title: Zahra-0_h_SS_control-3

status: Public on Jul 04 2026

city: Heidelberg

first: Rida

last: Zahra

address: Im Neuenheimer Feld 230

department: Centre for Organismal Studies (COS), Cytoskeleton, Cell division and Signalling Unit

country: Germany

institute: Heidelberg University

description: Library name: Sample 18

data_processing:
Quality of the raw data was assessed with FastQC.The adapter sequence was trimmed with Trimmomatic 0.39.
Assembly: After removal of the adapter sequence, reads were mapped against human genome hg38 using STAR with an annotation file from GENCODE (version 21). Later, SAMtools was used to sort the genearated BAM files and counting was done by QoRTs.
Supplementary files format and content: Raw counts are available in the form of .txt files or .csv files

growth_protocol: RPE1 cells were cultured in DMEM F12 supplemented with 10% FBS, 2 mM L-glutamine and 0.348% sodium bicarbonate with 5% CO2 at 37C.

extract_protocol:
Total RNA was harvested using NucleoSpin® RNA Plus (Macherey-Nagel) kit according to the manufacturer´s protocol.
Library peparation was carried out using TruSeq Stranded kit at the NGS core facility of German Cancer research center (DKFZ), Heidelberg, Germany according to the manufacturer´s protocol.

treatment_protocol: Bulk RNA sequencing was performed on RPE1 cells cultured on 1 kPa polyacrylamide hydrogel (coated with fibronectin) or glass-control (glass coated with fibronectin only) in the presence of serum for 24 hours. Furthermore, transcriptomic profile of serum starved cells with respect to their cyclin control was also analyzed. For that, RPE1 cells (cultured on uncoated glass) were serum starved for 6 and 24 hours and cyclin cells (0 hours of serum-starvation samples) were used as their respective controls.

tag: cell type

value: Retinal pigment epithelial cells

value: No serum starvation induced (cultured in the presence of serum)


title: Zahra-0_h_SS_control-1

type: SRA

description: Library name: Sample 16

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: treatment


title: NSCL/P_02

status: Public on Jul 05 2026

type: RNA

city: Beijing

first: Siyuan

last: Guo

state: Beijing

address: No. 9 Fanjiacun Road, Fengtai District

department: Department of Oral and Maxillofacial Plastic and Traumatic Surgery

country: China

institute: Beijing Stomatological Hospital, Capital Medical University

description: Gene expression data of peripheral blood from NSCL/P patients

hyb_protocol: Following labeling, fragmented cDNA was hybridized for 16 hr at 45C on GeneChip Clariom D Human Assay. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Peripheral blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: condition

value: Nonsyndromic cleft lip with or without cleft palate (NSCL/P)

tag: tissue

value: blood

tag: gender

value: female


title: Control rep1

city: JEONJU

first: SOO MI

last: KIM

state: JEONBUK

address: GUNGIRO 20

department: PHYSIOLOGY

country: South Korea

institute: JEONBUK NATIONAL UNIVERSITY

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Human HepG2 cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Hepatocellular carcinoma cell line


title: Zahra-24_h_SS-3

description: Library name: Sample 15

value: serum starvation induced for 24 hours


title: Zahra-0_h_SS_control-2

description: Library name: Sample 17


title: Zahra-24_h_SS-1

description: Library name: Sample 13


title: NSCL/P_01

value: male


title: Zahra-24_h_SS-2

description: Library name: Sample 14


title: Zahra_glass-control-plus_serum-3

description: Library name: Sample 6


title: Zahra_glass-control-plus_serum-2

description: Library name: Sample 5


title: Zahra_glass-control-plus_serum-1

description: Library name: Sample 4


title: Zahra_1_kPa-plus_serum-1

description: Library name: Sample 1


title: Zahra_1_kPa-plus_serum-3

description: Library name: Sample 3


title: GLUT3 overexpressed Aged HUVECs RNAseq rep1

city: aaaaaaaa

first: Wanzhou

last: Wu

address: aaaaaaaaa

institute: aaaaaaa

description:
Library name: Sample 8
OEC-GLUT3-OE2
Expression_Transcript.xlsx

data_processing:
Raw sequencing reads were assessed using FastQC. Adapter sequences and low-quality bases were removed using Cutadapt.  For RNA-seq data, clean reads were aligned to the Mus musculus reference genome (GRCm38) using HISAT2. Transcript assembly and abundance estimation were performed using StringTie based on GENCODE gene annotations. Gene and transcript expression levels were quantified as FPKM values. Differential expression analysis was performed using Ballgown. Alternative splicing events were identified using rMATS, and coding potential of novel transcripts was evaluated using CPAT.  For Ribo-seq data, reads shorter than 22 nt or longer than 34 nt after trimming were discarded. Reads mapping to rRNA, tRNA, snRNA, and snoRNA were removed using Bowtie. Remaining reads were aligned to the Mus musculus reference genome (GRCm38) using STAR. Only uniquely mapped reads were retained for downstream analyses. Ribosome footprint quality control analyses were performed using RiboTish. Transcript-level ribosome occupancy was quantified using Plastid and normalized as RPKM values. Differential translation analysis was performed using edgeR, translational efficiency (TE) was analyzed using RiboDiff, and ORF prediction was performed using RiboCode.
Assembly: GRCh38
Supplementary files format and content: Processed data files are provided as .xlsx table files. RNA-seq outputs include raw gene count matrices. Ribo-seq outputs include raw ribosome-protected fragment (RPF) count matrices.

source_name: Vascular

extract_protocol:
Samples were collected and immediately frozen in liquid nitrogen and stored at −80°C until processing. For RNA-seq samples, total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer's instructions. RNA quality and concentration were assessed using agarose gel electrophoresis and a NanoDrop ND-1000 spectrophotometer. Poly(A)+ mRNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), while ribosomal RNA depletion was performed when necessary.  For ribosome profiling (Ribo-seq) samples, tissues were homogenized in polysome lysis buffer supplemented with cycloheximide and RNase inhibitors. Cell debris was removed by centrifugation and lysates were treated with RNase I to digest unprotected RNA. Ribosome-protected fragments (RPFs) were isolated and purified. RNA quantity and integrity were evaluated prior to library preparation.
RNA-seq libraries were prepared using the KAPA Stranded RNA-Seq Library Prep Kit (Roche). Briefly, enriched mRNA or rRNA-depleted RNA was fragmented and reverse-transcribed into first-strand cDNA using random primers. Second-strand cDNA synthesis was performed with dUTP incorporation to preserve strand specificity. Double-stranded cDNA was end-repaired, A-tailed, ligated to Illumina-compatible adapters, PCR-amplified, and purified.  Ribo-seq libraries were prepared using the NEB Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs). Ribosome-protected fragments corresponding to 26–34 nt footprints were size-selected and ligated to 3′ and 5′ adapters. Reverse transcription was performed to generate cDNA, followed by PCR amplification. PCR products corresponding to 146–154 bp were purified by PAGE gel extraction.  Library quality and fragment size distributions were evaluated using an Agilent 2100 Bioanalyzer and quantified by qPCR. Sequencing was performed on the Illumina NovaSeq 6000 platform. RNA-seq libraries were sequenced in paired-end 150 bp mode, whereas Ribo-seq libraries were sequenced in single-end mode.

value: Vascular

value: Primary Cell

value: Human Umbilical Vein Endothelial Cells

tag: genotype

value: GLUT3 overexpress

tag: age

value: Aged


title: GLUT3 overexpressed Aged HUVECs RNAseq rep2

description:
Library name: Sample 7
OEC-GLUT3-OE1
Expression_Transcript.xlsx


title: Young HUVECs RNAseq rep3

description:
Library name: Sample 3
YEC3
Expression_Transcript.xlsx

value: Young


title: Aged HUVECs RNAseq rep3

description:
Library name: Sample 6
OEC3
Expression_Transcript.xlsx


title: Aged HUVECs RNAseq rep1

description:
Library name: Sample 4
OEC1
Expression_Transcript.xlsx


title: Young HUVECs RNAseq rep1

description:
Library name: Sample 1
YEC1
Expression_Transcript.xlsx


title: Oral_Biopsy_CrohnsDiseasePatient_Experiment4_TCR

city: Kiel

first: Philipp

last: Hofmann

address: Michaelisstraße 5

department: Institute of Medical Immunology

institute: Christian-Albrecht-University of Kiel

description:
Library name: Oral_CD_Experiment4_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript

library_source: transcriptomic single cell

data_processing:
Raw sequencing base calls were converted to FASTQ files using cellranger mkfastq. The resulting FASTQ files were then processed with Cell Ranger (v7.1.0) and aligned to the GRCh38 human reference genome (Cell Ranger 2020-A release). Paired single-cell RNA and single-cell TCR data were processed using cellranger multi, utilizing the Cell Ranger VDJ reference 7.1.0 for TCR read alignment. Sample-specific demultiplexing for single cell experiments involving hashtag antibodies was achieved by employing a modified Cell Ranger workflow, adapting the 3’ CellPlex pipleline for 5’ chemistry as described in the 10X Genomics online protocol (https://www.10xgenomics.com/analysis-guides/demultiplexing-and-analyzing-5’-immune-profiling-libraries-pooled-with-hashtags). Briefly, a customized cell multiplexing oligo reference was created, specifying each hashtag antibody sequence and incorporating an updated sequence pattern “^NNNNNNNNNN(BC)NNNNNNNNN” to define the barcode position within the hashtag antibody FASTQ files. An initial run of cellranger multi was performed using FASTQ files for the gene expression and hashtag antibody libraries along with the customized cell multiplexing oligo reference to enable sample demultiplexing. The resulting sample-specific BAM files were converted to FASTQ format using 10X Genomics bamtofastq (v1.4.1) and utilized in a second cellranger multi run to allow fully demultiplexed processing of paired single-cell RNA and TCR data.
Assembly: GRCh38
Supplementary files format and content: CellRanger count pipeline output: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger vdj pipeline output: filtered_contig_annotations.csv

source_name: Oral tissue

extract_protocol:
C. albicans-reactive CD154+ Tmem from peripheral blood or CD3+CD4+CD45RO+ cells from tissues were sorted with FACS and labeled with barcoded hashtag antibodies for sample multiplexing. In brief, PBMCs were stimulated with C. albicans, Th17 targets and Non-Th17 Targets for 6 h in the presence of 1 μg ml−1 of CD40 and 1 μg ml−1 of CD28 pure antibody. Cells were labeled with CD154-Biotin, followed by anti-biotin MicroBeads, and magnetically enriched by MS Columns (all from Miltenyi Biotec). Cells were stained on the column with TotalSeq-C anti-human hashtag antibodies (LNH-94, 1:50) in the presence of Human TruStain FcX (1:20) in 50 μl of staining volume. Columns were washed twice, and cells were eluted with 1000 μl of sterile filtered 1x PBS supplemented with 0.5% (v/v) human AB-serum. Subsequently, cells were sorted via FACS into precoated, low-bind collection tubes, containing sterile, filtered 1xPBS supplemented with 0.5% (v/v) human AB-serum. For intestinal tissue, up to four biopsies were pooled, whereas single biopsies were used  for oral samples (from the roof of the mouth, 4mm). Intestinal and oral biopsies were processed by mincing the tissue with scalpels and enzymatically digesting in 1mL of HBSS Ca2+Mg+ (Gibco) supplemented with 0.5% (v/v) human AB-serum (GemCell), 100 IU/mL penicillin, 100 mg/mL streptomycin, 0.25 mg/mL amphotericin B (Antibiotic Antimycotic Solution, Sigma Aldrich), 20uL/mL DNAseI (CellSystems), 1mg/mL collagenase type CLS IV (Biochrom). Tissue digestion was performed at 37°C while shaking for 30 minutes. Cells were passed through a sterile filter and stained with fluorochrome-conjugated antibodies to CD4-Vioblue or CD4-FITC, CD3-PE or CD3-VioGreen, CD45-AlexaFlour700, CD8/CD14/CD20-PerCP (Dump channel), CD45RO-APC, CLA-BV605 and Integrin-b7-PE-Vio770. Oral samples were stained with TotalSeq-C anti-human hashtag antibodies (LNH-94, 1:50) in the presence of Human TruStain FcX (1:20) in 50 μl of staining volume. Cells were sorted via FACS into precoated, low-bind collection tubes, containing sterile, filtered 1xPBS supplemented with 0.5% (v/v) human AB-serum.  After sorting, cells reactive for each antigen or oral cells derived from multiple donors were combined for sample multiplexing. FACS-enriched cells fractions from intestinal samples were processed individually.
FACS-enriched cells were loaded on a Chromium Next GEM Chip K (10X Genomics) for processing with the Chromium Next GEM Single Cell 5′ Kit v2 according to the manufacturer’s instructions. Sequencing libraries were generated as detailed in the manufacturer’s user guide (CG000511 Rev D).

value: Oral tissue

value: CD4+ T cells

value: Healthy Control and Crohn's disease patient

value: mixed sample (Oral CD4 +Tcells from CD8. CD9)

tag: library type

value: TCR


title: Young HUVECs RNAseq rep2

description:
Library name: Sample 2
YEC2
Expression_Transcript.xlsx


title: Oral_Biopsy_CrohnsDiseasePatient_Experiment4_HTO

description:
Library name: Oral_CD_Experiment4_HTO
Hashtag-derived oligonucleotide
HTO (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: HTO

tag: hto

value: TotalSeq-C0257 anti-human Hashtag 7 (CD8), TotalSeq-C0260 anti-human Hashtag 10 (CD9)


title: TSs-2

city: Lanzhou

first: jinqiang

last: huang

address: Yintanlu Stress

institute: Gansu Agricultural University

description:
Library name: Sample 11
IHNV-infected spleen tissue from rainbow trout, biological replicate 2, used for small RNA sequencing and miRNA expression profiling.

data_processing:
Raw reads from long RNA-seq, small RNA-seq and mRNA-seq libraries were filtered to remove adapter sequences, low-quality reads and reads containing excessive unknown bases; small RNA-seq reads outside the expected length range were also removed.
Clean reads from long RNA-seq and mRNA-seq libraries were aligned to the Oncorhynchus mykiss reference genome using HISAT2, whereas clean small RNA-seq reads were mapped to the reference genome using Bowtie.
mRNA, lncRNA and hepatocyte mRNA expression levels were quantified using StringTie, and raw count and normalized FPKM expression matrices were generated for the corresponding samples.
CircRNAs were identified using find_circ and quantified based on back-splice junction reads. CircRNA raw counts and normalized expression values were generated for all spleen long RNA-seq samples.
Known and novel miRNAs were identified using miRDeep2 and annotated by comparison with public miRNA databases. miRNA expression levels were quantified as raw counts and normalized TPM values for all spleen small RNA-seq samples.
Differential expression analyses were performed between IHNV-infected and uninfected spleen samples and between circUSP47-overexpressing and empty vector control hepatocytes. Differentially expressed circRNAs, miRNAs, lncRNAs and mRNAs were integrated to construct ceRNA networks and to identify commonly regulated mRNAs and immune-related pathways associated with circUSP47-mediated antiviral regulation.
Assembly: Oncorhynchus mykiss reference genome, USDA_OmykA_1.1, GCF_013265735.2.
Supplementary files format and content: Tab-delimited text files containing raw count and normalized expression matrices for mRNAs, lncRNAs, circRNAs and miRNAs across the corresponding samples. mRNA and lncRNA files include raw count and FPKM values; circRNA files include back-splice junction read counts, normalized expression values and circRNA annotation information including circRNA identifier, genomic position, strand and host gene; miRNA files include raw count and TPM values; hepatocyte mRNA-seq files include raw count and FPKM values for mRNAs or genes.

organism: Oncorhynchus mykiss

source_name: spleen

growth_protocol: For the in vivo infection experiment, rainbow trout (Oncorhynchus mykiss) were maintained under standard aquaculture conditions before IHNV challenge. Fish were acclimated prior to the experiment, and water quality parameters, including temperature and dissolved oxygen, were monitored throughout the experiment. For the in vitro overexpression experiment, rainbow trout hepatocytes were cultured under standard conditions in DMEM supplemented with 10% fetal bovine serum at 18°C.

extract_protocol:
Total RNA was extracted from rainbow trout spleen tissues or hepatocytes using Trizol reagent according to the manufacturer's instructions. RNA concentration and purity were assessed using NanoDrop, and RNA integrity was evaluated by agarose gel electrophoresis. RNA samples meeting quality requirements were used for long RNA-seq, small RNA-seq or mRNA-seq library construction.
For spleen long RNA-seq, ribosomal RNA was removed from total RNA, and strand-specific long RNA-seq libraries were constructed for mRNA, lncRNA and circRNA expression profiling. These libraries were sequenced on an Illumina HiSeq 4000 platform using paired-end 150 bp reads. For spleen small RNA-seq, small RNAs of approximately 18-30 nt were enriched, ligated to adapters, reverse transcribed and PCR amplified; libraries were sequenced on an Illumina HiSeq Xten platform using single-end 50 bp reads. For hepatocyte mRNA-seq, messenger RNA was enriched from total RNA using poly(A) selection, fragmented, reverse transcribed and amplified to generate libraries, which were sequenced on an Illumina NovaSeq 6000 platform using paired-end 150 bp reads.

treatment_protocol: For the IHNV infection experiment, rainbow trout in the infection group were challenged with infectious hematopoietic necrosis virus (IHNV), whereas fish in the control group were maintained without IHNV infection. Spleen tissues were collected from three biological replicates per group at 48 h post infection, immediately frozen in liquid nitrogen, and stored at -80°C until RNA extraction. For the circUSP47 overexpression experiment, rainbow trout hepatocytes were transfected with a circUSP47 overexpression vector or empty vector control using INVI DNA RNA transfection reagent, and cells were collected at 48 h after transfection for RNA extraction.

value: spleen

value: wild-type

value: IHNV infection

tag: batch

value: batch 1


title: Oral_Biopsy_CrohnsDiseasePatient_Experiment4_GEX

description:
Library name: Oral_CD_Experiment4_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: mRNA


title: Oral_Biopsy_CrohnsDiseasePatient_Experiment3_TCR

description:
Library name: Oral_CD_Experiment3_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript

value: mixed sample (Oral CD4 +Tcells from CD3_replicate2. CD5_replicate2)


title: Oral_Biopsy_CrohnsDiseasePatient_Experiment3_GEX

description:
Library name: Oral_CD_Experiment3_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Oral_Biopsy_CrohnsDiseasePatient_Experiment2_TCR

description:
Library name: Oral_CD_Experiment2_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript

value: mixed sample (Oral CD4 +Tcells from CD1_replicate2. CD4_replicate2)


title: Oral_Biopsy_CrohnsDiseasePatient_Experiment3_HTO

description:
Library name: Oral_CD_Experiment3_HTO
Hashtag-derived oligonucleotide
HTO (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: TotalSeq-C0257 anti-human Hashtag 7 (CD5_replicate2), TotalSeq-C0259 anti-human Hashtag 9 (CD3_replicate2)


title: Oral_Biopsy_CrohnsDiseasePatient_Experiment2_HTO

description:
Library name: Oral_CD_Experiment2_HTO
Hashtag-derived oligonucleotide
HTO (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: TotalSeq-C0252 anti-human Hashtag 2 (CD1_replicate2), TotalSeq-C0260 anti-human Hashtag 10 (CD4_replicate2)


title: Oral_Biopsy_CrohnsDiseasePatient_Experiment1_TCR

description:
Library name: Oral_CD_Experiment1_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript

value: mixed sample (Oral CD4 +Tcells from CD3, CD4. CD5)


title: Oral_Biopsy_CrohnsDiseasePatient_Experiment1_HTO

description:
Library name: Oral_CD_Experiment1_HTO
Hashtag-derived oligonucleotide
HTO (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: Oral tissue

value: TotalSeq-C0257 anti-human Hashtag 7 (CD3), TotalSeq-C0258 anti-human Hashtag 8 (CD4), TotalSeq-C0259 anti-human Hashtag 9 (CD5)


title: CD2_Oral_Biopsy_GEX

description:
Library name: CD2_Oral_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: CD4+ T cells

value: Healthy Control and Crohn's disease patient


title: Oral_Biopsy_CrohnsDiseasePatient_Experiment2_GEX

description:
Library name: Oral_CD_Experiment2_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CD2_Oral_Biopsy_TCR

description:
Library name: CD2_Oral_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript

value: TCR


title: Oral_Biopsy_TCR

description:
Library name: Oral_Experiment1_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript

value: mixed sample (Oral CD4 +Tcells from HC1, HC2. HC3. HC4. CD1)


title: Oral_Biopsy_GEX

description:
Library name: Oral_Experiment1_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CD10_PBMCs_Calbicans_Th17targets_nonTh17targets_TCR

description:
Library name: CD10_blood_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript

source_name: PBMCs

value: PBMCs

value: Crohn's disease patient

tag: Sex

value: female

value: mixed sample (Calbicans-reactive, Th17-targets-reactive, nonTh17-targets-reactive)


title: CD10_PBMCs_Calbicans_Th17targets_nonTh17targets_GEX

description:
Library name: CD10_blood_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CD9_PBMCs_Calbicans_Th17targets_nonTh17targets_TCR

description:
Library name: CD9_blood_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript

value: male


title: CD10_PBMCs_Calbicans_Th17targets_nonTh17targets_HTO

description:
Library name: CD10_blood_HTO
Hashtag-derived oligonucleotide
HTO (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: HTO

value: TotalSeq-C0252 anti-human Hashtag 2 (Calbicans-reactive), TotalSeq-C0254 anti-human Hashtag 4 (nonTh17-target-reactive), TotalSeq-C0256 anti-human Hashtag 6 (Th17-target-reactive)


title: CD9_PBMCs_Calbicans_Th17targets_nonTh17targets_GEX

description:
Library name: CD9_blood_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: mRNA


title: CD8_PBMCs_Calbicans_Th17targets_nonTh17targets_HTO

description:
Library name: CD8_blood_HTO
Hashtag-derived oligonucleotide
HTO (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads


title: CD8_PBMCs_Calbicans_Th17targets_nonTh17targets_TCR

description:
Library name: CD8_blood_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript


title: CD7_PBMCs_Calbicans_Th17targets_nonTh17targets_TCR

description:
Library name: CD7_blood_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript


title: CD8_PBMCs_Calbicans_Th17targets_nonTh17targets_GEX

description:
Library name: CD8_blood_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CD7_PBMCs_Calbicans_Th17targets_nonTh17targets_HTO

description:
Library name: CD7_blood_HTO
Hashtag-derived oligonucleotide
HTO (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: TotalSeq-C0253 anti-human Hashtag 3 (Calbicans-reactive), TotalSeq-C0254 anti-human Hashtag 4 (nonTh17-target-reactive), TotalSeq-C0256 anti-human Hashtag 6 (Th17-target-reactive)


title: CD7_PBMCs_Calbicans_Th17targets_nonTh17targets_GEX

description:
Library name: CD7_blood_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CD6_PBMCs_Calbicans_Th17targets_nonTh17targets_TCR

description:
Library name: CD6_blood_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript


title: CD6_PBMCs_Calbicans_Th17targets_nonTh17targets_HTO

description:
Library name: CD6_blood_HTO
Hashtag-derived oligonucleotide
HTO (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads


title: CD5_PBMCs_Calbicans_Th17targets_nonTh17targets_TCR

description:
Library name: CD5_blood_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript


title: CD6_PBMCs_Calbicans_Th17targets_nonTh17targets_GEX

description:
Library name: CD6_blood_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CD5_PBMCs_Calbicans_Th17targets_nonTh17targets_HTO

description:
Library name: CD5_blood_HTO
Hashtag-derived oligonucleotide
HTO (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads


title: CD4_PBMCs_Calbicans_Th17targets_nonTh17targets_TCR

description:
Library name: CD4_blood_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript


title: CD3_PBMCs_Calbicans_Th17targets_nonTh17targets_TCR

description:
Library name: CD3_blood_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript


title: CD4_PBMCs_Calbicans_Th17targets_nonTh17targets_GEX

description:
Library name: CD4_blood_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CD3_PBMCs_Calbicans_Th17targets_nonTh17targets_HTO

description:
Library name: CD3_blood_HTO
Hashtag derived oligonucleotide (HTO)
HTO (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads


title: CD5_PBMCs_Calbicans_Th17targets_nonTh17targets_GEX

description:
Library name: CD5_blood_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CD2_PBMCs_Calbicans_Th17targets_nonTh17targets_TCR

description:
Library name: CD2_blood_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript


title: CD2_PBMCs_Calbicans_Th17targets_nonTh17targets_HTO

description:
Library name: CD2_blood_HTO
Hashtag-derived oligonucleotide
HTO (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads


title: CD3_PBMCs_Calbicans_Th17targets_nonTh17targets_GEX

description:
Library name: CD3_blood_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CD2_PBMCs_Calbicans_Th17targets_nonTh17targets_GEX

description:
Library name: CD2_blood_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CD1_PBMCs_Calbicans_Th17targets_nonTh17targets_HTO

description:
Library name: CD1_blood_HTO
Hashtag derived oligonucleotide (HTO)
HTO (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: TotalSeq-C0257 anti-human Hashtag 7 (Calbicans-reactive), TotalSeq-C0258 anti-human Hashtag 8 (nonTh17-target-reactive), TotalSeq-C0259 anti-human Hashtag 9 (Th17-target-reactive)


title: CD1_PBMCs_Calbicans_Th17targets_nonTh17targets_TCR

description:
Library name: CD1_blood_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript


title: HealthyControls_PBMCs_Experiment2_Calbicans_Th17targets_nonTh17targets_HTO

description:
Library name: Healthy_blood_exp2_HTO
Hashtag-derived oligonucleotide
HTO (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: Healthy Control

value: mixed sample (Calbicans-reactive, Th17-targets-reactive, nonTh17-targets-reactive for HC3 and HC4)

value: TotalSeq-C0253 anti-human Hashtag 3 (HC3 Calbicans-reactive), TotalSeq-C0254 anti-human Hashtag 4 (HC3 nonTh17-target-reactive), TotalSeq-C0256 anti-human Hashtag 6 (HC3 Th17-target-reactive), TotalSeq-C0257 anti-human Hashtag 7 (HC4 Calbicans-reactive), TotalSeq-C0258 anti-human Hashtag 8 (HC4 nonTh17-target-reactive), TotalSeq-C0259 anti-human Hashtag 9 (HC4 Th17-target-reactive)


title: CD1_PBMCs_Calbicans_Th17targets_nonTh17targets_GEX

description:
Library name: CD1_blood_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: CD4+ T cells


title: HealthyControls_PBMCs_Experiment2_Calbicans_Th17targets_nonTh17targets_TCR

description:
Library name: Healthy_blood_exp2_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript


title: HealthyControls_PBMCs_Experiment2_Calbicans_Th17targets_nonTh17targets_GEX

description:
Library name: Healthy_blood_exp2_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: HealthyControls_PBMCs_Experiment1_Calbicans_Th17targets_nonTh17targets_TCR

description:
Library name: Healthy_blood_exp1_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript

value: mixed sample (Calbicans-reactive, Th17-targets-reactive, nonTh17-targets-reactive for HC1 and HC2)


title: HealthyControls_PBMCs_Experiment1_Calbicans_Th17targets_nonTh17targets_HTO

description:
Library name: Healthy_blood_exp1_HTO
Hashtag derived oligonucleotide (HTO)
HTO (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: TotalSeq-C0253 anti-human Hashtag 3 (HC1 Calbicans-reactive), TotalSeq-C0254 anti-human Hashtag 4 (HC1 nonTh17-target-reactive), TotalSeq-C0256 anti-human Hashtag 6 (HC1 Th17-target-reactive), TotalSeq-C0257 anti-human Hashtag 7 (HC2 Calbicans-reactive), TotalSeq-C0258 anti-human Hashtag 8 (HC2 nonTh17-target-reactive), TotalSeq-C0259 anti-human Hashtag 9 (HC2 Th17-target-reactive)


title: HealthyControls_PBMCs_Experiment1_Calbicans_Th17targets_nonTh17targets_GEX

description:
Library name: Healthy_blood_exp1_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CD10_GutBiopsy_CrohnsDiseasePatient_TCR

description:
Library name: CD10_gut_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript

source_name: Ileum

value: Ileum

value: Infliximab

value: TCR


title: CD10_GutBiopsy_CrohnsDiseasePatient_GEX

description:
Library name: CD10_gut_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Crohn's disease patient

value: female


title: CD8_GutBiopsy_CrohnsDiseasePatient_TCR

description:
Library name: CD8_gut_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript

source_name: Neo terminal ileum

value: Neo terminal ileum

value: male

value: Budesonide


title: CD8_GutBiopsy_CrohnsDiseasePatient_GEX

description:
Library name: CD8_gut_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: mRNA


title: CD9_GutBiopsy_CrohnsDiseasePatient_GEX

description:
Library name: CD9_gut_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Risankizumab


title: CD7_GutBiopsy_CrohnsDiseasePatient_TCR

description:
Library name: CD7_gut_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript

value: Golimumab, Mesalamine, Methotrexate


title: CD7_GutBiopsy_CrohnsDiseasePatient_GEX

description:
Library name: CD7_gut_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CD6_GutBiopsy_CrohnsDiseasePatient_GEX

description:
Library name: CD6_gut_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Vedolizumab, Prednisolone


title: CD5_GutBiopsy_CrohnsDiseasePatient_GEX

description:
Library name: CD5_gut_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript

source_name: Sigma

value: Sigma

value: Infliximab, Mesalamine


title: CD4_GutBiopsy_CrohnsDiseasePatient_GEX

description:
Library name: CD4_gut_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: CD4+ T cells

value: Infliximab, Azathioprine


title: CD5_GutBiopsy_CrohnsDiseasePatient_TCR

description:
Library name: CD5_gut_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript


title: CD3_GutBiopsy_CrohnsDiseasePatient_GEX

description:
Library name: CD3_gut_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CD2_GutBiopsy_CrohnsDiseasePatient_TCR

description:
Library name: CD2_gut_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript


title: CD1_GutBiopsy_CrohnsDiseasePatient_TCR

description:
Library name: CD1_gut_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript


title: CD2_GutBiopsy_CrohnsDiseasePatient_GEX

description:
Library name: CD2_gut_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CD1_GutBiopsy_CrohnsDiseasePatient_GEX

description:
Library name: CD1_gut_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: HC4_GutBiopsy_HealthyControl_TCR

description:
Library name: HC4_gut_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript

value: Healthy Control


title: HC4_GutBiopsy_HealthyControl_GEX

description:
Library name: HC4_gut_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: HC3_GutBiopsy_HealthyControl_TCR

description:
Library name: HC3_gut_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript


title: HC3_GutBiopsy_HealthyControl_GEX

description:
Library name: HC3_gut_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: HC2_GutBiopsy_HealthyControl_TCR

description:
Library name: HC2_gut_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript


title: HC2_GutBiopsy_HealthyControl_GEX

description:
Library name: HC2_gut_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CnA Replicate 3

city: Muenster

first: Anika

last: Witten

address: Domagkstr. 3

department: Institute of Human Genetics, Department Genetic Epidemiology

institute: University of Muenster

hyb_protocol: standard

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version11.0.1.1).

data_processing: quantile normalization and GeneSpring GX v12.0 software package (Agilent Technologies) were used

organism: Mus musculus

source_name: cardiac tissue

label_protocol: standard

extract_protocol:
Total RNA extracted using Direct-zol RNA purification Kit following manufacturer's instructions
mRNA purification after removal of rRNA (mRNA-ONLY Eukaryotic mRNA isoaltion kti, epicentre)
amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method

tag: strain


title: HC1_GutBiopsy_HealthyControl_GEX

description:
Library name: HC1_gut_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CnA Replicate 2


title: A887177, SALI

city: Chongqing

first: Jialian

last: Wang

address: Jiankang Road No.1, Yuzhong District

institute: Chongqing University Central Hospital

description:
Library name: Sample16
A887177_count

data_processing:
fastp was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was also verified using fastp We used Bowtie2 and Tophat2 to map reads to the genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie. Then, all transcriptome from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the ﬁnal transcriptome was generated, StringTie was used to estimate the expression levels of all transcripts. Transcripts were annotated with known mRNAs, known long non-coding RNAs (lncRNAs) and transcripts shorter than 200 nt were discarded. Then we utilized CPC and CNCI to predict transcripts with coding potential. All transcripts with CPC score <-1 and CNCI score <0 were removed. The remaining transcripts with class code (I, j, o, u, x) were considered as lncRNAs. StringTie was used to perform expression level for mRNAs and lncRNAs by calculating FPKM (FPKM = [total_exon_fragments/mapped_reads(millions) × exon_length(kB)]).
Assembly: Ensembl, version v112
Supplementary files format and content: txt files include Count values for each Sample

source_name: Whole blood

extract_protocol:
Whole blood samples were collected by venipuncture into PAXGene Blood RNA tubes (BD, San Jose, CA, USA). Total RNA was extracted using on-column DNase digestion (Qiagen, Hilden, NRW, Germany). Excess globin transcripts were removed using the GLOBINclear kit (Ambion, Austin, TX, USA). RNA concentration was measured with a NanoDrop spectrophotometer, and RNA quality was evaluated with the Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) to determine its integrity, with confirmation by agarose gel electrophoresis. Samples were deemed suitable for downstream library preparation and sequencing only if they satisfied the following thresholds: concentration > 50 ng/μL, RNA integrity number (RIN) > 7.0, OD260/280 ratio > 1.8, and total RNA yield > 2 μg.
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. Approximately 2μg of total RNA was used to remove ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). Following purification, the ribo-minus 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.

value: Whole blood

value: sepsis-induced liver injury

tag: disease state

value: SALI


title: CnA Replicate 1


title: TAC Replicate 3

description: TAC surgery

value: B6SV129F1 wild-type


title: A885370, SALI

description:
Library name: Sample14
A885370_count

value: female


title: Epididymis single-cell RNA-seq (Illumina)

city: Kunming

first: Hai

last: Li

state: Yunnan

address: No. 452, Fengyuan Road, Panlong District

department: College of Animal Science and Technology

institute: Yunnan Agricultural University

description:
Library name: Epi_Illumina
10x Genomics single-cell 3' library; processed with Cell Ranger

data_processing:
Illumina single-cell RNA-seq data were processed with Cell Ranger (10x Genomics) to perform demultiplexing, alignment, barcode/UMI processing, and generation of cell-by-gene count matrices.
Oxford Nanopore single-cell long-read data were basecalled with Dorado, aligned to the Sus scrofa reference genome with minimap2, and processed with FLAMES to generate gene-level and transcript/isoform-level count matrices and isoform annotations. SQANTI3 was used for structural characterization and quality assessment of transcript isoforms. Downstream analyses were performed using cell-level count matrices and associated cell metadata.
Assembly: Sus scrofa Sscrofa11.1
Supplementary files format and content: Processed data files include cell-level expression matrices and accompanying metadata. For Illumina single-cell RNA-seq libraries, processed files include filtered cell-by-gene count matrices in HDF5 and/or MEX format.
Supplementary files format and content: For Oxford Nanopore single-cell long-read libraries, processed files include gene-by-cell count matrices, transcript/isoform-by-cell count matrices, and isoform annotation files in text-based formats (for example, CSV/TSV and GFF3).

molecule: polyA RNA

organism: Sus scrofa

source_name: epididymis

extract_protocol:
Fresh tissues from seven reproductive-axis organs (hypothalamus, pituitary, prostate, bulbourethral gland, seminal vesicle, epididymis, and testis) of an 18-month-old male Baoshan pig were collected and processed individually. Single-cell suspensions were prepared from each tissue by tissue dissociation and filtration to remove debris and cell aggregates, followed by cell counting and quality assessment. The resulting viable single-cell suspensions were used for downstream 10x Genomics barcoding and library preparation.
For short-read single-cell RNA sequencing, single-cell libraries were constructed using the 10x Genomics Chromium Single Cell 3' platform according to the manufacturer's instructions and sequenced on an Illumina instrument. For long-read single-cell RNA sequencing, 10x-barcoded full-length cDNA generated from the same single-cell workflow was subjected to Oxford Nanopore sequencing to capture full-length transcript isoforms while preserving cell barcode information.

value: epididymis

tag: breed

value: Baoshan

value: mixed single cells

value: wild type

value: untreated


title: A885326, SALI

description:
Library name: Sample13
A885326_count

value: male


title: Vesicle gland single-cell RNA-seq (Illumina)

description:
Library name: VG_Illumina
10x Genomics single-cell 3' library; processed with Cell Ranger

source_name: vesicle gland

value: vesicle gland


title: Bulbourethral gland single-cell RNA-seq (Illumina)

description:
Library name: BG_Illumina
10x Genomics single-cell 3' library; processed with Cell Ranger

source_name: bulbourethral gland

value: bulbourethral gland


title: A885189, SALI

description:
Library name: Sample12
A885189_count


title: Prostate gland single-cell RNA-seq (Illumina)

description:
Library name: PG_Illumina
10x Genomics single-cell 3' library; processed with Cell Ranger

source_name: prostate gland

value: prostate gland


title: WT Replicate 3


title: Pituitary single-cell RNA-seq (Illumina)

description:
Library name: Pit_Illumina
10x Genomics single-cell 3' library; processed with Cell Ranger

source_name: pituitary

value: pituitary


title: A885150, SALI

description:
Library name: Sample11
A885150_count


title: Hypothalamus single-cell RNA-seq (Illumina)

description:
Library name: Hyp_Illumina
10x Genomics single-cell 3' library; processed with Cell Ranger

source_name: hypothalamus

value: hypothalamus


title: CD9_GutBiopsy_CrohnsDiseasePatient_TCR

description:
Library name: CD9_gut_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript

value: Neo terminal ileum

value: CD4+ T cells

value: Crohn's disease patient

value: Risankizumab

value: TCR


title: WT Replicate 2

value: B6SV129F1 wild-type


title: CD4_GutBiopsy_CrohnsDiseasePatient_TCR

description:
Library name: CD4_gut_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript

value: Sigma

value: Infliximab, Azathioprine


title: Testis single-cell RNA-seq (Nanopore)

description:
Library name: Tes_Nanopore
10x-barcoded full-length cDNA long-read sequencing; processed with FLAMES

source_name: testis

value: testis

value: Baoshan

value: mixed single cells


title: A884985, SALI

description:
Library name: Sample10
A884985_count

value: Whole blood

value: sepsis-induced liver injury

value: male

value: SALI


title: CD6_GutBiopsy_CrohnsDiseasePatient_TCR

description:
Library name: CD6_gut_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript

value: female

value: Vedolizumab, Prednisolone


title: CD3_GutBiopsy_CrohnsDiseasePatient_TCR

description:
Library name: CD3_gut_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript

value: Infliximab


title: Epididymis single-cell RNA-seq (Nanopore)

description:
Library name: Epi_Nanopore
10x-barcoded full-length cDNA long-read sequencing; processed with FLAMES

value: epididymis

value: wild type

value: untreated


title: WT Replicate 1


title: Vesicle gland single-cell RNA-seq (Nanopore)

description:
Library name: VG_Nanopore
10x-barcoded full-length cDNA long-read sequencing; processed with FLAMES

value: vesicle gland


title: A861093, SALI

description:
Library name: Sample9
A861093_count


title: Bulbourethral gland single-cell RNA-seq (Nanopore)

description:
Library name: BG_Nanopore
10x-barcoded full-length cDNA long-read sequencing; processed with FLAMES

value: bulbourethral gland


title: Prostate gland single-cell RNA-seq (Nanopore)

description:
Library name: PG_Nanopore
10x-barcoded full-length cDNA long-read sequencing; processed with FLAMES

value: prostate gland


title: R16_lung_10X_single_cell_mRNA_lane2

city: Dallas

last: Zhang

address: 6001 Forest Park Rd

department: Department of Pathology

country: USA

institute: UT Southwestern Medical Center

description:
Library name: EA_LARRY_LIB_S1_L002
10x Genomics 3' RNA assay

data_processing:
Raw fastq files generated from the sequencing runs (mRNA, HTO, LARRY outputs) were processed through the 10x Genomics CellRanger pipeline (cellranger-6.0.0) to generate count matrices. Custom python scripts were used for LARRY barcode extraction, error correction, and processing.
Assembly: mm10
Supplementary files format and content: Tab separated files and matrix files
Library strategy: CITE-seq

source_name: lung

extract_protocol:
Cell suspensions were prepared by mechanical dissociation, followed by enyzmatic digestion using collagenase/hyaluronidase. The single cell suspension was then enriched for GFP+ cancer cells. Then, we stained each sample with it's own unique hashing antibody so that we could subsequently pool the samples for loading onto the 10x Chromium machine and later prepare sequencing libraries, and finally separate each sample in silico by it's unique hashing antibody.
3x libraries from each lane are sequenced separately on a NovaSeq machine. Transcriptome library preparation was conducted according to the Chromium Next GEM Single Cell 3’ Reagents Kits v3.1 with Feature Barcoding technology kit manual. Hashtag libraries were prepared using the standard CITE-seq protocol (https://citeseq.files.wordpress.com/2019/02/cite- seq_and_hashing_protocol_190213.pdf). LARRY barcode libraries were constructed using a custom nested PCR protocol followed by indexing.

value: lung

value: tumor

value: B6, female


title: HC1_GutBiopsy_HealthyControl_TCR

description:
Library name: HC1_gut_TCR
10X Genomics
TCR (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript

value: Sigma

value: CD4+ T cells

value: Healthy Control

value: TCR


title: WJL, healthy

description:
Library name: Sample8
WJL_count

value: Whole blood

value: healthy

value: Healthy


title: Pituitary single-cell RNA-seq (Nanopore)

description:
Library name: Pit_Nanopore
10x-barcoded full-length cDNA long-read sequencing; processed with FLAMES

value: pituitary

value: Baoshan

value: male

value: mixed single cells


title: R16_lung_10X_single_cell_mRNA_lane1

description:
Library name: EA_LARRY_LIB_S1_L001
10x Genomics 3' RNA assay


title: LB, healthy

description:
Library name: Sample7
LB_count

value: female


title: Hypothalamus single-cell RNA-seq (Nanopore)

description:
Library name: Hyp_Nanopore
10x-barcoded full-length cDNA long-read sequencing; processed with FLAMES

value: hypothalamus

value: wild type

value: untreated


title: R16_lung_HTO_lane2

description:
Library name: EA_LARRY_HTO_S2_L002
10x Genomics 3' RNA assay

library_source: other

molecule: protein

value: lung

value: tumor


title: Dual-species_ST_replicate1_day2_day4_MRSA_mouse_kidney_infection

city: Indianapolis

first: Takashi

last: Hato

state: IN

address: 950 W. Walnut St. R2 202

department: Medicine

institute: Indiana University

description:
Library name: Kidney_MRSA_day2-4_RegularDigestion
10X Genomics Visium FFPE

data_processing:
spaceranger-3.0.1
Assembly: mm10/GRCm38 and MRSA FPR3757 (NC_007793)
Supplementary files format and content: spaceranger-3.0.1
Library strategy: Spatial Transcriptomics

organism:
Staphylococcus aureus
Mus musculus

source_name: kidney

growth_protocol: On the day of bacterial injection, S. aureus was grown to O.D. of 0.6. All bacteria were cultured in tryptic soy broth.

extract_protocol:
FFPE tissue sections were cut at 5 µm thickness and mounted on Visium Spatial slides (Visium V5 Slide FFPE v2) according to the protocol CG000408. Deparaffinization, H&E staining, and decrosslinking were performed following the User Guide CG000409.
Library construction was done at the Indiana University Center for Medical Genomics Core following the Visium CytAssist Spatial Gene Expression for FFPE Reagent Kits User Guide (CG000495). During the probe hybridization step, we compared the effects of MRSA cell wall permeabilization using either the default Enzyme B (included in the Visium FFPE Reagent Kit, cat. no. 1000362) or achromopeptidase (Sigma A3547; working concentration 5 U/mL) on consecutive slides. The overall MRSA read counts were comparable between the two permeabilization methods. The custom probes were prepared as a combined spike-in pool (LHS and RHS) at a concentration of 24 nM per probe as described in the 10X technical note CG000621. cDNA libraries were then prepared and sequenced on an Illumina NovaSeq 6000.

treatment_protocol: The MRSA injection dose was adjusted to 1 x 10^7 CFU based on OD-CFU calibration curves, and administered via tail vein injection in 200 uL of PBS.

value: kidney


title: A886104, SALI

description:
Library name: Sample15
A886104_count

value: sepsis-induced liver injury

value: SALI


title: Dual-species_ST_replicate2_day2_day4_MRSA_mouse_kidney_infection

description:
Library name: Kidney_MRSA_day2-4_Achromopeptidase
10X Genomics Visium FFPE


title: XH, healthy

description:
Library name: Sample6
XH_count


title: TAC Replicate 2

description: TAC surgery

value: B6SV129F1 wild-type


title: Testis single-cell RNA-seq (Illumina)

description:
Library name: Tes_Illumina
10x Genomics single-cell 3' library; processed with Cell Ranger

value: testis


title: R16_lung_HTO_lane1

description:
Library name: EA_LARRY_HTO_S2_L001
10x Genomics 3' RNA assay

value: B6, female


title: Duodenal crypt organoid, treated with vehicle, rep3

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

data_processing:
Kallisto (v0.46.1) was used to build a GENCODE vM29 transcriptome index and perform paired-end alignment on the paired-end FASTQ files.
Output of Kallisto was inputted into IsoformSwitchAnalyzeR (v1.19.0) and DEXSeq (v1.43.0) against Comprehensive Annotation GTF and Transcripts FASTA files of the GENCODE vM29 annotation. This led to the creation of nucleotide FASTA and amino acid FASTA files.
biomaRt (v2.53.2) was utilized to match up gene and transcript IDs with gene symbols for TPM counts, which were also obtained from the Kallisto output.
After this, the outputted nucleotide FASTA file was inputted into the CPC2 external tool, while the outputted amino acid FASTA file was inputted into HmmScan (HmmerWeb v2.41.2), SignalP (v5.0), and IUPred2A external tools.
Using the output of the aforementioned external tools, IsoformSwitchAnalyzeR (v1.19.0) was again used to output a top transcript-based isoform switch list based on q value < 0.05 and absolute differential isoform fraction > 0.1.
The top transcript-based isoform switch list and the TPM counts tables were merged and further filtered for average TPM across all conditions > 1, which led to the creation of the deposited processed file.
Assembly: GENCODE vM29 (mm39)
Supplementary files format and content: ISARandKallistoOutput_VehvsBMP2_Table.txt, tab-delimited text file containing the top isoform switches filtered for q value < 0.05, absolute differential isoform fraction > 0.1, and average TPM > 1.

source_name: duodenal crypt organoid

extract_protocol:
For cultured organoids, QIAGEN RNeasy Micro Kit was used to extract RNA according to the manufacturer’s instructions.
BGI in-house kit (BGI-Shenzhen, China)

treatment_protocol: Vehicle or 100ng/ml BMP2 on Day 6 for 24h

value: duodenal crypt organoid

value: C57BL/6 WT

value: Vehcile


title: Duodenal crypt organoid, treated with vehicle, rep2

value: Vehicle


title: Duodenal crypt organoid, treated with BMP2, rep3


title: Duodenal crypt organoid, treated with vehicle, rep1


title: LJL, healthy

description:
Library name: Sample5
LJL_count

value: Whole blood

value: healthy

value: Healthy


title: R16_lung_CRISPR_feature_bc_lane2

description:
Library name: EA_LARRY_CRISPR_S3_L002
10x Genomics 3' RNA assay

molecule: other


title: LYJ, healthy

description:
Library name: Sample4
LYJ_count

value: female


title: Duodenal crypt organoid, treated with BMP2, rep2


title: R16_lung_CRISPR_feature_bc_lane1

description:
Library name: EA_LARRY_CRISPR_S3_L001
10x Genomics 3' RNA assay


title: Duodenal crypt organoid, treated with BMP2, rep1


title: CPF, healthy

description:
Library name: Sample3
CPF_count


title: TAC Replicate 1

description: TAC surgery


title: GMDC-LPS+HES-3

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

hyb_protocol: Processing was carried out in accordance with manufacturer's directions.  Briefly, the assay samples were pre-warmed at 65°C for 5 minutes, prior to addition to the chip and insertion of the BeadChips into the HHyb Chamber.  Incubatation was for 16-20 hours at 58°C with gentle agitation.  Post-hybridisation washing at room temperature and then high temperature (55 degrees C) for 10 minutes, followed by an ethanol rinse (10 minutes) prior to preparation for staining and detection using standard streptavidin-Cy3 procedures.

scan_protocol: HiScan H166

data_processing:
Data were quality controlled (arrayQualityMetrics Bioconductor package), the arrays normalized (robust spline normalization method after data transformation using a variance stabilizing method) and array features annotated. Fold changes were determined by group-wise comparisons and significance values for each fold change controlled for false discovery, adjusted p values of 0.05 or below have been defined as significant.
The normalised data are given with nuIDs, annotated, and expression levels converted to log2 values prior to linear modeling comparison with limma lmFit() foillowed by eBayes()

source_name: GMDC, LPS+HES treated

label_protocol: using Illumina® TotalPrep™ RNA Amplification Kit according to manufacturer's recommendations

growth_protocol: C57BL/6 strain murine bone marrow-derived dendritic cells at 2x10^6 cells in 10 mL RPMI 1640 were differentiated with 20 ng/mL GM-CSF for 10 days, adding 10 mL medium on day 3 and replacing medium on days 6 and 8.

extract_protocol: RNA was extracted using a phenol-chloroform extraction method: GMDCs were resuspended in 1ml Trizol before addition of 200µl chloroform; after centrifugation, the acqueous phase was mixed with 500µl isopropanol and incubated for 10min. After centrifugation, the resulting pellet was washed with ethanol, and cleaned further using the RNeasy® Mini Kit (Qiagen)

treatment_protocol: Cells were treated at 10^6 cells/mL in RPMI 1640 with 5ng/mL GM-CSF, 1µg/mL LPS and 10µg/mL HES, for 8h before extraction of RNA

value: LPS+HES

value: GMDC


title: GMDC-LPS+HES-2


title: R18_lung_mRNA_lane2

description:
Library name: EA-1017 LIB-02
10x Genomics 3' RNA assay

value: lung

value: tumor


title: YY, healthy

description:
Library name: Sample2
YY_count

value: male


title: GMDC-LPS+HES-1


title: R18_lung_mRNA_lane1

description:
Library name: EA-1017 LIB-01
10x Genomics 3' RNA assay


title: GMDC-LPS-3

source_name: GMDC, LPS stimulated

value: LPS


title: TXY, healthy

description:
Library name: Sample1
TXY_count


title: GMDC-LPS-2


title: R18_lung_CRISPR_feature_bc_lane2

description:
Library name: EA-1017 LARRY-02
10x Genomics 3' RNA assay


title: WPMY-1, sh61A-3,tRNA-seq

city: Shenzhen

first: Yuhan

last: Liu

state: Guangdong

address: Xueyuan avenue 1066

institute: Shenzhen University

data_processing:
First，a tRNA library was adapted from the tRNAScan-SE library by appending CCA to tRNAs from the genomic tRNA database (http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/eukaryota/Hsapi19/). Isodecoders with identical scores were consolidated for ease of identity assignment. Then, raw reads were generated after sequencing, image analysis, base calling and quality filtering on sequencer. Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software(v1.9.3). Then, trimmed reads from all samples were aligned using bowtie2 software to the aforementioned tRNA library with sensitive options. Mapped reads on each tRNA were counted using samtools. edgeR software was used to detect statistical differences in expression of tRNA between conditions.
Assembly: HG38
Supplementary files format and content: excel file include tRNA Expression Profiling

extract_protocol:
Total RNA was extracted using Trizol reagent
Total RNA was size-selected for small RNA fraction ( <200nt) with the MirVana Isolation Kit (ThermoFisher). The enriched small RNAs were demethylated with AlkB enzyme mix for 100 min at 37°C. The demethylated small RNA was used for library construction with GenSeq® Small RNA Library Prep Kit (GenSeq, Inc.) by following the manufacturer’s instructions. All libraries were size-selected for tRNA fraction before sequencing and then sequenced in a NovaSeq platform (Illumina, Inc., San Diego, CA, USA).

value: TRMT61A knockdown


title: R18_lung_CRISPR_feature_bc_lane1

description:
Library name: EA-1017 LARRY-01
10x Genomics 3' RNA assay


title: GMDC-LPS-1


title: GLUT3 overexpressed Aged HUVECs Riboseq rep3

description:
Library name: Sample 18
Ribo_OEC-GLUT3-OE3
Ribo-Seq_Expression.result.xlsx

data_processing:
Raw sequencing reads were assessed using FastQC. Adapter sequences and low-quality bases were removed using Cutadapt.  For RNA-seq data, clean reads were aligned to the Mus musculus reference genome (GRCm38) using HISAT2. Transcript assembly and abundance estimation were performed using StringTie based on GENCODE gene annotations. Gene and transcript expression levels were quantified as FPKM values. Differential expression analysis was performed using Ballgown. Alternative splicing events were identified using rMATS, and coding potential of novel transcripts was evaluated using CPAT.  For Ribo-seq data, reads shorter than 22 nt or longer than 34 nt after trimming were discarded. Reads mapping to rRNA, tRNA, snRNA, and snoRNA were removed using Bowtie. Remaining reads were aligned to the Mus musculus reference genome (GRCm38) using STAR. Only uniquely mapped reads were retained for downstream analyses. Ribosome footprint quality control analyses were performed using RiboTish. Transcript-level ribosome occupancy was quantified using Plastid and normalized as RPKM values. Differential translation analysis was performed using edgeR, translational efficiency (TE) was analyzed using RiboDiff, and ORF prediction was performed using RiboCode.
Assembly: GRCh38
Supplementary files format and content: Processed data files are provided as .xlsx table files. RNA-seq outputs include raw gene count matrices. Ribo-seq outputs include raw ribosome-protected fragment (RPF) count matrices.
Library strategy: Ribo-Seq

source_name: Vascular

value: Vascular

value: Primary Cell

value: Human Umbilical Vein Endothelial Cells

value: GLUT3 overexpress

value: Aged


title: GLUT3 overexpressed Aged HUVECs Riboseq rep1

description:
Library name: Sample 17
Ribo_OEC-GLUT3-OE2
Ribo-Seq_Expression.result.xlsx


title: WPMY-1, sh61A-2,tRNA-seq


title: GLUT3 overexpressed Aged HUVECs Riboseq rep2

description:
Library name: Sample 16
Ribo_OEC-GLUT3-OE1
Ribo-Seq_Expression.result.xlsx


title: R18_lung_HTO_lane2

description:
Library name: EA-1017 HTO-02
10x Genomics 3' RNA assay

value: B6, female


title: Aged HUVECs Riboseq rep3

description:
Library name: Sample 15
Ribo_OEC3
Ribo-Seq_Expression.result.xlsx


title: WPMY-1, sh61A-1,tRNA-seq


title: Aged HUVECs Riboseq rep2

description:
Library name: Sample 14
Ribo_OEC2
Ribo-Seq_Expression.result.xlsx


title: Aged HUVECs Riboseq rep1

description:
Library name: Sample 13
Ribo_OEC1
Ribo-Seq_Expression.result.xlsx


title: R18_lung_HTO_lane1

description:
Library name: EA-1017 HTO-01
10x Genomics 3' RNA assay


title: Young HUVECs Riboseq rep3

description:
Library name: Sample 12
Ribo_YEC3
Ribo-Seq_Expression.result.xlsx

value: Young


title: WPMY-1, shcontrol-3,tRNA-seq

value: TRMT61A wildtype


title: snRNA_Saline_control_Padi4WT

description:
Library name: JH04_snRNA
10X Genomics multiome

data_processing:
cellranger-arc-2.0.2 pipeline
Assembly: mm10/GRCm38
Supplementary files format and content: cellranger-arc-2.0.2 pipeline

extract_protocol:
Single nuclei were isolated from frozen kidney tissues using Singulator 100 v2. A quarter of a mouse kidney was placed into a Dual Filter Cartridge V2 150/40 (Nuclei Isolation Cartridge Pack 100-063-732) with 75 µl of Singulator RNase Inhibitor (100-255-644). Nuclei isolation was performed using the Standard Nuclei Run protocol. Lysates were centrifuged at 500 x g for 5 min at 4 °C. The resulting nuclei pellets were resuspended in 20% Nuclei Debris Removal Reagent (100-253-628), prepared in Nuclei Storage Reagent (100-063-405) and centrifuged at 500 x g for 15 min without brake. Pellets were then resuspended in Nuclei Storage Reagent for an additional wash and centrifuged at 500 x g for 5 min at 4 °C.
Samples were targeted for recovery of 10,000 nuclei and processed using the Single Cell Multiome ATAC + Gene Expression v1 chemistry (10X Genomics). cDNA synthesis and library preparation were performed according to the manufacturer’s instructions at the Indiana University Center for Medical Genomics Core. cDNA libraries were sequenced on an Illumina NovaSeq6000 in paired-end mode.

treatment_protocol: The MRSA injection dose was adjusted to 1 x 10^7 CFU based on OD-CFU calibration curves, and administered via tail vein injection in 150 uL of PBS.

value: kidney

value: WT

value: Saline


title: Young HUVECs Riboseq rep2

description:
Library name: Sample 11
Ribo_YEC2
Ribo-Seq_Expression.result.xlsx


title: WPMY-1, shcontrol-2,tRNA-seq


title: Young HUVECs Riboseq rep1

description:
Library name: Sample 10
Ribo_YEC1
Ribo-Seq_Expression.result.xlsx


title: ATAC_Saline_control_Padi4WT

description:
Library name: JH04_ATAC
10X Genomics multiome


title: WPMY-1, shcontrol-1,tRNA-seq


title: A886104, SALI

description:
Library name: Sample15
A886104_count

data_processing:
reads with more than 10% N (N means base information could not be determined) removed;
remove the reads contaminated with 5 'splice;
removes the reads without 3 'splice sequences and inserts;
removes polyA/T/G/C reads (most consecutive polyA/T/G/C, probably from sequencing errors, and with low information entropy, can not be analyzed).
Assembly: Ensembl, version v112
Supplementary files format and content: txt files include Count values for each Sample

extract_protocol:
Whole blood samples were collected by venipuncture into PAXGene Blood RNA tubes (BD, San Jose, CA, USA). Total RNA was extracted using on-column DNase digestion (Qiagen, Hilden, NRW, Germany). Excess globin transcripts were removed using the GLOBINclear kit (Ambion, Austin, TX, USA). RNA concentration was measured with a NanoDrop spectrophotometer, and RNA quality was evaluated with the Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) to determine its integrity, with confirmation by agarose gel electrophoresis. Samples were deemed suitable for downstream library preparation and sequencing only if they satisfied the following thresholds: concentration > 50 ng/μL, RNA integrity number (RIN) > 7.0, OD260/280 ratio > 1.8, and total RNA yield > 2 μg.
Small RNA libraries were constructed using the TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA) according to kit instructions. The specific procedures were as follows: 3 'splice sequence ligation, 5' splice sequence ligation, reverse transcription to generate cDNA strand, PCR amplification, electrophoresis purification of target fragment, sequencing. Instruments and Reagents for library quality Control, Inc Instrument: Bioanalyzer 2100 (Agilent, CA, USA) Library quality check Kit: High Sensitivity DNA Chip Kit (Agilent, CA, USA)

value: Whole blood

tag: disease

value: sepsis-induced liver injury

value: SALI


title: snRNA_MRSA_day5_3_Padi4WT

description:
Library name: JH03_snRNA
10X Genomics multiome


title: A887177, SALI

description:
Library name: Sample16
A887177_count

value: male


title: A885370, SALI

description:
Library name: Sample14
A885370_count

value: female


title: WPMY-1, sh61A-3,RNA-seq

data_processing:
After library construction is completed, Qubit 2.0 Fluorometer is first used for quantification, and the library is diluted to 1.5 ng/渭l. Subsequently, Agilent 4200 TapeStation is used to detect the insert size of the library to ensure library quality.
Assembly: HG38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent
Using the structural feature that most eukaryotic mRNAs have a poly(A) tail, mRNAs with poly(A) tails are enriched using Oligo(dT) magnetic beads. Subsequently, the obtained mRNA is randomly fragmented using divalent cations. Using the fragmented mRNA as a template and random oligonucleotides as primers, the first strand of cDNA is synthesized in a 1st Strand Enzyme reverse transcriptase system. Then, 2nd Strand Enzyme and dNTPs are used to synthesize the second strand of cDNA. After purification, the double-stranded cDNA undergoes end repair, A-tailing, and sequencing adapter ligation. cDNA fragments of around 200-300bp are selected, PCR amplified, and the PCR products are purified again, ultimately obtaining the library.

value: TRMT61A knockdown


title: A885326, SALI

description:
Library name: Sample13
A885326_count


title: ATAC_MRSA_day5_3_Padi4WT

description:
Library name: JH03_ATAC
10X Genomics multiome


title: A885189, SALI

description:
Library name: Sample12
A885189_count


title: A885150, SALI

description:
Library name: Sample11
A885150_count


title: WPMY-1, sh61A-2,RNA-seq


title: snRNA_MRSA_day5_2_Padi4WT

description:
Library name: JH02_snRNA
10X Genomics multiome


title: WPMY-1, sh61A-1,RNA-seq


title: A884985, SALI

description:
Library name: Sample10
A884985_count


title: A861093, SALI

description:
Library name: Sample9
A861093_count


title: WJL, healthy

description:
Library name: Sample8
WJL_count

value: healthy

value: Healthy


title: WPMY-1, shvector-3,RNA-seq


title: ATAC_MRSA_day5_2_Padi4WT

description:
Library name: JH02_ATAC
10X Genomics multiome


title: LB, healthy

description:
Library name: Sample7
LB_count


title: snRNA_MRSA_day5_1_Neut_specific_Padi4KO

description:
Library name: JH01_snRNA
10X Genomics multiome

value: Padi4KO (neutrophil specific)


title: XH, healthy

description:
Library name: Sample6
XH_count


title: WPMY-1, shvector-2,RNA-seq


title: LJL, healthy

description:
Library name: Sample5
LJL_count


title: ATAC_MRSA_day5_1_Neut_specific_Padi4KO

description:
Library name: JH01_ATAC
10X Genomics multiome


title: LYJ, healthy

description:
Library name: Sample4
LYJ_count


title: WPMY-1, shvector-1,RNA-seq


title: CPF, healthy

description:
Library name: Sample3
CPF_count


title: mrsa23_3

description: Library name: KK10D23RNAKID

data_processing:
STAR v2.7.11a
Assembly: mm10/GRCm38 and MRSA FPR3757 (NC_007793)
Supplementary files format and content: featureCounts

extract_protocol:
MRSA-infected and uninfected mouse kidneys were homogenized in 1200 µl TRI Reagent using a Minilys tissue homogenizer with a mixture of Soil Grinding beads (SK38) and Hard Tissue Homogenizing beads (CK28). Homogenization was done at the highest speed (5000 rpm) for 1 minute, followed by 1 minute on ice, for a total of 3 cycles. After centrifugation, RNA was extracted from the supernatant using the Zymo Direct-zol RNA miniprep Plus kit, including on-column DNase I digestion.
Stranded total RNA-sequencing was performed at the Indiana University Center for Medical Genomics Core. cDNA library preparation was carried out using the Illumina total RNA plus Microbiome kit (Ribo-Zero Plus Microbiome for rRNA removal). Pooled libraries were sequenced on a NovaSeq 6000 sequencer at a final concentration of 300 pM to obtain 150 bp paired-end sequencing. Due to the low proportion of bacterial reads in host tissues, approximately 150 million reads per library were generated.

treatment_protocol: The MRSA injection dose was adjusted to 5 x 10^7 CFU based on OD-CFU calibration curves. The tail vein injection volume was approximately 200 uL.


title: NSCL/P_03

description: Gene expression data of peripheral blood from NSCL/P patients

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Peripheral blood

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: Nonsyndromic cleft lip with or without cleft palate (NSCL/P)

value: blood


title: YY, healthy

description:
Library name: Sample2
YY_count


title: WPMY-1, sh61A-3,ribo-seq

data_processing:
Low quality reads were filtered by fastp. Raw reads without inserted fragment or containing over 10% of N bases were removed. Adapter sequences were trimmed. Reads with length between 25-36bp were retained for subsequent analysis. Short reads alignment tool Bowtie (v1.3.1) was used for mapping reads to ribosome RNA (rRNA) database. The reads mapped to rRNAs were removed.
Assembly: HG38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Library strategy: Ribo-seq

extract_protocol:
Total RNA was extracted using Trizol reagent
In order to digest the RNA other than ribosome-protected fragments (RPFs or RFPs), cell or tissue lysate was treated with unspecific endoribonuclease RNase I. Monosomes were purified from the lysateby fractionation on a linear sucrose gradient. Following PAGE purification, the both ends of RPF were phosphorylated and ligated with 5’ and 3’ adapters respectively. The RNA samples were then treated with rRNA depletion kit (Qiagen, Germany) to deplete as much rRNA contamination as possible before PAGE purification of the relatively short (25~35nt) RPFs. Then the fragments were reversely transcribed to the cDNAs and amplified by PCR. After library construction, the concentration of library was measured by Qubit® 2.0 Fluorometer and adjusted to 1ng/μL. Agilent 2100 Bioanalyzer was deployed to examine the insert size of the acquired library. At last, the accurate concentration of cDNA library was again examined using qPCR. Once the insert size and concentration of the library was correct, the samples can then be subjected for sequencing.


title: TXY, healthy

description:
Library name: Sample1
TXY_count


title: mrsa23_2

description: Library name: KK8D23RNAKID


title: WPMY-1, sh61A-2,ribo-seq


title: Zahra-cyclin-control-2

description: Library name: Sample 11

data_processing:
Quality of the raw data was assessed with FastQC.The adapter sequence was trimmed with Trimmomatic 0.39.
Assembly: After removal of the adapter sequence, reads were mapped against human genome hg38 using STAR with an annotation file from GENCODE (version 21). Later, SAMtools was used to sort the genearated BAM files and counting was done by QoRTs.
Supplementary files format and content: Raw counts are available in the form of .txt files or .csv files

extract_protocol:
Total RNA was harvested using NucleoSpin® RNA Plus (Macherey-Nagel) kit according to the manufacturer´s protocol.
Library peparation was carried out using TruSeq Stranded kit at the NGS core facility of German Cancer research center (DKFZ), Heidelberg, Germany according to the manufacturer´s protocol.

value: Retinal pigment epithelial cells

value: No serum starvation induced (cultured in the presence of serum)


title: mrsa23_1

description: Library name: KK5D23RNAKID


title: Zahra-cyclin-control-3

description: Library name: Sample 12


title: Zahra-cyclin-control-1

description: Library name: Sample 10


title: WPMY-1, sh61A-1,ribo-seq


title: Zahra-6h_SS-3

description: Library name: Sample 9

value: serum starvation induced for 6 hours


title: mrsa16_3

description: Library name: KP14D16RNAKID

value: kidney


title: Aged HUVECs RNAseq rep2

description:
Library name: Sample 5
OEC2
Expression_Transcript.xlsx

data_processing:
Raw sequencing reads were assessed using FastQC. Adapter sequences and low-quality bases were removed using Cutadapt.  For RNA-seq data, clean reads were aligned to the Mus musculus reference genome (GRCm38) using HISAT2. Transcript assembly and abundance estimation were performed using StringTie based on GENCODE gene annotations. Gene and transcript expression levels were quantified as FPKM values. Differential expression analysis was performed using Ballgown. Alternative splicing events were identified using rMATS, and coding potential of novel transcripts was evaluated using CPAT.  For Ribo-seq data, reads shorter than 22 nt or longer than 34 nt after trimming were discarded. Reads mapping to rRNA, tRNA, snRNA, and snoRNA were removed using Bowtie. Remaining reads were aligned to the Mus musculus reference genome (GRCm38) using STAR. Only uniquely mapped reads were retained for downstream analyses. Ribosome footprint quality control analyses were performed using RiboTish. Transcript-level ribosome occupancy was quantified using Plastid and normalized as RPKM values. Differential translation analysis was performed using edgeR, translational efficiency (TE) was analyzed using RiboDiff, and ORF prediction was performed using RiboCode.
Assembly: GRCh38
Supplementary files format and content: Processed data files are provided as .xlsx table files. RNA-seq outputs include raw gene count matrices. Ribo-seq outputs include raw ribosome-protected fragment (RPF) count matrices.

extract_protocol:
Samples were collected and immediately frozen in liquid nitrogen and stored at −80°C until processing. For RNA-seq samples, total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer's instructions. RNA quality and concentration were assessed using agarose gel electrophoresis and a NanoDrop ND-1000 spectrophotometer. Poly(A)+ mRNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), while ribosomal RNA depletion was performed when necessary.  For ribosome profiling (Ribo-seq) samples, tissues were homogenized in polysome lysis buffer supplemented with cycloheximide and RNase inhibitors. Cell debris was removed by centrifugation and lysates were treated with RNase I to digest unprotected RNA. Ribosome-protected fragments (RPFs) were isolated and purified. RNA quantity and integrity were evaluated prior to library preparation.
RNA-seq libraries were prepared using the KAPA Stranded RNA-Seq Library Prep Kit (Roche). Briefly, enriched mRNA or rRNA-depleted RNA was fragmented and reverse-transcribed into first-strand cDNA using random primers. Second-strand cDNA synthesis was performed with dUTP incorporation to preserve strand specificity. Double-stranded cDNA was end-repaired, A-tailed, ligated to Illumina-compatible adapters, PCR-amplified, and purified.  Ribo-seq libraries were prepared using the NEB Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs). Ribosome-protected fragments corresponding to 26–34 nt footprints were size-selected and ligated to 3′ and 5′ adapters. Reverse transcription was performed to generate cDNA, followed by PCR amplification. PCR products corresponding to 146–154 bp were purified by PAGE gel extraction.  Library quality and fragment size distributions were evaluated using an Agilent 2100 Bioanalyzer and quantified by qPCR. Sequencing was performed on the Illumina NovaSeq 6000 platform. RNA-seq libraries were sequenced in paired-end 150 bp mode, whereas Ribo-seq libraries were sequenced in single-end mode.

value: Vascular

value: Primary Cell

value: Human Umbilical Vein Endothelial Cells

value: Aged


title: Zahra-6h_SS-2

description: Library name: Sample 8


title: Zahra-6h_SS-1

description: Library name: Sample 7


title: WPMY-1, shcontrol-3,ribo-seq

value: TRMT61A wildtype


title: mrsa16_2

description: Library name: KP13D16RNAKID

value: WT


title: Tex1,DMSO (HiC)

city: Summit

first: Junfei

last: Zhao

address: 556 Morris Ave

institute: Bristol Myers Squibb

description: Library name: Tex1_DMSO

library_source: genomic

data_processing:
Hi-C data were processed using ENCODE Hi-C uniform processing pipeline (v1.15.1) which is based on Juicer to generate .hic files.
Assembly: GRCh38
Supplementary files format and content: hic

molecule: genomic DNA

source_name: cell line

extract_protocol:
Cells were washed in Dulbecco’s modified Eagle’s medium (DMEM) without serum then crosslinked with 2% formaldehyde for 10 min at room temperature. The crosslinking reaction was quenched by adding cold 1 M glycine to a final concentration of 0.125 M for 5 min at room temperature, followed by 15 min on ice. Crosslinked cells were washed in ice-cold PBS, the supernatant discarded and the pellets flash-frozen on dry ice and stored at −80 °C.
Hi-C data was generated by Arima Genomics using the Arima-Hi-C kit (A510008) according to the manufacturer’s protocols.

value: T-cell

value: DMSO


title: WPMY-1, shcontrol-2,ribo-seq


title: Tex1,Mezi (HiC)

description: Library name: Tex1_480

value: Mezi


title: mrsa16_1

description: Library name: KP12D16RNAKID


title: Tact1,DMSO (HiC)

description: Library name: Tact1_DMSO


title: WPMY-1, shcontrol-1,ribo-seq


title: MM12 Tact Mezi (scRNAseq)

description: Library name: MM12_act_Mezi

data_processing:
Cellranger was used to processes raw sequencing data to align reads, generate gene-cell matrices.
Assembly: GRCh38
Supplementary files format and content: HDF5 Feature-Barcode Matrix

extract_protocol:
MM PBMCs were thawed, treated with either DMSO or 1 nM Mezigdomide for 1 hour, and stimulated with anti-CD3/CD28 Dynabeads for another 3 days followed by library preparation.
Single-nucleus gene expression libraries were generated using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits v1, following the manufacturer’s protocol.


title: mrsa09_3

description: Library name: KP10D9RNAKID


title: MM12 Tact DMSO (scRNAseq)

description: Library name: MM12_act_DMSO


title: MM11 Tact Mezi (scRNAseq)

description: Library name: MM11_act_Mezi


title: mrsa09_2

description: Library name: KP8D9RNAKID


title: WPMY-1, sh61A-3.Input, m1A-MAP-seq

data_processing:
After sequencer sequencing, image analysis, base identification and quality control, raw data (raw reads) were obtained. Before the analysis begins, a tRNA database needs to be built. The high-confidence tRNA sequence corresponding to the reference genome was downloaded from the GtRNAdb website and three bases (CCA) were added to the 3' end of each tRNA sequence. Then, Q30 and cutadapt software (v1.9.3) were used to control the quality of the raw reads, including removing connectors and low-quality reads. Finally, reads of length >=15nt were reserved as clean reads. After quality control was complete, clean reads for each sample were aligned to the prepared tRNA database using bowtie2 software (v2.2.4), and the number of reads on each tRNA was counted using samtools (v1.3.1) as the original expression of that tRNA.The ratio of single base sites in the demethylase (-) and demethylase (+) samples was calculated to achieve single base site recognition. Modified tRNAs were annotated by the program annotations.
Assembly: HG38
Supplementary files format and content: excel file include Methylated_m1A_sites
Library strategy: m1A-MAP-seq

extract_protocol:
Total RNA was extracted using Trizol reagent
m1A-MAP-Seq service was provided by Cloud-Seq Biotech (Shanghai, China).The MirVana Isolation Kit (ThermoFisher) was used to enrich small RNAs which were less than 200 nt from total RNAs. The m1A-MeRIP reaction was performed using the GenSeq m1A-MeRIP Kit as follows: RNA was incubated with m1A antibody in IPP buffer for 2 h at 4 degrees. The reaction mixture was further immunoprecipitated with protein A magnetic beads (Thermo Fisher) at 4 degrees for 2 h. The bound RNA on the beads was then eluted with a free m1A adenosine analogue. The eluted RNA was further extracted by Trizol reagent (Thermo Fisher). The extracted and purified RNA was divided into two groups and treated respectively, one with the AlkB demethylase [demethylase(+)] and the other without treatment [demethylase(-)]. Finally, the samples obtained were constructed using RNA Library Establishment Kit (NEB) and sequenced on an illumina NovaSeq instrument with 150bp paired end reads.

value: TRMT61A knockdown


title: MM11 Tact DMSO (scRNAseq)

description: Library name: MM11_act_DMSO


title: MM2 Tact Mezi (scRNAseq)

description: Library name: MM2_act_Mezi


title: WPMY-1, sh61A-3.AlkB+, m1A-MAP-seq


title: mrsa09_1

description: Library name: KP6D9RNAKID


title: MM2 Tact DMSO (scRNAseq)

description: Library name: MM2_act_DMSO


title: WPMY-1, sh61A-3.AlkB-, m1A-MAP-seq


title: MM1 Tact Mezi (scRNAseq)

description: Library name: MM1_act_Mezi


title: MM1 Tact DMSO (scRNAseq)

description: Library name: MM1_act_DMSO


title: mrsa07_1

description: Library name: KP11D7RNAKID


title: mrsa04_3

description: Library name: KK13D4RNAKID


title: WPMY-1, sh61A-2.Input, m1A-MAP-seq


title: Kmt2d WT 971 cell Chipseq Input for C

city: Houston

first: Zhao

last: Zheng

state: TX

address: 1901 East Rd

department: Genomic Medicine

institute: md anderson cancer center

description: Library name: IBM_SKCM_M971_G_for_C, INPUT

data_processing:
1. Quality Control by using fastqc and multiqc, then trim the sequences if needed
2. aligning the sequences by BMA
3. filtering the data and remove the duplicates, downsampling
4. calling the peaks by using macs1 for narrow peaks and macs2 for broad peaks
5. generating bigwig files
Assembly: mm10
Supplementary files format and content: .narrowPeaks, .broadPeaks
Supplementary files format and content: bigwig

source_name: Kmt2d WT 971

growth_protocol: Mouse melanoma cells were grown in DMEM/F12 with 10% FBS and 1% Penicillin-Streptomycin

extract_protocol:
Following the protocol on: Terranova, Christopher, et al. "An integrated platform for genome-wide mapping of chromatin states using high-throughput ChIP-sequencing in tumor tissues." Journal of visualized experiments: JoVE 134 (2018).
NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina

value: Melanoma

value: Kmt2d WT 971

tag: chip antibody


title: Tex3 DMSO (RNAseq)

description: Library name: 7312-HC-0035

data_processing:
We used MACS version 3.0.1 to call peaks.
Assembly: GRCh38
Supplementary files format and content: readcount on gene level

extract_protocol:
Cells for RNAseq were prepared according to instructions from Discovery Life Sciences.
Five million cells per sample were collected, washed, fixed, and stored at -80 C prior to shipping to Discovery Life Sciences where downstream RNAseq was carried out.

tag: cell type


title: mrsa04_2

description: Library name: KK9D4RNAKID


title: Kmt2d WT 971 cell Chipseq H3K27ac

description: Library name: IBM_SKCM_M971_C, ChIP

tag: cell line

value: H3K27ac abcam ab4729


title: WPMY-1, sh61A-2.AlkB-, m1A-MAP-seq


title: Kmt2d mutant 493 cell Chipseq input for C

description: Library name: IBM_SKCM_M493_G_for_C, INPUT

source_name: Kmt2d Mutant 493

value: Kmt2d Mutant 493


title: mrsa04_1

description: Library name: KK7D4RNAKID

tag: treatment


title: Tex2 Mezi (RNAseq)

description: Library name: 7312-HC-0030


title: WPMY-1, sh61A-1.Input, m1A-MAP-seq


title: Tex2 DMSO (RNAseq)

description: Library name: 7312-HC-0029


title: mrsa03_3

description: Library name: KP4D3RNAKID


title: Kmt2d mutant 493 cell Chipseq H3K27ac

description: Library name: IBM_SKCM_M493_C, ChIP


title: Tex1 Mezi (RNAseq)

description: Library name: 7312-HC-0024


title: WPMY-1, sh61A-1.AlkB+, m1A-MAP-seq


title: mrsa03_2

description: Library name: KP2D3RNAKID


title: Tex3 Mezi (RNAseq)

description: Library name: 7312-HC-0036


title: WPMY-1, sh61A-1.AlkB-, m1A-MAP-seq


title: Tex1 DMSO (RNAseq)

description: Library name: 7312-HC-0023


title: Kmt2d WT 971 cell Chipseq Input for AEF

description: Library name: IBM_SKCM_M971_G_for_AEF, INPUT


title: WPMY-1, sh61A-2.AlkB+, m1A-MAP-seq


title: mrsa03_1

description: Library name: KK4D3RNAKID


title: Kmt2d WT 971 cell Chipseq H3K4me1

description: Library name: IBM_SKCM_M971_A, ChIP

value: H3K4me1 abcam ab8895


title: WPMY-1, Vector-3.Input, m1A-MAP-seq


title: Tact3 DMSO (RNAseq)

description: Library name: 7312-HC-0033


title: mrsa02_3

description: Library name: KP3D2RNAKID


title: Kmt2d WT 971 cell Chipseq H3K4me3

description: Library name: IBM_SKCM_M971_E, ChIP

value: H3K4me3 abcam ab8580


title: WPMY-1, Vector-3.AlkB+, m1A-MAP-seq


title: mrsa02_2

description: Library name: KK15D2RNAKID

value: kidney


title: Kmt2d WT 971 cell Chipseq H3K27me3

description: Library name: IBM_SKCM_M971_F, ChIP

value: H3K27me3 abcam ab6002


title: Tact2 DMSO (RNAseq)

description: Library name: 7312-HC-0027


title: Tact1 DMSO (RNAseq)

description: Library name: 7312-HC-0021


title: WPMY-1, Vector-3.AlkB-, m1A-MAP-seq


title: mrsa02_1

description: Library name: KK3D2RNAKID


title: Kmt2d mutant 493 cell Chipseq input for AEF

description: Library name: IBM_SKCM_M493_G_for_AEF, INPUT


title: WPMY-1, Vector-2.Input, m1A-MAP-seq


title: mrsa01_4

description: Library name: KP5D1RNAKID


title: Tex3,DMSO,H3K4me3 (ChIP)

description: Library name: Tex3-DMSO_H3K4me3

data_processing:
We used MACS version 3.0.1 to call peaks.
Assembly: GRCh38
Supplementary files format and content: narrowpeak

extract_protocol:
DNA was extracted and purified using the standard phenol chloroform method, followed by ethanol precipitation.
Library was prepared using an automated system (Apollo 342, Wafergen Biosystems/Takara).


title: WPMY-1, Vector-2.AlkB+, m1A-MAP-seq


title: Tex3,Mezi,H3K4me3 (ChIP)

description: Library name: Tex3-480_H3K4me3


title: Kmt2d mutant 493 cell Chipseq H3K4me3

description: Library name: IBM_SKCM_M493_E, ChIP


title: mrsa01_3

description: Library name: KK11D1RNAKID


title: WPMY-1, Vector-2.AlkB-, m1A-MAP-seq


title: mrsa01_2

description: Library name: KK6D1RNAKID


title: Kmt2d mutant 493 cell Chipseq H3K27me3

description: Library name: IBM_SKCM_M493_F, ChIP


title: Tex2,DMSO,H3K4me3 (ChIP)

description: Library name: Tex2-DMSO_H3K4me3


title: WPMY-1, Vector-1.Input, m1A-MAP-seq


title: mrsa01_1

description: Library name: KK2D1RNAKID


title: Tex2,Mezi,H3K4me3 (ChIP)

description: Library name: Tex2-480_H3K4me3


title: Kmt2d WT 971 cell cut&run seq TFAP2A

description: Library name: CR_kmt2d_SKCM_971_R, Cut_Run

data_processing:
1. Quality Control by using fastqc and multiqc, then trim the sequences if needed
2. aligning the sequences by Bowtie2
3. filtering the data and remove the duplicates, downsampling
4. calling the peaks by using macs1 for narrow peaks and macs2 for broad peaks
5. generating bigwig files
Assembly: mm10
Supplementary files format and content: peaks files: .narrowPeaks, .broadPeaks
Supplementary files format and content: bigwig files: .bw
Library strategy: CUT&RUN

extract_protocol:
Epicypher cut and run protocol v2.1
Epicypher CUTANA™ CUT&RUN Library Prep Kit

value: Anti-TFAP2A Proteintech 13019-3-AP


title: WPMY-1, Vector-1.AlkB+, m1A-MAP-seq


title: mrsa00_5

description: Library name: KR5coRNAKID


title: Tex1,DMSO,H3K4me3 (ChIP)

description: Library name: Tex1-DMSO_H3K4me3


title: Kmt2d WT 971 cell cut&run seq UTX

description: Library name: CR_kmt2d_SKCM_971_P, Cut_Run

value: Anti-UTX Millipore ABE1865


title: WPMY-1, Vector-1.AlkB-, m1A-MAP-seq


title: mrsa00_4

description: Library name: KR4coRNAKID


title: Kmt2d WT 971 cell cut&run seq Menin

description: Library name: CR_kmt2d_SKCM_971_O, Cut_Run

value: Anti-Menin Epicypher 13-2021


title: Tex3,DMSO,H3K4me1 (ChIP)

description: Library name: Tex3-DMSO_H3K4me1


title: Tex1,Mezi,H3K4me3 (ChIP)

description: Library name: Tex1-480_H3K4me3


title: mvi_yes5

city: HANGZHOU

first: Xin

last: Hu

address: YUHANGTANGROAD 866

institute: Zhejiang university

data_processing:
Raw reads were treated with Trimmomatictools(V0.36) to remove adapters. Following reads quality con- trol:Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below15, drop reads which are less than 35% of initiation read length. Then reads quality was inspected using theFastQC software then output statistical result.
Two algorithms, CIRI2 and CIRCexplorer2 were used to detect circRNAs. Reads were mapped to human- reference genome GRCh37/ hg19 (http://genome.ucsc.edu/) by BWA-MEM or Tophat, respectively. CIRI2 detectsthe paired chiastic clipping (PCC) signals from the mapping information of reads by local alignment withBWA-MEM and combines with systematic filtering steps to remove potential false positives.CIRCexplorer2 uses TopHat and TopHat-Fusion alignment output to detect circRNAs.
If a circRNA can be detected by both methods, it will be consided as an identified circRNA. The DEseq/DESeq2/edgeR/DEGse package in Bioconductor was used to determine differently expressed circRNAs, according to the criteria of |log2 (fold change) | >1 and p-value≤005
Assembly: hg38

source_name: liver - hepatocellular carcinoma

growth_protocol: The HCC tissues of the patients were preserved in -80 environment after resection

extract_protocol:
none
Total RNA was isolated from cells/tissues using the Magzol Reagent (Magen, China)according to the manufac- turer’s protocol, The quantity and integrity of RNA yield was assessed by using the K5500(BeijingKaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately. Briefly, the mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA).And then fragmented to approximately 200bp. Subsequently, theRNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycleaccording to in- structions ofNEBNext® UltraTM RNA Library Prep Kit for Illumina. The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit(Thermo Fisher Scientific, USA). The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp

value: liver - hepatocellular carcinoma


title: mrsa00_3

description: Library name: KR3coRNAKID

value: WT


title: mvi_yes4


title: Tex3,Mezi,H3K4me1 (ChIP)

description: Library name: Tex3-480_H3K4me1

value: T-cell


title: mrsa00_2

description: Library name: KR2coRNAKID


title: Kmt2d WT 971 cell cut&run seq PBRM1

description: Library name: CR_kmt2d_SKCM_971_M, Cut_Run

value: Anti-PBRM1 Bethyl A301-591A-T


title: mvi_yes3


title: mrsa00_1

description: Library name: Controlext-RNA


title: Tex2,DMSO,H3K4me1 (ChIP)

description: Library name: Tex2-DMSO_H3K4me1

value: DMSO


title: Kmt2d WT 971 cell cut&run seq Arid2

description: Library name: CR_kmt2d_SKCM_971_L, Cut_Run

value: Anti-Arid2 Bethyl A302-230A-T


title: mvi_yes2


title: Kmt2d WT 971 cell cut&run seq BRD9

description: Library name: CR_kmt2d_SKCM_971_N, Cut_Run

value: Melanoma

value: Anti-BRD9 Bethyl A303-781A-T


title: Tex2,Mezi,H3K4me1 (ChIP)

description: Library name: Tex2-480_H3K4me1

value: Mezi


title: Kmt2d WT 971 cell cut&run seq Arid1a

description: Library name: CR_kmt2d_SKCM_971_K, Cut_Run

value: Kmt2d WT 971

value: Anti-Arid1a Abcam ab182560


title: mvi_yes1


title: Tex1,DMSO,H3K4me1 (ChIP)

description: Library name: Tex1-DMSO_H3K4me1