title: CCI_DAY14_2

description: Rat dorsal root ganglia underwent CCI, and then released after 7day. mRNA sample was havested on post releasing Day 14

value: 14 day


title: CCI_DAY7_1

status: Public on Jan 01 2026

type: RNA

city: Tainan

first: Chunwei

last: Lin

address: No. 1, Daxue Rd., East Dist.

country: Taiwan

institute: National Cheng Kung University

description: Rat dorsal root ganglia underwent CCI, and then released after 7day. mRNA sample was havested on post releasing Day 7

hyb_protocol: Followed manufacturer's protocol

scan_protocol: Samles were loaded onto a nCounter cartridge and ran on a nCounter SPRINT

data_processing: Sample gene transcript counts were normalized before downstream analysis by geoNorm algorithm in NanoString’s nSolver software Version 4.0 to figure out stable housekeeping genes and positive control for normalization.

molecule: total RNA

organism: Rattus norvegicus

source_name: rat dorsal root ganglia

label_protocol: Followed manufacturer's protocol

growth_protocol: Animal housing and care, were approved by the Laboratory Animal Center and Institutional Animal Care and Use Committee (IACUC; Protocol No. 108032) of National Cheng Kung University in Tainan, Taiwan.

extract_protocol: The rat dorsal root ganglion RNA were extracted via Trizol, and RNA sample quality was confirmed by spectrophotometry (SpectraMax QuickDrop) to determine concentration and chemical purity (A260/230 and A260/280 ratios) and with a Bioanalyzer (model 2100, Agilent Technologies) to determine RNA integrity and degraded samples were re-placed with an alternative sample if available.

treatment_protocol: The left sciatic nerve was dissected from the surrounding tissues and exposed at the mid-thigh level. The area proximal to the trifurcation of the sciatic nerve was cleared of any adhering tissue. Four ligatures made of 5–0 nylon (Ethicon US, Bridgewater, NJ) were tied around the sciatic nerve, with approximately 1 mm of space between each ligature. After 7 days, the CCI rats underwent a second surgery for decompression.

tag: days post never compression releasing

value: 7 day

tag: tissue

value: rat dorsal root ganglia


title: CCI_DAY14_1


title: CCI_DAY7_3


title: CCI_DAY7_2


title: CCI_DAY0_1

description: Rat dorsal root ganglia underwent CCI, and then released after 7day. mRNA sample was havested on post releasing Day 0

value: 0 day


title: CCI_DAY3_1

description: Rat dorsal root ganglia underwent CCI, and then released after 7day. mRNA sample was havested on post releasing Day 3

value: 3 day


title: CCI_DAY0_2


title: 501M_shLENT_DHX_1

type: SRA

city: Illkirch-Graffenstaden

first: Guillaume

last: Davidson

address: 1 Rue Laurent Fries

country: France

institute: I.G.B.M.C. - Institut de génétique et de biologie moléculaire et cellulaire

description:
501M silenced by Dox-inducible shLENT and immunoprecipitated with DHX36-antibody
LRHR21

library_source: transcriptomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed in order to remove adapter and low-quality sequences (Phred quality score below 20) using cutadapt version 1.10.
Reads were mapped to rRNA sequences using bowtie version 2.2.8, and reads mapping to rRNA sequences were removed for further analysis. Reads were mapped to spike sequences using bowtie2 version 2.2.8, and reads mapping to spike sequences were removed for further analysis.
Sequence reads were mapped to reference genome hg19 using Tophat v2.0.10 51 and the bowtie2 v2.1.0 aligner. Only uniquely aligned reads were retained for further analyses.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version v0.6.1 with annotations from Ensembl version 75.
Data normalization and quantification of gene expression was performed using the DESeq2 Bioconductor package. Significantly deregulated genes were selected using a log2 fold change >1 and <1 and adjusted p-value cutoff of 0.05.
Assembly: hg19
Supplementary files format and content: Excel file containing raw read counts, normalized counts (by sequencing depth and median gene length) and log2(fold-change) with adjusted p-values for comparisons of interest. The file contains 3 distinct sheets for RNA-seq (501M whole extracts and fractions) and RIP-seq.

molecule: polyA RNA

organism: Homo sapiens

source_name: Skin

growth_protocol: 501mel were grown in RPMI1640 w/o HEPES medium supplemented with 10 % fetal calf serum (FCS) and gentamycin (40 µg/mL).

extract_protocol:
Cells were grown in 15 cm petri dishes, harvested by scraping, resuspended in lysis buffer (20 mM Tris-HCl pH 8, 200 mM NaCl, 2.5 mM MgCl2, 0.05 % Triton, DEPC water) supplemented with DTT (1 mM), protease/phosphatase inhibitor cocktail (Thermo Fisher Scientific) and RNAsin (Thermo Fisher Scientific) and kept on ice for 15 minutes, pipetting every 3 minutes. Membranes were pelleted 10 minutes at 10,000 g at 4 °C and the supernatant precleared 1 hour at 4 °C with protein G magnetic beads (Invitrogen). Lysate was quantified by Bradford protein quantification assay (Bio-Rad) and incubated overnight on a rotating wheel at 4 °C with 5 µg of the indicated antibodies. Then, 50 µL of resuspended Protein G magnetic beads were added for 3 hours to isolate RNA - protein complexes and washed five times in lysis buffer. After final wash, RNA was purified by TRI Reagent + isopropanol precipitation and proteins eluted by boiling beads at 95 °C for 15 minutes in Laemmli buffer. Ribosomal RNAs were depleted with the Ribo-Zero Plus rRNA depletion kit (Illumina) prior to library preparation.
Library preparation was performed at the GenomEast platform at the Institute of Genetics and Molecular and Cellular Biology using Clontech SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing User Manual - PN 091817 + Illumina Nextera XT DNA Library Prep Kit Reference Guide - PN 15031942. Full length cDNA were generated from 100 to 500 pg of total RNA using SMART-SeqX v4 UltraX Low Input RNA Kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer’s instructions with 15 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, USA) followed by 12 cycles of library amplification. Following purification with SPRIselect beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

treatment_protocol: 501M were silenced using doxycycline-inducible LENT shRNA (shLENT) or a scrambled control (shCTRL) that were cloned in LT3GEPIR (a gift from Johannes Zuber; Addgene plasmid #111177; http://n2t.net/addgene:111177; RRID: Addgene_111177).

value: Skin

tag: cell line

tag: treatment

value: shLENT

tag: antibody for_rip-seq


title: CCI_DAY14_3


title: CCI_DAY0_3


title: CCI_DAY3_2


title: H3K4me3_ChIP mrc1D rep2

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

country: USA

institute: Columbia University

description: synchronized to G2 ending, nascent DNA on S10 min

library_source: genomic

data_processing:
mapped to pombe reference genome by Bowtie2
Read coverage in a bin of 1bp was calculated from filtered bam files by deepTools2 and then normalized with total filtered reads number into reads per million (RPM).
Origins were called by MACS2 from BrdU-IP
Assembly: pombe
Supplementary files format and content: bw, bigwig format, contains the read density at each genomic position
Library strategy: eSPAN-seq

molecule: genomic DNA

organism: Schizosaccharomyces pombe

growth_protocol: Strains containing the cdc25-22 temperature-sensitive mutant were first grown at permissive temperature (25°C) until the early-mid log phase (OD 0.2~0.4). Cultures were then incubated at 36°C for 4 hours to arrest cells at the G2 phase of the cell cycle. Cells were then shifted to 25°C to allow them to enter the S phase synchronously.

extract_protocol:
Cells were crosslinked at 60 minutes after temperature shift with the addition of 1% formaldehyde and incubated for 20 minutes with shaking at 25°C. Immunoprecipitation was performed as described in ChIP. Crosslinking was reversed by Chelex-100. Briefly, total and ChIP DNA were incubated at 100°C for 5 minutes and then immediately cooled on ice for 5 minutes. DNA was diluted ten times with BrdU IP buffer (PBS, 0.0625% Triton X-100(v/v)), and incubated with BrdU antibody (BD Bioscience 555627) for two hours at 4°C. Next, Sepharose Protein G beads (Cytiva 17-0618-01) were added and incubated for an additional one hour at 4°C. The beads were then washed three times with BrdU IP buffer and once with TE. Finally, DNA was eluted with TES and purified with the QIAGEN MinElute PCR Purification kit (Qiagen 28004).
AccelNGS 1S Plus DNA library kit (Swift Bioscience, 10096).

treatment_protocol: BrdU was added to a final concentration of 650 μM at 25minutes after the temperature shift.

tag: strain

tag: sample type

value: fission yeast

tag: chip antibody

tag: genotype


title: AngiotensinII-1

city: Guangzhou

first: Sijia

last: Liang

address: 74 Zhongshan 2 Rd

department: Pharmacology

country: China

institute: Sun Yat-Sen University

description:
Library name: Sample 4
AngiotensinII-1

data_processing:
After library quality control, different libraries were pooled based on the effective concentration and targeted data amount. 5'-end of each library was phosphorylated and cyclized. Subsequently, loop amplification was performed to generate DNA nanoballs. We ultimately loaded these DNA  nanoballs into flow cytometry cells with DNBSEQ-T7 for 2×150bp paired-end sequencing  (Guangzhou Angte Biotechnology Co.,Ltd. guangzhou,China) following the vendor's recommended protocol.
Quality control.Clean datas were obtained by removing low quality reads with Fastp.
Reads mapping.Clean reads were mapped to mouse reference genome mm10 by hisat2.
Differential expression analysis of two conditions/groups was performed using the feartureCounts.
Assembly: mm10
Supplementary files format and content: counts

organism: Mus musculus

source_name: Primary mous endothelial cells

growth_protocol: Mice were anesthetized with pentobarbital sodium, and the aorta was dissected and immersed immediately in the Kreb’s solution containing 137 mmol/L NaCl, 5.4 mmol/L KCl, 2.0 mmol/L CaCl2, 1.1 mmol/L MgCl2, 40.4 mmol/L NaH2PO, 5.6 mmol/L Glucose, 11.9 mmol/L NaHCO3, and 1% penicillin/streptomycin. After removal of adipose and connective tissues, 2 mm sections of aortas were placed on matrigel-coated plates and cultured in Dulbecco’s modified Eagle’s medium supplemented with 20% fetal calf serum, 25 U/mL heparin, 10 ng/mL endothelial growth factor, and 1% penicillin/streptomycin at 37°C in 5% CO2. Endothelial cells began migrating from explants after 5–7 days.

extract_protocol:
Total RNA extraction was conducted by TRlzol Reagent. RNA detect concentration using qubit (Thermo Fisher Scientific, Q33226). RNA purity was checked using the NanoDrop PR-1(Thermo Fisher Scientific,CHEM-PR1-KIT). RNA integrity was assessed using the Qsep1 system (Qsep1 Technologies, CA, China).
Messenger RNA was purified from total RNA using attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Eight-week-old C57BL/6 mice were anesthetized using 2% pentobarbital sodium, and osmotic pumps were subcutaneously implanted to deliver AngII at a constant rate of 1000 ng/kg/min over 14 consecutive days. Sham-operated mice underwent the identical procedure, with osmotic pumps containing 0.9% saline implanted subcutaneously instead. Subsequently, mouse aortic endothelial cells were isolated.

tag: cell type

value: Primary mous endothelial cells

value: WT

value: AngiotensinII infusion


title: BrdU mcm22A_mrc1D rep1

value: anti-BrdU

value: mcm2-2A mrc1[delta]

value: BrdU


title: 501M_shCtrl_DHX_3

description:
501M silenced by Dox-inducible shControl and immunoprecipitated with IgG-antibody
LRHR17

value: shCtrl


title: Saline-3

description:
Library name: Sample 3
Saline-3

value: Saline infusion


title: WT_7d NAA and release for 12h_Bio2

city: ghent

first: Wei

last: Xiao

address: Technologiepark-Zwijnaarde 71 - 9052 Ghent - Belgium

country: Belgium

institute: VIB-UGent Center for Plant Systems Biology

description: Library name: WT_7d NAA and release for 12h_2

data_processing:
using Galaxy Belgium platform
Trimmomatic to remove adaptors
Salmon quant to align reads
tximport to count read
Deseq2 to differentially expressed gened
Assembly: TAIR10 on Galaxy (for Arabidopsis thaliana), Genome Selaginella moellendorffii v1.0 (for Selaginella moellendorffii)
Supplementary files format and content: tab-delimited file of count read for each sample

organism: Selaginella moellendorffii

source_name: Root

growth_protocol: 1/2 MS  plates 22°C constant light 4d old root of Arabidopsis thaliana, and 14d old root of Selaginella moellendorffii

extract_protocol:
ReliaPrep™ RNA Miniprep Systems
BGI RNA Library Prep Kit protocol

treatment_protocol: 0.2 cm of the root tip of the root. Rna extraction with ReliaPrep RNA Miniprep Systems kit (Z6112)

value: Root

value: 1μM NAA for 7d, and release for 12h


title: 501M_shCtrl_DHX_2

description:
501M silenced by Dox-inducible shControl and immunoprecipitated with IgG-antibody
LRHR16


title: 501M_shLENT_DHX_3

description:
501M silenced by Dox-inducible shLENT and immunoprecipitated with DHX36-antibody
LRHR23


title: 501M_shCtrl_IgG_3

description:
501M silenced by Dox-inducible shControl and immunoprecipitated with IgG-antibody
LRHR14


title: AngiotensinII-3

description:
Library name: Sample 6
AngiotensinII-3


title: AngiotensinII-2

description:
Library name: Sample 5
AngiotensinII-2


title: H3K4me3_eSPAN mrc1D rep1

value: anti-BrdU and anti-H3K4me4


title: 501M_shCtrl_IgG_2

description:
501M silenced by Dox-inducible shControl and immunoprecipitated with IgG-antibody
LRHR13


title: Input mrc1D rep2

value: Input


title: WT_7d NAA and release for 6h_Bio3

description: Library name: WT_7d NAA and release for 6h_3

value: 1μM NAA for 7d, and release for 9h


title: H3K4me3_eSPAN mrc1D rep2


title: BrdU mrc1D rep1


title: WT_7d NAA and release for 12h_Bio1

description: Library name: WT_7d NAA and release for 12h_1


title: Saline-2

description:
Library name: Sample 2
Saline-2


title: WT_7d NAA and release for 6h_Bio2

description: Library name: WT_7d NAA and release for 6h_2

value: 1μM NAA for 7d, and release for 6h


title: BrdU mrc1D rep2


title: H3K4me3_ChIP mrc1D rep1


title: WT_7d NAA and release for 6h_Bio1

description: Library name: WT_7d NAA and release for 6h_1


title: Saline-1

description:
Library name: Sample 1
Saline-1


title: DRG, Tmem45b-flox mice, RNA-seq, rep6

city: Zhuhai

first: Liang

last: Chen

state: 广东Guangdong

address: 6th Building, No. 2515, Huan Dao North Road, Hengqin New Area, Zhuhai, Guangdong Province, China

institute: Guangdong Institute of Intelligence Science and Technology

description:
Library name: Sample17
con_ML_2
raw counts

data_processing:
The raw sequencing data underwent quality control using fastp (version 0.23.2), during which low-quality sequences and adapter contaminants were removed. Cleaned reads were then aligned to the mouse reference genome (mm10) using bwa-mem2 (version 2.2.1). The alignment was sorted using samtools (version 1.14) to generate the count matrix. Differential gene expression analysis was performed using DESeq2 (version 1.40.2).
Assembly: mm10
Supplementary files format and content: Raw count files: These are tab-delimited text files containing the raw read counts for each gene in each sample. The raw counts file provides the number of reads mapped to each gene.

source_name: DRG

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific, Carlsbad, CA, USA), following the manufacturer's protocol.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). A certain amount of RNA are denatured at suitable temperature to open the secondary structure, and mRNA is enriched by oligo (dT) attached magnetic beads. After reacting at a suitable temperature for a fixed time period, RNAs are fragmented with fragmentation reagents. Then First-strand cDNA is generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesized double strand cDNA is subject to end repairment reaction. After cDNA end repairment, a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments through A tailing reaction. Then the reaction system for adaptor ligation configured to ligate adaptors with the cDNAs, and finally, the library products are amplified through PCR reaction and subjected to quality control. Next, the single-stranded library products are produced via denaturation. The reaction system for circularization is set up to get the single-stranded cyclized DNA products. Any uncyclized single stranded linear DNA molecules will be digested. The final single strand circularized library is amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs are loaded into the patterned nanoarray and PE150 bases reads are generated on T7 platform (BGI-Shenzhen, China).

value: DRG

value: Tmem45b-flox::Mrgprd-cre mice


title: H3K4me3_ChIP mrc1_2 rep1

value: fission yeast


title: WT_7d NAA and release for 3h_Bio1

description: Library name: WT_7d NAA and release for 3h_1

value: 1μM NAA for 7d, and release for 3h


title: DRG, Tmem45b-flox::Mrgprd-cre mice, RNA-seq, rep6

description:
Library name: Sample20
ko_MC_2
raw counts


title: 501M_shCtrl_DHX_1

description:
501M silenced by Dox-inducible shControl and immunoprecipitated with IgG-antibody
LRHR15

value: Skin


title: 501M_shCtrl_IgG_1

description:
501M silenced by Dox-inducible shControl and immunoprecipitated with IgG-antibody
LRHR12


title: MOLM13_Plad_100nM_3

city: NY

first: Bin

last: Lu

address: 417 East 68th Street New York,

institute: mskcc

data_processing:
Raw fastq files were first trimed using trim_galore
trimed reads were mapped to hg38 or mm10 using MACS2 with very-sensitive seting
mapped files were further removed out of duplicates, sorted and indexed.
bamCoverage was used to generate bigwig file for genome browser visualization.
Library strategy: CUT&Tag

source_name: cell line

growth_protocol: leukemia cell lines were cultured at RPMI. All primary cells were enriched from mouse bone marrow, human cord blood, or human adult blood sample.

extract_protocol:
All the cells were first fixed by methanol, mobilized on Concanavalin A beads, folllowed by S9.6 anbibody incubation and nanobody Tn5 binding. Mg2+ was added to activate the cutting of Tn5
Recovered chromotain DNA was first end repaired using Bst 2.0, followed by in vitro transcription of T7 promoter. Transcribed RNA was first reverse converted to first cDNA and second DNA strand. Double strand DNA was cut by second Tn5. Library was amplified by DNA polymerase.

treatment_protocol: ckit+positive enrichment kit was used to enrich HSPCs cells, mature cells were flow through of HSPC enrichment process. CD34+ kit was used to enrich human HSPCs, mature cells were flow through of cd34+ enrichment process.

value: cell line

tag: antibody

value: S9.6 antibody


title: DRG, Tmem45b-flox mice, RNA-seq, rep4

description:
Library name: Sample15
con_FC_3
raw counts


title: BrdU mrc1_2 rep1

description: synchronized to G2 ending, nascent DNA on S10 min

value: anti-BrdU


title: WT_7d NAA and release for 3h_Bio2

description: Library name: WT_7d NAA and release for 3h_2

value: WT


title: DRG, Tmem45b-flox::Mrgprd-cre mice, RNA-seq, rep7

description:
Library name: Sample21
ko_ML_2
raw counts


title: WT_7d NAA and release for 0h_Bio2

description: Library name: WT_7d NAA and release for 0h_2

value: 1μM NAA for 7d, and release for 0h


title: DRG, Tmem45b-flox::Mrgprd-cre mice, RNA-seq, rep5

description:
Library name: Sample19
ko_FC_2
raw counts


title: TIP_100_K562_H3K4me1_1

description: patient sample

data_processing:
Raw fastq files were first trimed using trim_galore
trimed reads were mapped to hg38 or mm10 using MACS2 with very-sensitive seting
mapped files were further removed out of duplicates, sorted and indexed.
bamCoverage was used to generate bigwig file for genome browser visualization.
Supplementary files format and content: hg38
Supplementary files format and content: bw
Library strategy: Cut & Tag


title: Input mrc1D rep1


title: NOMO1_DMSO_3

value: DMSO


title: WT_7d Mock_Bio2

description: Library name: WT_7d Mock_2

value: Root

value: 1μM Mock for 7d


title: MOLM13_DMSO_1


title: WT_7d NAA and release for 3h_Bio3

description: Library name: WT_7d NAA and release for 3h_3


title: WT_7d Mock_Bio3

description: Library name: WT_7d Mock_3


title: WT_7d NAA and release for 0h_Bio3

description: Library name: WT_7d NAA and release for 0h_3


title: TIP_100_K562_H3K4me1_3

description: patient sample


title: DRG, Tmem45b-flox mice, RNA-seq, rep2

description:
Library name: Sample13
WT2_LDRG
raw counts


title: WT_BAP_Bio3

description: Library name: WT_BAP_3

value: 10μM BAP


title: H3K4me3_eSPAN mrc1_2 rep1

value: anti-BrdU and anti-H3K4me4


title: DRG, Tmem45b-flox::Mrgprd-cre mice, RNA-seq, rep4

description:
Library name: Sample18
ko_FC_1
raw counts


title: H3K4me3_eSPAN mrc1_2 rep2


title: DRG, Tmem45b-flox mice, RNA-seq, rep1

description:
Library name: Sample12
WT1_LDRG
raw counts


title: WT_7d NAA and release for 0h_Bio1

description: Library name: WT_7d NAA and release for 0h_1


title: NOMO1_Plad_100nM_2


title: WT_BAP_Bio2

description: Library name: WT_BAP_2


title: TIP_10_K562_H3K4me1_2

description: patient sample


title: Input mrc1_2 rep1

value: Input


title: DRG, Tmem45b-flox::Mrgprd-cre mice, RNA-seq, rep2

description:
Library name: Sample10
KO2_LDRG
raw counts


title: DRG, Tmem45b-flox mice, RNA-seq, rep5

description:
Library name: Sample16
con_FL_1
raw counts


title: WT_NAA_Bio3

description: Library name: WT_NAA_3

value: 10μM NAA


title: TIP_100_K562_H3K4me1_2

description: patient sample


title: WT_7d Mock_Bio1

description: Library name: WT_7d Mock_1


title: TIP_10_K562_H3K4me1_1

description: patient sample


title: Input mrc1_2 rep2


title: WT_BAP_Bio1

description: Library name: WT_BAP_1


title: H3K4me3_ChIP mrc1_2 rep2


title: BrdU mrc1_2 rep2

value: BrdU


title: TIP_10k_K562_H3K4me1_2

description: patient sample


title: DRG, Tmem45b-flox mice, RNA-seq, rep3

description:
Library name: Sample14
WT3_LDRG
raw counts

value: DRG

value: Tmem45b-flox::Mrgprd-cre mice


title: H3K4me3_ChIP mrc1_1 rep2

value: fission yeast


title: TIP_10_K562_H3K4me1_3

description: patient sample


title: BrdU mrc1_1 rep2


title: DRG, Tmem45b-flox::Mrgprd-cre mice, RNA-seq, rep3

description:
Library name: Sample11
KO3_LDRG
raw counts


title: WT_NAA_Bio1

description: Library name: WT_NAA_1


title: H3K4me3_eSPAN mrc1_1 rep2


title: TIP_10k_K562_H3K4me1_1

description: patient sample


title: DRG, CFA model，Tmem45b-flox mice, RNA-seq, rep4

description:
Library name: Sample8
CFA_WT4
raw counts CFA model

value: CFA model


title: DRG, Tmem45b-flox::Mrgprd-cre mice, RNA-seq, rep1

description:
Library name: Sample9
KO1_LDRG
raw counts


title: DRG, CFA model，Tmem45b-flox mice, RNA-seq, rep2

description:
Library name: Sample6
CFA_WT2
raw counts CFA model


title: WT_NAA_Bio2

description: Library name: WT_NAA_2


title: DRG, CFA model，Tmem45b-flox mice, RNA-seq, rep1

description:
Library name: Sample5
CFA_WT1
raw counts CFA model


title: H3K4me3_eSPAN mrc1_1 rep1

description: synchronized to G2 ending, nascent DNA on S10 min


title: TIP_1_K562_H3K4me1_2

description: patient sample


title: H3K4me3_ChIP mrc1_1 rep1


title: TIP_10k_K562_H3K4me1_3

description: patient sample


title: Input mrc1_1 rep2


title: WT_Mock_Bio2

description: Library name: WT_Mock_2

value: Mock


title: DRG, CFA model，Tmem45b-flox mice, RNA-seq, rep3

description:
Library name: Sample7
CFA_WT3
raw counts CFA model


title: DRG, CFA model，Tmem45b-flox::Mrgprd-cre mice, RNA-seq, rep3

description:
Library name: Sample3
CFA_CKO3
raw counts CFA model


title: WT_Mock_Bio3

description: Library name: WT_Mock_3


title: WT_Mock_Bio1

description: Library name: WT_Mock_1


title: TIP_1_K562_H3K4me1_1

description: patient sample


title: DRG, CFA model，Tmem45b-flox::Mrgprd-cre mice, RNA-seq, rep2

description:
Library name: Sample2
CFA_CKO2
raw counts CFA model


title: BrdU mrc1_1 rep1


title: DRG, CFA model，Tmem45b-flox::Mrgprd-cre mice, RNA-seq, rep4

description:
Library name: Sample4
CFA_CKO4
raw counts CFA model


title: TIP_1_K562_H3K4me1_3

description: patient sample


title: Input mrc1_1 rep1


title: H3K4me3_eSPAN WT rep1

value: anti-BrdU and anti-H3K4me3


title: DRG, CFA model，Tmem45b-flox::Mrgprd-cre mice, RNA-seq, rep1

description:
Library name: Sample1
CFA_CKO1
raw counts CFA model


title: TIP_1k_K562_H3K4me1_3

description: patient sample


title: H3K4me3_eSPAN WT rep2


title: Control sample 10

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

description: Library name: MAC101_10

data_processing:
CLC Genomics Workbench version 24
Reads were mapped to the genome using CLC Genomics Workbench version 24 using default settings
Assembly: Bioproject: PRJNA1276037 SUBID SUB15383676
Supplementary files format and content: Expression browser in Excel format with total read counts, RPKM, TPM and CPM of the mapped reads for all samples
Supplementary files format and content: study versus control: Fold change, p value, FDR p  value, Bonferroni values

organism: Mycobacterium avium

growth_protocol: Bacterial cultures of strain MAC101 (ATCC 700898) were grown in were grown at 28.5°C in Middlebrook 7H9 broth with acid-albumindextrose- catalase (ADC) enrichment to late log phase.

extract_protocol:
Bacteria cultures of 10 ml were centrifuged in Falcon tubes and subsequently resuspended in 0.5 ml TRIzol reagent (Invitrogen) and transferred to 2 ml Eppendorf tubes containing 0.25 ml glass beads (0.1 mm, Qiagen).  Cell lysis was performed by bead-beating in a bullet blender (Next Advance), for 1 min  at highest speed, for 6 cycles. The tubes were suspended in ice for 2 min between cycles. After 5 minutes centrifugation at 20.238 RCF (at RT), the TRIzol layer was recovered and  chloroform added (1:5) and vortexed vigorously for 15 seconds. Samples were centrifuged for 15 min at 21.130 RCF (at 4° C), upper transparent aqueous layer was carefully removed and mixed with 0.3 ml isopropanol and spun down 10 minutes. Pellets were washed with 0.5 ml 70% ethanol and centrifuged for 15 minutes at 21.130 RCF (at 4 ° C). Ethanol was removed as much as possible and subsequently air dried  for 5 minutes and 20 microliter RNAse free water was added. Equipment: Centrifuge Eppendorf 5424 R (cooled max 21130 RCF) or 5424 (max 20.238 RCF)
The library and sequencing was performed by the company Novogene (UK). Firstly, ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. Following is the workflow of library construction: The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries have been pooled and sequenced on Illumina platforms, according to effective library concentration and data amount specified.

treatment_protocol: Bacteria at late log phase were transferred to 10 ml Falcon tubes and grown in the presence or absence of 10 micromolar of antibiotic (stock solution of 10 millimolar in DMSO). As a control equal volumes of the solvent DMSO was added (control samples 4 and 10) or PBS buffer (control samples 1 and 4) were added to the cultures. After 1.5 hours the tubes were centrifuged and frozen pellets were used for RNA isolation.


title: TNT_100_K562_H3K4me1_1

description: patient sample


title: TIP_1k_K562_H3K4me1_1

description: patient sample


title: TIP_1k_K562_H3K4me1_2

description: patient sample


title: Control sample 1

description: Library name: MAC101_1


title: TNT_100_K562_H3K4me1_2

description: patient sample


title: Study antibiotic 80998879 sample 11

description: Library name: MAC101_11


title: Control sample 7

description: Library name: MAC101_7


title: Study antibiotic 80998879 sample 6

description: Library name: MAC101_6


title: BrdU WT rep2

value: anti-BrdU


title: 386_Neurone_AG1_S

city: Würzburg

first: Silke

last: Appenzeller

address: Schweinfurter Str. 28

country: Germany

institute: University Wuerzburg

description: Gene expression data from cortical neuron clusters of SHRSP rats aged 24-25 weeks

data_processing:
Quality Assessment (FASTQC version 0.11.5)
Trimming (bbduk from BBTools v37.93)
Alignment (STAR v2.5.3a)
Gene read counts (HTSeq-count v0.6.1)
Differential expression analysis (DESeq2 v1.18.1)
Assembly: Rattus norwegicus (Rnor6)
Supplementary files format and content: Unnormalized count-table

source_name: Laser-microdissected cortical neuron clusters

extract_protocol:
Total RNA was extracted using the PicoPure RNA Isolation Kit (Thermo Fisher Scientific)
QuantSeq 3' mRNA-Seq Library Prep Kit FWD (Lexogen)

value: SHRSP

value: Cortical neuron clusters

tag: hypertension stage

value: Early (24-25 weeks)


title: Hpb_RNA-seq_iPrimer-seq

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

description: Library name: Hpb_RNA-seq_iPrimer-seq

data_processing:
The raw data was quality control using fastqc and then trimmed of the Nextera adaptor. Following trimming , the Drop-seq-Tools pipeline was used to filter the data with a Phred quality score threshold of 30 for sample barcode and UMI identify and poly(A) trimming. The filtered data was mapped to the mouse genome(mm10) using STAR 2.5.1a,and the reads counted using Drop-seq-Tools.
Assembly: mm10
Supplementary files format and content: xlsx & txt

source_name: peritoneal macrophage

extract_protocol:
Directly lysis the cell by Digitonin
The isolated RNA was eluted with the 20 μL reverse transcription mix consisting of 100 unit Hiscript III Reverse Transcriptase (Vazyme, R303), 40 unit RNase Inhibitor (Vazyme, R301),1 μL 25 mM dNTP mix, 1 μL 100 mM DTT, 1 μL 1 val Betaine (Sigma, B0300-1VL), 0.5 μL 5% Digitonin, 0.5 μL TSO-LNA and 0.5 μL 5 μM Probe. The reaction was incubated at 42℃ for 90 min. Following cDNA synthesis, the sample were pooled, cleaned and concentrated with cleanup beads at a 1:0.8 of DNA to beads ration and eluted in 30 μL of ddH2O. Second-strand synthesis and pre-amplification were performed in a 50 μL reaction, consisting of 2x KAPA HiFi Ready mix and 0.5 μM TSO-PCR primer, with the following PCR setup initial denaturation at 98 °C for 3 min, (denaturation at 98 °C for 15 s, annealing at 65 °C for 30 s, elongation at 72 °C for 6 min) repeated for 8 cycle, and a final elongation at 72 °C for 10 min. The DNA was cleanup using DNA cleanup beads at a ratio of 1:0.8 of DNA to beads and eluted with 30 μL of ddH2O. The library were prepared with the TruePrep DNA Library Prep Kit V2 for Illumina according to the manufacturer. Probe was designed by TSO, sample barcode(7-mer),UMI(8-mer) and Oligo(dT).

value: peritoneal macrophage

value: Wild type


title: Control sample 4

description: Library name: MAC101_4


title: Hpb_trained_3

description: Library name: Hpb_trained_3

data_processing:
Raw data was trimmed the adaptor by Trim_glore and qulity controlled via fastQC.
The clean reads were aligned to mm10 by bowtie2 and the options were as default.
The Peak identified by MACS2 and options were 'Fold [5,50], p value cut-off 0.01'.
The Bigwig file were built by bamCoverage with effective genome size of 2652783500.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Nuclei prepaed as previously described(William J Greenleaf 2013).
ATAC-seq libraries were prepared following standard protocol as described(Vazyme TD501).

value: Hpb infection+pyrantel pamoate


title: TNT_10_K562_H3K4me1_2

description: patient sample


title: BrdU WT rep1

value: WT


title: Hpb_trained_2

description: Library name: Hpb_trained_2


title: TNT_100_K562_H3K4me1_3

description: patient sample


title: Multiplexed_bulk

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

country: United Kingdom

institute: King's College London

description: Library name: Bulk multiplexed long read RNAseq

data_processing:
Raw data reads were filtered for low base pair quality (Q30).
A custom barcode deconvolution protocol was employed using BLAST to search for barcode sequences within 150 bp of either end of each transcript. In rare cases, where the barcodes at either end were incongruent with one another, the barcode with the lowest e value was used to label the transcript. Transcripts without barcodes at both ends were discarded. Transcripts were filtered for the presence of a poly A tail, and oriented such that poly A tail was located at the end pf the sequence.
Assembly: de-novo
Supplementary files format and content: FASTA file containing barcodes and barcode names by tissue
Supplementary files format and content: FASTA file containing reads (full length transcripts) which passed demultiplexing process, still containing untrimmed barcodes at either end.
Supplementary files format and content: FASTA file containing reads (full length transcripts) which passed demultiplexing process, with the barcodes trimmed off.

organism: Lumbricus rubellus

source_name: Gut, Calciferous gland, Nephridia, Crop, Gizzard, Nerve cord, Body wall, Seminal vesicles, Clitellum, Pharynx

growth_protocol: An adult  clade “B” earthworm was sampled from Cwmystwyth mine site and maintained in native soil until commencing with the RNA extraction.

extract_protocol:
Gut, nephridia, calciferous gland, crop, gizzard, seminal vesicles, clitellum, nerve cord, body wall, and pharynx tissues were dissected and the RNA was extracted using Trizol reagent and homogenisation with Qiagen Tissuelyser with a 5mm stainless steel ball
The SMRTbell Express Template Prep Kit 3.0 was used to prepare the HiFi SMRTbell Library of the Cwmystwyth worm RNA with PacBio barcoding primers. The library sequencing was performed on a PacBio Sequel IIe system (Pacific Biosciences) on a single 8M cell.

treatment_protocol: The animal was washed with deionized water, then transferred to a plastic dish with wet filter paper and kept for two days to void the gut contents before further processing.

value: Native to Cwmystwyth mine site


title: TNT_10_K562_H3K4me1_1

description: patient sample


title: Hpb_trained_1

description: Library name: Hpb_trained_1


title: Control_(T)_2

description: Library name: Control_(T)_2

value: pyrantel pamoate


title: 386_Endothel_AG1_S

description: Gene expression data from cortical blood vessels of SHRSP rats aged 24-25 weeks

source_name: Laser-microdissected cortical blood vessels

value: Cortical blood vessels


title: 383_Neurone_AG1_S


title: TNT_10k_K562_H3K4me1_1

description: patient sample


title: TNT_10_K562_H3K4me1_3

description: patient sample


title: Hpb_colonized_2

description: Library name: Hpb_colonized_2

value: Hpb infection


title: 384_Neurone_AG2_S

description: Gene expression data from cortical neuron clusters of SHRSP rats aged 32-34 weeks

value: Late (32-34 weeks)


title: 383_Endothel_AG1_S


title: Control_(T)_3

description: Library name: Control_(T)_3


title: 20_miRNA profiling in Healthy subject with moderate consumption of traditional beer

city: Barcelona

first: Lina

last: Badimon

state: BARCELONA

address: Carrer de Sant Antoni Maria Claret, 167

department: ICCC-Cardiovascular Program

country: Spain

institute: Research Institut- HSCSP

hyb_protocol: Hybridization was performed on Affymetrix miRNA 4.0 arrays and cartridges were incubated at 48°C with 60 rpm rotation for 17 h using Affymetrix Hybridization Oven 600. After, each array was washed and stained using the FS450_002 fluidics script in Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned by using the GeneChip scanner 3000 7G System

data_processing: The data were explored using the Transcriptome Analysis Console software (TAC 4.0) for data summarization and normalization by RMA+DABG procedure (implemented in TAC 4.0 software).

label: Biotin

source_name: Whole blood

label_protocol: We used Affymetrix FlashTag Biotin HSR RNA Labeling Kit (Affymetrix, Rev3) to label 250 ng of total RNA isolated with PAXgene Blood miRNA Kit (Qiagen Inc) from each sample, according to manufacturers instructions.

growth_protocol: Whole blood samples (2.5 mL) were used to isolate total mRNA, including miRNAs

extract_protocol: To isolate miRNAs, we used whole blood from healthy subjects and PAXgene Blood miRNA Kit (Qiagen Inc), according to manufacturer’s instructions.

treatment_protocol: No treatment

tag: groups

value: Whole blood


title: 18_miRNA profiling in Healthy subject with moderate consumption of traditional beer


title: 16_miRNA profiling in Healthy subject with moderate consumption of traditional beer


title: 384_Endothel_AG2_S

description: Gene expression data from cortical blood vessels of SHRSP rats aged 32-34 weeks


title: Control_(T)_1

description: Library name: Control_(T)_1


title: 19_miRNA profiling in Healthy subject with moderate consumption of traditional beer


title: Hpb_colonized_3

description: Library name: Hpb_colonized_3


title: Hpb_colonized_1

description: Library name: Hpb_colonized_1


title: TNT_10k_K562_H3K4me1_2

description: patient sample


title: 382_Neurone_AG2_S


title: 15_miRNA profiling in Healthy subject with moderate consumption of traditional beer


title: 17_miRNA profiling in Healthy subject with moderate consumption of traditional beer


title: TNT_1_K562_H3K4me1_2

description: patient sample


title: TNT_10k_K562_H3K4me1_3

description: patient sample


title: TNT_1_K562_H3K4me1_1

description: patient sample


title: 381_Neurone_AG2_S


title: Control_(C)_3

description: Library name: Control_(C)_3

value: water


title: 382_Endothel_AG2_S


title: 13_miRNA profiling in Healthy subject with moderate consumption of traditional beer


title: TNT_1_K562_H3K4me1_3

description: patient sample


title: 381_Endothel_AG2_S


title: Control_(C)_1

description: Library name: Control_(C)_1


title: 11_miRNA profiling in Healthy subject with moderate consumption of traditional beer


title: DSS+KS_3

city: Tianjin

first: Jing

last: Yan

address: 154 Anshan Road in Heping District

institute: Tianjin Medical University General Hospital

description: Library name: sample 6

data_processing:
RNA sequencing: The data obtained from sequencing are raw data. Subsequently, quality is performed on the raw reads to determine whether the sequencing data are suitable for downstream analysis. Then, filtered clean reads are aligned to the reference sequence. Following alignment, the distribution and coverage of reads on the reference sequence are analyzed to assess whether the alignment results pass the second QC (QC of alignment). If the criteria are met, further analyses are conducted, including: Gene expression quantification, alternative splicing analysis, novel transcript prediction, SNP detection, gene structure optimization. From the gene expression results, differentially expressed genes (DEGs) between samples are identified. Based on these DEGs, Gene Ontology (GO) functional enrichment analysis and KEGG pathway enrichment analysis are performed to determine significant biological functions and pathways. 16s rRNA sequencing: Greengenes database was used to perform taxonomic assignment. Microbiome bioinformatics was mainly performed with QIIME 2 2019.4, including the composition of gut microbiota, alpha and beta diversity index analysis. R and Linear discriminant analysis Effect Size (LEfSe) were used to analyze different species and principal components.
Assembly: RNA sequencing: Reference genome: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.26; 16s rRNA sequencing: Greengenes Release 13.8; Primers: 341F: 5’-ACTCCTACGGGRSGCAGCAG-3’, 806R: 5’-GGACTACVVGGGTATCTAATC-3’
Supplementary files format and content: group.fpkm DSS vs DSS+KS.xls; DSS_vs_DK.Differential_allgene.results.xls; otu_table_genus.xls

source_name: colon

extract_protocol:
For RNA sequencing, after extracting total RNA from the samples, eukaryotic mRNA was enriched using magnetic beads coated with Oligo(dT). For 16s rRNA sequencing, Total fecal bacterial DNA was extracted using a QIAamp® Fast DNA Stool Mini Kit (QIAamp, Germany).
For RNA sequencing, the mRNA was fragmented into short pieces by adding fragmentation buffer. Using the fragmented mRNA as a template, the first strand of cDNA was synthesized with random hexamer primers. Subsequently, the second cDNA strand was synthesized by adding buffer, dNTPs, RNase H, and DNA polymerase I. The double-stranded cDNA then underwent end repair, poly(A) tailing, and sequencing adapter ligation. The product was purified and size-selected using magnetic beads. Finally, PCR amplification was performed to generate the sequencing library. 16s rRNA sequencing: The 16S rRNA gene sequencing procedure was carried out by the Bioyigene Biotechnology Co. Ltd (Wuhan, China) using an Illumina HiSeq platform. We used the Thermo Scientific NanoDrop 2000 UV microspectrophotometer and 1.2 % agarose gel electrophoresis for quality control. Specific primers (341F: 5’-ACTCCTACGGGRSGCAGCAG-3’, 806R: 5’-GGACTACVVGGGTATCTAATC-3’) were prepared for PCR amplification using TransStart® FastPfu high fidelity DNA polymerase, and product purification was finished by Vazyme VAHTSTM DNA Clean Beads. First, the sequencing library was constructed and underwent quality inspection. Next, the libraries were sequenced using Illumina Novaseq. The library sequences were quality filtered, trimmed, denoised, and merged, and then the chimeric sequences were identified and removed to analyze the abundance, diversity and composition of the gut microbiota.

value: colon

tag: Sex

value: female

value: DSS plus 7-ketositosterol

tag: time

value: Day 21


title: TNT_1k_K562_H3K4me1_3

description: patient sample


title: 379_Neurone_AG2_S

value: SHRSP

value: Cortical neuron clusters


title: 12_miRNA profiling in Healthy subject with moderate consumption of traditional beer


title: TNT_1k_K562_H3K4me1_1

description: patient sample


title: DSS+KS_1

description: Library name: sample 4


title: General_K562_2_2_Rloop

data_processing:
*library strategy: cut&tag
Raw fastq files were first trimed using trim_galore
trimed reads were mapped to hg38 or mm10 using MACS2 with very-sensitive seting
mapped files were further removed out of duplicates, sorted and indexed.
bamCoverage was used to generate bigwig file for genome browser visualization.
Assembly: mm10/hg38

source_name: bone marrow

value: bone marrow

value: patient sample

value: cell culture


title: TNT_1k_K562_H3K4me1_2

description: patient sample


title: Control_(C)_2

description: Library name: Control_(C)_2

value: peritoneal macrophage

value: Wild type


title: 379_Endothel_AG2_S


title: DSS+KS_2

description: Library name: sample 5

value: WT


title: DSS_3

description: Library name: sample 3

value: DSS


title: 380_Endothel_AG1_S

value: Cortical blood vessels

value: Early (24-25 weeks)


title: 10_miRNA profiling in Healthy subject without moderate consumption of traditional beer

value: Whole blood


title: 8_miRNA profiling in Healthy subject without moderate consumption of traditional beer


title: 14_miRNA profiling in Healthy subject with moderate consumption of traditional beer


title: 380_Neurone_AG1_S


title: DSS_1

description: Library name: sample 1


title: 378_Endothel_AG2_S

value: Late (32-34 weeks)


title: 378_Neurone_AG2_S


title: 377_Neurone_AG1_S


title: 9_miRNA profiling in Healthy subject without moderate consumption of traditional beer


title: General_K562_1_Rloop


title: single cell cord blood rep1 R_loop

data_processing:
*library strategy: Cut&Tag
Raw fastq reader files were first mapped to hg38 or mm10 using bwa-mem2 with default setting. Generated bam files were indexed using samtools and then used to create fragment file using Sinto package with the parameter of - –barcode_regex ‘[^:]*’. Generated files were further coordinate sorted, compressed by bgzip, indexed by tabix, and used for all the downstream analysis.
To quantify the counts of genomic region of each single cell, the function of AggregateTiles in Signac was used with a binsize of 10,000, min_counts=1 using hg38 or mm10 genome. Cells with < 10,000 total counts and > 100 counts were retained for further analysis. Count matrix was first normalized by performing TF-IDF, followed by RunTFIDF and RunSVD function in package Signac with default setting. UMAP for visualization was generated by running RunUMAP, followed by clustering classification using function FindNeighbors and FindCluster with reduction and dims set as reduction=“lsi”, dim=”2:10”. DimPlot function was finally used to generate 2D UMAP.
To annotate each cluster of single cell data, cell barcodes x fragments matrix file was first obtained from Seurat project. This same fragment region was next used to quantify the reads of each purified hematopoietic cells and form a matrix file by using tool multicov from bedtools. Since no defined marker of R-loop within distinct hematopoietic cell types is available, we used Reference component analysis (RCA) package to compare the similarity of each cluster versus purified hematopoietic populations. HSC/MPP population was first annotated using the Pearson correlation matrix with sorted progenitor cells. When one cluster was predicted to resemble multiple sorted progenitor populations, manual annotation was then used to nominate it. The populations with less cell amounts were classified as mature cells, and Pearson correlation matrix was obtained by comparing with sorted mature cells. As done progenitor cells, manual annotation is used to separate similar groups in mature populations.
bamCoverage was used to generate bigwig file for genome browser visualization.
Supplementary files format and content: mm10/hg38

source_name: cord blood

extract_protocol:
All the cells were fixed by methanol first, and co-icubate with S9.6 antibody for 1 hour, followed by binding of nano body -Tn5 and activated by addition of Mg2+
For human cells, 1 million umbilical cord blood CD34+ positive cells were used as input for single cell R-loop mapping was performed. For mouse cells, 1 million c-Kit+ positive cells were used. Primary cells were firstly subjected to nuclear extraction with lysis buffer. Extracted nuclei were centrifugates and incubated with S9.6 containing antibody buffe. Unbound S9.6 was washed away with the same buffer followed by incubating cells with Dig300 washing buffer containing 5 mM nanobody Tn5 . Library preparation protocol was following the procedure of single cell nano-tag Tn5

value: cord blood

value: blood cell

value: normal people

value: cd34+ enrich


title: DSS_2

description: Library name: sample 2

value: colon

value: female

value: Day 21


title: MOLM13_2_Rloop

data_processing:
*library strategy: Cut&Tag
Raw fastq files were first trimed using trim_galore
trimed reads were mapped to hg38 or mm10 using MACS2 with very-sensitive seting
mapped files were further removed out of duplicates, sorted and indexed.
bamCoverage was used to generate bigwig file for genome browser visualization.
Assembly: hg38 or mm10
Supplementary files format and content: bw

value: bone marrow

value: patient sample


title: CT26_con_rep 2

city: Shang Hai

first: zhengke

last: lian

address: 500 Dongchuan Rd

institute: East China Normal University

description: Library name: CT26_PHF8_con_rep 2

data_processing:
Reads were mapped to the mouse mm10 genome using bowtie2 (v2.4.1) with the setting "-p 20 --phred33 --no-unal --end-to-end --very-sensitive --no-mixed -X 2000". For unique alignments, PCR duplicate reads were removed using Picard's MarkDuplicates tool (v2.23.8), which detects duplicates based on alignment coordinates and marks them to minimize redundancy in downstream analyses. Enriched peaks were called by MACS3 (3.0.0a6) or SICER2. ATAC-seq peaks were called using MACS3 (3.0.0a6).
To generate BigWig files, alignment bam files were converted into read coverage tracks using deepTools (v3.5.2) with the RPKM (Reads Per Kilobase per Million mapped reads) normalization method.
For visualization, BigWig files of biological replicates were merged using ucsc_tools (bigWigMerge and bedGraphToBigWig). Selected genomic regions were visualized in the IGV browser, illustrating continuous tag distributions across these intervals.
To compare peak enrichment across different samples, we divided the peak into evenly spaced 500 bp bins. Next, coverage signal for each bin was extracted using deepTools PyBigWig. Then, the bin with the maximum signal was used as the observed immunoprecipitation value, and differential peak criteria were set as |log₂FC| > 1 or |log₂FC| > 0.585.
For the randomly expected background value, the coverage signal of random genomic regions of the same size was measured. Heatmaps and pileups were generated using deepTools. Peak annotation and motif discovery were performed using HOMER.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
CT26 cells were digested and counted, then resuspended to obtain a suspension containing 1 × 10⁵ cells in 20 μL.
Cells were processed using the High-Sensitivity Open Chromatin Profile Kit according to the manufacturer’s instructions.DNA was extracted using Tagment DNA Extract Beads, purified with NovoNGS DNA Clean Beads, and amplified by PCR. Libraries that passed quality control were sequenced on an Illumina NovaSeq X Plus platform.

value: Mouse Colorectal Cancer


title: 5_miRNA profiling in Healthy subject without moderate consumption of traditional beer


title: 7_miRNA profiling in Healthy subject without moderate consumption of traditional beer


title: CT26_sg_rep 2

description: Library name: CT26_PHF8_ko_rep 2

value: sg PHF8


title: 377_Endothel_AG1_S

value: SHRSP


title: MOLM13_1_Rloop

value: cell culture


title: 6_miRNA profiling in Healthy subject without moderate consumption of traditional beer


title: single cell cord blood rep2 R_loop


title: 374_Endothel_AG1_S

value: Cortical blood vessels


title: 3_miRNA profiling in Healthy subject without moderate consumption of traditional beer


title: 2_miRNA profiling in Healthy subject without moderate consumption of traditional beer


title: 374_Neurone_AG1_S

value: Cortical neuron clusters

value: Early (24-25 weeks)


title: K562_32K_1_Rloop


title: CD34_2_Rloop

source_name: adult blood

value: adult blood


title: CT26_con_rep 1

description: Library name: CT26_PHF8_con_rep 1


title: K562_32K_2_Rloop


title: CT26_sg_rep 1

description: Library name: CT26_PHF8_ko_rep 1


title: 368_Endothel_AG1_W

description: Gene expression data from cortical blood vessels of Wistar rats aged 24-25 weeks

value: Wistar


title: CT26_PHF8_ko_rep 2

description: Library name: CT26_PHF8_ko_rep 2

data_processing:
Reads were mapped to the mouse mm10 genome using bowtie2 (v2.4.1) with the setting "-p 20 --phred33 --no-unal --end-to-end --very-sensitive --no-mixed -X 2000". For unique alignments, PCR duplicate reads were removed using Picard's MarkDuplicates tool (v2.23.8), which detects duplicates based on alignment coordinates and marks them to minimize redundancy in downstream analyses. Enriched peaks were called by MACS3 (3.0.0a6) or SICER2. ATAC-seq peaks were called using MACS3 (3.0.0a6).
To generate BigWig files, alignment bam files were converted into read coverage tracks using deepTools (v3.5.2) with the RPKM (Reads Per Kilobase per Million mapped reads) normalization method.
For visualization, BigWig files of biological replicates were merged using ucsc_tools (bigWigMerge and bedGraphToBigWig). Selected genomic regions were visualized in the IGV browser, illustrating continuous tag distributions across these intervals.
To compare peak enrichment across different samples, we divided the peak into evenly spaced 500 bp bins. Next, coverage signal for each bin was extracted using deepTools PyBigWig. Then, the bin with the maximum signal was used as the observed immunoprecipitation value, and differential peak criteria were set as |log₂FC| > 1 or |log₂FC| > 0.585.
For the randomly expected background value, the coverage signal of random genomic regions of the same size was measured. Heatmaps and pileups were generated using deepTools. Peak annotation and motif discovery were performed using HOMER.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
CT26 cells were digested and counted, then resuspended to obtain a suspension containing 1 × 10⁵ cells in 20 μL.
Cells were processed using the NovoNGS CUT&Tag 4.0 High-Sensitivity Kit according to the manufacturer’s instructions.DNA was extracted using Tagment DNA Extract Beads, purified with NovoNGS DNA Clean Beads, and amplified by PCR. Libraries that passed quality control were sequenced on an Illumina NovaSeq X Plus platform.


title: CT26_PHF8_ko_rep 1

description: Library name: CT26_PHF8_ko_rep 1


title: 354_Neurone_AG2_W

description: Gene expression data from cortical neuron clusters of Wistar rats aged 32-34 weeks

value: Late (32-34 weeks)


title: 368_Neurone_AG1_W

description: Gene expression data from cortical neuron clusters of Wistar rats aged 24-25 weeks


title: 1_miRNA profiling in Healthy subject without moderate consumption of traditional beer

value: Whole blood


title: CB1_2_Rloop

value: cord blood

value: blood cell

value: normal people

value: cd34+ enrich


title: Mock-transduced_4T1

city: Fukuoka

first: Satoru

last: Koyanagi

address: 3-1-1 Maidashim Higashi-ku

department: Pharmaceutical Sciences

country: Japan

institute: Kyushu University

hyb_protocol: biotin labeled miRNA was hybridized to Affymetrix GeneChip miRNA 4.0 array, washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner

data_processing: The data were analyzed with  with median polish summarization and quantile normalization by Affymetrix® Transcriptome Analysis Console Software, and obtained normalized intensity values.

label: biotin

source_name: 4T1 cells, mock-transduced

label_protocol: 130ng of total RNAs were labeled  using the FlashTag™ Biotin HSR RNA Labeling Kit (Affymetrix), following the manufacturer’s instructions (User manual of the FlashTag™ Biotin HSR RNA Labeling Kit, Affymetrix)

extract_protocol: Total RNAs including miRNAs were isolated and purified from cells using miRNeasy Mini Kit  (Qiagen)　according to the manufacturer's instructions.

value: Malignant neoplasms of the mouse mammary gland


title: 354_Endothel_AG2_W

description: Gene expression data from cortical blood vessels of Wistar rats aged 32-34 weeks


title: CT26_PHF8_con_rep 1

description: Library name: CT26_PHF8_con_rep 1


title: CD34_1_Rloop


title: 4_miRNA profiling in Healthy subject without moderate consumption of traditional beer


title: CB1_1_Rloop


title: UT-Input

city: Nanjing

first: Zhang

last: Mengyu

address: HanKou road 22

institute: Nanjing university

data_processing:
RIP-seq:
RIP-seq raw files (fastq, PE150) were aligned to the GRCh38/hg38 version of the human reference genome, using STAR with default parameters. Read counts were imported by FeatureCounts.  Differential PTBP1-binding genomic region was performed with DESeq2 packages from R. Transcripts with an adjusted p-value < 0.05 were considered as differentially PTBP1-binding genomic region.
STAR
Differential PTBP1-binding genomic region was performed with DESeq2 packages
R
Adjusted p-value < 0.05
Assembly: GRCh38/hg38
RNA-Seq:
RNA-seq raw files (fastq, PE150) were aligned to the GRCm38/mm10 version of the mouse reference genome, using TopHat2 with default parameters. Read counts were imported by FeatureCounts.  Differential gene expression was performed with DESeq2 packages from R. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
TopHat2
Differential gene expression was performed with DESeq2 packages from R
R
Adjusted p-value < 0.05
Assembly: GRCm38/mm10
Supplementary files format and content: BigWig files contain the gene expression tags counts.
Supplementary files format and content: The differential expression file was further provided (csv file).

source_name: cervical tissue

growth_protocol:
RIP-Seq: Human HeLa cells were cultured in DMEM (Life Technologies) plus 10% fetal bovine serum (FBS) and penicillin/streptomycin (Life Technologies) at 37 °C in an incubator with 95% humidified air and 5% CO2.
RNA-Seq: Neuro-2a cells (N2a) cells were cultured in DMEM (Life Technologies) plus 10% fetal bovine serum (FBS) and penicillin/streptomycin (Life Technologies) at 37 °C in an incubator with 95% humidified air and 5% CO2

extract_protocol:
RIP-Seq: The cells were collected into 1 ml of a polysome lysis buffer containing 10 mM HEPES (pH7.4), 100 mM KCl, 0.5% Nonidet P-40, 0.1% SDS, 0.5 mM DTT, and a cocktail of Roche EDTA-free protease inhibitors. The lysates were cleaned by centrifugation and used for immunoprecipitation by incubating at 4 °C with the antibody pre-bound to BeyoMag Protein A/G magnetic beads (P2108, Beyotime). The beads were washed with a buffer (50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 1 mM MgCl2, 1 mM DTT) for 5 times and then resuspended for proteinase K treatment (55 °C for 30 min). The supernatants were collected, treated with DNase I at 37 °C for 10 min to remove potential DNA contamination, and then cleaned by phenol-chloroform extraction. The RNA was ethanol precipitated and reverse transcribed into cDNA using HiScript® III SuperMix (Vazyme) and usedfor library construction.
The RNA-seq library preparation was followed by the instructions of genergy bio-technology CO., Ltd.
RNA-Seq: Total cellular RNA was extracted using the RNA Rapid Extraction Kit (Vazyme, Nanjing, China) and total tissue RNA was extracted using Trizol (Vazyme), according to the reagent instructions.

treatment_protocol:
RIP-Seq: HSV-1 infected (MOI = 3, for 12 h) or mock-infected HeLa cells were collected by scraping the cells from 10 cm plates.
RNA-Seq: The oligos of small interfering RNA (siRNA) targeting mouse PTBP1 were synthesized by GenePharma. For gene knockdown experiments, N2a cells were transfected with Lipofectamine-2000 and were used at approximately 48-60 h after transfection or as indicated.

value: cervical tissue

value: HeLa

value: cervical cancer cell

tag: rip antibody

value: WT

value: Mock infection


title: 353_Endothel_AG2_W

value: Cortical blood vessels


title: CT26_PHF8_con_rep 2

description: Library name: CT26_PHF8_con_rep 2

value: Mouse Colorectal Cancer


title: ADAR2-KD_4T1

source_name: 4T1 cells, ADAR2-KD


title: HSV-Input

value: HSV-1 infection


title: HSV-IgG3

value: IgG


title: P7-P213L-cortex-2

last: Wang

state: Zhuhai

address: Room 2007, Building 6, North HuanDao  Road 2515,

institute: Guangdong institute of intelligence and science technoloty

description: Library name: Sample6

data_processing:
RNA subjected to 50-bp single-end sequencing with a Novaseq-PE150 sequencer.
RNA-seq raw data were initially filtered to obtain clean data after quality control.
Clean data were aligned to the mouse genome (mm10) by HISAT2.
Raw counts for each gene were calculated by Htseq.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv fles include TPM values for each Sample

source_name: cortex

growth_protocol: Fresh tissue

extract_protocol:
Total RNA was extracted from tissues or cultured cells using TRIzol reagent according to the manufacturer’s instructions (Invitrogen).>1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Fresh tissue

value: cortex


title: P7-P213L-cortex-1

description: Library name: Sample5


title: P7-WT-cortex-4

description: Library name: Sample4


title: 350_Neurone_AG2_W

value: Wistar

value: Cortical neuron clusters

value: Late (32-34 weeks)


title: HSV-IgG2


title: HSV-IgG1


title: Neutro_2_Rloop

value: cord blood

value: blood cell


title: 353_Neurone_AG2_W


title: MPP_2_Rloop

value: normal people

value: cd34+ enrich


title: MPP_1_Rloop


title: HSV-IP3

value: cervical tissue


title: 350_Endothel_AG2_W


title: P7-P213L-cortex-3

description: Library name: Sample7


title: P7-WT-cortex-3

description: Library name: Sample3


title: HSV-IP2

value: HeLa


title: MONO_2_Rloop


title: 351_Endothel_AG2_W


title: P7-WT-cortex-2

description: Library name: Sample2


title: 349_Neurone_AG1_W

value: Early (24-25 weeks)


title: P7-WT-cortex-1

description: Library name: Sample1


title: 351_Neurone_AG2_W


title: Neutro_1_Rloop


title: HSV-IP1

value: cervical cancer cell

value: WT


title: 349_Endothel_AG1_W

value: Cortical blood vessels


title: MONO_1_Rloop


title: UT-IP2

value: Mock infection


title: 346_Neurone_AG1_W


title: MEP_2_Rloop


title: UT-IP3


title: PDAC_4

city: Tualatin

first: Peter

last: Pham

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Radiation Medicine

institute: OHSU

description: Library name: PDAC_4

data_processing:
Counts table were input into deseq2 for differential expression analysis
Assembly: mm10
Supplementary files format and content: counts table and metadata table.

source_name: iWAT

extract_protocol:
Wildtype C57BL/6J mice aged 12-15 weeks received orthotopic PDAC tumor injections (KrasG12D; p53R172H/+; Pdx1-cre) or sham injections.
Total RNA was extracted from cell pellets or tissues with the E.Z.N.A. Total RNA Kit II (Omega Bio-Tek Inc., Norcross, GA). cDNA was transcribed with the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Waltham, MA). Quantitative real‐time polymerase chain reaction (qPCR) was run on the ABI 7300 (Applied Biosystems) using TaqMan Fast Advanced PCR Master Mix (Applied Biosystems) or SYBR Green Master Mix (Applied Biosystems). The relative expression was calculated using the ΔΔCt method

value: iWAT


title: 343_Neurone_AG1_W


title: LMPP_2_Rloop


title: DKOP

city: Los Angeles

first: De-Chen

last: Lin

state: CA

address: CSA 210, 2250 Alcazar Street

department: Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center

institute: University of Southern California

description:
Library name: RA03
10x  Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v.7.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values fles and matrix files
Supplementary files format and content: Fastq files

source_name: tongue

growth_protocol: Organoid were embeded in Cultrex basement membrane extract and maintained in aDME/F12 based organoid condtion medium.

extract_protocol:
Mouse organoids were dissociated into single cells and resuspended in organoid culture medium for the library preparation.
The Chromium Next GEM Single-Cell 3ʹ Reagent Kit (10× Genomics) was used according to the manufacturer's protocols. Briefly, organoid cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI), and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR, and the appropriate sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction, Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences, and a sample index were added.

value: tongue

value: Mouse organoids

value: Epithelial cells

value: Trp53/Cdkn2a double knockout + PI3KCA E545k


title: PDAC_5

description: Library name: PDAC_5


title: PDAC_1

description: Library name: PDAC_1


title: LMPP_1_Rloop


title: HSC_2_Rloop


title: HSC_1_Rloop


title: PDAC_2

description: Library name: PDAC_2


title: UT-IP1


title: 346_Endothel_AG1_W

value: Wistar


title: Sham_4

description: Library name: Sham_4


title: Sham_5

description: Library name: Sham_5


title: MEP_1_Rloop

value: cord blood


title: amniotic fluid

type: genomic

city: Lianyungang

first: Fang

last: Zhang

state: Jiangsu

address: Qindongmen Street No.669

institute: Lianyungang Maternal and Child Health Hospital

description: Hybridized to 750K_Nsp

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Affymetrix protocol

source_name: amniotic fluid CMA14q

label_protocol: Affymetrix protocol

extract_protocol: Affymetrix protocol

tag: tag

value: uncultured amniotic fluid cells


title: 343_Endothel_AG1_W

data_processing:
Quality Assessment (FASTQC version 0.11.5)
Trimming (bbduk from BBTools v37.93)
Alignment (STAR v2.5.3a)
Gene read counts (HTSeq-count v0.6.1)
Differential expression analysis (DESeq2 v1.18.1)
Assembly: Rattus norwegicus (Rnor6)
Supplementary files format and content: Unnormalized count-table


title: DKOC

description:
Library name: RA02
10x  Genomics

value: Trp53/Cdkn2a double knockout


title: 340_Neurone_AG1_W

value: Cortical neuron clusters


title: CMP_1_Rloop

extract_protocol:
All the cells were first fixed by methanol, mobilized on Concanavalin A beads, folllowed by S9.6 anbibody incubation and nanobody Tn5 binding. Mg2+ was added to activate the cutting of Tn5
Recovered chromotain DNA was first end repaired using Bst 2.0, followed by in vitro transcription of T7 promoter. Transcribed RNA was first reverse converted to first cDNA and second DNA strand. Double strand DNA was cut by second Tn5. Library was amplified by DNA polymerase.

value: blood cell

value: normal people

value: cd34+ enrich


title: GMP_2_Rloop


title: Ctrl

description:
Library name: RA01
10x  Genomics


title: 340_Endothel_AG1_W

value: Early (24-25 weeks)


title: CLP_2_Rloop


title: EL4-NP68 specific memory CD8 T cell restimulated

city: Lyon

first: Simon

last: de Bernard

address: 30 rue Pré Gaudry

institute: AltraBio

description: Library name: EL4_R

data_processing:
Quality control of the raw data was performed using FastQC. The Nextera Transposase Sequence and low-quality bases were trimmed using Trim Galore. Transcript expression was quantified using Salmon and version M23 of GENCODE mouse genome and transcriptome. The gene/count matrix was generated with tximport. Cells were filtered using the metric_sample_filter function implemented in SCONE package. For each criterion (the number of reads, the number of detected genes and the areas under the false negative rate (FNR) curve employing housekeeping genes), values greater than three median absolute deviations from the median were excluded. Moreover, genes expressed in fewer than three cells were removed.
Assembly: GRCm38.p6
Supplementary files format and content: csv file

source_name: Spleen

extract_protocol:
B6 mice were transferred with naive CD8 T cells from F5 transgenic mice. The next day, mice were hallenge with vaccinia virus (VV) or EL4 tumor cells, both expressing NP68 peptide. CD45.1+ F5 memory cells were sorted from the spleens of VV- or EL4-immunised mice 9 weeks after the primary challenge. Naive F5 cells were sorted from the spleen of F5 x CD45.1 mice. Total CD8 T cells were first enriched from splenocytes using an autoMACS® Pro Separator with the CD8a+ T cell isolation kit (Miltenyi Bio-tec) according to manufacturer’s instructions. Enriched CD8 T cells were stimulated (VV-CD8_R, EL4-CD8_R, naive_R)  or not (VV-CD8, EL4-CD8, Naive) with NP68 peptide (10 nM) for 2h at 37 °C. F5 cells were then single-cell sorted according to their viability and their expression of CD45.1, CD8a, and CD44. Single cell dDNA were prepared using Smart-Seq2 protocol.
Cells were sorted into a 96-well plate containing 4 uL of lysis solution (PBS, 0,04% Triton 0,4%, 2 U/uL RNaseOut [TFS], 2,5 uM of poly(T) reverse transcription primers and 2,5 mM dNTPs), on a FACS Aria II (BD Biosciences). Library construction was performed following the Smart-seq2 protocol. Briefly, mRNA was reverse transcribed into cDNA and pre-amplified by PCR. cDNAs was then fragmented by tagmentation and Illumina sequencing adaptors containing in-dexes allowing for cell identification were added. The cDNA was amplified by PCR. Each 96-cells libraries were pooled together and both quality and quantity were tested using  a DNA high sensitivity D1000 ScreenTape on Tapestation 4200 (Ag-ilent). Libraries were sequenced on an Illumina HiSeq in paired-ends (2 x 150 bp) at an average sequencing depth of ∼1M reads/cells.

value: Spleen

value: CD8 T cells transgenic for F5 TCR and sorted from spleen

value: CD8 T cells transgenic for F5 TCR

value: Subcutaneous immunization with EL4 cells expressing NP68 peptide (EL4-NP68)  In vitro stimulation with NP68 peptide, after cell sorting


title: EL4-NP68 specific memory CD8 T cell

description: Library name: EL4

value: Subcutaneous immunization with EL4 cells expressing NP68 peptide (EL4-NP68)


title: Sham_3

description: Library name: Sham_3

value: iWAT


title: Naive F5 CD8 T cell

description: Library name: Naive


title: GMP_1_Rloop


title: Leaves from 3-week-old NPB rice plants, infected with Magnaporthe oryzae at 24 hpi, REP2

city: Changsha

first: Xuanning

last: Zeng

address: Hunan Agricultural University

institute: College of Plant Protection

data_processing:
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). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: CT836194
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Oryza sativa

source_name: Leaves from 3-week-old

growth_protocol: the rice seedlings were transplanted into pots with sterilized nutrient soil and grown in a greenhouse under conditions of 28 °C with a 16-hour light/8-hour dark photoperiod

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

treatment_protocol: Three-leaf stage rice seedlings were subjected to spray inoculation.

value: Leaves from 3-week-old

value: Nipponbare T3

tag: genetic background

value: Nipponbare

value: WT

value: Magnaporthe oryzae at 24 hpi


title: PDAC_3

description: Library name: PDAC_3

tag: tissue


title: CMP_2_Rloop

value: cord blood

tag: cell line


title: Leaves from 3-week-old OsWHY1-overexpressed-1 rice plants, infected with Magnaporthe oryzae at 24 hpi

value: OsWHY1-overexpressed-1 T3

tag: treatment


title: GES1 Control 1

city: Charlottesville

first: Robert

last: Cornelison

state: VA

address: 345 Crispell Drive Carter-Harrison Research Building MR6 B710 Carter-Harrison Research Building MR6 B710

department: pathology

institute: UVA School of Medicine

description: Library name: C1

data_processing:
sequences were checked for QC with fastqc, aligned using kallisto to hg38
Assembly: Homo_sapiens.GRCh38.112
Supplementary files format and content: kallisto abunances in TSV format

source_name: gastric epithelia

growth_protocol: The immortalized human gastric epithelium cell line GES1 was clitured DMEM plus 10% FBS and the gastric adenocarcinoma cell line AGS (ATCC® CRL-1739) were cultured in F-12K medium plus 10% FBS.

extract_protocol:
All cell samples were extracted by Trizol  first and then use Rneasy Mini Kit for RNA purification
Novogen company perform the sample quality check (QC) using (1) 1% Agarose gel electrophoresis, (2) Nanodrop reading to check for RNA amount and purity, and (3) Agilent2100 to check for RNA Integrating Number (RIN). At Novogene, they deploy each of these three methods to check the quality of the data you send to us, thereby ensuring you work only with the highest quality data. Once  confirm the quality of the extracted total RNA is good,  and  move on with the protocol and perform the Library Construction step. The polyA enrichment library preparation procedure is most commonly used when working with mRNA-Seq data and results in the construction of 250-300 bp insert cDNA library.

treatment_protocol: AGS cell line was treated compound A (final concentration 20uM) or DMSO two days.

value: gastric epithelia

value: gastric normal epithelia

value: control plasmid


title: CLP_1_Rloop

last: Lu

address: 417 East 68th Street New York,

institute: mskcc

value: blood cell

value: normal people

value: cd34+ enrich


title: GES1 AVIL overexpression 3

description: Library name: D3

value: AVIL overexpression


title: GES1 AVIL overexpression 2

description: Library name: D2


title: Sham_2

description: Library name: Sham_2


title: VV-NP68 specific memory CD8 T cell

description: Library name: VV

value: Spleen

value: CD8 T cells transgenic for F5 TCR and sorted from spleen

value: CD8 T cells transgenic for F5 TCR

value: Intranasal infection with vaccinia virus expressing NP68 peptide (VV-NP68)


title: CD71_1_Rloop


title: Leaves from 3-week-old OsWHY1-overexpressed-4 rice plants, infected with Magnaporthe oryzae at 24 hpi

value: Leaves from 3-week-old

value: OsWHY1-overexpressed-4 T3


title: Naive F5 CD8 T cell restimulated

description: Library name: Naive_R

value: In vitro stimulation with NP68 peptide, after cell sorting


title: GES1 AVIL overexpression 1

description: Library name: D1


title: CD71_2_Rloop


title: Sham_1

description: Library name: Sham_1

value: iWAT


title: SAC_WT_input_1

city: Daejeon

first: Ki-Jun

last: Yoon

address: 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
Illumina Real Time Analysis (RTA3) is used for base calling and blc2fastq is used for fastq file conversion.
Cutadapt (v3.5) is used for adapter trimming.
For aligment, STAR (v2.7.10a, --alignEndsType Local --outFilterMatchNminOverLread 0.66 --outFilterMatchNmin 15 --outFilterMismatchNmax 5 --outFilterMismatchNoverLmax 0.2 --outFilterMultimapNmax 50 --outSAMmultNmax -1) and bowtie2 (v2.4.5, -no-unal --end-to-end -L 16 -N 1 --mp 5 --un-conc) are used.
Peak calling is used with customized python code following published protocol (https://github.com/y9c/m6A-SACseq)
Assembly: mm10
Supplementary files format and content: tab-seperated text files including chromosome, position, mutated reference base, strand, depth, and captured mutated sequence  which are estimated as m6A peak
Library strategy: m6A-SAC-Seq

source_name: Forebrain

extract_protocol:
RNA was extracted using TRIzol (Qiagen), and mRNA was isolated using the Dynabeads™ mRNA DIRECT™ Purification Kit (Invitrogen). 50 ng of mRNA was used for sequencing library construction.
RNA libraries for m6A-SAC-Seq were prepared using a manual protocol. After the treatment protocol described above, cDNA was synthesized using HIV Reverse Transcriptase (Worthington) and Actinomycin D (Sigma). cDNA libraries were then prepared using NEBNext Ultra II Q5 Master Mix and NEBNext Multiplex Oligos for Illumina (NEB).

value: Forebrain

value: WT


title: SAC_cKO_2

value: Nestin-Cre Mettl14 cKO


title: VV-NP68 specific memory CD8 T cell restimulated

description: Library name: VV_R

value: Intranasal infection with vaccinia virus expressing NP68 peptide (VV-NP68)  In vitro stimulation with NP68 peptide, after cell sorting


title: AGS DMSO 3

description: Library name: B17231

source_name: gastric cancer

value: gastric cancer

value: AGS

value: DMSO CONTROL


title: Leaves from 3-week-old NPB rice plants, infected with Magnaporthe oryzae at 24 hpi, REP3

value: Nipponbare T3

value: Nipponbare

value: Magnaporthe oryzae at 24 hpi


title: SAC_cKO_input_2


title: CD4_1_Rloop

city: NY

first: Bin

value: cord blood

value: blood cell

value: normal people

value: cd34+ enrich


title: AGS DMSO 2

description: Library name: B17228


title: CD8_2_Rloop


title: Leaves from 3-week-old NPB rice plants, infected with Magnaporthe oryzae at 24 hpi, REP1

value: Leaves from 3-week-old


title: SAC_cKO_1


title: CD8_1_Rloop


title: SAC_cKO_input_1


title: GES1 Control 3

description: Library name: C3

value: gastric epithelia

value: gastric normal epithelia

value: control plasmid


title: Leaves from 3-week-old OsWHY1-overexpressed-18 rice plants, infected with Magnaporthe oryzae at 24 hpi

value: OsWHY1-overexpressed-18 T3


title: AGS Compound-A 3

description: Library name: B17232

value: Compound-A Avil inihbition


title: AGS Compound-A 2

description: Library name: B17229


title: GES1 Control 2

description: Library name: C2


title: SAC_WT_input_2

value: Forebrain

value: WT


title: IgG rep2

city: Wuhan

first: Fan

last: Fuqiang

address: 1 Shizishan St

institute: Huazhong Agricultural University

description: Library name: IgG rep2

data_processing:
To determine the target sequence of AP2XI-3-mAID-3HA, raw data were quality controlled by cutadapt and mapped to reference genome GT1 (ToxoDB, version 68) using bowtie2 and duplicated sequences were marked by picard (http://broadinstitute.github.io/picard/). Peak calling was performed using MACS2 and peak overlap was subjected to bedtools. For de novo motif search, the peak sequence falls within 2 kb or 3 kb distance from TSS were subjected to STREME with default parameters.
Assembly: ToxoDB TGGT1 v68
Supplementary files format and content: peak annotation in text file and bigwig files for each sample
Library strategy: CUT&Tag

organism: Toxoplasma gondii

source_name: Toxoplasma

growth_protocol: All parasites strain used in this study were cultured in human foreskin fibroblast cells in high-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 unit/mL penicillin, and 100 mg/mL streptomycin at 37 °C with 5% CO2.

extract_protocol:
Cleavage Under Targets and Tagmentation was performed by using commercial Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (TD904, Vazyme Biotech) according to the manufacturer’s instructions. The strain, RH iAP2XI-3-mAID-3HA was collected and bounded to Concanavalin A-coated beads. The anti-HA tag antibody (ab9110, Abcam) was used as primary antibody. After incubation of primary and secondary antibodies, the samples were subjected to transposon activation and tagmentation.
Then targeted DNA was isolated, amplified, and purified to construct library by using VAHTS DNA Clean Beads (N411, Vazyme Biotech). Finally, the library was quantified and sequenced on the Illumina novaseq 6000 sequencer with the PE150 model.

value: Toxoplasma

value: RH iAP2XI-3-mAID-3HA

value: IgG


title: HA rep2

description: Library name: HA rep2

value: HA


title: SAC_WT_2


title: CD4_2_Rloop


title: AGS Compound-A 1

description: Library name: B17226

value: gastric cancer

value: AGS


title: BCELL_2_Rloop

value: cord blood

value: blood cell


title: SAC_WT_1


title: AGS DMSO 1

description: Library name: B17225

value: DMSO CONTROL


title: BCELL_1_Rloop

value: normal people

value: cd34+ enrich


title: G:K:TG011

status: Public on Dec 31 2025

city: Glendale

first: Crystal

last: Marconett

address: 1856 Kirkby Rd

department: Translational Genomics

institute: Keck School of Medicine

description: 10X Genomics

data_processing:
Fastq data was put into the 10X Cell Ranger platform for alignment and data processing into HDF5 files
Assembly: mm39
Supplementary files format and content: Cell Ranger HDF5 Feature-Barcode Matrix Format

molecule: nuclear RNA

source_name: Lung

growth_protocol: All mice were be housed in microisolator cages within the specific pathogen-free (SPF) environment in Hoffman Medical Research Center (HMR) at USC. All animal protocols are reviewed semiannually and annually and monitored continuously by an Institutional Animal Care and Use Committee (IACUC). Veterinary care is provided by USC’s Animal Resources Center. The facility has received full AAALAC accreditation.

extract_protocol:
Mice were euthanized with 100 uL Euthasol by IP injection. Lungs were perfused with 20 mL PBS to flush peripheral blood from lungs. Lungs were snap frozen in liquid nitrogen, and 10x genomics nuclei isolation kit (1000494) was use to isolate, purify and enrich nuclei from tissues.
10X Genomics Next GEM 3' Gene Expression Library Construction

treatment_protocol: Oncogenic KRASG12D was induced by tamoxifen through IP injection. Control mice received corn oil administration by IP injection.

value: Lung

value: Tamoxifen


title: G:K:TG014

description: 10X Genomics


title: HA rep1

description: Library name: HA rep1


title: G:K:TG007

description: 10X Genomics

value: Corn Oil


title: G:K:TG004

description: 10X Genomics


title: IgG rep1

description: Library name: IgG rep1


title: mTmG001

description: 10X Genomics

value: ROSAmTmG


title: S:K:TG003

description: 10X Genomics


title: S:TG001

description: 10X Genomics


title: S:K:TG005

description: 10X Genomics


title: S:K:TG009

description: 10X Genomics


title: G:TG001

description: 10X Genomics


title: S:K:TG010

description: 10X Genomics


title: WT001

description: 10X Genomics


title: Group: CAR19/CXCR4S338X without CXCL12 (related to Figure 5, shown as sample b)

status: Public on Dec 28 2025

city: Changchun

first: Yushu

last: Mao

address: Xinzhu Road

institute: Jinlin university

description: Library name: DBW_SA

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Assembly: hg38
Supplementary files format and content: FPKM values for each sample; two files generated from independent analyses

source_name: peripheral blood

extract_protocol:
Cell samples were lysed in 1 mL TRIzol reagent and extraced according to manufacturer's protocol.
mRNA was enriched from total RNA using oligo(dT) magnetic beads. After fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. The resulting cDNA underwent end repair, A-tailing, adapter ligation, size selection, amplification, and purification to generate the final sequencing library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: 1×10^6 T cells were resuspended with 100 IU IL-2 in 600 μL T Cell Expansion Medium, and 100 ng/mL CXCL12 or the same volume of PBS was added into the culture system, RNA of the cells were extracted 6 hours later.

value: peripheral blood

value: primary T cells

value: Group:CAR19/CXCR4S338X without CXCL12


title: CAR19/CXCR4S338X with CXCL12 (related to Fig 4G, representative; related to Fig 5, shown as sample c)

description: Library name: HL_28SB

value: Group:CAR19/CXCR4S338X with CXCL12


title: S:K:TG008

description: 10X Genomics


title: Group: CAR19/CXCR4S338X without CXCL12 (related to Figure 4G, not shown 10)

description: Library name: MYS_28SA


title: Group: CAR19/CXCR4S338X with CXCL12 (related to Fig 4G, not shown 11; related to Fig 5, shown as sample a)

description: Library name: DQH_28SB


title: Group: CAR19/CXCR4S338X with CXCL12 (related to Figure 4G, not shown 12)

description: Library name: MYS_28SB


title: G:K:TG005

description: 10X Genomics


title: Group: CAR19/CXCR4S338X with CXCL12 (related to Figure 5, shown as sample b)

description: Library name: DBW_SB


title: Group: CAR19/CXCR4S338X without CXCL12 (related to Fig 4G, not shown 9; related to Fig 5, shown as sample a)

description: Library name: DQH_28SA


title: Group: CAR19/CXCR4WT without CXCL12 (related to Figure 4G, not shown 5)

description: Library name: DQH_28CA

value: Group:CAR19/CXCR4WT without CXCL12


title: Group: CAR19/CXCR4WT without CXCL12 (related to Figure 4G, representative)

description: Library name: HL_28CA


title: Group: CAR19/CXCR4WT with CXCL12 (related to Figure 4G, representative)

description: Library name: HL_28CB

value: Group:CAR19/CXCR4WT with CXCL12


title: Group: CAR19/CXCR4S338X without CXCL12 (related to Fig 4G, representative; related to Fig 5, shown as sample c)

description: Library name: HL_28SA


title: Group: CAR19 without CXCL12 (related to Figure 4G, not shown 2)

description: Library name: MYS_28ZA

value: Group:CAR19 without CXCL12


title: Group: CAR19/CXCR4WT with CXCL12 (related to Figure 4G, not shown 8)

description: Library name: MYS_28CB


title: Group: CAR19/CXCR4WT without CXCL12 (related to Figure 4G, not shown 6)

description: Library name: MYS_28CA


title: Dox1

status: Public on Dec 27 2025

city: Honolulu

first: Xue

state: HI

address: 701 Ilalo Street

department: Cancer Biology Program

institute: University of Hawaii Cancer Center

description:
Library name: Dox1
Column name in Processed data_fpkm.txt: Dox1

data_processing:
Poor quality reads were trimmed using the fastq-mcf (v1.05). Reads quality was checked using the fastqc (v0.11.7).
Gene read counts were in Ensembl Gene ID and converted to Entrez Gene ID.
Corresponding Symbol annotations and full gene names were added using the “org.Hs.eg.db” library. NA (Not Annotated), duplicate Entrez IDs and genes without symbols were removed.
After removing the duplicated genes, the fragments per kilobase of transcript per million mapped reads (FPKM) were calculated.
Assembly: GRCh38
Supplementary files format and content: The tab-delimited text file includes FPKM values for each sample

source_name: SNU449 liver cancer cells

growth_protocol: pInducer20-FOXO1AAA SNU449 cells were cultured in RPMI 1640 medium (DMEM) (Cat# 11875093, Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in an atmosphere of humidified air containing 5% CO2. Cell viability was more than 90% according to trypan blue exclusion analysis.

extract_protocol:
Total RNA was extracted from Cont (n=3) and Dox (n=3) groups using RNAiso Plus according to the manufacturer’s protocol.
RNA-seq libraries were prepared by poly(A) capture, followed by reverse transcription into cDNA.

treatment_protocol: pInducer20-FOXO1AAA SNU449 cells were treated with or without 2 μM doxycycline hydrochloride (Dox) for 48 hours.

value: SNU449 liver cancer cells

value: total RNA

value: WT


title: Cont2

description:
Library name: Cont2
Column name in Processed data_fpkm.txt: Cont2


title: Group: CAR19 with CXCL12 (related to Figure 4G, not shown 3)

description: Library name: DQH_28ZB

value: Group:CAR19 with CXCL12


title: Group: CAR19 with CXCL12 (related to Figure 4G, not shown 4)

description: Library name: MYS_28ZB


title: Group: CAR19 without CXCL12 (related to Figure 4G, not shown 1)

description: Library name: DQH_28ZA


title: Dox3

description:
Library name: Dox3
Column name in Processed data_fpkm.txt: Dox3


title: Group: CAR19/CXCR4WT with CXCL12 (related to Figure 4G, not shown 7)

description: Library name: DQH_28CB


title: Lymph node cells, remitter-rep3

status: Public on Dec 23 2025

city: New Haven

first: Ying

last: Wu

state: CT

address: 300 George St

institute: Yale University

description:
Library name: Remitter_NOD_3_pLN
10x Genomics

data_processing:
The demultiplexing, aligning reads, counting barcodes and UMIs, generating feature-barcode matrices, and performing clustering and gene expression analysis was performed using Cell Ranger software v7.1.0.
Assembly: Mouse mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lymph node

extract_protocol:
The isolated mouse islets were incubated in 2ml Accutase™ Cell Dissociation reagent at room temperature for 5 mins on a tube rotator. After incubation, islet cells were resuspened thoroughly by pipet up and down. Five-time volume of culture medium with 10% FBS was added to stop excessive dissociation reactions. Then dissociated islet cells were washed and resuspened in PBS with 0.04% BSA. Pancreatic draining lymph node cells were dispersed into single cells by grinding the samples using the blunt end of a syringe over a cell strainer. Alive cells were counted using trypan blue and hemacytometer.
Library was constructed according to the manufacturer's protocols (Chromium Next GEM Single Cell 5' v2, Dual Index, 10X Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). Gel bead primers contain an Illumina TruSeq Read 1 primer, a 10x Barcode, a unique molecular identifier (UMI), and template switch oligo (TSO). Then the poly-A mRNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which was amplified. The amplifiedd cDNA from poly-A mRNA and the amplified DNA from cell surface protein Feature Barcode are separated by size selection for generating V(D)J and/or 5' Gene Expression libraries and Cell Surface Protein (hashtag) libraries, respectively.

value: Lymph node

value: female

value: Lymph node cells

value: NOD

value: anti-CD3 mAb


title: Group: CAR19 without CXCL12 (related to Figure 4G, representative)

description: Library name: HL_28ZA


title: Primary HGSOC patients 006

city: Incheon

first: Mi-Ryung

last: Han

address: 265, Harmony-ro, Yeonsu-gu, Incheon, Republic of Korea

institute: Incheon National University

description: Library name: SS2171265

data_processing:
The quality of raw data was ensured using the FastQC v0.11.9.
Adapter sequences were trimmed using Trimfastq from Fabio v2.1.0, then trimmed FASTQ files were aligned to GRCh37.p13 using STAR v2.7.10.
Assembly: GRCh37.p13
Supplementary files format and content: TXT file containing detected gene fusions.
Supplementary files format and content: TXT file containing detected gene fusions.

source_name: Tumor tissue

extract_protocol:
RNA was extracted from formalin-fixed, paraffin-embedded (FFPE) tissue sections of HGSOC patients RNeasy Plus Kits (Qiagen, NY, USA).
Library preparation was performed using the TruSight Oncology 500 (TSO500) panel (Illumina, San Diego, CA, USA).

tag: disease status

value: Primary

tag: tumor stage

value: IIIB

value: Female

value: Tumor tissue


title: Cont1

description:
Library name: Cont1
Column name in Processed data_fpkm.txt: Cont2


title: Primary HGSOC patients 008

description: Library name: SS2166116

value: IVB


title: Primary HGSOC patients 003

description: Library name: SS2213255

value: IIIC


title: Primary HGSOC patients 002

description: Library name: SS2214517


title: Dox2

description:
Library name: Dox2
Column name in Processed data_fpkm.txt: Dox2


title: Primary HGSOC patients 007

description: Library name: SS2166736


title: Recurrent HGSOC patients 001

description: Library name: SS2215507

value: Recurrent


title: Lymph node cells, remitter-rep4

description:
Library name: Remitter_NOD_4_pLN
10x Genomics

tag: strain


title: Group: CAR19 with CXCL12 (related to Figure 4G, representative)

description: Library name: HL_28ZB

value: peripheral blood

value: primary T cells


title: Cont3

description:
Library name: Cont3
Column name in Processed data_fpkm.txt: Cont3

value: SNU449 liver cancer cells

value: total RNA


title: Lymph node cells, remitter-rep2

description:
Library name: Remitter_NOD_2_pLN
10x Genomics


title: Primary HGSOC patients 018

description: Library name: SS2115211


title: Primary HGSOC patients 005

description: Library name: SS2180551


title: Primary HGSOC patients 004

description: Library name: SS2209402


title: Primary HGSOC patients 009

description: Library name: SS2165809


title: Primary HGSOC patients 011

description: Library name: SS2159212


title: Recurrent HGSOC patients 013

description: Library name: SS2146489


title: Primary HGSOC patients 012

description: Library name: SS2153839


title: Primary HGSOC patients 021

description: Library name: SS2106755


title: Primary HGSOC patients 023

description: Library name: SS2071919


title: Primary HGSOC patients 010

description: Library name: SS2164961


title: Primary HGSOC patients 029

description: Library name: SS2053409


title: Primary HGSOC patients 024

description: Library name: SS2070425


title: Primary HGSOC patients 031

description: Library name: SS2053053


title: Primary HGSOC patients 017

description: Library name: SS2118814


title: Recurrent HGSOC patients 033

description: Library name: SS2051456

value: IIIA


title: Primary HGSOC patients 016

description: Library name: SS2123225


title: Primary HGSOC patients 030

description: Library name: SS2053339

value: IVA


title: Primary HGSOC patients 034

description: Library name: SS2051316


title: Primary HGSOC patients 036

description: Library name: SS2039846


title: Primary HGSOC patients 019

description: Library name: SS2112337


title: Primary HGSOC patients 035

description: Library name: SS2042190


title: Primary HGSOC patients 022

description: Library name: SS2104482


title: Primary HGSOC patients 039

description: Library name: SS2029051


title: Recurrent HGSOC patients 015

description: Library name: SS2131323

value: III


title: Primary HGSOC patients 014

description: Library name: SS2142849


title: Recurrent HGSOC patients 026

description: Library name: SS2057730


title: Primary HGSOC patients 046

description: Library name: SS2016863


title: Recurrent HGSOC patients 025

description: Library name: SS2066520


title: Recurrent HGSOC patients 028

description: Library name: SS2056315

value: R


title: Recurrent HGSOC patients 037

description: Library name: SS2039208


title: Primary HGSOC patients 032

description: Library name: SS2052569


title: Primary HGSOC patients 042

description: Library name: SS2026934


title: Primary HGSOC patients 041

description: Library name: SS2027136


title: Primary HGSOC patients 027

description: Library name: SS2056361


title: Primary HGSOC patients 044

description: Library name: SS2023142


title: Primary HGSOC patients 020

description: Library name: SS2112292


title: Primary HGSOC patients 047

description: Library name: SS2015449


title: Recurrent HGSOC patients 040

description: Library name: SS2028780