title: IMR90-5-FU for 24 hours rep 2

city: Rochester

first: Julia

last: Freewoman

state: NY

address: 1 Lomb Memorial Dr

department: Thomas H. Gosnell School of Life Sciences

institute: Rochester Institute of Technology

data_processing:
University of Rochester Genomics Research Center (URGRC) squenced the samples and the resulting raw reads were cleaned using Trimmomatic-0.32 with a cutoff 25 bp for the read size
The filtered fastq were further cleaned by FASTX-toolkit (version 0.0.13) with a quality score cutoff of 28. Then, cutadapt (version 1.10) was used to filter out all reads greater than 50bp.
Using the HG19 was aligned using Bowtie2 using the -k option set to 100 so that Bowtie2 would identify up to 100 alternate mapping sites.
Using the HG19 repeat GTF made from the GFF file output from Repeatmaker telescope was run and the repeat counts were produced for each sample
Each of the telescope final counts were merged together by the "transciprt" column.  The positions where no count was given in a paticular sample (NA in the file) were replaced with a 0.
The merged count file was then filtered so only the REs with a cpm (EdgeR function) of greater than 5 for each column were kept.
The filtered telescope counts were then anylized via DESeq2.
Assembly: HG19
Supplementary files format and content: IMR90_5_FU_time_course.csv. Matrix of all of the telescope count values the the first column (row labels) has the RE ID which contains the RE name and the location of the RE on the HG19 genome the following are each of the samples for each of the IMR90 Nutlin. treatments
Supplementary files format and content: IMR90_total_Nutlin.csv.  Matrix of all of the telescope count values the the first column (row labels) has the RE ID which contains the RE name and the location of the RE on the HG19 genome the following are each of the samples for each of the IMR90 5-FU treatments

source_name: Lung

growth_protocol: IMR90 cells were grown in Eagle's minimum media and antiboitoics to between 70-90%.

extract_protocol:
Total RNA was extracted using the RNeasy Plus kit using protocl 1 from the supllimentary protocol provided by Quiagen title Purification of miRNA from animal cells alternate protocol using the RNeasy® Plus Mini Kit and RNeasy MinElute® Cleanup Kit.
The Illuminia TruSeq Stranded Total kit was used following manufactor's instructions

treatment_protocol: Fresh media was changed for the none treatment control 12 hours prior to extraction.  For the treatments the drug treatments (Nutlin/5-FU) drug treated media (5 µM for Nutlin and 375 µM) were added for 6, 12, or 24 hours along with the associated DMSO treatment equivalent to the volume associated with volume of drug added.

value: Lung

value: Fibroblast

value: wildtype

tag: time

value: 24 hours


title: NOA_3_6_7

status: Public on Oct 01 2025

type: SRA

city: Guangzhou

first: Lin

last: Li

address: Shatai South Road

department: Pathophysiology

country: China

institute: Southern Medical University

description: Sample 198

library_source: genomic

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
For bisulfite-seq data, Trim Galore (v0.3.3) was used to remove the first 6 bases of random primer, adaptor sequences and low quality bases; for RNA-seq data, each single cell was separated by unique cell barcode, then template switch oligo (TSO), ployA tails, adaptors and low quality bases were removed.
For bisulfite-seq data, clean reads were first mapped to human reference genome hg19 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module; for RNA-seq data, clean reads were mapped to human genome hg19 with Tophat (v2.0.14), and then unique UMI counts were calculated by HTSeq.
WCG and GCH methylation level of cytosines was estimated using comstomized scripts.
Genome_build: hg19
Supplementary_files_format_and_content: UMI_count.txt files include UMI counts of RefSeq genes. While WCG.txt and GCH.txt files include the read counts of cytosines in WCG and GCH context respectively. The columns in WCG.txt or GCH.txt files represent "chr" "position" "unmethylated read counts" "methylated read counts".

molecule: genomic DNA

organism: Homo sapiens

source_name: testis

extract_protocol:
An individual cell was picked into the cell lysis buffer with vitro methylation (IVM) mixture containing 4 U RNase inhibitor (TAKARA, Cat. 2313B), 0.25% IGEPAL CA-630 (SIGMA, Cat. I3021), 1X GC reaction buffer and 2 U M. CviPI (NEB, Cat. M0227L). After gently vortexed for 10 sec, the cell lysate was incubated at 37 °C for 20 min and then at 65 °C for 25 min. Then, the cell lysate could be directly processed for RNA/DNA separation or stored at -80 °C.
For RNA part, a modified Smart-seq2 protocol was applied for single-cell RNA-seq. For DNA part, Bisulfite-converted DNA was amplified with biotinylated random primer and klenow exo– polymerase (NEB, M0212L) for 7 rounds and excess primer was removed by exonuclease I (NEB, M0293L). After second strands synthesis, the library was amplified by KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602) for 14 cycles.

tag: gender

value: male

tag: age

tag: condition

value: nonobstructive azoospermia (NOA)

tag: testis

value: testis


title: SA00798_SMM_529

city: Liège

first: Jo

last: Caers

address: Avenue de l'Hôpital

country: Belgium

institute: CHU de Liège

description:
5' barcoded RNA + Antibody-derived oligonucleotide library
The file name is constructed based on SampleID_Cohort_ExperimentID

library_source: transcriptomic single cell

data_processing:
Sample demultiplexing, barcode processing, alignment to the human transcriptome (GRCh38), single-cell 5′ gene, V(D)J and feature barcode counting were performed using Cell Ranger Single-Cell Software Suite (cellranger-4.0.0, 10x Genomics). Each data type (RNA, ADT, BCR) was then pre-processed per sample independently and subsequently concatenated into a single dataset for further downstream analysis. Unless stated otherwise, for each data analysis step, related functions from the scanpy (v1.6.1) Python package were used with default parameters.
Empty droplets and dying cells were filtered out based on UMI counts < 650, minimum number of genes < 300 and mitochondrial gene expression > 20%. Doublet detection was conducted by Scrublet (v0.2.1). Droplets with a Scrublet doublet score > 0.3 and genes expressed in <3 cells were excluded. Following the initial filtering, a cell per million (CPM) normalization was applied with a scale factor of 10^4 and the data were log transformed. Highly variable genes were detected with Seurat flavor. For the downstream analyses, immunoglobulin genes (IG) were removed from the dataset. Cell cycle scores were calculated using score_genes_cell_cycle function from scanpy using the gene sets identified by Kowalczyk et al..
Droplets with UMI counts  500 were excluded. The data were normalized using centered log-ratio (CLR) transformation
Cell Ranger filtered BCR-seq output contig files from individual samples were concatenated into a single file. Using the scirpy (v0.6.1) library, with parameters receptor_arms=all and dual_ir=primary only, observed clonotypes were defined based on CDR3 nucleic acid sequences. To assess clonal expansion, per-sample-clonotype definitions were generated using both CDR3 nucleic acid sequences and sample IDs. Per-sample-clonotypes observed in  10 cells were considered expanded malignant clonotypes.
Gene expression based principal component analysis (PCA) and Harmony (v1.0) batch correction, using theta=0, was performed. Nearest neighborhood networks were constructed using a cosine distance. Each integrated dataset was projected onto 2D space applying the UMAP algorithm based on the standard settings of scanpy. Cell typing was performed as described in the publication.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: raw_feature_bc_matrix.h5. Integrated_processed_data.h5ad file includes the following information: batch (SampleID), cohort, experimentID, clonotype, isExpandedClonotype (expansion status), cellType, isLowQuality (high mito or low nr of genes within the same cell type), highly_variable, gene_ids, feature_types, cohort_colors, X_umap (RNa based), log (log counts).

molecule: total RNA

source_name: BM aspirate mononuclear cells mRNA-derived cDNA and ADT-derived cDNA

extract_protocol:
BM-MNCs were isolated from BM aspirate using Ficoll-plaque gradient separation and processed for single cell 10x Genomics 5' Chromium single cell V(D)J with Feature Barcoding protocol.
The library was constructed using single cell 10x Genomics 5' Chromium single cell V(D)J with Feature Barcoding protocol.

tag: sample id

tag: cohort

value: smoldering MM (SMM)

tag: tissue

value: Bone Marrow

tag: cell type

value: BM aspirate mononuclear cells

tag: library type

value: mRNA and ADT


title: SA00797_SMM_529


title: T24_DMSO_2

city: Duesseldorf

first: Michèle

middle: J

last: Hoffmann

state: NRW

address: Moorenstr. 5

department: Urology

country: Germany

institute: Heinrich Heine University, Medical Faculty

description:
Library name: 1016-1
1016-1_RPKM

library_source: transcriptomic

data_processing:
Illumina BCL Convert Tool (version 3.8.4) was used for basecalling.
Sequenced reads were adapter trimmed and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides maximal 2). Mapping was done against the Homo sapiens (hg38; GRCh38.107) (July 20, 2022) genome sequence using CLC Genomics Workbench v23.0.5 with standard parameters.
Reads Per Kilobase and per Megabase (RPKM) were calculated using CLC Genomics Workbench v23.0.5 with standard parameters. Multi-group comparisons were calculated using the CLC Differential Expression for RNA-Seq tool (version 2.8, Qiagen, Venlo, Netherlands). The resulting p values were corrected for multiple testing by FDR and Bonferroni-correction. A p value of ≤ 0.05 was considered significant. Cut-off for differential gene expression was set to 1.5 fold.
Assembly: hg38
Supplementary files format and content: The excel file includes RPKM values for each sample

growth_protocol: UC cell lines were cultivated in Dulbecco’s Modified Eagle’s Medium (DMEM; 4.5 g/L glucose) with GlutaMAX, Pyruvate, and 10 % fetal bovine serum (FBS). Cells were maintained at 37 °C in a humidified atmosphere containing 5 % CO2.

extract_protocol:
Rneasy Mini Kit, Qiagen, according to manufacturer with optional DNAse treatment
Library preparation was performed according to the manufacturer’s protocol using the Lexogen® QuantSeq 3’ mRNA-Seq Library Prep Kit FWD with UMI’s. The Input mount was 200 ng totalRNA. Bead purified libraries were normalized and finally sequenced on the NextSeq2000 system (Illumina Inc. San Diego, CA, USA) with a read setup of 1x100 bp.

treatment_protocol: Indicated cell lines were treated with reduced dosage (as indicated in publication, additional file 1) with PARP inhibitor Olaparib or Talazoparib for 72h. Solvent control cells were treated with DMSO.

tag: cell line

value: urothelial carcinoma cell line

tag: treatment

value: DMSO


title: NOA_3_7_4

description: Sample 202


title: SA00795_MGUS_528

value: monoclonal gammopathy of unknown significance (MGUS)


title: Liver tissue, CD163WT, Western diet, rep H

city: Odense M

first: Jonas

last: Graversen

address: Campusvej 55

department: Health, IMM

country: Denmark

institute: University of Southern Denmark

description: Library name: D426

data_processing:
Reads were aligned to the mouse gene assembly (GRCm39) using STAR (v.2.7.8a) and FeatureCounts (v.2.0) was used for exon read quantification. FastQC and MultiQC was used to assess quality of raw sequencing.
Assembly: GRCm39
Supplementary files format and content: Raw counts supplied as a txt file.

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA was extracted from snap-frozen liver tissue. The tissue was homogenized in TRI reagent (T9424, Sigma-Aldrich) using the FastPrep-24 5G bead beating grinder. 1-bromo-3-chloropropane was added and vortexed thoroghly and incubated for 15min at RT followed by centrifugation (10000g, 10min, 4oC). The aqueous phase containing the RNA was mixed with cold 96% ethanol and loaded on a EconoSpin column (1920-250, Epoch Life Science) by centrifugation (13000g, 30sec, RT). After three washes with RPE buffer, the column was spinned dry for 2 minutes (13000g, RT) followed by 5 minutes to allow evapuration of ethanol. RNA was eluted by DEPC-treated water and centrifugation (16000g, 1min, RT).
Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) and RNA was paired-end sequenced on the NovaSeq 6000 Sequencing System (Illumina).

treatment_protocol: Male CD163 knockout and littermate wildtype mice were generated by crossing heterozygous C57BL/6NTac (CD163tm1(KOMP)Vlcg) mice. At six-weeks of age, mice were allocated randomly to receive either Western diet with fructose-supplemented water (n=15 per genotype) or control chow diet (Chow; #1320 maintenance diet, Altromin) with normal drinking water (n=4-5 per genotype) ad libitum for 8 weeks.

value: Liver

tag: genotype

value: Western diet, 8 weeks


title: SA00796_SMM_529


title: NOA_3_6_2

description: Sample 195


title: NOA_3_6_8

description: Sample 199


title: NOA_3_6_4

description: Sample 196


title: NOA_3_5_8

description: Sample 193


title: ECU72 cultivar, heat (42°C), 5 hours

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

description:
Library name: ECU72_Heat
total RNA

data_processing:
base-calling:bcl2fastq
adapter trim: trimmomatic
alignment: Bowtie2
In order to identify the transcription start site, the RECLU pipeline was used.
Assembly: Mesculenta_671_v8.0
Supplementary files format and content: bed

organism: Manihot esculenta

source_name: Leaf and stem

growth_protocol: Cassava (Manihot esculenta) plants (cultivars ECU72 and KU50) were propagated from stem cuttings and grown in controlled environment chambers under a 12-hour light/12-hour dark photoperiod at 25°C. One-month-old plants were used for stress treatments.

extract_protocol:
Total RNA was extracted using RNeasy Plant Mini Kit (QIAGEN) with DNaseI treatment. RNA quality was verified via Bioanalyzer (RIN >7.5).
nAnT-iCAGE-seq libraries were prepared with the previously described protocol (https://doi.org/10.1007/978-1-4939-0805-9_7).

treatment_protocol: Control: Plants were maintained at 25°C for 5 hours. Heat stress: Plants were transferred to 42°C chambers for 5 hours. Cold stress: Plants were transferred to 4°C chambers for 5 hours. After treatment, the youngest leaves and shoot apices were immediately harvested, flash-frozen in liquid nitrogen, and stored at –80°C until RNA extraction.

value: Leaf and stem

value: Heat

value: WT


title: Liver tissue, CD163WT, Western diet, rep G

description: Library name: D425


title: Liver tissue, CD163WT, Western diet, rep K

description: Library name: D429


title: NOA_3_7_1

description: Sample 200


title: IMR90-DMSO for 24 hours 5-FU control rep 1

country: USA

value: Lung

value: Fibroblast

value: wildtype


title: Liver tissue, CD163WT, Western diet, rep F

description: Library name: D424


title: NOA_3_6_1

description: Sample 194

value: male

value: nonobstructive azoospermia (NOA)


title: SA00794_HV_528

value: healthy volunteer (HV)


title: Liver tissue, CD163WT, Western diet, rep J

description: Library name: D428


title: IMR90-5-FU for 24 hours rep 1

value: 24 hours


title: SA00722_HV_472

value: Bone Marrow

value: BM aspirate mononuclear cells


title: Liver tissue, CD163KO, chow diet, rep D

description: Library name: D420

value: Chow diet, 8 weeks


title: NOA_3_5_5

description: Sample 190

value: testis


title: Liver tissue, CD163WT, Western diet, rep E

description: Library name: D423


title: IMR90-DMSO for 24 hours 5-FU control rep 2

value: DMSO


title: Liver tissue, CD163WT, Western diet, rep I

description: Library name: D427

value: Liver


title: SA00793_MM_528

value: active MM

value: mRNA and ADT


title: NOA_3_5_4

description: Sample 189


title: Liver tissue, CD163WT, Western diet, rep D

description: Library name: D422

value: Western diet, 8 weeks


title: Liver tissue, CD163WT, chow diet, rep D

description: Library name: D418


title: NOA_3_5_7

description: Sample 192


title: Liver tissue, CD163WT, Western diet, rep C

description: Library name: D421


title: SA00792_SMM_528

value: smoldering MM (SMM)


title: IMR90-5-FU for 6 hours rep 2

value: Lung

value: 6 hours


title: Liver tissue, CD163WT, chow diet, rep C

description: Library name: D417


title: NOA_3_5_6

description: Sample 191


title: IMR90-5-FU for 12 hours rep 1

value: Fibroblast

value: wildtype

value: 12 hours


title: NOA_3_5_3

description: Sample 188

value: male

value: nonobstructive azoospermia (NOA)


title: IMR90-5-FU for 12 hours rep 2


title: IMR90-DMSO for 12 hours 5-FU control rep 2


title: Liver tissue, CD163WT, chow diet, rep E

description: Library name: D419


title: SA00721_MM_472

value: Bone Marrow


title: NOA_3_5_1

description: Sample 186


title: SA00720_SMM_472

value: BM aspirate mononuclear cells


title: IMR90-DMSO for 12 hours 5-FU control rep 1


title: IMR90-DMSO for 6 hours 5-FU control rep 1


title: Liver tissue, CD163WT, Western diet, rep A

description: Library name: D414


title: SA00719_MGUS_472

value: monoclonal gammopathy of unknown significance (MGUS)


title: IMR90-Nutlin for 6 hours rep 2

value: Nutlin


title: NOA_3_5_2

description: Sample 187

value: testis


title: IMR90-5-FU for 6 hours rep 1


title: SA00718_MM_471


title: IMR90-Nutlin for 6 hours rep 1


title: Liver tissue, CD163KO, Western diet, rep L

description: Library name: D412

value: Liver


title: SA00713_MGUS_470


title: Liver tissue, CD163WT, chow diet, rep B

description: Library name: D416

value: Chow diet, 8 weeks


title: NOA_3_4_5

description: Sample 182


title: SA00717_SMM_471

value: mRNA and ADT


title: IMR90-DMSO for 6 hours 5-FU control rep 2

value: DMSO


title: SA00715_HV_471

value: healthy volunteer (HV)


title: SA00716_MGUS_471


title: Liver tissue, CD163KO, Western diet, rep M

description: Library name: D413

value: Western diet, 8 weeks


title: Liver tissue, CD163WT, Western diet, rep B

description: Library name: D415


title: NOA_3_4_7

description: Sample 184


title: SA00712_HV_470


title: NOA_3_4_3

description: Sample 181


title: SA00714_SMM_470

value: smoldering MM (SMM)


title: IMR90-DMSO for 6 hours Nutlin control rep 1

value: Lung

value: Fibroblast

value: 6 hours


title: IMR90-DMSO for 6 hours Nutlin control rep 2

value: wildtype


title: Liver tissue, CD163KO, Western diet, rep I

description: Library name: D409


title: NOA_3_4_6

description: Sample 183

value: male

value: nonobstructive azoospermia (NOA)


title: Liver tissue, CD163KO, Western diet, rep K

description: Library name: D411


title: SA00710_MGUS_469

value: Bone Marrow

value: BM aspirate mononuclear cells


title: NOA_3_3_8

description: Sample 179


title: SA00711_MM_470

value: active MM


title: NOA_3_4_2

description: Sample 180

value: testis


title: NOA_3_4_8

description: Sample 185


title: IMR90-Control rep 2

value: none-treatment

value: control


title: SA00709_HV_469

value: mRNA and ADT


title: NOA_3_3_6

description: Sample 177


title: Liver tissue, CD163KO, Western diet, rep H

description: Library name: D408

value: Liver


title: NOA_3_3_5

description: Sample 176


title: SA00707_SMM_469


title: CRISPR-MA4, CD133neg, rep3

city: Oxford

first: Joe

middle: Wilson

last: Cross

address: Wellington Square

country: United Kingdom

institute: University of Oxford

data_processing:
Data quality was assessed with fastqc (v0.11.9), quality filtered and trimmed using TrimGalore (v0.6.10), aligned to the hg38 reference genome with STAR (v2.7.11a) and transcript reads counted with featureCounts (v2.0.6).
Assembly: hg38
Supplementary files format and content: Counts tables generated using featureCounts (subread).

molecule: polyA RNA

source_name: FL CD34+

extract_protocol:
Total RNA was extracted using a RNAEasy Micro Kit (Qiagen)
PolyA selection was performed using a NEBNext Poly(A) mRNA Magnetic Isolation Module. Library generation was performed with a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

value: FL CD34+

value: Blast

value: FACS CD133-


title: CRISPR-MA4, CD133pos, rep3

value: FACS CD133+


title: Liver tissue, CD163KO, Western diet, rep G

description: Library name: D407

value: Western diet, 8 weeks


title: Liver tissue, CD163KO, Western diet, rep F

description: Library name: D406


title: SA00708_MM_469


title: CRISPR-MA4, CD133pos, rep2


title: Liver tissue, CD163KO, Western diet, rep D

description: Library name: D404


title: Liver tissue, CD163KO, Western diet, rep E

description: Library name: D405


title: NOA_3_3_4

description: Sample 175


title: CRISPR-MA4, CD133pos, rep1


title: Liver tissue, CD163KO, Western diet, rep J

description: Library name: D410


title: IMR90-Control rep 1

value: Lung

value: Fibroblast


title: SA00654_HV_429

value: healthy volunteer (HV)


title: NOA_3_3_1

description: Sample 172

value: male

value: nonobstructive azoospermia (NOA)


title: NOA_3_3_3

description: Sample 174


title: NOA_3_2_6

description: Sample 171


title: SA00653_MM_429

value: Bone Marrow

value: BM aspirate mononuclear cells


title: Liver tissue, CD163KO, Western diet, rep C

description: Library name: D403


title: SA00652_SMM_429

value: smoldering MM (SMM)


title: Liver tissue, CD163WT, chow diet, rep A

description: Library name: D400

value: Chow diet, 8 weeks


title: P+5 endometrium tissue in RIF patient114

city: GuangZhou

first: Yameng

last: Xu

address: 6 Chenggui Road, East District

institute: Boai Hospital of Zhongshan Affiliated to Southern Medical University

data_processing:
The raw data were filtered to exclude low-quality reads.
The reads were alternative alignment with RNASeQC.
Qualified reads were mapped to the human reference genome (GRCh37) by using STAR.
Calculate the count of each gene.
Estimate the RNA expression level by FPKM.
Assembly: Ensembl primary assembly, version GRCh37
Supplementary files format and content: Tab-delimited text files include raw counts for each Sample.
Supplementary files format and content: Comma-separated text file includes FPKM values for each Sample.

source_name: endometrium

growth_protocol: The tip of the endometrial sampler was placed into the uterine fundus, and 5–10 mm3 of endometrial tissues were aspirated into the sampler.

extract_protocol:
Total RNA extraction was performed using the RNeasy Micro Kit (74004; Qiagen, Germantown, MD, USA) and followed by quantification with a Qubit HS RNA Kit.
RNA reverse transcription was conducted using the MALBAC® Platinum Single Cell RNA Amplification Kit. Library construction was accomplished using a gene sequencing and library preparation kit (XY045; Yikon Genomics, Suzhou, Jiangsu, China).

treatment_protocol: The collected endometrial tissues were immediately placed into 1.5 mL RNA-later buffer for RNA stabilization, sealed, and cryopreserved at -20 °C.

value: endometrium

value: repeated implantation failure

tag: group

value: rsERT

tag: receptive/non-receptive

value: non-receptive


title: CRISPR-MA4, CD133neg, rep1

value: FL CD34+

value: Blast


title: NOA_3_3_7

description: Sample 178

value: testis


title: Liver tissue, CD163KO, Western diet, rep B

description: Library name: D402

value: Liver

value: Western diet, 8 weeks


title: SA00651_MGUS_429

value: monoclonal gammopathy of unknown significance (MGUS)

value: mRNA and ADT


title: Liver tissue, CD163KO, chow diet, rep C

description: Library name: D399


title: Liver tissue, CD163KO, chow diet, rep B

description: Library name: D398


title: NOA_3_2_4

description: Sample 169

value: male


title: P+5 endometrium tissue in RIF patient112


title: P+5 endometrium tissue in RIF patient115


title: SA00650_MM_428

value: active MM


title: NOA_3_2_5

description: Sample 170

value: nonobstructive azoospermia (NOA)


title: SA00646_SMM_427

value: Bone Marrow

value: BM aspirate mononuclear cells


title: Liver tissue, CD163KO, Western diet, rep A

description: Library name: D401


title: SA00649_SMM_428

value: smoldering MM (SMM)


title: NOA_3_2_2

description: Sample 167


title: P+5 endometrium tissue in RIF patient111

value: endometrium


title: CRISPR-MA4, CD133neg, rep2

value: FACS CD133-


title: SA00647_HV_428

value: healthy volunteer (HV)


title: SA00645_MGUS_427


title: NOA_3_2_3

description: Sample 168


title: NOA_3_3_2

description: Sample 173


title: P+5 endometrium tissue in RIF patient113

value: repeated implantation failure

value: rsERT

value: non-receptive


title: P0 Cochlea CutRun CTCF replicate 4

city: Omaha

first: Litao

last: Tao

state: NE

address: 2500 California Plaza

department: Biomedical Sciences

institute: Creighton University

description: Library name: P0_Cochlea_CutRun_CTCF_rep4

data_processing:
Micro-C paired-end reads were processed following the Micro-C analysis tutorial provided by Dovetail Genomics with minor adaptations (https://github.com/dovetail-genomics/Micro-C). Paired-end reads were aligned to the mm10 reference genome using BWA-MEM. Aligned reads were processed using pairtools to parse, sort, merge, deduplicate, and classify ligation products. PCR duplicates and self-ligation artifacts were removed, and high-confidence chimeric read pairs were retained. Filtered reads were converted into contact pairs (.pairs), and contact matrices were generated using Juicer Tools (.hic format) and HiCExplorer (.cool format) at multiple resolutions. For ATACseq and Cut&Run, data were processed using Encode ATACseq and ChIPseq pipelines.
Statistically significant chromatin interactions were identified using Fit-Hi-C (Kaul et al., 2020) at 10 kb resolution by computing contact frequencies and p-values from genome-wide interaction matrices.
Chromatin loops were detected with the Mustache algorithm (Roayaei Ardakany et al., 2020) on .hic files to capture enhancer-promoter and domain-level interactions.
Assembly: mm10
Supplementary files format and content: file with genome-wide contact matrices in hic track format (.hic)
Supplementary files format and content: one loop annotation file in tsv format generated by Mustache
Supplementary files format and content: bigwig files for ATACseq and Cut&Run samples
Library strategy: CUT&Run

source_name: cochlea

extract_protocol:
For Micro-C, cochleae were dissected from P0 mice, and approximately 6 × 10⁵ cells were harvested and crosslinked at room temperature using disuccinimidyl glutarate (DSG), followed by formaldehyde, according to the manufacturer’s protocol (Dovetail Micro-C Kit, Cantata Bio, Scotts Valley, CA, USA). Cells were then permeabilized and digested with micrococcal nuclease to generate mononucleosome-sized fragments, and DNA was purified following reverse crosslinking. For ATACseq and Cut&Run, ~10,000 cells from dissociated P0/1 cochleae were used for each biological replicates, and published ATACseq and Cut&RUN protocols were used to extract DNA fragments.
Micro-C libraries were constructed per manufacture instructions. ATACseq libraries were made using home-made Tn5 with the original ATACseq protocol. Cut&Run libraries were made using Takara DNA library construction kits.

value: cochlea


title: SA00634_MGUS_420


title: P+5 endometrium tissue in RIF patient110


title: SA00644_HV_427


title: Liver tissue, CD163KO, chow diet, rep A

description: Library name: D397

value: Liver

value: Chow diet, 8 weeks


title: P+5 endometrium tissue in RIF patient109


title: NOA_3_1_7

description: Sample 164

value: testis


title: P0 Cochlea CutRun CTCF replicate 2

description: Library name: P0_Cochlea_CutRun_CTCF_rep2


title: P+5 endometrium tissue in RIF patient108


title: SA00633_HV_420

value: mRNA and ADT


title: P+5 endometrium tissue in RIF patient107


title: SA00632_MM_420


title: P0 Cochlea CutRun CTCF replicate 3

description: Library name: P0_Cochlea_CutRun_CTCF_rep3


title: NOA_3_1_6

description: Sample 163

value: male


title: P0 Cochlea CutRun CTCF replicate 1

description: Library name: P0_Cochlea_CutRun_CTCF_rep1


title: NOA_3_1_5

description: Sample 162


title: P0 Cochlea CutRun H3K27ac replicate 3

description: Library name: P0_Cochlea_CutRun_H3K27ac_rep3


title: P+5 endometrium tissue in RIF patient106


title: P+5 endometrium tissue in RIF patient105


title: SA00630_MGUS_419

value: monoclonal gammopathy of unknown significance (MGUS)


title: SA00631_SMM_420


title: P0 Cochlea CutRun H3K27ac replicate 2

description: Library name: P0_Cochlea_CutRun_H3K27ac_rep2


title: NOA_3_1_4

description: Sample 161

value: nonobstructive azoospermia (NOA)


title: P0 Cochlea CutRun H3K27ac replicate 1

description: Library name: P0_Cochlea_CutRun_H3K27ac_rep1


title: SA00629_HV_419

value: Bone Marrow


title: NOA_3_1_3

description: Sample 160


title: P+5 endometrium tissue in RIF patient103


title: P0 Cochlea CutRun H3K4me1 replicate 3

description: Library name: P0_Cochlea_CutRun_H3K4me1_rep3


title: NOA_3_1_8

description: Sample 165


title: NOA_3_2_1

description: Sample 166


title: SA00628_MM_419

value: active MM

value: BM aspirate mononuclear cells


title: P0 Cochlea CutRun H3K4me1 replicate 2

description: Library name: P0_Cochlea_CutRun_H3K4me1_rep2


title: NOA_2_9_8

description: Sample 158


title: P+5 endometrium tissue in RIF patient102

value: endometrium


title: NOA_3_1_1

description: Sample 159


title: SA00627_SMM_419

value: smoldering MM (SMM)


title: P0 Cochlea CutRun H3K4me1 replicate 1

description: Library name: P0_Cochlea_CutRun_H3K4me1_rep1


title: NOA_2_9_7

description: Sample 157


title: SA00626_HV_418

value: healthy volunteer (HV)


title: SA00625_MM_418


title: NOA_2_9_6

description: Sample 156


title: P+5 endometrium tissue in RIF patient104

value: repeated implantation failure

value: receptive


title: P+5 endometrium tissue in RIF patient100

value: rsERT

value: non-receptive


title: SA00624_SMM_418


title: P+5 endometrium tissue in RIF patient99


title: P0 Cochlea replicate 4

description: Library name: P0_Cochlea_Micro_C_rep4

data_processing:
Micro-C paired-end reads were processed following the Micro-C analysis tutorial provided by Dovetail Genomics with minor adaptations (https://github.com/dovetail-genomics/Micro-C). Paired-end reads were aligned to the mm10 reference genome using BWA-MEM. Aligned reads were processed using pairtools to parse, sort, merge, deduplicate, and classify ligation products. PCR duplicates and self-ligation artifacts were removed, and high-confidence chimeric read pairs were retained. Filtered reads were converted into contact pairs (.pairs), and contact matrices were generated using Juicer Tools (.hic format) and HiCExplorer (.cool format) at multiple resolutions. For ATACseq and Cut&Run, data were processed using Encode ATACseq and ChIPseq pipelines.
Statistically significant chromatin interactions were identified using Fit-Hi-C (Kaul et al., 2020) at 10 kb resolution by computing contact frequencies and p-values from genome-wide interaction matrices.
Chromatin loops were detected with the Mustache algorithm (Roayaei Ardakany et al., 2020) on .hic files to capture enhancer-promoter and domain-level interactions.
Assembly: mm10
Supplementary files format and content: file with genome-wide contact matrices in hic track format (.hic)
Supplementary files format and content: one loop annotation file in tsv format generated by Mustache
Supplementary files format and content: bigwig files for ATACseq and Cut&Run samples

value: cochlea


title: SA00623_MGUS_418


title: NOA_2_9_4

description: Sample 154


title: P+5 endometrium tissue in RIF patient98


title: P0 Cochlea replicate 3

description: Library name: P0_Cochlea_Micro_C_rep3


title: SA00622_MM_417


title: P+5 endometrium tissue in RIF patient96


title: NOA_2_9_3

description: Sample 153


title: NOA_2_9_2

description: Sample 152


title: P0 Cochlea replicate 2

description: Library name: P0_Cochlea_Micro_C_rep2


title: SA00621_SMM_417


title: P+5 endometrium tissue in RIF patient101


title: P0 Cochlea replicate 1

description: Library name: P0_Cochlea_Micro_C_rep1


title: NOA_2_9_1

description: Sample 151


title: SA00620_MGUS_417


title: P0 Cochlea umiATAC replicate 2

description: Library name: P0_Cochlea_umiATAC_1K_rep2


title: P+5 endometrium tissue in RIF patient95


title: Lung, Repetitive bleomycin followed by treatment with engineered MSCs

city: Ann Arbor

first: Jae-Won

last: Shin

address: 1011 N University Ave Room K1030, Ann Arbor, MI 48109

institute: University of Michigan

description:
Library name: Sample 3
10X genomics
annotated_integrated_data.h5ad

data_processing:
Single-cell data were processed using 10x CellRanger v7.1.0 with the mm10-2020-A reference and default parameters. Doublets were filtered out from each sample using SCVI-tools v0.20.3[86] and Solo[87]. Quality control was conducted with scanpy v1.9.3[88], removing cells that had fewer than 200 genes, an n_genes_by_count value above the 99th percentile of cells, or more than 15% mitochondrial reads. Raw counts were normalized using scanpy's default normalization function (scanpy.pp.normalize_total()) followed by a shifted log transformation (scanpy.pp.log1p()). Data integration was performed using scanorama v1.7.3[89], focusing on the top 2000 most variable genes. The scanorama embedding was used to construct the neighborhood graph for Leiden clustering and UMAP dimensionality reduction, aimed at classifying CD45+ immune cells. Immune cell clusters were annotated at a resolution of 0.8 using SCVI-SCANVI by transferring labels from the Tabula Muris Senis dataset[90], with further validation through known cell-type marker genes. Macrophage subpopulations were further refined at a resolution of 0.5, validated using marker genes and through label projection with SingleR[59]. Imputed counts were generated using SCVI for the expression analysis of selected genes.
Assembly: Mouse mm10
Supplementary files format and content: Tab-seperated values and matrix files

extract_protocol:
Mouse lungs were harvested after perfusion through the right ventricle with 5 mL of PBS until they turned completely white. The lungs were then minced into small pieces (<1 mm³) in 200 µL of Enzyme Mix from the Tumor Dissociation Kit (#1119; Miltenyi). The enzyme mix consisted of 1119 µL DMEM combined with the following enzymes: 50 µL Enzyme H, 25 µL Enzyme R, and 6.25 µL Enzyme A. This mixture was prepared on a tissue culture plate placed at a 45° angle. The minced tissue was transferred using wide-bore tips to a 2 mL LoBind tube and digested at 37°C for 25 minutes with continuous rotation. Gentle pipetting every 5 minutes using a 1000-µL pipette tip ensured even digestion. After digestion, the suspension was vigorously pipetted for 2 minutes to ensure complete dissociation. The resulting cell suspension was filtered through a pre-wetted 40-µm strainer placed in a 50 mL tube, followed by a wash with 12 mL of DMEM to maximize cell recovery. The strainer was rinsed with 1 mL of PBS to collect any remaining cells. The cell suspension was then centrifuged at 300×g for 5 minutes at room temperature. The pellet was resuspended in PBS containing 0.04% BSA (in PBS, Ca2+- and Mg2+-free; Sigma) for washing and further processing. A total of three washes were performed. The final pellet was resuspended in cell resuspension buffer at a concentration of 1000 cells/μL, ensuring >90% viability for subsequent library preparation.
Cells were resuspended and diluted in DMEM supplemented with 10% FBS, followed by filtration through a 40-micron Flowmi Cell Strainer. The quality of the single-cell suspension was assessed by Trypan blue staining and inspection under a hemocytometer to evaluate cell viability. Samples exhibiting greater than 90% viability were used at a concentration of 1200 cells/µl. Gel bead-in-emulsions (GEMs) were generated by encapsulating the cells using the Chromium X platform at the Single-Cell Sequencing Core at the University of Illinois at Chicago. The 3’ Gene Expression Next GEM Assay v3.1 with dual indexing was performed following the protocol provided by 10x Genomics (CG000315). Library quality was assessed using the TapeStation High Sensitivity D5000 ScreenTape. The libraries were pooled and sequenced across three lanes of the Illumina NovaSeq 6000 SP flowcell (28 x 150) at the DNA Services facility at the University of Illinois at Urbana-Champaign.

value: Lung

value: Repetitive bleomycin + engineered MSCs


title: P+5 endometrium tissue in RIF patient94


title: NOA_2_8_7

description: Sample 150

value: testis


title: NOA_2_9_5

description: Sample 155

value: male


title: P+5 endometrium tissue in RIF patient93


title: P0 Cochlea umiATAC replicate 1

description: Library name: P0_Cochlea_umiATAC_1K_rep1


title: SA00619_HV_417

value: mRNA and ADT


title: NOA_2_8_6

description: Sample 149

value: nonobstructive azoospermia (NOA)


title: Lung, Repetitive bleomycin

description:
Library name: Sample 2
10X genomics
annotated_integrated_data.h5ad

value: Repetitive bleomycin


title: SA00612_HV_410

value: Bone Marrow


title: NOA_2_8_3

description: Sample 148


title: Lung, No bleomycin

description:
Library name: Sample 1
10X genomics
annotated_integrated_data.h5ad

value: PBS


title: P+5 endometrium tissue in RIF patient92

value: endometrium


title: P+5 endometrium tissue in RIF patient91


title: SA00611_MM_410

value: active MM

value: BM aspirate mononuclear cells


title: P+5 endometrium tissue in RIF patient97

value: repeated implantation failure


title: E16 miR-9-2 Wild-type male 2 cerebral cortex

city: Seattle

first: Timothy

last: Cherry

state: WA

department: Developmental Biology and Regenerative Medicine

institute: Seattle Children's Research Institute

description:
Library name: E16WTM2
10X Genomics

data_processing:
Sequencing reads were aligned to GRCm39/mm39 and UMI counts per gene and cell were quantified using Cellranger 7.2.0.  Cellbender 0.3.0 was used to remove background UMI counts.  Seurat v5 was used for subsequent analyses, including quality control, filtering, normalization, ordination, and integration.
Assembly: GRCm39/mm39
Supplementary files format and content: raw_feature_bc_matrix.h5 output files from cellranger

source_name: cerebral cortex

extract_protocol:
For nuclei isolation, samples were processed via a modified 10X Genomics Nuclei Isolation from Mouse Brain Tissue protocol (CG000212 Rev. B). 500 µl of cold 0.1X Lysis Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.01% Tween-20, 0.01% IGEPAL CA-360, 1% BSA, 1 U/µl RNase Inhibitor (Roche #03335402001)) was added to each sample-containing tube and triturated 15-20 times. The suspensions were further homogenized using dounce homogenizers by applying 10 dounces each with an A then B pestle. Following transfer of each sample to a new tube, the samples were incubated on ice for 5 minutes. Sample suspensions were pipette-mixed 10 times, then incubated on ice for 10 minutes. 500 µl of cold Wash Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20, 1 U/µl RNase Inhibitor) was then added, and samples were pipette-mixed 5 times and then passed through a 40 µm Flowmi Cell Strainer into a fresh tube. Dissociated sample nuclei were then washed 2 times by centrifugation pelleting at 500 rcf in a 4ºC swinging-bucket centrifuge and resuspension in 750 µl cold Wash Buffer. Sample nuclei concentrations were determined using propidium iodide and a Countess II FL Automated Cell Counter. Nuclei were then centrifuged at 500 rcf for 5 minutes at 4ºC. The supernatant was discarded and the nuclei were resuspended in cold Nuclei Buffer (1X 10X Genomics Nuclei Buffer) to achieve a nuclei concentration range of 700-1200 nuclei/ µl, which is recommended for targeting 10,000 cells in the 10x Genomics snRNA-seq protocol.
Sample libraries were generated following the 10X Genomics Chromium Next GEM Single Cell 3’ v3.1 snRNA-seq protocol and subsequently sequenced per 10X Genomics’ recommended cycles and sequencing depth using either a NovaSeq SP or NovaSeq S1 100-cycle flow cell, according to the number of samples submitted for sequencing (SP for 4 or S1 for 5-9 samples).

value: cerebral cortex

value: embryonic day 16

tag: Sex

value: miR-9-2 wild-type

tag: batch


title: SA00610_SMM_410

value: smoldering MM (SMM)


title: NOA_2_8_1

description: Sample 147


title: P+5 endometrium tissue in RIF patient90

value: rsERT

value: non-receptive


title: NOA_2_7_8

description: Sample 146

value: testis


title: SA00608_MM_409


title: E16 miR-9-2 Wild-type male 1 cerebral cortex

description:
Library name: E16WTM1
10X Genomics

value: male


title: P+5 endometrium tissue in RIF patient85

value: receptive


title: NOA_2_7_7

description: Sample 145

value: nonobstructive azoospermia (NOA)


title: E16 miR-9-2 Wild-type female 2 cerebral cortex

description:
Library name: E16WTF2
10X Genomics

value: female


title: SA00607_SMM_409

value: Bone Marrow

value: mRNA and ADT


title: E16 miR-9-2 Knock-out male 2 cerebral cortex

description:
Library name: E16KOM2
10X Genomics

value: miR-9-2 homozygous knock-out


title: NOA_2_7_6

description: Sample 144


title: P+5 endometrium tissue in RIF patient84

value: endometrium


title: NOA_2_7_3

description: Sample 142


title: E16 miR-9-2 Knock-out male 1 cerebral cortex

description:
Library name: E16KOM1
10X Genomics


title: NOA_2_7_5

description: Sample 143


title: SA00606_MGUS_409

value: monoclonal gammopathy of unknown significance (MGUS)

value: BM aspirate mononuclear cells


title: P+5 endometrium tissue in RIF patient82

value: repeated implantation failure


title: E16 miR-9-2 Knock-out female 2 cerebral cortex

description:
Library name: E16KOF2
10X Genomics

value: cerebral cortex

value: embryonic day 16


title: P+5 endometrium tissue in RIF patient80


title: P+5 endometrium tissue in RIF patient89


title: E12 miR-9-2 Wild-type male 2 cerebral cortex

description:
Library name: E12WTM2
10X Genomics

value: embryonic day 12

value: miR-9-2 wild-type


title: SA00603_MGUS_408


title: NOA_2_6_5

description: Sample 139


title: E16 miR-9-2 Knock-out female 1 cerebral cortex

description:
Library name: E16KOF1
10X Genomics


title: P+5 endometrium tissue in RIF patient81

value: rsERT

value: non-receptive


title: SA00604_SMM_408

value: smoldering MM (SMM)


title: NOA_2_7_2

description: Sample 141

value: male

value: testis


title: NOA_2_6_8

description: Sample 140

value: nonobstructive azoospermia (NOA)


title: SA00602_HV_408

value: healthy volunteer (HV)

value: Bone Marrow


title: E12 miR-9-2 Wild-type male 1 cerebral cortex

description:
Library name: E12WTM1
10X Genomics


title: SA00609_MGUS_410

value: mRNA and ADT


title: NOA_2_6_4

description: Sample 138


title: P+5 endometrium tissue in RIF patient79

value: endometrium


title: P+5 endometrium tissue in RIF patient78


title: SA00601_MM_408

value: active MM


title: P+5 endometrium tissue in RIF patient77


title: SA00605_HV_409

value: BM aspirate mononuclear cells


title: P+5 endometrium tissue in RIF patient76

value: repeated implantation failure


title: E12 miR-9-2 Wild-type female 2 cerebral cortex

description:
Library name: E12WTF2
10X Genomics

value: cerebral cortex

value: female


title: E12 miR-9-2 Wild-type female 1 cerebral cortex

description:
Library name: E12WTF1
10X Genomics

value: embryonic day 12


title: SA00600_MGUS_407

value: monoclonal gammopathy of unknown significance (MGUS)


title: NOA_2_6_3

description: Sample 137


title: NOA_2_6_2

description: Sample 136


title: E12 miR-9-2 Knock-out male 2 cerebral cortex

description:
Library name: E12KOM2
10X Genomics

value: miR-9-2 homozygous knock-out


title: NOA_2_5_8

description: Sample 134


title: P+5 endometrium tissue in RIF patient74

value: rsERT

value: receptive


title: SA00597_SMM_407

value: smoldering MM (SMM)


title: SA00599_HV_407


title: P+5 endometrium tissue in RIF patient75

value: non-receptive


title: NOA_2_6_1

description: Sample 135

value: male

value: nonobstructive azoospermia (NOA)

value: testis


title: E12 miR-9-2 Knock-out female 2 cerebral cortex

description:
Library name: E12KOF2
10X Genomics


title: P+5 endometrium tissue in RIF patient73


title: E12 miR-9-2 Knock-out female 1 cerebral cortex

description:
Library name: E12KOF1
10X Genomics


title: E12 miR-9-2 Knock-out male 1 cerebral cortex

description:
Library name: E12KOM1
10X Genomics


title: NOA_2_5_7

description: Sample 133


title: SA00582_HV_387

value: healthy volunteer (HV)

value: Bone Marrow

value: mRNA and ADT


title: SA00598_MM_407

value: active MM

value: BM aspirate mononuclear cells


title: mice, hippocampi, oxygen, 6h, rep3

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description:
Library name: Old_C3H
10x Genomics

data_processing:
We applied fastp with default parameter filtering the adaptor sequence and removed the low quality reads to achieve the clean data. Then the feature-barcode matrices were obtained by aligning reads to the rhesus mouse genome (mm10 Ensemble:version 100) using CellRanger v7.1.0 with intron including mode for the data characteristics of snRNA-Seq and utilized the cellranger aggr function with mapped reads.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated  values files and matrix files

source_name: hippocampi

extract_protocol:
The samples were surgically removed and the frozen tissue was used to intact nucleus isolation. Briefly, the frozen tissue was homogenized in NLB buffer, which contains 250 mM Sucrose, 10 mM Tris–HCl, 3 mM MgAc2, 0.1% Triton X-100 (SigmaAldrich, USA), 0.1 mM EDTA, and 0.2 U/μL RNase Inhibitor (Takara, Japan). Various concentrations of sucrose were used to purify the nucleus.
The snRNA-Seq libraries were generated using the 10×Genomics Chromium Controller Instrument and Chromium Single Cell 3' V3.1 Reagent Kits (10× Genomics, Pleasanton, CA). Briefly, nuclei were concentrated to approximately 1000 nuclei/μL and loaded into each channel to generate single-cell gel bead-in-emulsions (GEMs). After the RT step, GEMs were broken and barcoded-cDNA was purified and amplified. The amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors, and index-PCR amplified. The final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific), and the size distribution of the libraries were determined using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent). All libraries were sequenced by the Illumina sequencer (Illumina, San Diego, CA) on a 150 bp paired-end run.

treatment_protocol: Aged mice were randomly divided into the sevoflurane (SEV) or control (Ctrl) groups. In the SEV group, aged mice were exposed to 2% sevoflurane and 60% O2 (at a flow rate of 1L/min) for 6 h,while the mice in the Ctrl group were exposed to 60% O2 alone (at a flow rate of 1 L/min) for the same duration. As described in our previous study, we monitored the blood levels of electrolytes, including sodium, potassium, and chloride to ensure they remained within the normal range [10]. The monitored heart rate and saturation of pulse oxygen (SpO2) were consistent with normal physiological parameters. Importantly, no hypoxia or carbon dioxide accumulation was observed throughout the monitoring period. During general anesthesia, spontaneous respiration was maintained in the mice, with strict monitoring, to ensure that their rectal temperature remained within the range of 37°C ± 0.5°C.

value: hippocampi

value: 18-20 months old

value: oxygen


title: P+5 endometrium tissue in RIF patient71

value: endometrium

value: repeated implantation failure


title: P+5 endometrium tissue in RIF patient72

value: rsERT


title: NOA_2_5_5

description: Sample 132


title: SA00581_MM_387


title: mice, hippocampi, oxygen, 6h, rep2

description:
Library name: Old_C2H
10x Genomics


title: P+5 endometrium tissue in RIF patient70

value: receptive


title: NOA_2_5_4

description: Sample 131


title: SA00579_MGUS_387

value: monoclonal gammopathy of unknown significance (MGUS)


title: P+5 endometrium tissue in RIF patient69

value: non-receptive


title: mice, hippocampi, oxygen, 6h, rep1

description:
Library name: Old_C1H
10x Genomics

value: male


title: NOA_2_5_3

description: Sample 130

value: nonobstructive azoospermia (NOA)


title: mice, hippocampi, sevoflurane, 6h, rep2

description:
Library name: Old_S2H
10x Genomics

value: sevoflurane


title: NOA_2_4_8

description: Sample 128

value: testis


title: P+5 endometrium tissue in RIF patient68


title: NOA_2_4_7

description: Sample 127


title: P+5 endometrium tissue in RIF patient64


title: NOA_2_5_2

description: Sample 129


title: mESC cells, AC106872.1-KI-D11, Hi-C

city: Beijing

first: Liu

last: He

address: No. 5, Dongdan Sanjo, Dongcheng District

institute: Peking Union Medical College

description: Library name: sample5

data_processing:
Hi-C reads were aligned to mouse genome version mm10 and knock in sequence simultaneously with default settings of HiC-Pro (v3.1.0), and then uniquely mapped reads were used to build contact pairs, and then valid pairs were used to build contact matrix in 10kb resolution. Hic-Pro (v3.1.0) raw matrix was then converted matrices into .h5 format files with hicConvertFormat subcommand in HiCExplorer (v3.4.3). Different samples’s matrix was then normalized by hicNormalize subcommand in HiCExplorer (v3.4.3) with parameters ‘--normalize smallest’ and then corrected with ‘--filterThreshold -3 5 --iterNum 20’ of hicCorrectMatrix subcommand. Then the matrix was then converted into .hic format for Visualization using FanC (v0.9.24). Insulation scores and TAD boundary strengths were calculated by FanC (v0.9.24) with parameter -w 1mb.
Assembly: mm10
Supplementary files format and content: .hic file include contact matrix of each sample

extract_protocol:
1) Lyse cells by grinding and lysing in an ice bath of lysate to obtain nuclei samples; 2) Restriction enzyme (DpnII) digestion was followed to break the original genomic DNA structure to form a molecular group in units of "protein-DNA cross-linking complex"; 3) Cleave the cleavage site using dNTP-labeled repair enzymes with biotin labeling; 4) Using DNA ligase treatment, the flat ends of DNA molecules on the same "protein-DNA crosslinking complex" were connected to each other, so that the DNA fragment reconstructs the structure based on spatial location to form Hi-C molecules. The junction of the reconstituted molecule would be marked with biotin; 5) Protease 65°C high temperature treatment, unlink protein cross-linking and release DNA, and then use phenolic chloroform extraction to obtain Hi-C characteristic DNA molecules; 6) Remove unsuccessfully ligated DNA fragment ends using T4 DNA polymerase exonuclease activity to eliminate residual biotin labeling. 7) Fragmented DNA molecules were interrupted using ultrasound, followed by terminal repair, A-tail ligation, streptavidin-activated magnetic beads to retrieve biotin marker molecules, sequencing linker ligation, PCR enrichment for library preparation, and finally recovered the fragments of interest using AMPure XP beads or agarose gel electrophoresis to obtain the final Hi-C library.
Hi-C

tag: strain

value: mouse embryonic stem cells

value: AC106872.1 knock in


title: P+5 endometrium tissue in RIF patient67


title: NOA_2_4_6

description: Sample 126

tag: gender


title: SA00577_SMM_386

value: smoldering MM (SMM)

value: Bone Marrow

value: mRNA and ADT


title: P+5 endometrium tissue in RIF patient63


title: mESC cells, AC106872.1-KI-B9, Hi-C

description: Library name: sample4


title: P+5 endometrium tissue in RIF patient62


title: NOA_2_4_5

description: Sample 125

tag: age


title: SA00580_SMM_387

value: BM aspirate mononuclear cells


title: SA00572_HV_385

value: healthy volunteer (HV)


title: mice, hippocampi, sevoflurane, 6h, rep3

description:
Library name: Old_S3H
10x Genomics

value: hippocampi

value: 18-20 months old

value: female


title: NOA_2_4_3

description: Sample 123

tag: condition


title: SA00573_MGUS_385


title: SA00571_MM_385

value: active MM


title: mESC cells, KRT18P67-KI-B5, Hi-C

description: Library name: sample3

value: KRT18P67 knock in


title: mice, hippocampi, sevoflurane, 6h, rep1

description:
Library name: Old_S1H
10x Genomics


title: SA00576_MGUS_386

value: monoclonal gammopathy of unknown significance (MGUS)


title: NOA_2_4_4

description: Sample 124

value: male

tag: testis


title: SA00578_MM_386

tag: sample id


title: P+5 endometrium tissue in RIF patient61

value: endometrium

value: repeated implantation failure

value: rsERT

value: non-receptive


title: P+5 endometrium tissue in RIF patient60

value: receptive


title: SA00575_HV_386

tag: cohort


title: mESC cells, WT, Hi-C

description: Library name: sample1

value: mouse embryonic stem cells

value: WT


title: SA00569_HV_384

tag: tissue

value: Bone Marrow

value: mRNA and ADT


title: CM-3

city: Shanghai

first: Yazhuo

last: Zhang

state: Shanghai

address: 320 Yueyang Road, Xuhui District

department: CAS Center for Excellence in Molecular Cell Science

institute: Chinese Academy of Sciences

description:
Library name: Smaple 6
Column name in all.fpkm_anno.xls: CM-3

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Alignment: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome (GRCm39.107 Mus musculus reference genome) via software Hisat2 (v2.0.1).
Expression analysis: In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis: Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
Assembly: GRCm39.107 Mus musculus reference genome
Supplementary files format and content: Excel files inculde FPKM values and raw counts for each sample

source_name: bone

growth_protocol: BMSCs from mice were cultured in α-minimum essential medium (α-MEM) supplemented with 10% FBS and 1% penicillin/streptomycin solution. All cell lines and primary cells were cultured at 37°C in humidified incubators containing an atmosphere of 5% CO2.

extract_protocol:
Differentiated osteoblasts were harvested into TRIzol LS buffer and RNA was extracted using chloroform.
The RNA library construction utilized RNA Reagent Kit (P/N CLS960010).The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina NovaSeg6000 platform for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

treatment_protocol: For osteoblast differentiation, the BMSCs isolated from mice and grown in α-MEM supplemented with 10% FBS and 1% penicillin/streptomycin solution were digested and seeded with 2x104 cells per well in 96-well plate and also cultured in α-MEM supplemented with 10% FBS and 1% penicillin/streptomycin solution. The next day, BMSCs culture medium was changed into α-MEM containing 10% FBS, 1% penicillin/streptomycin, 50 μg/ml L-ascorbic acid, and 1.08 mg/mL β-Glycerophosphate disodium salt hydrate with Hepa 1-6-derived-CM, compared with control medium. The culture medium changed every 2 days and differentiated for 7 days

value: bone

value: BMSCs

tag: cell type

value: mesenchymal stem cells

value: osteoblast differentiation


title: NOA_2_4_1

description: Sample 122

value: nonobstructive azoospermia (NOA)

value: testis


title: P+5 endometrium tissue in RIF patient59


title: NOA_2_3_7

description: Sample 120


title: CM-2

description:
Library name: Smaple 5
Column name in all.fpkm_anno.xls: CM-2


title: NOA_2_3_5

description: Sample 119


title: SA00567_SMM_384

description:
5' barcoded RNA + Antibody-derived oligonucleotide library
The file name is constructed based on SampleID_Cohort_ExperimentID

value: smoldering MM (SMM)

value: BM aspirate mononuclear cells

tag: library type


title: NOA_2_3_8

description: Sample 121

value: male


title: SA00574_SMM_385


title: CM-1

description:
Library name: Smaple 4
Column name in all.fpkm_anno.xls: CM-1

tag: cell line


title: Control-3

description:
Library name: Smaple 3
Column name in all.fpkm_anno.xls: Control-3

tag: treatment


title: NOA_2_3_4

description: Sample 118


title: Control-2

description:
Library name: Smaple 2
Column name in all.fpkm_anno.xls: Control-2

tag: genotype


title: SA00548_MM_374

value: active MM


title: SA00547_SMM_374


title: P+5 endometrium tissue in RIF patient54

value: endometrium

value: repeated implantation failure

tag: group

value: rsERT


title: P+5 endometrium tissue in RIF patient58

tag: receptive/non-receptive

value: receptive


title: SA00568_MM_384


title: SA00546_MGUS_374

value: monoclonal gammopathy of unknown significance (MGUS)


title: P+5 endometrium tissue in RIF patient53

value: non-receptive


title: NOA_2_3_3

description: Sample 117


title: Control-1

description:
Library name: Sample 1
Column name in all.fpkm_anno.xls: Control-1

value: WT


title: NOA_2_2_7

description: Sample 114


title: Allograft, rep4

first: Jifu

last: Ge

address: Wujin Road

institute: Shanghai General Hospital

description: Library name: A4

data_processing:
Illumina adapter sequences were trimmed using Skewer (v0.2.2). And the quality checking was performed using FastQC (v0.11.5)
Then clean reads were mapped to human genome version mm10 using STAR (v2.5.3a)
StringTie (v1.3.1c) was used to generate gene expression data and differential gene expression
Differentially expression analysis between matched case and control samples were performed by the R package DESeq2 version 1.16.1 with the likelihood ratio test option
Gene ontology analysis was performed using TopGO (https://www.bioconductor.org/packages/release/bioc/html/topGO.html), pathway analysis was performed using the KEGG PATHWAY Database (https://www.genome.jp/kegg/pathway.html)
Assembly: mm10
Supplementary files format and content: csv files include raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: heart

extract_protocol:
RNA was extracted with theQuick-RNA™ Microprep Kit (TR150, ZYMO RESEARCH) according to the manufacturer’s instructions
cDNA synthesis and amplification were using by Single Cell Full Length mRNA-Amplification Kit (N712-03, Vazyme),cDNA libraries were prepared using the QuarPrep EZ DNA Library Kit 1.0 for Illumina (NL1002A, Dynegene)

value: heart

value: Type 2 Innate lymphoid cells

tag: time

value: 7 days


title: mESC cells, KRT18P67-KI-C4, Hi-C

description: Library name: sample2

value: mouse embryonic stem cells

value: KRT18P67 knock in


title: Allograft, rep3

description: Library name: A3


title: SA00545_MM_373

value: Bone Marrow

value: mRNA and ADT


title: P+5 endometrium tissue in RIF patient57


title: P+5 endometrium tissue in RIF patient51


title: NOA_2_2_6

description: Sample 113

value: nonobstructive azoospermia (NOA)

value: testis


title: Allograft, rep1

description: Library name: A1


title: P+5 endometrium tissue in RIF patient55


title: NOA_2_3_2

description: Sample 116

value: male


title: SA00543_HV_373

value: healthy volunteer (HV)

value: BM aspirate mononuclear cells


title: P+5 endometrium tissue in RIF patient52

value: endometrium

value: repeated implantation failure

value: rsERT


title: NOA_2_3_1

description: Sample 115


title: P+5 endometrium tissue in RIF patient49

value: non-receptive


title: NOA_2_2_5

description: Sample 112


title: P+5 endometrium tissue in RIF patient56

value: receptive


title: SA00544_MGUS_373

value: monoclonal gammopathy of unknown significance (MGUS)


title: SA00549_HV_374


title: NOA_2_2_4

description: Sample 111


title: Naïve heart, rep2

description: Library name: N2

value: heart

value: Type 2 Innate lymphoid cells


title: NOA_2_2_3

description: Sample 110


title: P+5 endometrium tissue in RIF patient48


title: SA00542_MM_373

value: active MM


title: SA00541_MM_354


title: Naïve heart, rep1

description: Library name: N1

value: 7 days


title: Allograft, rep2

description: Library name: A2


title: Naïve heart, rep3

description: Library name: N3


title: SA00540_SMM_354

value: smoldering MM (SMM)

value: Bone Marrow


title: P+5 endometrium tissue in RIF patient47


title: NOA_2_2_2

description: Sample 109

value: nonobstructive azoospermia (NOA)


title: P+5 endometrium tissue in RIF patient50


title: P+5 endometrium tissue in RIF patient46


title: NOA_2_12_8

description: Sample 108

value: testis


title: SC-HTO seq of mus musculus: adult female thymus_CD8

first: Wenhua

last: Liang

address: 227 South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

description:
Library name: Sample 8
10x Genomics

library_source: other

data_processing:
The Cell Ranger software (version 6.0.1) was used to process the single-cell expression data and align data to the GRCm38 reference genome, of which the corresponding vdj package was used for TCR v/d/j analysis.
Assembly: Mouse mm10/GRCm38
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger output files:filtered_contig_annotations.csv
Supplementary files format and content: CellRanger output files: feature_ref.csv

molecule: protein

source_name: Thymus

extract_protocol:
Thymocyte suspension from WT and CD3εI173A were stained with different TotalSeq™-C0304 and -C0306 anti-mouse Hashtag 4/6 Antibody hashtag reagents, then following stained with CD4, CD8 fluorescent antibodies and Live/Dead dye with recommended concentrations at 4℃ for 30 min. Then sorted CD4 SP (CD4+CD8-), CD8 SP (CD4-CD8+) and DP (CD4+CD8+) T cells by flow cytometry. The CD4 SP, CD8 SP and DP T cells were mixed to 3 samples for single-cell sequencing.
The Chromium Single-Cell 5’ v2 Reagent Kit (10X Genomics, Pleasanton, USA) was used as per the manufacturer’s instructions. T cells were resuspended in the master mix andloaded together with partitioning oil and gel beads into the chip to generate the gelbead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in everysingle GEM was retrotranscripted to cDNA, which contains an llumina R1 primersequence, Unigue Molecular ldentifier (UMl) and the 10x Barcode. The pooledbarcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR andthe apropiated sized fragments were selected with SPRlselect reagent forsubsequent library construction.

value: Thymus

value: T cell

tag: hto

value: TotalSeq™-C0304 anti-mouse Hashtag 4 Antibody (WT mice); TotalSeq™-C0306 anti-mouse Hashtag 6 Antibody (CD3εI173A mice)


title: SA00538_HV_354

value: healthy volunteer (HV)

value: BM aspirate mononuclear cells

value: mRNA and ADT


title: P+5 endometrium tissue in RIF patient44

value: endometrium

value: repeated implantation failure

value: rsERT

value: non-receptive


title: SA00536_MGUS_353

value: monoclonal gammopathy of unknown significance (MGUS)


title: SC-HTO seq of mus musculus: adult female thymus_DP

description:
Library name: Sample 9
10x Genomics


title: P+5 endometrium tissue in RIF patient45

value: receptive


title: SA00537_SMM_353


title: SC-HTO seq of mus musculus: adult female thymus_CD4

description:
Library name: Sample 7
10x Genomics


title: SA00539_MGUS_354


title: SA00535_HV_353


title: NOA_2_12_7

description: Sample 107

value: male


title: NOA_2_12_2

description: Sample 105


title: SC-TCR seq of mus musculus: adult female thymus_DP

description:
Library name: Sample 6
10x Genomics


title: P+5 endometrium tissue in RIF patient42


title: SC-TCR seq of mus musculus: adult female thymus_CD8

description:
Library name: Sample 5
10x Genomics


title: NOA_2_11_5

description: Sample 103


title: P+5 endometrium tissue in RIF patient43


title: SC-TCR seq of mus musculus: adult female thymus_CD4

description:
Library name: Sample 4
10x Genomics


title: NOA_2_11_7

description: Sample 104


title: SA00534_MM_353

value: active MM


title: P+5 endometrium tissue in RIF patient40


title: Sc-RNA seq of mus musculus: adult female thymus_DP

description:
Library name: Sample 3
10x Genomics


title: SA00488_HV_323

value: Bone Marrow


title: NOA_2_11_3

description: Sample 102

value: nonobstructive azoospermia (NOA)


title: P+5 endometrium tissue in RIF patient39


title: NOA_2_12_5

description: Sample 106

value: testis


title: Sc-RNA seq of mus musculus: adult female thymus_CD8

description:
Library name: Sample 2
10x Genomics

value: Thymus


title: P+5 endometrium tissue in RIF patient41


title: NOA_2_11_1

description: Sample 100


title: P+5 endometrium tissue in RIF patient38


title: NOA_2_11_2

description: Sample 101


title: P+5 endometrium tissue in RIF patient36


title: Sc-RNA seq of mus musculus: adult female thymus_CD4

description:
Library name: Sample 1
10x Genomics

value: T cell


title: P+5 endometrium tissue in RIF patient37


title: SA00485_HV_322


title: SA00486_SMM_323

value: smoldering MM (SMM)


title: SA00484_MM_322


title: Kupffer_2000

first: Runping

last: Liu

state: Beijing

address: 11 Beisanhuandonglu

institute: Beijing University of Chinese Medicine

description: Library name: Sample 18

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: liver

value: Kupffer-like cells (Kupffer)

value: BDL


title: NOA_2_10_6

description: Sample 98

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
For bisulfite-seq data, Trim Galore (v0.3.3) was used to remove the first 6 bases of random primer, adaptor sequences and low quality bases; for RNA-seq data, each single cell was separated by unique cell barcode, then template switch oligo (TSO), ployA tails, adaptors and low quality bases were removed.
For bisulfite-seq data, clean reads were first mapped to human reference genome hg19 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module; for RNA-seq data, clean reads were mapped to human genome hg19 with Tophat (v2.0.14), and then unique UMI counts were calculated by HTSeq.
WCG and GCH methylation level of cytosines was estimated using comstomized scripts.
Genome_build: hg19
Supplementary_files_format_and_content: UMI_count.txt files include UMI counts of RefSeq genes. While WCG.txt and GCH.txt files include the read counts of cytosines in WCG and GCH context respectively. The columns in WCG.txt or GCH.txt files represent "chr" "position" "unmethylated read counts" "methylated read counts".


title: Kupffer_1969

description: Library name: Sample 17


title: P+5 endometrium tissue in RIF patient34

value: endometrium


title: NOA_2_10_4

description: Sample 96


title: Kupffer_1957

description: Library name: Sample 16


title: SA00487_MM_323

data_processing:
Sample demultiplexing, barcode processing, alignment to the human transcriptome (GRCh38), single-cell 5′ gene, V(D)J and feature barcode counting were performed using Cell Ranger Single-Cell Software Suite (cellranger-4.0.0, 10x Genomics). Each data type (RNA, ADT, BCR) was then pre-processed per sample independently and subsequently concatenated into a single dataset for further downstream analysis. Unless stated otherwise, for each data analysis step, related functions from the scanpy (v1.6.1) Python package were used with default parameters.
Empty droplets and dying cells were filtered out based on UMI counts < 650, minimum number of genes < 300 and mitochondrial gene expression > 20%. Doublet detection was conducted by Scrublet (v0.2.1). Droplets with a Scrublet doublet score > 0.3 and genes expressed in <3 cells were excluded. Following the initial filtering, a cell per million (CPM) normalization was applied with a scale factor of 10^4 and the data were log transformed. Highly variable genes were detected with Seurat flavor. For the downstream analyses, immunoglobulin genes (IG) were removed from the dataset. Cell cycle scores were calculated using score_genes_cell_cycle function from scanpy using the gene sets identified by Kowalczyk et al..
Droplets with UMI counts  500 were excluded. The data were normalized using centered log-ratio (CLR) transformation
Cell Ranger filtered BCR-seq output contig files from individual samples were concatenated into a single file. Using the scirpy (v0.6.1) library, with parameters receptor_arms=all and dual_ir=primary only, observed clonotypes were defined based on CDR3 nucleic acid sequences. To assess clonal expansion, per-sample-clonotype definitions were generated using both CDR3 nucleic acid sequences and sample IDs. Per-sample-clonotypes observed in  10 cells were considered expanded malignant clonotypes.
Gene expression based principal component analysis (PCA) and Harmony (v1.0) batch correction, using theta=0, was performed. Nearest neighborhood networks were constructed using a cosine distance. Each integrated dataset was projected onto 2D space applying the UMAP algorithm based on the standard settings of scanpy. Cell typing was performed as described in the publication.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: raw_feature_bc_matrix.h5. Integrated_processed_data.h5ad file includes the following information: batch (SampleID), cohort, experimentID, clonotype, isExpandedClonotype (expansion status), cellType, isLowQuality (high mito or low nr of genes within the same cell type), highly_variable, gene_ids, feature_types, cohort_colors, X_umap (RNa based), log (log counts).

value: BM aspirate mononuclear cells

value: mRNA and ADT


title: NOA_2_10_5

description: Sample 97


title: Kupffer_2136

description: Library name: Sample 14

value: Sham


title: NOA_2_10_3

description: Sample 95


title: SA00480_SMM_312


title: Kupffer_2140

description: Library name: Sample 13


title: P+5 endometrium tissue in RIF patient32

value: repeated implantation failure

value: rsERT

value: non-receptive


title: SA00481_MM_312

value: active MM


title: SA00483_SMM_322

value: Bone Marrow


title: P+5 endometrium tissue in RIF patient35

value: receptive


title: SA00479_MGUS_312

value: monoclonal gammopathy of unknown significance (MGUS)


title: SA00482_MGUS_322


title: Kupffer_2137

description: Library name: Sample 15


title: SA00478_HV_312

value: healthy volunteer (HV)


title: P+5 endometrium tissue in RIF patient33


title: BECs_2011

description: Library name: Sample 10

value: Biliary epithelial cells (BECs)


title: P+5 endometrium tissue in RIF patient29


title: NOA_2_10_2

description: Sample 94

value: male

value: nonobstructive azoospermia (NOA)

value: testis


title: NOA_2_1_6

description: Sample 91


title: NOA_2_10_8

description: Sample 99


title: P+5 endometrium tissue in RIF patient31


title: NOA_2_1_7

description: Sample 92


title: BECs_2153

description: Library name: Sample 12

value: liver

value: BDL


title: P+5 endometrium tissue in RIF patient30

value: endometrium


title: P+5 endometrium tissue in RIF patient28


title: SA00477_SMM_311

value: smoldering MM (SMM)

value: BM aspirate mononuclear cells

value: mRNA and ADT


title: BECs_2036

description: Library name: Sample 9

value: Sham


title: NOA_2_1_4

description: Sample 90


title: SA00476_MGUS_311


title: P+5 endometrium tissue in RIF patient27

value: repeated implantation failure

value: rsERT

value: non-receptive


title: NOA_2_1_8

description: Sample 93


title: SA00475_HV_311

value: Bone Marrow


title: P+5 endometrium tissue in RIF patient26

value: receptive


title: BECs_2550

description: Library name: Sample 8


title: BECs_2548

description: Library name: Sample 7


title: BECs_2154

description: Library name: Sample 11


title: MPH_1964

description: Library name: Sample 6

value: Primary hepatocytes (MPH)


title: P+5 endometrium tissue in RIF patient25


title: SA00455_MGUS_310

value: monoclonal gammopathy of unknown significance (MGUS)


title: NOA_2_1_2

description: Sample 88

value: male


title: NOA_1_9_8

description: Sample 87

value: nonobstructive azoospermia (NOA)


title: SA00474_MM_311

value: active MM


title: P+5 endometrium tissue in RIF patient24


title: MPH_1957

description: Library name: Sample 5

value: liver


title: P+5 endometrium tissue in RIF patient23


title: SA00454_HV_310

value: healthy volunteer (HV)


title: NOA_1_9_7

description: Sample 86

value: testis


title: MPH_1956

description: Library name: Sample 4

value: BDL


title: P+5 endometrium tissue in RIF patient22

value: endometrium


title: SA00453_MM_310

value: BM aspirate mononuclear cells

value: mRNA and ADT


title: NOA_1_9_2

description: Sample 84


title: NOA_1_9_6

description: Sample 85


title: SA00451_HV_309


title: NOA_1_9_1

description: Sample 83


title: MPH_2136

description: Library name: Sample 2

value: Sham


title: NOA_2_1_3

description: Sample 89


title: P+5 endometrium tissue in RIF patient21

value: repeated implantation failure

value: rsERT


title: SA00452_SMM_310

value: smoldering MM (SMM)

value: Bone Marrow


title: P+5 endometrium tissue in RIF patient20

value: non-receptive


title: SA00450_MM_309


title: MPH_2143

description: Library name: Sample 1

value: Primary hepatocytes (MPH)


title: NOA_1_8_8

description: Sample 82

value: male


title: P+5 endometrium tissue in RIF patient19


title: NOA_1_8_7

description: Sample 81

value: nonobstructive azoospermia (NOA)


title: NOA_1_8_4

description: Sample 80


title: P+5 endometrium tissue in RIF patient18

value: receptive


title: SA00447_SMM_308


title: SA00449_MM_309

value: active MM


title: P+5 endometrium tissue in RIF patient17


title: MDR_H1

description: Library name: Sample 10

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.   RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA).  RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: liver


title: MPH_2140

description: Library name: Sample 3


title: SA00446_MGUS_308

value: monoclonal gammopathy of unknown significance (MGUS)


title: NOA_1_8_3

description: Sample 79

extract_protocol:
An individual cell was picked into the cell lysis buffer with vitro methylation (IVM) mixture containing 4 U RNase inhibitor (TAKARA, Cat. 2313B), 0.25% IGEPAL CA-630 (SIGMA, Cat. I3021), 1X GC reaction buffer and 2 U M. CviPI (NEB, Cat. M0227L). After gently vortexed for 10 sec, the cell lysate was incubated at 37 °C for 20 min and then at 65 °C for 25 min. Then, the cell lysate could be directly processed for RNA/DNA separation or stored at -80 °C.
For RNA part, a modified Smart-seq2 protocol was applied for single-cell RNA-seq. For DNA part, Bisulfite-converted DNA was amplified with biotinylated random primer and klenow exo– polymerase (NEB, M0212L) for 7 rounds and excess primer was removed by exonuclease I (NEB, M0293L). After second strands synthesis, the library was amplified by KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602) for 14 cycles.

value: testis


title: P+5 endometrium tissue in RIF patient16

value: endometrium


title: MDR3

description: Library name: Sample 9


title: NOA_1_7_8

description: Sample 78


title: SA00445_MM_308

extract_protocol:
BM-MNCs were isolated from BM aspirate using Ficoll-plaque gradient separation and processed for single cell 10x Genomics 5' Chromium single cell V(D)J with Feature Barcoding protocol.
The library was constructed using single cell 10x Genomics 5' Chromium single cell V(D)J with Feature Barcoding protocol.

value: BM aspirate mononuclear cells


title: MDR2

description: Library name: Sample 8


title: P+5 endometrium tissue in RIF patient15


title: NOA_1_7_5

description: Sample 76


title: P+5 endometrium tissue in RIF patient14


title: SA00444_HV_308

value: healthy volunteer (HV)

value: mRNA and ADT


title: MDR1

description: Library name: Sample 7


title: NOA_1_7_7

description: Sample 77


title: P+5 endometrium tissue in RIF patient13

value: repeated implantation failure


title: MDR_H2

description: Library name: Sample 11


title: P+5 endometrium tissue in RIF patient12

value: rsERT


title: M1hiPSC_RPE, D28, rep2

first: Xiufeng

last: Zhong

address: 54 xianlie Rd

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

description: CLCN2 mutation

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: HiPSC-RPE cells were cultured following our published protocol with minor modifications (Liu, S, et.al., 2018). Briefly, hiPSC-RPE cells were seeded onto Matrigel-coated Transwell inserts at approximately 5 × 104 cells/cm2 in retinal culture medium 1, consisting of 50% DMEM/F12 (1:1 ratio) (C11330500BT, Gibco), 35% basic DMEM (C11995500BT, Gibco), 10% fetal bovine serum (FBS) (10099-141, Gibco), 100 μM Taurine (T-0625, Sigma Aldrich), 2% B27 supplement (12587-010, Gibco), 1% GlutaMAX (35050061, Gibco), 1% MEM NEAA (11140050, Gibco), and 1% antibiotic antimycotic (AA) (15240, Gibco). From day 7, the medium was switched to RPE medium, consisting of 59% DMEM/F12, 37% basic DMEM, 2% B27 supplement , 1% FBS, and 1% AA. Cells were collected at day 28 for RNA-seq analysis.

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

value: CLCN2 c.2257C>T (p.R753X) homozygous mutation

value: Maintain the culture of hiPSC_RPE cells onto Matrigel-coated Transwell insert for 28 days

value: Day 28


title: NOA_1_7_4

first: Lin

last: Li

institute: Southern Medical University

description: Sample 75


title: BDL_H2

description: Library name: Sample 5


title: MDR_H3

description: Library name: Sample 12


title: NOA_1_7_3

description: Sample 74


title: M1hiPSC_RPE, D28, rep1

description: CLCN2 mutation


title: NOA_1_7_1

description: Sample 73


title: C1hiPSC_RPE, D28, rep3

description: Control

value: WT


title: NOA_1_6_7

description: Sample 72

value: male


title: P+5 endometrium tissue in RIF patient11

value: non-receptive


title: P+5 endometrium tissue in RIF patient9


title: C1hiPSC_RPE, D28, rep2

description: Control


title: P+5 endometrium tissue in RIF patient10


title: P+5 endometrium tissue in RIF patient8


title: M1hiPSC_RPE, D28, rep3

description: CLCN2 mutation


title: BDL_H3

description: Library name: Sample 6


title: BDL3

description: Library name: Sample 3


title: BDL_KO_2371

description: Library name: Sample 20


title: C1hiPSC_RPE, D28, rep1

description: Control


title: BDL1

description: Library name: Sample 1


title: NOA_1_6_2

description: Sample 69

value: nonobstructive azoospermia (NOA)


title: HCASMCs,ox-LDL treated, 24 hours input rep3

city: Nanjing

first: Yahong

last: Fu

state: Jiangsu

address: Guangzhou Road

institute: the First Affiliated Hospital of Nanjing Medical University

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of input libraries were aligned to reference genome (UCSC HG19) by STAR software
Then circRNAs were identified by DCC software using the STAR alignment results. After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software
Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA, LncRNA and circRNA were figured out and chosen by home-made scripts.
Assembly: hg19
Supplementary files format and content: MACS peak

source_name: HCASMCs

growth_protocol: Human coronary artery smooth muscle cells were purchased from Sigma. HCASMCs were cultured in a humidified incubator at 37◦C supplied with 5% CO2 using Dulbecco’s modified Eagle’s medium (DMEM; Gibco, United States) supplemented with 10% fetal bovine serum (FBS; Gibco) and 1% penicillin (100 m/ml) and streptomycin (100 mg/ml) (Beyotime, Shanghai, China)

extract_protocol:
RNA samples were prepared using Trizol regent (Vazyme, Nanjing, China) following the instruction of the manufacture. Then we used NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA) to measure the concentration and quantification of each sample
m6A RNA-Seq service was provided by Cloudseq Biotech Inc. (Shanghai, China). Briefly, m6A RNA immunoprecipitation was performed with the GenSeqTM m6A RNA IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Novaseq instrument with 150bp paired-end reads..

treatment_protocol: The cells were divided into two groups. One was cultured with basic DMEM, and the other was administered 50ug/mL ox-LDL purchased from Yiyuan Biotechnologies (Guangzhou, China) to simulate an abnormal lipid environment and build proliferation and migration models.

value: HCASMCs

value: ox-LDL treated

value: 50ug/ml ox-LDL

value: 24 hours


title: NOA_1_6_6

address: Shatai South Road

description: Sample 71

value: testis


title: BDL_KO_2370

description: Library name: Sample 19

value: liver


title: NOA_1_6_1

description: Sample 68


title: P+5 endometrium tissue in RIF patient6

value: endometrium


title: BDL_H1

description: Library name: Sample 4


title: P+5 endometrium tissue in RIF patient5


title: HCASMCs,ox-LDL treated, 24 hours input rep1

value: Human coronary artery smooth muscle cells


title: NOA_1_6_4

description: Sample 70


title: BDL_KO_2248

description: Library name: Sample 18


title: BDL_KO_2365

description: Library name: Sample 17


title: NOA_1_5_6

description: Sample 67


title: BDL2

description: Library name: Sample 2


title: HCASMCs,control, 24 hours input rep3

value: Control


title: NOA_1_4_7

description: Sample 66


title: P+5 endometrium tissue in RIF patient3

value: repeated implantation failure

value: rsERT

value: receptive


title: P+5 endometrium tissue in RIF patient4


title: P+5 endometrium tissue in RIF patient7


title: HCASMCs,control, 24 hours input rep2


title: BDL_Wt_2240

description: Library name: Sample 15


title: NOA_1_4_6

description: Sample 65


title: HCASMCs,control, 24 hours input rep1


title: HCASMCs,ox-LDL treated, 24 hours input rep2


title: HCASMCs,ox-LDL treated, 24 hours IP rep3


title: P+5 endometrium tissue in RIF patient1


title: P+5 endometrium tissue in RIF patient2


title: HCASMCs,ox-LDL treated, 24 hours IP rep2


title: NOA_1_3_8

description: Sample 64


title: NOA_1_3_6

description: Sample 63


title: BDL_Wt_2236

description: Library name: Sample 13


title: HCASMCs,ox-LDL treated, 24 hours IP rep1


title: BDL_Wt_2237

description: Library name: Sample 14


title: NOA_1_3_4

description: Sample 62


title: G449P_treated_exp3

city: Glasgow

first: Katarzyna

middle: Kinga

last: Modrzynska

state: Glasgow (City of)

address: B627 Sir Graeme Davies Building, 120 University Place

institute: Wellcome Trust Centre for Molecular Parasitology

data_processing:
The quality of the raw sequencing reads were assessed using FastQC and MultiQC platforms.
The RNA-seq reads (FASTQ) was mapped against Plasmodium falciparum reference genome (downloaded from PlasmoDB ver 56) using splice-aware aligner hisat2 (v. 2.2.1). Resulting BAM files were sorted, indexed and filtered for the mapping quality (only reads with MAPQ>10 were kept) using samtools suite (v. 1.17) and visually inspected using IGV genome browser.
Initially a featureCounts function from subread software has been used in a -J mode to count the number of reads supporting each splicing junction. All identified splicing events were used to construct a genome feature file with all mapped junctions. Next featureCounts was used again to in –nonSplitOnly mode to count the number of reads covering the junctions (not spliced).
R software with data table package was used to combine data from all samples, with reads spanning each intron or covering it forming separate columns. Only the introns supported by >15 spliced reads between all the samples and present within the annotated genes were carried forward to further analysis. .
The edgeR package statistical framework has been adapted to splicing analysis as described previously (PMID: 29333247). The resulting table containing log-fold changes of the proportion of the reads spliced and P-values with Bonferroni correction was generated and used to filter the differentially spliced intron. Introns with >25% changes in splicing proportions between the conditions and q values <0.01 were considered as differentially spliced/retained.
Assembly: 3D7
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: "*spliced.txt" is tab-delimited text file including the number of reads supporting each of the splicing junctions detected in each of the samples."*non_spliced.txt" files cotain number of non-spliced reads spanning each of these junctions

organism: Plasmodium falciparum 3D7

source_name: 30_hpi trophozoites

growth_protocol: Asexual blood stage 3D7 Plasmodium falciparum parasites were grown in RPMI media supplemented with 0.5% Albumax II, 0.292g/L L-glutamine, 0.05g/L hypoxanthine, 2.3g/L sodium bicarbonate, 0.025g/L gentamicin, 5.957g/L HEPES and 4g/L dextrose in human O+ anonymous male blood donor maintained at 4% haemtocrit maintained at 37 degrees celsuis.

extract_protocol:
RNA was isolated using Rneasy mini kit according to the manufactirer's instructions.
Using 500ng of RNA for each sample, libraries were prepared for sequencing using Roche’s KAPA RNA Hyperprep kit (part No. KK8540). The samples were then paired-end multiplex sequenced (2x 150 base pairs) on the illumina HiSeq 2500 platform, and at least 30 million reads were generated for each sample.

treatment_protocol: Previously synchronised 30-hpi old trophozoites were treated with 1𝛍M selective PfCLK3 inhibitor TCMDC135051 for 1-hour at 37 degrees celsius

tag: strain

value: 30_hpi trophozoites


title: NOA_1_3_3

description: Sample 61

tag: gender


title: HCASMCs,control, 24 hours IP rep3


title: G449P_treated_exp2


title: BDL_Wt_2235

description: Library name: Sample 12


title: G449P_treated_exp1


title: HCASMCs,control, 24 hours IP rep2


title: BDL_KO_2359

description: Library name: Sample 16


title: Sham_KO_2353

description: Library name: Sample 10


title: G449P_untreated_exp3

value: DMSO


title: HCASMCs,control, 24 hours IP rep1


title: NOA_1_3_2

description: Sample 60

value: male

tag: age


title: NOA_1_3_1

description: Sample 59

tag: condition


title: Sham_KO_2350

description: Library name: Sample 8


title: NOA_1_2_8

description: Sample 58

tag: testis


title: Patient2, CITE-seq and Hashtag

city: Hamburg

first: Yu

last: Zhao

address: Falkenried 94

department: Institute of Medical Systems Biology

institute: University Medical Center Hamburg-Eppendorf

description:
10x Genomics
Patient2_ADT_HTO

data_processing:
10x Genomics raw sequencing data were processed using CellRanger software (version 5.0.0, 10x Genomics, Pleasanton, CA) and the human genome GRCh38-2020-A release as the reference (function cellranger count). The matrices of cells and the unique molecular identifier (UMI) count were obtained and further processed by the R package Seurat (version 4.0.1)
To remove potential doublets, cutoff values for number of expressed genes (nGene) were determined for samples following visual inspection of the distribution of nGene and nUMI for each cell. The cells with higher nGene values were excluded. We further removed low-quality cells with high mitochondrial genes of all detected genes
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

molecule: other

source_name: kidney and blood mixded

growth_protocol: For single cell suspension kidneys were dissected and incubated for 40 min at 37°C in RPMI medium (including 0.01 M HEPES; 0.5 mL filtered FBS and 0.4µg/ mL DNase and 8 µg/ mL collagenase D). The samples were homogenized using a gentleMACS (Miltenyi Biotec).

extract_protocol:
Cells were loaded on a 10x Chromium single cell instrument.
All steps were performed according to standard protocol of the Chromium single cell 5’ v2 kit to generate high-quality cDNA libraries.

value: T cells

value: kidney and blood mixded

tag: disease

value: ANCA-GN

tag: patientid

tag: molecule subtype

value: surface protein


title: G449P_untreated_exp2

tag: cell type


title: Sham_KO_2352

description: Library name: Sample 9

tag: tissue


title: G449P_untreated_exp1


title: Patient2, scRNAseq

description:
10x Genomics
Patient2_GEX


title: Sham_KO_2349

description: Library name: Sample 7


title: NOA_1_2_7

description: Sample 57

value: nonobstructive azoospermia (NOA)


title: Patient1, CITE-seq and Hashtag

description:
10x Genomics
Patient1_ADT_HTO


title: NOA_1_2_6

description: Sample 56


title: 3D7_treated_exp3

value: WT


title: NOA_1_2_5

description: Sample 55

value: testis


title: Patient1, scRNAseq

description:
10x Genomics
Patient1_GEX


title: Sham_KO_2347

description: Library name: Sample 6

value: liver


title: BDL_Wt_2233

description: Library name: Sample 11


title: NOA_1_2_4

description: Sample 54


title: ZNF808-KO, S7, 4

city: Exeter

first: Nick

last: Owens

state: Exeter

address: Barrack Road

institute: University of Exeter Medical School

data_processing:
Stranded paired end 150bp RNA-seq reads were aligned to the hg19 genome using STAR and quantified against Gencode v36 release liftover to hg19 by RSEM using the RSEM-STAR pipeline, with additional options “--seed 1618 --calc-pme --calc-ci --estimate-rspd --paired-end”. RSEM estimated read counts per sample were rounded.
Assembly: hg19
Supplementary files format and content: tab delimited file with raw counts for each gene

growth_protocol: Human embryonic stem cells (hESC) (WA01/H1 line, Wicell) were cultured on Matrigel-coated plates (BD Biosciences) in Essential 8 (E8) medium (Life technologies, A1517001) and passaged using EDTA. To carry out the differentiation experiments, hPSC were dissociated using EDTA, then seeded on new Matrigel-coated plates in E8 medium supplemented with 10 µM Rho-Associated kinase inhibitor (ROCKi, catalog no. Y-27632; Selleckchem catalog no. S1049) at a density of 0.21 million cells cm-1. After 24 h, the differentiation was started by washing the cells with PBS, then changing the medium to D0 medium. The differentiation was carried out using our optimized seven-stage protocol as previously described in doi:10.1038/s41587-022-01219-z.

extract_protocol: RNA extraction and library preparation for stranded polyA+ RNA-seq libaries was performed by NovoGene Co Ltd.

tag: cell line

value: human embryonic stem cells (hESC)

tag: Stage

tag: replicate


title: Sham_Wt_2229

description: Library name: Sample 5


title: 3D7_untreated_exp3

tag: genotype

tag: treatment


title: Sham_Wt_2228

description: Library name: Sample 4


title: NOA_1_2_2

city: Guangzhou

description: Sample 53


title: 3D7_treated_exp2


title: WT-H1, S7, 4


title: 3D7_untreated_exp2


title: Sham_Wt_2227

description: Library name: Sample 3


title: NOA_1_2_1

description: Sample 52


title: 3D7_untreated_exp1


title: Sham_Wt_2224

description: Library name: Sample 2


title: ZNF808-KO, S7, 3


title: Sham_Wt_2223

description: Library name: Sample 1


title: NOA_1_12_8

description: Sample 51


title: WT-H1, S7, 3


title: NOA_1_12_7

description: Sample 50


title: 3dpf_fibroblasts_sort_500_cells_injury_sample3

city: Shenzhen

first: Zhao

last: Shizheng

address: Shenzhen

department: LIFS

institute: Undefined

description: Library name: Injury-fibroblast-3

data_processing:
STAR(v2.7.10a)
Assembly: Zebrafish reference genome (GRCz11.111)
Supplementary files format and content: csv files with TPM value of each sample

organism: Danio rerio

extract_protocol:
The fibroblasts were isolated by FACS sorting and cDNA library was constructed by Smartseq2 protocol.
In this experiment, we have conducted acetic acid corrosion in four trunk sites in 2 dpf embryos,cut the trunk region at 3 dpf, dissociated the embryos into single cell suspension and performed FACS sorting of dsRed positive fibroblasts. In each biological replicate, around 30 embryos were harvested and 500 fibroblsts were sorted into lysis buffer. Smartseq2 protocol was utilized for double strand cDNA library construction. After acquiring the cDNA from sorted fibroblasts, 0.5 ng cDNA input was tagmented using the TruePrep DNA Library Prep Kit V2 for Illumina (TD503, Vazyme). Following tagmentation, the samples were amplified using the TruePrep Index Kit V2 for Illumina (TD202, Vazyme) for 12 cycles and subsequently purified using Ampure XP beads (A63881, Beckman Coulter). The quality of the libraries was evaluated using the Agilent Fragment Analyzer System and then sent to Novogene for Illumina Hiseq X Ten 150-bp paired-end sequencing, with an average sequencing depth of 8 × 10^6 raw reads per sample.

value: fibroblast


title: WT-H1, S7, 2