsil

label_protocol: cDNA was prepared from 1 ng total RNA using Ovation PicoSL WTA System V2 Regent(NuGEN Technologies) following manufacturer's instruction.  Cyanine-3(Cy3) labeled cRNA was prepared from 2 ug this cDNA using SureTag DNA Labeling Kit(Agilent Technologies) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted with TRIzol reagent (Life Technologies) following the manufacturer's recommendations.  RNA was checked with a 2100 Bioanalyzer (Agilent Technologies) and NanoDrop microvolume spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: Tissues were mechanically disrupted and lymphocytes in single cell suspensions were prepared by density gradient centrifugation with Lymphoprep (Axis-Shield). Then cells were subjected to standard staining with specific surface markers for flow cytometry. Cells were analyzed using FACS Aria II for careful cell sorting (BD Biosciences) in combination with magnet beads (Miltenyi Biotec).

value: CD4+CD8+ Tfh cell

value: Tonsil

tag: gender

value: male


title: 200130_Tn_CD8+Tfh_003_007

value: female


title: PC3_1

city: Sherbrooke

first: Sherif

middle: Abou

last: Elela

state: Québec

address: 3201 Jean Mignault

department: Département de microbiologie et infectiologie

country: Canada

institute: Université de Sherbrooke

data_processing:
Trimming of paired-end reads was performed using Trimmomatic v0.36 (parameters: ILLUMINACLIP:<fastaWithAdaptersEtc>:2:12:10:8, TRAILING:30, LEADING:30, MINLEN:20) in order to remove adapters and low-quality reads.
FastQC v0.11.5 was used before and after trimming to assess the quality of the reads.
Alignment of reads to the reference human genome hg38 (v101) was performed using STAR v2.7.6 (parameters: --runMode alignReads, --outSAMunmapped None, --outSAMtype BAM SortedByCoordinates,   outFilterScoreMinOverLread 0.3, --outFilterMatchNminOverLread 0.3, --outFilterMultimapNmax 100, --winAnchorMultimapNmax 100, --alignEndsProtrude 5 ConcordantPair). The index needed to align reads was generated using STAR v2.7.6 (parameters: --runMode genomeGenerate, --sjdbOverhang 99), the reference human genome hg38 (v101) and the annotation file were obtained from ENSEMBL (v101) and supplemented with missing snoRNAs and tRNAs (available at https://zenodo.org/record/4570182/files/hg38_Ensembl_V101_Scottlab_2020.gtf).
Gene expression normalized in count per million (CPM) and transcript per million (TPM) were obtained using CoCo v0.2.3 (parameters: cc, --countType both, --strand 1 --paired), a software optimizing the quantification of small non-coding RNAs nested in host genes.
Assembly: hg38
Supplementary files format and content: Tab-separated value (.tsv) file containing the gene id, gene name and abundance in each sample (in TPM) for all the genes
Library strategy: TGIRT-seq

extract_protocol:
Total RNA extraction for HCT-116, MCF-7, PC3 and TOV-112D cell lines was performed using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions, using on column DNase digestion with RNase-Free DNase Set (Qiagen). To keep smaller RNA molecules, 1.5 volumes Ethanol 100% were used instead of the 1 volume of ethanol 70% recommended. Agilent 2100 Bioanalyzer was used to assess the quality of the RNA of each sample.
2 ug of DNAse treated RNA was ribodepleted using Ribo-Zero Gold (Illumina), following the manufacturer’s instructions. The resulting rRNA free RNA was purified with RNA Clean and Concentrator (RCC) kit (Zymo Research) using a slightly modified protocol (400 ul ethanol 100% per 50 ul sample) allowing us to retain RNA ≤ 80 nucleotides, followed by a fragmentation for 2-4 min using NebNext Magnesium RNA Fragmentation Module (New England Biolabs). The sample was purified once again with the RCC kit and was then dephosphorylated using T4 Polynucleotide Kinase (Epicentre) followed by an additional purification with the RCC kit. For cDNAs preparation, we used 1 uM TGIRT-III reverse transcriptase (Ingex, LLC) for 15 minutes at 60 °C, which also permits the binding of an Illumina Read 2 sequencing primer DNA complement to the 5’ end of the cDNA. Next, an Illumina Read 1 sequencing adenylated DNA oligonucleotide complement was ligated to the 3’ end of the cDNA using Thermostable 5’ AppDNA / RNA Ligase (New England Biolabs). The resulting product was amplified using a 12 cycle PCR reaction in order to synthesize the second strand and add sequences for Illumina flowcell capture and indexing. A two-round purification step was performed using Ampure XP beads (Beckman-Coulter). The quality of the product was assessed on a 2100 Bioanalyzer (Agilent). The pooled libraries were sequenced on a NextSeq 500 platform (Illumina) (2 x 75 nt) using a NextSeq500 High Output Kit v2.5 (150 cycles) (Illumina). HCT-116, MCF-7, PC3 and TOV-112D were all sequenced in two replicates together multiplexed in one sequencing run.

value: epithelial

value: WT


title: 200130_M_CD8+Tfh_004_004

description: Gene expression of CD4+CD8+ GC-Tfh in lesion of IgG4-RD

source_name: submandibular gland

value: submandibular gland


title: PC3_2


title: 200130_M_CD8+Tfh_002_002


title: TOV112D_1


title: TOV112D_2


title: Unstimulated HK-2 6 hours rep 2


title: MCF7_2


title: MCF7_1


title: HCT116_2

source_name: HCT 116

value: HCT 116


title: 200130_Tn_CD8+Tfh_004_008


title: HCT116_1


title: 180509_Tn_CD8+Tfh_004_008

description: Gene expression of CD4+CD8+ GC-Tfh

data_processing: The scanned images were analyzed with Feature Extraction Software v.11.5.1.1 (Agilent Technologies) using default parameters (protocol GE1_1105_Oct12 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3(Cy3) labeled cRNA was prepared from 100 ng total RNA using the Low Input Quick Amp Labeling Kit(Agilent Technologies) according to the manufacturer's instructions.

value: CD4+CD8+ Tfh cells


title: 200130_Tn_CD8+Tfh_002_006


title: 200130_M_CD8+Tfh_001_001


title: 180509_Tn_CD8+Tfh_003_006

description: Gene expression of CD4+CD8+ GC-Tfh


title: 180509_Tn_CD8-Tfh_004_007

description: Gene expression of CD4+CD8- GC-Tfh

value: CD4+CD8- Tfh cells


title: 200130_M_CD8+Tfh_003_003


title: 180509_Tn_CD8+Tfh_002_004

description: Gene expression of CD4+CD8+ GC-Tfh


title: 180509_Tn_CD8-Tfh_003_005

description: Gene expression of CD4+CD8- GC-Tfh


title: RCC24, Female, Nonprogr

city: Bergen

first: Philipp

last: Strauss

address: Haukeland Universitetssykehus Laboratoriebygget, 7. etg. Heis øst

country: Norway

institute: University of Bergen

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Counts per millions were log transformed and Trimmed mean of M values normalization was applied to adjust for variation in library size.
Tophat (https://ccb.jhu.edu/software/tophat/index.shtml) and Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) were used for assembly of reads and alignment of the contigs to the human genome assembly
Assembly: GRch38
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: renal tissue, FFPE

extract_protocol:
Small RNA sequencing of the 24 samples/libraries was performed using the NEXTflex small RNA-seq kit v3 (Bio Scientific, Austin, TX, USA). The adapter-dimer   reduction   technology   incorporated   into   this   kit   allows   low   input   library preparation. Briefly, 100 ng total RNA, extracted from solid tissues, were used as template for 3' 4N and 5' 4N adenylated adapter ligation, followed by reverse transcription-first strand synthesis. By applying these products as template for second-strand synthesis, double-stranded cDNA was prepared by PCR amplification (22 cycles). Fragments/libraries were run on a Labchip GX   (Caliper/PerkinElmer),   for   quality   control   and   quantitation.   Individual   libraries   were normalized to 25 nM and pooled. The library pool was purified with the QIAquick PC Purification Kit (Qiagen AB, Sweden), according to providers’ instructions. Automated size selection was performed using the Blue Pippin technology (Sage Science, Beverly, MA, USA), with a range of 135-165 bp to select the ~ 152 bp fragment.
Sequencing libraries were generated using the TruSeq RNA library kit (Illumina, San Diego, CA, USA), according to manufacturers’ instructions.

treatment_protocol: Four 10 μm sections per FFPE block were cut for total RNA extraction, which was performed using the miRNeasy FFPE kit (cat no. 217504 ; Qiagen, Venlo, The Netherlands), as previously described    (22, 23) . Total RNA concentration was measured using a Qbit RNA HS assay kit on a Qubit 2.0 fluorimeter (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity was assessed using an Agilent RNA 6000 Nano kit on a 2100 bioanalyser (Agilent Technologies, Santa Clara, CA, USA), and DV200 values (percentage of fragments >200 nucleotides) were calculated. Following RNA extraction, samples were stored at −80°C.

value: renal tissue, FFPE

value: Female

tag: pt

tag: fuhrmann grade

tag: necrosis

value: No

tag: creatinine

tag: leibovich score

tag: analysis group

value: Nonprogr

tag: block (pair id)


title: RCC22, Male, Nonprogr

value: Male


title: RCC21, Male, Nonprogr


title: RCC19, Male, Nonprogr


title: RCC17, Male, Nonprogr


title: RCC18, Female, Nonprogr


title: RCC16, Male, Nonprogr


title: RCC15, Male, Nonprogr


title: 180509_Tn_CD8-Tfh_001_001

description: Gene expression of CD4+CD8- GC-Tfh


title: RCC23, Male, Nonprogr


title: 180509_Tn_CD8+Tfh_001_002

description: Gene expression of CD4+CD8+ GC-Tfh


title: 170203_M_Tfh_004_008

description: Gene expression of IgG4RD-SMG GC-Tfh

data_processing: The scanned images were analyzed with Feature Extraction Software v.10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.


title: 170203_Tn_Tfh_003_003

description: Gene expression of Tonsil GC-Tfh


title: RCC14, Male, Nonprogr


title: 170203_Tn_Tfh_002_002

description: Gene expression of Tonsil GC-Tfh


title: RCC20, Male, Nonprogr


title: BCP rep1

first: Xinran

last: Hou

state: Hunan

address: Xiangya Road 87

data_processing:
Raw reads were processed by FASTX Tool kit (version 0.0.13) to filter out the low-quality reads, as well as sequences with 3' primers, with 5'primer, with poly-A tails, or with insert tags to get clean reads
By confining the length to 18-40 nucleotides, clean reads were mapped to rat referenced genome (Rnor 6.0) by Bowtie (v2.2.3) to obtain different types of small RNA.
Known miRNAs were identified by the length (21-22 nucleotides) and the annotation in miRbase (version: 22.0) and quantified by TPM (Transcripts Per Kilobase of exon model per Million mapped reads), then edgeR was used to identify differentially expressed miRNAs
Assembly: Rnor_6.0
Supplementary files format and content: Matrix table with counts and known maturemiRNA names for every sample and replicate

organism: Rattus norvegicus

source_name: spinal cord

extract_protocol:
The lumbar enlargement spinal cord was quickly isolated out, removed the meninges, and dissected longitudinally on ice; then the ipsilateral spinal cord was snap-frozen and preserved in liquid nitrogen.Total RNA was extracted from the lumbar spinal cord tissue using a RNeasy Mini Kit (Cat# 74106,  Qiagen)  according to manufacturer instructions and the quality was assessed by Agilent 2100 Bioanalyzer (Agilent technologies Santa Clara,US).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Approximately (1-5) ×10^5 living or heat-killed Walker 256 breast cancer cells were implanted into medullary cavity of left tibia

value: spinal cord

value: Wistar

value: 14 days after tumor innoculation

tag: condition

value: Bone cancer pain (BCP)


title: sham rep3

tag: tissue

value: sham


title: RCC12, Male, Nonprogr


title: BCP rep3


title: BCP rep2


title: RCC11, Male, Progr

value: Yes

value: Progr


title: sham rep1


title: 170203_M_Tfh_001_005

description: Gene expression of IgG4RD-SMG GC-Tfh

value: male


title: 170203_Tn_Tfh_004_004

description: Gene expression of Tonsil GC-Tfh

value: Tonsil


title: 170203_M_Tfh_002_006

description: Gene expression of IgG4RD-SMG GC-Tfh

value: submandibular gland

value: female


title: 180509_Tn_CD8-Tfh_002_003

description: Gene expression of CD4+CD8- GC-Tfh

value: CD4+CD8- Tfh cells


title: 170203_M_Tfh_003_007

description: Gene expression of IgG4RD-SMG GC-Tfh


title: sham rep2


title: RCC09, Female, Progr

value: renal tissue, FFPE


title: RCC08, Male, Progr


title: BCBL1 shN Depletion BCBL1_Brunelo_shN_cFLIP_A

description: BCBL1 shN Depletion

tag: cell line

value: BCBL-1/Cas9 Clone C2

value: primary effusion lymphoma

value: shN-cFLIP


title: BCBL1 shM Depletion BCBL1_Brunello_shM_cFLIP_A

description: BCBL1 shM Depletion

tag: treatment

value: shM-cFLIP


title: RCC07, Male, Nonprogr

value: Male

value: No

value: Nonprogr


title: BCBL1 sh1 Control BCBL1_Brunello_sh1_cFLIP_A

description: BCBL1 sh1 Control


title: RCC13, Male, Nonprogr


title: RCC06, Male, Progr


title: BCBL1 shRen713 Control BCBL1_Brunello_shRen713_A

description: BCBL1 shRen713 Control


title: BCBL1 shRen308 Control BCBL1_Brunello_shRen308_A

description: BCBL1 shRen308 Control


title: RCC05, Male, Progr


title: RCC04, Male, Nonprogr


title: BCBL1 sgCFLIP Depletion BCBL1_Brunello_sgCFLIP

description: BCBL1 sgCFLIP Depletion

value: sgCFLIP


title: RCC02, Male, Progr


title: BCBL1 sgAAVS1 Control BCBL1_Brunello_sgAAVS1

description: BCBL1 sgAAVS1 Control


title: RCC10, Female, Nonprogr

value: Female


title: RCC03, Male, Progr


title: RCC01, Female, Progr


title: GSK343+XL413 replicate_2

city: Birmimgham

first: Romi

last: Gupta

state: Alabama

address: 720, 20th street south

institute: University of Alabama at Birmingham

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

source_name: A375 CELLS

growth_protocol: A375 cells were grown in DMEM medium  with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: A375 cells were treated with  either DMSO, CDC7 inhibitor  XL413  (1 micomolar), EZH2 inhibitor GSK343  (1 micomolar) or combination of GSK343  (1 micomolar) and XL413  (1 micomolar)  for 24 hours, cells were harvested and were used to prepare the total RNA to perfrom RNA Seq.


title: GSK343+XL413 replicate_3


title: 170203_Tn_Tfh_001_001

description: Gene expression of Tonsil GC-Tfh


title: JM19 plasma_NSCLC -QiAseq

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

data_processing:
Raw sequences were analysed using the Qiagen Online Data Analysis Center with default settings
Assembly: HG38, miRBase
Supplementary files format and content: normalization performed using the TMM method for each sample

extract_protocol:
Total RNA was extracted from 200 μl of plasma using the automatic nucleic acid extractor Maxwell 48 (Promega, Madison, WI, USA)
preparation of small RNA libraries was performed according to manufacturer’s procedures (QiaSeq miRNA Library kit; Qiagen)

value: plasma

tag: msc status


title: JM21 plasma_Control -QiAseq

tag: cell type


title: JM17 plasma_NSCLC -QiAseq


title: JM18 plasma_Control -QiAseq


title: GSK343 replicate_2


title: GSK343 replicate_1


title: XL413 replicate_3


title: GSK343 replicate_3


title: JM16 plasma_Control -QiAseq


title: XL413 replicate_2


title: JM15 plasma_NSCLC -QiAseq


title: JM14 plasma_Control -QiAseq


title: XL413 replicate_1


title: JM13 plasma_NSCLC -QiAseq


title: DMSO replicate_3

value: DMSO


title: JM12 plasma_Control -QiAseq


title: JM11 plasma_NSCLC -QiAseq


title: DMSO replicate_1


title: JM10 plasma_Control_rep2c -QiAseq


title: OF1+XL413 replicates3

description: OF1+XL413 replicates3 XO3

treatment_protocol: A375 cells were treated with  either DMSO, CDC7 inhibitor  XL413  (1 micomolar),  BRPF1/2/3 inhibitor OF1 (1 micomolar) or combination of XL413  (1 micomolar) and OF1 (1 micomolar) for 24 hours, cells were harvested and were used for preparing the total RNA to perfrom RNA Seq.

value: tumor


title: JM09 plasma_NSCLC_rep2b -QiAseq


title: JM20 plasma_Control -QiAseq


title: OF1+XL413 replicates2

description: OF1+XL413 replicates2 XO2


title: JM08 plasma_Control-rep2a -QiAseq


title: OF1+XL413 replicates1

description: OF1+XL413 replicates1 XO1


title: OF1 replicates3

description: OF1 replicates3 O3


title: OF1 replicates1

description: OF1 replicates1 O1


title: JM07 plasma_NSCLC -QiAseq


title: JM06 plasma_Control_rep1c -QiAseq


title: XL413  replicates2

description: XL413  replicates2 X2


title: JM04 plasma_Control_rep1a -QiAseq


title: XL413  replicates3

description: XL413  replicates3 X3


title: JM05 plasma_NSCLC_rep1b -QiAseq


title: XL413  replicates1

description: XL413  replicates1 X1


title: JM03 plasma_NSCLC -QiAseq


title: DMSO replicate_2


title: JM02 plasma_Control -QiAseq


title: JM01 plasma_NSCLC -QiAseq


title: DMSO  replicates3

description: DMSO  replicates3 D3


title: JM00 plasma_Control -QiAseq


title: JL99 plasma_NSCLC -QiAseq


title: Hypoxia #3

city: Stanford

first: Anastasia

last: Hains

email: hainsa@uchicago.edu, hains@stanford.edu

state: CA

address: 269 Campus Drive

institute: Stanford University

data_processing:
fastq reads were aligned to hg19 reference genome with BWA/0.7.17
Peaks were called by MACS2 for each sample using input as control
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files containing peak positions

source_name: SK-N-BE(2) cell line

growth_protocol: RPMI 1640 with 10% FBS

extract_protocol:
Fixed chromatin was sheared for HIF-1alpha ChIP. ChIPed DNA was reverse-crosslinked and purified for sequencing
Library was prepared with standard Illumina protocol by the University of Chicago Sequencing Core

treatment_protocol: normoxia (21% O2) vs hypoxia (1% O2) for 48 hours

value: SK-N-BE(2) cell line

value: Neuroblastoma

value: 1% oxygen

tag: treatment length

value: 48 hours

tag: antibody


title: Hypoxia #2


title: JM21 plasma_Control-HTG

data_processing:
raw counts were corrected by background subtraction of the maximum value of the five ANT probes. In addition, control miRs were removed and miRs with negative counts after background correction set to 0 for the subsequent normalization performed using the TMM method
Assembly: HG38, miRBase
Supplementary files format and content: normalization performed using the TMM method for each sample

source_name: plasma

extract_protocol: multiplexed nuclease protection assay

tag: disease state

value: control


title: JM20 plasma_Control-HTG

tag: gender


title: OF1 replicates2

description: OF1 replicates2 O2


title: Hypoxia #1


title: JM19 plasma_NSCLC-HTG

value: NSCLC


title: JM18 plasma_Control-HTG


title: Normoxia #3

value: 21% oxygen


title: Normoxia #2


title: JM17 plasma_NSCLC-HTG


title: Normoxia #1


title: JM15 plasma_NSCLC-HTG


title: input #2

value: input


title: JM16 plasma_Control-HTG


title: input #3


title: input #1


title: JM12 plasma_Control-HTG


title: JM13 plasma_NSCLC-HTG


title: MYCN ON 3

data_processing:
Sequence reads aligned to reference genome and transcriptome by Tophat2/Bowtie2
Initial quantification by Cufflinks
Statistical test by Cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing genes and FPKM quantification

source_name: SHEPTET21n cell line

growth_protocol: Human primary erythroblasts were generated by culturing CD34+ early hematopoietic stem and progenitor cells initially isolated from growth factor-mobilized peripheral blood (purchased from ALL Cells, Inc.) using a CliniMacs device. The culture contained 15% fetal bovine serum, 15% human serum, Isocove’s modified Dulbecco’s medium (IMDM), 10 ng/ml interleukin-3, 2 units/ml EPO, and 50 ng/ml SCF. During the initial 8 days of culture, cells were fed on days 3 and 6 by adding equal volumes of fresh culture media supplemented with growth factors. However, no new interleukin-3 was added after the initial addition on day 0, and the amount of SCF added to the fresh media was gradually decreased at each feeding (day 3, 25 ng/ml; day 6, 10 ng/ml; day 8, 2 ng/ml). The amount of EPO added was 2 units/ml during each feeding until d8 of culture. Cells were fed one more time on day 10 of culture by adding equal volumes of fresh media with only EPO (2 units/ml) during this final feeding. Cells were collected at various time points during the culture and stained with benzidine and hematoxylin  and Flow cytometry was done with CD71 and GlyA  to monitor the differentiation program.

extract_protocol:
RNA was extracted by Trizol.
mRNA library was prepared by KAPA mRNA HyperPrep Kit.

treatment_protocol: normoxia (21% O2) vs hypoxia (1% O2)

value: SHEPTET21n cell line

tag: time point

value: Day 4

value: water

tag: genotype

value: WT


title: DMSO  replicates2

description: DMSO  replicates2 D2


title: DMSO  replicates1

description: DMSO  replicates1 D1


title: MYCN ON 2


title: JM11 plasma_NSCLC-HTG


title: MYCN OFF 3

value: 1 mg/mL doxycycline


title: JM09 plasma_NSCLC_rep2b-HTG

value: Female


title: JM10 plasma_Control_rep2c-HTG

value: plasma

value: Male


title: MYCN OFF 2


title: JM14 plasma_Control-HTG


title: JM07 plasma_NSCLC-HTG


title: 72 hour

data_processing:
Library strategy: hMe-SEAL
fastq reads were aligned to hg19 reference genome with BWA/0.7.17
Peaks were called by MACS2 for each sample using input as control
Numbers of reads in each peak quantified by Htseq-count
Counts normalized to FPKM
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files containing peak positions and calculated FPKM value of each peak

source_name: SK-N-BE2 Neuroblastoma cell line

growth_protocol: SK-N-BE(2) neuroblastoma cell line cultured in RPMI with 10% FBS

extract_protocol:
DNA was from cell pellets were sheared to 300bp. 5-hmC was labeled with UDP-6'-azide-glucose by T4 glucosyltransferase, then biotin-S-S-DBCO via Click reaction. 5-hmC containing DNA fragments were then captured using streptavidin beads, washed, released from beads by DTT cleavage of S-S bond, and purified for sequencing
Library was prepared with standard Illumina protocol by the University of Chicago Sequencing Core

value: SK-N-BE2 Neuroblastoma cell line

value: Hour 72


title: JM06 plasma_Control_rep1c-HTG


title: ROP5

first: Yedi

last: Zhou

address: No. 139, Middle Renmin Road

department: Department of Ophthalmology

institute: The Second Xiangya Hospital, Central South University

description: circRNA

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.

source_name: PBMCs

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol.

growth_protocol: PBMCs from treatment-requiring ROP patients and controls

extract_protocol: RNA was isolated from the PBMCs by using Trizol RNA extraction kit

treatment_protocol: Venous blood from each study subject was collected in an Ethylene Diamine Tetraacetic Acid anticoagulant tube in the early morning and sent to the laboratory within 2 h. PBMCs were isolated from the blood by density gradient centrifugation using Ficoll-Paque PLUS (GE Healthcare, NJ, USA). Total RNAs were extracted using TRIzol reagent (Invitrogen, Carlsbad, USA), and the samples were stored at -80℃.

value: PBMCs

value: male

value: ROP patient


title: JM05 plasma_NSCLC_rep1b-HTG


title: MYCN ON 1


title: 48 hour

value: Hour 48

value: 1% oxygen


title: 24 hour

value: Hour 24


title: ROP4

description: circRNA

value: female


title: wound-1

city: Daejeon

first: Hyo-Jun

last: Lee

address: Gwahak-ro

department: Plant Systems Engineering Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Sequencing adapters and low quality bases were trimmed by CLC Genomics Workbench software
High quality reads were mapped to the reference genome by CLC Genomics Workbench software
To quantify the mapped reads on the reference genome, CLC Genomics Workbench software was used
Only genes showing log2 fold change > 1 and P < 0.01 with mean total counts ≥ 100 for heat or wound-treated group were considered as DEGs
Assembly: Niben.genome.v1.0.1.scaffolds.nrcontigs.fasta.gz
Supplementary files format and content: An excel file containing read counts and differentially expressed genes

organism: Nicotiana benthamiana

source_name: Leaves, wound

growth_protocol: Plants were grown in soil for 5 weeks under long-day conditions at light intensity of 100 mmol m-2 s-1

extract_protocol:
Total RNA was extracted using Trizol
Library construction was performed according to the protocol of Seeders, an RNA-sequencing company in South Korea

treatment_protocol: Plants were wounded and then incubated at 23oC for 1 h. For heat, plants were exposed to 37oC for 1 h.

value: Leaves were wounded with scissors and then incubated at 23oC for 1 h

tag: developmental stage

value: 5-week-old plants grown in soil

value: Leaves


title: wound-3


title: wound-2


title: ROP2

description: circRNA


title: ROP3

description: circRNA


title: ROP1

description: circRNA


title: Con4

description: circRNA

value: control


title: Con3

description: circRNA


title: JM08 plasma_Control-rep2a-HTG


title: Con5

description: circRNA


title: JM04 plasma_Control_rep1a-HTG


title: Heat-3

source_name: Leaves, heat

value: Exposed to 37oC for 1 h


title: Heat-2


title: 12 hour

value: Hour 12

value: WT


title: MYCN OFF 1

value: SHEPTET21n cell line

value: Day 4

value: 1 mg/mL doxycycline


title: Con1

description: circRNA

value: PBMCs


title: JM03 plasma_NSCLC-HTG

value: plasma

value: Male

value: NSCLC


title: 6 hour

value: SK-N-BE2 Neuroblastoma cell line

value: Hour 6

value: 1% oxygen


title: Heat-1


title: Con2

description: circRNA

value: female


title: JM02 plasma_Control-HTG


title: 0 hour

value: Hour 0

value: 21% oxygen


title: Mock-2

source_name: Leaves, mock

value: Left at 23oC without wound for 1 h

value: 5-week-old plants grown in soil

value: Leaves


title: Mock-1


title: JM01 plasma_NSCLC-HTG


title: input

value: WT


title: JM00 plasma_Control-HTG

value: control


title: JL99 plasma_NSCLC-HTG


title: stage 4, Treated, Obese, replicate 2

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and hg19 genome with ensemble transcriptome information.
Assembly: hg19
Supplementary files format and content: iPSC_RNAseq.txt: Processed data file contains the raw counts for each gene.

source_name: Induced pluripotent stem cells

extract_protocol:
Total RNA was isolated using MasterPure™ RNA Purification Kit from Epicentre (Cat.#MCR 85102) according to the manufacturer’s instructions from normal and obese (control and palmitate treated) iPSCs from days 0, 6, 13 and 17 of hepatocyte differentiation.
Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7775) using the manufacturer’s instructions.

value: Induced pluripotent stem cells differentiated into hepatocytes

tag: differentiation stage

tag: differentiation days

value: palmitate

tag: donor weight

value: obese

tag: replicate


title: JM20 plasma_Control MiRCURY

data_processing: text files were downloaded from the QuantStudio 12K Flex and were imported in R as data tables. Expression matrices in qPCRset format were created for every dataset using the HTqPCR R package

label: SYBR Green

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (miRCURY LNA miRNome PCR Panels (miRCURY) (Qiagen)).

extract_protocol: Total RNA was extracted from 200 μl of plasma using the automatic nucleic acid extractor Maxwell 48 (Promega, Madison, WI, USA)

value: Female

value: heathy


title: JM21 plasma_Control MiRCURY

value: Male


title: stage 4, Treated, Obese, replicate 1


title: Mock-3


title: JM19 plasma_NSCLC MiRCURY

value: NSCLC


title: JM15 plasma_NSCLC MiRCURY


title: JM16 plasma_Control MiRCURY


title: 375-2

city: Boston

first: Mark

last: Feinberg

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's

description:
mRNA from whole-cell lysate
miR-375 Mimic Sample 2

data_processing:
All samples were processed using an RNA-seq pipeline implemented by Genewiz (South Plainfield, NJ).
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 Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
BAM files were generated as a result
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GRCh38

source_name: HUVECs

extract_protocol:
Total RNA was extracted with QIAzol reagent and miRNeasy micro kit (Qiagen)
RNA-Seq analysis was performed with polyA selection and standard library construction using Illumina HiSeq2500 V4 2x100 PE  (Genewiz, South Plainfield, NJ).

treatment_protocol: Treated with 50nM miRNA-375 mimics for 48 hours

value: Endothelial Cell

tag: cell isolated from tissue

value: primary


title: JM13 plasma_NSCLC MiRCURY


title: 375-4

description:
mRNA from whole-cell lysate
miR-375 Mimic Sample 4

value: Treated with 50nM miRNA-375 mimics for 48 hours


title: JM14 plasma_Control MiRCURY


title: 375-5

description:
mRNA from whole-cell lysate
miR-375 Mimic Sample 5


title: stage 4, Treated, normal, replicate 2

value: normal


title: 375-3

description:
mRNA from whole-cell lysate
miR-375 Mimic Sample 3


title: stage 4, Treated, normal, replicate 1


title: 375-1

description:
mRNA from whole-cell lysate
miR-375 Mimic Sample 1


title: NS-5

description:
mRNA from whole-cell lysate
Non-Specific Mimic Sample 5

value: Treated with 50nM non-specific miRNA mimics for 48 hours


title: JM12 plasma_Control MiRCURY


title: JM10 plasma_Control_rep2c MiRCURY


title: JM09 plasma_NSCLC_rep2b MiRCURY


title: JM11 plasma_NSCLC MiRCURY


title: JM17 plasma_NSCLC MiRCURY


title: NS-4

description:
mRNA from whole-cell lysate
Non-Specific Mimic Sample 4


title: stage 4, control, Obese, replicate 2


title: stage 4, control, Obese, replicate 1


title: JM18 plasma_Control MiRCURY


title: JM07 plasma_NSCLC MiRCURY


title: JM08 plasma_Control-rep2a MiRCURY


title: NS-3

description:
mRNA from whole-cell lysate
Non-Specific Mimic Sample 3


title: JM06 plasma_Control_rep1c MiRCURY


title: NS-2

description:
mRNA from whole-cell lysate
Non-Specific Mimic Sample 2


title: JM05 plasma_NSCLC_rep1b MiRCURY


title: stage 4, control, normal, replicate 2


title: GSK343+XL413 replicate_1


title: stage 3, Treated, Obese, replicate 2


title: stage 4, control, normal, replicate 1


title: NS-1

description:
mRNA from whole-cell lysate
Non-Specific Mimic Sample 1


title: JM03 plasma_NSCLC MiRCURY


title: JM04 plasma_Control_rep1a MiRCURY


title: JM01 plasma_NSCLC MiRCURY


title: JM02 plasma_Control MiRCURY


title: stage 3, Treated, Obese, replicate 1


title: SKOV3 cells, ILUC, 96 hours SN96_3

city: Pittsburgh

first: Santiago

last: Panesso

address: 204 Craft Ave B330

department: Obstetrics and Gynecology

institute: Magee Womens Research Institute

description: SKOV3 cells, ILUC, 96 hours

data_processing:
CASAVA base recognition
aw image data file from high-throughput sequencing(like Illumina ) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit (Qiagen, 217004) according to the manufacture’s guidelines
RNA quality was determined using Bioanalyser chip and RNA Integrity Number (RIN) >7 was deemed acceptable. Novogene Bioinformatics Technology Co., Ltd., (Beijing, China) constructed 250-300 bp insert polyA selected cDNA library and ran the sequencing on the NextSeq platform (Illumina) according to 150 bp paired-ends protocol.

value: Ovarian Cancer Cells

value: Quiescent Cells Differentitation

tag: time

value: 96 hours


title: JL99 plasma_NSCLC MiRCURY


title: JM00 plasma_Control MiRCURY


title: SKOV3 cells, ILUC, 96 hours SN96_2

description: SKOV3 cells, ILUC, 96 hours

tag: cell line


title: stage 3, Treated, normal, replicate 2

tag: treatment


title: SKOV3 cells, ILUC, 96 hours SN96_1

description: SKOV3 cells, ILUC, 96 hours


title: Oocyte Type 3 rep 2

city: East Lansing

first: Peter

last: Schall

address: 474 S. Shaw Lane

department: CMIB ANS

institute: Michigan State University

data_processing:
Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1
Trimming was conducted utilizing TrimGalore with the following parameters: minimum quality threshold of 20, minimum length of 20 basepairs, removal of Ns from ends of reads, and a hard trim of the first 5 basepairs.
The cow cDNA genome (ARS-UCD1.20, build 102) was downloaded from Ensembl and indexed and transcript abundance quantified with Kallisto (v0.44.0), using standard settings.
Genome_build: ARS-UCD1.20
Supplementary_files_format_and_content: tab-delimited Kallisto output files for each sample

source_name: Oocyte

extract_protocol:
A subset of ovulatory-size (≥10 mm) follicles (5-15/heifer) were individually dissected from pairs of ovaries. Individual follicles were aspirated, the COCs recovered and the remaining follicular fluid used for measurement of progesterone, estradiol and oxytocin. The cumulus cells were removed from the oocyte, whilst granulosa cells were recovered from the follicle wall. Based on the morphology of the COC (compact or expanded) and the ratio of estradiol:progesterone (E:P) in follicular fluid (estrogen-active (EA) E:P≥1, or estrogen-inactive (EI) E:P < 1), follicles were classified into four types. Type 1 follicles (control group) were those from cattle that receive the industry standard dose (70 IU) of cpFSH, contained a compact COC and were EA. Types 2-4 were the follicular phenotypes chosen from heifers that received the excessive (210 IU) dose of cpFSH, the characteristics of which are as follows: Type 2 follicles contained compact COC and were EA, Type 3 follicles contained expanded follicles and were EA, and Type 4 follicles contained expanded COC and were EI (described in SAMPLES section). One follicle, per follicle type, per heifer was randomly selected and total RNA was isolated from the oocyte, a cumulus cell and a granulosa cell sample from follicles using the PicoPure™ RNA Isolation Kit with a DNase digestion step included.
The Ovation® SoLo RNA-Seq System kit with Bovine AnyDeplete primers (TECAN) was used to prepare RNAseq libraries for the oocyte. The Universal RNA-Seq with NuQuant kit including Bovine AnyDeplete primers (TECAN) was used to prepare the cumulus and granulosa cell libraries.

treatment_protocol: SOR heifers (11-12mo) were treated with either 70 IU (40 mg, n = 7 heifers) or 210 IU (120 mg, n = 6) cpFSH (Folltropin-V, Lot# 499213, Vetoquinol USA Inc) per injection. SOR heifers were synchronized with two prostaglandin F2α injections ten days apart and a third PG injection 12 h later. At the time of ovulation or emergence of the first follicular wave (~36 h after the last PG injection), animals received either a standard, 70 IU, or excessive, 210 IU, cpFSH twice daily for four days. Instead of an ovulatory dose of human chorionic gonadotropin (hCG) standard for this superovulation protocol,  the ovaries were recovered 12 h after the final cpFSH injection for follicle extraction.

value: Oocyte

value: FSH dose 210 IU

tag: sample group

value: Type 3, Expanded, E/P>1.0


title: Oocyte Type 1 rep 3

tag: cell type

value: FSH dose 70 IU

value: Type 1, Compact, E/P>1.0


title: Oocyte Type 1 rep 2


title: stage 3, Treated, normal, replicate 1

value: Induced pluripotent stem cells differentiated into hepatocytes

value: palmitate


title: Oocyte Type 2 rep 2

value: Type 2, Compact, E/P>1.0


title: Oocyte Type 2 rep 1


title: Oocyte Type 3 rep 1


title: stage 3, control, Obese, replicate 2

value: control

value: obese


title: Oocyte Type 1 rep 1


title: SKOV3 cells, ILUC, 48 hours SN48_2

description: SKOV3 cells, ILUC, 48 hours

value: 48 hours


title: Granulosa cell Type 4 rep 4

source_name: Granulosa Cell

value: Granulosa Cell

value: Type 4, Expanded, E/P<0.1


title: Oocyte Type 4 rep 1


title: SKOV3 cells, ILUC, 48 hours SN48_1

description: SKOV3 cells, ILUC, 48 hours


title: stage 3, control, Obese, replicate 1


title: Granulosa cell Type 3 rep 6


title: stage 3, control, normal, replicate 2

value: normal


title: Granulosa cell Type 2 rep 6


title: Granulosa cell Type 3 rep 5


title: stage 3, control, normal, replicate 1


title: SKOV3 cells, ILUC, 24 hours SN24_3

description: SKOV3 cells, ILUC, 24 hours

value: Ovarian Cancer Cells

value: 24 hours


title: Oocyte Type 4 rep 2


title: SKOV3 cells, ILUC, 24 hours SN24_2

description: SKOV3 cells, ILUC, 24 hours

value: Quiescent Cells Differentitation


title: Granulosa cell Type 2 rep 4


title: Granulosa cell Type 3 rep 4


title: SKOV3 cells, ILUC, 48 hours SN48_3

description: SKOV3 cells, ILUC, 48 hours


title: SKOV3 cells, ILUC, 24 hours SN24_1

description: SKOV3 cells, ILUC, 24 hours


title: stage 2, Treated, Obese, replicate 1


title: SKOV3 cells, IcNFATc4 , 96 hours SL96_3

description: SKOV3 cells, IcNFATc4 , 96 hours

value: ILUC

value: 96 hours


title: stage 2, Treated, normal, replicate 2


title: Granulosa cell Type 4 rep 3

value: FSH dose 210 IU


title: Granulosa cell Type 2 rep 3


title: Granulosa cell Type 3 rep 3

value: Type 3, Expanded, E/P>1.0


title: Granulosa cell Type 4 rep 2


title: SKOV3 cells, IcNFATc4 , 96 hours SL96_2

description: SKOV3 cells, IcNFATc4 , 96 hours


title: stage 2, control, Obese, replicate 2


title: SKOV3 cells, IcNFATc4 , 96 hours SL96_1

description: SKOV3 cells, IcNFATc4 , 96 hours


title: Granulosa cell Type 4 rep 1


title: stage 2, Treated, normal, replicate 1


title: Granulosa cell Type 2 rep 2


title: stage 2, Treated, Obese, replicate 2


title: Granulosa cell Type 2 rep 5


title: SKOV3 cells, IcNFATc4 , 48 hours SL48_3

description: SKOV3 cells, IcNFATc4 , 48 hours


title: Granulosa cell Type 1 rep 7

value: FSH dose 70 IU

value: Type 1, Compact, E/P>1.0


title: stage 2, control, Obese, replicate 1

value: Induced pluripotent stem cells differentiated into hepatocytes


title: SKOV3 cells, IcNFATc4 , 48 hours SL48_2

description: SKOV3 cells, IcNFATc4 , 48 hours


title: Granulosa cell Type 1 rep 5


title: stage 2, control, normal, replicate 2


title: Granulosa cell Type 1 rep 4


title: SKOV3 cells, IcNFATc4 , 24 hours SL24_3

description: SKOV3 cells, IcNFATc4 , 24 hours


title: Granulosa cell Type 1 rep 1


title: Granulosa cell Type 1 rep 2


title: stage 2, control, normal, replicate 1


title: Granulosa cell Type 1 rep 3


title: stage 1, Treated, Obese, replicate 2

value: palmitate


title: Cumulus cell Type 4 rep 4

source_name: Cumulus Cell

value: Cumulus Cell


title: SKOV3 cells, IcNFATc4 , 24 hours SL24_2

description: SKOV3 cells, IcNFATc4 , 24 hours


title: stage 1, Treated, Obese, replicate 1

value: obese


title: Granulosa cell Type 2 rep 1

value: Type 2, Compact, E/P>1.0


title: Granulosa cell Type 3 rep 2

value: Granulosa Cell


title: stage 1, Treated, normal, replicate 2


title: Granulosa cell Type 1 rep 6


title: SKOV3 cells, IcNFATc4 , 24 hours SL24_1

description: SKOV3 cells, IcNFATc4 , 24 hours


title: Cumulus cell Type 3 rep 5


title: HEY1 cells, IcNFATc4 , 96 hours HP96_3

description: HEY1 cells, IcNFATc4 , 96 hours


title: stage 1, Treated, normal, replicate 1


title: SKOV3 cells, IcNFATc4 , 48 hours SL48_1

description: SKOV3 cells, IcNFATc4 , 48 hours

value: 48 hours


title: Cumulus cell Type 3 rep 4


title: Cumulus cell Type 2 rep 4


title: stage 1, control, Obese, replicate 2

value: control


title: Cumulus cell Type 3 rep 6


title: Cumulus cell Type 4 rep 3

value: Type 4, Expanded, E/P<0.1


title: HEY1 cells, IcNFATc4 , 96 hours HP96_2

description: HEY1 cells, IcNFATc4 , 96 hours

value: Ovarian Cancer Cells


title: Cumulus cell Type 3 rep 3


title: HEY1 cells, IcNFATc4 , 96 hours HP96_1

description: HEY1 cells, IcNFATc4 , 96 hours

value: Quiescent Cells Differentitation


title: stage 1, control, Obese, replicate 1


title: Cumulus cell Type 2 rep 3


title: Cumulus cell Type 3 rep 2


title: Cumulus cell Type 4 rep 2


title: stage 1, control, normal, replicate 2

value: normal


title: HEY1 cells, IcNFATc4 , 48 hours HP48_3

description: HEY1 cells, IcNFATc4 , 48 hours


title: HEY1 cells, IcNFATc4 , 48 hours HP48_2

description: HEY1 cells, IcNFATc4 , 48 hours


title: Cumulus cell Type 2 rep 2


title: Cumulus cell Type 4 rep 1


title: Cumulus cell Type 2 rep 5


title: Cumulus cell Type 2 rep 6


title: stage 1, control, normal, replicate 1


title: HEY1 cells, IcNFATc4 , 24 hours HP24_2

description: HEY1 cells, IcNFATc4 , 24 hours

value: 24 hours


title: Cumulus cell Type 1 rep 4


title: Cumulus cell Type 1 rep 1


title: HEY1 cells, IcNFATc4 , 48 hours HP48_1

description: HEY1 cells, IcNFATc4 , 48 hours


title: Cumulus cell Type 2 rep 1

value: FSH dose 210 IU


title: HEY1 cells, IcNFATc4 , 24 hours HP24_3

description: HEY1 cells, IcNFATc4 , 24 hours


title: Cumulus cell Type 3 rep 1

value: Type 3, Expanded, E/P>1.0


title: Low concentration rep 1

city: Ithaca

first: Chieh-Ren

last: Hsia

state: New York (NY)

address: 526 Campus Road

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
Adapter sequences were removed using fastp v0.20.0
reads were aligned to the hg38 genome assembly using bowtie2 v2.4.3
pileup signal tracks were generated using deepTools bamCoverage v3.5.0
alignment files were merged using samtools merge v1.1
peaks were called using macs2 v2.2.7.1
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files of raw pileup signal for each sample, bigWig files of merged raw signal for each collagen concentration, and narrowPeak file of peaks called on all replicates and conditions using macs2

source_name: fibrosarcoma cell

growth_protocol: To generate single cell-containing collagen matrices at specified collagen concentrations (low: 0.3 mg/mL; medium: 1.0 mg/mL; high: 1.7 mg/mL), acidic solution of rat tail type-I collagen (Corning) was supplemented with complete DMEM (Gibco, with 10% FBS and pen/strep) and NaOH to reach a neutral pH of 7.4, and then mixed with cell suspension to reach a final density of 100,000 cells per mL, and a volume of 800 μL per dish. Cells were incubated in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Single cell-containing collagen was carefully collected by pipette tip into microcentrifuge tubes, and an equal volume of 5,000 U (μmol/min) collagenase type 7 (Worthington) dissolved in DPBS (Gibco) was added into each tube for incubation for 15 minutes at 37°C. After digestion, cells were spun down at 4°C, and then resuspended into freezing media (10% DMSO, 20% FBS, and 70% culture media) for freeze-down.
Viable frozen cells were thawed rapidly at 37°C, and then slowly diluted using DMEM supplemented with 10% FBS until the diluted volume reached at least 10-fold of the initial volume. If needed, samples were concentrated by centrifuging at 500 RCF for 5 minutes, followed by removal of supernatant. Omni-ATAC protocol (Corces, M. R. et al., Nature Methods, 2017) was followed, with the following modifications: a cell count of up to 25,000 per sample was used, and cells were washed twice in ATAC-RSB (resuspension buffer) containing 0.1% Tween-20 prior to lysis and transposition. A reaction volume of 25 μL was used for transposition. After the transposition, half of the reaction product was amplified by PCR using a total of 11 cycles without qPCR testing, followed by SPRIselect bead (Beckman Coulter) clean-up (2:1 bead ratio). All the buffers (RSB-Tween, lysis buffer, and TD buffer) were made fresh before use. After the library preparation, samples were quantified by a Qubit (Thermo Fisher) and the size distribution was determined by a Fragment Analyzer (Agilent). If necessary, a digital PCR assay (Bio-Rad QX200) was used to accurately quantify the sequenceable molarity. The libraries were then sequenced on an Illumina HiSeqX at Novogene with 2x150 paired-end reads.
ATAC-seq. Omni-ATAC (Corces, M. R. et al., Nature Methods, 2017)

treatment_protocol: Cells were treated with a broad matrix metalloproteinases (MMP) inhibitor, GM6001 (Millipore, 20 μM). Fresh media was changed every 24 hours.

value: MMP inhibitor GM6001 (Millipore, 20 μM)

tag: collagen matrix concentration

value: 0.3 mg/mL of rat tail type-I collagen (Corning)


title: Low concentration rep 4


title: Low concentration rep 3


title: Low concentration rep 2


title: Cumulus cell Type 1 rep 6

value: FSH dose 70 IU

value: Type 1, Compact, E/P>1.0


title: Cumulus cell Type 1 rep 5

value: Cumulus Cell


title: Cumulus cell Type 1 rep 3


title: HEY1 cells, ILUC, 96 hours HN96_3

description: HEY1 cells, ILUC, 96 hours

value: ILUC

value: 96 hours


title: HEY1 cells, ILUC, 96 hours HN96_2

description: HEY1 cells, ILUC, 96 hours


title: Medium concentration rep 4

value: 1.0 mg/mL of rat tail type-I collagen (Corning)


title: Oocyte Type 1 rep 5

value: Oocyte


title: Oocyte Type 4 rep 4


title: Oocyte Type 4 rep 3


title: HEY1 cells, ILUC, 96 hours HN96_1

description: HEY1 cells, ILUC, 96 hours


title: Oocyte Type 3 rep 6


title: Medium concentration rep 2


title: HEY1 cells, IcNFATc4 , 24 hours HP24_1

description: HEY1 cells, IcNFATc4 , 24 hours


title: Cumulus cell Type 1 rep 2


title: Oocyte Type 3 rep 5


title: HEY1 cells, ILUC, 48 hours HN48_2

description: HEY1 cells, ILUC, 48 hours

value: 48 hours


title: Medium concentration rep 1


title: Oocyte Type 3 rep 4


title: Oocyte Type 3 rep 3


title: HEY1 cells, ILUC, 48 hours HN48_3

description: HEY1 cells, ILUC, 48 hours


title: Medium concentration rep 3


title: High concentration rep 3

value: 1.7 mg/mL of rat tail type-I collagen (Corning)


title: Oocyte Type 2 rep 3

value: Type 2, Compact, E/P>1.0


title: Oocyte Type 1 rep 4


title: HEY1 cells, ILUC, 24 hours HN24_2

description: HEY1 cells, ILUC, 24 hours

value: Ovarian Cancer Cells

value: Quiescent Cells Differentitation


title: High concentration rep 4


title: HEY1 cells, ILUC, 48 hours HN48_1

description: HEY1 cells, ILUC, 48 hours


title: HEY1 cells, ILUC, 24 hours HN24_3

description: HEY1 cells, ILUC, 24 hours

value: 24 hours


title: mouse fibroblast cells, control, rep3

city: Wuhan

first: Junjie

last: Zhang

state: Hubei

address: Donghu Road, No. 115

department: Medical Research Institute

institute: Wuhan University

description:
NC3_1
L929-control-3

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)
he clean reads in FASTQ format were mapped to the reference genome using HISAT2(v2.0.4)
Bowtie2 (v2.2.5) was used to align the clean reads to the reference coding gene set
the gene expression level was calculated by RSEM (v1.2.12)
Differential expression analysis was performed using DESeq2(v1.4.5)
Assembly: NCBI genome build number (GRCm38 (mm10) ) were used for alignment
Supplementary files format and content: normalized abundance measurements, output from DESeq2

extract_protocol:
total RNA was isolated with TRIzol reagent (#9109, Takara) according to the manufacturer’s instructions
Oligo(dT)-attached magnetic beads were used to purified mRNA. Sequencing library was constructed based on standard protocol

value: mouse fibroblast cells

value: WT


title: mouse fibroblast cells, STING KO, rep1

description:
KO1_1
L929-STING KO-1

value: STING KO


title: mouse fibroblast cells, STING KO, rep3

description:
KO3_1
L929-STING KO-3


title: mouse fibroblast cells, control, rep1

description:
NC1_1
L929-control-1


title: mouse fibroblast cells, STING KO, rep2

description:
KO2_1
L929-STING KO-2


title: mouse fibroblast cells, control, rep2

description:
NC2_1
L929-control-2


title: High concentration rep 1

value: MMP inhibitor GM6001 (Millipore, 20 μM)


title: BC-1 (ATCC CRL-2230)

first: Eva

last: Gottwein

address: 320 E Superior St., Tarry building, Room 6-752

data_processing:
Un-trimmed reads were aligned to the Gencode 41 annotation of GRCh38.p13 with STAR
Assembly: GRCh38.p13
Supplementary files format and content: Tab-separated values containing gene-level read counts

growth_protocol: RPMI 1640 with L-glutamine (Corning, MT10040CM) supplemented with 10% Serum Plus-II (Sigma-Aldrich, catalog number 14009C, lots 15H243 and 21C421), 10 µg/mL gentamycin (ThermoFisher, 15710064) and 0.05 mM β-mercaptoethanol (Sigma-Aldrich, M3148-25ML).

extract_protocol: Pelleted cells were resuspended and frozen in Trizol reagent

value: primary effusion lymphoma


title: High concentration rep 2


title: HEY1 cells, ILUC, 24 hours HN24_1

description: HEY1 cells, ILUC, 24 hours


title: ATAC_seq_PS_6

city: Shanghai

first: Jiali

last: Hu

address: No.419, Fangxie Road

institute: Obstetrics and Gynecology Hospital of Fudan University

data_processing:
The reads were mapped to human genome (hg38) by hisat2 and peaks were called by MACS3.
Assembly: Human (hg38)
Supplementary files format and content: Tab-delimited text files include raw peaks counts for each Sample.

source_name: endometrium lesion

extract_protocol:
Frozen tissue was digested and grinded by trypsin and washed three times in PBS. Then the broken tissue was centrifuged and resuspended in lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40) for 10 minutes. Next, the cells after lysis were centrifuged at 500 g at 4°C for 5 minutes. Carefully discarded the supernatant and the sediment were nuclei. Nuclei were counted after addition of trypan blue, which stains all nuclei due to membrane permeabilization from freezing. 50,000 counted nuclei were then transferred to a tube containing 1 ml of ATAC-seq RSB with 0.1% Tween-20. Nuclei were pelleted by centrifugation at 500r.c.f. for 10 min in a pre-chilled (4°C) fixed-angle centrifuge. Supernatant was removed using the two pipetting steps described above. Because the nuclei were already permeabilized, no lysis step was performed, and the transposition mix (25μl 2× TD buffer, 2.5μl transposase (100nM final), 16.5μl PBS, 0.5μl 1% digitonin, 0.5μl 10% Tween-20, 5μl water) was added directly to the nuclear pellet and mixed by pipetting up and down six times. Transposition reactions were incubated at 37°C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Polymerase chain reaction amplification and size selection (150-500 bp) were performed using Agencourt AMPure XP (Beckman Coulter) and Bioanalyzer 2100 (Agilent).
The library concentration and quality were assayed using the 2100/2200 Bioanalyzer (Agilent) prior to sequencing. Libraries were pooled at equimolar ratios with barcodes and sequenced on the BGISEQ-500 platform (BGI, Shenzhen, China).

tag: tissue

value: endometrium lesion

tag: diagnosis

value: endometrial atypical hyperplasia

tag: phenotype

value: progestin sensitivity

tag: age


title: ATAC_seq_PS_5


title: ATAC_seq_PS_4


title: L24_3: 24 hours after cold treatment sample3

city: Shenyang

first: Xiaoyu

last: Duan

address: Dongling street 120

institute: Shenyang Agricultrual University

description: 24 hours after cold treatment sample3

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Cucumis sativus.Cucumber (Chinese Long) v3
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Cucumis sativus

source_name: leaves

growth_protocol: The cucumber seeding were cultivated in a phytotron.when they werer three ture leaves, the plnat was subjected to cold stress and the cucumber leaves were sampled.

extract_protocol:
The samples of cucumber leaves under cold stress were collected and frozen in liquid nitrogen. The tatal RNA was extracted using Trizol reagent and checked its integrity. The qualified RNA was used to construct cDNA libraries.
cDNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When cucumber seedlings had three true leaves, they were subjected to cold stress at 15/6 ℃ and 12 h/12 h day and night for 24 h.

value: leaves

value: 24 hours after cold treatment


title: RNA_SES3

city: Milano

first: Luca

last: Massimino

address: Via Olgettina, 58

institute: Ospedale San Raffaele

description:
SES-transduced SNB19; RNA-Seq
Human_Normalized_counts.tsv

data_processing:
ChIP-Seq/ATAC-Seq/Cut-n-Tag: Trimming and QC by Trimmomatic. Genome mapping by Bowtie2. Peak calling by MACS3. Coverage analysis by DeepTools.
RNA-Seq: Trimming and QC by Trimmomatic. Genome mapping and gene quantification by STAR. Differential analysis by DESeq2.
Assembly: hg38, mm10
Supplementary files format and content: DESeq2 normalized counts, MACS3 peaks

extract_protocol:
For RNA-seq RNA was extracted using the TRI Reagent isolation system (Sigma-Aldrich) according to the manufacturer’s instructions.RNA libraries were generated starting from 1 mg of total RNA (deriving from U87, SNB19 and murine hippocampi) which quality was assessed by using a TapeStation instrument (Agilent). ATAC-seq was performed using 50000 cells for each experimental condition (SNB19 infected with SOX2V5 or SESV5), 2 technical replicates each. Briefly, cells were detached, counted, collected, and then washed by performing a centrifuge at 500 rcf for 5’ at 4° in PBS. Subsequently cells were gently lysed by suspending them in 50 ul of ATAC-RSB (Corces et al., 2017) supplemented with 0.1% NP-40, 0.1% Tween-20 and 0.01% digitonin for 5’ on ice. After the lysis cells were washed using 1ml of ATAC-RSB with Tween-20, but no NP-40 or digitonin. Transposition was then performed using Tn5 trasposase and buffer from Illumina (cod. 20034197). for meDiP 1μg of purified genomic DNA (gDNA) was used with qiAMP DNA mini kit (Qiagen, cat. 51304). In brief, for methylated DNA immune precipitation and purification MagMeDIPseq kit was used (Diagenode, cod. C02010040). First, gDNA was sonicated to obtain a fragment size between 150- 300 bp, then, it was de-naturated to ssDNA and immune-precipitated using α-metyl-cytosine antibody provided by the kit. The next day, immunoprecipitated DNA and Input were purified and eluted. Chromatins were isolated from SNB19. Cells were plated in adherent condition using Matrigel coated 15mm plates at a density of 6x10^6 per plate. When the plates reached 90% of confluence, cells were fixed adding formaldehyde directly to the cell culture media to reach a final concentration of 1%, then were incubated for 10 min at RT. The reaction was quenched adding glycine to a final concentration of 125 mM and incubated 5 min at RT. Medium was then removed and cells were washed 3 times with cold, sterile PBS + protease inhibitors, then cells were gently scraped and collected for centrifugation at 4°C for 50 at 1200 rpm. ChIP experiments were performed as previously described (Sessa et al. 2019). Briefly, collected cell pellets were lysed in lysis buffer (50 mM Tris-HCl pH 8, 0.1% SDS, 10 mM EDTA pH 8, 1 mM phenylmethylsulfonyl fluoride (PMSF, Sigma # P7626), protease inhibitor cocktail (Roche #04693159001) and chromatin was sonicated with a Branson D250 sonifier (4 cycles of 30 s, 20% amplitude), to reach an average fragment size of 0.1–0.5 kb. Following quantification, 100 mg of sonicated chromatin were used in each immunoprecipitation and incubated O/N at 4° C with 4 mg of V5 antibody (mouse, 1:5, ThermoFisher Scientific, R96025).
RNA was processed according to the TruSeq Stranded mRNA Library Prep Kit protocol. ChIP-seq libraries were produced using 5 ng of each immunoprecipitated and purified DNA. End  repair of DNA fragments was achieved by sequential 15 min incubations at 12°C and 25°C with 0.15  U/ml T4 PNK (NEB #M0201L), 0.04 U/ml T4 POL (NEB #M0203L) and 0.1 mM dNTPs (NEB  #N0446S). A-base addition was performed by an incubation with 0.25 U/ml of Klenow fragment  (NEB # M0212L) and 167 mM dATP (NEB N0440S) for 30 min at 30°C. Adaptor ligation was  achieved by using the Quick ligation kit (NEB #M2200L) and performing an incubation of 15 min at  25°C. DNA fragments were finally amplified for 14 cycles, by using the PfuUltra II Fusion HS DNA  Pol kit (Agilent #600674). DNA purification steps after each enzymatic reaction were performed  using Agencourt AMPure XP SPRI beads (Beckman #A63882). MeDIP immunoprecipitated DNA and Input were purified and eluted. Library preparation was performed using NEBNext Ultra II kit for Illumina (cod. E7645), following  manufacturer instruction. ATAC-seq DNA After transposition was purified and libraries were amplified for the required amount of cycles  as previously described (Buenrostro et al., 2013).

value: glioblastoma cells

value: SES-transduced SNB19


title: ATAC_seq_PS_3

value: endometrial endometrioid carcinoma


title: ATAC_seq_PS_1


title: RNA_SES2


title: L24_2: 24 hours after cold treatment sample2

description: 24 hours after cold treatment sample2


title: ATAC_seq_PS_2


title: ATAC_seq_PIS_6

value: progestin insensitivity


title: ATAC_seq_PIS_5


title: L24_1: 24 hours after cold treatment sample1

description: 24 hours after cold treatment sample1


title: L12_3: 12 hours after cold treatment sample3

description: 12 hours after cold treatment sample3

value: 12 hours after cold treatment


title: RNA_Mock2

description:
Mock-transduced SNB19; RNA-Seq
Human_Normalized_counts.tsv

value: Mock-transduced SNB19


title: RNA_Mock3


title: RNA_SES1


title: RNA_seq_PS_5

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 hisat2.
Fragment Per Kilobase of exon per Megabase of library size (FPKM) and read count were calculated by Stringtie and ballgown pipeline. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Human (hg38)
Supplementary files format and content: Tab-delimited text files include raw gene counts for each Sample.

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 purify 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 pair end 100 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).


title: ATAC_seq_PIS_2


title: ATAC_seq_PIS_4


title: L12_1: 12 hours after cold treatment sample1

description: 12 hours after cold treatment sample1


title: ATAC_seq_PIS_3


title: L3_3: 3 hours after cold treatment sample3

description: 3 hours after cold treatment sample3

value: 3 hours after cold treatment


title: ATAC_seq_PIS_1


title: RNA_seq_PS_4


title: RNA_seq_PS_3


title: RNA_seq_PS_6


title: SMNB19_SOX2_3

description: SOX2-transduced SNB19; SOX2-V5 Cut-n-Tag

data_processing:
Library strategy: CUT&TAG
ChIP-Seq/ATAC-Seq/Cut-n-Tag: Trimming and QC by Trimmomatic. Genome mapping by Bowtie2. Peak calling by MACS3. Coverage analysis by DeepTools.
RNA-Seq: Trimming and QC by Trimmomatic. Genome mapping and gene quantification by STAR. Differential analysis by DESeq2.
Assembly: hg38, mm10
Supplementary files format and content: DESeq2 normalized counts, MACS3 peaks

value: SOX2-transduced SNB19


title: L3_2: 3 hours after cold treatment sample2

description: 3 hours after cold treatment sample2


title: RNA_seq_PS_2


title: RNA_seq_PS_1


title: L12_2: 12 hours after cold treatment sample2

description: 12 hours after cold treatment sample2


title: RNA_Mock1


title: L0_3: without cold treatment sample3

description: without cold treatment sample3

value: without cold treatment


title: RNA_seq_PIS_6


title: SMNB19_SOX2_1


title: L0_2: without cold treatment sample2

description: without cold treatment sample2


title: RNA_seq_PIS_4


title: L3_1: 3 hours after cold treatment sample1

description: 3 hours after cold treatment sample1


title: MCAO-rTMS-3

city: Nanjing

first: Ye

last: Hong

address: No.68, Changle Road, Nanjing, Jiangsu Province, China

department: Department of Neurology

institute: Nanjing First Hospital

data_processing:
Illumina Bcl2FastQ  software used for basecalling
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 17 nt.
Total clean reads were mapped to the Rat reference genome using the bwa aligner.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org) and pirnabank (www.pirnabank.ibab.ac.in) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA
Genome_build:   rn6
Supplementary_files_format_and_content: The "miRNA_expression.txt" contains the values calculated by DEseq2 against the Count value and the 'miRNA_differential_expression.txt' contains all values greater than 200 and fold change >2, and P<0.05 between MCAO group and MCAO + rTMS group after counting the count value according to DEseq2 algorithm.

source_name: peri-infarct cortex tissue

extract_protocol:
Total RNA was isolated from  tissues using the Magzol Reagent (Magen, China)according to the manufacturer's protocol.
Briefly, total RNAs were ligated with 3' RNA adapter, and followed by 5' adapter ligation. Subsequently, the adapter-ligated RNAs were subjected to RT-PCR and amplified with a low-cycle. Then the PCR products were size selected by PAGE gel according to instructions of NEBNext Multiplex Small RNA Library Prep Set for Illumina (Illumina, USA)

tag: strain

value: Sprague-Dawley

value: The right middle cerebral artery (MCA) was occluded for 90 min, and received 10 Hz  rTMS treatment 10 min a day for  7 consecutive days

value: brain; peri-infarct cortex


title: RNA_seq_PIS_3

value: endometrium lesion


title: RNA_seq_PIS_2


title: SMNB19_SES_3

description: SES-transduced SNB19; SES-V5 Cut-n-Tag


title: MCAO-rTMS-2


title: MCAO-rTMS-1


title: L0_1: without cold treatment sample1

description: without cold treatment sample1


title: SMNB19_SOX2_Input

description: SOX2-transduced SNB19; Input


title: SMNB19_SES_2

description: SES-transduced SNB19; SES-V5 Cut-n-Tag


title: Spatial meta-transcriptomic data for LI

first: seqcore

last: sii

address: Southern Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
SpaceRanger 1.0.0
blastn 2.10.1+
phyloseq 1.32.0
Seurat 4.0.1
Assembly: mm10-3.0.0
Supplementary files format and content: rds was created from Seurat object in R
Supplementary files format and content: tsv was generated from blast output
Library strategy: Spatial Transcriptomics

organism:
Mus musculus
mouse gut metagenome

source_name: large intestine

extract_protocol:
10x Genomics, Visium Spatial, Rev B for ST and TRIzol Reagent (#15596026, InvitrogenTM) for total RNA isolation extraction
The spatial gene libraries were constructed using Visium Spatial Library Construction kit (10X Genomics,PN-3000394). The cDNA was break into fragments of about 200-300bp, add poly(A) tails and connected the P7 adapter, 3’ end sequencing was performed using Illumina Novaseq 6000 sequencer with a sequencing depth of at least 100,000 reads per spot with pair-end 150 bp (PE150) reading strategy.

value: large intestine

tag: Sex

value: male

value: 6 weeks


title: RNA_seq_PIS_1


title: MCAO-3

value: The right middle cerebral artery (MCA) was occluded for 90 min,cortex tissues were obtained at 7 days post surgery.


title: SOX2V5ChIPSeq2S4

description: SOX2-transduced SNB19; SOX2-V5 ChIP-Seq

value: glioblastoma cells


title: SMNB19_SOX2_2


title: Spatial meta-transcriptomic data for SI

source_name: small intestine

value: small intestine


title: RNA_seq_PIS_5

value: endometrial atypical hyperplasia


title: MSC-M+

city: Guangzhou

first: Jing

last: Liu

state: Guangdon

address: 190 Kai Yuan Avenue, Science Park,Guangzhou

department: CAS Key Laboratory of Regenerative Biology

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China

data_processing:
raw fastq data were trimed by trim_galore(version 0.6.0).
RNAseq reads were aligned to the mm10 genome assembly using rsem with options --bowtie2 --bowtie2-sensitivity-level very_sensitive
expected_count were extract from the sample_name.genes.results and merged together to get a big table
RNAseq data was normalized by TPM(Transcripts Per Million)
Assembly: mm10
Supplementary files format and content: tsv file was generated form normalized RNAseq data, it include all samples' RNAseq data

source_name: human mesenchymal stem cells

growth_protocol: The human umbilical cord-derived MSCs used in this project were isolated from Wharton’s Jelly, a gelatinous tissue around umbilical vessels. The human umbilical cord was obtained from the healthy cesarean section fetus. The MSCs samples were donated from The Fifth Affiliated Hospital of Guangzhou Medical University. MSCs were cul-tured in a medium with Dulbecco's modified Eagle's medium (DMEM)/F12 and 10% fe-tal bovine serum (FBS) in a 37 °C 5% CO2 incubator.

extract_protocol:
TRIzol was used to extract the total RNA. HiScript II Reverse Transcriptase (Vazyme biotech R222-01) was used to reverse-transcribe cDNA from 2 μg of total RNA.
The VAHTSTM mRNA-seq V3 Library Prep Kit for Illumina® (NR611-01/02) was used to prepare sequencing libraries, and the libraries were sequenced on an Illumina Novaseq platform, and 150 bp paired-end reads were generated.

value: human mesenchymal stem cells


title: MCAO-2

value: The right middle cerebral artery (MCA) was occluded for 90 min,cortex tissues were obtained at 7 days post reperfusion.


title: SOX2V5ChIPSeq1S3

description: SOX2-transduced SNB19; SOX2-V5 ChIP-Seq