title: MDS1047

description: MDS


title: MDS1046

status: Public on Jul 08 2026

type: SRA

city: Taipei

first: Yu-Hung

last: Wang

address: N0 7, Chung-Shan South Rd

country: Taiwan

institute: National Taiwan University Hospital

description: MDS

library_source: transcriptomic

data_processing:
Reads were then aligned to the human genome (GRCh38) and gene annotated with its corresponding GTF files (GENCODE GRCh38) using STAR version 2.4.2a with the settings –outFilterMultimapNmax 20 –outFilterType BySJout –alignSJoverhangMin 8 –quantMode GeneCounts.
Assembly: GRCh38
Supplementary files format and content: Read counts in .csv format

molecule: total RNA

organism: Homo sapiens

source_name: human BM Mononuclear cells

extract_protocol:
RNA was extracted from fresh BM samples of patients and healthy donors and sent for RNA sequencing.
The purified RNA was used to prepare the sequencing library using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations. Briefly, mRNA was purified from total RNA (1 μg) using oligo(dT)-coupled magnetic beads and fragmented into small pieces at elevated temperatures.
First-strand cDNA was synthesized using reverse transcriptase and random primers. After the generation of double-strand cDNA and adenylation on the 3’ ends of DNA fragments, the adaptors were ligated and purified with the AMPure XP system (Beckman Coulter, Beverly, USA). The quality of the libraries was assessed using an Agilent Bioanalyzer 2100 system and a real-time polymerase chain reaction (PCR) system. The qualified libraries were then sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads generated by Genomics, BioSci & Tech Co., New Taipei City, Taiwan. The bases with low quality and sequences from adapters in the raw data were removed using Cutadapt (v 3.0).

tag: cell type

value: human BM Mononuclear cells


title: 15659_mouse_LDA_Day_19

city: Aurora

first: Jo

last: Hendrix

state: CO

department: Pulmonology

country: USA

institute: University of Colorado

description: Library name: mm_15659

data_processing:
After sequencing, bacterial reads were trimmed by Skewer v0.2.2 using an adapter sequence of 5’- CTGTCTCTTATACACATCT-3’, a length of 50-175 bases, and an end quality of 20. Individual reads were reunited with their mate pair using PairFQ lite v0.17.0. Paired-end reads were then aligned to the 2016 Mtb Erdman reference assembly using Bowtie2 v2.5.0 with default parameters. Mapped sequences were counted using HtSeq v1.0 with the default parameters. The SEARCH-TB panel amplifies Mtb 3,568 genes. Genes with high incidences of 0 expression values were excluded.
Sequenced mouse reads were processed using Trimmomatic v0.39 to remove TruSeq3-PE-2 adapter sequences, trim leading and trailing bases with a quality score below 3, and filter for reads longer than 36 bases after trimming. Reads were aligned to the mm39 genome assembly (GCA_000001635.9) and using Star v2.7.10b with default parameters. The genome assembly and associated annotation file were acquired from the University of California Santa Cruz Genomics Institute. Additional alignment metrics were collected using Picard v2.27.5. Genes with excessive number of zero values (>90%) or low variance across samples were removed from analysis, resulting in a final dataset of 29,579 host genes.
Assembly: 2016 Mtb Erdman reference assembly for Mtb sequencing reads. mm39 genome assembly (GCA_000001635.9) for murine sequencing reads.
Supplementary files format and content: Read counts per organism gene are provided in .txt format

organism: Mus musculus

source_name: Lung homogenate

growth_protocol: All animal procedures were conducted according to relevant national and international guidelines and approved by the Colorado State University Animal Care and Use Committee as described in the Supplemental Information. For the chronic infection model, 30 BALB/c female mice (7-9 weeks old) were infected with a low dose aerosol (LDA) of Mtb Erdman using the Glas-Col Inhalation Exposure System. This resulted in the deposition of 2.40 ± 0.07 (SEM) log10 CFU in lungs one day post-infection. Five mice were sacrificed on days 1, 7, 11, 19, 28, and 56 post-infection for lung specimen collection, respectively. Following sacrifice, the lungs were aseptically harvested and sectioned into the left lobe, upper right lob, and lower right robes for subsequent analysis.

extract_protocol:
Murine tissue samples were snap frozen in 7 mL Precellys tubes (Bertin) under liquid nitrogen. To each tissue sample, 1.5 mL GTC-TCEP buffer was added and samples were homogenized at 7,200 rpm for 16s using a Precellys Evolution (Bertin). Homogenates were incubated at room temperature for 5 minutes while protected from light. Unlysed mycobacterial cells were pelleted at 10,000g for 3 minutes, then resuspended in 0.8 mL RLT+ BME buffer (Qiagen, TCEP concentration 0.75 mM). Mycobacterial cells were lysed on a Precellys Evolution (Bertin) at 6,500 rpm for 30s three times, resting on ice for 5 minutes each time, and stored at -80C. After storage at -80C, murine lysates were thawed, and RNA was purified using the Maxwell simplyRNA tissue kit (murine samples) using the Maxwell RSC instrument following the manufacturer’s instructions with the following modifications. Additional kit DNase was added at twice the manufacturer’s recommended amount. Purified RNA was quantified using the Quantifluor RNA system (Promega).
Murine RNA was purified with Maxwell simplyRNA tissue kit while bacterial RNA was prepared for SEARCH-TB using Illumina’s AmpliSeq for Illumina Custom and Community RNA Panels kit.

treatment_protocol: no treatment was given.

tag: tissue

value: Lung homogenate

tag: strain

value: BALB/c


title: OCI-AML-3 WT1 cells, H3K9me3 (ChIP)

city: Marseille

first: Estelle

middle: Anna

last: Duprez

address: 23 bvd lei roure

department: OHIO

country: France

institute: CRCM-INSERM

description: Library name: ChIPseq_OCI3_WT1_H3K27me3

library_source: genomic

data_processing:
Sequencing quality control was determined using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aggregated across samples using MultiQC (v1.7)
Reads with a Phred quality score of less than 30 were filtered out and mapped to a human (Hg38) genome using using default parameters of Bowtie2 (v2.3.4.3) Only mapped reads were filtered in using samtools (v1.9). Duplicate tags were removed using Picard Tools
Peaks were called  using MACS2 callpeak (v2.1.2)  in broad mode (--broad broad-cutoff=0.05 -q 0.01 --nomodel)
bigWigs files were generated  using the deepTools suite (v3.2.1)
Assembly: GRCh38 reference genome
Supplementary files format and content: Bigwig

molecule: genomic DNA

source_name: OCI-AML-3 parental

growth_protocol: Cells were growth in MEMα medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 U/mL streptomycin under standard culture conditions (37°C, 5% CO2)

extract_protocol:
Cells were fix with 1% formaldehyde. Cell lysates were clarified from sonicated nuclei using a Diagenode Bioruptor, and histone-DNA complexes were isolated with antibody incubated over-night. Rabit IgG (Cell signaling; #2729S) was used as a control. Genomic DNA was purified using the i-Pure V2 kit (Diagenode)
Libraries were generated using the MicroPlex Library Preparation Kit (Diagenode) following the manufacturer's instructions and analyzed on a 2100 Bioanalyzer system (Agilent) prior sequencing

treatment_protocol: H1.3-V5 DNA was cloned into a doxycycline-inducible plasmid pLix-403 (Addgene) using the GATEWAY strategy. The plasmid (pLix403-H1.3-V5) was transfected into OCI-AML3 cells by electroporation using the Amaxa Kit V (program X-001) according to the manufacturer’s protocol. Transfected cells were selected 48 h after electroporation with puromycin 2 µg/mL, which was kept in the culture medium to maintain pressure selection. Expression of the H1.3-V5 construct was obtained with 1 µg/mL doxycycline and induction of expression was assessed by Western blot

tag: cell line

value: OCI-AML-3 parental

value: Acute myeloid leukemia

tag: genotype

value: WT

tag: treatment

tag: chip antibody

value: H3K27me3 (Cell Signaling; #9733S)


title: MDS1044

description: MDS


title: OCI-AML-3 WT1 cells, H3K27me3 (ChIP)

description: Library name: ChIPseq_OCI3_WT1_H3K9me3

value: H3K9me3 (Active Motif; #39161)


title: MDS1040

description: MDS


title: 15658_mouse_LDA_Day_19

description: Library name: mm_15658


title: MDS1039

description: MDS


title: OCI-AML-3 WT1 cells, H1 antibody (ChIP)

description: Library name: ChIPseq_OCI3_WT1_H1

value: H1 (Active Motif; #39707)


title: MDS1038

description: MDS


title: 15657_mouse_LDA_Day_11

description: Library name: mm_15657


title: MDS1035

description: MDS


title: MDS1036

description: MDS


title: 15656_mouse_LDA_Day_11

description: Library name: mm_15656


title: ATACseq OCI-AML3 H1.3 KO clone 2

description: Library name: ATACseq_OCI3_H1.3_KO2

data_processing:
paired-end reads were aligned to the human GRCh38 reference genome using Bowtie2 (v2.3.4.3)  with default options. SAMtools (v1.9) were used to filter out the low-quality alignment using the flag 3844. High confidence binding sites were determined using MACS2 peak caller (v2.1.2). Each sample’s fragment size was previously computed by deepTools
Assembly: GRCh38 reference genome
Supplementary files format and content: Bigwig

source_name: OCI-AML-3 H1-3 KO 2

extract_protocol:
ATAC-Seq were performed with the Diagenode ATAC-seq kit; (#C01080001) following the manufacturer’s instructions. Nuclei were collected by centrifugation, and a transposition reaction was performed by adding 50 μL of transposition mixture (containing Tagmentation buffer, Tagmentase, 2% Digitonin, 10% Tween20, PBS and Nuclease-free water) for 30 min at 37°C. DNA was isolated using supplied spin columns and eluted in 12 μL of DNA elution buffer. Transposed DNA fragments were amplified using 8 UDI for Tagmented libraries (Diagenode; #C01011035) and libraries were purified using AMPure XP beads (Beckman Coulter; #A63881)
Libraries were prepared using the ATAC-seq kit (Diagenode) with 24 unique dual indexes (UDI) for tagmented libraries (Set I), according to the manufacturer's protocol, and analyzed on an Agilent 2100 Bioanalyzer prior to sequencing.

value: OCI-AML-3 H1-3 KO 2

value: non


title: MDS1029

description: MDS


title: ATACseq OCI-AML3 H1.3 KO clone 1

description: Library name: ATACseq_OCI3_H1.3_KO1

source_name: OCI-AML-3 H1-3 KO 1

value: OCI-AML-3 H1-3 KO 1


title: MDS1028

description: MDS


title: 15655_mouse_LDA_Day_11

description: Library name: mm_15655


title: MDS1027

description: MDS


title: ATACseq OCI-AML3 WT1 parental

description: Library name: ATACseq_OCI3_WT1

value: OCI-AML-3 WT


title: MDS1026

description: MDS


title: MDS1053

description: MDS


title: 15654_mouse_LDA_Day_11

description: Library name: mm_15654


title: MCF10A, XRCC1-KO, repl 3

city: Naples

first: Stefano

last: Amente

address: via pansini, 5

department: Department of  Molecular Medicine and Medical Biotechnologies

country: Italy

institute: University of Naples "FEDERICO II"

description:
Library name: Sample 9
sheet name in DE_all_genes.xlsx: XRCC1-KO vs CRTL-KO

data_processing:
Trim Galore
Salmon version 1.4.0
edgeR
filterByExpr edgeR
Assembly: hg19
Supplementary files format and content: excell file containing differential analysis

molecule: polyA RNA

source_name: breast

growth_protocol: MCF10A cells (non-transformed mammary epithelial cell line) were maintained in DMEM/F-12 medium (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 5% horse serum, 20 ng/mL epidermal growth factor (EGF), 100 ng/mL cholera toxin, 10 µg/mL insulin, and 500 ng/mL hydrocortisone.

extract_protocol:
RNA was extracted from MCF10 CTRL, APE1- and XRCC1-deficient cells using the RNeasy Mini Kit (QIAGEN, Hilden, Germany), according to the manufacturer’s protocol
Illumina Stranded mRNA Prep

value: breast

value: breast cell line

tag: batch


title: MDS1025

description: MDS


title: 15653_mouse_LDA_Day_11

description: Library name: mm_15653


title: MDS1020

description: MDS


title: MDS1019

description: MDS


title: MCF10A, XRCC1-KO, repl 2

description:
Library name: Sample 8
sheet name in DE_all_genes.xlsx: XRCC1-KO vs CRTL-KO


title: MDS1018

description: MDS


title: 15652_mouse_LDA_Day_7

description: Library name: mm_15652


title: MCF10A, XRCC1-KO, repl 1

description:
Library name: Sample 7
sheet name in DE_all_genes.xlsx: XRCC1-KO vs CRTL-KO


title: MDS1007

description: MDS


title: MDS1014

description: MDS


title: 15651_mouse_LDA_Day_7

description: Library name: mm_15651


title: MCF10A, APE1-KO, repl 3

description:
Library name: Sample 6
sheet name in DE_all_genes.xlsx: APE1-KO vs CRTL-KO


title: MDS1005

description: MDS


title: MDS1002

description: MDS


title: MCF10A, APE1-KO, repl 2

description:
Library name: Sample 5
sheet name in DE_all_genes.xlsx: APE1-KO vs CRTL-KO


title: MDS1004

description: MDS


title: MDS1001

description: MDS


title: 15649_mouse_LDA_Day_7

description: Library name: mm_15649


title: Donor7

description: donor


title: Donor8

description: donor


title: MCF10A, APE1-KO, repl 1

description:
Library name: Sample 4
sheet name in DE_all_genes.xlsx: APE1-KO vs CRTL-KO


title: 15648_mouse_LDA_Day_7

description: Library name: mm_15648


title: MCF10A, Control-KO, repl 3

description: Library name: Sample 3


title: Donor6

description: donor


title: Donor5

description: donor


title: SFRP1 WT, PDGFRa+, P0, biol rep 5

city: New York

first: Jeanine

last: D'Armiento

address: 622 W. 168th street

institute: Columbia University Medical Center

description: Library name: JN016

data_processing:
CLC Genomics Workbench 26
Assembly: mouse reference genome (GRCm38)
Supplementary files format and content: text file contains TPM values

source_name: Lung

extract_protocol:
RNA was extracted from the sorted cells RNA using the RNeasy Mini Kit (Qiagen)
mRNA was enriched by rRNA depletion, then proceed with library construction using Illumina TruSeq chemistry. The final PCR step has been modified using the KAPA HiFi HotStart Ready Mix.For CLONTECH: We use the Clontech Ultra Low v4 kit for cDNA synthesis followed by NexteraXT.

value: Lung

value: PDGFRa+ cells from lung

value: SFRP1 WT


title: Donor4

description: donor

value: human BM Mononuclear cells


title: Donor3

description: donor


title: SFRP1 WT, PDGFRa+, P0, biol rep 4

description: Library name: JN015


title: MCF10A, Control-KO, repl 2

description: Library name: Sample 2


title: Donor2

description: donor


title: MCF10A, Control-KO, repl 1

description: Library name: Sample 1


title: Donor20

description: donor


title: 15650_mouse_LDA_Day_7

description: Library name: mm_15650

value: Lung homogenate

value: BALB/c


title: SFRP1 WT, PDGFRa+, P0, biol rep 3

description: Library name: JN014


title: Donor1

description: donor


title: Donor19

description: donor


title: Case 28 ATRT-MYC recurrence

city: Hamburg

first: Lea

last: Altendorf

address: Martinistraße 52

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

description: Library name: Case_28_recurrence

library_source: transcriptomic single cell

data_processing:
The 10x Genomics Cell Ranger v8.0.1 software was used for demultiplexing, barcode processing and assignment, single-nucleus counting, alignment to the human reference genome GRCh38-2024-A, and finally for Feature Barcode Matrix generation
Normalization, scaling, principal component analysis (PCA), shared nearest-neighbor graph construction (snn-graph), clustering and uniform manifold approximation and projection (UMAP) were performed via the Seurat (version 5.1.0) pipeline17. Data were merged and normalized using the SCTransform() function, correcting for the percentage of mitochondrial counts. Only cells with more than 200 and less than 2500 detected genes and less than 5% mitochondrial reads were included in further analysis
Assembly: hg38
Supplementary files format and content: Filtered Feature Barcode Matrices including barcodes.tsv, features.tsv, and matrix.mtx for each sample
Supplementary files format and content: CSV file containing the SCT-normalized count table including all samples

molecule: nuclear RNA

source_name: FFPE AT/RT primary tumor

extract_protocol:
snRNA-seq was performed using the Chromium Single Cell Flex Gene Expression Assay from 10x Genomics. Cells were isolated according to the demonstrated protocol “Isolation of Cells from FFPE Tissue Sections for Chromium Fixed RNA Profiling”, Document Number CG000632 Rev B, from 10x Genomics, using a gentleMACS Octo Dissociator (#130-134-029, Miltenyi Biotec). FFPE scrolls were dissociated using the Enzyme Mix containing Liberase TH (# 5401151001, Millipore Sigma)
Probe hybridization and multiplex library preparation were performed using the 10x Genomics Sample Preparation Kit PN-1000414, 16 rxns, according to the protocol “Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples”, Document Number CG000527 Rev E, from 10x Genomics. A recovery of 80,000 cells for each library was targeted.

value: FFPE AT/RT primary tumor

value: B


title: SFRP1 WT, PDGFRa+, P0, biol rep 2

description: Library name: JN013


title: Donor18

description: donor


title: Donor17

description: donor


title: Case 28 ATRT-MYC primary

description: Library name: Case_28_primary


title: SFRP1 WT, PDGFRa+, P0, biol rep 1

description: Library name: JN012


title: Donor16

description: donor


title: Case 27 ATRT-MYC recurrence

description: Library name: Case_27_recurrence


title: Donor15

description: donor


title: SFRP1 KO, PDGFRa+, P0, biol rep 5

description: Library name: JN011

value: SFRP1 KO


title: Case 27 ATRT-MYC primary

description: Library name: Case_27_primary


title: SFRP1 KO, PDGFRa+, P0, biol rep 4

description: Library name: JN010


title: Donor14

description: donor


title: Donor12

description: donor


title: Donor13

description: donor


title: Case 26 ATRT-TYR recurrence

description: Library name: Case_26_recurrence


title: Donor11

description: donor


title: SFRP1 KO, PDGFRa+, P0, biol rep 3

description: Library name: JN009


title: Case 26 ATRT-TYR primary

description: Library name: Case_26_primary


title: CMML90

data_processing:
Reads were aligned to the human genome (GRCh38 GENCODE release 25) and gene annotated with their corresponding GTF file (GENCODE GRCh38 release 25) using STAR version 2.4.2a with the settings --outFilterMultimapNmax 20 ,--outFilterType BySJout, --alignSJoverhangMin 8, --quantMode GeneCounts (Dobin A, et al. STAR: ultrafast universal RNA-seq aligner.Bioinformatics. 2013;29(1):15–21). DEseq2 was used to perform differential gene expression analysis and calculate FPKM (fragments per kilobase of transcript per million mapped reads) values for each gene (Love et al., 2014).
Assembly: GRCh38

growth_protocol: not applicable

extract_protocol:
RNA was extracted from cells using the RNeasy Kit (Qiagen) following the instructions of the manufacturer. The purified RNA was used to prepare the sequencing library using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA) following the manufacturer’s recommendations. Briefly, mRNA was purified from total RNA (1 mg) using oligo(dT)-coupled magnetic beads and fragmented into small pieces at elevated temperatures. First-strand cDNA was synthesized using reverse transcriptase and random primers. After the generation of doublestrand cDNA and adenylation on the 39 ends of DNA fragments, the adaptors were ligated and purified with the AMPure XP system (Beckman Coulter, Beverly, MA). The quality of the libraries was assessed using an Agilent Bioanalyzer 2100 system and a real-time polymerase chain reaction system.
The quality of the libraries was assessed using an Agilent Bioanalyzer 2100 system and a real-time polymerase chain reaction system. The qualified libraries were then sequenced on an Illumina NovaSeq 6000 platform with 150-bp paired-end reads generated by Genomics, BioSci & Tech Co. (New Taipei City, Taiwan).

treatment_protocol: not applicable

tag: disease

value: CMML

tag: age

tag: Sex

value: M


title: SFRP1 KO, PDGFRa+, P0, biol rep 2

description: Library name: JN008


title: Case 18 ATRT-MYC recurrence

description: Library name: Case_18_recurrence

value: A


title: CMML89

value: F


title: SFRP1 KO, PDGFRa+, P0, biol rep 1

description: Library name: JN007


title: CMML88


title: CMML87


title: Case 18 ATRT-MYC primary

description: Library name: Case_18_primary


title: CMML86


title: SFRP1 KO, whole lung, P0, biol rep 3

description: Library name: JN006

value: Whole lung


title: CMML85


title: CMML84


title: SFRP1 KO, whole lung, P0, biol rep 2

description: Library name: JN005


title: CMML83


title: Case 17 ATRT-TYR primary

description: Library name: Case_17_primary


title: CMML82


title: SFRP1 KO, whole lung, P0, biol rep 1

description: Library name: JN004


title: CMML81


title: Case 7 ATRT-SHH recurrence

description: Library name: Case_7_recurrence


title: CMML80


title: SFRP1 WT, whole lung, P0, biol rep 3

description: Library name: JN003


title: CMML79


title: Donor10

description: donor


title: Case 7 ATRT-SHH primary

description: Library name: Case_7_primary


title: SFRP1 WT, whole lung, P0, biol rep 2

description: Library name: JN002


title: CMML78


title: CMML77


title: Case 6 ATRT-MYC recurrence

description: Library name: Case_6_recurrence


title: CMML76


title: SFRP1 WT, whole lung, P0, biol rep 1

description: Library name: JN001


title: CMML75


title: Case 6 ATRT-MYC primary

description: Library name: Case_6_primary


title: Case 17 ATRT-TYR recurrence

description: Library name: Case_17_recurrence


title: CMML74


title: CMML73


title: HFD+AAV-BCKDK_3

city: Nanjing

first: Yu

last: Liu

state: Jiangsu

address: No.87 Dingjiaqiao Street

country: China

institute: Southeast University

description: Library name: HB.3

data_processing:
Reads were mapped to the mm10 reference mouse genome using HISAT2 (v2.0.5) and assigned to Ensembl genes.
Assembly: mm10
Supplementary files format and content: csv file includs counts for each sample

source_name: heart

extract_protocol:
Total RNA from left ventricular tissues was extracted with Trizol Reagent (Invitrogen Life Technologies, USA) and quantified with a Nanodrop (Thermo scientific, USA).
After RNA quality control was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies), sequencing libraries were generated using VAHTS mRNA-seq v2 Library Prep Kit (Illumina, USA).

value: heart

value: WT

value: HFD+AAV-BCKDK


title: MDS1251

description: MDS


title: Case 3 ATRT-TYR recurrence

description: Library name: Case_3_recurrence


title: CMML72


title: HFD+AAV-BCKDK_2

description: Library name: HB.2


title: CMML71


title: HFD+AAV-BCKDK_1

description: Library name: HB.1


title: Case 3 ATRT-TYR primary

description: Library name: Case_3_primary


title: CMML69


title: CMML70


title: DKD 23

city: Beijing

first: Qi

last: Jin

address: No.5, Beixiange, Xicheng District, Beijing

institute: Guang'anmen Hospital, China Academy of Chinese Medical Sciences

description: Library name: Sample 36

data_processing:
Afterwards, the DNA sequences are PCR amplified, library constructed and purified, and then sequenced by the Illumina platform (NextSeq550/NovaSeq 6000), where the NGS reads will be traced back to the specific location of the tissue and used for in-situ target abundance studies at the spatial level.
Assembly: GRCm39
Supplementary files format and content: Normalization data for each Sample

source_name: Kidney

extract_protocol:
Routine FFPE sections of kidney tissue are deparaffinised, hydrated and antigenically repaired before overnight incubation with a pre-designed RNA hybridisation probe (WTA) that, in addition to containing a portion that binds to the target RNA, also joins a section of DNA sequence with a specific label via a UV-dissolvable linker moiety. The next day, a polychromatic fluorescent antibody (Nephrin, AQP1) was incubated to enable morphological observation of the tissue and to guide the selection of subsequent ROIs.
Subsequent UV irradiation of selected ROIs results in the release of DNA oligonucleotide strands with photolysable linkers, which are then absorbed by capillary tubes into 96-well plates. The collected DNA oligonucleotide sequence is composed of a section of RNA target-specific marker, specific molecular tag UMI and primer binding site for RNA identification, spatial position reduction and splitting of the sample after sequencing.

value: Kidney

tag: sample group

value: DKD

tag: tissue type

value: Renal tubules


title: CMML68


title: HFD+AAV-CON_3

description: Library name: HC.3

value: HFD+AAV-CON


title: DKD 22

description: Library name: Sample 35


title: CMML66


title: CMML67


title: HFD+AAV-CON_2

description: Library name: HC.2


title: CMML65


title: DKD 21

description: Library name: Sample 34


title: CMML63


title: CMML64


title: CMML62


title: DKD 20

description: Library name: Sample 33


title: HFD+AAV-CON_1

description: Library name: HC.1


title: ND+AAV-CON_3

description: Library name: NC.3

value: ND+AAV-CON


title: DKD 19

description: Library name: Sample 32


title: CMML61


title: CMML60


title: DKD 18

description: Library name: Sample 31


title: ND+AAV-CON_2

description: Library name: NC.2


title: CMML59


title: CMML58


title: ND+AAV-CON_1

description: Library name: NC.1


title: CMML57


title: DKD 17

description: Library name: Sample 30


title: CMML55


title: Prefrontalcortex_snRNAseq_R848_57

city: Austin

first: Roy

middle: Dayne

last: Mayfield

state: Texas

address: 2500 Speedway, MBB 1.124

department: Neuroscience

institute: University of Texas at Austin

description: Library name: PFC57_R848

data_processing:
Fastq files were processed using the CellRanger (v7.0.0) pipeline. CellRanger outputs were imported to Seurat (v4.3.0) for further processing.
Assembly: mouse reference genome (mm10, GENCODE v32/Ensembl98) with introns included
Supplementary files format and content: Tab-separated values files, comma-separated values files, matrix files

source_name: Prefrontal cortex (PFC)

growth_protocol: adult C57BL6/J mice (Jax) were used for this study

extract_protocol:
Brains were extracted and flash frozen in isopentane. dmPFC and AMG were cryosectioned and nuclei were isolated with the Chromium Nuclei Isolation Kit following manufacturer's protocol with lysis time reduced to 4.5 min (10X Genomics)
libraries were prepared utilizing the Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics), and sequenced on a NovaSeq 6000 using an S4 flow cell at the Genomic Sequencing and Analysis Core Facility at UT Austin

treatment_protocol: i.p. injections of R848 (50 µg in 50 µl, Invitrogen) or vehicle (50 µl saline) were given to mice every other day for 20 days (10 total injections). Mice were then given 10 treatment free days, and tissue was harvested.

value: Prefrontal cortex (PFC)

value: male

value: wildtype


title: CMML56


title: DKD 16

description: Library name: Sample 29


title: CMML54


title: Prefrontalcortex_snRNAseq_R848_55

description: Library name: PFC55_R848


title: CMML53


title: DKD 15

description: Library name: Sample 28


title: CMML52


title: DKD 14

description: Library name: Sample 27


title: MDS1852

description: MDS

value: human BM Mononuclear cells


title: Prefrontalcortex_snRNAseq_R848_35

description: Library name: PFC35_R848


title: CMML51

value: CMML


title: CMML50


title: Prefrontalcortex_snRNAseq_R848_31

description: Library name: PFC31_R848


title: CMML48

value: M


title: DKD 13

description: Library name: Sample 26


title: CR 3 Month AAV-TBG-Cre Mouse 2

city: Philadelphia

first: Abhinav

last: Illendula

address: 333 Cottman Avenue

institute: Fox Chase Cancer Center

description:
Library name: CR_3_Month_Sample2
10X Genomics

data_processing:
Raw sequencing data files were processed using Cell Ranger v.8.0.1 from 10x Genomics, and reads were mapped to the GRCm39 reference genome modified to include the tdTomato sequence found in RtdT mice. All other parameters were kept as default. The resultant data was then processed using the Seurat 5.0.2 package in R.
Cells which did not meet QC criteria (n_feature count between 400-7000 and mitochondrial genes <20% for the normal liver samples and 950-7000, <20% for the CLD samples) were filtered out prior to downstream analysis.
Assembly: GRCm39
Supplementary files format and content: Matrix h5

source_name: Liver

extract_protocol:
The abdominal  vena cava was cannulated with the thoracic vena cava clamped. The portal vein was snipped and 20 mL HBSS -/- buffer was perfused. Then, HBSS +/+ with 4 mg/mL Liberase was perfused until the liver was digested to acheive a single-cell suspension. Cells were washed with HBSS -/- and incubated with DAPI. Cells were sorted on FACAria II into DMEM supplemented with 10% FBS.
Cell partitioning into Gel Beads-in-emulsions (GEMs) and barcoding was carried out using the Chromium Controller, following the manufacturer’s protocol. Barcoded cDNA libraries were prepared from GEMs for each mouse, and sequencing was performed on an Illumina HiSeq X platform (PE150).

treatment_protocol: AAV8-TBG-Cre tail-vein injection

value: Liver

value: AAV8:TBG>Cre 3 month


title: CMML49


title: Prefrontalcortex_snRNAseq_Saline_44

description: Library name: PFC44_Sal

value: Saline


title: CMML47


title: DKD 12

description: Library name: Sample 25


title: CMML46


title: Prefrontalcortex_snRNAseq_Saline_5

description: Library name: PFC5_Sal


title: CMML45


title: Prefrontalcortex_snRNAseq_Saline_4

description: Library name: PFC4_Sal


title: DKD 11

description: Library name: Sample 24


title: CMML44


title: CMML43

value: F


title: DKD 10

description: Library name: Sample 23


title: CMML42


title: CMML38


title: DKD 9

description: Library name: Sample 22


title: CMML41


title: CMML40


title: Prefrontalcortex_snRNAseq_Saline_2

description: Library name: PFC2_Sal


title: Prefrontalcortex_snRNAseq_Saline_3

description: Library name: PFC3_Sal


title: CMML39


title: DKD 8

description: Library name: Sample 21


title: Amygdala_snRNAseq_R848_57

description: Library name: Amy57_R848

source_name: Amygdala (Amy)

value: Amygdala (Amy)


title: CMML37


title: DKD 7

description: Library name: Sample 20


title: Amygdala_snRNAseq_R848_55

description: Library name: Amy55_R848


title: CMML36


title: CMML34


title: CMML35


title: Amygdala_snRNAseq_R848_35

description: Library name: Amy35_R848


title: Normal 13

description: Library name: Sample 19

value: normal (paraneoplastic tissue)


title: CMML33


title: Normal 12

description: Library name: Sample 18

value: Kidney


title: CMML32


title: CMML31


title: Amygdala_snRNAseq_R848_31

description: Library name: Amy31_R848


title: DKD 6

description: Library name: Sample 17

value: DKD


title: CMML30


title: Amygdala_snRNAseq_Saline_44

description: Library name: Amy44_Sal

value: Salne


title: CMML29


title: CMML28


title: DKD 5

description: Library name: Sample 16

value: Renal tubules


title: CMML27


title: Amygdala_snRNAseq_Saline_5

description: Library name: Amy5_Sal


title: DKD 4

description: Library name: Sample 15


title: CMML26


title: CMML25


title: CMML24


title: Amygdala_snRNAseq_Saline_4

description: Library name: Amy4_Sal


title: Amygdala_snRNAseq_Saline_3

description: Library name: Amy3_Sal


title: DKD 3

description: Library name: Sample 14


title: CMML22


title: DKD 2

description: Library name: Sample 13


title: IL17KO3

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

description: Library name: IL17KO5

data_processing:
The NextSeq basecalls files were converted to fastq files using the bcl2fastq program with default parameters (without trimming or filtering applied at this stage).
Raw reads (fastq files) were inspected for quality issues with FastQC. Following that, the 3 first bases of each read were trimmed ( according to library preparation guidelines) and reads were subjected to quality-trimmed with cutadapt, using a quality threshold of 32 for both ends, poly-G sequences (NextSeq’s no signal) and adapter sequences were removed from the 3' end, and poly-T stretches were removed from the 5' end (being the reverse-complement of poly-A tails). The cutadapt parameters included using a minimal overlap of 1, allowing for read wildcards, and filtering out reads that became shorter than 15 nt. Finally, low quality reads were filtered out using fastq_quality_filter, with a quality threshold of 20 at 90 percent or more of the read's positions.
Alignment and counting
The processed reads were aligned to the mouse transcriptome and genome with TopHat, allowing for 10 mismatches (see full command below). The genome version was GRCm39, with annotations from Ensembl release 106.
Quantification was done with htseq-count. Strand information was set to 'forward', and an annotation file that lacked information for genes of type IG, TR, Artifact, miRNA, Mt_rRNA, Mt_tRNA, ncRNA, piRNA, pre_miRNA, rRNA, ribozyme, sRNA, scRNA, scaRNA, siRNA, snRNA, snoRNA, tRNA and vaultRNA was used.
Assembly: GRCm39
Supplementary files format and content: raw_and_norm_counts.xlsx
Supplementary files format and content: raw_and_norm_counts.xlsx contains row per gene with Ensembl gene id, Symbol, name, raw counts per sample and normalized (DESeq2 base mean) counts per sample

source_name: Soft tissue (Muscle and soft callus)

growth_protocol: mice were breeded in SPF conditions, and the soft tussue was extracted 5 days post injury

extract_protocol:
RNEASY MINI KIT protocol
Kapa stranded mRNA

treatment_protocol: soft tissues from the vicinity of the drill hole were collected on the fifth day from Il17af-/- mice and their littermates for RNA sequencing

value: Soft tissue (Muscle and soft callus)

value: 1.5-mm drill hole defect in the mandible


title: Co_L1_48_8K

city: San Diego

first: Yasmin

last: Vasquez

state: CA

address: 3612 Mount Ariane Dr

institute: Lassen Therapeutics

description: Library name: Sample 77

data_processing:
Raw image data from Illumina sequencing were converted to FASTQ format using CASAVA base calling. Low-quality reads were filtered out by removing reads containing adapter contamination, reads with >10% undetermined bases (N), and reads with >50% low-quality bases (Q < 5).
Clean reads were aligned to the Homo sapiens (hg38) reference genome using HISAT2, a graph-based alignment algorithm. Gene expression quantification was performed using FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Assembly: Homo sapiens (hg38)
Supplementary files format and content: FASTQ (.fq), Raw sequencing reads (four-line format: identifier, sequence, +, quality)
Supplementary files format and content: FPKM matrix, Normalized expression values (FPKM per gene per sample)

source_name: Orbital adipose/connective tissue

growth_protocol: Following collection, tissues were minced into 1–2 mm pieces, placed in T75 culture flasks containing 15 mL of growth media high glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 20% fetal bovine serum and 1% penicillin/ streptomycin, and incubated at 37°C with 5% CO2. Culture medium was renewed every 3–4 days and tissue was maintained in culture for 2-3 weeks to allow the orbital fibroblasts to migrate out of the tissue and adhere.  Floating debris was cleared, and attached cells were expanded and used up to 6 passages.

extract_protocol:
RNA was isolated from orbital fibroblast cells using the RNeasy Plus Mini kit (Cat#74134, Qiagen) according to manufacturer instructions.
Messenger RNA (mRNA) was purified from total RNA using poly-T oligo–attached magnetic beads to isolate polyadenylated transcripts. The purified mRNA was then fragmented into short fragments, which served as templates for first-strand cDNA synthesis using random hexamer primers. The second-strand cDNA was synthesized using dTTP, generating non-directional libraries. Following cDNA synthesis, fragments were subjected to end repair, A-tailing, and adapter ligation. Ligated products were then size-selected, PCR-amplified, and purified to obtain the final sequencing libraries. Library quality and quantity were assessed using a Qubit fluorometer for concentration measurement, real-time PCR for accurate quantification, and a Bioanalyzer for insert size distribution. Final libraries were pooled according to effective concentration and sequenced on an Illumina platform to generate paired-end reads.

treatment_protocol: Orbital fibroblasts were seeded in 6-well plates at a density of 1 x 10^5 cells/well (2 mL volume) in growth media and incubated at 37°C with 5% CO2. After 24 hours media was replaced with DMEM supplemented with penicillin, streptomycin and 1% FBS for an additional 24 hours (starvation media).  Serum-starved cells were pretreated with LASN01 antibody at 1 µg/mL or 10 µg/mL Teprotumumab in starvation media for 1hr. Cells were subsequently treated with agonists IL-11 (10ng/mL), or a combination of IL-11 and IGF-1 (100ng/mL) for 6 or 48hr.

value: Orbital adipose/connective tissue

value: primary fibroblast

value: thyroid eye disease


title: CMML23

value: CMML


title: MDS1833

description: MDS

value: human BM Mononuclear cells


title: CMML21


title: CMML19

value: M


title: IL17KO2

description: Library name: IL17KO2


title: Normal 10

description: Library name: Sample 11


title: Normal 11

description: Library name: Sample 12


title: CMML18


title: CMML20


title: CMML16


title: Normal 9

description: Library name: Sample 10


title: CMML17


title: Normal 8

description: Library name: Sample 9


title: CMML14


title: Normal 7

description: Library name: Sample 8


title: WT3

description: Library name: WT5

value: WT


title: IL17KO1

description: Library name: IL17KO1


title: CMML12


title: CMML15


title: CMML13


title: WT4

description: Library name: WT6


title: CMML11


title: Normal 6

description: Library name: Sample 7


title: CMML10


title: WT2

description: Library name: WT4


title: WT1

description: Library name: WT3


title: CMML9


title: Normal 5

description: Library name: Sample 6


title: CMML8


title: CPC;ApcPten3

city: Hiroshima-shi

first: Hikaru

last: Nakahara

address: kasumi 1-2-3, minami-ku

country: Japan

institute: Hiroshima University

description: Library name: K120

data_processing:
Sequencing reads were pre-processed using fastp v0.20.
RSEM was used for mapping and quantification to the human genome GRCh38.p13. STAR was selected as the parameter for mapping.
Assembly: GRCm38
Supplementary files format and content: txt file includes raw counts for each sample
Supplementary files format and content: txt file includes transcripts per million (TPM) value for each sample

source_name: colon

extract_protocol:
RNA was extracted from frozen samples using the RNeasy Mini Kit (Qiagen)
TruSeq Stranded mRNA library was prepared from total RNA using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) according to the TruSeq Stranded mRNA Reference Guide (Document #1000000040498, v00). The procedure included poly(A)+ RNA purification, fragmentation, first- and second-strand cDNA synthesis, adapter ligation, and PCR amplification, selecting fragments of approximately 200–400 bp in length.

value: colon

value: Apc and Pten conditional knockout


title: CMML7

value: F


title: Normal 4

description: Library name: Sample 5

value: normal (paraneoplastic tissue)


title: CPC;Apc3

description: Library name: K88

value: Apc conditional knockout


title: CMML5


title: CPC;Apc2

description: Library name: K82


title: Normal 3

description: Library name: Sample 4

value: Kidney


title: CMML6


title: CMML4


title: CMML3


title: CMML2


title: Normal 2

description: Library name: Sample 3


title: CMML1


title: Normal 1

description: Library name: Sample 2


title: CPC;ApcPten2

description: Library name: K80


title: LPS immunized, day 4, Blimp1+ plasma cell, biol rep 4

first: Brian

middle: Thomas

last: Gaudette

state: PA

address: 3620 Hamilton Walk, Pathology and Laboratory Medicine

department: Pathology and Lab Medicine

institute: University of Pennsylvania

description: Library name: 84-6-PC

data_processing:
Fastq data files were generated tvia the illumina Basespace bcl2fastq pipeline.
Paired-end sequences were aligned to mm10 mouse genome with Bowtie2
ATAC-seq BAM files from FO, MZ, and PC-B cells were processed to generate genome-wide signal tracks
Coverage was computed using BEDTools genomecov, converted to bedGraph format, and transformed into BigWig files using bedGraphToBigWig with mm10 chromosome sizes
Assembly: GRCm38 (mm10)
Supplementary files format and content: 83-1-FO.bw, sample specific BigWig genome trace
Supplementary files format and content: 83-1-MZ.bw, sample specific BigWig genome trace
Supplementary files format and content: 83-3-FO.bw, sample specific BigWig genome trace
Supplementary files format and content: 83-3-MZ.bw, sample specific BigWig genome trace
Supplementary files format and content: 84-1-FO.bw, sample specific BigWig genome trace
Supplementary files format and content: 84-1-MZ.bw, sample specific BigWig genome trace
Supplementary files format and content: 84-2-FO.bw, sample specific BigWig genome trace
Supplementary files format and content: 84-2-MZ.bw, sample specific BigWig genome trace
Supplementary files format and content: 84-3-PC.bw, sample specific BigWig genome trace
Supplementary files format and content: 84-4-PC.bw, sample specific BigWig genome trace
Supplementary files format and content: 84-5-PC.bw, sample specific BigWig genome trace
Supplementary files format and content: 84-6-PC.bw, sample specific BigWig genome trace
Supplementary files format and content: FO_merged.bw, follicular B cell (n=4) merged BigWig genome trace
Supplementary files format and content: MZ_merged.bw, marginal zone B cell (n=4) merged BigWig genome trace
Supplementary files format and content: PC_merged.bw, plasma cell (n=4) merged BigWig genome trace

source_name: spleen

extract_protocol:
ATAC-seq was performed according to modified published protocol in Buenrostro et al Curr Protoc Mol Biol 2015: 50K cells were sorted into 500 mL indicator-free RPMI supplemented with 10% FBS and10 mM HEPES and centrifuged at 600 x g at 4°C. Cells were washed with cold 1X PBS and lysed with 45 L lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and quickly spun at 600 x g for 10 minutes at 4°C. Nuclei pellets were resuspended in 50 μL transposition reaction containing 2.5 μL Tn5 transposase (Nextera) and incubating at 37°C for 30 minutes.
Tagmented DNA was purified using Qiagen MinElute Reaction Cleanup Kit, and transposed DNA was eluted in 10 mL elution buffer (10mM Tris HCL, pH 8). Transposed DNA was amplified in 0.2 mL PCR tubes containing 10 mL transposed DNA, 10 mL nuclease-free water, 2.5 mL 25 uM PCR primer 1, 2.5 mL 25 mM Barcoded PCR primer 2, and 25 mL NEBNext High-Fidelity 2x PCR master mix, and amplified. Optimal cycle number of 12 was determined empircally. Equal molar pooling was performed using quantitation by Tapestation 2200 and Qubit.

treatment_protocol: Follicular (CD19+, CD93-, CD23+, CD21int) and marginal zone (CD19+, CD93-, CD23-, CD21high) B cells were sorted from untreated 10 week old C57BL6 mouse spleens. Plasma cells (IgD-, lineage[CD4, CD8a, F4/80, Ter119]-, CD138+, GFP(Blimp1)+) were sorted from 10 week old B6.Blimp1GFP/+ spleens 4 days post immunization with 50 ug LPS i.p.

value: spleen

value: plasma cell

value: 50 ug LPS i.p. day 4


title: CPC;ApcPten1

description: Library name: K79


title: DKD 1

description: Library name: Sample 1

value: DKD

value: Renal tubules


title: MF40

city: Pittsburgh

first: Patrizia

last: Fuschiotti

address: 200 Lothrop St

institute: University of Pittsburgh

description:
Library name: Sample 23
Treatments hashed together, HTO5-ctr,HTO6-regn

data_processing:
Chromium scRNA-seq data produced by the 10X Chromium Platform were processed to generate sample-specific fastq files.
Processed reads were then examined by quality metrics, mapped to a reference human genome using RNA-seq aligner STAR and assigned to individual cells of origin according to the cell specific barcodes, using the Cell Ranger pipeline (10X Genomics).
To ensure that PCR amplified transcripts were counted only once, only single UMIs were counted for gene expression level 10. In this way, cell x gene UMI counting matrices were generated for downstream analyses.
Seurat, an R package developed for single-cell analysis, was used to identify distinct cell populations and visualize cell clusters in graphs. Specifically, the UMI matrix was filtered such that only cells expressing at least 200 genes were utilized in downstream analysis.
Unwanted sources of variation were regressed out of the data by constructing linear models to predict gene expression based on the number of UMIs per cell as well as the percentage of mitochondrial gene content. Hashtags were demultiplexed based on the Seurat package, https://satijalab.org/seurat/articles/hashing_vignette.html
Assembly: GrCh38A genome
Supplementary files format and content: H5 files for gene expression, CSV files for TCR outputs

source_name: Skin

extract_protocol:
Skin biopsies were minced and digested enzymatically (Whole Dissociation Skin Kit, Miltenyi Biotec) for 2 hours at 37°C and further dispersed using the Miltenyi gentleMACS Octo Dissociator. Skin biopsies were hashed together 2 at a time per protocol: https://www.biolegend.com/en-us/protocols/totalseq-b-or-c-with-10x-feature-barcoding-technology.
Experimental procedures followed established techniques using the Chromium Single Cell 5’ Library V2 kit +V(D)J Enrichment Kit, Human T Cell (10x Genomics).

value: Skin

tag: health status

value: mycosis fungoides

tag: chemistry


title: LPS immunized, day 4, Blimp1+ plasma cell, biol rep 3

description: Library name: 84-5-PC


title: LPS immunized, day 4, Blimp1+ plasma cell, biol rep 2

description: Library name: 84-4-PC


title: marginal zone B cell, biol rep 4

description: Library name: 84-2-MZ

value: marginal zone B cell

value: Wildtype

value: untreated


title: follicular B cell, biol rep 4

description: Library name: 84-2-FO

value: follicular B cell


title: CPC;Apc1

description: Library name: K66

value: colon


title: marginal zone B cell, biol rep 3

description: Library name: 84-1-MZ


title: MF35

description:
Library name: Sample 22
Treatments hashed together, HTO3-ctr,HTO4-regn


title: LPS immunized, day 4, Blimp1+ plasma cell, biol rep 1

description: Library name: 84-3-PC


title: Ctrl

city: Xiamen

first: Lingjuan

last: Zhang

address: Xiangan South Street

institute: Xiamen University

description:
Library name: Sam1
Female C57BL/6J mice (7 weeks old) were subjected to dorsal hair removal using depilatory cream (Nair) 24 hours before initiating experimental interventions. For the control treatment, a volume of 100% ethanol containing no active agent was topically applied daily to a 2 cm × 2 cm depilated dorsal skin area for 10 consecutive days. On day 10, all mice were euthanized to collect samples for subsequent analyses.

data_processing:
The raw sequencing data was demultiplexed and aligned to the reference genome ensembl-release111 using Cell Ranger v3.1.0 pipiline (10x Genomics). The generated raw gene expression matrix was converted into Seurat objects using the R package Seurat v5.0.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: dorsal skin

extract_protocol:
Mouse dorsal skin biopsies were collected from mice, and skin biopsies were subjected to mincing and enzymatic digestion by collagenase D and DNase1 to isolate single cell.
Dead cells were removed using Dead Cell Removal kit (Miltenyi Biotic,130-090-101) according to manufacturer’s instruction. Live single cells (>85% viability) were loaded on a 10x Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Barcoded, full-length cDNAs were reverse-transcribed from polyadenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from post GEM reaction mixture. Next, libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. R1 (read 1 primer sequence) were added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification.

value: dorsal skin

value: EtOH-treated


title: AD

description:
Library name: Sample2
Female C57BL/6J mice (7 weeks old) were subjected to dorsal hair removal using depilatory cream (Nair) 24 hours before initiating experimental interventions. MC903 (calcipotriol; MedChemExpress, catalog no. HY-10001) was dissolved in 100% ethanol and freshly diluted to a final concentration delivering 4.5 nmol per application. This solution was topically applied daily to a 2 cm × 2 cm depilated dorsal skin area for 10 consecutive days. On day 10, mice were euthanized for sample collection and subsequent analyses.


title: follicular B cell, biol rep 3

description: Library name: 84-1-FO


title: MF34

description:
Library name: Sample 21
Treatments hashed together, HTO1-ctr,HTO2-regn


title: follicular B cell, biol rep 2

description: Library name: 83-3-FO


title: marginal zone B cell, biol rep 2

description: Library name: 83-3-MZ


title: Hippocampus, DEK WT, male, 3

city: Cincinnati

first: Taylor

last: Lange

state: OH

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

description: Library name: CMV421

data_processing:
Kallisto was used to generate TPM
AltAnalyze v2.1.4.4 (EnsMart100 database) was used to perform the subsequent differential expression analysis.
The AltAnalyze supplied empirical Bayes moderated t-test was performed followed by Benjamini-Hochberg adjustment for false discovery (FDR).
Final threshold cutoffs were an raw p-value < 0.05 and linear fold change ≥ 1.2.
Assembly: mm10
Supplementary files format and content: CMVDEK_TPM.txt
Supplementary files format and content: tab-delimited file of TPM for each sample

source_name: brain, hippocampus

extract_protocol:
Mice were euthanized by isoflurane inhalation followed by decapitation within 6 weeks of the completion of the final behavior assay. Brains were microdissected to remove the hippocampus and stored in RNA-Later at -20 oC. Tissue was homogenized in 1 mL of trizol using a tissue disruptor (Qiagen) and RNA isolated using standard Trizol/chloroform extraction and precipitation with isopropanol.
RNA libraries were prepared for sequencing using standard Illumina protocols by the CCHMC Genomics Sequencing Facility (RRID:SCR_022630)

value: brain, hippocampus

value: DEK WT


title: MF31

description:
Library name: Sample 20
Treatments hashed together, HTO3-ctr,HTO4-regn


title: marginal zone B cell, biol rep 1

description: Library name: 83-1-MZ


title: follicular B cell, biol ep 1

description: Library name: 83-1-FO


title: Hippocampus, DEK WT, male, 2

description: Library name: CMV419


title: follicular B cell cultured on OP9 cells unstimulated for 68 hrs rep 3

description: Library name: Op9_Utx_68_3

data_processing:
basecalling: Illumina basespace pipeline (and concatenation of 4 lanes)
pseudoalignment: Kallisto (param: -b 100 --single -l 250 -s 30 -t 16)
differential expression: Voom (normalization), and limma linear fit: empirical Bayes method, for differential expression
all data display and additional statistics: R statistical environment
Assembly: GRCm38/mm10 cDNA
Supplementary files format and content: Op9_DL1.rawTPM.txt: matrix file of transript per million (TPM) values from pseudoalignment (Kallisto).
Supplementary files format and content: Op9_DL1.normExp.txt: matrix file of normalized TPM values for analyses performed (voom, limma).

extract_protocol:
Pure cell populations were FACS-sorted into Trizol reagent supplemented with 0.5% 2-mercaptoethanol. Phenol-Chloroform RNA isolation and precipitation was performed with glycogen carrier according to manufacturer protocol.
cDNA was prepared using Takara Clonetech SMART-seq HT kit and Illumina Nextera XT kits according to SMART-seq HT kit protocol.

treatment_protocol: Cell populations were purified from mouse spleens and co-cultured on confluent OP9 or OP9-DL1 cultures for 20, 44, or 68 hours in 96-well plates at 2x10^5 per well with B cell stimulation culture media  Cells were stimulated with the following, where indicated: Unstimulated (just B cell stimulation media), LPS (purified from salmonella enterica), or anti-IgM (F(ab'2)), all at 10 ug/mL. Cultures were maintained for 20-68 hours as indicated at 5% CO2, 37 degrees C.


title: follicular B cell cultured on OP9 cells unstimulated for 68 hrs rep 1

description: Library name: Op9_Utx_68_1


title: Hippocampus, DEK KO, male, 3

description: Library name: CMV416

value: DEK KO


title: Hippocampus, DEK KO, male, 2

description: Library name: CMV403


title: follicular B cell cultured on OP9 cells unstimulated for 68 hrs rep 2

description: Library name: Op9_Utx_68_2

value: spleen


title: MF22

description:
Library name: Sample 17
Treatments hashed together, HTO3-ctr,HTO4-regn


title: follicular B cell cultured on OP9 cells stimulated with LPS for 68 hrs rep 2

description: Library name: Op9_LPS_68_2

value: LPS


title: MF28

description:
Library name: Sample 18
Treatments hashed together, HTO1-ctr,HTO2-regn


title: follicular B cell cultured on OP9 cells stimulated with LPS for 68 hrs rep 3

description: Library name: Op9_LPS_68_3


title: MF30

description:
Library name: Sample 19
Treatments hashed together, HTO1-ctr,HTO2-regn


title: PF3CULTURE

description:
Library name: Sample 16
Treatments hashed together, HTO3-ctr,HTO4-regn

value: healthy control


title: follicular B cell cultured on OP9 cells stimulated with LPS for 68 hrs rep 1

description: Library name: Op9_LPS_68_1


title: Hippocampus, DEK KO, male, 1

description: Library name: CMV395


title: follicular B cell cultured on OP9 cells stimulated with LPS for 44 hrs rep 3

description: Library name: Op9_LPS_44_3


title: follicular B cell cultured on OP9 cells stimulated with LPS for 44 hrs rep 2

description: Library name: Op9_LPS_44_2


title: Hippocampus, DEK KO, female, 3

description: Library name: CMV389


title: PF2CULTURE

description:
Library name: Sample 15
Treatments hashed together, HTO1-ctr,HTO2-regn


title: NS17CULTURE

description:
Library name: Sample 14
Treatments hashed together, HTO5-ctr,HTO6-regn


title: follicular B cell cultured on OP9 cells stimulated with LPS for 44 hrs rep 1

description: Library name: Op9_LPS_44_1


title: follicular B cell cultured on OP9 cells stimulated with LPS for 20 hrs rep 2

description: Library name: Op9_LPS_20_2


title: follicular B cell cultured on OP9 cells stimulated with LPS for 20 hrs rep 3

description: Library name: Op9_LPS_20_3


title: Hippocampus, DEK KO, female, 2

description: Library name: CMV386


title: Hippocampus, DEK KO, female, 1

description: Library name: CMV374


title: follicular B cell cultured on OP9 cells stimulated with LPS for 20 hrs rep 1

description: Library name: Op9_LPS_20_1


title: Hippocampus, DEK WT, male, 1

description: Library name: CMV350


title: follicular B cell cultured on OP9 cells stimulated with anti-IgM F(ab)'2 for 68 hrs rep 1

description: Library name: Op9_IgM_68_1

value: a-IgM


title: NS14CULTURE

description:
Library name: Sample 13
Treatments hashed together, HTO3-ctr,HTO4-regn


title: follicular B cell cultured on OP9 cells stimulated with anti-IgM F(ab)'2 for 68 hrs rep 3

description: Library name: Op9_IgM_68_3


title: follicular B cell cultured on OP9 cells stimulated with anti-IgM F(ab)'2 for 68 hrs rep 2

description: Library name: Op9_IgM_68_2


title: follicular B cell cultured on OP9 cells stimulated with anti-IgM F(ab)'2 for 44 hrs rep 3

description: Library name: Op9_IgM_44_3


title: Hippocampus, DEK WT, female, 3

description: Library name: C57147


title: follicular B cell cultured on OP9 cells stimulated with anti-IgM F(ab)'2 for 44 hrs rep 2

description: Library name: Op9_IgM_44_2


title: NS17

description: Library name: Sample 11


title: NS13CULTURE

description:
Library name: Sample 12
Treatments hashed together, HTO1-ctr,HTO2-regn


title: Hippocampus, DEK WT, female, 2

description: Library name: C57146


title: NS16

description: Library name: Sample 10


title: follicular B cell cultured on OP9 cells stimulated with anti-IgM F(ab)'2 for 44 hrs rep 1

description: Library name: Op9_IgM_44_1


title: follicular B cell cultured on OP9 cells stimulated with anti-IgM F(ab)'2 for 20 hrs rep 3

description: Library name: Op9_IgM_20_3


title: NS14

description: Library name: Sample 9


title: follicular B cell cultured on OP9-DL1 cells unstimulated for 68 hrs rep 3

description: Library name: DL1_Utx_68_3


title: follicular B cell cultured on OP9 cells stimulated with anti-IgM F(ab)'2 for 20 hrs rep 2

description: Library name: Op9_IgM_20_2


title: Hippocampus, DEK WT, female, 1

description: Library name: C57145


title: PF2/PF3

description: Library name: Sample 7


title: follicular B cell cultured on OP9-DL1 cells unstimulated for 68 hrs rep 1

description: Library name: DL1_Utx_68_1


title: follicular B cell cultured on OP9 cells stimulated with anti-IgM F(ab)'2 for 20 hrs rep 1

description: Library name: Op9_IgM_20_1


title: Mov10 KO HSC cells at 12 days post-4.5 Gy-2

city: Chongqing

first: Chang

middle: Lin

last: Zhen

address: Baianba

institute: Chongqing Three Gorges Medical College

description: Library name: SAMPLES 5

library_source: other

data_processing:
CLC Genomics workbench v 11.0.1
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Library strategy: Ribo-Seq

molecule: other

source_name: Mov10 KO

extract_protocol:
Ribosome profiling libraries were prepared per established methods [52]. Cells underwent 100 mg/ml cycloheximide treatment (5 min, 37°C) before harvesting in ribosome lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl₂, 1 mM DTT, 1% Triton X-100, 25 U/ml Turbo DNase I) with equivalent cycloheximide. Cytoplasmic RNA was digested with RNase I (45 mins, RT, nutator), terminated by SuperRNaseIn addition. Ribosome-protected fragments were isolated via sucrose cushion centrifugation (2 ml 1 M sucrose in Triton-free lysis buffer; SW-32 rotor, max speed, 4°C, 7 hr). Pellet resuspension in Trizol was followed by RNA extraction per manufacturer.
Size selec-tion (15% TBE-urea PAGE) used 24 and 36nt RNA markers; 24-36nt fragments were excised and extracted by freezing in dry ice bath with RNA extraction buffer (300 mM NaOAc pH 5.5, 1.0 mMEDTA, 0.25% SDS) for 30 minutes, followed by an overnight incubation at room temperature on a nutator and isopropanol-precipitated. Adaptor ligation (NEB miRNA adaptor), gel purifica-tion (15 % PAGE), SuperScript III reverse transcription, and CircLigase circularization preceded PCR amplification.

value: Mov10 KO

value: hematopoietic stem cells

value: 4.5 Gy IR

value: 12 days


title: NS13

description: Library name: Sample 8

value: Skin


title: follicular B cell cultured on OP9-DL1 cells unstimulated for 68 hrs rep 2

description: Library name: DL1_Utx_68_2


title: Mov10 KO HSC cells at 12 days post-4.5 Gy-3

description: Library name: SAMPLES 6


title: Mov10 KO HSC cells at 12 days post-4.5 Gy-1

description: Library name: SAMPLES 4


title: follicular B cell cultured on OP9-DL1 cells stimulated with LPS Blimp1+ rep 3

description: Library name: DL1_LPS_BlimpPos_3

value: DL1, LPS


title: follicular B cell cultured on OP9-DL1 cells stimulated with LPS Blimp1+ rep 2

description: Library name: DL1_LPS_BlimpPos_2

value: follicular B cell


title: MF48

description: Library name: Sample 6

value: mycosis fungoides


title: follicular B cell cultured on OP9-DL1 cells stimulated with LPS Blimp1+ rep 1

description: Library name: DL1_LPS_BlimpPos_1


title: WT HSC cells at 12 days post-4.5 Gy IR-3

description: Library name: SAMPLES 3

source_name: WT

value: WT


title: MF36

description: Library name: Sample 5


title: follicular B cell cultured on OP9-DL1 cells stimulated with LPS for 68 hrs rep 2

description: Library name: DL1_LPS_68_2


title: MF25

description: Library name: Sample 3


title: follicular B cell cultured on OP9-DL1 cells stimulated with LPS for 68 hrs rep 1

description: Library name: DL1_LPS_68_1


title: WT HSC cells at 12 days post-4.5 Gy IR-2

description: Library name: SAMPLES 2


title: follicular B cell cultured on OP9-DL1 cells stimulated with LPS for 68 hrs rep 3

description: Library name: DL1_LPS_68_3


title: follicular B cell cultured on OP9-DL1 cells stimulated with LPS for 44 hrs rep 1

description: Library name: DL1_LPS_44_1


title: HSC cells at 12 days post-4.5 Gy IR-IgG-3

description: Library name: SAMPLES 6

data_processing:
CLC Genomics workbench v 11.0.1
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: hematopoietic stem cells

extract_protocol:
Rip-seq was performed using Magna RIP Kit (Merck Millipore, Darmstadt, Germany, 17-700) according to the manufacturer’s instructions. Bone marrow cells from femurs and tibiae were collected, red blood cells lysed with red blood cell lysis buffer, and cells resuspended in PBS containing 2% FBS. Lin-c-kit+ cells were sequentially enriched using EasySep™ Mouse Hematopoi-etic Progenitor Cell Isolation Kit  and EasySep™ Mouse CD117 (cKIT) Positive selection Kit (StemCell Technologies, Vancouver, BC, Canada).Cell were lysed in complete RIP lysis buff-er-containing protease inhibitors and RNase inhibitor. Mov10 protein was pulled down using a Dynabeads-associated Mov10 antibody. A mock pull-down was carried out with normal rabbit IgG (Cell Signaling Technologies, Danvers, Massachusetts, USA, 2729). After rigorous washing, co-precipitated RNA was isolated by Trizol.
The pre-amplified cDNA was fragmented using Tn5 enzyme, and libraries were generated using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme Biotech, Nanjing, Jiangsu, China). The libraries were then subjected to paired-end se-quencing on the Illumina HiSeq X Ten platform


title: follicular B cell cultured on OP9-DL1 cells stimulated with LPS for 44 hrs rep 3

description: Library name: DL1_LPS_44_3


title: follicular B cell cultured on OP9-DL1 cells stimulated with LPS for 20 hrs rep 3

description: Library name: DL1_LPS_20_3


title: MF24

description: Library name: Sample 2


title: WT HSC cells at 12 days post-4.5 Gy IR-1

description: Library name: SAMPLES 1


title: follicular B cell cultured on OP9-DL1 cells stimulated with LPS for 44 hrs rep 2

description: Library name: DL1_LPS_44_2


title: MF26

description: Library name: Sample 4


title: HSC cells at 12 days post-4.5 Gy IR-IgG-2

description: Library name: SAMPLES 5


title: follicular B cell cultured on OP9-DL1 cells stimulated with LPS for 20 hrs rep 1

description: Library name: DL1_LPS_20_1


title: RNA-seq in THP1 cells: IRF7 RE Haplotype Unstimulated Replicate 2

status: Public on Jul 09 2026

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

description: Library name: RNA-seq_THP1_RE02_E007061

data_processing:
RNA-seq reads were mapped to the hg19 genome using the nf-core RNA-seq pipeline with the default alignment options (STAR and Salmon).
Transcription abundance estimates generated by Salmon
Assembly: hg19
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing CPM --binSize 10. The reads aligned to the forward strand were processed separately from the reads aligned to the reverse strand. The parameter --scaleFactor -1 was used when generating the reads on the reverse strand.

growth_protocol: THP-1 IRF7 deficient and HEK Blue hTLR7 cells were purchased from InvivoGen. THP-1 cells were grown in RPMI 1640 medium supplemented with 10% FBS, 10,000 units/mL of penicillin, 10,000 ug/mL of streptomycin, and Normocin. Following transduction, THP-1 cell lines stably expressing IRF7 variants were also cultured in 1 ug/mL puromycin. HEK Blue hTLR7 cells were grown in DMEM medium supplemented with 10% FBS, 10,000 units/mL of penicillin, and 10,000 ug/mL of streptomycin. All cells were kept at 37°C and 5% CO2 and were determined to be mycoplasma free.

extract_protocol:
Total RNA was isolated using the mirVana RNA extraction kit
rRNA depleted, stranded libraries were generated by and sequenced at the Cincinnati Children’s Hospital Medical Center Genomics Sequencing Facility (CCHMC)

treatment_protocol: THP-1 cells were stimulated using 2.5ug/mL of low molecular weight Poly(I:C) transfected using Lipofectamine 2000. HEK Blue hTLR7 cells were stimulated using 1ug/mL of Resiquimod (R848).

tag: irf7 genotype

value: Protective

tag: stimulation


title: MF21

description: Library name: Sample 1


title: 3190115_JWH004-C32_resistant

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

description: Library name: sample 8

data_processing:
Paired-end 100-cycle sequencing was performed on NovaSeq6000 sequencer following the manufacturer’s instructions (Illumina). Raw reads were first trimmed using TrimGalore (v0.6.3) with parameters ‘--paired --retain_unpaired’
Filtered reads were then mapped to the Homo sapiens reference genome GRC38 using STAR (v2.7.9a). Gene-level read quantification was done using RSEM (v1.3.1)on the Gencode annotation v31. To identify the differentially expressed genes, normalization factors are first estimated using the trimmed mean of M values (TMM) and genes with CPM < 1 in all samples were removed.
Next, the TMM normalization factors and raw counts were then used for the Limma-voom analysis using the “voom”, “lmFit” and “eBayes” functtions from the limma R package.
Assembly: hg38
Supplementary files format and content: gene-based raw counts and TPM tsv file

source_name: Blood

growth_protocol: The knockin clones of SEM were cultured in RPMI-1640 medium (Lonza) containing 10 % fetal bovine serum (Hyclone), 2 mM glutamine (Sigma), and 1% penicillin/streptomycin (Thermo Fisher Scientific) in an incubator at 37°C, 5 % CO2 and 95 % humidity. A high-titer virus for TRE3G-HA-MBNL1-Zeocin was generated using 293T cells, which were cultured in DMEM (GIBCO, Life Technologies) with 10% heat-inactivated fetal bovine serum (Hyclone) and 2 mM L-glutamine (Sigma) at 37°C in 5% CO2. All cell lines were validated by STR and verified to be free of mycoplasma by Lookout Mycoplasma PCR Detection Kit (Sigma, #MP0035).

extract_protocol:
Total RNA was extracted from cells using Trizol (Thermo Fisher Scientific, 15596026) with the zymo RNA clean and concentrator kit 5 kit.
The RNA-seq library was constructed  for deep sequencing using a Novaseq system (illumina) for single-end 100-bp reads.

treatment_protocol: The CTCF-miniAID-mClover3 knockin cells were treated by 1uM 5-Ph-IAA with or without 100ug/ml Zeocin for long-term culture until day 36. Fresh medium with drug were changed every 3 days.

value: Blood

value: SEM

tag: cell type

value: B-ALL

tag: clone

value: C3.2 resistant


title: HSC cells at 12 days post-4.5 Gy IR-3

description: Library name: SAMPLES 3

tag: tissue


title: follicular B cell cultured on OP9-DL1 cells stimulated with anti-IgM F(ab)'2 for 68 hrs rep 1

description: Library name: DL1_IgM_68_1

value: spleen

value: DL1, a-IgM


title: follicular B cell cultured on OP9-DL1 cells stimulated with LPS for 20 hrs rep 2

description: Library name: DL1_LPS_20_2


title: follicular B cell cultured on OP9-DL1 cells stimulated with anti-IgM F(ab)'2 for 44 hrs rep 3

description: Library name: DL1_IgM_44_3


title: follicular B cell cultured on OP9-DL1 cells stimulated with anti-IgM F(ab)'2 for 20 hrs rep 3

description: Library name: DL1_IgM_20_3


title: follicular B cell cultured on OP9-DL1 cells stimulated with anti-IgM F(ab)'2 for 68 hrs rep 3

description: Library name: DL1_IgM_68_3


title: HSC cells at 12 days post-4.5 Gy IR-IgG-1

description: Library name: SAMPLES 4


title: follicular B cell cultured on OP9-DL1 cells stimulated with anti-IgM F(ab)'2 for 68 hrs rep 2

description: Library name: DL1_IgM_68_2


title: follicular B cell cultured on OP9-DL1 cells stimulated with anti-IgM F(ab)'2 for 44 hrs rep 2

description: Library name: DL1_IgM_44_2


title: HSC cells at 12 days post-4.5 Gy IR-2

description: Library name: SAMPLES 2


title: follicular B cell cultured on OP9-DL1 cells stimulated with anti-IgM F(ab)'2 for 44 hrs rep 1

description: Library name: DL1_IgM_44_1


title: 3190114_JWH003-C32_resistant

description: Library name: sample 7

tag: cell line


title: follicular B cell cultured on OP9-DL1 cells stimulated with anti-IgM F(ab)'2 for 20 hrs rep 1

description: Library name: DL1_IgM_20_1

tag: genotype


title: 3190113_JWH002-C32_parental

description: Library name: sample 6

value: C3.2 parental


title: WTD-ZZ

description: Library name: Sample 2

data_processing:
The raw sequence data were firstly quality trimmed by fatsp software to obtain the clean reads. Then the clean reads were aligned to the (input your reference genome and version, eg, the musculus GRCm39) using Bowtie2 and subsequently analyzed by the SEACR software based the ‘stringent’parameter to detect genomic regions enriched for multiple overlapping DNA fragments (peaks) that we considered to be putative binding sites. Visualization of peak distribution along genomic regions of interested genes was performed with IGV.Peaks were then annotated using chipseeker software to obtain the genes and gene annotations about peaks. Significant Motif of peaks were analyzed by MEME and DREME software and aligned to the motif database.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Normalized_read_density for each Sample
Library strategy: CUT&Tag

source_name: Primary tubular epithelial cells

growth_protocol: Sirt6fl/fl and Sirt6ΔTEC mice were kept in the same environment.

extract_protocol:
prepared concanavalin A-coated magnetic beads (ConA beads) were added to resuspended cells and incubated at room temperature to bound cells. Non-ionic detergent Digitonin was used to permeate cell membrane. Then, primary H3K9ac antibody (A21107, Abclonal), secondary antibody and the Hyperactive pA-Tn5 Transposase were incubated with the cells that were bounded by ConA beads in order.
Therefore, the Hyperactive pA-Tn5 Transposase can exactly cut off the DNA fragments that were bound with target protein. In addition, the cut DNA fragments can be ligated with P5 and P7 adaptors by Tn5 transposase and the libraries were amplified by PCR with the P5 and P7 primers. The purified PCR products were evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Finally, these libraries were sequenced on the Illumina NovaSeq6000 platform and 150bp paired-end reads were generated for the following analysis.

treatment_protocol: DKD was induced in Sirt6fl/fl and Sirt6ΔTEC mice through uninephrectomy followed by STZ and HFD administration.

value: Primary tubular epithelial cells

tag: treatment

value: Uninephrectomy+STZ+HFD


title: 3171952_JWH004-C172_resistant

description: Library name: sample 4

value: C17.2 resistant


title: S6D-ZZ

description: Library name: Sample 1

value: SIRT6 knockdown


title: follicular B cell cultured on OP9-DL1 cells stimulated with anti-IgM F(ab)'2 for 20 hrs rep 2

description: Library name: DL1_IgM_20_2


title: 3190112_JWH001-C32_parental

description: Library name: sample 5


title: WTD-3

description: Library name: Sample 6

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. Then about xxxxxx clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM, count values for each Sample

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). Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.


title: 3171950_JWH002-C172_parental

description: Library name: sample 2

value: C17.2 parental


title: IP4_M14KD

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
The 5’-UMI of the forward RNA-seq reads was trimmed using UMI-tools, while the 3’-adapter sequences were removed using Cutadapt. Trimmed reads were aligned to the UCSC mouse genome (mm10) using STAR, and PCR duplicates were removed with UMI-tools. Cross-linked sites were identified with PureCLIP and aligned read counts for IP and input RNA samples per site were obtained with multiBamSummary.
Assembly: mm10
Supplementary files format and content: CSV with chromosome, start, end, and read counts for each input and IP sample.

extract_protocol:
An anti-m6A antibody (Millipore Sigma #ABE572-I-1MG) was added, and samples were UV-C crosslinked. Antibody-RNA complexes were then coupled overnight to protein G beads.
We performed adapter ligations, SDS-PAGE electrophoresis and nitrocellulose membrane transfer, reverse transcription, and PCR amplification.

value: alpha cells

value: METTL14 siRNA KD

value: IP


title: Input2_SCR

value: scramble siRNA controls (SCR)

value: Input


title: Input4_M14KD


title: IP2_SCR


title: WTD-2

description: Library name: Sample 5

value: WT


title: Input1_SCR


title: 3171951_JWH003-C172_resistant

description: Library name: sample 3

value: Blood

value: SEM


title: IP3_M14KD


title: WTD-1

description: Library name: Sample 4


title: 3171949_JWH001-C172_parental

description: Library name: sample 1

value: B-ALL


title: S6D-3

description: Library name: Sample 3


title: IP1_SCR


title: LLPSEp53_2_3

city: Hangzhou

first: Guozhen

last: Wang

state: Zhejiang Province

address: No.866 Yuhangtang Road

institute: Zhejiang University

data_processing:
Sequencing data were processed using Trimmomatic (0.39) for quality control and adapter trimming.
the reads were then aligned to the human reference genome (Homo_sapiens.GRCh38.106) using STAR (2.7.10a).
Assembly: GRCh38.106
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: lung

growth_protocol: H1299 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
total RNA was isolated using Trizol regent (Simgen, 5301100)，10 μg total RNA was used as input material for Illumina high-throughput sequencing (RNA-seq).
Sequencing libraries were generated using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB，E7775L) according to manufacturer’s protocol.

value: lung

value: cancer cell

value: data collected year 2022


title: Input3_M14KD


title: BAC plasmid CenU 65_128

city: Yonago

first: Junichiro

last: Ohzeki

address: 86 Nishi-cho

department: Chromosome Engineering Research Center

institute: Tottori University

description:
Library name: PC count  BAC plasmid CenU 65_128
Competitive PCR product derived from BAC plasmid DNA

data_processing:
Fastq files were generated by Miseq base calling.
Sequencing reads were trimmed with cutadapt 4.0 using Python 3.9.13.
Trimmed reads were matched against the indexed list of the position code DNA using bowtie.
The number of reads for each the position code was obtained using samtools idxstats (1.11).
Note that to minimize deviations in counts at each position caused by competitive PCR, the ratio of position code DNA in genomic DNA was normalized by the ratio of position code DNA in the original input BAC plasmid.
Assembly: The index list of the position code DNA (See also supplementary Inofrmation)
Supplementary files format and content: Tab-delimited text file includes raw counts for each the position code.

organism: Escherichia coli str. K-12 substr. DH10B

growth_protocol: Human HT1080 and derived cells were cultured in the DMEM Glutamax I (10569010, Gibco) supplemented with the 10% tet-system approved Fetal Bovine Serum (631101, TAKARA) at 37˚ C and 5% CO2. The E. coli (DH10B)-derived strain carrying the BAC was cultured at 30°C.

extract_protocol:
Genomic DNA was extracted from each cell line carrying the human artificial chromosome using Genomic tip 100 (Qiagen). BAC plasmid was also prepared using Large construction kit (Qiagen).
Then 100 ng of the genomic DNA or 1 ng of BAC plasmid DNA was used for competitive PCR to the construction of sequencing library.

treatment_protocol: A hundred ng of the genomic or BAC plasmid DNA was used for competitive PCR to the construction of sequencing library.

value: carrying pBAC KMN CenU.64


title: BAC plasmid CenU 1_96

description:
Library name: PC count  BAC plasmid CenU 1_96
Competitive PCR product derived from BAC plasmid DNA

value: carrying pBAC Alone CenU.96


title: LLPSEp53_2_2


title: BAC plasmid NCU 1_96

description:
Library name: PC count  BAC plasmid NCU 1_96
Competitive PCR product derived from BAC plasmid DNA

value: carrying pBAC Alone NCU.96


title: FX_84_6

city: Tsu

first: Yuhei

last: Nishimura

state: Mie

address: 2-174 Edobashi

department: Integrative Pharmacology

institute: Mie University Graduate School of Medicine

description: Library name: FX_84_6

data_processing:
Sequencing of 150-bp paired-end reads was conducted using a HiSeq X Ten system (Illumina).
Assembly: Quantification of gene expression was conducted using Danio_rerio.GRCz11.cdna.all.fa as described previously (Kashima et al., 2022).
Supplementary files format and content: csv (count.csv and metadata.csv)

organism: Danio rerio

source_name: whole body

extract_protocol:
total RNA was extracted from each larva using Direct-TRI, and RNA concentrations were determined using a QuantiFluor RNA System Kit with a Quantus Fluorometer.
a library was prepared for RNA-Seq as described previously (Kamitani et al., 2019, Taya et al., 2025).

value: whole body

tag: hpf

tag: idents


title: RNA-seq in THP1 cells: IRF7 KO PolyIC Transfected Replicate 1

description: Library name: RNA-seq_THP1_KOP31_E007045

value: KO

value: PolyIC


title: LLPSEp53_2_1

tag: batch


title: S6D-1

first: Qi

last: Jin

address: No.5, Beixiange, Xicheng District, Beijing

description: Library name: Sample 1

value: Primary tubular epithelial cells

value: SIRT6 knockdown

value: Uninephrectomy+STZ+HFD


title: F_84_6

description: Library name: F_84_6


title: S6D-2

description: Library name: Sample 2


title: OSKM, replicate 1, snRNAseq

city: Seoul

first: Seunghee

last: Hong

address: 50 Yonsei-ro, Seodaemun-gu

department: Biochemistry

country: South Korea

institute: Yonsei university

description: 10x Genomics

data_processing:
cellranger (v7.0.1) and bcl2fastq (v2.20.0) software used for basecalling and demultiplexing for other samples.
cellranger (v7.1.0) software used for alignment and aggregation (with no depth normalization)
Assembly: mm10
Supplementary files format and content: h5 format, containing integrated samples and read counts for each cell

source_name: Whole liver

extract_protocol:
Prepare nuclei using a singulator 100 system (S2 Genomics). The singulator 100 system is designed to automatically process solid tissues into suspensions of nuclei using mechanical disruption coupled with chemical dissociation in a single-use cartridge. A mass of 20~100mg of tissue is recommended. Determine the nuclei concentration using a LUNA-FL™ Automated Fluorescence Cell Counter (logos biosystems) and examine the nuclei morphology using microscopy. Libraries were prepared using the Chromium controller according to the 10x chromium Next GEM Single Cell 3’ v3.1 protocol(CG000315). Briefly, the cell suspensions were diluted in nuclease-free water to achieve a targeted cell count of 10,000. Cell suspension was mixed with master mix and loaded with Single Cell 3’V3.1 Gel Beads and Partitioning Oil into a chromium Next GEM chip G. RNA transcripts from single cells were uniquely barcoded and reverse transcribed within droplets.cDNA molecules were pooled and the cDNA pool then go through an end repair process, the  addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified andenriched with PCR to create the final cDNA library. The purified libraries were quantified using    qPCR according to the qPCR Quantification Protocol Guide(KAPA) and qualified using the Agilent Technologies 4200 TapeStation(Agilent technologies). And then the libraries were sequenced usingNovaSeq platform(Illumina) according to the read length in the user guide.
LibrarieswerepreparedusingtheChromiumcontrolleraccordingtothe10xchromium Next GEM SingleCell3’v3.1protocol(CG000315).Briefly,thecellsuspensionsweredilutedinnuclease‑free watertoachieveatargetedcellcountof10,000.Cellsuspensionwasmixedwithmastermixand loadedwithSingleCell3’V3.1GelBeadsandPartitioningOilintoachromium Next GEM chip G.RNAtranscriptsfromsinglecellswereuniquelybarcodedandreverse‑transcribedwithindroplets.cDNAmoleculeswerepooledandthecDNApoolthengothroughanendrepairprocess,the additionofasingle‘A’base,andthenligationoftheadapters.TheproductsarethenpurifiedandenrichedwithPCRtocreatethefinalcDNAlibrary.Thepurifiedlibrarieswerequantifiedusing   qPCRaccordingtotheqPCRQuantificationProtocolGuide(KAPA)andqualifiedusingtheAgilentTechnologies4200TapeStation .

value: Whole liver

value: hepatic cell

value: Col1A1TetO-OSKM;ROSA26rtTA mice (iOSKM mice)

value: OSKM induction (Doxycycline 0.15 mg/kg in water)


title: FX_37_6

description: Library name: FX_37_6


title: F_60_6

description: Library name: F_60_6


title: F_37_6

description: Library name: F_37_6


title: F_36_6

description: Library name: F_36_6


title: FX_60_6

description: Library name: FX_60_6


title: LLPSEp53_1_3


title: FX_84_5

description: Library name: FX_84_5


title: LLPSEp53_1_1


title: FX_36_6

description: Library name: FX_36_6


title: Cont, replicate 1, snRNAseq

description: 10x Genomics

value: Mock treatment (PBS I.P. injection)


title: LLPSEp53_1_2

value: lung


title: p53_3

value: cancer cell


title: APAP, replicate 1, snRNAseq

description: 10x Genomics

value: APAP treatment (Acetaminophen 300 mg/kg I.P. injection)


title: ATAC-seq in BACH1-overexpressing wild-type BMDMs (rep3)

city: Debrecen

first: Laszlo

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

description: Library name: mm_BMDM_C57_ATAC_lenti_BACH1_vector_rep3.fastq.gz

data_processing:
[mm_RNA_Lung_*.bw, mm_BMDM_RNA_*.bw]
alignment to mm10 reference genome with HISAT2 (v2.1.0) using default parameters
transcript assembly with StringTie (v1.3.4d)
BAM file indexing with SAMtools (v1.7)
coverage (bigwig) file generation with bamCoverage program of deepTools (v3.0.2)
[mm_ATAC_AM_*.bedgraph.gz]
alignment to mm10 reference genome with BWA v0.7.10 using default parameters
bam generation with SAMtools v1.7 using default parameters
tag directory generation with HOMER's makeTagDirectory using -checkGC parameter
generation of coverage (bedgraph) files with HOMER's makeUCSCfile using -fsize 1e50 -norm parameters
peak prediction with callpeak function of MACS2
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: bedgraph
[mm_BMDM_C57_ATAC_*.bw]
alignment to mm10 reference genome with BWA v0.7.10 using default parameters
bam generation with SAMtools v1.7 using default parameters
tag directory generation with HOMER's makeTagDirectory using -checkGC parameter
generation of coverage (bedgraph) files with HOMER's makeUCSCfile followed by conversation to bigwig using UCSC bedGraphToBigWig
peak prediction with callpeak function of MACS2

source_name: bone marrow-derived macrophage

growth_protocol:
For the alveolar macrophages (AMs) profiling experiment, tissue-derived CD45.1⁺ WT and CD45.2⁺ Bach1 fl/flLyz2-Cre alveolar macrophages (AMs) were FAC-Sorted from Bone Marrow chimeric mice (lethally irradiated recipients ≥8 weeks after transfer of a 1:1 mixture of donor BM cells).
For the alveolar macrophages (AMs) profiling experiment, WT and Bach1 fl/flLyz2-Cre alveolar macrophages (AMs) were FAC-Sorted and were lysed with the following lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL). After lysis, nuclei were subjected to tagmentation. Nextera DNA Library Prep Kit was used for library generation according to manufacturer's protocol.
For the Lentiviral transduction of BMDMs, a high titer (>1x108 TU/ml) lentiviral vector containing the full-length cDNA of mouse BACH1 was designed and ordered as packaged virus from VectorBuilder (pLV[Exp]-Neo-CMV>3xFLAG/mBach1). Transduction efficiency was tested with control virus: pLV[Exp]-EGFP/Puro-EF1A>mCherry. 5x105 BMDMs were transduced at Day 3 of differentiation at MOI:5 and used for RNA-seq after 48-72 hours in the presence of 10ug/ml doxycycline.
For the Lentiviral transduction of BMDMs, a high titer (>1x108 TU/ml) lentiviral vector containing the full-length cDNA of mouse BACH1 was designed and ordered as packaged virus from VectorBuilder (pLV[Exp]-Neo-CMV>3xFLAG/mBach1). Transduction efficiency was tested with control virus: pLV[Exp]-EGFP/Puro-EF1A>mCherry. 5x105 BMDMs were transduced at Day 3 of differentiation at MOI:5 and used for ATAC-seq after 48-72 hours in the presence of 10ug/ml doxycycline.

extract_protocol:
AMs were sorted directly to 500μl Tri Reagent (MRC) and total RNA was isolated according to the manufacturer’s protocol.
Indexed cDNA libraries were prepared following the TruSeq™ RNA Sample Preparation Kit (Illumina, Inc.) protocol.
WT and Bach1 fl/flLyz2-Cre alveolar macrophages (AMs) were FAC-Sorted and were lysed with the following lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL).
Nextera DNA Library Prep Kit was used for library generation according to manufacturer's protocol.
Total RNA was extracted from transduced BMDMs 48–72 hours post-transduction.
Indexed cDNA libraries were prepared following the TruSeq™ RNA Sample Preparation Kit (Illumina, Inc.) protocol.

value: bone marrow-derived macrophage

value: wild-type

value: vehicle


title: FX_60_5

description: Library name: FX_60_5

value: whole body


title: F_60_5

description: Library name: F_60_5


title: F_84_5

description: Library name: F_84_5


title: Replicate 4, gastronemius, K/BxN+Dipyridamole mice

city: Madrid

first: Aranzazu

last: Mediero

state: Madrid

address: Avda. Reyes Catolicos 2

department: Rheumatology

country: Spain

institute: Fundacion Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz

description: Gastronemius of K/BxN+Dipyridamole mice 4

data_processing:
aligned to the GRCm38.p6/mm10 mouse genome using STAR (version 2.7.3a).
Read counts were extracted using htseq-count in non-stranded mode.
Assembly: GRCm38.p6/mm10
Supplementary files format and content: .txt (counts)

source_name: gastronemius

extract_protocol:
For the generation of RNA libraries for NGS with polyA+RNA purification, the TruSeq system was used.
TruSeq system was employed
The finally obtained libraries were validated and quantified by TapeStation and an equimolecular pool was made, purified using AMPure XP beads (Beckman Coulter)and titrated by PicoGreen. Library pool was sequenced on a NovaSeq6000 (Illumina) where clusters were formed and sequenced in a 1x100single-read sequencing run.

treatment_protocol: Dipyridamole daily for 16 days (25mg/kg)

value: gastronemius

value: K/BxN


title: FX_37_5

description: Library name: FX_37_5


title: p53_1

value: data collected year 2022


title: FX_36_5

description: Library name: FX_36_5


title: Replicate 3, gastronemius, K/BxN+Dipyridamole mice

description: Gastronemius of K/BxN+Dipyridamole mice 3

value: Dipyridamole daily for 16 days (25mg/kg)


title: F_37_5

description: Library name: F_37_5


title: p53_2

value: data collected year 2022 (sample collected in different batch)


title: Replicate 2, gastronemius, K/BxN+Dipyridamole mice

description: Gastronemius of K/BxN+Dipyridamole mice 2


title: Ctrl-3

value: Ctrl

value: data collected year 2023


title: F_84_4

description: Library name: F_84_4


title: Replicate 1, gastronemius, K/BxN+Dipyridamole mice

description: Gastronemius of K/BxN+Dipyridamole mice 1


title: FX_60_4

description: Library name: FX_60_4


title: Ctrl-2


title: FX_84_4

description: Library name: FX_84_4


title: Replicate 4, gastronemius, K/BxN mice

description: Gastronemius of K/BxN mice 4


title: F_60_4

description: Library name: F_60_4


title: FX_37_4

description: Library name: FX_37_4


title: Ctrl-1


title: Replicate 3, gastronemius, K/BxN mice

description: Gastronemius of K/BxN mice 3


title: ATAC-seq in BACH1-overexpressing wild-type BMDMs (rep1)

description: Library name: mm_BMDM_C57_ATAC_lenti_BACH1_vector_rep1.fastq.gz


title: WT-3

value: WT


title: F_37_4

description: Library name: F_37_4


title: F_36_4

description: Library name: F_36_4


title: RNA-seq in THP1 cells: IRF7 QK Haplotype PolyIC Transfected Replicate 1

description: Library name: RNA-seq_THP1_QKP31_E007054

value: Risk

value: PolyIC


title: Replicate 2, gastronemius, K/BxN mice

description: Gastronemius of K/BxN mice 2


title: FX_36_4

description: Library name: FX_36_4


title: Replicate 1, gastronemius, K/BxN mice

description: Gastronemius of K/BxN mice 1


title: WT-2

value: lung


title: F_84_3

description: Library name: F_84_3


title: TRA_F14_3N_FH_A52

city: Nanjing

first: Xuan

last: Li

address: No. 666, Binjiang Avenue, Jiangbei New Area

institute: Nanjing Agricultural University

description:
Library name: A52
TRA_F14_3N_FH_A52

data_processing:
Alignment was performed with STAR (v2.7.11a) against the reference genome using a pre-built STAR genome index. STAR was run with “--outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts” to generate sorted alignment files and gene-level count profiles. Gene-level expression quantification was carried out using RSEM (v1.3.1) with STAR-generated transcriptome BAM files as input (--paired-end --no-bam-output --alignments).
Assembly: Nasonia vitripennis reference genome (RefSeq No. GCF_009193385.2, NCBI GenBank)
Supplementary files format and content: Tab-delimited text file includes raw counts and tpm value for each sample

organism: Nasonia vitripennis

source_name: Head

extract_protocol:
RNA extraction was performed using Quick-RNATM Tissue/Insect Microprep (Catalogue No. R2030 Zymo Research, Germany) (without DNase treatment). For sequencing, RNA was resuspended in 10 µL DNase/RNase-free water and the RNA concentration and purity was measured using a fluorometer (Qubit 2.0, Life Technologies); poor quality samples judged by A260/A280 and A260/A230 ratios were discarded. The extracted RNA was sent to Novogene (UK) Company Limited for sequencing. Novogene Hongkong prepared the sample library.
Unique index codes were added to each sample using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, USA). mRNA was purified from total RNA using poly-T magnetic beads, and libraries were prepared according to the manufacturer's instructions (Illumina).

value: Head

value: female

tag: age

value: 1 day after emergence

tag: strain

value: TRA


title: FX_84_3

description: Library name: FX_84_3


title: Male, GFP-RNAi, Thorax, replicate 5

city: Wageningen

first: Julien

last: Rougeot

address: Droevendaalsesteeg 1

department: Plant Science Group

country: Netherlands

institute: Wageningen University and Research (Netherlands)

data_processing:
Raw data filtering was performed to remove reads with adaptor contamination, uncertain nucleotides on more than 10% of the sequence (N>10%) and reads with low-quality nucleotides (<20) on more than 50% of the sequence.
Clean paired-end reads were mapped on the Nasonia vitripennis genome Nvit_psr_1.1 (GCA_009193385.2 Nvit_psr_1.1) using HISAT2 (v2.0.5) and default parameters.
Gene counts were obtained using HTSeq (v0.6.1) and the union method on the annotation GCF_009193385.1_Nvit_psr_1.
Assembly: Nvit_psr_1.1
Supplementary files format and content: tab-delimited text file includes raw counts for each samples

source_name: thorax

growth_protocol: Nasonia vitripennis lab strain AsymCX was reared on Calliphora sp. under a 16 hours light / 8 hours dark cycle at 25°C.

extract_protocol:
After 3 days post-injection, five samples with three individuals were collected for each time point and sex and flash-frozen in liquid nitrogen. For adult parts, seven adults were collected one day after emergence, between 7 and 8 days after pupae injection. Adults were flash-frozen in liquid nitrogen, then immediately dissected apart on ice into head, thorax, and abdomen, and finally flash-frozen back in liquid nitrogen. All samples were stored at −80 °C until RNA extraction. For 1 day-old embryo (parental RNAi), F0 female pupae 8 days after oviposition were injected as described above, kept until emergence, and then crossed with uninjected AsymCX males or kept virgin. Every female was then set up individually with one host, changed every 4 hours. Virgin females produce only male progeny while mated females produce between 90-95% females. Batches of 100 embryos were collected  24 hours later by dissecting the host, transfer into a microcentrifugation tube on ice without buffer, flash-frozen in liquid nitrogen, and stored at −80 °C until RNA extraction. Total RNA was extracted with Quick-RNA Tissue/Insect Kit coupled with on column DNase treatment (ZymoResearch - R2030) according to manufacturer's protocol.
Library preparation was performed at the Novogene (HK) Company Limited. Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Sequencing libraries were paired-end sequenced (150 bp read-length) on an Illumina NovaSeq platform.

treatment_protocol: Larval RNAi knockdown was induced in AsymCX males or females at 4, 6, and 8 days after oviposition. Larvae at 4 and 6 days were injected on PBS-1%agar plates. After injection, the 4 day-old larvae were transferred back to host (6-8 per host) and sealed with the host shell, while 6 day-old larvae were kept on the PBS-agar plate. Pupae at 8 days were fixed on microscopy slides with double-sided tape, inject, and kept until emergence. Larvae and pupae were injected in the posterior part with 4 μg/μl dsx or GFP dsRNA diluted in milliQ water mixed with red food dye in the ratio 9:1. Injections were performed using custom made capillary needles and a Femtojet (Eppendorf).

value: thorax

value: AsymCX

tag: Sex

value: Male

tag: developmental stage

value: adult

value: GFP-RNAi


title: F_60_3

description: Library name: F_60_3

value: whole body


title: FX_60_3

description: Library name: FX_60_3


title: Male, GFP-RNAi, Thorax, replicate 4


title: WT-1

value: cancer cell


title: FX_37_3

description: Library name: FX_37_3


title: ccRCC tumor Spatial RNA-seq P_19

city: PARIS

first: Isaias

last: Hernandez-Verdin

state: Ile-de-France

address: GH PITIE SALPETRIERE ICM IHU A, 47 Boulevard DE L'HOPITAL

department: Genetics and Development of Nervous System Tumors

institute: Institut du cerveau

description: Corresponds to bulk sample dee4

data_processing:
Raw fastqs were processed with SpaceRanger (v1.3.0)
Assembly: Genome build: hg38
Supplementary files format and content: TLS_annotation.csv: A comma-separated values file containing the spatial barcodes and indicating whether or not they are associated with TLS presence which was determined by chromogenic staining using CD3 and CD20.
Supplementary files format and content: TumoralZone_annotation.csv: comma-separated values file containing the spatial barcodes and indicating the tumoral area which was detected by a trained pathologist.
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image.
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots.
Supplementary files format and content: scalefactors_json.json: scalefactors in json format.
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue.
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue.
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots.
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 file containing only tissue-associated barcodes (columns) and number of UMIs associated with a feature (rows).
Supplementary files format and content: raw_feature_bc_matrix.h5: HDF5 file containing all barcodes (columns) and number of UMIs associated with a feature (rows).
Library strategy: Spatial Transcriptomics

source_name: Kidney

extract_protocol:
Spatial transcriptomics: RNA extraction with the 10X Visium protocol
Libraries were prepared with Truseq Illumina libraries and sequenced on a NovaSeq (Illumina)

value: Kidney

tag: disease state

value: renal cell cancer

tag: cancer type

value: Clear cell renal cell carcinoma


title: F_37_3

description: Library name: F_37_3


title: FX_36_3

description: Library name: FX_36_3


title: RNA-seq in THP1 cells: IRF7 RE Haplotype Unstimulated Replicate 1

description: Library name: RNA-seq_THP1_RE01_E007060

tag: irf7 genotype

value: Protective


title: F_36_3

description: Library name: F_36_3