title: U2OS cells, Hydroxyurea (HU) treated, Rep 1

status: Public on Sep 30 2025

type: SRA

city: Liverpool

first: Claire

last: Wilson

address: Ashton Street

country: United Kingdom

institute: University of Liverpool

description: Library name: H1A

library_source: other

data_processing:
Quality assessed using FastQC(v0.11.9).
Sequence reads were trimmed for adapters and low-quality reads using TrimGalore (v0.6.6).
Genome mapping was performed with STAR (v2.7.10b) against the human reference genome (hg38 assembly).
Read coverage performed to calculate raw counts using samtools/1.13.
RPKM calculated and differential analysis was performed using R Studio.
Assembly: hg38
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample
Library strategy: Chromatin-RNA-Seq

molecule: other

organism: Homo sapiens

source_name: Bone

growth_protocol: Cells were authenticated by STR profiling (ATCC) and grown in Dulbecco’s modified Eagle’s Medium (DMEM) with 10% foetal bovine serum (FBS), L-Glutamine (2 mM), Streptomycin (50 μg/mL) and Penicillin (50 U/mL) in a humidified atmosphere containing 5% CO2

extract_protocol:
Cells were resuspended in cytoplasmic lysis buffer (0.15% NP-40, 10 mM Tris-HCl pH 7.0, 150 mM NaCl) before being incubated with ice for 5 min. The lysate was then poured on top of Sucrose buffer (10 mM Tris-HCl pH 7.0, 150 mM NaCl, 25% sucrose) and centrifuged at 16,000g for 10 min. The nuclei were resuspended in nuclei wash buffer (0.1% Triton X-100, 1 mM EDTA, in 1x PBS) before being centrifuged at 1500g for 1 min. The pellet was resuspended in glycerol buffer (20 mM Tris-HCl pH 8.0, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol, 0.85 mM DTT), and then nuclei lysis buffer (1% NP-40, 20 mM HEPES pH 7.5, 300 mM NaCl, 1M Urea, 0.2 mM EDTA, 1 mM DTT) was added before the sample was vortexed and put on ice. The sample was centrifuged further for 2 min at 18,500g, and the nucleoplasm fraction was extracted by removing the supernatant. The chromatin was resuspended in chromatin resuspension buffer (25 μM α-amanitin, 50 Units SUPERaseIN, Protease inhibitors cOmplete, in 1x PBS). The chromatin fraction was extracted using the Zymol RNA extraction kit following manufacturer’s instructions. RNA quality and concentration was determined using the 4200 tapestation system.
NEBNext® Ultra™ II RNA Library Prep Kit for Illumina

treatment_protocol: Cells were plated, treated with camptothecin (10 mM, 2h), hydroxyurea (200 mM, 2h) or DMSO control (2h) and harvested.

tag: tissue

value: Bone

tag: cell line

tag: cell type

value: Human osteosarcoma cells

tag: treatment


title: U2OS cells, Hydroxyurea (HU) treated, Rep 3

description: Library name: H3C


title: U2OS cells, Camptothecin (CPT,) treated, Rep 3

description: Library name: C3C

value: CPT, 10 mM, 2 h


title: U2OS cells, Hydroxyurea (HU) treated, Rep 2

description: Library name: H2B


title: U2OS cells, Camptothecin (CPT) treated, Rep 1

description: Library name: C1A


title: Parental U2OS cells, Control, Rep 2

description: Library name: U2B

value: dimethylsulfoxide (DMSO), 2h


title: Parental U2OS cells, Control, Rep 3

description: Library name: U3C


title: U2OS cells, Camptothecin (CPT) treated, Rep 2

description: Library name: C2B


title: Parental U2OS cells, Control, Rep 1

description: Library name: U1A


title: CTRL00021

city: Chicago

first: Amir

middle: M.

last: Alhajjat

state: Illinois

address: 225 E Chicago Ave

country: USA

institute: Ann & Robert H. Lurie Children's Hospital of Chicago

description: Library name: CTRL0021_S2

data_processing:
The quality of reads was evaluated using FastQC in FASTQ format. Reads were trimmed to remove Illumina adapters from the 3’ ends using cutadapt.
Assembly: Read counts for each gene were calculated using htseq-count in conjunction with a gene annotation file for hg38 obtained from miRbase.
Supplementary files format and content: Samples were identified as technical outliers when the overall miRNA expression (counts) fell outside of an established cutoff of 100–1000 reads per million (RPM) and subsequently removed. Differential expression in disease and clinical severity was performed after duplicate miRNAs were removed and counts data was filtered to only include miRNAs with at least 10 counts across 75 % of samples through normalization and analysis in DESeq2 which utilizes the Wald test for significance (normalized counts files not included).

source_name: plasma

extract_protocol:
miRNA was isolated from frozen patient plasma using a miRNeasy kit (Qiagen, Hilden, Germany), snap frozen, and stored at −80 °C prior to sequencing. Small RNA-seq was performed via the Illumina Sequencing Platform.
Small RNA Sequencing library preparation. Trimmed reads were aligned to the human miRBase database using bowtie2.

value: plasma

tag: condition

value: healthy


title: CTRL00163

description: Library name: CTRL00163_S7


title: CTRL00318

description: Library name: CTRL00318_S11


title: CTRL00173

description: Library name: CTRL00173_S8


title: CTRL00200

description: Library name: CTRL00200_S10


title: CTRL00139

description: Library name: CTRL00139_S6


title: CTRL00196

description: Library name: CTRL00196_S9


title: CDH00494

description: Library name: CDH00494_S31

value: congenital diaphragmatic hernia


title: CDH00528

description: Library name: CDH00528_S40


title: CDH00432

description: Library name: CDH00432_S28


title: CTRL00127

description: Library name: CTRL00127_S4


title: CDH00439

description: Library name: CDH00439_T0_S29


title: CDH00292

description: Library name: CDH00292_S23


title: CDH00362

description: Library name: CDH00362_S25


title: CDH00374

description: Library name: CDH00374_S26


title: CDH00497

description: Library name: CDH00497_S39


title: CDH00378

description: Library name: CDH00378_T1_S27


title: CDH00269

description: Library name: CDH00269_S35


title: CDH00253

description: Library name: CDH00253_S34


title: CDH00215

description: Library name: CDH00215_S20


title: CDH00208

description: Library name: CDH00208_S19


title: CDH00193

description: Library name: CDH00193_S18


title: CDH00094

description: Library name: CDH0094_S22


title: CDH00059

description: Library name: CDH0059_S13


title: CDH00087

description: Library name: CDH0087_S21


title: CDH00189

description: Library name: CDH00189_S17


title: CDH00154

description: Library name: CDH00154_S16


title: BPH1 ZC3H13 KO replicate 3

city: Salamanca

first: Sandra

last: Blanco

address: Campus Universitario

country: Spain

institute: CSIC

description:
Library name: ZC3KOR3
RNA-Seq library preparation of BPH1 Prostate cancer cell line

library_source: transcriptomic

data_processing:
Kallisto
Assembly: hg38
Supplementary files format and content: Excel file with counts per transcript

molecule: total RNA

source_name: Prostate

growth_protocol: BPH-1 cells were cultured in RPMI supplemented with 20% FBS, 20 ng/ml dihydrotestosterone (DHT, Sigma-Aldrich, D0731), 5 µg/ml transferrin (Sigma-Aldrich, T8158), 5 ng/ml sodium selenite (Sigma-Aldrich, 214485) and 5 µg/ml insulin (Sigma-Aldrich, 10516). All cultures were maintained in a humidified atmosphere at 37°C, 5% CO2. Cell cultures were tested for mycoplasma monthly and maintained mycoplasma-free.

extract_protocol:
For RNA-seq and MeRIP experiments, total RNA was extracted from ZC3H13 control, ZC3H13 KO, ZC3H13-dCas9, and ZC3H13-overexpressing BPH-1 cells using QIAzol Lysis Reagent (Qiagen, 79306) according to the manufacturer's instructions. After isopropanol precipitation, DNAse I Turbo (ThermoFisher Scientific, AM2239) treatment was performed to remove any remaining DNA contamination.  For the MeRIP protocol, mRNA enrichment was performed using Dynabeads® mRNA Purification Kit (ThermoFisher Scientific, 61006) following the manufacturer’s instructions. Three replicates per experimental condition were generated. 5 µg of mRNA was fragmented by adding 1 µl of 10X fragmentation reagent (Invitrogen, AM8740) before ethanol precipitation. The fragmented mRNA was recovered by centrifugation at 17,000 g for 30 min at 4ºC. The mRNA pellets were resuspended in DEPC water and 10% of the sample was used for inputs. Fragmented mRNA was diluted with 100 µl of 5X IP buffer (250 mM Tris pH 7.4, 500 mM NaCl, 0.25% NP-40) and incubated with 10 µg of anti-m6A antibody (Abcam, ab151230, RRID:AB_2753144) in the presence of RNase inhibitors, for 3 hours at 4ºC. 30 µl of SureBeads Protein A Magnetic beads (Bio-Rad, 1614013) were added to the mRNA-antibody mixture and incubated for 2 hours at 4ºC. The beads were washed three times with high salt IP buffer (50 mM Tris pH 7.4, 1 M NaCl, 1 mM EDTA, 1% NP-40), and twice with 1X IP buffer. To elute the immunoprecipitated mRNA, 200 µl of PK buffer (100 mM Tris-HCl pH 7.5, 50 mM NaCl, 10 mM EDTA) and Proteinase K (Invitrogen, AM 2548, Compound CID: 118855431) were added to the beads. To isolate RNAs, 1:1 Phenol:Chloroform was added and gently vortexed and kept at room temperature for 5 min. After centrifugation at 12,000 g, the aqueous phase containing the immunoprecipitated RNA was ethanol precipitated overnight. The immunoprecipitated RNA was resuspended in DEPC-treated water.
RNA-seq library preparation was performed from three biological replicates for each condition following standard protocols. In brief, mRNA was enriched from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit (RRID:SCR_020553) and real-time PCR for quantification and bioanalyzer (RRID:SCR_019715) for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms (RRID:SCR_016387).

value: Prostate

value: Epithelial

tag: genotype

value: ZC3H13 knock out


title: BPH1 dCas9 replicate 3

description:
Library name: DCAS9R3
RNA-Seq library preparation of BPH1 Prostate cancer cell line

value: wild type


title: BPH1 ZC3H13 KO replicate 2

description:
Library name: ZC3KOR2
RNA-Seq library preparation of BPH1 Prostate cancer cell line


title: BPH1 ZC3H13 OE replicate 3

description:
Library name: OESG1R3
RNA-Seq library preparation of BPH1 Prostate cancer cell line

value: ZC3H13 overexpression


title: BPH1 Empty_Vector replicate 2

description:
Library name: EMPVECR2
RNA-Seq library preparation of BPH1 Prostate cancer cell line


title: BPH1 ZC3H13 OE replicate 2

description:
Library name: OESG1R2
RNA-Seq library preparation of BPH1 Prostate cancer cell line


title: CDH00079

description: Library name: CDH0079_S14


title: BPH1 Empty_Vector replicate 3

description:
Library name: EMPVECR3
RNA-Seq library preparation of BPH1 Prostate cancer cell line


title: BPH1 ZC3H13 KO replicate 1

description:
Library name: ZC3KOR1
RNA-Seq library preparation of BPH1 Prostate cancer cell line


title: BPH1 Empty_Vector replicate 1

description:
Library name: EMPVECR1
RNA-Seq library preparation of BPH1 Prostate cancer cell line


title: GTEA1, rep4

city: Fuzhou

first: Zhiyun

last: Cao

state: 福建Fujian

address: 1# Qiu Yang Road

country: China

institute: Fujian university

description:
Library name: SAMPLES 7
A1_4

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. 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, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence by STAR. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome.
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK3 or Samtools software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.
HTSeq(v 0.5.4) was used to count the reads numbers mapped to each gene. Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped (FPKM). The formula is shown as follow: FPKM = cDNA Fragments \{Mapped Fragments(Millions) * TranscriptLength(kb)}
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.10.1). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value < 0.05 found by DESeq were assigned as differentially expressed.
Assembly: mm 10
Supplementary files format and content: tab-delimited text file including raw counts data for each samples

source_name: Human colon

extract_protocol:
RNA was extracted using the TRIzol method (Invitrogen, CA, USA) and treated with RNase-free DNase I (Takara, Kusatsu, Japan). RNA degradation and contamination was monitored on 1% agarose gels. RNA was quantified using Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA), the quality and integrity were assessed by NanoDrop spectrophotometer (Thermo Scientific, DE, USA).
A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 200-250 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The library preparations were sequenced on an Illumina Novaseq 6000 platform by the Beijing Allwegene Technology Company Limited (Beijing, China) and paired-end 150bp reads were generated.

value: Human colon

value: epithelial cells

value: ras mutation

value: GTEA1 treatment

tag: batch


title: GTEA7, rep3

description:
Library name: SAMPLES 10
A7_3

value: GTEA7 treatment


title: GTEA7, rep2

description:
Library name: SAMPLES 9
A7_2


title: BPH1 ZC3H13 OE replicate 1

description:
Library name: OESG1R1
RNA-Seq library preparation of BPH1 Prostate cancer cell line


title: GTEA1, rep3

description:
Library name: SAMPLES 6
A1_3


title: GTEA7, rep1

description:
Library name: SAMPLES 8
A7_1


title: BPH1 dCas9 replicate 1

description:
Library name: DCAS9R1
RNA-Seq library preparation of BPH1 Prostate cancer cell line


title: BPH1 dCas9 replicate 2

description:
Library name: DCAS9R2
RNA-Seq library preparation of BPH1 Prostate cancer cell line


title: SA2

city: guangzhou

first: han

last: shunxin

address: Guangzhou North Road

institute: southern medical university

description:
Library name: ATGEL
Compare the regeneration effects of SVF cells obtained by one non-enzymatic and two enzymatic methods, and analyze the cell composition of ADRC produced by commercial cell isolation systems.

library_source: transcriptomic single cell

data_processing:
The default parameters of Cell Ranger single-cell software (10x Genomics) were used for data alignment, unique molecular identifier (UMI) counting, cell counting and clustering analysis. The quality of the sample-specific FASTQ files was assessed via Cell Ranger's counts. The expression level of each transcript is determined by the quantity of UMI assigned to it. The filtered gene expression matrix was then employed for downstream analysis. RStudio (v.4.4.1) was used to visualize clustering and gene expression with the Seurat software package (v.5.1.0). The uniform manifold approximation and projection (UMAP) method in Seurat software was used for dimensionality reduction. The differential gene expression among clusters was analyzed via the Seurat function FindMarkers and the Wilcoxon test. Violin plots, heatmaps and individual UMAP maps of the given genes were generated via the VlnPlot, DoHeatmap and FeaturePlot functions of the Seurat toolkit, respectively.
Assembly: hg38
Supplementary files format and content: tab-separated values files and matrix files

molecule: nuclear RNA

source_name: adipose tissue

extract_protocol:
The improved nuclear separation method was utilized to isolate nuclei from frozen human white adipose tissue (WAT) and C-SVF.
Single-cell 3' v2 chemistry was employed to produce single-cell barcoded droplets (GEMs), and upon capturing the nuclei, the GEM solution appeared as a uniform milky white liquid. The GEM solution was subsequently withdrawn and transferred to PCR tubes for reverse transcription and library construction for sequencing. The "gene expression library" was quantified via a Qubit instrument, and the fragment size of the "gene expression library" was analyzed via Qpcr.

value: adipose tissue


title: GTEA1, rep1

description:
Library name: SAMPLES 4
A1_1


title: GTEA7, rep4

description:
Library name: SAMPLES 11
A7_4


title: SA1

description:
Library name: ADRCGEL
Compare the regeneration effects of SVF cells obtained by one non-enzymatic and two enzymatic methods, and analyze the cell composition of ADRC produced by commercial cell isolation systems.

source_name: SVF

value: SVF


title: GTEA1, rep2

description:
Library name: SAMPLES 5
A1_2


title: DMSO, rep3

description:
Library name: SAMPLES 3
Control_3

value: DMSO as control


title: DMSO, rep2

description:
Library name: SAMPLES 2
Control_2


title: DMSO, rep1

description:
Library name: SAMPLES 1
Control_1


title: Fed_48h

city: Seoul

first: Minjeong

last: Jang

state: Asia/Oceania

address: 75, Nowon-ro, Nowon-gu, Seoul, Republic of Korea

country: South Korea

institute: Korea Institute of Radiological and Medical Sciences (KIRAMS)

description: Library name: H_48

data_processing:
the libraries were evaluated using the TapeStation HS D1000 Screen Tape (Agilent Technologies, Santa Clara, CA, USA) to determine the mean fragment size. Quantification was performed using a library quantification kit and StepOne Real-Time PCR System (Life Technologies, Carlsbad, CA, USA). High-throughput sequencing was performed via paired-end 100 sequencing using NovaSeq 6000 (Illumina, San Diego, CA, USA).
Assembly: hg19
Supplementary files format and content: tab-delimited text file included raw counts for each Samples

source_name: ReN

extract_protocol:
Total RNA was isolated using the QIAzol lysis reagent (79306, Qiagen, Germantown, MD, USA). RNA quality was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies, Amstelveen, The Netherlands), and RNA quantification was performed using an NanoDrop-2000 spectrophotometer (ND-2000, Thermo Fisher Scientific).
Libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA-Seq Kit (New England BioLabs, Hitchin, UK). mRNA isolation was performed using a Poly(A) RNA Selection Kit (LEXOGEN, Wein, Austria). The isolated mRNAs were used for cDNA synthesis and shearing by following the manufacturer’s instructions. Indexing was performed using Illumina indexes 1–12.

value: ReN


title: Fast_48h

description: Library name: 0_48


title: siNC repeat 1

city: Harbin

first: yc

last: z

address: the Second Affiliated Hospital of Harbin Medical University

institute: HMU

description: Library name: sinc1

data_processing:
Raw sequencing reads (FASTQ files) were processed using Fastp (version 0.23.2) with default parameters to remove adapter sequences and filter out low-quality reads. This preprocessing step ensured that only high-quality reads—termed "clean data"—were retained for subsequent analyses.Clean reads were aligned to the reference genome using HISAT2 (version 2.2.1) with default settings, except for the parameter --dta to optimize for downstream transcript assembly and quantification. Alignment quality was assessed to ensure high mapping rates.Gene expression quantification was performed by counting the number of reads aligned to each gene using HTSeq-count (version 0.13.5), with default parameters and the --mode=union option for read assignment. The gene annotation file in GTF format corresponding to the reference genome was used for accurate feature assignment.Normalized gene expression values were calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) to facilitate comparison across samples.
Assembly: GRCh38 hg38
Supplementary files format and content: Count file includes raw counts for each Sample

extract_protocol:
For RNA extraction, the Trizol method is utilized. Cells are first washed twice with PBS. 1ml of Trizol reagent is added to the cell culture dish, and cells are thoroughly dissolved by repetitive pipetting or scraping. The Trizol-cell mixture is transferred to an EP tube, to which 200μL of chloroform is added and mixed thoroughly. It is then centrifuged at 4°C for 10 minutes at 12000g. The supernatant is carefully transferred to a new RNase-free centrifuge tube, and an equal volume of RNase-free alcohol is added and mixed. The RNA is then precipitated in a -20°C freezer. After another round of centrifugation, the supernatant is discarded, and the residue is washed with 70% ethanol. Finally, the precipitate is dissolved in DEPC water to obtain the final RNA, which is stored at -80°C.
Total RNA was extracted from samples using standard protocols. For transcriptomic library construction, the VAHTS Universal V5 RNA-seq Library Prep Kit (Vazyme) was employed according to the manufacturer’s instructions. This kit facilitates high-efficiency and high-fidelity library preparation, which is critical for accurate transcriptome profiling. The resulting libraries were assessed for quality and quantity using an Agilent Bioanalyzer 2100 system and Qubit fluorometer. Libraries passing quality control were sequenced on the Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads, enabling robust transcript coverage and reliable downstream analysis.

value: colorectal cancer cell line

value: siNC


title: siNC repeat 2

description: Library name: sinc2


title: siNC repeat 3

description: Library name: sinc3


title: siOSBPL3 repeat 1

description: Library name: si1


title: siOSBPL3 repeat 2

description: Library name: si2


title: siha_KD2

city: Hangzhou

first: Boya

last: Zhang

state: Zhejiang

address: Qingchun East Road

institute: Department of dermatology,Sir Run Run Shaw Hospital, Zhejiang University, School of Medicine

description: Library name: Sample2

data_processing:
We used the featureCounts tool in the subread software to quantify the expression levels of genes. The featureCounts mainly utilized the parameters -Q 10, -B, and -C to filter out reads with alignment quality values lower than 10, reads with non-unique alignments, and reads that aligned to multiple regions of the genome, respectively.
Assembly: not provided
Supplementary files format and content: siha_KDvssiha_NC_deg_all.xls

source_name: Siha

extract_protocol:
Total RNA from each sample was extracted using TRIzol® Reagent according to the manufacturer’s instructions (Invitrogen, Carlsbard, CA, USA) and genomic DNA was removed using DNase I (TaKara, Shiga, Japan)
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep Ligation from Illumina (San Diego, CA) using 1μg of total RNA.

value: Siha

value: knockdown of HPV 16E7


title: siha_NC1

description: Library name: Sample4

value: control


title: siOSBPL3 repeat 3

description: Library name: si3


title: siha_NC2

description: Library name: Sample5


title: 3M

city: nantong

first: liang

last: wang

state: chongchuan

address: nantong,jiangsu Province

institute: nantong university

description:
Library name: sample2
10x genomics

data_processing:
low-quality reads and adapter sequences were trimmed using FastQC (version 0.11.7) and Cutadapt (version 1.17). Reads were aligned to the GRCm38 genome (Ensembl V. 92 annotation) with STAR (version 020201). Gene and unique molecular identifier (UMI) counts were generated using FeatureCounts (version 1.6.2). The CeleScope pipeline facilitated a series of analytical steps, leading to the construction of a gene expression matrix.
Assembly: The reference genome (fasta format) and gene annotation (gtf format) files were downloaded from Ensembl database (release version 94).
Supplementary files format and content: matrix files

source_name: temporomandibular joint condyle

extract_protocol:
The isolated TMJC tissue was cut into 2–3 mm sections and rinsed with Hanks' Balanced Salt Solution (HBSS). Enzymatic digestion was performed for 15 minutes using a tissue dissociation solution (Singleron Biotechnologies, Nanjing, China). The resulting cell suspension was filtered through a sterile 40-μm filter (Corning, NY, USA) and centrifuged at 150 g for 5 minutes. Erythrocytes were removed with a lysis reagent (Singleron Biotechnologies, Nanjing, China) for 10 minutes. The cells were resuspended in phosphate-buffered saline (PBS) and stained with trypan blue (T6146, Sigma, Burlington, VT, USA). Cell viability was assessed using a TC20 automated cell counter (Bio-Rad, Hercules, CA, USA).
A cell suspension at a concentration of 1×10^5 cells/mL was prepared and loaded into a microfluidic plate. The scRNA-seq libraries were constructed using the Single-Cell RNA Library Kit (Singleron Biotechnologies, Nanjing, China). The prepared libraries were pooled and sequenced on an Illumina NovaSeq 6000 platform. Raw sequencing reads were processed with the CeleScope pipeline (https://github.com/singleron-RD/CeleScope).

value: temporomandibular joint condyle

value: various cells

tag: age

value: Human embryos at 3 months


title: siha_NC3

description: Library name: Sample6


title: 4M

description:
Library name: sample3
10x genomics

value: Human embryos at 4 months


title: siha_KD3

description: Library name: Sample3


title: siha_KD1

description: Library name: Sample1


title: 24132XR-06-02

city: New York

first: Won-Min

last: Song

state: NY

address: 1399 Park Avenue

department: Genetics and Genomic Sciences

institute: Icahn school of medicine at Mount Sinai

description:
Library name: 24132XR-06-02
count_matrix.SKMEL147.txt

data_processing:
High-throughput RNA-sequencing data is subjected to adapter removal with cutadapt and base quality trimming to remove 3′ read sequences if more than 20 bases with Q<20 were present. The reads are mapped to GRCh38 by STAR aligner, the gene counts for fragments mapped into exonic regions are called by featureCounts, then are normalized by Counts Per Million (CPM), followed by Trimmed Mean of M (TMM) scaling normalization
Assembly: GRCh38
Supplementary files format and content: Raw count matrices for each of A375 and SKMEL147 cell lines

growth_protocol: Cell line SKmel147 was obtained from Dr. Alan Houghton’s laboratory (MSKCC, New York). The A375 and Yumm1.7 cell line were sourced from American type culture collection. A375 and SKmel147 cells were maintained in DMEM (Corning #10-013-CV), while Yumm1.7 cells were cultured in DMEM-F12 (GIBCO #11320-082). Both media were supplemented with 10% (v/v) fetal bovine serum and 1% (v/v) penicillin/streptomycin. All cell lines were kept in a humidified incubator at 37°C with 5% CO2 and were regularly tested to confirm the absence of mycoplasma contamination.

extract_protocol:
Total RNA was extracted using miRNeasy QIAGEN mini kit according to the manufacturer’s protocol (QIAGEN #1038703). Totally, 1000 ng of RNA were reverse transcribed using superscript IV Uniprime (Invitrogen #12596025) with random hexamers following the manufacturer’s recommendations. cDNA was diluted with RNase and DNase free water prior to use in a quantitative real-time polymerase chain reaction (qRT-PCR).
RNA was isolated from samples using RNeasy® Plus Mini Kit (Qiagen, Hilden, Germany) per the manufacturer’s instructions. Isolated RNA sample quality was assessed by RNA Tapestation (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Massachusetts, USA). Libraries were constructed with KAPA™ RNA HyperPrep with RiboErase (Roche, Indiana, USA) and performed based on manufacturer’s recommendations. Final library quantity was measured by KAPA SYBR® FAST qPCR and library quality evaluated by TapeStation HSD1000 ScreenTape (Agilent Technologies, CA, USA). The final library size was about 400bp with an insert size of about 250bp. Illumina® 8-nt unique dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq (Illumina, California, USA) with a read length configuration of 150 PE for 60M PE reads per sample (30M in each direction).

treatment_protocol: Totally, 4 × 106 HEK293T cells were seeded per 10 cm tissue culture plate and incubated overnight at 37 °C and 5% CO2. After seeding, HEK293T were co-transfected with bacterial glycerol clones PLKO-puro-shNTC (sigma # SHC016-1EA) , ZNF180_shZ1 (shRNA sequence : TGTCCTTGTTGTGCATCAAAG) ZNF180_shZ2 (shRNA sequence : GCTCGACTTATTGTGCATCAA), shZFP180 (shRNA sequence: GAAGTCGTTCATCCAGAGTTA) lentiviral expression constructs (12 μg), viral packaging plasmid (psPAX2, 8 μg), and viral envelope plasmid (VSVG, 4 μg) using Lipofectamine 2000 (Invitrogen # 52887) following manufacturer’s recommendations. Viral supernatant was collected and 0.45 mm filtered at 48 h post-transfection and stored at -80 °C for long-term usage (1-30 days). Cells were transduced with lentivirus in the presence of polybrene   (8 μg/ml) and selected with puromycin (1–2 μg/ml) for 4–6 days.

value: Epithelial

value: NRAS mutant

value: shNTC


title: 24132XR-06-03

description:
Library name: 24132XR-06-03
count_matrix.SKMEL147.txt


title: 24132XR-06-05

description:
Library name: 24132XR-06-05
count_matrix.SKMEL147.txt


title: 24132XR-06-01

description:
Library name: 24132XR-06-01
count_matrix.SKMEL147.txt


title: 24132XR-06-06

description:
Library name: 24132XR-06-06
count_matrix.SKMEL147.txt


title: 24132XR-01-05

description:
Library name: 24132XR-01-05
count_matrix.A375.txt

value: BRAF mutant


title: 24132XR-06-04

description:
Library name: 24132XR-06-04
count_matrix.SKMEL147.txt


title: 24132XR-01-06

description:
Library name: 24132XR-01-06
count_matrix.A375.txt


title: 24132XR-01-04

description:
Library name: 24132XR-01-04
count_matrix.A375.txt


title: 24132XR-01-03

description:
Library name: 24132XR-01-03
count_matrix.A375.txt


title: Fed_24h

description: Library name: H_24


title: 24132XR-01-02

description:
Library name: 24132XR-01-02
count_matrix.A375.txt


title: Fast_24h

description: Library name: 0_24


title: 24132XR-01-01

description:
Library name: 24132XR-01-01
count_matrix.A375.txt


title: TP487 TWIST1

city: Oxford

first: Alison

last: Simmons

address: John Radcliffe Hospital/Headley Way

department: The MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

description: Library name: TP487TWIST1

data_processing:
For analysis, adapters/low-quality bases were trimmed with Cutadapt; reads were aligned with STAR to hg38 augmented with full lentiviral insert sequences (Addgene plasmids) to capture transgene/PAC expression; duplicates were marked with Picard; gene-level counts were obtained with featureCounts;
Assembly: hg38
Supplementary files format and content: tab delimited text file containing raw counts for each sample

molecule: polyA RNA

source_name: intestinal fibroblasts

extract_protocol:
Total RNA was extracted from each condition using the RNeasy Plus Micro kit (Qiagen).
Library preparation were performed by Novogene (UK) Company Limited (Cambridge, United Kingdom)

value: intestinal fibroblasts

value: primary fibroblasts

tag: donor


title: TP487 Control

description: Library name: TP487Control

value: Control


title: TP487 OSR2

description: Library name: TP487OSR2


title: TP430 TWIST1

description: Library name: TP430TWIST1


title: TP430 OSR2

description: Library name: TP430OSR2


title: RG591 OSR2

description: Library name: RG591OSR2


title: Si2

city: jinan

first: jingyu

last: ma

address: Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Lixia, Jinan, Shandong , P.R.China

institute: shandong university

description: Library name: sample5

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38 . The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38 . The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters.
Supplementary files format and content: 1_genes_fpkm_expression.txt

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using 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 is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are 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 are 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 library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using 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 is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are 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 are 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 library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

tag: disease

value: thyroid cancer


title: Si1

description: Library name: sample4


title: Si3

description: Library name: sample6


title: NC1

description: Library name: sample1


title: RG547 OSR2

description: Library name: RG547OSR2


title: RG591 Control

description: Library name: RG591Control


title: NC3

description: Library name: sample3


title: TP430 Control

description: Library name: TP430Control


title: RG559 Control

description: Library name: RG559Control


title: RG559 TWIST1

description: Library name: RG559TWIST1


title: Human chondrocytes, CCN6 p.Cys52, replicate 2

city: Istanbul

first: Eda

last: Tahir Turanli

address: Kayisdagi St.

country: Turkey

institute: Acibadem University

description: Library name: CCN6c-156C_ABR2

data_processing:
Raw reads were quality-filtered (adapter trimming and low-quality base removal) using standard practices, then aligned to the human reference genome GRCh38 with HISAT2 v2.2.1 using default splice-aware settings. Comprehensive gene annotations were supplied from GENCODE v48. Gene-level read counts were obtained with featureCounts v2.0.8 using the GENCODE v48 annotation as the reference.
Genes were retained for downstream differential expression analysis only if they met both of the following criteria: (a) achieved ≥1 CPM (counts per million, approximately ≥10 raw reads) in at least the two samples representing the smallest genotype group, and (b) were detectable at this threshold in ≥70% of samples within each genotype group. Filtered gene-level counts were analyzed using edgeR’s quasi-likelihood pipeline (edgeR v4.0.16). Tag-wise dispersions were estimated while accounting for the biological replicate structure. Differential expression was assessed via separate contrasts of each variant genotype versus the wild-type reference. Genes with a false discovery rate (FDR) < 0.05 were considered significant.
Significant genes, ranked by differential expression statistics, were tested for enrichment of biological processes using clusterProfiler v4.6.2’s implementation of fgsea, against the MSigDB v2025.1.Hs Gene Ontology gene sets to identify enriched pathways and processes.
Assembly: GRCh38
Supplementary files format and content: CCN6_PPD_TPM

growth_protocol: Human chondrocytes (402-05A, Cell Applications, Inc., USA) were maintained in high-glucose DMEM (Sigma-Aldrich) supplemented with 10% FBS (Gibco) and 1% penicillin–streptomycin (Thermo Fisher Scientific) at 37 °C in 5% CO₂.

extract_protocol:
Total RNA isolation was performed 48 hours after transfection using the RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. Further purification was carried out using the DNA Clean & Concentrator Kit (Zymo Research, Irvine, CA, USA). RNA concentration and purity were assessed by spectrophotometric measurement using a NanoDrop spectrophotometer (Thermo Fisher Scientific, MA, USA), and concentrations were further validated fluorometrically using a Qubit Fluorometer (Thermo Fisher Scientific, MA, USA). RNA quality and integrity were evaluated using the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). The resulting RNA integrity numbers (RINs) ranged from 9.6 to 10.
RNA sequencing libraries were prepared using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit (Illumina, San Diego, CA, USA), following the manufacturer’s protocol. This protocol includes enzymatic ribosomal RNA depletion, strand-specific cDNA synthesis, adapter ligation, and PCR amplification with unique dual indexes. Libraries were quantified, normalized, and prepared for sequencing according to Illumina's standard pipeline.

value: Human chondrocyte

value: Overexpressed CCN6 p.Cys52


title: Human chondrocytes, CCN6 p.Cys52, replicate 1

description: Library name: CCN6c-156C_ABR1


title: Human chondrocytes, CCN6 p.Cys114Trp, replicate 2

description: Library name: CCN6c-342T_GBR2

value: Overexpressed CCN6 p.Cys114Trp


title: RG547 TWIST1

description: Library name: RG547TWIST1


title: SH-SY5Y KI/del RA treatment, Day7 replicate 3

first: Artemiy

last: Kurishev

address: Kashirskoe Sh., 34

country: Russia

institute: Menatal Health National Center

description:
Library name: sample 18
Raw FASTQ R1 and R2 for sample KI_del_ATRA_rep3

data_processing:
Trimmed reads were quality-checked using FastQC.
Reads were aligned to the human reference genome (GRCh38/hg38) using STAR v2.7.10b in paired-end mode.
PCR duplicates were marked and removed with Picard v2.27.4.
Gene-level counts were generated with HTSeq v2.0.2 (union mode, stranded).
Raw reads were trimmed for adapters and low-quality bases with FastP.
Assembly: Gene-level counts were generated with HTSeq v2.0.2 (union mode, stranded).
Supplementary files format and content: format and content Tab-delimited “count_matrix.txt” containing raw gene counts for all 18 samples.
Supplementary files format and content: format and content Tab-delimited “DESeq2_results.txt” containing gene IDs, log₂ fold-changes, p-values, and adjusted p-values from differential expression analysis.

growth_protocol: SH-SY5Y cells were maintained in DMEM/F12 (Paneco LLC) supplemented with 10% fetal bovine serum, 50 U/mL penicillin and 50 µg/mL streptomycin at 37 °C, 5% CO₂; medium was changed every 2–3 days.

extract_protocol:
Total RNA was extracted using ExtractRNA reagent (Evrogen), treated with DNase I (NEB) to remove genomic DNA, and RNA integrity verified via Qubit RNA IQ assay (RIN > 7.0).
Poly(A)+ RNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module, and strand-specific libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (average insert size ~283 bp).

treatment_protocol: For neuronal differentiation, cells at ~30% confluency were switched to DMEM with 1% FBS plus 10 µM all-trans retinoic acid (ATRA) and cultured for 7 days, with medium refreshed every 48 hours.

value: neuroblastoma cell

value: ZNF536 KI/del

value: ATRA neuronal differenetiation


title: SH-SY5Y KI/del RA treatment, Day7 replicate 2

description:
Library name: sample 17
Raw FASTQ R1 and R2 for sample KI_del_ATRA_rep2


title: SH-SY5Y KI/del RA treatment, Day7 replicate 1

description:
Library name: sample 16
Raw FASTQ R1 and R2 for sample KI_del_ATRA_rep1


title: RG547 Control

description: Library name: RG547Control


title: Human chondrocytes, CCN6 wild type, replicate 1

description: Library name: CCN6-WT-BR1

value: Overexpressed CCN6 Wild Type


title: NC2

description: Library name: sample2

value: control


title: RG591 TWIST1

description: Library name: RG591TWIST1


title: SH-SY5Y KI/KI RA treatment, Day7 replicate 2

description:
Library name: sample 14
Raw FASTQ R1 and R2 for sample KI_KI_ATRA_rep2

value: ZNF536 KI/KI


title: SH-SY5Y KI/KI RA treatment, Day7 replicate 1

description:
Library name: sample 13
Raw FASTQ R1 and R2 for sample KI_KI_ATRA_rep1


title: Human chondrocytes, CCN6 p.Cys114Trp, replicate 1

description: Library name: CCN6c-342T_GBR1


title: RG559 OSR2

description: Library name: RG559OSR2


title: Human chondrocytes, CCN6 wild type, replicate 2

description: Library name: CCN6-WT-BR2


title: SH-SY5Y NTC RA treatment, Day7 replicate 3

description:
Library name: sample 12
Raw FASTQ R1 and R2 for sample NTC_ATRA_rep3

value: WT


title: SH-SY5Y NTC RA treatment, Day7 replicate 2

description:
Library name: sample 11
Raw FASTQ R1 and R2 for sample NTC_ATRA_rep2


title: SH-SY5Y NTC RA treatment, Day7 replicate 1

description:
Library name: sample 10
Raw FASTQ R1 and R2 for sample NTC_ATRA_rep1


title: SH-SY5Y KI/KI basal replicate 3

description:
Library name: sample 6
Raw FASTQ R1 and R2 for sample KI_KI_basal_rep3


title: SH-SY5Y NTC basal replicate 1

description:
Library name: sample 1
Raw FASTQ R1 and R2 for sample NTC_basal_rep1


title: SH-SY5Y KI/KI basal replicate 1

description:
Library name: sample 4
Raw FASTQ R1 and R2 for sample KI_KI_basal_rep1


title: iMECLCs_DDX6_KD_2

city: Boulder

first: Mika

last: Nevo

state: Colorado

address: 2315 Walnut St

institute: CU Boulder

description:
Library name: 22017FL-26-01-96
202507_iMECLCs.RawCount.hg38.v40.csv

data_processing:
RNA-seq was analyzed by mapping reads using hisat2.1.0150 to the mouse mm39 genome assembly, human hg38 assembly. Gene counts were annotated using featureCounts v1.6.2.
Assembly: hg38, mm39
Supplementary files format and content: raw counts

source_name: TFAP2C-GFP/BLIMP1-TOMATO BTAG hIPSC

extract_protocol:
miRNeasy Micro Kit (QIAGEN)
SNAP-total seq

value: TFAP2C-GFP/BLIMP1-TOMATO BTAG hIPSC

value: iMECLC


title: SH-SY5Y KI/del basal replicate 1

description:
Library name: sample 7
Raw FASTQ R1 and R2 for sample KI_del_basal_rep1


title: iMECLCs_Ctrl_KD_1

description:
Library name: 22017FL-26-01-93
202507_iMECLCs.RawCount.hg38.v40.csv


title: iMECLCs_Ctrl_KD_2

description:
Library name: 22017FL-26-01-94
202507_iMECLCs.RawCount.hg38.v40.csv


title: hESC_TBL_naïve_DDX6_KD_TPRX1GFP_2

description:
Library name: 22017FL-26-01-92
202507_hESC_TBL.RawCount.hg38.v40.csv

source_name: TPRX1-GFP hESC

value: TPRX1-GFP hESC


title: hESC_TBL_naïve_DDX6_KD_TPRX1GFP_1

description:
Library name: 22017FL-26-01-91
202507_hESC_TBL.RawCount.hg38.v40.csv


title: hESC_TBL_naïve_DDX6_KD_NEG_1

description:
Library name: 22017FL-26-01-89
202507_hESC_TBL.RawCount.hg38.v40.csv

value: NEG


title: hESC_TBL_naïve_DDX6_KD_NEG_2

description:
Library name: 22017FL-26-01-90
202507_hESC_TBL.RawCount.hg38.v40.csv


title: hESC_TBL_naïve_CTRL_KD_TPRX1GFP_1

description:
Library name: 22017FL-26-01-87
202507_hESC_TBL.RawCount.hg38.v40.csv


title: SH-SY5Y KI/KI RA treatment, Day7 replicate 3

description:
Library name: sample 15
Raw FASTQ R1 and R2 for sample KI_KI_ATRA_rep3


title: hESC_TBL_naïve_CTRL_KD_NEG_2

description:
Library name: 22017FL-26-01-86
202507_hESC_TBL.RawCount.hg38.v40.csv


title: hESC_TBL_naïve_CTRL_KD_NEG_1

description:
Library name: 22017FL-26-01-85
202507_hESC_TBL.RawCount.hg38.v40.csv


title: SH-SY5Y KI/del basal replicate 2

description:
Library name: sample 8
Raw FASTQ R1 and R2 for sample KI_del_basal_rep2


title: hESC_TBL_E8_CTRL_KD_1

description:
Library name: 22017FL-26-01-77
202507_hESC_TBL.RawCount.hg38.v40.csv


title: hESC_TBL_E8_CTRL_KD_2

description:
Library name: 22017FL-26-01-78
202507_hESC_TBL.RawCount.hg38.v40.csv


title: SH-SY5Y KI/del basal replicate 3

description:
Library name: sample 9
Raw FASTQ R1 and R2 for sample KI_del_basal_rep3


title: SH-SY5Y KI/KI basal replicate 2

description:
Library name: sample 5
Raw FASTQ R1 and R2 for sample KI_KI_basal_rep2


title: BTAG_iPS_DDX6_KD_2

description:
Library name: 22017FL-26-01-76
202507_BTAG.RawCount.hg38.v40.csv


title: SH-SY5Y NTC basal replicate 2

description:
Library name: sample 2
Raw FASTQ R1 and R2 for sample NTC_basal_rep2


title: BTAG_iPS_Ctrl_KD_2

description:
Library name: 22017FL-26-01-74
202507_BTAG.RawCount.hg38.v40.csv


title: iMECLCs_DDX6_KD_1

description:
Library name: 22017FL-26-01-95
202507_iMECLCs.RawCount.hg38.v40.csv


title: PGCs_DDX6_KD_neg_2

description:
Library name: 22017FL-26-01-70
202507_PGC.RawCount.hg38.v40.csv

value: PGC

value: neg


title: PGCs_DDX6_KD_double_positive_1

description:
Library name: 22017FL-26-01-71
202507_PGC.RawCount.hg38.v40.csv


title: SH-SY5Y NTC basal replicate 3

description:
Library name: sample 3
Raw FASTQ R1 and R2 for sample NTC_basal_rep3


title: PGCs_Ctrl_KD_double_positive_2

description:
Library name: 22017FL-26-01-68
202507_PGC.RawCount.hg38.v40.csv


title: PGCs_DDX6_KD_neg_1

description:
Library name: 22017FL-26-01-69
202507_PGC.RawCount.hg38.v40.csv


title: PGCs_Ctrl_KD_neg_2

description:
Library name: 22017FL-26-01-66
202507_PGC.RawCount.hg38.v40.csv


title: hESC_TBL_naïve_CTRL_KD_TPRX1GFP_2

description:
Library name: 22017FL-26-01-88
202507_hESC_TBL.RawCount.hg38.v40.csv


title: PGCs_Ctrl_KD_neg_1

description:
Library name: 22017FL-26-01-65
202507_PGC.RawCount.hg38.v40.csv


title: DMBC21PLXR

city: Lodz

first: Michal

last: Wozniak

address: Mazowiecka 6/8

country: Poland

institute: Medical University of Lodz

description: Library name: Sample 3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-houseperl scripts. 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, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
StringTie (1.3.1) was used to calculate FPKMs of coding genes in each sample . Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Assembly: In this project, Homo_sapiens was used as the reference genome in the following analysis and it can be downloaded on Homo_sapiens.GRCh38.113.HW.genome.fa.
Supplementary files format and content: one single tab delimited text file contains raw counts and FPKM for all three samples

source_name: melanoma

growth_protocol: The study received approval from the Ethical Commission of the Medical University of Lodz (identification code: RNN/84/09/KE), and informed consent was signed by the patient before tissue acquisition. Drug-naïve cell lines were named after the Department of Molecular Biology of Cancer (DMBC) with consecutive numbers. The DMBC21 cell line was acquired from a tumor specimen obtained from the back of a 65-year-old female patient. The melanoma was characterized as Clark level IV, with a Breslow thickness of 10 mm, a mitotic index (MI) of 1, and classified as pIIC according to the seventh edition of the American Joint Committee on Cancer (AJCC) staging guidelines for melanoma. A fragment of the tumor obtained from the patient was sectioned and digested for 2-3 h at 37 °C with 1 mg/mL collagenase IV in Hanks’ Balanced Salt Solution (HBSS; Sigma-Aldrich, St Louis, MO, USA) supplemented with 3 mM calcium chloride. Then DNase I (10 μg/mL) was added, and cells were filtered through a 70 μm pore size filter and cultured in a complete medium (RPMI-1640 with 10% FBS) for 24 h to remove dead and nonadherent cells. In the next step, living adherent cells were transferred to serum-free stem cell medium (SCM), consisting of Dulbecco’s Modified Eagle’s Medium (DMEM)/F12 (Lonza, Basel, Switzerland), 10 ng/mL basic fibroblast growth factor (bFGF) (Corning, Corning, NY, USA), 20 ng/mL epidermal growth factor (EGF) (Corning, Corning, NY, USA), B-27 supplement (Gibco, Paisley, UK), insulin (10 µg/mL) (Sigma-Aldrich, St Louis, MO, USA), heparin (1 ng/mL) (Sigma-Aldrich, St Louis, MO, USA), and antibiotics (100 IU/mL penicillin, 100 μg/mL streptomycin and 2 µg/mL fungizone B.). Cell cultures were maintained in low-adherent flasks (NUNC) at 37ºC in a humidified atmosphere containing 5% CO2, and the medium was exchanged twice a week [Sztiller-Sikorska M 2015]. To obtain cell lines resistant to vemurafenib (PLX, 21_PLXR) or trametinib (TRA, 21_TRAR), DMBC21 melanoma cells were cultured in SCM in the presence of increasing concentrations of respective drugs for 4-5 months to achieve high viability in the final concentration 10 μM and 50 nM, respectively.

extract_protocol:
total RNA was harvested using RNeasy Mini Kit (Qiagen). A total amount of 1.5 μg RNA per sample was used for library construction.
rRNA removal was prepared using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA). Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer （ 5X）. First strand cDNA was synthesized using random hexamer primer and Reverse Transcriptase. Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select insert fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP Beads (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 and qPCR.

treatment_protocol: cell cultures were not treated prior to RNA preparation

value: melanoma

value: cell line resistant to vemmurafenib


title: DMBC21TRAR

description: Library name: Sample 2

value: cell line resistant to trametinib


title: DMBC21

description: Library name: Sample 1


title: A549 RBM10KD, rep2

city: Cincinnati

first: Nathan

last: Salomonis

state: Ohio

address: 3401 Burnet Ave, Cincinnati, OH 45229

department: Biomedical Informatics

institute: Cincinnati Children's Medical Hospital

description:
Library name: A549-RBM10KD-rep2
Column name in processed data files: A549-RBM10KD-rep2.bed

data_processing:
Fastq files were aligned to grcg38 using STAR (STAR 2.6.1). Alternative splicing was assessed using AltAnalyze (version 2.1.4) with the Ensembl-91 human database, computing ASEs with the previously described MultiPath-PSI algorithm (see: https://altanalyze.readthedocs.io/en/latest/Algorithms/#multipath-psi-splicing-algorithm).
Assembly: hg38
Supplementary files format and content: Tab-delimited text file of the gene expression (RPKM) values for each sample.
Supplementary files format and content: Tab-delimited text file of the splicing (PSI) values for each sample.

source_name: cell line

growth_protocol: A549 cells were maintained in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics (Antibiotic-Antimycotic and Normocin) in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol: Total RNA was extracted from approximately 5×10e6 A549 cells using the QIAGEN RNeasy Mini Kit according to the manufacturer's instructions, including on-column DNase digestion. RNA was washed, eluted in nuclease-free water, quantified by NanoDrop, and stored at -80°C. Library prep and sequencing was performed at the Cincinnati Children's Hospital Medical Center DNA Sequencing and Genotyping Core. Between 150 to 300 ng of total was used for poly-A selection and library preparation with the TruSeq® Stranded mRNA Library Prep Kit (Illumina). Libraries were sequenced on an Illumina NovaSeq 6000, generating ~40 million stranded 100 bp paired end reads per sample.

treatment_protocol: For RBM10 knockdown experiments, A549 cells were transduced with lentiviral particles encoding RBM10-targeting shRNA (TRCN0000233280; Sigma-Aldrich). Wells were pre-treated with Retronectin to enhance transduction efficiency. Transduced cells were selected with puromycin (1 µg/mL) for 10–14 days to enrich for stable knockdown populations. Knockdown efficiency was confirmed by Western blot using a rabbit anti-RBM10 antibody (HPA034972, Sigma-Aldrich) at a 1:10,000 dilution.

value: Lung Adenocarcinoma

value: RBM10 knockdown

value: October 13, 2021


title: A549 RBM10wt, rep1

description:
Library name: A549wt-rep1
Column name in processed data files: A549wt-rep1.bed

value: RBM10 wild type


title: A549 RBM10wt, rep2

description:
Library name: A549wt-rep2
Column name in processed data files: A549wt-rep2.bed


title: hESC_TBL_E8_DDX6_KD_2

description:
Library name: 22017FL-26-01-80
202507_hESC_TBL.RawCount.hg38.v40.csv


title: A549 RBM10KD, rep1

description:
Library name: A549-RBM10KD-rep1
Column name in processed data files: A549-RBM10KD-rep1.bed


title: hESC_TBL_E8_DDX6_KD_1

description:
Library name: 22017FL-26-01-79
202507_hESC_TBL.RawCount.hg38.v40.csv


title: BTAG_iPS_DDX6_KD_1

description:
Library name: 22017FL-26-01-75
202507_BTAG.RawCount.hg38.v40.csv


title: BTAG_iPS_Ctrl_KD_1

description:
Library name: 22017FL-26-01-73
202507_BTAG.RawCount.hg38.v40.csv


title: 150si-1

city: JiNan

first: Lin

last: Lv

state: Student

address: Department of Thoracic Surgery, Shandong University, Jinan, 250013, Shandong, P.R.China;

institute: Department of Thoracic Surgery, Jinan Central Hospital, Shandong University

description:
Library name: Sample4
150si-1_FPKM

data_processing:
The raw reads were filtered by Seqtk before mapping to genome using Hisat2 (version:2.0.4). The fragments of genes were counted using stringtie(v1.3.3b) followed by TMM (trimmed mean of M values) normalization. Significant differential expressed genes (DEGs) were identified as those with a False Discovery Rate (FDR) value above the threshold (Q< 0.05) and fold-change >2 using edgeR software.
Assembly: hg38
Supplementary files format and content: FPKM, counts

source_name: Oesophagus

growth_protocol: The KYSE-150 cells were cultured in RPMI 1640 medium containing 10% fetal bovine serum (FBS) in a humidified incubator at 37°C with 5% carbon dioxide.

extract_protocol:
Total RNA was extracted from EC cells using TRIzol™ reagent, with procedures performed in strict accordance with the manufacturer's guidelines. Reverse transcription of 1 μg mRNA into cDNA was performed using the Evo M-MLVRT Mix Kit Ver.2
The Illumina standard protocol (VAHTS General V6 RNA Sequencing Library Preparation Kit) was used for library preparation. The cDNA library concentration and size distribution were evaluated using the Agilent 4200 bioanalyzer, followed by sequencing using the Illumina novaseq6000.

treatment_protocol: The experimental group KYSE-150 was treated with ZNF514 knockout (siZNF514)

value: Oesophagus

value: Esophageal cancer cells

value: knockout ZNF514 (siZNF514)


title: PGCs_DDX6_KD_double_positive_2

description:
Library name: 22017FL-26-01-72
202507_PGC.RawCount.hg38.v40.csv


title: 150nc-2

description:
Library name: Sample2
150nc-2_FPKM


title: 150nc-3

description:
Library name: Sample3
150nc-3_FPKM


title: 150si-2

description:
Library name: Sample5
150si-2_FPKM


title: 150si-3

description:
Library name: Sample6
150si-3_FPKM


title: HCT116 cells p21 -/-, treated, biol rep1

city: Education City

first: Georges

last: Nemer

state: Doha

address: Penrose Road

department: College of Health and Life Sciences

country: Qatar

institute: Hamad Bin Khalifa University

description: Library name: Sample 11

data_processing:
CLC Genomics Workbench version 22.0.2 software.
Raw sequence reads were trimmed to eliminate contaminant DNA, PCR duplicates, and adaptor sequences. Reads with a quality lower than Q20 were filtered using CLC Genomics Workbench software.
CLC Genomics Workbench was employed for assembly and mapping of all paired end reads against the latest version of the human genome (Homo sapiens, GRCh38). Outlier samples and genes with average raw counts below 10 were excluded.
Read counts were extracted utilizing CLC Genomics Workbench with default parameters.
Assembly: GRCh38
Supplementary files format and content: Comma-separated values (CSV) file contains raw counts for all samples.
Supplementary files format and content: CVS file includes reads count data

source_name: human colorectal carcinoma line

growth_protocol: All cells were cultured in DMEM with (4.5 g/L) high D-Glucose, (2 mM) Glutamine, and (1 mM) Sodium Pyruvate, supplemented with 10% fetal bovine serum (FBS) and (1X) antibiotic-antimycotic (Gibco). All cell lines were grown under sterile conditions in a monolayer culture at 37°C, with a 5% CO2 atmosphere and 95% air humidity. At 70% to 80% confluency, all cells were harvested through treatment with 0.25% EDTA.

extract_protocol:
Total RNA was isolated from cell lines using 1 mL TRIzol reagent (Invitrogen), according to the manufacturer's guidelines. Subsequently, equivalent amounts of high-quality RNA pools (100–200 ng) were precipitated in a 75% ethanol solution and shipped to Macrogen Inc. (http://macrogen.com, Korea) for total RNA-sequencing library construction and next-generation sequencing.
RNA sequencing libraries were prepared with the TruSeq Stranded Total RNA Library Prep Kit (1000000040499, Illumina), following the instructions.

treatment_protocol: Cells were treated with Metformin 4mM

value: human colorectal carcinoma line

value: spontaneously immortalized, human colorectal carcinoma line

value: p21 -/- treated

value: Metformin 4mM


title: 150nc-1

description:
Library name: Sample1
150nc-1_FPKM


title: PGCs_Ctrl_KD_double_positive_1

description:
Library name: 22017FL-26-01-67
202507_PGC.RawCount.hg38.v40.csv

value: TFAP2C-GFP/BLIMP1-TOMATO BTAG hIPSC


title: HCT116 cells p21 -/-, treated, biol rep2

description: Library name: Sample 12


title: HCT116 cells p53 -/-, treated, biol rep1

description: Library name: Sample 7

value: p53 -/- treated


title: HCT116 cells p21 -/-, control, biol rep2

description: Library name: Sample 10

value: p21 -/- control

value: No


title: HCT116 cells p53 -/-, treated, biol rep2

description: Library name: Sample 8


title: HCT116 cells p53 -/-, control, biol rep2

description: Library name: Sample 6

value: p53 -/- control


title: HCT116 cells, treated, biol rep1

description: Library name: Sample 3

value: wild-type treated


title: HCT116 cells p53 -/-, control, biol rep1

description: Library name: Sample 5


title: HCT116 cells, treated, biol rep2

description: Library name: Sample 4


title: U937 cells, non-template control, rep 2

city: North Chicago

first: Fedik

last: Rahimov

state: IL

address: 1 N. Waukegan Road

department: Genomics Research Center

institute: AbbVie

description:
Library name: U937NTC24hrLPS2
U937NTCrep2

data_processing:
FastQ files were aligned to human genome reference using STAR (v2.7.10b) with GRCh38 primary assembly (v2.7.4a) gene annotations. Gene expression levels were counted using featureCounts (v2.4.3). Differential expression was compared using the test in limma R package (v3.54.2).
UMI-labeled reads were deduplicated using UMI-tools.
Assembly: GRCh38
Supplementary files format and content: Count matrix showing CPM values in a tab-delimited text file

growth_protocol: Cells were maintained in RPMI 1640 (Gibco) supplemented with 10% heat inactivated fetal bovine serum (FBS, Gibco) and 1% Pen/Strep (Gibco).

extract_protocol:
Total RNA was isolated using the Direct-zol RNA Miniprep Plus kit (R2072, Zymo Research)
500 nanograms of total RNA were used for NEBNext Ultra II Directional RNA Library Prep Kit (NEB # E7760L). Poly-A selection (NEBNext Poly (A) Magnetic Isolation Module; NEB # E7490) and cDNA synthesis were performed according to NEB protocol. The NEBNext UMI RNA Adaptors were diluted 50-fold in ice-cold UMI Adaptor dilution buffer. Ligation reaction was purified using Ampure XP beads. (Beckman Coulter, # A63881) and the adaptor ligated cDNA was amplified with 12 cycles of PCR with NEBNext Primer Mix (96 Unique Dual Index UMI Adaptors RNA set1, (NEB #E7416). Equimolar amounts of the samples were then pooled and sequenced using NextSeq 500/550 70 base read lengths in paired-end mode.

treatment_protocol: Cells were differentiated by addition of 10 ng/ml phorbol 12-myristate 13-acetate (Sigma, P1585) for 24 hours and treated with 100 mg/ml lipopolysaccharide (LPS) (Sigma, L26375MG)for designated times.

value: pro-monocytic cell

value: WT

value: LPS


title: U937 cells, non-template control, rep 1

description:
Library name: U937NTC24hrLPS1
U937NTCrep1


title: U937 cells, WIPI2 knockout, 24hr LPS treatment rep 3

description:
Library name: U937WIPI2KO24hrLPS3
U937WIPI2KOrep3


title: U937 cells, WIPI2 knockout, 24hr LPS treatment rep 2

description:
Library name: U937WIPI2KO24hrLPS2
U937WIPI2KOrep2


title: U937 cells, WIPI2 knockout, 24hr LPS treatment rep 1

description:
Library name: U937WIPI2KO24hrLPS1
U937WIPI2KOrep1


title: Thawed_withDMSO_wt_D44_c

city: Rennes

first: Pascal

last: Loyer

address: CHU Pontchaillou

country: France

institute: Inserm

description: Library name: J14TH1Wc

data_processing:
Quality control and preprocessing of data were performed by SciLicium (Rennes, France).
The first read contains 16 bases that must have a quality score higher than 10. The first 6 bp correspond to a unique sample-specific barcode and the following 10 bp to a unique molecular identifier (UMI).
The second reads were aligned to the mus musculus reference transcriptome from the UCSC website (release mm10) using BWA version 0.7.4.4 with the parameter “-l 24”
Assembly: hg38
Supplementary files format and content: Expression file in tab-separated format. Contains for each sample (row), the number of unique umis (unique molecular identifier) associated with 28,307 genes (columns).

source_name: HepaRG

growth_protocol: HepaRG cells were maintained for two weeks in William's E medium supplemented with 10% FCS, 100 units/ml penicillin, 100 μg/ml streptomycin, 5 μg/ml insulin, and 5 × 10−5 M hydrocortisone hemisuccinate

extract_protocol:
RNA was harvested using Direct-zol™-96 RNA kit from Zymo Research (R2055).10ng of total RNA was used for the construction of sequencing libraries.
Briefly a first step of reverse transcription and template switching reactions were performed using 4 µL total RNA at 2.5 ng/µL. Then cDNAs were purified and Double strand (ds) cDNAs were generated by PCR. The sequencing libraries were built by tagmentation using 50 ng of ds cDNA with the Illumina Nextera XT Kit (Illumina, #FC-131-1024) following the manufacturer’s recommendations. The sequencing libraries were built by tagmentation using 50 ng of ds cDNA with the Illumina Nextera XT Kit (Illumina, #FC-131-1024) following the manufacturer’s recommendations.

treatment_protocol: HepaRG cells differentiation was induced by treatment for two more weeks with 1,7% DMSO

value: HepaRG

value: wt

value: withDMSO

tag: cell status

value: Thawed


title: Thawed_withDMSO_wt_D44_b

description: Library name: J14TH1Wb


title: Thawed_withDMSO_wt_D37_c

description: Library name: J7TH1Wc


title: Thawed_withDMSO_wt_D37_b

description: Library name: J7TH1Wb


title: Thawed_withDMSO_wt_D37_a

description: Library name: J7TH1Wa


title: Thawed_withDMSO_wt_D32_c

description: Library name: J2TH1Wc


title: Thawed_withDMSO_wt_D32_b

description: Library name: J2TH1Wb


title: Thawed_withDMSO_wt_D44_a

description: Library name: J14TH1Wa


title: HCT116 cells p21 -/-, control, biol rep1

description: Library name: Sample 9

value: human colorectal carcinoma line


title: Thawed_withDMSO_wt_D32_a

description: Library name: J2TH1Wa


title: HCT116 cells, control, biol rep2

description: Library name: Sample 2

value: spontaneously immortalized, human colorectal carcinoma line

value: wild-type control


title: Thawed_withDMSO_CYP2D6_D37_b

description: Library name: J7TH1Lb


title: Thawed_withDMSO_CYP2D6_D37_a

description: Library name: J7TH1La


title: Thawed_withDMSO_CYP2D6_D37_c

description: Library name: J7TH1Lc


title: Thawed_withDMSO_CYP2D6_D44_a

description: Library name: J14TH1La


title: Thawed_withDMSO_CYP2D6_D32_c

description: Library name: J2TH1Lc


title: HCT116 cells, control, biol rep1

description: Library name: Sample 1


title: Thawed_withDMSO_CYP2D6_D32_a

description: Library name: J2TH1La


title: Thawed_noDMSO_wt_D32_b

description: Library name: J2TH0Wb

value: noDMSO


title: Thawed_withDMSO_CYP2D6_D44_c

description: Library name: J14TH1Lc


title: U937 cells, non-template control, rep 3

description:
Library name: U937NTC24hrLPS3
U937NTCrep3


title: Thawed_noDMSO_wt_D32_c

description: Library name: J2TH0Wc


title: Thawed_noDMSO_wt_D30_c

description: Library name: J0TH0Wc


title: Thawed_noDMSO_wt_D32_a

description: Library name: J2TH0Wa


title: Thawed_noDMSO_wt_D30_a

description: Library name: J0TH0Wa


title: Thawed_noDMSO_wt_D30_b

description: Library name: J0TH0Wb


title: Thawed_noDMSO_CYP2D6_D32_c

description: Library name: J2TH0Lc


title: Thawed_noDMSO_CYP2D6_D32_b

description: Library name: J2TH0Lb


title: Thawed_noDMSO_CYP2D6_D32_a

description: Library name: J2TH0La


title: Thawed_noDMSO_CYP2D6_D30_c

description: Library name: J0TH0Lc


title: Progenitor_noDMSO_wt_D14_c

description: Library name: J14PR0Wc

value: Progenitor


title: Thawed_withDMSO_CYP2D6_D44_b

description: Library name: J14TH1Lb


title: Thawed_noDMSO_CYP2D6_D30_a

description: Library name: J0TH0La


title: Thawed_noDMSO_CYP2D6_D30_b

description: Library name: J0TH0Lb


title: Thawed_withDMSO_CYP2D6_D32_b

description: Library name: J2TH1Lb


title: Progenitor_noDMSO_wt_D7_c

description: Library name: J7PR0Wc


title: Progenitor_noDMSO_wt_D7_b

description: Library name: J7PR0Wb


title: Progenitor_noDMSO_wt_D4_b

description: Library name: J4PR0Wb


title: Progenitor_noDMSO_wt_D2_a

description: Library name: J2PR0Wa


title: Progenitor_noDMSO_wt_D4_c

description: Library name: J4PR0Wc


title: Progenitor_noDMSO_wt_D7_a

description: Library name: J7PR0Wa


title: Progenitor_noDMSO_wt_D4_a

description: Library name: J4PR0Wa


title: Progenitor_noDMSO_wt_D0_c

description: Library name: J0PR0Wc


title: Progenitor_noDMSO_wt_D2_b

description: Library name: J2PR0Wb


title: Progenitor_noDMSO_wt_D2_c

description: Library name: J2PR0Wc


title: Progenitor_noDMSO_wt_D14_b

description: Library name: J14PR0Wb


title: Progenitor_noDMSO_wt_D14_a

description: Library name: J14PR0Wa


title: Progenitor_noDMSO_CYP2D6_D14_c

description: Library name: J14PR0Lc


title: Progenitor_noDMSO_CYP2D6_D14_b

description: Library name: J14PR0Lb


title: Progenitor_noDMSO_CYP2D6_D14_a

description: Library name: J14PR0La


title: Progenitor_noDMSO_wt_D0_a

description: Library name: J0PR0Wa


title: Progenitor_noDMSO_CYP2D6_D7_c

description: Library name: J7PR0Lc


title: Progenitor_noDMSO_CYP2D6_D4_c

description: Library name: J4PR0Lc


title: Progenitor_noDMSO_CYP2D6_D7_b

description: Library name: J7PR0Lb


title: Progenitor_noDMSO_CYP2D6_D4_b

description: Library name: J4PR0Lb


title: Progenitor_noDMSO_CYP2D6_D4_a

description: Library name: J4PR0La


title: Progenitor_noDMSO_CYP2D6_D7_a

description: Library name: J7PR0La


title: Progenitor_noDMSO_wt_D0_b

description: Library name: J0PR0Wb


title: Progenitor_noDMSO_CYP2D6_D2_b

description: Library name: J2PR0Lb


title: Progenitor_noDMSO_CYP2D6_D2_a

description: Library name: J2PR0La


title: Progenitor_noDMSO_CYP2D6_D2_c

description: Library name: J2PR0Lc


title: Progenitor_noDMSO_CYP2D6_D0_a

description: Library name: J0PR0La


title: Progenitor_noDMSO_CYP2D6_D0_c

description: Library name: J0PR0Lc


title: Progenitor_noDMSO_CYP2D6_D0_b

description: Library name: J0PR0Lb


title: FreshDifferentiated_withDMSO_wt_D44_b

description: Library name: J14FD1Wb

value: FreshDifferentiated


title: FreshDifferentiated_withDMSO_wt_D44_c

description: Library name: J14FD1Wc


title: FreshDifferentiated_withDMSO_wt_D37_a

description: Library name: J7FD1Wa


title: FreshDifferentiated_withDMSO_wt_D37_b

description: Library name: J7FD1Wb


title: FreshDifferentiated_withDMSO_wt_D37_c

description: Library name: J7FD1Wc


title: FreshDifferentiated_withDMSO_wt_D32_b

description: Library name: J2FD1Wb


title: FreshDifferentiated_withDMSO_wt_D32_c

description: Library name: J2FD1Wc


title: FreshDifferentiated_withDMSO_wt_D32_a

description: Library name: J2FD1Wa


title: FreshDifferentiated_withDMSO_CYP2D6_D37_a

description: Library name: J7FD1La


title: FreshDifferentiated_withDMSO_wt_D44_a

description: Library name: J14FD1Wa


title: FreshDifferentiated_withDMSO_CYP2D6_D37_c

description: Library name: J7FD1Lc


title: FreshDifferentiated_withDMSO_CYP2D6_D37_b

description: Library name: J7FD1Lb


title: FreshDifferentiated_withDMSO_CYP2D6_D44_b

description: Library name: J14FD1Lb


title: FreshDifferentiated_withDMSO_CYP2D6_D44_a

description: Library name: J14FD1La


title: FreshDifferentiated_withDMSO_CYP2D6_D44_c

description: Library name: J14FD1Lc


title: FreshDifferentiated_withDMSO_CYP2D6_D32_a

description: Library name: J2FD1La


title: FreshDifferentiated_noDMSO_wt_D32_c

description: Library name: J2FD0Wc


title: FreshDifferentiated_noDMSO_wt_D30_c

description: Library name: J0FD0Wc


title: FreshDifferentiated_noDMSO_wt_D32_a

description: Library name: J2FD0Wa


title: FreshDifferentiated_noDMSO_wt_D30_b

description: Library name: J0FD0Wb


title: FreshDifferentiated_withDMSO_CYP2D6_D32_c

description: Library name: J2FD1Lc


title: FreshDifferentiated_noDMSO_wt_D32_b

description: Library name: J2FD0Wb


title: FreshDifferentiated_noDMSO_CYP2D6_D32_b

description: Library name: J2FD0Lb


title: FreshDifferentiated_noDMSO_CYP2D6_D30_b

description: Library name: J0FD0Lb


title: FreshDifferentiated_noDMSO_CYP2D6_D32_c

description: Library name: J2FD0Lc


title: FreshDifferentiated_noDMSO_CYP2D6_D30_c

description: Library name: J0FD0Lc


title: FreshDifferentiated_noDMSO_CYP2D6_D30_a

description: Library name: J0FD0La


title: FreshDifferentiated_noDMSO_wt_D30_a

description: Library name: J0FD0Wa


title: FreshDifferentiated_noDMSO_CYP2D6_D32_a

description: Library name: J2FD0La


title: AGS, Input

city: Nanjing

first: Han

last: Chen

state: Jiangsu

address: #300 Guzhou Road, Gulou District

institute: Nanjing Medical University

description: Library name: AGS, Input

library_source: genomic

data_processing:
The VAHTS Universal DNA Library Prep Kit for Illumina V3 (ND607, Vazyme) was utilized for high-throughput DNA sequencing library preparation. Library products ranging from 200 to 500 bp were enriched, quantified, and sequenced on a Novaseq 6000 sequencer (Illumina) using the PE150 model.
Assembly: hg38

molecule: genomic DNA

source_name: stomach

extract_protocol:
The AGS cells were cross-linked with 1% (vol/vol) formaldehyde for 10 minutes. Following this, the cells were lysed, dissociated by sonication, and immunoprecipitated with anti-H3K18la (ChIP Grade) at 4°C overnight, using the input sample as a control. DNA was extracted using the phenol-chloroform method.
ChIP sequencing (ChIP-seq) was performed on AGS cells by Geneseed Co., Ltd. (Guangzhou, China). The AGS cells were cross-linked with 1% (vol/vol) formaldehyde for 10 minutes. Following this, the cells were lysed, dissociated by sonication, and immunoprecipitated with anti-H3K18la (ChIP Grade) at 4°C overnight, using the input sample as a control. DNA was extracted using the phenol-chloroform method.

value: stomach

value: AGS

value: cancer cell

tag: ip antibody

value: input


title: AGS, ChIP

description: Library name: AGS, ChIP

value: with anti-H3K18la antibodies


title: FreshDifferentiated_withDMSO_CYP2D6_D32_b

description: Library name: J2FD1Lb


title: 41_ad_en_4B_GEX-v3

first: Davide

last: Simone

address: Roosevelt Drive

department: Kennedy Institute of Rheumatologt

description: Library name: bone_R4

data_processing:
CellRanger v7.1.0 was used for demultiplexing and initial barcode selection. Ambient RNA removal was performed using CellBender v0.3.0 on the raw feature-barcode matrix generated from a custom reference built with the Ensembl GRCh38 Homo Sapiens v110 anotations. Cell barcodes of predicted cells were retained after identifying and removing background signal.
For further downstream analysis, predicted doublets were removed using Scrublet with default parameters (expected doublet rate of 6%). Additionally, cells with more than 10% mitochondrial reads or fewer than 200 detected genes were excluded from further analysis.
Assembly: Custom reference built with the Ensembl GRCh38 Homo Sapiens v110 anotations.
Supplementary files format and content: Processed files represent respectively cellranger and cellbender ("filtered") output
Supplementary files format and content: The h5ad files represent post-QC single cell data in AnnData format

source_name: perientheseal bone

extract_protocol:
Human entheseal tissue from spinal surgeries was collected from individuals undergoing scoliosis correction or vertebral decompression. Samples were dissected into perispinous entheseal bone (PEB) and interspinous ligament entheseal soft tissue (EST) and enzymatically digested with a collagenasd solution before processing.
Isolated single cells were suspended in DMEM media with 10% FCS and transported in cooler box with ice (temperature 5°C) and processed within four hours. Viable cells were sorted using 7-AAD dye (Biolegend 420403) and processed on the 10X Genomics Chromium Controller (Chip G) in accordance with the manufacturer's guidelines to capture approximately 10,000 cells per sample. Gene expression libraries were generated using the 10x Genomics Single Cell 3' Reagent Kits v3.1, following the instructions provided in the user guide (CG000330 Rev B). The resulting libraries were combined and sequenced on an Illumina NovaSeq6000 platform using a custom paired-end, dual-indexing configuration (28, 8, 98 bp) as recommended by 10X Genomics. This procedure was carried out twice, with two paired PEB/EST samples processed in each batch.

value: perientheseal bone

value: live cell


title: 36_ad_en_2B_GEX-v3

description: Library name: bone_R2


title: 38_ad_en_3B_GEX-v3

description: Library name: bone_R3


title: 42_ad_en_4EN_GEX-v3

description: Library name: enthesis_R4

source_name: entheseal soft tissue

value: entheseal soft tissue


title: 39_ad_en_3EN_GEX-v3

description: Library name: enthesis_R3


title: 44_ad_en_5EN_GEX-v3

description: Library name: enthesis_R5


title: THESCSRF1, siNT, THESC 1

city: Research Triangle Park

first: Francesco

middle: John

last: DeMayo

state: North Carolina

address: 111 T W Alexander Dr

department: DIR

institute: NIEHS

description: Library name: THESCSRF1

data_processing:
Raw reads were trimmed to a minimum quality score of 20 using Trimmomatic v0.39.
Paired-end alignment to the mouse mm10 reference genome from the Genome Reference Consortium was performed using HISAT2 v2.2.1.
Alignment files were indexed by Samtools v1.16.1.
Count matrices were generated using Subread’s featureCounts tool (v2.0.6).
Normalization and differential expression analysis was performed using DESeq2 v1.38.3  in R v4.2.2.
Assembly: hg38
Supplementary files format and content: THESC_raw_counts.csv contains raw counts for each sample
Supplementary files format and content: THESC_normalized_counts.csv contains DESeq2-normalized counts for each sample

source_name: hTERT-immortalized human endometrial stromal cells

growth_protocol: THESCs were cultured in DMEM/F12 (Gibco #11320033) supplemented with 10% fetal bovine serum (FBS, Gibco #10082147) and 1% Penicillin-Streptomycin (Sigma #P0781) at 37°C in a 5% CO2 humidified incubator.

extract_protocol:
Total RNA was isolated from THESCs using the RNeasy mini kit (Qiagen #74106) and treated with RNase-free DNase (Qiagen #79254).
Libraries were prepared by the NIEHS Epigenomics and DNA Sequencing Core Facility with an Illumina Tru-seq stranded mRNA library prep kit.

treatment_protocol: Transfections of 100 nM ON-TARGETplus SMARTpool siNT (D-001810-10-50, Dharmacon, Lafayette, CO) or siSRF (L-009800-00-0010, Dharmacon) were performed in Opti-MEM (Gibco #31985070) with 2% charcoal stripped FBS (Gibco #12676029) using Lipofectamine RNAiMAX (Invitrogen #13778150) according to the manufacturer’s instructions for 48 hours. After completion of transfection, the media was replaced with Opti-MEM (Gibco #31985070) with 2% charcoal stripped FBS (Gibco #12676029) and 1% Penicillin-Streptomycin (Sigma #P0781), and cells were cultured for 3 more days before collection to allow optimal drop in target protein levels.

value: siSRF


title: 43_ad_en_5B_GEX-v3

description: Library name: bone_R5


title: THESCSRF3, siNT, THESC 3

description: Library name: THESCSRF3

value: hTERT-immortalized human endometrial stromal cells


title: THESCNT3, siNT, THESC 3

description: Library name: THESCNT3

value: siNT (non-targetting control)


title: THESCSRF2, siNT, THESC 2

description: Library name: THESCSRF2


title: 37_ad_en_2EN_GEX-v3

description: Library name: enthesis_R2


title: SRF74, siSRF, ME-HESC 3

description: Library name: SRF74

data_processing:
Raw reads were trimmed to a minimum quality score of 20 using Trimmomatic v0.39.
Paired-end alignment to the mouse mm10 reference genome from the Genome Reference Consortium was performed using HISAT2 v2.2.1.
Alignment files were indexed by Samtools v1.16.1.
Count matrices were generated using Subread’s featureCounts tool (v2.0.6).
Normalization and differential expression analysis was performed using DESeq2 v1.38.2 in R v4.2.2 with both treatment condition and cell donor included as factors in the model.
Assembly: hg38
Supplementary files format and content: ME-HESC_raw_counts.csv contains raw counts for each sample
Supplementary files format and content: ME-HESC_normalized_counts.csv contains DESeq2-normalized counts for each sample

source_name: Menstrual effluent-derrived endometrial stromal cells

growth_protocol: ME-HESCs were cultured in DMEM/F12 (Gibco #11320033) supplemented with 10% fetal bovine serum (FBS, Gibco #10082147) and 1% Penicillin-Streptomycin (Sigma #P0781) at 37°C in a 5% CO2 humidified incubator.

extract_protocol:
Total RNA was isolated from ME-HESCs using the RNeasy mini kit (Qiagen #74106) and treated with RNase-free DNase (Qiagen #79254).
Libraries were prepared by the NIEHS Epigenomics and DNA Sequencing Core Facility with an Illumina Tru-seq stranded mRNA library prep kit.


title: SRF49, siSRF, ME-HESC 1

description: Library name: SRF49

value: Menstrual effluent-derrived endometrial stromal cells


title: NT74, siNT, ME-HESC 3

description: Library name: NT74


title: SRF50, siSRF, ME-HESC 2

description: Library name: SRF50


title: THESCNT2, siNT, THESC 2

description: Library name: THESCNT2


title: THESCNT1, siNT, THESC 1

description: Library name: THESCNT1


title: NT50, siNT, ME-HESC 2

description: Library name: NT50


title: HELA_EZRKO_4

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description:
Library name: S_20210906095404_8
Transcriptome profile of experiment Ezrin knockout biological rep3

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: Hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files including raw counts

source_name: HeLa

growth_protocol: DMEM with 10% FBS

extract_protocol:
For gene expression analyses, total RNA was extracted according to the manufacturer's instructions (RNeasy Mini Kit). Total RNA was quantified using the Qubit 4.0 fluorimetric Assay (Thermo Fisher Scientific). RNA extracted was precisely quantified and mixed at 10ng/µL.
NEGEDIA Digital mRNAseq research grade sequencing service (NEGEDIA srl) (NEGEDIA srl)

value: HeLa

value: immortal human cell

value: Ezrin knockout


title: HELA_EZRKO_2

description:
Library name: S_20210906095404_6
Transcriptome profile of experiment Ezrin knockout biological rep2


title: HeLA_WT_3

description:
Library name: S_20210906095404_3
Transcriptome profile of control wild-type biological rep3

value: wild-type


title: HeLA_WT_4

description:
Library name: S_20210906095404_4
Transcriptome profile of control wild-type biological rep4


title: HELA_EZRKO_1

description:
Library name: S_20210906095404_5
Transcriptome profile of experiment Ezrin knockout biological rep1


title: HeLA_WT_1

description:
Library name: S_20210906095404_1
Transcriptome profile of control wild-type biological rep1


title: HeLa_ezr-inhibitor_4

description:
Library name: S_20210525173143_8
Transcriptome profile of Ezr-inhibitor-treated wild-type biological rep3

treatment_protocol: 6 hours of NSC668394 for Ezrin Inhibition; 6 hours of DMSO as control


title: HeLa_ezr-inhibitor_2

description:
Library name: S_20210525173143_6
Transcriptome profile of Ezr-inhibitor-treated wild-type biological rep2


title: HeLa_ezr-inhibitor_1

description:
Library name: S_20210525173143_5
Transcriptome profile of Ezr-inhibitor-treated wild-type biological rep1


title: HeLa_dmso_3

description:
Library name: S_20210525173143_3
Transcriptome profile of DMSO-treated wild-type biological rep3


title: HeLa_dmso_4

description:
Library name: S_20210525173143_4
Transcriptome profile of DMSO-treated wild-type biological rep4


title: HeLa_dmso_1

description:
Library name: S_20210525173143_1
Transcriptome profile of DMSO-treated wild-type biological rep1


title: CD8_TRB, CD4 = 842 cells/ul

city: Hefei

first: Lina

last: Huang

state: 安徽

address: Hefei in Anhui Province

institute: university of science and technology in China

description: Library name: 35#_CD8_TRB

data_processing:
Sequencing was performed on the Illumina Novaseq 6000 platform, yielding 10M of PE150 reads for the BCR library and 5M of PE150 reads for the TCR library. Data processing of raw reads was quality checked by using fastqc v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed for low-quality bases and adaptors, if necessary, by using TrimGalore
MiGEC software was used to identify primers for each gene in the sequences, followed by demultiplexing of the quality-filtered sequences based on their primer sequences
MiGEC software was used to analyze the CDR3 sequences and identity VDJ segment positions for each gene
Assembly: hg38
Supplementary files format and content: xlsx files about BCR and TCR repertoires and Frequency
Library strategy: TCR-Seq

source_name: PBMC

extract_protocol:
Total RNA was extracted using TRIzol reagents and quantified by Qubit. RNA integrity was measured using Agilent 2100 bioanalyzer and only samples with RIN higher than 7 were used for library preparation.
For PBMC samples, typically 100 ng of total RNA was used as a template. cDNA synthesis was performed according to smart-seq2 protocol with some modifications

value: PBMC

value: Lymphocyte

value: CD8+T cell


title: HeLa_dmso_2

description:
Library name: S_20210525173143_2
Transcriptome profile of DMSO-treated wild-type biological rep2


title: CD8_TRB, CD4 = 1467 cells/ul

description: Library name: 33#_CD8_TRB


title: CD8_TRB, CD4 = 1484 cells/ul

description: Library name: 32#_CD8_TRB


title: CD8_TRB, CD4 = 248 cells/ul

description: Library name: 26#_CD8_TRB


title: CD8_TRB, CD4 = 236 cells/ul

description: Library name: 27#_CD8_TRB


title: CD8_TRB, CD4 = 871 cells/ul

description: Library name: 34#_CD8_TRB


title: CD8_TRB, CD4 = 212 cells/ul

description: Library name: 30#_CD8_TRB


title: CD8_TRB, CD4 = 34 cells/ul

description: Library name: 25#_CD8_TRB


title: CD8_TRB, CD4 = 886 cells/ul

description: Library name: 31#_CD8_TRB


title: CD8_TRB, CD4 = 202 cells/ul

description: Library name: 28#_CD8_TRB


title: CD8_TRB, CD4 = 58 cells/ul

description: Library name: 22#_CD8_TRB


title: CD8_TRB, CD4 = 28 cells/ul

description: Library name: 24#_CD8_TRB


title: CD8_TRB, CD4 = 214 cells/ul

description: Library name: 29#_CD8_TRB


title: NT49, siNT, ME-HESC 1

description: Library name: NT49


title: CD8_TRB, CD4 = 63 cells/ul

description: Library name: 23#_CD8_TRB


title: CD8_TRB, CD4 = 87 cells/ul

description: Library name: 21#_CD8_TRB


title: HeLA_WT_2

description:
Library name: S_20210906095404_2
Transcriptome profile of control wild-type biological rep2


title: CD4_TRB,  CD4 = 1484 cells/ul

description: Library name: 32#_CD4_TRB

value: CD4+T cell


title: CD4_TRB,  CD4 = 1467 cells/ul

description: Library name: 33#_CD4_TRB


title: CD4_TRB,  CD4 = 886 cells/ul

description: Library name: 31#_CD4_TRB


title: CD4_TRB,  CD4 = 842 cells/ul

description: Library name: 35#_CD4_TRB


title: CD4_TRB,  CD4 = 871 cells/ul

description: Library name: 34#_CD4_TRB


title: CD4_TRB,  CD4 = 212 cells/ul

description: Library name: 30#_CD4_TRB


title: CD4_TRB,  CD4 = 214 cells/ul

description: Library name: 29#_CD4_TRB


title: CD4_TRB,  CD4 = 202 cells/ul

description: Library name: 28#_CD4_TRB


title: CD4_TRB,  CD4 = 236 cells/ul

description: Library name: 27#_CD4_TRB


title: CD4_TRB,  CD4 = 34 cells/ul

description: Library name: 25#_CD4_TRB


title: CD4_TRB,  CD4 = 63 cells/ul

description: Library name: 23#_CD4_TRB


title: CD4_TRB,  CD4 = 58 cells/ul

description: Library name: 22#_CD4_TRB


title: CD4_TRB,  CD4 = 28 cells/ul

description: Library name: 24#_CD4_TRB


title: CD4_TRB,  CD4 = 87 cells/ul

description: Library name: 21#_CD4_TRB


title: CD4_TRB,  CD4 = 248 cells/ul

description: Library name: 26#_CD4_TRB


title: CD8_TRA, CD4 = 842 cells/ul

description: Library name: 35#_CD8_TRA


title: CD8_TRA, CD4 = 871 cells/ul

description: Library name: 34#_CD8_TRA


title: CD8_TRA, CD4 = 1484 cells/ul

description: Library name: 32#_CD8_TRA


title: CD8_TRA, CD4 = 236 cells/ul

description: Library name: 27#_CD8_TRA


title: CD8_TRA, CD4 = 214 cells/ul

description: Library name: 29#_CD8_TRA


title: CD8_TRA, CD4 = 34 cells/ul

description: Library name: 25#_CD8_TRA


title: CD8_TRA, CD4 = 212 cells/ul

description: Library name: 30#_CD8_TRA


title: CD8_TRA, CD4 = 886 cells/ul

description: Library name: 31#_CD8_TRA


title: CD8_TRA, CD4 = 248 cells/ul

description: Library name: 26#_CD8_TRA


title: CD8_TRA, CD4 = 202 cells/ul

description: Library name: 28#_CD8_TRA


title: CD8_TRA, CD4 = 1467 cells/ul

description: Library name: 33#_CD8_TRA


title: CD8_TRA, CD4 = 28 cells/ul

description: Library name: 24#_CD8_TRA


title: CD8_TRA, CD4 = 58 cells/ul

description: Library name: 22#_CD8_TRA


title: CD8_TRA, CD4 = 63 cells/ul

description: Library name: 23#_CD8_TRA


title: CD8_TRA, CD4 = 87 cells/ul

description: Library name: 21#_CD8_TRA


title: CD4_TRA,  CD4 = 842 cells/ul

description: Library name: 35#_CD4_TRA


title: CD4_TRA,  CD4 = 1484 cells/ul

description: Library name: 32#_CD4_TRA


title: CD4_TRA,  CD4 = 886 cells/ul

description: Library name: 31#_CD4_TRA


title: CD4_TRA,  CD4 = 212 cells/ul

description: Library name: 30#_CD4_TRA


title: CD4_TRA,  CD4 = 214 cells/ul

description: Library name: 29#_CD4_TRA


title: CD4_TRA,  CD4 = 871 cells/ul

description: Library name: 34#_CD4_TRA


title: CD4_TRA,  CD4 = 202 cells/ul

description: Library name: 28#_CD4_TRA


title: CD4_TRA,  CD4 = 1467 cells/ul

description: Library name: 33#_CD4_TRA


title: CD4_TRA,  CD4 = 236 cells/ul

description: Library name: 27#_CD4_TRA


title: CD4_TRA,  CD4 = 248 cells/ul

description: Library name: 26#_CD4_TRA


title: CD4_TRA,  CD4 = 34 cells/ul

description: Library name: 25#_CD4_TRA


title: CD4_TRA,  CD4 = 63 cells/ul

description: Library name: 23#_CD4_TRA


title: CD4_TRA,  CD4 = 28 cells/ul

description: Library name: 24#_CD4_TRA


title: CD4_TRA,  CD4 = 58 cells/ul

description: Library name: 22#_CD4_TRA


title: CD4_TRA,  CD4 = 87 cells/ul

description: Library name: 21#_CD4_TRA


title: PBMC_IgG+ B cells, CD4 = 842 cells/ul

description: Library name: 35#_BCR

data_processing:
Sequencing was performed on the Illumina Novaseq 6000 platform, yielding 10M of PE150 reads for the BCR library and 5M of PE150 reads for the TCR library. Data processing of raw reads was quality checked by using fastqc v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed for low-quality bases and adaptors, if necessary, by using TrimGalore
MiGEC software was used to identify primers for each gene in the sequences, followed by demultiplexing of the quality-filtered sequences based on their primer sequences
MiGEC software was used to analyze the CDR3 sequences and identity VDJ segment positions for each gene
Assembly: hg38
Supplementary files format and content: xlsx files about BCR and TCR repertoires and Frequency
Library strategy: BCR-Seq

value: B cell


title: PBMC_IgG+ B cells, CD4 = 886 cells/ul

description: Library name: 31#_BCR


title: PBMC_IgG+ B cells, CD4 = 1467 cells/ul

description: Library name: 33#_BCR


title: PBMC_IgG+ B cells, CD4 = 202 cells/ul

description: Library name: 28#_BCR


title: PBMC_IgG+ B cells, CD4 = 248 cells/ul

description: Library name: 26#_BCR


title: PBMC_IgG+ B cells, CD4 = 212 cells/ul

description: Library name: 30#_BCR


title: PBMC_IgG+ B cells, CD4 = 236 cells/ul

description: Library name: 27#_BCR


title: PBMC_IgG+ B cells, CD4 = 63 cells/ul

description: Library name: 23#_BCR


title: PBMC_IgG+ B cells, CD4 = 58 cells/ul

description: Library name: 22#_BCR


title: PBMC_IgG+ B cells, CD4 = 214 cells/ul

description: Library name: 29#_BCR


title: PBMC_IgG+ B cells, CD4 = 871 cells/ul

description: Library name: 34#_BCR


title: PBMC_IgG+ B cells, CD4 = 87 cells/ul

description: Library name: 21#_BCR


title: PBMC_IgG+ B cells, CD4 = 860 cells/ul

description: Library name: 19#


title: PBMC_IgG+ B cells, CD4 = 1250 cells/ul

description: Library name: 20#


title: PBMC_IgG+ B cells, CD4 = 28 cells/ul

description: Library name: 24#_BCR


title: PBMC_IgG+ B cells, CD4 = 576 cells/ul

description: Library name: 18#


title: PBMC_IgG+ B cells, CD4 = 570 cells/ul

description: Library name: 17#


title: PBMC_IgG+ B cells, CD4 = 318 cells/ul

description: Library name: 14#


title: PBMC_IgG+ B cells, CD4 = 469 cells/ul

description: Library name: 15#


title: PBMC_IgG+ B cells, CD4 = 486 cells/ul

description: Library name: 13#


title: PBMC_IgG+ B cells, CD4 = 418 cells/ul

description: Library name: 16#


title: PBMC_IgG+ B cells, CD4 = 217 cells/ul

description: Library name: 12#


title: PBMC_IgG+ B cells, CD4 = 88 cells/ul

description: Library name: 9#


title: PBMC_IgG+ B cells, CD4 = 368 cells/ul

description: Library name: 11#


title: PBMC_IgG+ B cells, CD4 = 83 cells/ul

description: Library name: 10#


title: PBMC_IgG+ B cells, CD4 = 1484 cells/ul

description: Library name: 32#_BCR


title: PBMC_IgG+ B cells, CD4 = 163 cells/ul

description: Library name: 8#


title: PBMC_IgG+ B cells, CD4 = 142 cells/ul

description: Library name: 7#


title: PBMC_IgG+ B cells, CD4 = 43 cells/ul

description: Library name: 5#


title: PBMC_IgG+ B cells, CD4 = 47 cells/ul

description: Library name: 1#


title: PBMC_IgG+ B cells, CD4 = 165 cells/ul

description: Library name: 6#


title: PBMC_IgG+ B cells, CD4 = 34 cells/ul

description: Library name: 25#_BCR