title: CD45+ cells isolated from muscle of mice with TB mice

status: Public on Nov 15 2024

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

description: 10x Genomics

data_processing:
Sequencing data were mapped to the reference genome of Mus musculus (GRCm39) and analyzed using the CellRanger (v. 7.0.1) provide by 10X Genomic.
Assembly: Mus musculus (GRCm39)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: gastrocnemius (GA)

growth_protocol: All mice used in this study were approved and cared for in accordant with guidelines of the International Animal Care and Use Committee (IACUC) of the Yonsei University (2023-0074).

extract_protocol:
Freshly isolated tissues were finely minced and enzymatically digested with RPMI1640 containing 0.3 mg/ml Liberase TL (5401119001, Sigma-Aldrich, St. Louis, MA, USA) and 0.4 μg/ml deoxyribonuclease I (DN25, Sigma-Aldrich) for 2 h at 37°C with gentle agitation. The digested cells were further disaggregated using 18G and 21G syringes (Korea Vaccine Co., Ltd, Seoul, Korea) and filtration with a 100-μm cell strainer (93100, SPL Life Sciences, CITY, Korea). After red blood cell depletion with ammonium-chloride-potassium lysis buffer (A10492-01, Gibco), CD45+ immune cells were positively isolated with magnetic beads (130-052-301, Miltenyi Biotec, Bergisch Gladbach, Germany) according to the manufacturer’s instruction, and then subjected to flow cytometry or scRNA-seq.
Single-cell RNA sequencing (scRNA-seq) data were generated by GENINUS Inc. (Seoul, Korea). Barcoded sequencing libraries were prepared using the Chromium Single Cell 5' v2 Reagent Kits (10x Genomics), and sequencing was performed on the Illumina NovaSeq 6000 platform.

value: gastrocnemius (GA)

value: CD45+ cells

value: CAC mouse model


title: Mouse 4, Sample 4-1 (10x72), Trunk, E8.5 GFP-virus (pMR532), GEX

status: Public on Nov 14 2024

type: SRA

city: Vienna

first: Sergey

last: Isaev

address: Spitalgasse, 4

department: Department of Neuroimmunology

country: Austria

institute: Medical University of Vienna

description:
Gene expression library
Mouse 4, Sample 4-1 (10x72), Trunk, E8.5 GFP-virus (pMR532), Gene expression library

library_source: transcriptomic single cell

data_processing:
In the course of the experiments, one to three libraries were generated for each sample: (1) 10x v3 Gene Expression, and (2-3) viral barcode-containing cDNA libraries (two in the case of double injection). Detailed descriptions of each sample, corresponding libraries, and FP sequences are provided in Supplementary Table X. Reads from experiments (1) and (2) were aligned to a chimeric mm39 and FP genome reference using Cell Ranger 7.0.1.
Clonal barcodes were identified using an algorithm suggested in [PMID: 35210624] with modifications available at https://github.com/serjisa/TREX.modified. Firstly, barcode sequence corrections were performed individually for each cell, enhancing robustness against artificial merging but slightly increasing clonal dropout rates.
Assembly: Chimeric mm39 with FP-CloneID contigs added
Supplementary files format and content: h5-containers, h5ad-containers and comma-separated values

molecule: polyA RNA

organism: Mus musculus

source_name: Ectodermal and mesodermal derivatives

extract_protocol:
The embryos were removed from the uterus, sacrificed, and placed into a petri dish containing Hank’s Balanced Salt Solution (HBSS) on ice. Embryos were screened for expression of Tomato or GFP using a benchtop fluorescence stereoscope. Limbs, liver, and the ventral skin were removed. Body regions, primarily lower trunk, middle trunk, and cranial regions, were dissected separately and placed into a small Petri dish containing 2.5 mL of a cell dissociation buffer consisting of 2mg/mL Collagenase P (Roche, Sigma-Aldrich), 1X TrypLE, and 1uL/mL DNASe I, fully dissolved in HBSS (without phenol red, including Ca2+ and Mg2+). Tissue was chopped finely with a scalpel and forceps under control of stereomicroscope and transferred to 15mL falcon tubes. The tissue pieces were triturated 10X using a transfer pipette, and then 10X using a 1mL pipette. Samples were then incubated for 20 minutes at 37 C in a preheated shaking incubator set at 150 RPM, with the tubes tilted to ~60 degrees. During this time every 6-8 minutes, the samples were vortexed and triturated using a 1mL pipette. After the tissue clumps disappeared, 12.5 mL of 2% Fetal Bovine Serum (FBS) diluted in ice-cold HBSS (without phenol red, without Ca2+ and Mg2+, H6648 SIGMA) was added. The samples were centrifuged in a cold centrifuge (4C) for 15 minutes at 500 g. The supernatant was carefully removed and the pellet was resuspended in 1mL HBSS + 2% FBS and kept on ice thereafter. After centrifugation and resuspension, the cells were filtered into round-bottom polypropylene test tubes (Falcon) using a cell strainer with a 40 micrometer woven polyethylene terephthalate mesh (pluriSelect pluriStrainer SKU 43-10040-40) for downstream cell sorting.
Cells were loaded into the Chromium machine (aiming for ~10,000 cells per reaction) using the V3.1 single-cell reagent kit (10X Genomics). Following GEM creation and cell lysis, cDNA was synthesized by reverse transcription, then amplified by PCR for 12 cycles as per the manufacturer’s protocol (10X Genomics). A portion of the amplified cDNA was used to generate Gene expression libraries and then indexed using the Single Index Plate T Set A. CloneID enrichment from cDNA libraries was additionally performed based on Ratz et al 2022 to increase the retrieval of the barcodes by ~5-10%. Briefly, two nested PCR reactions were performed using Q5 error-correcting DNA polymerase to amplify the CloneID-containing region, and a third reaction was used for sample indexing using the Single Index Plate T Set A. In between each reaction, amplicons were purified by 0.8X AMPure beads using a DynaMag Magnetic separator. Indexed GE and CloneID-enrichment libraries were quantified using BioAnalyzer and/or Qubit, and then pooled prior to Illumina sequencing on a NovaSeq 6000 S2-200 v1.5 flow cell with read setup 28-8-0-166.

treatment_protocol: Injections for lentiviral gene delivery were performed according to previously published protocols. At embryonic day E7.5-E8.5, the females were anesthetized with isoflurane (4% induction, maintained at 1.5-2.5%) and placed on a heated plate for surgery. Depth of anesthesia was tested through pinching the paw. Eye gel was applied to prevent dehydration. Pain relief e.g. Buprenorphine 0.05-0.1 mg/kg was administered via subcutaneous injection 30 minutes before the first incision. All instruments were autoclaved and disinfected with chlorhexidine alcohol before surgery. The skin was disinfected with chlorhexidine alcohol, and the hair on the abdomen was removed with a shaver or hair removal agent such as Veet. A small incision was placed in the abdomen and the uterus was exposed and placed on top of gauze soaked in sterile NaCl solution, placed around the opening. The uterus was kept moist with warm NaCl solution (37C). Using a glass capillary, lentivirus (from 23-206 nL) was injected through the uterine wall into the amniotic cavity. After the embryos were injected, the uterus was brought back into the abdomen and the incisions in the muscle wall were sewn together with absorbent suture thread, and the skin was closed with suture thread or staples. The mice were taken off isoflurane and allowed to wake up in their own cage on a heating pad under supervision. Postoperative pain relief was given in the form of a subcutaneous injection of Buprenorphine (0.05-0.1 mg/kg). For embryo retrieval, the mother was euthanized via CO2 overdose and cervical dislocation, and the embryos were collected at E13.5 and euthanized via decapitation.

tag: Sex

value: Male

tag: tissue

value: Ectodermal and mesodermal derivatives

tag: strain

tag: genotype

value: Wild type

tag: developmental stage


title: Input, ESCs

status: Public on Dec 05 2024

city: Athens

first: Dimitris

last: Valakos

address: Soranou Ephessiou 4

department: Center of Basic Research

country: Greece

institute: Biomedical Reasearch Foundation Academy of Athens

library_source: genomic

data_processing:
The quality of the generated fastq files was examined with the FASTQC software. FASTQ files were aligned against mm10 mouse genome with Bowtie2 aligner. The output file was filtered for low quality reads, duplicates, blacklist regions and mitochondrial genome entries with custom-made pipeline from Bedtools  and Samtools packages. Peak calling was performed with MACS2 with default parameters.
Assembly: mm10
Supplementary files format and content: The bed file Nanog_ESCs_peaks.bed contains the peaks generared with MACS2 compared to the respective Input file.

molecule: genomic DNA

growth_protocol: Bruce-4 ESCs were cultured in complete ESC medium [Knock Out DMEM (Gibco, Cat. No. 10829018), 20% ES-tested FBS (Pansera, Cat. No. P30-2602), Penicillin/Streptomycin 1X (Thermo Fischer Scientific, Cat. No. 15140122), GlutaMAX 1X (Gibco, Cat. No. 35-050-061). Non-Essential Amino Acids 1X (Gibco, Cat. No. 11140050) and mLIF 20ng/mL (Santa Cruz Biotechnology, sc-4378).

extract_protocol:
ESCs were cultured under optimum conditions and were fixed at a high‐confluence stage at room temperature for 15 min using 1% formaldehyde in fixing buffer, followed by quenching with 0.125 M glycine at room temperature for 7 min. Cells were resuspended in lysis buffer [50 mM Hepes (pH 7.9), 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP‐40, 0.25% Triton X‐100] and then in sonication buffer [0.1% SDS, 1 mM EDTA, 10 mM Tris (pH 8.1)]. Chromatin shearing was carried out in the Covaris S2 sonicator using the Covaris TC12 × 12 mm tubes (Tube AFA Fiber and Cap, Covaris) for 12 min (duty factor: 75, peak power: 25, cycles per burst: 200) allowing the shearing of chromatin within a range of 250–500 base pairs DNA fragments. Triton X‐100 and NaCl were then added in the sheared chromatin to final concentrations of 1% and 150 mM, respectively. ChIPs were carried out by incubating 100 μg of chromatin with the proper dilution of the anti-Nanog antibody (1:100) per ChIP reaction [anti‐Nanog, D1G10 Rabbit mAb ChIP Formulated #8785, Cell Signalling]. Next, protein G‐Dynabeads (10004D, Thermo Fisher Scientific) pre‐equilibrated in IP buffer [0.1% SDS, 1 mM EDTA, 10 mM Tris (pH 8.1), 1% Triton X‐100, 150 mM NaCl] were incubated with the chromatin‐antibody solution in an orbital mixer at 4°C for 4 hours. The recovered resin was subsequently washed with 150mM NaCl buffer (1%Triton, 0.1%SDS, 2mM EDTA, 20mM Tris pH 8.0, 150mM NaCl), 250 mM  NaCl buffer (1%Triton, 0.1%SDS, 2mM EDTA, 20mM Tris pH 8.0, 250mM NaCl), once with LiCl buffer (0.25M LiCl, 1% NP-40, 1% DOC, 1mM EDTA, 10mM Tris pH 8.0) and once with TE (1mM EDTA, 10mM Tris pH 8.0). The captured chromatin fragments were subjected to 30ug RnaseA for 1 hr at 37°C , then 40ug/ml PK for 1 hr at 50°C  and finally 0.3M NaCl at 65°C overnight for reverse crosslinking. All DNA present in each sample was purified with Nucleomag DNA purification beads (Macherey-Nagel) and eluted in TE buffer.
Libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina, according to the manufacturer’s guidelines.

tag: cell line

tag: cell type

value: Embryonic Stem Cells

tag: chip antibody

value: none (input)


title: Adult_HPT_WT_Female_05 [ATAC-Seq]

status: Public on Dec 18 2024

city: St. Louis

first: Joseph

middle: D

last: Dougherty

state: MO

address: 4370 Duncan Ave

department: Genetics

country: USA

institute: Washington University in St. Louis

data_processing:
Adapator trimming using Trimmomatic
Reads alignment using Bowtie2 and STAR
Peak calling using MASC2
Reads counts using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Peak, Reads counts

source_name: Hypothalamus

extract_protocol:
Zymo RNA extraction kit
SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech)
ATAC-seq: Corces et al., 2017, Nature Methods

value: WT

value: f

tag: mouse age


title: Coc_D2_SS_6

status: Public on Oct 09 2024

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

library_source: transcriptomic

data_processing:
Raw sequencing reads were mapped to the mm10 genome using the NGS-Data-Charmer pipeline.  In brief, reads were trimmed to remove adaptor and low-quality sequences, then the reads were aligned to the reference genome. Duplicate alignments were removed prior to gene counting and downstream analysis. Counts of mapped reads were obtained using featureCounts against the GENCODE m25 annotation.
Assembly: mm10
Supplementary files format and content: Cocaine_raw_counts_v2.txt: Tab-delimited text file containing the raw read counts for annotated genes, with individual samples present as columns. Cocaine_FPKM_v2.txt: Tab-delimited text file containing the normalized read counts (in fragments per kilobase per million) for annotated genes, with individual samples present as columns. DEGs.xlsx: DESeq2 differential expression analysis among D1 or D2 cells pertaining to cocaine-treated mice.

molecule: total RNA

source_name: Nucleus Accumbens

extract_protocol:
Direct-zol RNA microprep kit (Zymo Research)
SMARTer Stranded Total RNA-seq kit v3-Pico Input Mammalian (Takara Bio, CA)

treatment_protocol: Mice were euthanized by cervical dislocation, and bilateral NAc tissue was rapidly dissected on ice from 1-mm thick coronal sections using a 14G punch and flash frozen on dry ice. Nuclei were purified using fluorescence activated nuclei sorting (FANS)

value: Nucleus Accumbens

tag: drug

value: Coc

tag: treatment

value: SS


title: Coc_D2_SS_4


title: Coc_D2_SS_7


title: Mouse 1, Sample 1-1 (10X_19_IA_02_R31), Head, E8.5 GFP-virus (pMR532), GEX

description:
Gene expression library
Mouse 1, Sample 1-1 (10X_19_IA_02_R31), Head, E8.5 GFP-virus (pMR532), Gene expression library


title: Coc_D2_SS_3


title: Coc_D2_SS_1


title: Coc_D2_SC_7

value: SC


title: atac_smarca5_ko1

city: New Haven

first: Bluma

middle: J

last: Lesch

state: CT

address: 333 Cedar Street

institute: Yale University

description: 150bp PE ATAC-seq from Smarca5 cKO testes

data_processing:
Adapter trimming was performed using Cutadapt (Martin, 2011). Trimmed reads were aligned to the mouse genome (mm10) using Bowtie2 in very sensitive mode (Langmead and Salzberg, 2012). Mitochondrial reads were removed by excluding any reads aligning to chrMT. Peak calling was performed using MACS2 with default parameters.
Assembly: mm10
Supplementary files format and content: scRNA-seq: index (.tsv), feature (.tsv), and matrix (.mtx) files
Supplementary files format and content: ATAC-seq: .bed files of peaks

source_name: sorted testicular cells

extract_protocol:
A polypropylene collection tube was coated with 3 ml Collection Buffer (20% FBS in 1X PBS) for 2 hours at RT with end-over-end mixing. Seminiferous tubules were mechanically isolated from the tunica and transferred to a 15ml conical tube containing 5ml Digestion Solution I [0.75 mg/ml collagenase type IV (Gibco, 17104-019) in Dulbecco’s modified Eagle’s media (DMEM, Gibco, 11965092) supplemented with 1:1000 with 1 mg/ml DNase I (StemCell Technologies, 07900)] warmed to 37 °C, followed by incubation at 37 °C for 10 mins with end-over-end rotation. 5ml of cold DMEM was added and tubules allowed to settle on ice. The supernatant was discarded and the tubules were washed again with 5ml cold DMEM to deplete Leydig cells. 5ml of DMEM was added followed by centrifugation at 500xg for 5 mins at 4°C. The supernatant was removed and 5ml of Digestion Solution II [Accutase (Gibco, A1110501) supplemented with 1 mg/ml DNase I at 1:1000 at room temperature)] was added to the tubules followed by incubation with end-over-end rotation for 10 mins at RT with gentle pipetting after 5 mins to disperse the tubules. 5ml of cold Complete Media (10% FBS in DMEM) was added and the sample was centrifuged at 500 xg for 5 mins at 4 °C. The cell pellet was then resuspended in 5 ml of cold Complete Medium, filtered through a 100 μm strainer, and the cell suspension was transferred to a fresh 15 ml conical tube and centrifuged at 500 xg for 5 mins at 4 °C.Cells were stained with Hoechst dye and isolated by flow cytometry based on 4C DNA content.  50,000 sorted pachytene or pachytene-like cells were processed for each ATAC-seq library using the Active Motif kit (53150) as per the manufacturer’s protocol.
50,000 sorted cKIT+ cells were processed for each ATAC-seq library using the Active Motif kit (53150) as per the manufacturer’s protocol.

value: sorted testicular cells

value: Smarca5 fl/delta; Ddx4-Cre+ (Smarca5 cKO)


title: Coc_D2_SC_6


title: Coc_D2_SC_4


title: atac_wt1

description: 150bp PE ATAC-seq from control testes

value: wild type C57BL6


title: Coc_D2_SC_5


title: Coc_D2_SC_3


title: Mouse 3, Sample 3-1 (10x71), Trunk, E8.5 GFP-virus (pMR532), GEX

description:
Gene expression library
Mouse 3, Sample 3-1 (10x71), Trunk, E8.5 GFP-virus (pMR532), Gene expression library

value: Female


title: Coc_D2_CS_9

value: CS


title: Coc_D2_SC_1


title: Coc_D2_SS_9


title: Coc_D2_SS_8


title: Coc_D2_SS_5


title: Coc_D2_SS_2


title: Coc_D2_CS_4


title: Coc_D2_CS_1


title: Coc_D2_CS_3


title: Coc_D2_CC_10

value: CC


title: Coc_D2_CS_2


title: Coc_D2_CC_9


title: Coc_D2_SC_9


title: Coc_D2_SC_8


title: Adult_HPT_Het_Female_19 [ATAC-Seq]

value: Het


title: CD45+ cells isolated from lung of mice with TB mice

description: 10x Genomics

source_name: lung

value: lung

value: CD45+ cells

value: CAC mouse model


title: Coc_D2_CS_6


title: Coc_D2_CC_1


title: Coc_D2_SC_2


title: Coc_D2_CS_5


title: Coc_D2_CS_10


title: Coc_D2_CS_8


title: Coc_D1_SC_9


title: Coc_D2_CC_7


title: Coc_D1_SC_8


title: Coc_D2_CS_7


title: Coc_D1_SC_7


title: Coc_D2_CC_4


title: Coc_D2_CC_2


title: Coc_D1_SC_4


title: Coc_D2_CC_6


title: Coc_D1_SC_3


title: Coc_D2_CC_5


title: Coc_D2_CC_3


title: Coc_D1_SC_1


title: Coc_D1_SS_10


title: Coc_D1_CS_8


title: Coc_D1_SS_9


title: Coc_D1_SS_8


title: Coc_D1_SS_7


title: Coc_D1_CS_6


title: Coc_D1_CS_4


title: Coc_D1_SS_6


title: Coc_D1_CS_2


title: Coc_D1_SS_5


title: Coc_D1_SS_2


title: Coc_D2_CC_8


title: Coc_D1_SS_3


title: Coc_D1_SS_4


title: Coc_D1_SS_1


title: Coc_D1_CC_8


title: Coc_D1_SC_2


title: Coc_D1_SC_5


title: Coc_D1_CS_7


title: Coc_D1_CC_4


title: Coc_D1_CS_5


title: Coc_D1_SC_6


title: Coc_D1_CS_3


title: Coc_D1_CS_1


title: Coc_D1_CC_10


title: Coc_D1_CC_9


title: Sample_01_healthy

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

country: Italy

institute: IRCCS Humanitas Research Hospital

data_processing:
Raw blc files were converted into fastq files using the Cell Ranger pipeline suite of 10X Genomics (version 3.0.2).
The CellRanger analysis pipeline was used to generate a digital gene expression matrix starting from raw data.
Gene expression matrices were used as input for Seurat clustering (R version 4.0.3; Seurat version 3.2.2)
Assembly: Pre-build Human genome (version GRCh38) was used as genome reference.
Supplementary files format and content: UMI counts per gene per cell

source_name: Prostate tissue

extract_protocol:
Mouse prostatic tumoral tissue was dissociated to single cell suspension. Briefly, tumors were digested for 45 minutes in a Collagenase type I solution (1 mg/ml) at 37°C, 5% CO2 on a rocking platform. Cells digestion was then pelleted and incubated in 2.5% Trypsin for five minutes at 37°C, 5%CO2. Trypsin was then inactivated by complete medium with FBS and cells suspension was further passed through a syringe needle until complete dissociation and filtered through a 40 μm cell strainer. CD45+ and CD45- cells were sorted by flow cytometry, resuspended in 1ml PBS plus 0.04% BSA and washed two times by centrifugation at 450 rcf for 7min. After the second wash cells were resuspended in 30 ul and counted with an automatic cell counter (Countess II, Thermo Fisher) to get a precise estimation of total number of cells recovered.
CD45+ and CD45- cells of each sample were loaded into one channel of the Single Cell Chip A using the Single Cell 3’ v2 single cell reagent kit (10X Genomics) for Gel bead Emulsion generation into the Chromium system.
Following capture and lysis, cDNA was synthesized and amplified for 14 cycles following the manufacturer’s protocol (10X Genomics). 50 ng of the amplified cDNA were then used for each sample to construct Illumina sequencing libraries. Sequencing was performed on the NextSeq500 Illumina sequencing platform following 10x Genomics instruction for reads generation. A sequencing depth of at least ~ 10,000 reads/cell was obtained for each sample.

value: CD45+  and epithelial cells

value: Prostate tissue

tag: tissue type

value: Normal tissue adjacent to tumor


title: Coc_D1_CC_7

value: Nucleus Accumbens


title: Coc_D1_CC_6

value: Coc


title: anti-PD-L1_2

status: Public on Oct 08 2024

data_processing:
Read length: 100
The adapter sequences were trimmed using TrimGalore (https://www.bioinformatics.babraham.ac.uk/).
Trimmed sequence reads were aligned to the Mus musculus reference genome (NCBI accession GCF_000001635.27) using the STAR aligner (v. 2.7.9a)
Transcript quantification was performed using RSEM (v. 1.3.3)
Assembly: Mus musculus (NCBI accession GCF_000001635.27)
Supplementary files format and content: Tab-deliminated text file includes raw counts for each sample
Supplementary files format and content: Tab-deliminated text file includes TPM values for each sample

source_name: tibialis anterior (TA)

extract_protocol:
KrasIKKaL cell line was maintained in RPMI1640 medium (Gibco, Waltham, MA, USA), supplemented with 10% fetal bovine serum (FBS, Gibco), 1% antibiotic-antimycotic mixture (Gibco), and 100 mg/L normocin (InvivoGen, San Diego, CA, USA). 6-8 week-old male C57BL/6 mice were intratracheally injected with 5 ´ 10^6 of KrasIKKaL cells.
RNA libraries were prepared using MGIEasy RNA Directional Library PrepKit.

treatment_protocol: 6-8 week-old male C57BL/6 mice were intratracheally injected with 5 ´ 106 of KrasIKKaL cells. Mice were randomly divided into treatment groups. then mice were treated with 200 μg/kg of anti-mouse PD-L1 antibody (clone 10F.9G2™, BE0101, BioXCell, Lebanon, NC, USA) or 200 μg of anti-mouse CD8a antibody (clone 2.43, BE0061, BioXCell) three times a week by intraperitoneal injection. IgG group was injected with an isotype IgG (rat IgG2b, clone LTF-2, BE0090, BioXCell). Control mice are the non-tumor injected group.

value: tibialis anterior (TA)

value: C57BL/6 (C57BL/6NCrlOri)


title: Coc_D1_CC_5


title: Coc_D1_CC_3


title: IgG_1

value: anti-IgG


title: Sample_01_tumor

value: Tumor tissue


title: Coc_D1_CC_2


title: Coc_D1_CC_1


title: anti-CD8a_2


title: CON_5

value: control


title: anti-CD8a_1


title: CON_3


title: CON_1


title: anti-PD-L1_3


title: anti-CD8a_3


title: lung_TB_4

status: Public on Oct 01 2024

description: Read legnth: 100

data_processing:
The adapter sequences were trimmed using TrimGalore (https://www.bioinformatics.babraham.ac.uk/).
Trimmed sequence reads were aligned to the Mus musculus reference genome (NCBI accession GCF_000001635.27) using the STAR aligner (v. 2.7.9a)
Transcript quantification was performed using RSEM (v. 1.3.3)
Assembly: Mus musculus (NCBI accession GCF_000001635.27)
Supplementary files format and content: Tab-deliminated text file includes raw counts for each sample
Supplementary files format and content: Tab-deliminated text file includes TPM values for each sample


title: CON_2


title: IgG_4


title: lung_TB_2

description: Read legnth: 100


title: IgG_3


title: lung_TB_3

description: Read legnth: 100


title: lung_CON_2

description: Read legnth: 100


title: CON_4


title: IgG_2


title: lung_CON_3

description: Read legnth: 100


title: lung_CON_1

description: Read legnth: 100


title: anti-PD-L1_1


title: lung_TB_5

description: Read legnth: 100


title: muscle_TB_2

description: Read legnth: 100

value: gastrocnemius (GA)


title: muscle_CON_3

description: Read legnth: 100


title: muscle_CON_1

description: Read legnth: 100


title: muscle_CON_2

description: Read legnth: 100


title: 7101

status: Public on Sep 27 2024

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

data_processing:
Reads were filtered, trimmed, and deduplicated using fastp version 0.23.1 with default parameters
Read conversion, alignment to the Bos taurus reference genome (ARS-UCD1.2.104)
Methyl calling were performed using Bismark. This process was implemented in the DRAGEN Methylation Pipeline,  which was run on an Illumina DRAGEN server using default parameters
Methylation calls from Bismark were filtered to retain CpG sites covered by at least six reads in a minimum of five samples per group.
The annotation was performed using the annotatePeak function in the default mode of the R ChIPseeker (version 1.32.1).
Assembly: ARS-UCD1.2
Supplementary files format and content: A tab-delimited text file includes information about differential methylated positions with q-values less than 0.01 and methylation  differences greater than the absolute value of 25 and their annotations.
Supplementary files format and content: A tab-delimited text file includes information about differential methylated regionss with q-values less than 0.01 and methylation  differences greater than the absolute value of 25 and their annotations. The regional analysis used a 500-bp sliding window with a 250-bp overlap and a minimum of five CpG per regions
Library strategy: Enzymatic methyl-seq (EM-seq)

organism: Bos taurus

source_name: Blood

growth_protocol: The cows were raised in the same conditions on the farm

extract_protocol:
One mL of blood was sent to the Génome Québec sequencing platform for DNA extraction
DNA conversion step involves in three primary enzymes: TET2 and T4-BGT detect and transform 5mC and 5hmC into a product that cannot be deaminated by the APOBEC3A enzyme. Subsequently, APOBEC3A deaminates unmodified cytosines by converting them to uracils. As a result, unmethylated cytosines are transformed into uracils and then to thymines during PCR amplification, while methylated cytosines remain as cytosines

value: Blood

value: MRG


title: 7163


title: 7048


title: 50_13258657

status: Public on Sep 18 2024

city: Chicago

first: Raghavendra

middle: G

last: Mirmira

state: IL

address: 900 E. 57th Street

department: Medicine

institute: University of Chicago

data_processing:
All sequenced libraries were then mapped to the human genome (GENCODE GRCh37) using the STAR RNA-seq aligner.  Read distributions across the genome were assessed using bamutils (from ngsutils).
Alternative splicing events were analyzed using replicated multivariate analysis of transcript splicing (rMATs 4.1.1), which computes a percentage splicing index (PSI) and false discovery rate (FDR) for five different types of splicing events, including skipped exons, mutually exclusive exons, retained introns, alternative 5’ splice sites, and alternative 3’ splice sites.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include splicing output from rMATs.

organism: Homo sapiens

source_name: Human blood

extract_protocol:
Total RNA was isolated from whole blood collected in Tempus® Blood RNA Tubes (ThermoFisher, catalog #4342792). RNA isolation was performed using the Tempus® Spin RNA Isolation Kit (ThermoFisher, catalog t#4380204) according to the manufacturer’s instructions.
RNA was first evaluated for its quantity and quality using Qubit and Agilent Bioanalyzer; an RNA Integrity Number (RIN) of 7 or higher was used for downstream applications. Five hundred nanograms of total RNA were used for library preparation. For the training cohort, the cDNA library preparation included mRNA enrichment/purification, RNA fragmentation, cDNA synthesis, ligation of index adaptors, and amplification using TruSeq Stranded mRNA Sample Preparation Guide (Illumina, Inc, RS-122-9004DOC, Part #15031047 Rev. E).  Each resulting indexed library with average insert size of 150-200b was quantified, and its quality was assessed by Qubit and Agilent Bioanalyzer, and multiple libraries were pooled in equal molarity. Five microliters of 2 nM pooled libraries per lane were then denatured, neutralized, and applied to the cBot for flow cell deposition and cluster amplification before loading to HiSeq 4000 for 75b paired-end read sequencing (Illumina, Inc.).

value: Human blood


title: 53_13258660


title: 51_13258658

value: Healthy Control


title: 49_13258656


title: 46_13258653


title: 47_13258654


title: 44_13258651


title: 54_13258661


title: muscle_TB_3

description: Read legnth: 100


title: 42_13258649


title: 43_13258650


title: 48_13258655


title: 38_13258645


title: lung_TB_1

description: Read legnth: 100

value: lung


title: muscle_TB_1

description: Read legnth: 100


title: 45_13258652


title: 40_13258647


title: 33_13257136


title: 37_13258644


title: 7_13256001


title: 34_13257137


title: 36_13257139


title: 1_13255995


title: 2_13255996


title: T1D-014


title: T1D-017


title: 4_13255998


title: T1D-013


title: HC-19


title: T1D-012


title: T1D-016


title: T1D-010


title: HC-18


title: HC-15


title: T1D-011


title: HC-13


title: HC-17


title: T1D-08


title: T1D-05


title: T1D-01


title: T1D-06


title: HC-10


title: 3_13255997


title: HC-12


title: 5_13255999


title: WT CFP-cnp1, Input

status: Public on Sep 15 2024

city: Wroclaw

first: Karol

last: Kramarz

address: Kanonia 6/8

department: Faculty of Biological Sciences

country: Poland

institute: University of Wrocław

data_processing:
Raw sequencing data was quality controlled by Q30. Low-quality reads and adapter sequences were cut off using Cutadapt. Filtered reads were then mapped against the target genome (S. pombe assembly ASM294v2) and against the spike-in genome (S. cerevisiae S288C assembly SacCer3) using Bowtie2. Unmapped reads, rDNA regions, mitochondrial DNA and duplicates were filtered out using Samtools. Samtools was also used to count reads uniquely mapped to ASM294v2 and SacCer3, and these values were used to calculate the occupancy ratio value. Using MACS3, we computed the local bias by taking the maximum bias from surrounding 1kb, 10kb, the size of fragment length d, and the whole genome background. Finally, we combined and generated the maximum background noise, and scaled the ChIP and control to the same sequencing depth. Spike-in calibration was performed according to Hu et al. (2015). Peaks were called using MACS3 bdgpeakcall function. bigWig files were created using deepTools.
Assembly: Schizosaccharomyces pombe assembly ASM294v2
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

organism: Schizosaccharomyces pombe

source_name: yeast

growth_protocol: The growth of relevant mutants was done in rich medium (YES).

extract_protocol:
100 mL of exponential culture (OD600 ~1) of untagged strain, WT CFP-cnp1 and SUMO-KallR CFP-cnp1 were mixed with 10 mL of budding yeast exponential culture Scc1-Pk, used as a calibrator and then crosslinked 1% formaldehyde (Sigma, F-8775) for 15 min. Formaldehyde crosslinking was quenched with 2.5 M glycine and cells were washed with 1x TBS. Next, samples were frozen in liquid nitrogen and cells were extracted by bead beating in FA-lysis buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1% Triton X100, 0.1% NaDeoxycholate, 1 mM EDTA with 1 mM PMSF and protease inhibitors (Sigma-Aldrich, P8215). Chromatin sonication was done in a DiagenodeBioruptor Pico using Easy mode 10 cycles of 30 s ON and 30 s OFF. Immunoprecipitation was carried o/n: 300 µL of extract was incubated on the wheel with anti-GFP antibody (Invitrogen, A11122) at 1:150 concentration. 20 µL of extract was preserved as INPUT fraction. Next morning Protein G Dynabeads (Invitrogen, 10003D) were added for 1 h, stringency washes to remove unspecific proteins were done and immunoprecipitated complexes were decrosslinkedover night at 65° C. Next morning samples were digested with RNAse A (Thermo) for 30 min at 37oC and then with proteinase K at 65oC for 1h. The DNA associated with CFP-cnp1 was precipitated with isopropanol/glycogene/3M Kac for 1h in -20oC. Precipitated DNA was centrifuged for 20 min at 4oC and then washed with cold 70% ethanol.Finally, DNA pellet was resuspended in 30 µL of ultra pure water (Sigma). DNA concentration was determined by qubit and test qPCR was ran on 10x dilution of obtained DNA suspension with SsoAdvanced Universal SYBR® Green Supermix (Biorad #1725274).
NEBNext®Ultra™ II DNA Library Prep Kit for Illumina E7645L

value: yeast


title: HC-06


title: HC-04


title: HC-03


title: SUMO-KallR CFP-cnp1, Input


title: VUHD090_Unaffected_TMA5-Run1_3mm

status: Public on Sep 10 2024

type: other

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

hyb_protocol: A total of 343 unique genes were included in the analysis of this dataset. 246 genes came from an early version of the Xenium human lung base panel (PD_336) and 97 genes from a custom designed panel (CVEVZD). The custom panel was curated based on human lung single cell analysis data (Habermann et al. 2020), selecting for genes useful in cell type identification and/or with suspected involvement in IPF. Gene panel probe hybridization occurred overnight for 18 hours at 50°C (Bio-Rad DNA Engine Tetrad 2). Subsequent washes the next day removed unbound probes. Ligase was added to circularize the paired ends of bound probes (2 hours at 37°C) and followed by enzymatic rolling circle amplification (2 hours at 30°C). Slides were washed in TE buffer before background fluorescence was chemically quenched; autofluorescence is a known issue in lung tissue as well as a byproduct of formalin-fixation (Davis et al. 2014). Following PBS and PBS-T washes, DAPI was used to stain sample nuclei. Finalized slides were stored in PBS-T in the dark at 4°C for ≤5 days until being loaded onto the Xenium Analyzer instrument. Stepwise Xenium FFPE preparation guidelines and buffer recipes can be found in 10X Genomics Demonstrated Protocol CG000578.

scan_protocol: Xenium Analyzer is fully automated. The user marks regions for analysis by manually selecting sample location on an initial low-resolution image. After loading consumable reagents and slides, internal sample and liquid handling mechanics control experiment progression. Data collection occurs in cycles of fluorescently labeled probe binding, image acquisition, and probe stripping. Localized points of fluorescence intensity detected during the rounds of imaging are then defined as potential RNA puncta. Each gene on the panel has a unique fluorescence pattern across the image channels. Puncta that match a specific pattern are then decoded and labeled according to the gene ID. All image FOVs (4240 x 2960 pixels) and associated detected transcripts are computationally stitched together via the DAPI-stained image. The data for TMAs 1-4 was acquired on instrument software version 1.1.2.4 and analysis version xenium-1.1.0.2. The data for TMA5 was acquired on instrument software version 2.0.1.0 and analysis version xenium-2.0.0.10.Detailed instructions on instrument operation and consumable preparation can be found in 10X Genomics’ Demonstrated Protocol CG000582.

data_processing:
To be updated.
Supplementary files format and content: HE_annotations.tar: This file contains geojson polygons of pathology annotations of regions mentioned in the paper for each sample as well as a csv assigning cells to the annotations they fall within.

molecule: other

source_name: Lung, unaffected

label_protocol: Deparaffinization and decrosslinking was performed to make subcellular RNA targets accessible (10X Genomics Demonstrated Protocol CG000580).

growth_protocol: A 5um section of each archived lung FFPE block was H&E stained and presented to a physician who identified areas of interest and labeled them as less or more fibrotic (LF or MF) relative to the sample. For TMAs 1-4, blocks were designed in a 3x3 or 2x2 pattern for 3mm and 5mm cores, respectively. Sample cores were punched and placed manually using a “Quick-Ray Manual Tissue Microarrayer Full Set” and “Quick-Ray Molds”, according to the manufacturer’s directions. Empty core spaces were filled with core punches taken from blank paraffin blocks (VWR 76548-194). Once complete, blocks are placed face down on a clean glass slide and briefly heated in a warm drawer (~45°C) to slightly melt the paraffin together and even the block face. TMA blocks were then cooled to room temperature, removed from the slide, sealed, and stored at 4°C. For TMA5, a custom 3mm square punch was made to fit the specifications of the “Quick-Ray Manual Tissue Microarrayer Full Set”, and a new 3x6 layout was designed. These cores were punched and placed tissue-side down on double-sided tape in a FFPE block mold. Paraffin wax (VWR 76548-194) was then poured slowly into the back of mold with tapping to release trapped air pockets between the cores. The block was allowed to cool completely overnight. TMA5 was then placed in the warm drawer and cooled as TMAs 1-4.

extract_protocol: Sectioning was performed at 5um on a Leica RM2135 with a water float temperature of 40°C. Sections were placed on Xenium slides (10X Genomics) and left to dry overnight. Slides were then stored in a sealed dessicator at room temperature for up to a maximum of 10 days.

treatment_protocol: All protocol workstations and equipment were cleaned using RNase Away (RPI 147002) followed by 70% Isopropanol. All reagents, including water, were molecular grade nuclease-free.

tag: age

tag: gender

value: F

tag: ethnicity

value: European

tag: tobacco

value: Unknown

tag: status

value: Unaffected

value: Lung, unaffected

tag: tma

tag: run

tag: punch size

tag: clinical diagnosis

value: Control

tag: sample type


title: TILD315_More-affected_TMA5-Run1_3mm

source_name: Lung, more affected

value: African American

value: Y

value: Affected

tag: tissue

value: Lung, more affected


title: VUHD038_Unaffected_TMA5-Run1_3mm

value: N


title: WT CFP-cnp1, ChIP

tag: cell type

value: anti-GFP antibody (Invitrogen, A11122)


title: SUMO-KallR CFP-cnp1, ChIP

tag: chip antibody


title: VUILD142_More-affected_TMA5-Run1_3mm

value: M

value: CPFE


title: HC-14

value: Human blood

tag: cell line

value: Healthy Control


title: TILD299_More-affected_TMA5-Run1_3mm

value: Hispanic

value: IPF


title: VUILD141_More-affected_TMA5-Run1_3mm

value: F

value: European

value: cHP


title: T1D-07


title: TILD113_Less-affected_TMA5-Run1_3mm

source_name: Lung, less affected

value: Lung, less affected


title: untagged strain, ChIP

value: yeast


title: HC-09


title: TILD117_More-affected_TMA5-Run1_3mm

value: ILD


title: TILD111_Less-affected_TMA5-Run1_3mm


title: TILD167_Less-affected_TMA5-Run1_3mm


title: untagged strain, Input


title: TILD049_More-affected_TMA5-Run1_3mm


title: TILD080_Less-affected_TMA5-Run1_3mm


title: TILD028_Less-affected_TMA5-Run1_3mm

value: Y


title: VUILD58_More-affected_TMA5-Run1_3mm

value: Affected


title: Paw skin bulk RNA-seq female, rep3

status: Public on Aug 08 2024

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC mouse genome build mm9) using TopHat2 default settings (Trapnell et al., 2012).
The BAM files obtained after alignment were processed using HTSeq-count to obtain the counts per gene in all samples (Anders et al., 2015).
Assembly: UCSC mouse genome build mm9
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: Non-neuronal cells

extract_protocol:
Dissection of hind paw skin and DRG
Approximately 500ng Total RNA was used for RNA-seq library preparation by following TruSeq stranded mRNA-seq library preparation kit ( Cat. No: 20020595, Illumina, USA). Following mRNA enrichment by oligodT beads,  the RNA was fragmented into small pieces using divalent cautions under elevated temperature and magnesium. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). The incorporation of dUTP in second strand synthesis effectively quenches the second strand during amplification, since the polymerase used in the assay will not incorporate past this nucleotide. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-Seq library for sequencing by 50bp single-end protocol with Illumina HiSeq 3000 platform.

treatment_protocol: Mice were treated by injecting systemically with PTX (6mg/kg) at day -6, -3 and 0

value: Non-neuronal cells

tag: genotype

value: WT

value: Vehicle

tag: time

value: Day 0 (control)


title: VUILD49_Less-affected_TMA5-Run1_3mm

value: M


title: Paw skin bulk RNA-seq female, rep2

tag: treatment


title: VUHD049_Unaffected_TMA5-Run1_3mm

tag: age

value: Unknown

value: Unaffected

value: Lung, unaffected

value: Control


title: Paw skin bulk RNA-seq female, rep1


title: Paw skin bulk RNA-seq male, rep3


title: Paw skin bulk RNA-seq male, rep2


title: TILD130_Less-affected_TMA5-Run1_3mm

tag: gender

value: IPF


title: DRG bulk RNA-seq female, rep3

source_name: Non-neuronal cells and DRG neurons

value: Non-neuronal cells and DRG neurons


title: DRG bulk RNA-seq male, rep3


title: DRG bulk RNA-seq female, rep1


title: DRG bulk RNA-seq female, rep2


title: DRG bulk RNA-seq male, rep2


title: DRG bulk RNA-seq male, rep1


title: Paw skin bulk RNA-seq 31d post-PTX female, rep3

value: Chemotherapy (Pacletaxol) treatment

value: Day 31


title: Paw skin bulk RNA-seq 31d post-PTX female, rep2


title: Paw skin bulk RNA-seq 16d post-PTX female, rep2

value: Day 16


title: Paw skin bulk RNA-seq 1d post-PTX female, rep3

value: Day 1


title: Paw skin bulk RNA-seq male, rep1


title: Paw skin bulk RNA-seq 16d post-PTX female, rep3


title: Paw skin bulk RNA-seq 16d post-PTX female, rep1


title: Paw skin bulk RNA-seq 31d post-PTX female, rep1


title: Paw skin bulk RNA-seq 1d post-PTX female, rep1


title: Paw skin bulk RNA-seq 31d post-PTX male, rep3


title: Paw skin bulk RNA-seq 1d post-PTX female, rep2


title: Paw skin bulk RNA-seq 31d post-PTX male, rep4


title: Paw skin bulk RNA-seq 31d post-PTX male, rep2


title: Paw skin bulk RNA-seq 16d post-PTX male, rep3


title: Paw skin bulk RNA-seq 31d post-PTX male, rep1


title: Paw skin bulk RNA-seq 16d post-PTX male, rep2


title: Paw skin bulk RNA-seq 16d post-PTX male, rep1


title: Paw skin bulk RNA-seq 1d post-PTX male, rep3


title: Paw skin bulk RNA-seq 1d post-PTX male, rep4


title: Paw skin bulk RNA-seq 1d post-PTX male, rep2


title: Paw skin bulk RNA-seq 1d post-PTX male, rep1


title: DRG bulk RNA-seq 31d post-PTX female, rep3


title: DRG bulk RNA-seq 31d post-PTX female, rep2


title: DRG bulk RNA-seq 16d post-PTX female, rep2


title: DRG bulk RNA-seq 16d post-PTX female, rep3


title: DRG bulk RNA-seq 31d post-PTX female, rep1


title: DRG bulk RNA-seq 16d post-PTX female, rep1


title: DRG bulk RNA-seq 1d post-PTX female, rep3


title: DRG bulk RNA-seq 1d post-PTX female, rep1


title: DRG bulk RNA-seq 31d post-PTX male, rep3


title: DRG bulk RNA-seq 31d post-PTX male, rep4


title: DRG bulk RNA-seq 31d post-PTX male, rep2


title: DRG bulk RNA-seq 16d post-PTX male, rep2


title: DRG bulk RNA-seq 31d post-PTX male, rep1


title: DRG bulk RNA-seq 1d post-PTX male, rep2


title: DRG bulk RNA-seq 1d post-PTX male, rep1


title: DRG bulk RNA-seq 1d post-PTX female, rep2


title: DRG bulk RNA-seq 16d post-PTX male, rep3


title: Patient_24_NT

status: Public on Aug 02 2024

data_processing:
the fastq files were generated using bcl2fastq v2.19.0.316 with --no-lane-splitting option
the fastq files have been aligned to GRCh38 genome reference with STAR Aligner tool v2.7.0a
the raw count matrix of mapped reads has been generated from the bam files made after alignment with featureCounts function of Rsubread package with the gtf file of comprensive gene annotation file of GENCODE38 and with the option: isPairedEnd=T, strandSpecific=1, GTF.featuresType="CDS" , GTF.attrType="gene_name", isGTFAnnotationFile=T,  countChimericFragments=F, autosort=T.
Differential Gene Expression analysis was performed using DESeq2 1.30.1 indicating as design formula the surrogate variables identified with the package DaMiRseq  2.2.0 R version 4.0.5 . padj < 0.05
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files with numbers of mapped reads for gene expressed as raw count

source_name: Control

extract_protocol:
Tissue biopsies for RNA sequencing were stored in RNA later and frozen at -80°C. Then, RNA was extracted with RNeasy Mini kit (QIAGEN).
Libraries were prepared with the SMARTer Stranded Total RNA Sample Prep Kit-HI Mammalian (Takara).
Sequencing was performed on the Illumina Next Seq550 platform by generating at least 80 million reads 75bp paired-end per sample.

value: YES Neoadj

tag: disease stage

value: progression


title: DRG bulk RNA-seq 1d post-PTX male, rep3


title: Patient_21_NT

value: NO Neoadj

value: relapse


title: Patient_14_NT


title: Patient_20_NT


title: Patient_19_NT


title: DRG bulk RNA-seq 1d post-PTX male, rep4

value: WT


title: DRG bulk RNA-seq 16d post-PTX male, rep4


title: Patient_23_NT


title: DRG bulk RNA-seq 16d post-PTX male, rep1


title: Patient_18_NT


title: Patient_16_NT


title: Patient_22_NT


title: Patient_15_NT


title: Patient_06_NT


title: Patient_03_NT


title: Patient_13_NT


title: Patient_24_T

source_name: Tumor

value: Tumor


title: Patient_10_NT


title: Patient_11_NT


title: Patient_01_NT


title: Patient_12_NT


title: Patient_22_T


title: Patient_21_T


title: Patient_23_T


title: Patient_20_T


title: Patient_19_T


title: Patient_18_T


title: Patient_16_T


title: Patient_12_T


title: Patient_14_T


title: Patient_08_T


title: Patient_09_T


title: Patient_07_T


title: Patient_13_T


title: Patient_05_T


title: Patient_11_T


title: Patient_03_T


title: Patient_02_T


title: Patient_15_T


title: Patient_08_NT


title: patient_25_NT

data_processing:
reads were mapped to the reference genome GRCh38 using the CellRanger Software
We used the emptyDrops function to remove all the droplets with a false discovery rate greater than 0.05, and all cells with a number of UMIs, detected genes or a percentage of mitochondrial and ribosomal genes that were outliers compared to the median absolute deviation.
All genes that did not have a minimum of 10 counts in the entire dataset were removed
Performed Seurat scRNA analysis workflow
Assembly: GRCh38
Supplementary files format and content: mtx. tsv. Of raw and filtered cellranger output
Supplementary files format and content: rds object of analized dataset

source_name: Non Tumor

extract_protocol:
cells were stained with live dead eFluor780 and CD45+ antibody and sorted with FacsAria III. An average of 7000 cells were loaded into the Chromium controller System (10X Genomics) for Gel bead Emulsion generation.
Single-cell 3’ library preparation, (Chromium Single Cell 3’ Reagent Kits v2-rev C).
Libraries were sequenced on the Illumina NextSeq550 platform and an average of 40.000 reads per single cell was obtained

treatment_protocol: Fresh tissue biopsies were dissociated to obtain a single-cell suspension with the Tumor Dissociation Kit, human (Miltenyibiotec)

value: Non Tumor


title: Patient_06_T


title: Patient_01_T


title: patient_25_T


title: patient_26_T


title: patient_21_T


title: Patient_10_T


title: patient_21_NT


title: Responder2_CD8

status: Public on Jul 04 2024

type: genomic

city: Berlin

first: Julia

middle: K

last: Polansky

address: Augustenburger Platz 1

country: Germany

institute: Berlin Institute of Health @ Charité Universitätsmedizin Berlin

hyb_protocol: After bisulfite conversion, the gDNA, was fragmented, hybridized, and stained as per the guidelines of the Infinium HD protocol.

scan_protocol: Bead arrays were scanned using the iScan.

data_processing: The raw intensity data files (IDAT) were preprocessed using minfi version 1.42.0 by quantile normalization. Probes were filtered based on not meeting the detection p-value threshold against the background (p<0.01), being reported as cross-reactive, revisions of Illumina's manifest (Infinium MethylationEPIC v1.0 13.03.2020), or being at a SNP, using the minfi function dropLociWithSnps. To account for differences between the 10 matched responder/non-responder pairs (e.g. matched comorbidities, age, sex, etc.) batch correction was performed using the ComBat function from the sva package version 3.44.0.

label: Cy3, Cy5

label_protocol: Infinium HD Methylation Assay Reference Guide.

extract_protocol:
DNA_extraction_and_Bisulfite_Conversion
genomic DNA was extracted using Zymo’s Quick-DNA MicroPREP Kit (Zymo Research) following instructions provided by the manufacturer. Samples with cell counts <25,000 cells were not subjected to DNA extraction. Instead, the cell pellets were directly taken up in a mix of 40 µl lysate buffer from the Zymo’s Quick-DNA MicroPREP Kit (Zymo Research) with 1.25 mg/ml Proteinase K (Sigma-Aldrich 3115828001) and incubated for 3 hours at room temperature. Isolated genomic DNA and cell lysates from Proteinase K digestion were subjected to bisulfite conversion using Zymo’s EZ DNA Methylation-Gold Kit (Zymo Research) according to manufacturer's instructions.

treatment_protocol: Dexamethasone treatment, sample collected within the first 4 days of treatment.

value: Responder

tag: donor

tag: Sex

value: F


title: Non_Responder9_CD8

extract_protocol:
ProtK_digestion_and_Bisulfite_Conversion
genomic DNA was extracted using Zymo’s Quick-DNA MicroPREP Kit (Zymo Research) following instructions provided by the manufacturer. Samples with cell counts <25,000 cells were not subjected to DNA extraction. Instead, the cell pellets were directly taken up in a mix of 40 µl lysate buffer from the Zymo’s Quick-DNA MicroPREP Kit (Zymo Research) with 1.25 mg/ml Proteinase K (Sigma-Aldrich 3115828001) and incubated for 3 hours at room temperature. Isolated genomic DNA and cell lysates from Proteinase K digestion were subjected to bisulfite conversion using Zymo’s EZ DNA Methylation-Gold Kit (Zymo Research) according to manufacturer's instructions.

value: M


title: Responder5_CD8


title: Non_Responder5_CD8


title: Responder6.2_CD8


title: Responder8.1_CD4


title: Responder1_CD8


title: Responder8.1_CD8


title: Non_Responder7_CD4


title: Responder3_CD8


title: Non_Responder6_CD8


title: Non_Responder10_CD4


title: Non_Responder9_CD4


title: Responder7_CD8


title: Responder10_CD4


title: Non_Responder2_CD8


title: Responder9_CD8


title: Non_Responder1_CD8


title: Responder4.2_CD8


title: Non_Responder4_CD8


title: Non_Responder10_CD8


title: Non_Responder7_CD8


title: Non_Responder8_CD8


title: Responder9_CD4


title: Responder7_CD4


title: Non_Responder8_CD4


title: Non_Responder3_CD8


title: Responder10_CD8


title: Non_Responder6_CD4


title: Responder6.2_CD4


title: Non_Responder2_CD4


title: Non_Responder4_CD4


title: Non_Responder3_CD4


title: Non_Responder1_CD4


title: Responder3_CD4


title: Non_Responder7_CD19


title: Responder6_CD19


title: Non_Responder8_CD19


title: Responder8_CD19


title: Responder10_CD19


title: Responder7_CD19


title: Responder1_CD4


title: Non_Responder5_CD19


title: Non_Responder6_CD19


title: Non_Responder3_CD19


title: Non_Responder5_CD4


title: Responder4_CD19


title: Non_Responder4_CD19


title: Responder1_CD19


title: Non_Responder10_CD19


title: Responder2_CD19


title: VUILD48-1_Less-affected_TMA2-Run1_3mm

status: Public on Jun 04 2024

scan_protocol: Xenium Analyzer is fully automated. The user marks regions for analysis by manually selecting sample location on an initial low-resolution image. After loading consumable reagents and slides, internal sample and liquid handling mechanics control experiment progression. Data collection occurs in cycles of fluorescently labeled probe binding, image acquisition, and probe stripping. Localized points of fluorescence intensity detected during the rounds of imaging are then defined as potential RNA puncta. Each gene on the panel has a unique fluorescence pattern across the image channels. Puncta that match a specific pattern are then decoded and labeled according to the gene ID. All image FOVs (4240 x 2960 pixels) and associated detected transcripts are computationally stitched together via the DAPI-stained image. The data in this paper was acquired on instrument software version 1.1.2.4 and analysis version xenium-1.1.0.2. Detailed instructions on instrument operation and consumable preparation can be found in 10X Genomics’ Demonstrated Protocol CG000582.

data_processing:
Transcript-based niche embedding files (node_meta.csv and .npy files) were genetared using GraphSAGE.
Information about output files can be found here:
https://www.10xgenomics.com/support/in-situ-gene-expression/documentation/steps/onboard-analysis/understanding-xenium-outputs
Supplementary files format and content: HE_annotations.tar: This file contains geojson polygons of pathology annotations of regions mentioned in the paper for each sample as well as a csv assigning cells to the annotations they fall within.

growth_protocol: A 5um section of each archived lung FFPE block was H&E stained and presented to a physician who identified areas of interest and labeled them as less or more fibrotic (LF or MF) relative to the sample. TMA blocks were designed in a 3x3 or 2x2 pattern for 3mm and 5mm cores, respectively. Sample cores were punched and placed manually using a “Quick-Ray Manual Tissue Microarrayer Full Set” and “Quick-Ray Molds”, according to the manufacturer’s directions. Empty core spaces were filled with core punches taken from blank paraffin blocks (VWR 76548-194). Once complete, blocks are placed face down on a clean glass slide and briefly heated in a warm drawer (~45°C) to slightly melt the paraffin together and even the block face. TMA blocks were then cooled to room temperature, removed from the slide, sealed, and stored at 4°C.

tag: ethnicity

value: European

tag: tobacco

value: Y

tag: status

value: Disease

value: Lung

tag: tma

value: NSIP


title: Non_Responder9_CD14


title: Responder3_CD19


title: Responder10_CD14


title: Non_Responder10_CD14


title: pca31, rep3

status: Public on Apr 29 2024

city: GWANGJU

first: Cheol Soo

last: Kim

address: 77 YONGBONG-RO, BUK-GU

institute: Chonnam National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to TAIR10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

organism: Arabidopsis thaliana

source_name: 2-week-old seedlings

growth_protocol: 2-week-old seedlings were grown on the MS media

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

value: 2-week-old seedlings


title: Responder8_CD14


title: Non_Responder8_CD14


title: Responder4.2_CD4


title: 10X_balf [FixedRNA-Pilot2_NGS23-B119]

status: Public on May 30 2024

city: Liège

first: Thomas

last: Marichal

address: Avenue de l'Hopital 11

department: GIGA Institute

country: Belgium

institute: University of Liege

description: 10X genomics

data_processing:
The Cell Ranger (v7.1.0) application (10x Genomics) was then used to demultiplex the BCL files into FASTQ files (cellranger mkfastq), to perform alignment (to Cell Ranger human genome references GRCh38) and unique molecular identifier counting to produce gene-barcode matrices.
Raw matrix files were used for further scRNA-seq analyses with R Bioconductor (3.17) and Seurat
Assembly: GRCh38
Supplementary files format and content: barcode sequences corresponding to column indices
Supplementary files format and content: tsv files containing for each feature the feature ID, the name and the type of features (Gene, antibody)
Supplementary files format and content: mtx files describing the count of genes for all cells

source_name: Bronchoalveolar lavage

extract_protocol:
The cells were fixed and barcoded using the Chromium Next Gem Single Cell Fixed RNA Sample Preparation Kit for multiplexed samples.
A Gene Expression Library was generated following the chromium  Fixed RNA Profiling workflow

value: Bronchoalveolar lavage


title: Non_Responder1_CD19


title: Non_Responder2_CD19


title: VUILD105-1_More-affected_TMA2-Run1_3mm

tag: run

tag: punch size

tag: clinical diagnosis

value: IPF

tag: sample type


title: Responder5_CD14

tag: cell type


title: Responder7_CD14


title: WT, rep2

tag: tissue

tag: genotype


title: WT, rep1


title: Responder9_CD14


title: MDA231_chip2

status: Public on Apr 22 2024

city: Houston

last: Navin

state: Texas

address: 6565 MD Anderson Blvd

department: Systems Biology

institute: MD anderson Cancer Center

data_processing:
The scRNA-seq FASTQ files were trimmed with Trimmomatic to remove sequencing and library adaptors
The trimmed reads were alignment to the reference genomes of human (hg19 reference) with STARsolo
The processed rds (count matrix) files were generated with Seurat 4.1.0
Assembly: hg19
Supplementary files format and content: Gene count

source_name: Breast

extract_protocol:
The genomic DNA and RNA was extract from isolated single nuclei
The in house nanowell based DNA-RNA sequencing (wellDA-seq) protocol

value: Breast

tag: cell line

tag: biomaterial provider

value: MD Anderson

tag: histology


title: Non_Responder6_CD14

tag: age


title: Responder5_CD4

tag: donor


title: atrzf1, rep3


title: MDA231_chip1


title: pca31, rep2


title: pca31, rep1


title: Responder3_CD14

tag: Sex


title: Non_Responder7_CD14


title: I148M 24hr biol rep5

status: Public on Apr 09 2024

city: Thousand Oaks

first: David

middle: Joseph

last: Sherman

state: California

address: 1 Amgen Center Drive, B29 DZ 2H

department: Discovery Research

institute: Amgen Inc.

data_processing:
Sequencing reads QC, mapping and gene quantification were performed using ArrayStudio.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Human liver cancer cell line

growth_protocol: Hep3B-PNPLA3-HiBiT (WT) and Hep3B-PNPLA3-I148M-HiBiT (I148M) cells were maintained in EMEM (ATCC) supplemented with 10% dialyzed fetal bovine serum (FBS) in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
100 ‒ 2,000 ng of human total RNA was used for cDNA library preparation by using a modified protocol based on the TruSeq® RNA Sample Preparation Kit (Illumina) and the published methods for strand-specific RNA-Seq.
RNA libraries for RNA-Seq were prepared using TruSeq® RNA Sample Preparation Kit (Illumina) following manufactuer's protocols.

treatment_protocol: Enough 6-well plates were seeded (500,000 cells/well) to allow for 5 replicates of the following conditions: WT & I148M cells basal (EMEM + 10% FBS), WT & I148M cells with 30 min, 1, 2, 4, and 24 h oleic acid (200 μM) added to the basal media (EMEM + 10% FBS).

value: Human liver cancer cell line

value: Cancer cell

value: mutant PNPLA3 (PNPLA3-I148M)

tag: treatment

value: oleic acid,24h


title: WT, rep3


title: Responder6_CD14

value: Responder


title: I148M 24hr biol rep4


title: Responder2_CD4

value: F


title: I148M 4hr biol rep4

value: oleic acid,4h


title: I148M 2hr biol rep5

value: oleic acid,2h


title: I148M 2hr biol rep4


title: I148M 4hr biol rep5


title: Responder4_CD14


title: I148M 1hr biol rep4

value: oleic acid,1h


title: Non_Responder5_CD14


title: VUILD104-2_More-affected_TMA2-Run1_3mm

tag: gender

value: M

tag: ethnicity

value: European

tag: tobacco

value: Y

value: Disease


title: I148M 30min biol rep5

value: oleic acid,0.5h


title: Non_Responder3_CD14


title: atrzf1, rep2

value: 2-week-old seedlings


title: I148M 30min biol rep4


title: atrzf1, rep1


title: I148M untreated biol rep5

value: untreated


title: I148M untreated biol rep4


title: WT 24hr biol rep4

value: wild-type PNPLA3


title: I148M 1hr biol rep5

value: Human liver cancer cell line


title: Responder1_CD14


title: Responder5_CD19


title: Non_Responder1_CD14


title: Non_Responder4_CD14


title: WT 4hr biol rep5

value: Cancer cell


title: Non_Responder2_CD14


title: WT 4hr biol rep4


title: WT 24hr biol rep3


title: WT 2hr biol rep5


title: WT 4hr biol rep3


title: Responder2_CD14


title: WT 2hr biol rep4


title: WT 30min biol rep5


title: WT 1hr biol rep3


title: WT 1hr biol rep5


title: WT 1hr biol rep4


title: WT 30min biol rep3


title: WT untreated biol rep5


title: WT 30min biol rep4


title: I148M 4hr biol rep1

value: mutant PNPLA3 (PNPLA3-I148M)


title: WT untreated biol rep4


title: I148M 4hr biol rep3


title: I148M 24hr biol rep3

value: oleic acid,24h


title: I148M 2hr biol rep3


title: I148M 4hr biol rep2


title: I148M 24hr biol rep2


title: I148M 24hr biol rep1


title: I148M 2hr biol rep1


title: I148M 2hr biol rep2


title: I148M 1hr biol rep1


title: I148M 1hr biol rep2


title: I148M 30min biol rep3


title: I148M 1hr biol rep3


title: WT 2hr biol rep3


title: I148M 30min biol rep2


title: I148M untreated biol rep2


title: I148M untreated biol rep3


title: I148M 30min biol rep1


title: I148M untreated biol rep1


title: WT untreated biol rep3


title: WT 24hr biol rep2


title: WT 24hr biol rep5


title: WT 24hr biol rep1


title: WT 4hr biol rep2


title: WT 2hr biol rep2


title: WT 2hr biol rep1


title: WT 1hr biol rep2


title: WT 30min biol rep1


title: WT 30min biol rep2


title: WT untreated biol rep2


title: WT untreated biol rep1


title: PRL01_M3

status: Public on Feb 27 2024

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC mouse genome build mm9) using TopHat2 default settings (Trapnell et al., 2012).
The BAM files obtained after alignment were processed using HTSeq-count to obtain the counts per gene in all samples (Anders et al., 2015).
Genome_build: UCSC mouse genome build mm9
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: paw

extract_protocol:
Fresh tissues were homogenized in Rn-easy solution using Bead Mill Homogenizer (Omni International, Kennesaw, GA).
Approximately 500ng Total RNA was used for RNA-seq library preparation by following TruSeq stranded mRNA-seq library preparation kit ( Cat. No: 20020595, Illumina, USA). Following mRNA enrichment by oligodT beads,  the RNA was fragmented into small pieces using divalent cautions under elevated temperature and magnesium. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). The incorporation of dUTP in second strand synthesis effectively quenches the second strand during amplification, since the polymerase used in the assay will not incorporate past this nucleotide. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-Seq library for sequencing by 50bp singlle-end protocol with Illumina HiSeq 3000 platform.

treatment_protocol: PBS single i.pl. injection; PBS 12d i.pl. injection (one per day); PRL (0.1ug) i.pl. injection; PRL (0.1ug) 12d i.pl. injection (one per day)

tag: strain

value: male

value: 0.1ug 12d PRL


title: PRL01_F4

value: female


title: PRL01_M1


title: PRL01_F1


title: PRL01_M2


title: PRL01_M4


title: 200MOI_1hpi_3

status: Public on Jan 30 2024

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq Fastq reads were aligned with combined reference genome using TopHat2 default settings (Trapnell et al., 2012).
The BAM files obtained after alignment were processed using htseq-count to obtain the counts per gene in all samples (Anders et al., 2015).
Assembly: Combined genome including Chlamydia trachomatis 434/Bu chromosome (GCF_000068585.1_ASM6858v1), C_trachomatis_pL2_plasmid_AM886278, and mouse genome (mm10).
Supplementary files format and content: tab-delimited text files include raw count values for each sample

organism: Chlamydia trachomatis

growth_protocol: L2-infected L929 cells were cultured in DMEM supplemented with 5% fetal bovine serum (FBS) at 37 ℃.

extract_protocol:
RNA was harvested using Tri Reagent (MilliporeSigma). Genomic DNA was removed using RNase-free DNase I-XT (New England Biolab).
2000 ng Total RNA was used for RNA-seq library preparation using Illumina TruSeq stranded mRNA-seq sample preparation protocol with the modifications to remove host and bacterial rRNAs and host mRNAs.

tag: group

value: 200 MOI

tag: time

value: 1 hpi


title: 200MOI_1hpi_1


title: PRL01_F2


title: 200MOI_0hpi_2

value: 0 hpi


title: 200MOI_0hpi_1


title: 200MOI_0hpi_3


title: 50MOI_1hpi_3

value: 50 MOI


title: 50MOI_1hpi_2


title: 50MOI_1hpi_1


title: WT 4hr biol rep1

value: oleic acid,4h


title: 50MOI_0hpi_3


title: 50MOI_0hpi_2


title: WT 1hr biol rep1

value: oleic acid,1h


title: 50MOI_0hpi_1


title: CLM 02

status: Public on Jan 29 2024

description: FFPE Spatial transcriptome sequencing

data_processing:
Raw sequencing data were converted into fastqs using Illumina BCL Convert software (version 3.8.2).
Fastq files were aligned to the human reference genome GRCh38 with Space Ranger (10X Genomics) version 1.3.1 using the human probe set v1 (Visium_Human_Transcriptome_Probe_Set_v1.0_GRCh38–2020-A.csv).
The generated filtered feature matrices were analyzed individually using Scanpy package (version 1.9.1).
Assembly: Pre-build Human genome (version GRCh38) was used as genome reference.
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene Ids
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Visium Spatial Transcriptomics

source_name: CLM

growth_protocol: not applicable

extract_protocol:
After deparaffinization and rehydration, sections were stained with hematoxylin (Histo-Line, catalog no. 01HEMH1000) for 15 minutes, followed by eosin (Histo-Line, catalog no. 01EOY101000) for 7 minutes. RNA quality of the FFPE tissue blocks was determined before performing spatial transcriptomics assay, according to the manufacturer's instructions.
H&E image preparation was performed according to protocol. Brightfield histologic images were acquired using the Axio Scan.Z1 (ZEISS). Libraries were prepared using 10X Genomics Visium Spatial for FFPE Gene Expression Kit, following the manufacturer's protocol, and sequenced on a NextSeq2000 (Illumina) at a minimum sequencing depth of 50,000 read pairs per spatial spot.

treatment_protocol: not applicable

value: CLM


title: PRL01_F3


title: HCT116_k27me3_chip_rep_1_ChIPseq

status: Public on Jan 22 2024

city: Edinburgh

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

data_processing:
All ChIP-seq experiments were processed previously described (Masalmeh et al., 2021, PMID: 33514701). Read quality was checked using FASTQC (v0.11.4, https://www.bioinformatics.babraham.ac.uk/projects/fastqc), with low quality reads and adaptors removed using TrimGalore with default settings (v0.4.1). Reads were aligned to hg38 using bowtie 2 (v2.3.1, with settings: -N 1 -L 20 --no-unal) (Langmead and Salzberg, 2012, PMID: 22388286). For paired end data, additional settings were used during alignment to remove discordant reads: --no-mixed –nodiscordant -X 1000. ChIP-Rx-seq reads were aligned to a combination of hg38 and dm6 genomes. Multimapping reads excluded using SAMtools (v1.6, with settings: -bq 10) (Li et al., 2009) and PCR duplicates excluded using SAMBAMBA (v0.5.9) (Tarasov et al., 2015, PMID: 25697820). For T7 ChIP-Rx-seq UMIs were used for de-duplication instead of SAMBAMBA. We first extracted UMIs from the appropriate read and placed them in the read FASTQ headers using UMI tools extract (v1.0.0 and setting: --bc-pattern=NNNNNNNNNNN). Then deduplication was performed using the UMI tools dedup function (v1.0.0 and setting: --paired). Tracks for visualisation of histone ChIP-seq were generated using Deeptools (v3.2.0) (Ramirez et al., 2016, PMID: 27079975). Counts per million normalised tracks were generated using the bamCoverage function (settings: --normalizeUsing CPM) with the default bin size of 50 bp. The mean of replicate tracks and normalisation over the input was calculated using the bigwigCompare function (settings: --operation mean). For the single-ended H3K36me3 ChIP-seq, the estimated fragment length of 150 bp was used. For the other paired-end experiments the actual fragment size was used.
Assembly: hg38
Supplementary files format and content: Processed data files are bigWig files generated by normalisation over input and from the mean of the two replicates as described under data processing.

source_name: HCT116 cells

growth_protocol: HCT116 and DNMT3B cells were gifts from B. Vogelstein (Rhee et al 2002 PMID: 11932749). Cells were cultured in McCoy’s 5A medium (Gibco) supplemented with 10% fetal calf serum (Life technologies) and penicillin-streptomycin antibiotics at 140 and 400 µg/ml respectively.

extract_protocol:
ChIP-seq was performed as previously described (Masalmeh et al., 2021, PMID: 33514701). For T7-DNMT3B ChIP-Rx-seq experiments, 1×107 cells were harvested, washed and crosslinked with 1% methanol-free formaldehyde in PBS for 8 min at room temperature. Crosslinked cells were lysed for 10 min on ice in 50 μl of lysis buffer (50 mM Tris-HCl pH 8, 150 mM NaCl, 1 mM EDTA, 1% SDS) freshly supplemented with proteinase inhibitor (Sigma-Aldrich). IP dilution buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 1 mM EDTA, 0.1% Triton X-100) freshly supplemented with proteinase inhibitor, DTT and PMSF was added to the samples to reach a final volume of 500 μl. As prolonged sonication caused T7-DNMT3B degradation, chromatin was fragmented using Benzonase (Pchelintsev et al., 2016, PMID: 26821228): samples were sonicated on ice with Soniprep 150 twice for 30 s to break up nuclei; then 200 U of Benzonase Nuclease (Sigma) and MgCl2 (final concentration 2.5 mM) were added and samples were incubated on ice for 15 min. The reaction was blocked by adding 10 μl of 0.5 M EDTA pH 8. Following centrifugation for 30 min at 18,407 g at 4 °C, supernatants were collected and supplemented with Triton X-100 (final concentration 1%) and 5% input aliquots were retained for later use. Protein A Dynabeads (Invitrogen) previously coupled with 10 μl of T7-Tag antibody per 1×107 cells in blocking solution (1x PBS, 0.5% BSA) were added and the samples incubated overnight under rotation at 4 °C. Beads were then washed for 10 min at 4 °C with the following buffers: IP dilution buffer 1% Triton X-100 (20 mM Tris-HCl pH 8, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100), buffer A (50mM HEPES pH 7.9, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS), buffer B (20 mM Tris pH 8, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate), TE buffer (1mM EDTA pH 8, 10 mM Tris pH 8). Chromatin was eluted by incubating the beads in extraction buffer (0.1 M NaHCO3, 1% SDS) for 15 min at 37 °C. To reverse the cross-linking Tris-HCl pH 6.8 and NaCl were added to final concentrations of 130 mM and 300 mM respectively, and immunoprecipitations were incubated at 65 °C overnight. Samples were then incubated at 37 °C for 1 h after addition of 2 μl of RNase Cocktail Enzyme Mix (Ambion). Then 40 μg of Proteinase K (Roche) were added, followed by 2 h incubation at 55 °C. Input material was similarly de-crosslinked. Samples were purified with the MinElute PCR purification kit (QIAGEN). For ChIP-Rx-seq of endogenous T7-DNMT3B and ectopic T7-DNMT3B expressed in DNMT3B KO cells, 20 μg of Spike-in chromatin (ActiveMotif 53083) was added to each sample after sonication. 2 μl of spike-in antibody per sample (ActiveMotif 61686) was also added in a ratio 1:5 versus the T7 antibody. A similar protocol was used for H3K4me3, H3K9me3, H3K27me3 and H3K36me3 ChIP-seq experiments, except: 0.5×107 cells were harvested and crosslinked with 1% methanol-free formaldehyde in PBS for 5 min at room temperature. For H3K36me3 ChIP-Rx-seq crosslinked Drosophila S2 cells were spiked into samples before sonication at a ratio of 20:1 human to Drosophila cells. Following nuclei rupture by sonication on ice with Soniprep 150, chromatin was fragmented using Bioruptor Plus sonicator (Diagenode) for 40 cycles (30 s on/30 s off on high setting at 4 °C). 2 μl /1×106 cells of the following antibodies were used for immunoprecipitations: H3K4me3 (EpiCypher 13-00041), H3K9me3 (Active Motif 39161), H3K27me3 (Cell Signaling Technology C36B11) and H3K36me3 (Abcam ab9050).
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645) according to the manufacturer instructions. NEBNext Multiplex Oligos for Illumina (NEB) barcode adapters were used. Specifically, Illumina Index Primers Set 1 (E7335) for endogenous T7-DNMT3B and H3K36me3, and Unique Dual Index UMI Adaptors DNA Set 1 (E7395) for the other libraries.  For histone modifications ChIP-seq, adapter-ligated DNA was size selected for an insert size of 150 bp using Agencourt AMPure XP beads. Libraries were quantified using the Qubit dsDNA HS or BR assay kit and assessed for size and quality using the Agilent Bioanalyser. Endogenous T7-DNMT3B and H3K36me3 ChIP-Rx-seq libraries were sequenced using the NextSeq 500/550 high-output version 2.5 kit (75 bp paired end reads, DNMT3B or 75 bp single end reads, H3K36me3). The other ChIP-seq libraries were sequenced using the NextSeq 2000 P3 (50 bp paired end reads). Libraries were combined into equimolar pools to run within individual flow cells. Sequencing was performed by the Edinburgh Clinical Research Facility.

tag: cell line_background

value: colorectal cancer cell line

value: WT

tag: chip antibody


title: HCT116_k9me3_chip_rep_2_ChIPseq

tag: cell type

value: H3K9me3 (Active Motif 39161)


title: HCT116_k27me3_chip_rep_2_ChIPseq

tag: genotype

value: H3K27me3 (Cell Signaling Technology C36B11)


title: 200MOI_1hpi_2


title: HCT116_k9me3_k27me3_input_rep_2_ChIPseq

description:
HCT116_k9me3_norm_mean_ChIPseq.bigWig
HCT116_k27me3_norm_mean_ChIPseq.bigWig

value: none (input)


title: CLM 01

description: FFPE Spatial transcriptome sequencing

tag: tissue


title: HCT116_k36me3_chip_rep_1_ChIPseq

value: H3K36me3 (Abcam ab9050)


title: HCT116_k36me3_input_rep_1_ChIPseq


title: HCT116_k4me3_input_rep_1_ChIPseq


title: HCT116_k4me3_chip_rep_1_ChIPseq

value: H3K4me3 (EpiCypher 13-00041)


title: HCT116_k36me3_input_rep_2_ChIPseq


title: HCT116_k4me3_chip_rep_2_ChIPseq


title: MM_Co_6d_M3

status: Public on Jan 02 2024

source_name: Masseter muscle

extract_protocol:
Dissection of masseter muscle
Approximately 500ng Total RNA was used for RNA-seq library preparation by following TruSeq stranded mRNA-seq library preparation kit ( Cat. No: 20020595, Illumina, USA). Following mRNA enrichment by oligodT beads,  the RNA was fragmented into small pieces using divalent cautions under elevated temperature and magnesium. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). The incorporation of dUTP in second strand synthesis effectively quenches the second strand during amplification, since the polymerase used in the assay will not incorporate past this nucleotide. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-Seq library for sequencing by 50bp single-end protocol with Illumina HiSeq 3000 platform.

treatment_protocol: Mice were treated by injecting complete Freund's adjuvant (CFA), collagenase type 2 0.2U, collagenase type 2 10U or vehicle into masseter muscle.

value: male

tag: cell types

value: All muscle cells

value: Collagenase type 2 10U


title: HCT116_k36me3_chip_rep_2_ChIPseq


title: MM_Co_6d_M1


title: 12d_post_col_1


title: MM_Co_6d_M2


title: 12d_post_col_2


title: 12d_post_col_4


title: 2d_post_col_4


title: 2d_post_col_3


title: HCT116_k9me3_k27me3_input_rep_1_ChIPseq


title: 2d_post_col_1


title: 2d_post_col_2


title: HCT116_k9me3_chip_rep_1_ChIPseq


title: Contr_2

value: Vehicle


title: C_RPC_4

value: Collagenase type 2 0.2U


title: Contr_1


title: C_RPC_3


title: HCT116_k4me3_input_rep_2_ChIPseq


title: C_RPC_2


title: C_RPC_1


title: C_1C_4


title: C_1C_2


title: C_1C_1


title: 12d_post_col_3


title: CFA_control_3


title: CFA_control_1


title: CFA_control_2


title: CFA_1d_2

value: CFA


title: CFA_1d_1


title: CFA_1d_3


title: CFA_5d_3


title: CFA_5d_1


title: CFA_5d_2


title: Contr_3


title: C42B_EnzR_RNA-seq_siNON_rep1

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Basecalls performed using CASAVA
For RNA-seq, the reads were trimmed using trimmomatic version 0.33 and poly-A tails were removed using homerTools in HOMER. Contaminants reported in iGENOME were removed using Bowtie2 and remaining reads were mapped to human hg38 transcriptome and genome with tophat2 software version 2.0.31. Differential expression of genes was analyzed using edgeR using HOMER.
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph (HOMER makeUCSCfile command) from alignment file.

source_name: C42B prostate cancer cells, EnzR, siNON, RNA

growth_protocol: C42B cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum, 25 U/ml penicillin and 25 µg/ml streptomycin, kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
For RNA-seq, RNA was extracted using Qiagen RNeasy Mini kit.
For RNA-seq, NEBNext Poly(A) mRNA Magnetic Isolation Module kit and NEBNext Ultra II Directional RNA Library Prep kit.

treatment_protocol: Treatment-induced NE-like Enzalutamide resistant C42B EnzR cells were constantly cultured with 10 µM Enzalutamide. C42B EnzR cells were plated on 10 cm plates and transfected the following day with 25 nM of siRNA using OPTI-MEM and Lipofectamine 2000. Medium was changed after 4 hours incubation and samples were collected after 48 hours. Plasmid overexpressing (OE) DPYSL5 was created by inserting DPYSL5 to pLVX-IRES-ZsGreen1 by using In-Fusion HD Cloning Kit. DPYSL5 overexpression vector was introduced to C42B cells using multiplicity of infection (MOI) of 40 and cells were monitored one week before sample collection.

tag: cell line

value: LNCaP C4-2B

tag: long-term treatment

value: 10 µM Enzalutamide

tag: sirna treatment

value: Non-targeting control siRNA (Dharmacon, D-001810-10)

tag: sirna concentration

value: 25 nM

tag: sirna time


title: C42B_RNA-seq_plvx-OE-CTRL_rep2

source_name: C42B prostate cancer cells, plvx-OE-CTRL, RNA


title: C42B_EnzR_RNA-seq_siDPYSL5_rep1

source_name: C42B prostate cancer cells, EnzR, siDPYSL5, RNA

value: ON-TARGETplus SMARTpool against DPYSL5 (Dharmacon, L-008581-01)


title: C42B_RNA-seq_DPYSL5-OE_rep1

source_name: C42B prostate cancer cells, DPYSL5-OE, RNA


title: C42B_RNA-seq_plvx-OE-CTRL_rep1


title: C42B_RNA-seq_DPYSL5-OE_rep2


title: C42B_EnzR_RNA-seq_siDPYSL5_rep2


title: C42B_EnzR_RNA-seq_siNON_rep2


title: LNCaP-EnzR_RNA-seq_siNON_rep1

source_name: LNCaP prostate cancer cells, EnzR, siNON, RNA

growth_protocol: LNCaP cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum, 25 U/ml penicillin and 25 µg/ml streptomycin, kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

treatment_protocol: Treatment-induced NE-like Enzalutamide resistant LNCaP EnzR cells were constantly cultured with 10 µM Enzalutamide. LNCaP EnzR cells were plated on 10 cm plates and transfected the following day with 25 nM of siRNA using OPTI-MEM and Lipofectamine 2000. Medium was changed after 4 hours incubation and samples were collected after 72 hours. Plasmid overexpressing (OE) DPYSL5 was created by inserting DPYSL5 to pLVX-IRES-ZsGreen1 by using In-Fusion HD Cloning Kit. DPYSL5 overexpression vector was introduced to LNCaP cells using multiplicity of infection (MOI) of 40 and cells were monitored one week before sample collection.

value: LNCaP-EnzR

value: Lymph Node Carcinoma of the Prostate

value: Non-targeting control siRNA (Dharmacon, D-001810-10), 25 nM, 72 h


title: LNCaP-EnzR_RNA-seq_siDPYSL5_rep1

source_name: LNCaP prostate cancer cells, EnzR, siDPYSL5, RNA

value: ON-TARGETplus SMARTpool against DPYSL5 (Dharmacon, L-008581-01), 25 nM, 72 h


title: LNCaP-EnzR_RNA-seq_siDPYSL5_rep2

treatment_protocol: Treatment-induced NE-like Enzalutamide resistant LNCaP EnzR cells were constantly cultured with 10 µM Enzalutamide. LNCaP EnzR cells were plated on 10 cm plates and transfected the following day with 25 nM of siRNA using OPTI-MEM and Lipofectamine 2000. Medium was changed after 4 hours incubation and samples were collected after 48 hours. Plasmid overexpressing (OE) DPYSL5 was created by inserting DPYSL5 to pLVX-IRES-ZsGreen1 by using In-Fusion HD Cloning Kit. DPYSL5 overexpression vector was introduced to LNCaP cells using multiplicity of infection (MOI) of 40 and cells were monitored one week before sample collection.


title: C_1C_3

tag: Sex

tag: treatment


title: LNCaP_RNA-seq_DPYSL5-OE_rep2

source_name: LNCaP prostate cancer cells, DPYSL5-OE, RNA

value: LNCaP


title: LNCaP_RNA-seq_DPYSL5-OE_rep1


title: LNCaP_RNA-seq_plvx-OE-CTRL_rep1

source_name: LNCaP prostate cancer cells, plvx-OE-CTRL, RNA


title: Ccr2- Dapa HFD 1

status: Public on Dec 22 2023

data_processing:
Sequence reads were processed with nf-core/rnaseq versione 3.6 with --aligner star_rsem
Assembly: GrCM38/mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Ccr2- macrophages

extract_protocol:
According Maxwell RSC simply/RNA kit protocol
According SMART-Seq Stranded Kit (Clontech-Takara).

treatment_protocol: intragastric dapagliflozin (AstraZeneca) through gavage, 1.0 mg/kg/d for 12-weeks

value: high fat diet

value: Ccr2- macrophages

value: ApoE KO

value: 12 weeks treatment


title: Ccr2- vehicle HFD 2

value: intragastric vehicle (Hbss) through gavage 1/die


title: Ccr2- vehicle HFD 1


title: Ccr2- vehicle CD 2

value: chow diet


title: Ccr2- Dapa CD 1

value: intragastric dapagliflozin (AstraZeneca) through gavage, 1.0 mg/kg/d for 12-weeks


title: Ccr2- vehicle CD 1


title: Ccr2+ Dapa HFD 2

source_name: Ccr2+ macrophages

value: Ccr2+ macrophages


title: Ccr2+ Dapa HFD 1


title: Ccr2+ vehicle HFD 1


title: Ccr2+ Dapa CD 2


title: Ccr2+ Dapa CD 1


title: LNCaP_RNA-seq_plvx-OE-CTRL_rep2


title: WT_HFD_a, replicate 1,scRNAseq

description: 10x Genomics

data_processing:
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
10x Genomics

source_name: Heart

extract_protocol:
According Maxwell RSC simply/RNA kit protocol
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol:
chow diet
high fat diet

value: CD45+ cells

value: Heart

value: Wild type

tag: age

value: 14 months old


title: ApoE_KO_HFD_a, replicate 1,scRNAseq

description: 10x Genomics

tag: strain

value: APOE KO


title: Ccr2+ vehicle CD 1


title: Ccr2- Dapa HFD 2


title: WT_HFD_b, replicate 2,scRNAseq

description: 10x Genomics


title: ApoE KO HFD, replicate 2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.39 with the following settings (TruSeq3-PE.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 MINLEN:36)
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR v2.7a with the following settings (--quantMode GeneCounts --readFilesIn $FASTQS --outFilterType BySJout--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate)
Read count was performed with HTSeq v0.13.5 with the following settings (f bam -m intersection-nonempty -r name -s reverse -t exon -i gene_id)
Assembly: GrCM38/mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: cardiomyocytes

value: cardiomyocytes

value: 7 weeks of diet


title: WT_CD_a, replicate 1,scRNAseq

description: 10x Genomics


title: WT_CD_b, replicate 2,scRNAseq

description: 10x Genomics


title: ApoE_KO_HFD_b, replicate 2,scRNAseq

description: 10x Genomics


title: ApoE_KO_CD_b, replicate 2,scRNAseq

description: 10x Genomics


title: ApoE_KO_CD_a, replicate 1,scRNAseq

description: 10x Genomics


title: ApoE KO CD, replicate 3


title: ApoE KO CD, replicate 1


title: Wt HFD, replicate 1

value: WT


title: Ccr2+ vehicle HFD 2


title: Wt HFD, replicate 2


title: Ccr2- Dapa CD 2


title: ApoE KO HFD, replicate 1


title: Wt CD, replicate 2


title: ApoE KO CD, replicate 2


title: Wt HFD, replicate 3


title: Patient 10  post CAR  PB VDJ T

status: Public on Dec 15 2023

city: Leipzig

first: Maximilian

last: Merz

address: Liebigstr. 22

department: Department for Hematology, Cell Therapy and Hemostaseology

institute: University Hospital Leipzig

description:
10x Genomics
VDJ T

data_processing:
The CAR sequences for Ide-cel and Cilta-cel were obtained from the respective patents. Two separate custom references for Cilta and Ide-cel have been created by adding the corresponding CAR sequences  to the reference genome (GRCh38, Ensembl release 98) and GENCODE v32 annotation using the mkref function from Cellranger v7.1.0. The Cellranger multi pipeline was used to process the single cell gene-expression, cell surface protein and V(D)J libraries. The feature reference CSV file, declaring Antibody Capture constructs and associated barcodes can be found in the supplementary files. The reference dataset required for the V(D)J contigs is provided by 10X Genomics (GRCh38 Human V(D)J Reference - 7.1.0 (December 7, 2022)).
Assembly: hg38
Supplementary files format and content: filtered and tab-separated value files and matrix files
Library strategy: TCRseq

source_name: Peripheral Blood

extract_protocol:
For single cell sequencing, mononuclear cells from bone marrow (BMMCs) and peripheral blood (PBMCs) were isolated following standardized operating procedures using Leucosep tubes (Greiner Bio One, Frickenhausen, Germany) with a Ficoll gradient (Ficoll-Paque™ PLUS, VWR Avantor, Spring House, Pennsylvania). Cells were frozen using a CoolCell LX container (Corning, USA) and stored in the vapour phase of liquid nitrogen in an Askion HS200S freezer (Askion, Gera, Germany). Prior to single cell staining and library construction, samples with initial viability < 80% were subjected to dead cell removal using Viahance™ from BioPAL, Inc. following the manufacturer’s instructions.
A custom panel of61oligonucleotide-coupled antibodies directed against cell surface proteins was used for surface proteome analyses. The oligonucleotides consist of a linker to the antibody, a polymerase chain reaction (PCR) handle, an antibody-specific barcode and a binding site for the cell identifying capture oligonucleotide. The antibody-oligonucleotide conjugate was afterwards incubated with the cells followed by the removal of unbound antibody. After single cell droplet encapsulation, the antibody-bound oligonucleotides act as synthetic transcripts and were then processed with 10x Genomics 5’ v2 chemistry to generate libraries for BCR, TCR, gene expression and surface protein expression.
scRNA + surface protein expression seq, BCRseq, TCRseq

tag: timepoint

value: post CAR T cell infusion

value: PBMC

value: Peripheral Blood

tag: patient sex

value: m

tag: patient age

tag: sample type

value: VDJ T


title: Patient 12  apheresis  PB VDJ T

description:
10x Genomics
VDJ T

value: time of leukapheresis

tag: cell type

value: f


title: Patient 13  post CAR  PB VDJ T

description:
10x Genomics
VDJ T


title: Patient 10  apheresis  PB VDJ T

description:
10x Genomics
VDJ T


title: Wt CD, replicate 3

tag: genotype

value: chow diet

tag: time


title: Ccr2+ vehicle CD 2

value: Ccr2+ macrophages

value: ApoE KO

value: intragastric vehicle (Hbss) through gavage 1/die

value: 12 weeks treatment


title: ApoE KO HFD, replicate 3

value: high fat diet


title: Patient 9  post CAR  BM VDJ T

description:
10x Genomics
VDJ T

source_name: Bone Marrow

value: BMMC

tag: tissue

value: Bone Marrow


title: Patient 8  apheresis  PB VDJ T

description:
10x Genomics
VDJ T


title: Patient 8  post CAR  PB VDJ T

description:
10x Genomics
VDJ T


title: Patient 14 post CAR  PB VDJ T

description:
10x Genomics
VDJ T


title: Patient 13 apheresis  PB VDJ T

description:
10x Genomics
VDJ T


title: Patient 1  apheresis  PB VDJ T

description:
10x Genomics
VDJ T


title: Patient 9  apheresis  PB VDJ T

description:
10x Genomics
VDJ T


title: Patient 12  post CAR  BM VDJ T

description:
10x Genomics
VDJ T


title: Patient 6  post CAR  PB VDJ T

description:
10x Genomics
VDJ T


title: Wt CD, replicate 1

value: cardiomyocytes

value: 7 weeks of diet


title: Patient 11  post CAR  PB VDJ T

description:
10x Genomics
VDJ T

value: post CAR T cell infusion


title: Patient 10  post CAR  BM VDJ T

description:
10x Genomics
VDJ T


title: Patient 6  apheresis  PB VDJ T

description:
10x Genomics
VDJ T

value: PBMC


title: Patient 11  apheresis  PB VDJ T

description:
10x Genomics
VDJ T

value: Peripheral Blood


title: Patient 7  post CAR BM VDJ T

description:
10x Genomics
VDJ T

value: m


title: Patient 14  apheresis  PB VDJ T

description:
10x Genomics
VDJ T

value: VDJ T


title: Patient 8  post CAR  BM VDJ T

description:
10x Genomics
VDJ T


title: Patient 9  post CAR  PB VDJ T

description:
10x Genomics
VDJ T


title: Patient 12  post CAR  PB VDJ T

description:
10x Genomics
VDJ T


title: Patient 10  post CAR  PB VDJ B

description:
10x Genomics
VDJ B

data_processing:
The CAR sequences for Ide-cel and Cilta-cel were obtained from the respective patents. Two separate custom references for Cilta and Ide-cel have been created by adding the corresponding CAR sequences  to the reference genome (GRCh38, Ensembl release 98) and GENCODE v32 annotation using the mkref function from Cellranger v7.1.0. The Cellranger multi pipeline was used to process the single cell gene-expression, cell surface protein and V(D)J libraries. The feature reference CSV file, declaring Antibody Capture constructs and associated barcodes can be found in the supplementary files. The reference dataset required for the V(D)J contigs is provided by 10X Genomics (GRCh38 Human V(D)J Reference - 7.1.0 (December 7, 2022)).
Assembly: hg38
Supplementary files format and content: filtered and tab-separated value files and matrix files
Library strategy: BCR-seq

value: VDJ B


title: Patient 7  apheresis  PB VDJ T

description:
10x Genomics
VDJ T

value: time of leukapheresis


title: Patient 1  post CAR  BM VDJ T

description:
10x Genomics
VDJ T


title: Patient 8  apheresis  PB VDJ B

description:
10x Genomics
VDJ B


title: Patient 12  apheresis  PB VDJ B

description:
10x Genomics
VDJ B

value: f


title: Patient 10  apheresis  PB VDJ B

description:
10x Genomics
VDJ B


title: Patient 9  post CAR  BM VDJ B

description:
10x Genomics
VDJ B


title: Patient 14 post CAR  PB VDJ B

description:
10x Genomics
VDJ B


title: Patient 13  post CAR  PB VDJ B

description:
10x Genomics
VDJ B


title: Patient 12  post CAR  BM VDJ B

description:
10x Genomics
VDJ B


title: Patient 6  post CAR  PB VDJ B

description:
10x Genomics
VDJ B


title: Patient 1  apheresis  PB VDJ B

description:
10x Genomics
VDJ B


title: Patient 9  apheresis  PB VDJ B

description:
10x Genomics
VDJ B


title: Patient 10  post CAR  BM VDJ B

description:
10x Genomics
VDJ B


title: Patient 14  apheresis  PB VDJ B

description:
10x Genomics
VDJ B


title: Patient 9  post CAR  PB VDJ B

description:
10x Genomics
VDJ B


title: Patient 11  post CAR  PB VDJ B

description:
10x Genomics
VDJ B


title: Patient 8  post CAR  BM VDJ B

description:
10x Genomics
VDJ B


title: Patient 13 apheresis  PB VDJ B

description:
10x Genomics
VDJ B


title: Patient 12  post CAR  PB VDJ B

description:
10x Genomics
VDJ B


title: Patient 7  post CAR BM VDJ B

description:
10x Genomics
VDJ B


title: Patient 1  post CAR  BM VDJ B

description:
10x Genomics
VDJ B


title: Patient 7  apheresis  PB VDJ B

description:
10x Genomics
VDJ B


title: Patient 1  post CAR  PB VDJ B

description:
10x Genomics
VDJ B


title: Patient 11  apheresis  PB VDJ B

description:
10x Genomics
VDJ B


title: Patient 6  apheresis  PB VDJ B

description:
10x Genomics
VDJ B


title: Patient 13  post CAR  PB ADT

description:
10x Genomics
ADT
MXMERZ002A_25_barcodes.tsv.gz
MXMERZ002A_25_features.tsv.gz
MXMERZ002A_25_matrix.mtx.gz

library_source: other

data_processing:
The CAR sequences for Ide-cel and Cilta-cel were obtained from the respective patents. Two separate custom references for Cilta and Ide-cel have been created by adding the corresponding CAR sequences  to the reference genome (GRCh38, Ensembl release 98) and GENCODE v32 annotation using the mkref function from Cellranger v7.1.0. The Cellranger multi pipeline was used to process the single cell gene-expression, cell surface protein and V(D)J libraries. The feature reference CSV file, declaring Antibody Capture constructs and associated barcodes can be found in the supplementary files. The reference dataset required for the V(D)J contigs is provided by 10X Genomics (GRCh38 Human V(D)J Reference - 7.1.0 (December 7, 2022)).
Assembly: hg38
Supplementary files format and content: filtered and tab-separated value files and matrix files
Library strategy: ADT

molecule: protein

value: ADT


title: Patient 12  apheresis  PB ADT

description:
10x Genomics
ADT
MXMERZ002A_24_barcodes.tsv.gz
MXMERZ002A_24_features.tsv.gz
MXMERZ002A_24_matrix.mtx.gz


title: Patient 1  post CAR  PB VDJ T

description:
10x Genomics
VDJ T


title: Patient 8  post CAR  PB VDJ B

description:
10x Genomics
VDJ B


title: Patient 8  post CAR  PB ADT

description:
10x Genomics
ADT
MXMERZ002A_20_barcodes.tsv.gz
MXMERZ002A_20_features.tsv.gz
MXMERZ002A_20_matrix.mtx.gz


title: Patient 10  post CAR  PB ADT

description:
10x Genomics
ADT
MXMERZ002A_23_barcodes.tsv.gz
MXMERZ002A_23_features.tsv.gz
MXMERZ002A_23_matrix.mtx.gz


title: Patient 10  apheresis  PB ADT

description:
10x Genomics
ADT
MXMERZ002A_22_barcodes.tsv.gz
MXMERZ002A_22_features.tsv.gz
MXMERZ002A_22_matrix.mtx.gz


title: Patient 9  post CAR  BM ADT

description:
10x Genomics
ADT
MXMERZ002A_21_barcodes.tsv.gz
MXMERZ002A_21_features.tsv.gz
MXMERZ002A_21_matrix.mtx.gz


title: Patient 8  apheresis  PB ADT

description:
10x Genomics
ADT
MXMERZ002A_19_barcodes.tsv.gz
MXMERZ002A_19_features.tsv.gz
MXMERZ002A_19_matrix.mtx.gz


title: Patient 14 post CAR  PB ADT

description:
10x Genomics
ADT
MXMERZ002A_18_barcodes.tsv.gz
MXMERZ002A_18_features.tsv.gz
MXMERZ002A_18_matrix.mtx.gz


title: Patient 13 apheresis  PB ADT

description:
10x Genomics
ADT
MXMERZ002A_17_barcodes.tsv.gz
MXMERZ002A_17_features.tsv.gz
MXMERZ002A_17_matrix.mtx.gz


title: Patient 12  post CAR  BM ADT

description:
10x Genomics
ADT
MXMERZ002A_16_barcodes.tsv.gz
MXMERZ002A_16_features.tsv.gz
MXMERZ002A_16_matrix.mtx.gz


title: Patient 9  apheresis  PB ADT

description:
10x Genomics
ADT
MXMERZ002A_15_barcodes.tsv.gz
MXMERZ002A_15_features.tsv.gz
MXMERZ002A_15_matrix.mtx.gz