title: R3_Response_RNA

city: 河南省

first: 艳茹

last: 张

state: Henan

address: 金水区经八路

institute: 郑州大学第二附属医院

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by  Removing reads containing sequencing adapter, Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%;  Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set;
The expression level of gene was calculated by RSEM.
Assembly: grch38
Supplementary files format and content: tab-delimited text files includes  FPKM values for each Sample

source_name: peripheral blood leukocyte

extract_protocol:
Total RNA was extracted using Trizol
Take a certain amount of RNA sample, prepare a reaction system, and use the RNase H method kit to remove rRNA. React at an appropriate temperature for a certain period of time to fragment RNA Add a pre prepared one strand synthesis reaction system to the interrupted RNA and set up a reaction program to synthesize one strand cDNA; Prepare a double stranded synthesis reaction system (including dUTP) and set up a reaction program to synthesize double stranded cDNA. Repair the double stranded cDNA end and add an A base at the 3 'end to prepare a linker connection reaction system. Set up a reaction program to connect the linker to the cDNA and amplify the product. After denaturing the PCR product into a single stranded form, a cyclization reaction system is prepared and a reaction program is set up to obtain a single stranded circular product. The linear DNA molecules that have not been cyclized are digested.

tag: patient diagnosis

value: Crohn's disease

value: peripheral blood leukocyte

tag: condition

value: response to vedolizumab treatment


title: Spleen-YG-6dpi-3

status: Public on Aug 01 2025

type: SRA

city: Daejeon

first: Dongbin

last: Park

address: 55, Expo-ro

country: South Korea

institute: Institute for Basic Science

description:
Library name: 99_S1_L002
10x Genomics

library_source: transcriptomic single cell

data_processing:
Cellranger (v5.1.2)
Assembly: MuSPutFur1.0 and SFTSV (CB1)
Supplementary files format and content: matrix files

molecule: total RNA

organism: Mustela putorius furo

source_name: Spleen

extract_protocol:
young-adult (20–24 months; YG, n = 26) and aged (36–40months; AG, n = 26) ferrets were inoculated intramuscularly with 0.5 ml of SFTSV CB1/2014 (10^6.0 TCID50/ml) and spleen, PBMC, and BM were collected from three ferrets per group at 2, 4, and 6 dpi, using separate tools to avoid cross-contamination
10x Genomics Chromium Single Cell 3′ GEM, Library & Gel Bead kit v3.1 (PN-1000121; 10X Genomics)

tag: tissue

value: Spleen


title: Firefighter-ID-12 Dermal tape wrist [1-012-W]

type: RNA

city: Oklahoma City

first: Chao

last: Xu

state: Oklahoma

address: 801 N. E. 13th Street

department: Biostatistics and Epidemiology

country: USA

institute: University of Oklahoma Health Sciences Center

hyb_protocol: The quantity and quality of miRNA were assessed using the NanoDrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Wilmington, DE) and the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). The expression levels of miRNA were ligated with bridge oligos and miRNA tags, making them long enough to hybridize to the probes using the nCounter Human v3 miRNA Expression panel with 800 endogenous human-associated miRNAs (NanoString Technologies, Seattle, WA). Prepared miRNA samples were then hybridized with the capture and reporter probes for 16 hours at 65C.

scan_protocol: Immediately after hybridization, the samples were loaded onto the NanoString nCounter Max Analysis System for clean-up and detection. Each run contained miRNA from six skin samples and six serum samples.

data_processing: The raw data were logarithm 2-transformed and then normalized as the manufacturer suggests.30,31 The RCC and RLF files were imported into NanoString’s nSolver Advanced Analysis Software v 4.0. Analysis of the normalized data was performed with the background correction threshold count value set to 30, no positive control correction, and normalization by geometric mean set at the top 100 genes. The normalization file was then imported into ROSALIND and processed through the miRNA nSolver normalized counts pipeline.

label: mirna

organism: Homo sapiens

source_name: Dermal tape wrist

label_protocol: The RNA yield for both sample types was too low to quantify using Qubit RNA HS Assay Kits or Agilent Bioanalyzer RNA system. Therefore, the maximum 3 µL of RNA was deposited into the nCounter miRNA Expression Assay Kit provided with the panels.

extract_protocol: RNeasy Micro Kits (Qiagen, Chatsworth, CA) were used to isolate RNA from the STS and serum samples according to the manufacturer’s protocol. RNA was isolated using Qiagen’s miRNeasy Serum/Plasma Advanced Kit and established protocols. Upon completion, the samples were then concentrated using RNA Clean & Concentrator-5 (DNase Included) (Zymo Research, Irvine, CA).

tag: batch

tag: fire exposure

value: Pre

tag: firefighter type

value: Volunteer

tag: firefighter years served

tag: gender

value: Male

tag: age

tag: height (m)

tag: weight (kg)

tag: race

value: Non_Hispanic White/European


title: Firefighter-ID-13 Dermal tape wrist [1-013-W]

value: Career


title: Firefighter-ID-11 Blood serum [1-011]

source_name: Blood serum

value: Female


title: Firefighter-ID-13 Blood serum [1-013]


title: R2_Response_RNA

country: China

library_source: transcriptomic

tag: cell type


title: Firefighter-ID-11 Dermal tape wrist [1-011-W]


title: nphp1/nphp4 morphant embryos (48 hpf), treatment (Omarigliptin), sample 1

city: Freiburg im Breisgau

first: Toma

middle: Antonov

last: Yakulov

address: Hugstetter Str. 55

department: Department of Medicine

country: Germany

institute: University Freiburg Medical Center

description: Library name: Omarigliptin 1

data_processing:
Raw RNA sequencing reads were quality-controlled with FastQC (v0.11.8) and pre-processed with cutadapt (v4.0) to trim low-quality bases, adapter sequences, and remove low-quality reads. Processed reads were aligned against the zebrafish reference genome GRCz11 from Ensembl (v110) using STAR (v2.6.1e). Gene counts were obtained during alignment using the "--quantMode GeneCounts" option.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file containing raw counts (as generated by the STAR aligner)

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish were maintained according to standard protocols and in compliance with the guidelines of the local animal ethics committee at the Regierungspräsidium Freiburg (permit G-21/146).

extract_protocol:
Total RNA was extracted from 15-50 embryos at 48 hpf using the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol.
Samples were sent for sequencing to Novogene (Cambridge, UK) on an Illumina platform.

treatment_protocol: Antisense morpholino oligonucleotides (MO) were diluted in 100mM KCL, 10mM 4- (2-hydroxyethyl)-1-piperazineethanesulfonic acid and 0.1% phenol red (Sigma-Aldrich). 4nl of this solution was microinjected into fertilized eggs at the one-cell stage (respectively 0.15mM nphp1 MO and 0.25mM nphp4 MO). All MO were co-injected with p53-MO to reduce off-target effects. At 24 hpf, embryos were dechorionated and incubated with DMSO or 25μM Omarigliptin. All embryos were additionally incubated in PTU (0.003% 1-phenyl-2-thiourea) to avoid skin pigmentation. Total RNA was extracted from 15-50 embryos at 48 hpf.

value: whole embryo

tag: treatment

value: nphp1 & nphp4 MO, Omarigliptin


title: Firefighter-ID-9 Blood serum [1-009]


title: Spleen-YG-2dpi-3

description:
Library name: 75_S1_L004
10x Genomics


title: R1_Response_RNA


title: nphp1; nphp4 homozygous double mutants 2

description: Library name: dm2

data_processing:
(FastQC v0.11.9, MultiQC v1.11) quality control, no data processing
Cutadapt v4.4 with Python 3.10.11
RNA STAR v2.7.10b with GRCz11 v110
(MultiQC v1.11), no data processing
featureCounts v2.0.3
DESeq2 v2.11.40.7
goseq v1.50.0
Assembly: GRCz11 v110
Supplementary files format and content: Normalized_counts.tabular

growth_protocol: 48 hpf @ 28°C, no PTU

extract_protocol:
Rneasy Mini Kit (Qiagen, Venlo, NED), chloroform extraction
Eurofins Genomics (Constance, GER)

treatment_protocol: anesthetized with tricaine, transfer to RNAprotect tissue reagent, stored @ -80°C

tag: genotype


title: Spleen-YG-2dpi-2

description:
Library name: 5_S6_L004
10x Genomics


title: Firefighter-ID-14 Dermal tape wrist [1-014-W]


title: Spleen-YG-6dpi-1

description:
Library name: 93_S6_L004
10x Genomics


title: Spleen-YG-2dpi-1

description:
Library name: 9_S1_L004
10x Genomics


title: Firefighter-ID-9 Dermal tape wrist [1-009-W]


title: Siblings control 4

description: Library name: ctrl4

value: wild-type


title: nphp1; nphp4 homozygous double mutants 1

description: Library name: dm1


title: Spleen-YG-4dpi-1

description:
Library name: 84_S10_L004
10x Genomics


title: NR5_Non-response_RNA

value: nonresponse to vedolizumab treatment


title: Firefighter-ID-7 Blood serum [1-007]


title: BrainPanel_2

city: Vancouver

first: Freda

last: Miller

state: BC

address: 2185 East Mall

country: Canada

institute: University of British Columbia

description: Mouse brain gene panel

hyb_protocol: Sections were incubated in a probe solution for 22 hours at 50°C for hybridization. The probe solution contained a set of 347 or 480 gene-targeting probes (described in methods) in TE buffer (Fisher). The rest of the Xenium workflow for fresh frozen tissue (fixation, permeabilization, ligation, amplification, etc) was performed as recommended by 10x Genomics.

scan_protocol: Full sections were imaged and analyzed using the Xenium Analyzer, software v1.7.6.0.

data_processing: Output files (transcripts, cell boundaries, features, etc) were generated directly by the Xenium onboard analysis pipeline (analysis v1.7.1.0). **Important note on file names** File names have been pre-fixed with their associated sample to ensure they are unumbigious when contained in the upload folder (e.g. "BrainPanel1_" for BrainPanel_1). However, the experiment.xenium file will try to pull paths from non-prefixed files (e.g. "morphology.ome.tif", rather than "BrainPanel1_morphology.ome.tif"). Hence, data users should remove these pre-fixes prior to using the data. The probeset panel design file is listed as gene_panel.json, with the prefix either ‘Brain’ or ‘Mesenchymal’ to indicate which sample it’s associated with.  Remove the prefix before using the data.

label: Gene targeting probes

organism: Mus musculus

label_protocol: Single cell spatial transcriptomics was performed using a panel targeting 347 (Brain) or 480 (Mesenchymal)  mRNA transcripts. 247 of these probes were from the mouse brain panel designed by 10x Genomics (10xgenomics.com/products/xenium-panels) for the Brain Panel. An additional 100 custom probes were added which are documented in Ebert et al. supplementary table 9 and in the gene_panel.json raw data file attached. The mesenchymal panel consists of a fully custom 480 probe panel set also described in supplementary table 9

extract_protocol: Once dissected, brains were immediately embedded in O.C.T. compound (Tissue-Tek) on dry ice, stored at -70°C, and cryosectioned coronally onto Xenium slides (chemistry v1) to produce 10 μm sections.

value: F

tag: strain

value: brain, forebrain

value: adult


title: NR3_Non-response_RNA

value: Crohn's disease


title: Spleen-YG-CTRL-3

description:
Library name: 81_S8_L004
10x Genomics


title: Siblings control 3

description: Library name: ctrl3


title: Firefighter-ID-7 Dermal tape wrist [1-007-W]


title: NR2_Non-response_RNA

value: peripheral blood leukocyte


title: Spleen-YG-CTRL-2

description:
Library name: 30_S4_L001
10x Genomics


title: Siblings control 1

description: Library name: ctrl1


title: Du145-DtxR, MeninKnockout3, Replica #3

status: Public on Jul 31 2025

city: Istanbul

first: Hamzah

last: Syed

address: Rumelifeneri Yolu

department: School of Medicine

country: Turkey

institute: Koç University

description:
Library name: DtxR-MENKO3-3
VST_normalised_counts.xlsx

data_processing:
STAR was used to align Fastq files to the latest human reference transcriptome
Salmon was used for quantification
Tximport and DEseq2 used for normalisation of counts
chipseq - The raw FASTQ files were processed using the nf-core CUT&RUN pipeline (v3.2.2). Adapter sequences and low-quality bases were trimmed using Trim Galore (v0.6.6), followed by quality assessment with FastQC (v0.12.1). The cleaned reads were aligned to the hg38 reference genome using Bowtie2 (v2.4.4). To minimize bias in downstream analyses, PCR duplicates were removed using Picard or SAMtools. Peak calling was performed with SEACR (v1.3) & MACS3, and consensus peaks were merged using bedtools (v2.31.0). Genomic tracks were visualized using IGV desktop (v2.16.1). Final outputs, including peak statistics, fragment size distribution, and signal tracks, were summarized and visualized using deepTools and other relevant tools. HOMER's annotatePeaks.pl  used for the annotation of the peaks.
Assembly: GRCh38
Supplementary files format and content: XLSX files of all sample counts
Supplementary files format and content: xls &.bed files of peaks

growth_protocol: Du145-P and Du145-DtxR cancer cells (ATCC no. HTB-81) were cultured in RPMI 1640 medium (Gibco, 11875093) supplemented with 10% FBS (Biowest, S1810), 1% penicillin-streptomycin (Biowest, L0022), and incubated at 37°C, 5% CO2 in a humidified environment.

extract_protocol:
Total RNA was extracted with NucleoSpin™ RNA Plus Isolation Kit (Macherey Nagel, 740984). Cell Signaling Technology, CUT&RUN Assay Kit #86652  was used and DNA elution was performed according to manufacturer's protocols.
Eukaryotic Strand-specific Transcriptome Library Construction & NEBNext® Ultra™ II DNA Library Prep Kit for Illumina

treatment_protocol: Gene knockouts were obtained with CRISPR/cas9 technology and single colonies were isolated and grown. 125.000 cells were collected and proceeded with RNA isolation step. MEN1-FLAG overexpression was conducted through lentiviral overexpression system and validated via western blot.

tag: cell line

value: prostate cancer cell line

value: Menin knockout

value: Menin-guide


title: Du145-DtxR, MeninKnockout3, Replica #2

description:
Library name: DtxR-MENKO3-2
VST_normalised_counts.xlsx


title: Du145-DtxR, Menin-FLAG

description:
Library name: M-FLAG
M_FLAG_REP1_summits.bed
M_FLAG_REP1_peaks.txt

library_source: genomic

molecule: genomic DNA

value: Menin-FLAG overexpression

tag: chip antibody

value: Sigma Aldrich F3165-Monoclonal anti-FLAG M2


title: Spleen-YG-CTRL-1

description:
Library name: 12_S3_L004
10x Genomics

value: Spleen


title: Siblings control 2

description: Library name: ctrl2


title: Firefighter-ID-6 Dermal tape wrist [1-006-W]

value: Pre

value: Volunteer

value: Male

value: Non_Hispanic White/European


title: NR1_Non-response_RNA

tag: patient diagnosis

tag: condition


title: Firefighter-ID-6 Blood serum [1-006]

tag: batch


title: Du145-DtxR, MeninKnockout2, Replica #3

description:
Library name: DtxR-MENKO2-3
VST_normalised_counts.xlsx


title: Du145-DtxR, Menın-IGG-control

description:
Library name: M-IGG
M_FLAG_REP1_summits.bed
M_FLAG_REP1_peaks.txt

value: Thermo Fisher Scientific-Mouse IgG Isotype Control (10400C)


title: nphp1; nphp4 homozygous double mutants 3

description: Library name: dm3

tag: tissue

value: whole embryo


title: Du145-DtxR, MeninKnockout2, Replica #2

description:
Library name: DtxR-MENKO2-2
VST_normalised_counts.xlsx


title: Du145-DtxR, MeninKnockout2, Replica #1

description:
Library name: DtxR-MENKO2-1
VST_normalised_counts.xlsx


title: Du145-P, MeninKnockout3, Replica #2

description:
Library name: P-MENKO3-2
VST_normalised_counts.xlsx


title: Du145-P, MeninKnockout3, Replica #1

description:
Library name: P-MENKO3-1
VST_normalised_counts.xlsx


title: Du145-P, Non-targeting guide, Replica #3

description:
Library name: P-NT3
VST_normalised_counts.xlsx

value: control

value: Non-targeting guide


title: Du145-DtxR, MeninKnockout3, Replica #1

description:
Library name: DtxR-MENKO3-1
VST_normalised_counts.xlsx


title: CAR99 manufactured CD19 CAR-T infusion product

status: Public on Jul 30 2025

city: Tampa

first: Michael

middle: D

last: Jain

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

description:
Library name: CAR99
10x Genomics

library_source: other

data_processing:
Data analysis included demultiplexing, barcode processing, alignment, and gene counting using 10x Genomics CellRanger v3.0.0 or v2.2.0
Assembly: Human GRCh38
Supplementary files format and content: Tab-separated matrix files.
Supplementary files format and content:
Supplementary files format and content: meta.rds: cell type annotation and clinical response data.
Supplementary files format and content: rawcount.rds: raw count data with the engineered chimeric antigen receptor.

molecule: other

source_name: CAR T-cell

extract_protocol:
Patient CAR T-cells were obtained by washes from commercial product infusion bags after patient infusion, and cryopreserved for batch analysis.
Cells were washed with calcium and magnesium-free 1x PBS containing 0.04% BSA. After staining for viability using AO/PI and quantification with the Nexcelom Cellometer K2, cells were loaded onto the 10x Genomics Chromium Single Cell Controller at 1,000 cells/µl to encapsulate approximately 5,000 cells per sample. Inside nanoliter-sized Gelbeads in Emulsion (GEMs), single cells, reagents, and 10x Genomics gel beads underwent reverse transcription of poly-adenylated mRNA at 53°C. cDNA libraries were prepared using the 10x Genomics Chromium NextGEM Single Cell 5’ Reagent Kit v2

value: CAR T-cell

tag: manufacture

value: YESCARTA


title: Du145-DtxR, Non-targeting guide, Replica #3

description:
Library name: DtxR-NT3
VST_normalised_counts.xlsx


title: CAR94 manufactured CD19 CAR-T infusion product

description:
Library name: CAR94
10x Genomics

value: KYMRIAH


title: Du145-DtxR, Non-targeting guide, Replica #2

description:
Library name: DtxR-NT2
VST_normalised_counts.xlsx

value: prostate cancer cell line


title: CAR78 manufactured CD19 CAR-T infusion product

description:
Library name: CAR78
10x Genomics


title: CAR59 manufactured CD19 CAR-T infusion product

description:
Library name: CAR59
10x Genomics


title: Du145-DtxR, Non-targeting guide, Replica #1

description:
Library name: DtxR-NT1
VST_normalised_counts.xlsx


title: Du145-P, MeninKnockout2, Replica #3

description:
Library name: P-MENKO2-3
VST_normalised_counts.xlsx

value: Menin knockout


title: CAR65 manufactured CD19 CAR-T infusion product

description:
Library name: CAR65
10x Genomics


title: Du145-P, MeninKnockout2, Replica #2

description:
Library name: P-MENKO2-2
VST_normalised_counts.xlsx

value: Menin-guide


title: Du145-P, Non-targeting guide, Replica #2

description:
Library name: P-NT2
VST_normalised_counts.xlsx


title: CAR245 manufactured CD19 CAR-T infusion product

description:
Library name: CAR245
10x Genomics


title: CAR240 manufactured CD19 CAR-T infusion product

description:
Library name: CAR240
10x Genomics


title: Du145-P, MeninKnockout2, Replica #1

description:
Library name: P-MENKO2-1
VST_normalised_counts.xlsx


title: CAR237 manufactured CD19 CAR-T infusion product

description:
Library name: CAR237
10x Genomics


title: Du145-P, Non-targeting guide, Replica #1

description:
Library name: P-NT1
VST_normalised_counts.xlsx


title: CAR227 manufactured CD19 CAR-T infusion product

description:
Library name: CAR227
10x Genomics


title: CAR219 manufactured CD19 CAR-T infusion product

description:
Library name: CAR219
10x Genomics


title: NR4_Non-response_RNA

value: Crohn's disease

value: peripheral blood leukocyte

value: nonresponse to vedolizumab treatment


title: CAR89 manufactured CD19 CAR-T infusion product

description:
Library name: CAR89
10x Genomics


title: CAR80 manufactured CD19 CAR-T infusion product

description:
Library name: CAR80
10x Genomics


title: CAR200 manufactured CD19 CAR-T infusion product

description:
Library name: CAR200
10x Genomics


title: CAR210 manufactured CD19 CAR-T infusion product

description:
Library name: CAR210
10x Genomics


title: CAR56 manufactured CD19 CAR-T infusion product

description:
Library name: CAR56
10x Genomics


title: CAR72 manufactured CD19 CAR-T infusion product

description:
Library name: CAR72
10x Genomics


title: CAR74 manufactured CD19 CAR-T infusion product

description:
Library name: CAR74
10x Genomics


title: Du145-P, MeninKnockout3, Replica #3

description:
Library name: P-MENKO3-3
VST_normalised_counts.xlsx


title: CAR42 manufactured CD19 CAR-T infusion product

description:
Library name: CAR42
10x Genomics


title: CAR187 manufactured CD19 CAR-T infusion product

description:
Library name: CAR187
10x Genomics


title: CAR190 manufactured CD19 CAR-T infusion product

description:
Library name: CAR190
10x Genomics


title: CAR180 manufactured CD19 CAR-T infusion product

description:
Library name: CAR180
10x Genomics


title: CAR239 manufactured CD19 CAR-T infusion product

description:
Library name: CAR239
10x Genomics


title: CAR172 manufactured CD19 CAR-T infusion product

description:
Library name: CAR172
10x Genomics


title: CAR218 manufactured CD19 CAR-T infusion product

description:
Library name: CAR218
10x Genomics


title: CAR247 manufactured CD19 CAR-T infusion product

description:
Library name: CAR247
10x Genomics


title: CAR214 manufactured CD19 CAR-T infusion product

description:
Library name: CAR214
10x Genomics


title: CAR161 manufactured CD19 CAR-T infusion product

description:
Library name: CAR161
10x Genomics


title: CAR158 manufactured CD19 CAR-T infusion product

description:
Library name: CAR158
10x Genomics


title: CAR201 manufactured CD19 CAR-T infusion product

description:
Library name: CAR201
10x Genomics


title: CAR196 manufactured CD19 CAR-T infusion product

description:
Library name: CAR196
10x Genomics


title: CAR184 manufactured CD19 CAR-T infusion product

description:
Library name: CAR184
10x Genomics


title: CAR186 manufactured CD19 CAR-T infusion product

description:
Library name: CAR186
10x Genomics


title: CAR193 manufactured CD19 CAR-T infusion product

description:
Library name: CAR193
10x Genomics


title: CAR153 manufactured CD19 CAR-T infusion product

description:
Library name: CAR153
10x Genomics


title: CAR213 manufactured CD19 CAR-T infusion product

description:
Library name: CAR213
10x Genomics


title: CAR178 manufactured CD19 CAR-T infusion product

description:
Library name: CAR178
10x Genomics


title: CAR146 manufactured CD19 CAR-T infusion product

description:
Library name: CAR146
10x Genomics


title: CAR167 manufactured CD19 CAR-T infusion product

description:
Library name: CAR167
10x Genomics


title: CAR138 manufactured CD19 CAR-T infusion product

description:
Library name: CAR138
10x Genomics


title: CAR144 manufactured CD19 CAR-T infusion product

description:
Library name: CAR144
10x Genomics


title: CAR136 manufactured CD19 CAR-T infusion product

description:
Library name: CAR136
10x Genomics


title: CAR159 manufactured CD19 CAR-T infusion product

description:
Library name: CAR159
10x Genomics


title: CAR154 manufactured CD19 CAR-T infusion product

description:
Library name: CAR154
10x Genomics


title: CAR160 manufactured CD19 CAR-T infusion product

description:
Library name: CAR160
10x Genomics


title: CAR135 manufactured CD19 CAR-T infusion product

description:
Library name: CAR135
10x Genomics


title: CAR134 manufactured CD19 CAR-T infusion product

description:
Library name: CAR134
10x Genomics


title: CAR133 manufactured CD19 CAR-T infusion product

description:
Library name: CAR133
10x Genomics


title: CAR143 manufactured CD19 CAR-T infusion product

description:
Library name: CAR143
10x Genomics


title: CAR130 manufactured CD19 CAR-T infusion product

description:
Library name: CAR130
10x Genomics


title: CAR114 manufactured CD19 CAR-T infusion product

description:
Library name: CAR114
10x Genomics


title: WVGAS15_M92 _iMLS_ERY_REP_3

status: Public on Jul 24 2025

city: Morgantown

first: Lei

last: Wang

state: West Virginia

address: 64 Medical Center Drive

department: Department of Microbiology, Immunology and Cell Biology

institute: west virginia university

description: Library name: Sample 12

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence with the QIAGEN CLC Genomics Workbench (version 23) "Rule-based" proprietary trimming tool in the transcriptomic analysis tools according to a quality score of 0.05 (https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/801/index.php?manual=Sequencing_data_analyses.html)
Trimmed reads were mapped in pairs to the MGAS2221 genome (Bioproject accession PRJNA562873) and the pRW35-like plasmid sequence (GenBank accession NZ_CP032701) using the CLC genomic workbench proprietary CLC Mapper tool. (parameters were as follows: mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.8, similarity fraction 0.8)   (https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/801/index.php?manual=Read_mapping.html)
The CLC genomics workbench proprietary RNA-Seq analysis pipeline was used to perform read count extraction and normalization. Normalization was done using median-of-ratios (DESeq2). (https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/801/index.php?manual=Statistical_analysis_identifying_differential_expression.html)
Differential gene expression was determined using DESeq2 as part of the CLC genomics workbench proprietary RNA-Seq analysis pipeline. The analysis of erythromycin treatment versus control was done for each strain (cMLS vs iMLS phenotype) independently, resulting in two pairwise comparisons. DESeq2 uses a generalized linear model framework based on negative binomial distribution.
Assembly: the MGAS2221 genome
Supplementary files format and content: reads_count.txt
Supplementary files format and content: First colum: Name; second column: Chromosome; third column: region; columns thereafter: reads count  for each sample
Supplementary files format and content: WVGAS10_cMLS_NO_ERY_versus_WVGAS10_cMLS_ERY.txt,  and WVGAS15_iMLS_NO_ERY_versus WVGAS15_iMLS_ERY.txt
Supplementary files format and content: First colum: Name; second column: Chromosome; third column: region; fourth column: Max Group Mean; fifth group column: Log2 fold change; sixth column: fold change; seventh column: p-value; eight column: FDR p-value; nineth column Bonferroni

organism: Streptococcus pyogenes

extract_protocol:
Cells collected in RNA protect and total RNA was extracted using the the IBI Scientific rBAC Mini RNA Bacteria Kit protocol adapted for GAS. RNA was isolated from cells. DNAse treated.
RNA libraries of cDNA for RNA sequencing were prepared by Admera Health using the QIAseq FastSelect rRNA 5S/16S/23S (Bacteria) kit + NEB Ultra II and the Directional RNA Library Prep Kit 2x150, according to Manufactor Instructions.

treatment_protocol: Bacterial isolates were cultured overnight on brain heart infusion agar at 37°C with 5% CO2. Cultures were used to inoculate Todd Hewitt Yeast media at a starting OD600nm of 0.05. At log-phase (OD600nm 0.5) a final concentration of 10 g/mL erythromycin was added to half of the culture, followed by 1-hour of incubation.

tag: mlsb sub-phenotype

value: iMLS

value: 10 µg/mL erythromycin

tag: time

value: 1 hour


title: CAR147 manufactured CD19 CAR-T infusion product

description:
Library name: CAR147
10x Genomics


title: WVGAS15_M92_iMLS_NO_ERY_REP_3

description: Library name: Sample 9

value: No erythromycin


title: WVGAS15_M92 _iMLS_ERY_REP_2

description: Library name: Sample 11


title: WVGAS15_M92 _iMLS_ERY_REP_1

description: Library name: Sample 10


title: CAR127 manufactured CD19 CAR-T infusion product

description:
Library name: CAR127
10x Genomics


title: CAR113 manufactured CD19 CAR-T infusion product

description:
Library name: CAR113
10x Genomics


title: WVGAS15_M92_iMLS_NO_ERY_REP_1

description: Library name: Sample 7


title: WVGAS15_M92_iMLS_NO_ERY_REP_2

description: Library name: Sample 8


title: CAR120 manufactured CD19 CAR-T infusion product

description:
Library name: CAR120
10x Genomics


title: WVGAS10_M92_cMLS_ERY_REP_1

description: Library name: Sample 4

value: cMLS


title: WVGAS10_M92_cMLS_NO_ERY_REP_3

description: Library name: Sample 3


title: CAR149 manufactured CD19 CAR-T infusion product

description:
Library name: CAR149
10x Genomics


title: WVGAS10_M92_cMLS_NO_ERY_REP_1

description: Library name: Sample 1


title: CAR152 manufactured CD19 CAR-T infusion product

description:
Library name: CAR152
10x Genomics


title: HGG5B(GBM5B)

status: Public on Jul 14 2025

city: NEW YORK

first: Nadejda

middle: M

last: Tsankova

state: NY

address: 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B

department: Pathology

institute: Icahn School of Medicine at Mount Sinai

description: Library name: 21804_B

data_processing:
Gene expression count matrices were generated with CellRanger(v7.1.0)
Seurat metadata was generated using Seurat(v4.3.0), Filtering step: i) Doublets were removed using DoubletFinder(v3) ii)Low quality nuclei removal (< 400 unique genes, < 1,000 UMI counts, or > 15% mitochondrial genes)
UMAP embeddings: "Dimensionality reduction was applied on the scaled expression of top 2,000 variable genes by Principal component analysis (PCA) (Seurat::RunPCA). Integrated data was normalized using the SCTransform workflow in Seurat. PCA was re-computed using the top 3,000 variable features followed by nearest-neighbor graph construction (Seurat::FindNeighbors), unbiased Louvain clustering (Seurat::FindClusters), and Uniform Manifold Approximation and Projection (UMAP) (Seurat::RunUMAP) for visualization of the data in two dimensions."
AvgExpression_ConfidentSamples.csv"; "AvgExpression_allGBM.csv": "Processed,SCT normalized average gene expression data calculated for each of the following integrated objects: all GBM (n=6) or confident dissected GBM (n=4)
Assembly: GRCh38 human genome
Supplementary files format and content: "barcodes.tsv.gz" contains barcodes sequences, "features.tsv.gz" contains feature ID and names, "matrix.mtx.gz" contains matrices with gene ID, cell ID and UMI information
Supplementary files format and content: "Seuratmetadata" files: comma separated file with Seurat metadata including barcode information for individual samples
Supplementary files format and content: "UMAP_embedding": comma separated file with UMAP cordinates
Supplementary files format and content: "AvgExpression_ConfidentSamples_nov2024.csv"; "AvgExpression_allGBM_nov2024.csv" comma separated file.

molecule: nuclear RNA

source_name: Brain tumor

extract_protocol:
Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3’ gene expression (3’ GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. ( (Nuclei from same dissociates were used for snRNA-seq and snATAC-seq related to this data)
P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus.

value: Brain tumor


title: HGG4C(GBM4C)

description: Library name: 27419_C

tag: region

value: Core

tag: age (average)

tag: Sex

value: Female

value: Glioblastoma, IDH-wildtype, CNS WHO grade 4, MGMT unmethylated, NF1 splice site 2850+1G>A, PTEN M199del, CDKN2A/B loss, TERT -146C>T, TP53 T211_H214del, Right frontal lobe, Primary


title: HGG6M(GBM6M)

description: Library name: MA20195_I

value: Margin


title: HGG6C(GBM6C)

description: Library name: MA20195_C

value: Male

value: Glioblastoma, IDH-wildtype, CNS WHO grade 4, MGMT unmethylated, FGFR3 amplification, FGFR3:TACC3 fusion, PIK3R1 p.L573P, TERT c.-124C>T, Left parietal lobe, Recurrent


title: HGG3B(GBM3B)

description: Library name: 17257_B


title: HGG5A(GBM5A)

description: Library name: 21804_A

value: Glioblastoma, IDH-wildtype, CNS WHO grade 4, MGMT methylated, PDGFRA amplification, MDM4 amplification, PTEN p.D24N, TP53 c.673-2A>T, NF1 p.Q2263*, Right temporal lobe, Primary


title: HGG2M(GBM2M)

description: Library name: 24340_I


title: HGG4M(GBM4M)

description: Library name: 27419_I


title: HGG3A(GBM3A)

description: Library name: 17257_A

value: Glioblastoma, IDH-wildtype, CNS WHO grade 4, MGMT unmethylated, PTEN c. 1003C>T, RB1 and WT1 mutations, Right temporal lobe, Primary


title: HGG2C(GBM2C)

description: Library name: 24340_C

value: High-grade glioma, EGFR-amplified and IDH-mutant, CNS WHO grade 4, MGMT methylated, EGFR amplification, PIK3CA E545G, CDKN2A/B loss, MTAP loss, IDH1R132H, TP53 V272M, ATRX S567fs*16, Left frontal lobe, Primary


title: CAR122 manufactured CD19 CAR-T infusion product

description:
Library name: CAR122
10x Genomics

value: CAR T-cell

value: YESCARTA


title: WVGAS10_M92_cMLS_ERY_REP_3

description: Library name: Sample 6


title: HGG6C(GBM6C)

description: Library name: MA20195_C

library_source: genomic single cell

data_processing:
Count matrices were generated with CellRanger(v7.1.0)
Seurat metadata was generated using Seurat(v4.3.0), Filtering step: i) Doublets were removed using DoubletFinder(v3) ii)Low quality nuclei removal (< 400 unique genes, < 1,000 UMI counts, or > 15% mitochondrial genes), nuclei were additionally filtered based on TSS enrichment less than 4 and fragment number less than 3000 and greater than 30,000
UMAP embeddings: Dimensionality reduction was performed using the default TileMatrix and the addIterativeLSI function with 15,000 variable features, 2:30 dimensions, 10000 sample cells, 15 maximum clusters, n.start 10, and 0.5 cluster resolution. Clusters were computed using addClusters. Dimensionality reduction and clustering were repeated with the PeakMatrix using the same parameters described above. Batch effect correction was performed using Harmony followed by addUMAP and addClusters.
Assembly: GRCh38 human genome
Supplementary files format and content: "barcodes.tsv.gz" contains barcodes sequences, "features.tsv.gz" contains feature ID and names, "matrix.mtx.gz" contains matrices with gene ID, cell ID and UMI information , "fragments.tsv" contains fragments information .
Supplementary files format and content: "Seuratmetadata" files: comma separated file with Seurat metadata including barcode information for individual samples
Supplementary files format and content: "UMAP_embedding": comma separated file with UMAP cordinates

extract_protocol:
Nuclei from same dissociates were used for snATAC-seq and sn-RNAseq related to this data. Briefly, 50-200 mg of tissue was dounced in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation: a sucrose solution (1.8 M sucrose, 3 mM magnesium acetate, and 1 mM DTT in 10 mM Tris-HCl, pH 8.0) was layered under the lysate solution followed by centrifugation at 4°C for 1 hour (h) at 24,400 rotations per minute. Nuclei were resuspended in 0.04% bovine serum albumin (BSA) in Ca2+/Mg2+-free phosphate buffered saline (PBS) at 1x106 cells/mL concentration and loaded to achieve optimal recovery of 6,000 sequenced nuclei/sample with minimal doublet/triplet formation. Concentrations were verified using an automated cell counter (Countless 3, ThermoFisher). Trypan blue staining was used to assess nuclei quality and quantity prior to library preparation.
Nuclei  were transposed and processed according to Chromium Single Cell ATAC kit (10X Genomics, Pleasanton, CA) using manufacturer’s guidelines. An estimated 10,000 nuclei were loaded onto each channel with a targeted nuclei recovery of 6000 nuclei/sample. Fragmented DNA underwent RT and cleanup followed by amplification 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using Tapestation (Agilent) and Qubit (ThermoFisher) analysis. Libraries were sequenced in paired end mode on a NovaSeq instrument (Illumina, San Diego, CA) targeting a depth of 50,000-100,000 reads per cell.


title: HGG5A(GBM5A)

description: Library name: 21804_A


title: HGG3B(GBM3B)

description: Library name: 17257_B


title: HGG4M(GBM4M)

description: Library name: 27419_I


title: HGG5B(GBM5B)

description: Library name: 21804_B


title: HGG2C(GBM2C)

description: Library name: 24340_C


title: HGG1M(GBM1M)

description: Library name: 17273_I


title: HGG1C(GBM1C)

description: Library name: 17273_C

value: Glioblastoma, IDH-wildtype, CNS WHO grade 4, MGMT unmethylated, EGFR amplification, Right frontal lobe, Primary


title: HGG4C(GBM4C)

description: Library name: 27419_C


title: HGG6M(GBM6M)

description: Library name: MA20195_I


title: bf.hd45

city: Barcelona

first: Giancarlo

last: Castellano

address: 2 Passeig Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain

department: PCCB

country: Spain

institute: Hospital Sant Joan de Déu Barcelona

description:
Library name: bf.hd45
10x Genomics

data_processing:
The gene expression (GEX) and V(D)J sc-RNA seq data were aligned and quantified using the Cell Ranger (v 5.0) pipeline (https://www.10xgenomics.com/) and Seurat pipeline (v 4.4.0,) was used to analyze expression matrices.
Assembly: human genome GRCh38
Supplementary files format and content: Tab-separated values and matrix files

source_name: Bone marrow

extract_protocol:
MNCs were washed thrice with 1X Phosphate-Buffered Saline (PBS, free of calcium and magnesium) containing0.04% weight/volume FBS (Gibco, Cat# 70011-044). Thereafter MNCs were counted by the Burker chamber. CD138+ BM cells were prepared using the EasySep CD138 Positive selection kit II (STEMCELL Technologies, Cat#17887A), after erythrocyte lysis (Cytognos, Cat# CYT-BL), following manufacturer’s instructions.
The Chromium Next GEM Single Cell 5’ v2 protocol (CG000330 Rev E) was used to calculate the volume of cells to load for each sample, with the aim of recovering 9,000 cells. The Chromium Next GEM Chip K (10X Genomics; PN-2000286) with Master Mix from Chromium Next GEM Single Cell 5’ Reagent Kits v2 (Dual Index) (10X Genomics; PN-1000263) and Chromium Single Cell Human TCR Amplification Kit, (10X Genomics; PN-1000252) were employed to generate Single-cell 5′ RNA-seq libraries. After the GEM was generated and the barcoded full-length cDNA amplificated, the SPRIselect Reagent (Cat# B23318) was used to purify cDNA. The latter was then quantified by Picogreen dsDNA assay kit (Cat# P7589). To assess quality, the Agilent 4150 TapeStation machine was employed by using High Sensitivity D5000 ScreenTape (Agilent, Cat# 5067-5592) with High Sensitivity D5000 Reagents (Agilent, Cat# 5067-5593).

value: Bone marrow

value: Whole Bone Marrow, CD138 neg fraction

value: healthy donor


title: bf.hd44

description:
Library name: bf.hd44
10x Genomics


title: bf.hdmipos

description:
Library name: bf.hdmipos
10x Genomics

source_name: Bone marrow, CD138 purified Plasmacells

value: Bone marrow, CD138 purified Plasmacells

value: Bone marrow plasma cells


title: bf23, Remission_pts4

description:
Library name: bf23
10x Genomics

value: Whole Bone Marrow

value: Remission


title: bf16, Diagnosis_pts4

description:
Library name: bf16
10x Genomics

value: Diagnosis


title: HGG2M(GBM2M)

description: Library name: 24340_I

value: Brain tumor

value: Margin


title: WVGAS10_M92_cMLS_NO_ERY_REP_2

description: Library name: Sample 2

value: cMLS

value: No erythromycin

value: 1 hour


title: HGG3A(GBM3A)

description: Library name: 17257_A

value: Male

value: Glioblastoma, IDH-wildtype, CNS WHO grade 4, MGMT unmethylated, PTEN c. 1003C>T, RB1 and WT1 mutations, Right temporal lobe, Primary


title: bf7, Diagnosis_pts3

description:
Library name: bf7
10x Genomics


title: HGG1M(GBM1M)

description: Library name: 17273_I


title: ST2

description: Library name: 44564 / G4

data_processing:
Gene expression count matrices were generated withSpaceRnager(v2.1.0)
Seurat metadata was generated using Seurat(v4.3.0), Filtering step: Low quality nuclei removal (< 400 unique genes, < 1,000 UMI counts, or > 15% mitochondrial genes)
UMAP embeddings: "Dimensionality reduction was applied on the scaled expression of top 2,000 variable genes by Principal component analysis (PCA) (Seurat::RunPCA). To mitigate inter-sample technical variation when analyzing multiple samples, we normalized and integrated the data using the SCTransform workflow in Seurat, which finds mutual nearest neighbors (or anchors) to integrate different samples. PCA was re-computed using the top 3,000 variable features followed by nearest-neighbor graph construction (Seurat::FindNeighbors), unbiased Louvain clustering (Seurat::FindClusters), and Uniform Manifold Approximation and Projection (UMAP) (Seurat::RunUMAP) for visualization of the data in two dimensions."
"Spatial.gz" contains images and coordinates of the 10X visium data
Assembly: GRCh38 human genome
Supplementary files format and content: "barcodes.tsv.gz" contains barcodes sequences, "features.tsv.gz" contains feature ID and names, "matrix.mtx.gz" contains matrices with gene ID, cell ID and UMI information
Supplementary files format and content: "Seuratmetadata" files: comma separated file with Seurat metadata including barcode information for individual samples
Supplementary files format and content: "UMAP_embedding": comma separated file with UMAP cordinates
Library strategy: Spatial transcriptomics

extract_protocol:
Slides for 10X Visium were freshly cut (10uM) from Formalin fixed paraffin embeded GBM tissues, after determining RNA quality.
10X-Visium was used to perform spatial transcriptomics (ST) on two GBM specimens, with distinct genetic background and patient sex, in which highest RNA quality was obtained and full Core-to-Margin transition was captured histologically. Tissue permeabilization and library preparation was done according to the manufacturer’s protocol. The Visium spatial gene expression for FFPE assays (10X Genomics) was used to generates spatially-resolved cDNA libraries from FFPE tissue. Tissue slices were sectioned onto the assay slide, which consists of four 6.5mm x 6.5mm arrays of spatially-barcoded poly T capture probes (arranged as 5,000 55 um spots) and permeabilized. Captured mRNA then underwent reverse transcription and cleavage from the slide, followed by cDNA amplification and fragmenting, end-repair, poly A-tailing, adapter ligation, and 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using Tapestation and Qubit and sequenced in paired end mode on NovaSeq instrument targeting a depth of 50,000-100,000 reads per capture spot.

value: Core-to-Margin

value: Glioblastoma, IDH-wildtype, CNS WHO grade 4, MGMT unmethylated,EGFR amplification, EGFR A289V, EGFRvIII, MTAP loss, CDKN2A/B loss, JAK2 V617F, TERT -146C>T, Right temporal lobe, Primary


title: bf6, Diagnosis_pts2

description:
Library name: bf6
10x Genomics

value: Bone marrow


title: HGG1C(GBM1C)

description: Library name: 17273_C

value: Core

value: Glioblastoma, IDH-wildtype, CNS WHO grade 4, MGMT unmethylated, EGFR amplification, Right frontal lobe, Primary


title: bfc2, RR4

description:
Library name: bfc2
10x Genomics

value: relapse/refractory


title: bf.hd45pos

description:
Library name: bf.hd45pos
10x Genomics

value: Bone marrow, CD138 purified Plasmacells

value: Bone marrow plasma cells

value: healthy donor


title: bfc1, RR3

description:
Library name: bfc1
10x Genomics

value: Whole Bone Marrow


title: uBT_SC_MG_4m_WT_4_LPS

status: Public on Jul 09 2025

city: Paris

first: Isadora

last: Lenoel

address: 47 Boulevard de l'hopital

country: France

institute: Paris Brain Institute

description: Library name: uBT_SC_MG_4m_WT_4_LPS

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads
Illumina DRAGEN bio-IT Plateform (v3.8.4) was used for mapping on mm10 reference genome and quantification with gencode v25 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Assembly: mm10, mm39
Supplementary files format and content: LPS_uG_SpCBr_mappedmm39_global_expression_genes_tpm.xlsx file contains the raw tpm genes expression values of the three experimental groups at 4 months of age : Spinal cord microglia unstimulated, Spinal cord microglia stimulated with LPS, and brain microglia stimulated with LPS, of two genotypes : Tbk1- G-KO and control Tbk1- G-WT. All are mapped on mm39.
Supplementary files format and content: SpC_uG_4m22m_mappedmm10_global_expression_genes_tpm.xlsx file contains the raw tpm genes expression values of two experimental groups : Spinal cord microglia unstimulated at 4 months, and Spinal cord microglia unstimulated at 22 months, of two genotypes : Tbk1- G-KO and control Tbk1- G-WT. All are mapped on mm10.

source_name: Spinal cord

extract_protocol:
Microglial isolation was performed as previously described (Hammond et al.). Mice were all females and were deeply anesthetized using xylazine (Rompun 0.2%) and ketamine (Imalgene 500) and transcardially perfused with ice-cold 0.1 M PBS and whole brains were collected. Brains were Dounce homogenized in ice cold Hank’s balanced salt solution (HBSS) 10 times with the loose and 5 times with tight pestles. Tissues were passed through a 70-μm cell strainer (Corning). Cells were pelleted by centrifugation (300g, 5 minutes), resuspended in 40% Percoll solution (GE Healthcare), HBSS and centrifugated (30 minutes, 500g, 4°C). Myelin was then removed with the Percoll. Cell pellet was washed in HBSS and resuspended in PBS/2mM EDTA (Life Technologies).  Cells were stained with Zombie Green (1/1000, Biolegend) for 15 minutes at 4°C. All samples were then washed and resuspended in ice cold FACS buffer (5% FCS, 2mM EDTA, in 1x PBS) with TruStain FcX (Biolegend) for 10 minutes. Antibodies were then added Cd11b (PE, 1/100, Biolegend 101207), CD45 (SBB700, 1/20, Biorad, MCA1031) and incubated for 20 minutes at 4°C. Finally, cells were sorted using Biorad S3 cell sorter. Approximately 10000 to 30000 cells were isolated per sample and directly lysed with RNA lysis buffer (RNeasy micro kit, Qiagen). Lysates were stored at -80°C before RNA extraction according to manufacturer’s protocol (RNeasy micro kit, Qiagen). Quantity of RNA used for sequencing was adjusted to the number of cells sorted, and 2500 to 5000 cells were sequenced.
Since the RNAconcentration was too low to be detected using a Nanodrop, test samples were used to assess  RIN quality. RNA quantity sequenced was adjusted to the number of FAC-sorted cells, to sequence between 2500 and 5000 cells per sample.cDNA synthesis was performed using the Smartseq V4 TAKARA kit with linear pre-amplification. Library preparation was made with amplified cDNA for every sample using the Nextera XT DNA Library Preparation Kit (Illumina). 35 samples were run with a 1200 million cartridge to reach an average coverage of 34 million reads per sample (100bp, paired-ends). Sequencing was performed using the Novaseq 6000 sequencer (Illumina). Library preparations and sequencing were performed by the ICM iGenSeq core facility.

value: Spinal cord

value: Microglial cells

value: WT

value: LPS

tag: age

value: 4 months


title: ST1

description: Library name: 56691 / G740

value: Brain tumor

value: Female

value: Glioblastoma, IDH-wildtype, CNS WHO grade 4, MGMT methylated,CDK4 amplification, MDM2 amplification, PTEN E242fs*1, TERT -124C>T, Left temporal lobe, Primary


title: uBT_SC_MG_4m_WT_3_LPS

description: Library name: uBT_SC_MG_4m_WT_3_LPS

tag: cell type


title: bfa2, RR2

description:
Library name: bfa2
10x Genomics


title: uBT_SC_MG_4m_WT_1_LPS

description: Library name: uBT_SC_MG_4m_WT_1_LPS

tag: treatment


title: uBT_SC_MG_4m_KO_4_LPS

description: Library name: uBT_SC_MG_4m_KO_4_LPS

tag: genotype

value: KO


title: bf.hd44pos

description:
Library name: bf.hd44pos
10x Genomics


title: uBT_SC_MG_4m_KO_2_LPS

description: Library name: uBT_SC_MG_4m_KO_2_LPS


title: bf9, Remission_pts1

description:
Library name: bf9
10x Genomics

value: Bone marrow

value: Remission


title: uBT_SC_MG_4m_KO_1_LPS

description: Library name: uBT_SC_MG_4m_KO_1_LPS


title: uBT_BR_MG_22m_WT_4_LPS

description: Library name: uBT_BR_MG_22m_WT_4_LPS

source_name: Brain

value: Brain


title: bf17, Diagnosis_pts5

description:
Library name: bf17
10x Genomics

value: Diagnosis


title: bf8, Remission_pts2

description:
Library name: bf8
10x Genomics


title: bf5, Diagnosis_pts1

description:
Library name: bf5
10x Genomics


title: bfa1, RR1

description:
Library name: bfa1
10x Genomics

value: relapse/refractory


title: uBT_BR_MG_22m_KO_4_LPS

description: Library name: uBT_BR_MG_22m_KO_4_LPS


title: uBT_SC_MG_4m_WT_2_LPS

description: Library name: uBT_SC_MG_4m_WT_2_LPS


title: bf.hdmi

description:
Library name: bf.hdmi
10x Genomics

value: Whole Bone Marrow, CD138 neg fraction


title: uBT_BR_MG_22m_KO_1_LPS

description: Library name: uBT_BR_MG_22m_KO_1_LPS


title: uBT_SC_MG_22m_KO_3

description: Library name: uBT_SC_MG_22m_KO_3

value: 22 months


title: uBT_SC_MG_4m_KO_3_LPS

description: Library name: uBT_SC_MG_4m_KO_3_LPS


title: uBT_SC_MG_22m_KO_2

description: Library name: uBT_SC_MG_22m_KO_2


title: uBT_SC_MG_22m_WT_2

description: Library name: uBT_SC_MG_22m_WT_2


title: uBT_SC_MG_22m_WT_3

description: Library name: uBT_SC_MG_22m_WT_3


title: uBT_SC_MG_22m_KO_1

description: Library name: uBT_SC_MG_22m_KO_1


title: uBT_SC_MG_4m_KO_5

description: Library name: uBT_SC_MG_4m_KO_5


title: uBT_BR_MG_22m_WT_3_LPS

description: Library name: uBT_BR_MG_22m_WT_3_LPS


title: uBT_BR_MG_22m_KO_3_LPS

description: Library name: uBT_BR_MG_22m_KO_3_LPS


title: uBT_BR_MG_22m_WT_2_LPS

description: Library name: uBT_BR_MG_22m_WT_2_LPS


title: uBT_SC_MG_4m_KO_4

description: Library name: uBT_SC_MG_4m_KO_4


title: uBT_BR_MG_22m_KO_2_LPS

description: Library name: uBT_BR_MG_22m_KO_2_LPS


title: uBT_SC_MG_4m_WT_5

description: Library name: uBT_SC_MG_4m_WT_5


title: uBT_SC_MG_4m_WT_4

description: Library name: uBT_SC_MG_4m_WT_4


title: uBT_BR_MG_22m_WT_1_LPS

description: Library name: uBT_BR_MG_22m_WT_1_LPS


title: uBT_SC_MG_4m_KO_3

description: Library name: uBT_SC_MG_4m_KO_3


title: uBT_SC_MG_22m_WT_5

description: Library name: uBT_SC_MG_22m_WT_5


title: uBT_SC_MG_4m_KO_2

description: Library name: uBT_SC_MG_4m_KO_2


title: uBT_SC_MG_4m_KO_1

description: Library name: uBT_SC_MG_4m_KO_1


title: uBT_SC_MG_4m_WT_3

description: Library name: uBT_SC_MG_4m_WT_3


title: uBT_SC_MG_22m_KO_4

description: Library name: uBT_SC_MG_22m_KO_4


title: uBT_SC_MG_22m_WT_4

description: Library name: uBT_SC_MG_22m_WT_4


title: uBT_SC_MG_4m_WT_2

description: Library name: uBT_SC_MG_4m_WT_2


title: ChIP_anti_SMC_BWX3212

status: Public on Jul 07 2025

city: Bloomington

first: Xindan

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

description: Library name: ChIP_anti_SMC_BWX3212

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Bacillus subtilis Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.  For ChIP-seq and WGS, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) genome was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of Bacillus subtilis (PY79) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Assembly: Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1)
Supplementary files format and content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv files are comma-separated values files of ChIP-seq/WGS results.

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79

extract_protocol:
Wild type and mutant cells of Bacillus subtilis PY79 growing in CH were crosslinked using 3% formaldehyde and then lysed by treatment of lysosome and 1% SDS as previouly discribed (Wang et al 2015).
Standard library construction protocol was used for Illumina MiSeq sequencing platforms. Illumina Truseq indexes were used.

value: Bacillus subtilis PY79

value: Bacterial

value: parS{delta}9 no a.b.

value: Cells were grown in CH medium at 37°C


title: WGS_input_BWX3212

description: Library name: WGS_input_BWX3212


description: Library name: ChIP_anti_SMC_BWX4310_42C_HPUraIPTG25min_T40

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Bacillus subtilis Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.  For ChIP-seq and WGS, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) genome was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of Bacillus subtilis (PY79) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle: mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Assembly: Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1)
Supplementary files format and content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv files are comma-separated values files of ChIP-seq/WGS results.

extract_protocol:
Wild type and mutant cells of Bacillus subtilis PY79 growing in CH were crosslinked using 3% formaldehyde and then lysed by treatment of lysosome and 1% SDS as previouly discribed (Wang et al 2015).
Standard library construction protocol was used for Illumina Nextseq500/Nextseq2000 sequencing platforms. Illumina Truseq indexes were used.

value: parSdelta9 no a.b., deltaspo0J (remains wt parS at -1degree)::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30°C for 2h, then shifted up to 42°C for 45min, then shifted down to 30°C for 15min, finally shifted up to 42°C with the treatment of 1mM IPTG and 162 µM HPUra for 25min


description: Library name: ChIP_anti_SMC_BWX4310_42C_HPUraIPTG20min_T35

value: Cells were grown in CH medium at 30°C for 2h, then shifted up to 42°C for 45min, then shifted down to 30°C for 15min, finally shifted up to 42°C with the treatment of 1mM IPTG and 162 µM HPUra for 20min


description: Library name: ChIP_anti_SMC_BWX4310_42C_HPUraIPTG15min_T30

value: Cells were grown in CH medium at 30°C for 2h, then shifted up to 42°C for 45min, then shifted down to 30°C for 15min, finally shifted up to 42°C with the treatment of 1mM IPTG and 162 µM HPUra for 15min


title: uBT_SC_MG_22m_WT_1

description: Library name: uBT_SC_MG_22m_WT_1

value: Spinal cord

value: Microglial cells

value: WT


title: WGS_BWX5297_42C10m_T0

description: Library name: WGS_BWX5297_42C10m_T0

value: parSdelta9 no a.b., -59degree parS no a.b, deltaspo0J::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30°C for 2h, then shifted up to 42°C for 45min, then shifted down to 30°C for 15min, finally shifted up to 42°C for 10min.


description: Library name: ChIP_anti_SMC_BWX4310_42C_HPUraIPTG30min_T45

value: Cells were grown in CH medium at 30°C for 2h, then shifted up to 42°C for 45min, then shifted down to 30°C for 15min, finally shifted up to 42°C with the treatment of 1mM IPTG and 162 µM HPUra for 30min


title: WGS_BWX4310_42C_HPUraIPTG30min_T45_rep2

description: Library name: WGS_BWX4310_42C_HPUraIPTG30min_T45_rep2


title: Ventricular cardiomyocytes, control, rep2

status: Public on Jul 05 2025

city: Moscow

first: Stanislav

last: Shilejko

address: Ostrovityanova str., 1

country: Russia

institute: RSMU

description: Library name: Sample 5

data_processing:
Raw sequencing reads were subjected to quality control using FastQC. Adapter trimming and quality filtering were performed with Trimmomatic. Processed reads were aligned to the rat reference genome using HISAT2 with default parameters. Gene expression quantification was performed using HTSeq-count to generate raw counts. Normalization of gene expression was conducted using the Transcripts Per Kilobase Million (TPM) method, enabling comparability across samples.
Assembly: Rat reference genome mRatBN7.2 (Ensembl Release 104)
Supplementary files format and content: counts

organism: Rattus

source_name: Ventricular cardiomyocytes

extract_protocol:
Total RNA was extracted from isolated ventricular cardiomyocytes using the TRIzol reagent, followed by chloroform phase separation and purification with the RNeasy Mini Kit. RNA integrity and concentration were assessed using a NanoDrop spectrophotometer and Agilent Bioanalyzer to ensure high-quality RNA for downstream processing. Poly(A)+ RNA was subsequently enriched using the NEBNext Poly(A) Magnetic Isolation Module. All steps were performed according to the manufacturer’s protocols to ensure reproducibility and sample integrity.
Library preparation was performed according to the TruSeq Stranded mRNA library preparation assay

value: Ventricular cardiomyocytes

tag: strain

value: Wistar rat

value: wild-type

value: male

value: control (no hypergravity)

tag: developmental stage

value: adult (8 weeks old)


title: Ventricular cardiomyocytes, control, rep3

description: Library name: Sample 6


title: Ventricular cardiomyocytes, hypergravity, rep3

description: Library name: Sample 3

value: hypergravity (4g for 14 days)


title: Ventricular cardiomyocytes, control, rep1

description: Library name: Sample 4


title: Ventricular cardiomyocytes, hypergravity, rep2

description: Library name: Sample 2


title: Ventricular cardiomyocytes, hypergravity, rep1

description: Library name: Sample 1


title: RNA-Seq, dissected germline, ESC422, GRWD-1 depletion via 1 mM IAA, rep 2

status: Public on Jun 24 2025

city: Austin

first: Elif

last: Sarinay Cenik

state: TX

address: 2500 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

description:
Library name: ESC-HSl-611
multimapping_fractional_counts_for_rRNA_expression.csv

data_processing:
Read trimming: Trim Galore! v0.6.10 used with default parameters.
Genome indexing: HISAT2 v2.2.1 used to build WBcel235 genome index with hisat2-build --seed 40.
Read mapping: HISAT2 v2.2.1 used with hisat2 --seed 40 and default parameters.
Alignment sorting: Picard SortSam v3.1.1 used with -SORT_ORDER coordinate --CREATE_INDEX true.
Feature quantification: featureCounts v2.0.6 used with -t exon -g gene_id -p.
Gene filtering: Retained 19,985 protein-coding genes from WBcel235 annotation and removed genes with fewer than 5 counts across 3 biological replicates.
Assembly: WBcel235
Supplementary files format and content: Comma-delimited file containing filtered raw counts of reads within 19,985 protein coding genes (Wormbase identifiers from WBcel235) across all samples. Note that genes with fewer than 5 counts across 3 biological replicates were filtered out.

For multimapping_fractional_counts_for_rRNA_expression.csv:
Read trimming: Trim Galore! v0.6.10 used with default parameters.
Genome indexing: HISAT2 v2.2.1 used to build WBcel235 genome index with hisat2-build --seed 40.
Read mapping: HISAT2 v2.2.1 used with hisat2 -U --seed 40 --all, and all other default parameters.
Alignment sorting: Picard SortSam v3.1.1 used with -SORT_ORDER coordinate --CREATE_INDEX true.
Curated gene annotions: To quantify rDNA transcription, we manually curated “gene” annotations for the two unique internal transcribed spacers (ITS) and appended them to the WBcel235 annotation. See command: `echo -e 'I\tcurated_RMT\tgene\t15061160\t15062082\t.\t+\t.\tgene_id "5ETS"; gene_name "5ETS"; gene_source "curated_RMT"; gene_biotype "rRNA";' >> WBcel235_w_ITS.gtf echo -e 'I\tcurated_RMT\tgene\t15063837\t15064300\t.\t+\t.\tgene_id "ITS1"; gene_name "ITS1"; gene_source "curated_RMT"; gene_biotype "rRNA";' >> WBcel235_w_ITS.gtf echo -e 'I\tcurated_RMT\tgene\t15064454\t15064837\t.\t+\t.\tgene_id "ITS2"; gene_name "ITS2"; gene_source "curated_RMT"; gene_biotype "rRNA";' >> WBcel235_w_ITS.gtf echo -e 'I\tcurated_RMT\tgene\t15068356\t15069279\t.\t+\t.\tgene_id "3ETS"; gene_name "3ETS"; gene_source "curated_RMT"; gene_biotype "rRNA";' >> WBcel235_w_ITS.gtf`
Feature quantification: featureCounts v2.0.6 used with -a WBcel235_w_ITS.gtf -t gene -g gene_id -M -O --fraction.
Multi-mapping fractional counts were rounded for downstream analyses. We provided the fractional read counts as the processed data file.
Assembly: WBcel235
Supplementary files format and content: Comma-delimited file containing fractional counts of multi-mapping reads to the WBcel235 genome annotatation with additional curated rDNA loci including ITS regions (Wormbase identifiers from WBcel235). Note that reads were re-mapped separately for protein coding gene expression and ITS expression analyses (PCG expression: default hisat2 params and featureCounts -t exon -g gene; ITS expression: hisat2 --all and featureCounts -M --fraction).

organism: Caenorhabditis elegans

source_name: dissected germline

growth_protocol: Maintained and treated at 20°C on non-enriched plated seeded with OP50.

extract_protocol:
Dissected gonads were transferred to 1 mL of TRIzol, vortexed, then incubated for 5 minutes at room temperature. RNA was extracted by adding 200 µL of chloroform to the lysate, spinning for 10 minutes at 15,000 rpm, and isolating the supernatant. The isolated RNA was precipitated overnight at −20°C using 50 mM sodium acetate, 5 mM MgCl2, 15 mg/mL GlycoBlue™ Coprecipitant, and isopropanol.
RNA pellets were washed in 80% ethanol and processed with the SMARTer Stranded RNA-Seq kit. RNA was fragmented, converted to cDNA, and PCR amplified (1 min at 94°C; 15-17 cycles of 15 sec at 98°C, 15 sec at 55°C, 30 sec at 68°C). Libraries were purified using Agencourt AMPure XP beads, quantified with the Qubit™ dsDNA HS Assay Kit, and sequenced on a NovaSeq 6000 v1.5 SP flow cell.

treatment_protocol: Auxin (IAA) plates were prepared by diluting Alfa Aesar (#A10556) to 1 mM in NGM agar, while control plates contained an equivalent EtOH volume. Plates were poured, solidified, seeded with OP50, and incubated at 20°C overnight. Synchronized late L4 worms were transferred to control or auxin plates for 18 hours at 20°C.

value: dissected germline

value: young adult

value: hermaphrodite

value: 1 mM auxin (IAA)


title: RNA-Seq, dissected germline, ESC422, GRWD-1 depletion via 1 mM IAA, rep 1

description:
Library name: ESC-HSl-605
multimapping_fractional_counts_for_rRNA_expression.csv


title: RNA-Seq, dissected germline, ESC422, GRWD-1 control, rep 2

description:
Library name: ESC-HSl-610
multimapping_fractional_counts_for_rRNA_expression.csv

value: EtOH control


title: uBT_SC_MG_4m_WT_1

description: Library name: uBT_SC_MG_4m_WT_1

value: Spinal cord

value: Microglial cells

value: 4 months


title: HiC_BWX5297_42C10m_T0

description: Library name: HiC_BWX5297_42C10m_T0

tag: cell line

value: Bacillus subtilis PY79

value: Bacterial

value: parSdelta9 no a.b., -59degree parS no a.b, deltaspo0J::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30°C for 2h, then shifted up to 42°C for 45min, then shifted down to 30°C for 15min, finally shifted up to 42°C for 10min.


title: RNA-Seq, dissected germline, ESC422, GRWD-1 control, rep 1

description:
Library name: ESC-HSl-604
multimapping_fractional_counts_for_rRNA_expression.csv


title: RNA-Seq, dissected germline, ESC332, RPOA-2 depletion via 1 mM IAA, rep 2

description:
Library name: ESC-HSL-457
multimapping_fractional_counts_for_rRNA_expression.csv


title: RNA-Seq, dissected germline, ESC332, RPOA-2 depletion via 1 mM IAA, rep 3

description:
Library name: ESC-HSL-458
multimapping_fractional_counts_for_rRNA_expression.csv


title: RNA-Seq, dissected germline, ESC332, RPOA-2 depletion via 1 mM IAA, rep 1

description:
Library name: ESC-HSL-456
multimapping_fractional_counts_for_rRNA_expression.csv


title: RNA-Seq, dissected germline, ESC332, RPOA-2 control, rep 2

description:
Library name: ESC-HSL-460
multimapping_fractional_counts_for_rRNA_expression.csv


title: RNA-Seq, dissected germline, ESC332, RPOA-2 control, rep 1

description:
Library name: ESC-HSL-459
multimapping_fractional_counts_for_rRNA_expression.csv


title: RNA-Seq, dissected germline, ESC332, RPOA-2 control, rep 3

description:
Library name: ESC-HSL-461
multimapping_fractional_counts_for_rRNA_expression.csv


title: Xu-17_S65_L001, Senescent Preadipocytes , DMSO

status: Public on May 30 2025

city: Rochester

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

data_processing:
Raw reads were trimmed using fastp (v0.20.1).
Trimmed reads were then aligned to the GRCh38 reference genome using STAR (v2.7.9a).
Gene expression levels were quantified by generating a count matrix using STAR with the --quantMode GeneCounts option.
Assembly: GRCh38
Supplementary files format and content: A .txt file containing gene expression values

source_name: ADIPOSE TISSUE

extract_protocol:
Trizol/ Chloroform
TruSeq Stranded mRNA kit

value: ADIPOSE TISSUE

value: Senescent Preadipocytes

value: Healthy Donors

value: DMSO


title: Xu-15_S63_L001, Senescent Preadipocytes , DASATINIB

value: DASATINIB


title: Xu-14_S62_L001, Senescent Preadipocytes , DMSO


title: Xu-12_S60_L001, Senescent Preadipocytes , DASATINIB


title: Xu-18_S66_L001, Senescent Preadipocytes , DASATINIB


title: Xu-11_S59_L001, Senescent Preadipocytes , DMSO


title: Xu-9_S57_L001, Senescent Preadipocytes , DASATINIB


title: Xu-5_S53_L001, Senescent Preadipocytes , DMSO


title: Xu-2_S50_L001, Senescent Preadipocytes , DMSO


title: Xu-3_S51_L001, Senescent Preadipocytes , DASATINIB


title: Xu-8_S56_L001, Senescent Preadipocytes , DMSO


title: RNA-Seq, dissected germline, ESC422, GRWD-1 control, rep 3

description:
Library name: ESC-HSl-616
multimapping_fractional_counts_for_rRNA_expression.csv

value: dissected germline


title: RNA-Seq, dissected germline, ESC422, GRWD-1 depletion via 1 mM IAA, rep 3

description:
Library name: ESC-HSl-617
multimapping_fractional_counts_for_rRNA_expression.csv

value: young adult


title: Slide 8, Xenium In Situ Spatial Gene Expression

city: Hamburg

first: Robin

last: Khatri

address: Falkenried 94

department: Institute of Medical Systems Biology

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: The Xenium samples underwent several rounds of fluorescent probe hybridization, imaging, and probe removal. The Xenium Analyzer captured a Z-stack of images every cycle and in every channel, which needed to be processed and stitched to build a spatial map of the transcripts across the tissue section.

scan_protocol: Xenium In Situ Analyzer

data_processing:
Baysor (v0.6.2) was used to re-segment cells with prior being default segmentations (cell_boundaries.parquet). Scanpy (v1.10.1) workflows were used for normalization to the median the downstream analysis.
The processed anndata object (processed_data.h5ad) contains cells after re-segmentation and integration. .X contains log-normalized counts.

label: Xenium Human Probe Set

source_name: 5 µm kidney section

label_protocol: Xenium Human Probe Set

extract_protocol: 5 μm sections were taken for Xenium.

value: kidney


title: Slide 1, Xenium In Situ Spatial Gene Expression


title: Slide 5, Xenium In Situ Spatial Gene Expression


title: Lamp5_Gaba.9mo

status: Public on Apr 30 2025

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
Library name: sample 56
read length: 151

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Supplementary files format and content: tab-delimited files (CONTACT files) describing the raw contact number between two genome regions . Columns are: 1. Strand1 (0 for forward, anything else for reverse), 2. Chromosome1, 3. Position1, 4. restriction site fragments, 5. Strand2 (0 for forward, anything else for reverse), 6.  Chromosome2, 7. Position2, 8. restriction site fragments, 9. the score imputed to this read
Library strategy: snm3C-seq

source_name: brain

extract_protocol:
Mouse brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

treatment_protocol: For all snm3C-seq samples, in-situ 3C treatment was done during the nuclei preparation that allows capturing the chromatin conformation modality as described previously. These steps were carried out using the Arima-3C BETA Kit (Arima Genomics). The nuclei were isolated and sorted into 384-well plates using previous methods21. Briefly, single-nuclei were stained with AlexaFluor488-conjugated anti-NeuN antibody (MAB377X, Millipore) and Hoechst 33342 (62249, ThermoFisher) followed by FANS using a BD Influx sorter with single-cell (1 drop single) mode.

value: brain

value: female


title: MEA-BST_Gaba.9mo

description:
Library name: sample 59
read length: 151


title: Lamp5_Gaba.8wk

description:
Library name: sample 55
read length: 151


title: MEA-BST_Gaba.18mo

description:
Library name: sample 57
read length: 151


title: LDT-PCG-CS_Gata3_Lhx1_Gaba.8wk

description:
Library name: sample 52
read length: 151


title: LDT-PCG-CS_Gata3_Lhx1_Gaba.9mo

description:
Library name: sample 53
read length: 151


title: LDT-PCG-CS_Gata3_Lhx1_Gaba.18mo

description:
Library name: sample 51
read length: 151


title: LA-BLA-BMA-PA_Glut.9mo

description:
Library name: sample 50
read length: 151


title: LA-BLA-BMA-PA_Glut.8wk

description:
Library name: sample 49
read length: 151


title: Xu-6_S54_L001, Senescent Preadipocytes , DASATINIB


title: L6bCT_ENT_Glut.18mo

description:
Library name: sample 45
read length: 151


title: L6bCT_ENT_Glut.9mo

description:
Library name: sample 47
read length: 151


title: L6bCT_ENT_Glut.8wk

description:
Library name: sample 46
read length: 151


title: FaTTy rep3

city: Midlothian

first: Xavier

last: Donadeu

address: Easter Bush

country: United Kingdom

institute: Roslin Institute, University of Edinburgh

description:
NovaSeq 2x150 bp sequencing
FaTTy_C

data_processing:
Raw sequence data converted to fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software
Trimming for adapters and poor quality reads was performed using Trimmomatic v0.36
Mapping performed using STAR aligner v2.5.2b
Gene hit counts calculated using feature Counts from the Subread package v1.5.2
Differential expression analysis performed using DESeq2 v1.16.1
Assembly: Sscrofa10.2
Supplementary files format and content: raw_counts: comma separated values containing raw reads, Ensembl ID, and associated hgnc symbols where applicable for each sample

organism: Sus scrofa

source_name: FaTTy

growth_protocol: Cells were obtained from a subcutaneous adipose tissue sample and grown in high glucose DMEM with 10% FBS, 1% penicillin/streptomycin, and 5ng/ul human basic fibroblast growth factor at 39C and 5% CO2

extract_protocol:
RNA was extracted from confluent wells using TRIzol/BCP and an RNeasy Mini kit (Qiagen)
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufaturer's instructions

value: FaTTy

value: Immortalised Mesenchymal Stem Cell


title: FaTTy rep4

description:
NovaSeq 2x150 bp sequencing
FaTTy_D


title: FaTTy rep2

description:
NovaSeq 2x150 bp sequencing
FaTTy_B


title: MSC rep2

description:
NovaSeq 2x150 bp sequencing
MSC_B

source_name: MSC

value: MSC

value: Mesenchymal Stem Cell

value: WT


title: Slide 2, Xenium In Situ Spatial Gene Expression


title: FaTTy rep1

description:
NovaSeq 2x150 bp sequencing
FaTTy_A


title: MSC rep3

description:
NovaSeq 2x150 bp sequencing
MSC_C


title: MSC rep4

description:
NovaSeq 2x150 bp sequencing
MSC_D


title: AD_4C_3 (IP)

status: Public on Mar 28 2025

city: Fuzhou

first: Kunqi

last: Chen

address: Fujian Medical University

institute: Fujian Medical University

description: Library name: sample24

data_processing:
The raw MeRIP-seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for RNA modification (RM) peak calling and thesignificant methylation was identified by exomepeak2, and the RM peakcalling can be visualized by IGV software.
The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME was used to determine if the RM peaks contained theconsensus of RM motif sequences.
For mRNA-seq, the mRNA expression level was analyzed by StringTie, and differentially expressed mRNAs were calculated by DEseq.
The substrates of RM regulators were obtained from starBase v2.0.
The statistical enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for differentially expressed genes (DEGs) and differentially methylated mRNAs were applied by DAVID.
genome build/assembly: hg38
processed data files format and content: The processed data files is in CSV format, containing the expression levels and RM status changes for each gene.

source_name: liver

extract_protocol:
Total RNA was extracted according to manufacturer’s instruction.
The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched

value: liver

value: human hepatocellular carcinoma cell line

value: human organ cells

value: Wild type


title: AD_A727

description: Library name: sample27


title: LA-BLA-BMA-PA_Glut.18mo

description:
Library name: sample 48
read length: 151


title: MSC rep1

description:
NovaSeq 2x150 bp sequencing
MSC_A


title: MEA-BST_Gaba.8wk

description:
Library name: sample 58
read length: 151


title: AD_4C_3 (Input)

description: Library name: sample23


title: AD_A716

description: Library name: sample26


title: AD_4C_2 (IP)

description: Library name: sample22


title: Lamp5_Gaba.18mo

description:
Library name: sample 54
read length: 151


title: AD_4C_1 (Input)

description: Library name: sample19


title: AD_4C_1 (IP)

description: Library name: sample20


title: AD_7G_3 (IP)

description: Library name: sample18


title: AD_7G_3 (Input)

description: Library name: sample17


title: AD_4C_2 (Input)

description: Library name: sample21


title: AD_7G_2 (IP)

description: Library name: sample16


title: AD_7G_2 (Input)

description: Library name: sample15


title: AD_7G_1 (Input)

description: Library name: sample13


title: AD_5C_3 (IP)

description: Library name: sample12


title: AD_5C_2 (IP)

description: Library name: sample10


title: AD_5C_3 (Input)

description: Library name: sample11


title: AD_5C_2 (Input)

description: Library name: sample9


title: AD_5C_1 (IP)

description: Library name: sample8


title: AD_5C_1 (Input)

description: Library name: sample7


title: AD_A710

description: Library name: sample25


title: AD_1A_3 (Input)

description: Library name: sample5


title: AD_1A_1 (IP)

description: Library name: sample2


title: AD_1A_3 (IP)

description: Library name: sample6


title: AD_1A_2 (IP)

description: Library name: sample4


title: AD_1A_1 (Input)

description: Library name: sample1


title: MT4_I0037_A3

description: Library name: sample37

data_processing:
The raw MeRIP-seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for RNA modification (RM) peak calling and thesignificant methylation was identified by exomepeak2, and the RM peakcalling can be visualized by IGV software.
The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME was used to determine if the RM peaks contained theconsensus of RM motif sequences.
For mRNA-seq, the mRNA expression level was analyzed by StringTie, and differentially expressed mRNAs were calculated by DEseq.
The substrates of RM regulators were obtained from starBase v2.0.
The statistical enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for differentially expressed genes (DEGs) and differentially methylated mRNAs were applied by DAVID.
genome build/assembly:  hg38
processed data files format and content: The processed data files is in CSV format, containing the expression levels and RM status changes for each gene.

source_name: Lymphocyte

value: Lymphocyte

value: human T cell leukaemia cell line


title: MT4_I0037_A1

description: Library name: sample35


title: MT4_hm5C_2 (IP)

description: Library name: sample34


title: MT4_hm5C_2 (Input)

description: Library name: sample33


title: MT4_hm5C_1 (Input)

description: Library name: sample31


title: MT4_hm5C_1 (IP)

description: Library name: sample32


title: MT4_4C_3 (IP)

description: Library name: sample30


title: MT4_4C_2 (Input)

description: Library name: sample27


title: MT4_4C_3 (Input)

description: Library name: sample29


title: AD_7G_1 (IP)

description: Library name: sample14


title: MT4_7G_3 (IP)

description: Library name: sample24


title: MT4_7G_3 (Input)

description: Library name: sample23


title: MT4_4C_2 (IP)

description: Library name: sample28


title: MT4_7G_2 (IP)

description: Library name: sample22


title: MT4_7G_1 (Input)

description: Library name: sample19


title: MT4_5C_3 (Input)

description: Library name: sample17


title: MT4_5C_3 (IP)

description: Library name: sample18


title: MT4_5C_2 (Input)

description: Library name: sample15


title: MT4_I0037_A2

description: Library name: sample36


title: MT4_5C_1 (IP)

description: Library name: sample14


title: MT4_7G_2 (Input)

description: Library name: sample21


title: AD_1A_2 (Input)

description: Library name: sample3


title: MT4_6A_3 (Input)

description: Library name: sample11


title: MT4_6A_2 (Input)

description: Library name: sample9


title: MT4_5C_2 (IP)

description: Library name: sample16


title: MT4_6A_1 (Input)

description: Library name: sample7


title: MT4_1A_3 (IP)

description: Library name: sample6


title: MT4_5C_1 (Input)

description: Library name: sample13


title: MT4_1A_2 (IP)

description: Library name: sample4


title: MT4_1A_3 (Input)

description: Library name: sample5


title: MT4_1A_2 (Input)

description: Library name: sample3


title: MT4_4C_1 (IP)

description: Library name: sample26


title: MT4_4C_1 (Input)

description: Library name: sample25


title: MT4_1A_1 (Input)

description: Library name: sample1


title: MT4_1A_1 (IP)

description: Library name: sample2


title: HepAD38 - DOX_3 (IP)

description: Library name: sample12

value: HepAD38 - DOX


title: HepAD38 - DOX_3 (Input)

description: Library name: sample11


title: MT4_7G_1 (IP)

description: Library name: sample20


title: HepAD38 - DOX_2 (IP)

description: Library name: sample10


title: HepAD38 - DOX_2 (Input)

description: Library name: sample9


title: HepAD38 - DOX_1 (IP)

description: Library name: sample8


title: MT4_6A_3 (IP)

description: Library name: sample12


title: HepAD38 + DOX_3 (IP)

description: Library name: sample6

value: HepAD38 + DOX


title: HepAD38 + DOX_3 (Input)

description: Library name: sample5


title: MT4_6A_2 (IP)

description: Library name: sample10


title: HepAD38 + DOX_2 (Input)

description: Library name: sample3


title: PBMCs, TCR, 6mo post-CAR T, P32

status: Public on Mar 04 2025

city: Boston

first: Dimitra

last: Karagkouni

address: Brookline 330

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

description:
Library name: Sample 182
10x Genomics

data_processing:
Cellranger v.4.0.0 for scRNA-seq data, cellranger v.4.0.0 V(D)J Annotation pipeline for scTCR-seq data
Assembly: hg38
Supplementary files format and content: Gene expression,  TCR sequences
Library strategy: TCR-Seq

source_name: PBMC

extract_protocol: Library was performed according to the manufacter's indtructions. For each sample, 8,000-10,000 cells were loaded in one channel of a Chromium Chip K (10x Genomics, PN-1000286) and profiled using the Chromium Next GEM Single Cell 5' Kit v2 (10x Genomics, PN-1000263). Full-length paired α/β TCR libraries were obtained using the Chromium Single Cell V(D)J Enrichment Human T Cell (10x Genomics,  PN-1000252). cDNA, gene expression, and TCR libraries were assessed using the DNA High Sensitivity Bioanalyzer Chip (Agilent, 5067-4626).

value: PBMC

value: CAR T

value: 6mo post-CAR T


title: PBMCs, RNA, 12mo post-CAR T, P32

description:
Library name: Sample 183
10x Genomics

data_processing:
Cellranger v.4.0.0 for scRNA-seq data, cellranger v.4.0.0 V(D)J Annotation pipeline for scTCR-seq data
Assembly: hg38
Supplementary files format and content: Gene expression,  TCR sequences

value: 12mo post-CAR T


title: PBMCs, TCR, 12mo post-CAR T, P32

description:
Library name: Sample 184
10x Genomics


title: PBMCs, TCR, Leukapheresis, P32

description:
Library name: Sample 180
10x Genomics

value: Leukapheresis


title: PBMCs, RNA, 6mo post-CAR T, P32

description:
Library name: Sample 181
10x Genomics


title: PBMCs, RNA, Leukapheresis, P32

description:
Library name: Sample 179
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P31

description:
Library name: Sample 173
10x Genomics

value: 4wk post-CAR T


title: PBMCs, TCR, 4wk post-CAR T, P31

description:
Library name: Sample 174
10x Genomics


title: PBMCs, RNA, 6mo post-CAR T, P31

description:
Library name: Sample 175
10x Genomics


title: MT4_6A_1 (IP)

description: Library name: sample8


title: HepAD38 + DOX_1 (IP)

description: Library name: sample2


title: PBMCs, RNA, Leukapheresis, P31

description:
Library name: Sample 171
10x Genomics


title: HepAD38 + DOX_1 (Input)

description: Library name: sample1


title: HepAD38 + DOX_2 (IP)

description: Library name: sample4


title: PBMCs, TCR, 4wk post-CAR T, P30

description:
Library name: Sample 168
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P30

description:
Library name: Sample 167
10x Genomics


title: PBMCs, RNA, Leukapheresis, P30

description:
Library name: Sample 165
10x Genomics


title: PBMCs, TCR, 12mo post-CAR T, P29

description:
Library name: Sample 164
10x Genomics


title: PBMCs, TCR, Leukapheresis, P30

description:
Library name: Sample 166
10x Genomics


title: PBMCs, RNA, 6mo post-CAR T, P30

description:
Library name: Sample 169
10x Genomics


title: PBMCs, TCR, 6mo post-CAR T, P30

description:
Library name: Sample 170
10x Genomics


title: HepAD38 - DOX_1 (Input)

description: Library name: sample7


title: PBMCs, RNA, 12mo post-CAR T, P29

description:
Library name: Sample 163
10x Genomics


title: PBMCs, RNA, 6mo post-CAR T, P29

description:
Library name: Sample 161
10x Genomics


title: PBMCs, TCR, 6mo post-CAR T, P29

description:
Library name: Sample 162
10x Genomics


title: PBMCs, TCR, 4wk post-CAR T, P29

description:
Library name: Sample 160
10x Genomics


title: PBMCs, TCR, Leukapheresis, P29

description:
Library name: Sample 158
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P29

description:
Library name: Sample 159
10x Genomics


title: PBMCs, RNA, Leukapheresis, P29

description:
Library name: Sample 157
10x Genomics


title: PBMCs, TCR, 6mo post-CAR T, P28

description:
Library name: Sample 154
10x Genomics


title: PBMCs, TCR, Leukapheresis, P28

description:
Library name: Sample 152
10x Genomics


title: PBMCs, RNA, Leukapheresis, P28

description:
Library name: Sample 151
10x Genomics


title: PBMCs, TCR, 12mo post-CAR T, P28

description:
Library name: Sample 156
10x Genomics


title: PBMCs, RNA, 6mo post-CAR T, P28

description:
Library name: Sample 153
10x Genomics


title: PBMCs, RNA, 12mo post-CAR T, P28

description:
Library name: Sample 155
10x Genomics


title: PBMCs, TCR, 12mo post-CAR T, P27

description:
Library name: Sample 150
10x Genomics


title: PBMCs, TCR, 12mo post-CAR T, P31

description:
Library name: Sample 178
10x Genomics


title: PBMCs, TCR, 6mo post-CAR T, P27

description:
Library name: Sample 148
10x Genomics


title: PBMCs, RNA, 12mo post-CAR T, P27

description:
Library name: Sample 149
10x Genomics


title: PBMCs, RNA, 6mo post-CAR T, P27

description:
Library name: Sample 147
10x Genomics


title: PBMCs, TCR, 4wk post-CAR T, P26

description:
Library name: Sample 138
10x Genomics


title: PBMCs, TCR, 4wk post-CAR T, P27

description:
Library name: Sample 146
10x Genomics


title: PBMCs, RNA, 12mo post-CAR T, P26

description:
Library name: Sample 141
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P26

description:
Library name: Sample 137
10x Genomics


title: PBMCs, RNA, 6mo post-CAR T, P26

description:
Library name: Sample 139
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P27

description:
Library name: Sample 145
10x Genomics


title: PBMCs, TCR, Leukapheresis, P26

description:
Library name: Sample 136
10x Genomics


title: PBMCs, TCR, Leukapheresis, P27

description:
Library name: Sample 144
10x Genomics


title: PBMCs, RNA, Leukapheresis, P27

description:
Library name: Sample 143
10x Genomics


title: PBMCs, RNA, Leukapheresis, P26

description:
Library name: Sample 135
10x Genomics


title: PBMCs, TCR, 12mo post-CAR T, P26

description:
Library name: Sample 142
10x Genomics


title: PBMCs, TCR, 12mo post-CAR T, P25

description:
Library name: Sample 134
10x Genomics


title: PBMCs, TCR, 4wk post-CAR T, P25

description:
Library name: Sample 132
10x Genomics


title: PBMCs, RNA, 12mo post-CAR T, P25

description:
Library name: Sample 133
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P25

description:
Library name: Sample 131
10x Genomics


title: PBMCs, TCR, Leukapheresis, P25

description:
Library name: Sample 130
10x Genomics


title: PBMCs, RNA, Leukapheresis, P25

description:
Library name: Sample 129
10x Genomics


title: PBMCs, RNA, 12mo post-CAR T, P24

description:
Library name: Sample 127
10x Genomics


title: PBMCs, TCR, 12mo post-CAR T, P24

description:
Library name: Sample 128
10x Genomics


title: PBMCs, TCR, 6mo post-CAR T, P24

description:
Library name: Sample 126
10x Genomics


title: PBMCs, TCR, 6mo post-CAR T, P26

description:
Library name: Sample 140
10x Genomics


title: PBMCs, RNA, 6mo post-CAR T, P24

description:
Library name: Sample 125
10x Genomics


title: PBMCs, TCR, Leukapheresis, P24

description:
Library name: Sample 122
10x Genomics


title: PBMCs, TCR, 4wk post-CAR T, P24

description:
Library name: Sample 124
10x Genomics


title: PBMCs, RNA, Leukapheresis, P24

description:
Library name: Sample 121
10x Genomics


title: PBMCs, TCR, 12mo post-CAR T, P23

description:
Library name: Sample 120
10x Genomics


title: PBMCs, RNA, 12mo post-CAR T, P23

description:
Library name: Sample 119
10x Genomics


title: PBMCs, TCR, 4wk post-CAR T, P22

description:
Library name: Sample 110
10x Genomics


title: PBMCs, RNA, Leukapheresis, P23

description:
Library name: Sample 113
10x Genomics


title: PBMCs, RNA, 12mo post-CAR T, P22

description:
Library name: Sample 111
10x Genomics


title: PBMCs, TCR, Leukapheresis, P23

description:
Library name: Sample 114
10x Genomics


title: PBMCs, RNA, 6mo post-CAR T, P23

description:
Library name: Sample 117
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P22

description:
Library name: Sample 109
10x Genomics


title: PBMCs, TCR, 12mo post-CAR T, P22

description:
Library name: Sample 112
10x Genomics


title: PBMCs, TCR, 6mo post-CAR T, P23

description:
Library name: Sample 118
10x Genomics


title: PBMCs, RNA, Leukapheresis, P22

description:
Library name: Sample 107
10x Genomics


title: PBMCs, TCR, Leukapheresis, P22

description:
Library name: Sample 108
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P24

description:
Library name: Sample 123
10x Genomics


title: PBMCs, TCR, 12mo post-CAR T, P21

description:
Library name: Sample 106
10x Genomics


title: PBMCs, TCR, 6mo post-CAR T, P21

description:
Library name: Sample 104
10x Genomics


title: PBMCs, RNA, 12mo post-CAR T, P21

description:
Library name: Sample 105
10x Genomics


title: PBMCs, TCR, 6mo post-CAR T, P31

description:
Library name: Sample 176
10x Genomics


title: PBMCs, RNA, Leukapheresis, P21

description:
Library name: Sample 101
10x Genomics


title: PBMCs, RNA, 12mo post-CAR T, P20

description:
Library name: Sample 99
10x Genomics


title: PBMCs, TCR, 12mo post-CAR T, P20

description:
Library name: Sample 100
10x Genomics


title: PBMCs, TCR, Leukapheresis, P21

description:
Library name: Sample 102
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P23

description:
Library name: Sample 115
10x Genomics


title: PBMCs, TCR, Leukapheresis, P31

description:
Library name: Sample 172
10x Genomics


title: PBMCs, TCR, 6mo post-CAR T, P20

description:
Library name: Sample 98
10x Genomics


title: PBMCs, TCR, Leukapheresis, P20

description:
Library name: Sample 94
10x Genomics


title: PBMCs, TCR, 12mo post-CAR T, P19

description:
Library name: Sample 92
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P20

description:
Library name: Sample 95
10x Genomics


title: PBMCs, RNA, Leukapheresis, P20

description:
Library name: Sample 93
10x Genomics


title: PBMCs, TCR, 6mo post-CAR T, P19

description:
Library name: Sample 90
10x Genomics


title: PBMCs, TCR, 4wk post-CAR T, P19

description:
Library name: Sample 88
10x Genomics


title: PBMCs, TCR, Leukapheresis, P19

description:
Library name: Sample 86
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P19

description:
Library name: Sample 87
10x Genomics


title: PBMCs, RNA, Leukapheresis, P19

description:
Library name: Sample 85
10x Genomics


title: PBMCs, TCR, 12mo post-CAR T, P18

description:
Library name: Sample 84
10x Genomics


title: PBMCs, RNA, 6mo post-CAR T, P19

description:
Library name: Sample 89
10x Genomics


title: PBMCs, RNA, 12mo post-CAR T, P18

description:
Library name: Sample 83
10x Genomics


title: PBMCs, RNA, 12mo post-CAR T, P19

description:
Library name: Sample 91
10x Genomics


title: PBMCs, TCR, 4wk post-CAR T, P18

description:
Library name: Sample 82
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P18

description:
Library name: Sample 81
10x Genomics


title: PBMCs, TCR, 12mo post-CAR T, P17

description:
Library name: Sample 78
10x Genomics


title: PBMCs, RNA, 6mo post-CAR T, P20

description:
Library name: Sample 97
10x Genomics


title: PBMCs, RNA, Leukapheresis, P18

description:
Library name: Sample 79
10x Genomics


title: PBMCs, TCR, 4wk post-CAR T, P20

description:
Library name: Sample 96
10x Genomics


title: PBMCs, RNA, 6mo post-CAR T, P21

description:
Library name: Sample 103
10x Genomics


title: PBMCs, RNA, 12mo post-CAR T, P17

description:
Library name: Sample 77
10x Genomics


title: PBMCs, TCR, Leukapheresis, P18

description:
Library name: Sample 80
10x Genomics


title: PBMCs, RNA, 6mo post-CAR T, P17

description:
Library name: Sample 75
10x Genomics


title: PBMCs, RNA, Leukapheresis, P17

description:
Library name: Sample 73
10x Genomics


title: PBMCs, RNA, Leukapheresis, P16

description:
Library name: Sample 71
10x Genomics


title: PBMCs, TCR, Leukapheresis, P17

description:
Library name: Sample 74
10x Genomics


title: PBMCs, TCR, 6mo post-CAR T, P17

description:
Library name: Sample 76
10x Genomics


title: PBMCs, TCR, Leukapheresis, P16

description:
Library name: Sample 72
10x Genomics


title: PBMCs, RNA, Leukapheresis, P15

description:
Library name: Sample 67
10x Genomics


title: PBMCs, TCR, Leukapheresis, P14

description:
Library name: Sample 64
10x Genomics


title: PBMCs, TCR, 4wk post-CAR T, P15

description:
Library name: Sample 70
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P15

description:
Library name: Sample 69
10x Genomics


title: PBMCs, RNA, Leukapheresis, P14

description:
Library name: Sample 63
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P14

description:
Library name: Sample 65
10x Genomics


title: PBMCs, TCR, 6mo post-CAR T, P12

description:
Library name: Sample 58
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P13

description:
Library name: Sample 61
10x Genomics


title: PBMCs, TCR, 4wk post-CAR T, P14

description:
Library name: Sample 66
10x Genomics


title: PBMCs, TCR, Leukapheresis, P15

description:
Library name: Sample 68
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P12

description:
Library name: Sample 55
10x Genomics