title: MOLM13_shALKBH1_Ribo_rep2

description: Ribosome-profiling


title: MOLM13_shALKBH1_Venetoclax_rep3

status: Public on Jul 23 2025

type: SRA

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

country: USA

institute: Beckman Research Institute of City of Hope

library_source: transcriptomic

data_processing:
The adapter sequences were trimmed by use of Cutadapt29 with parameter “--minimum-length 20” and Truseq illumine adapters.  Then the trimmed reads were mapped to the human transcriptome built with genome sequences (hg38 version) and gene annotations (GENCODE v3730) by STAR software31. The gene expressions were calculated by RSEM32 and quantified as expected count and Transcript Per Million (TPM). The expected count matrixes were used as the input of DESeq233 package to estimate the differential expressions (DE) of genes between different conditions. The average TPM values of two biological replicates were used for estimating the gene expression level. To obtain high-confidence DE genes, lowly expressed genes (average TPM < 1) in corresponding condition and DE genes with p-value less than 0.05 were filtered. The t-test was employed to estimate the significance of gene changes (ratio of ratios) among multiple conditions.
Assembly: hg38
Supplementary files format and content: tab-seperated results from RSEM, containing gene expression information

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: MOLM13 cells were cultured in RPMI 1640 medium supplemented with 10% FBS

extract_protocol:
Qiagen miRNeasy Mini Kit
Each RNA sample was supplemented with Mix1 or Mix2 in accordance with Life Technologies' guidelines, targeting an approximate 1% representation of the total RNA-Seq reads mapped to the 92 ERCC control sequences. In total, 300 ng of RNA from each sample was used for this purpose.
Sequencing was performed using an Illumina®HiSeq 2500 system, utilizing a 51 bp paired-end configuration via the TruSeq SR Cluster Kit V4-cBot-HS (Illumina, San Diego, CA, USA).

treatment_protocol: Tet-shNS or Tet-shALKBH1 transduced MOLM13 cells were treated with doxycycline (1 ug/ml) for 4 days to induce ALKBH1 KD. Then cells were split into two groups for DMSO or 100 nM Venetoclax treatment for 48 hours

tag: cell line

tag: cell type

value: acute myeloid leukemia

tag: treatment

value: Tet-shALKBH1, Venetoclax, 48h


title: vancomycin_start_3

city: Philadelphia

first: Andrea

last: Facciabene

state: PA

address: 3400 Civic Center Bulevard

department: Radiation Oncology

institute: University of Pennsylvania

data_processing:
Raw RNA-Seq datasets were quality checked and pre-processed using FastQC and Cutadapt. Alignment of the trimmed sequencing reads was conducted against the Homo sapiens (version GRCh38) genome using the STAR aligner.
Isoform-level quantification was performed using RSEM and expected counts for each gene were extracted for downstream analysis.
Trimmed mean of M-values (TMM) normalization was applied to RSEM read counts and differential expression analysis was conducted using edgeR.
Assembly: hg38
Supplementary files format and content: tab-delimited text files that includes raw counts for each sample

molecule: total RNA

source_name: PBMCs

extract_protocol:
Total RNA was extracted using standard trizol protocol, following RNA concentrations were measured with Qubit Flourometric Quantification (Theromo Fisher Scientific), RNA integrity number (RIN) was determined with Bioanalyzer on RNA 6000 Nano Kit (Agilent Technologies), all samples were high quality with RIN > 9.
RNA-seq libraries were generated using NEBNext Poly(A) + ultra–Directional RNA library Prep Kit for Illumina (New England BioLabs) according to manufacturer’s instructions.  For sequencing (150 bp paired-end) at Genewiz NJ, USA

treatment_protocol: SBRT was administered per institutional guidelines for peripheral or centrally located tumors under 5 cm. Treatment was delivered as 50 Gy across 4 or 5 fractions on non-consecutive days. Patient setup involved 4D CT simulation with upper and lower vaclok bags for reproducibility and a compression belt for tumors in the lower lobe to reduce motion. Treatment volumes were defined using the 4D CT images to create an IGTV, with an isotropic 5 mm margin added to form the PTV. Established dose constraints from previous publications were followed

value: PBMCs

value: RT + Vancomycin

tag: time

value: start


title: kidney biopsy N237

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

source_name: kidney biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: All human kidney biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

tag: mmdx (abmr, mixed, nr[no rejection], pabmr, ptcmr, tcmr)

value: NR


title: kidney biopsy N96

value: pABMR


title: PDAC-CA-Tumor-15

city: Birmingham

first: Sooryanarayana

last: Varambally

state: Alabama

address: 1824 6th Avenue S

department: Pathology

institute: University of Alabama

description: Library name: 28_C5_S8

data_processing:
Adapter sequences and low quality reads were trimmed from fastq files using trim_galore.
With HISAT, trimmed raw read sequences were mapped to Homo sapiens reference genome (hg38)
The aligned reads were sorted via samtools (Version: 1.3.1). HTSeq-count (version 0.6.0) was used to obtain raw read counts for each annotated human gene. Differential expression analysis was carried out using DESeq2.  Genes with an adjusted p-value <0.05 and a log2-fold change >= 1 or <= -1 were considered significantly differentially expressed
Assembly: hg38
Supplementary files format and content: tab delimited text file include normalized read counts for each sample from DESeq.

source_name: Pancreas

extract_protocol:
Total RNA (including small RNAs) was extracted from FFPE tissue sections using Qiagen AllPrep DNA/RNA FFPE kits (Cat #80234), following the manufacturer’s protocol. RNA integrity and quantification were assessed using the Agilent TapeStation instrument with High Sensitivity RNA ScreenTapes (Cat #5067-5579) and Qubit RNA assay kits (Cat#: Q32855, Invitrogen, Thermo Fisher).
Library preparation from input RNA was performed using SureSelectXT Low Input Library Preparation and Target Enrichment Kits (Cat #5190-9686). Final pooled libraries (12-plex) were run to obtain 30M read depth for single-end reads using NextSeq 500/550 High Output Reagent Cartridge v2 (Cat # 15057934) on an Illumina NextSeq 500/550 instrument.

tag: tissue

value: Pancreas

tag: race

value: Caucasian

tag: condition

value: Tumor


title: kidney biopsy N6


title: vancomycin_end_1

value: end


title: kidney biopsy N107


title: MOLM13_shALKBH1_Venetoclax_rep2


title: MOLM13_shALKBH1_Venetoclax_rep1


title: MOLM13_shALKBH1_mRNA_rep2

description: RNA-seq

data_processing:
The raw reads (R1 only) were adapter trimmed by Cutadapt with parameters: -m 25 -M 40 -a AGATCGGAAGAGCACACGTCT. The human tRNA, rRNA and snoRNA sequences were removed from trimmed reads by using Bowtie software. Then the clean reads were mapped to human transcriptome (hg38 version + GENCODE v37) by utilizing STAR software. The reads counts and TPM on gene level were estimated by RSEM.
Assembly: hg38
Supplementary files format and content: tab-seperated results from RSEM, containing gene expression information

extract_protocol:
The ribosomes from the cell lysates were separated in the sugrose gredient by ultracentrifugation and were collected. ribosome protecting RNA fracgments were recovered from polyacrylamide TBE-Urea gel. The end structures of the RNA fragments were repaired by T4 polynucleotide kinase (T4 PNK, M0201S, New England Biolabs): (1) 3’ end healing reaction (10 μl): 7 μl RNA sample, 1 μl 10×T4 PNK buffer, 1 μl T4 PNK, and 1 μl SUPERase In RNase Inhibitor were mixed and incubated for 1 h at 37 ℃; (2) 5’-end phosphorylation: 1 μl 10 mM ATP and 1 μl extra T4 PNK were added to the reaction and the mixture was kept for 30 min at 37 ℃. The RNA was purified by ethanol precipitation.
The libraries were constructed after depletion of rRNA using NEBNext small RNA library prep set for Illumina (NEB)
Sequencing was performed using an Illumina®HiSeq 2500 system, utilizing a 51 bp paired-end configuration

treatment_protocol: Tet-shNS or Tet-shALKBH1 transduced MOLM13 cells were treated with doxycycline (1 ug/ml) for 4 days to induce ALKBH1 KD. Then cells were treated with 100 μg/ml cycloheximide for 7 min at 37 ℃ to prevent translation before standard ribosome profiling protocol.


title: MOLM13_shALKBH1_DMSO_rep3

value: Tet-shALKBH1, DMSO, 48h


title: vancomycin_start_1


title: PDAC-CA-Tumor-17

description: Library name: 30_C12_S5


title: PDAC-CA-Tumor-13

description: Library name: 26_F10_S3


title: PDAC-CA-Tumor-14

description: Library name: 27_D8_S7


title: PDAC-CA-Tumor-12

description: Library name: 25_B26_S6


title: MOLM13_shALKBH1_DMSO_rep2


title: primary tumor, discovery cohort, YCC-231, 5' scRNA-seq

city: Seoul

first: IlSeok

last: Choi

address: 50, Yonsei-ro, Seodaemun-gu

department: Biotechnology

country: South Korea

institute: Yonsei University

description: 10X Genomics 5'

library_source: transcriptomic single cell

data_processing:
Sequencing reads were aligned to the human reference genome (GRCh38) using Cell Ranger software (v6.0.0).
Assembly: GRCh38
Supplementary files format and content: CellRanger output .h5 file containing filtered gene by cell count data

source_name: colorectal adenocarcinoma

extract_protocol:
Single-cell isolation was performed using a Human Tumor Dissociation Kit (Miltenyi Biotec, USA) following the manufacturer’s instructions. Fresh surgical tissues were cut into small pieces (<1 mm3) and placed into a gentleMACS C Tube (Miltenyi Biotec, USA) containing a mixture of Enzyme H, Enzyme R, and Enzyme A in RPMI 1640 medium. The tube was then processed on a gentleMACS Dissociator (Miltenyi Biotec, USA) using the GentleMACS programs h_tumor_01 and h_tumor_02, each followed by a 30-minute incubation at 37°C with rotation. The dissociated tissues were filtered through a 70 μm MACS SmartStrainer (Miltenyi Biotec, USA) to achieve a single-cell suspension. The filtrate was centrifuged at 300 × g for 10 minutes at 4°C. The resultant cell pellet was resuspended in 4 mL of RPMI 1640 medium (Thermo Fisher Scientific, USA), and dead cells were removed using Ficoll-Paque PLUS (GE Healthcare, USA). The cells were subsequently washed and resuspended in PBS supplemented with 0.1% bovine serum albumin (BSA, Invitrogen, USA). Cell viability was assessed using the LIVE/DEAD™ Viability/Cytotoxicity Kit (Invitrogen, USA), and the single-cell suspension was further enriched for viability with a Dead Cell Removal Kit (Miltenyi Biotec, USA).
Single-cell suspensions were processed on a Chromium system (10x Genomics, USA). For the discovery cohort consisting of 24 samples, we prepared 5’ scRNA-seq libraries using the Chromium Next GEM Single Cell 5′ Library and Gel Bead Kit v1.1 (PN-1000165). For the validation cohort of 18 samples, 3’ scRNA-seq libraries were generated using the Chromium Next GEM Single Cell 3ʹ v3.1 Library and Gel Bead Kit v3.1 (PN-1000121). The libraries were sequenced on an Illumina NovaSeq 6000 for the 5’ scRNA-seq and an Illumina HiSeq 2000 for the 3’ scRNA-seq.

value: colorectal adenocarcinoma

tag: Sex

value: Male

tag: primary tumor_location

value: rectum

tag: msi

value: MSS

tag: kras

tag: fusobacterium positivity

value: POS


title: PDAC-CA-Tumor-11

description: Library name: 24_A14_S2


title: PDAC-CA-Tumor-16

description: Library name: 29_E6_S4


title: vancomycin_baseline_1

value: baseline


title: MOLM13_shNS_Venetoclax_rep3

value: acute myeloid leukemia

value: Tet-shNS, Venetoclax, 48h


title: MOLM13_shALKBH1_DMSO_rep1


title: PDAC-CA-Tumor-10

description: Library name: 23_B7_S1


title: kidney biopsy N68

value: ABMR


title: PDAC-CA-Tumor-29

description: Library name: 60_A6_S5


title: MOLM13_shNS_Venetoclax_rep2


title: kidney biopsy N66


title: PDAC-CA-Tumor-9

description: Library name: 21_C6_S7


title: primary tumor, discovery cohort, YCC-225, 5' scRNA-seq

description: 10X Genomics 5'

value: ascending

value: wild

value: NEG


title: kidney biopsy N50

value: NR


title: MOLM13_shNS_Venetoclax_rep1


title: PDAC-CA-Tumor-8

description: Library name: 20_F6_S1

value: Pancreas

value: Caucasian


title: MOLM13_shNS_DMSO_rep3

value: Tet-shNS, DMSO, 48h


title: primary tumor, discovery cohort, YCC-223, 5' scRNA-seq

description: 10X Genomics 5'

value: Female

value: sigmoid


title: primary tumor, discovery cohort, YCC-212, 5' scRNA-seq

description: 10X Genomics 5'

value: colorectal adenocarcinoma

value: Male


title: primary tumor, discovery cohort, YCC-230, 5' scRNA-seq

description: 10X Genomics 5'

value: MSS


title: kidney biopsy N38


title: PDAC-CA-Tumor-7

description: Library name: 15_C13_2_S6

value: Tumor


title: MOLM13_shNS_DMSO_rep2


title: PDAC-CA-Tumor-6

description: Library name: 13_C1_S11


title: primary tumor, discovery cohort, YCC-211, 5' scRNA-seq

description: 10X Genomics 5'

value: POS


title: kidney biopsy N215


title: primary tumor, discovery cohort, YCC-227, 5' scRNA-seq

description: 10X Genomics 5'

value: rectosigmoid junction


title: MOLM13_shNS_DMSO_rep1

value: acute myeloid leukemia


title: primary tumor, discovery cohort, YCC-197, 5' scRNA-seq

description: 10X Genomics 5'


title: kidney biopsy N120

value: ABMR


title: primary tumor, discovery cohort, YCC-195, 5' scRNA-seq

description: 10X Genomics 5'

value: trans


title: sh3

city: jinan

first: qian

last: zhou

state: li xia

address: wenhua western road

country: China

institute: shandong university

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)   by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) 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，then expression level of gene was calculated by RSEM (v1.2.12)
Differential expression was performed using DESeq2 (version 1.4.5).
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Text Document  include Raw read counts for each Sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent. RNA quality and quantity were determined using a Nano Drop and Agilent 2100 bioanalyzer
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBSEQ  platform.

value: PLEK2 knockdown


title: PDAC-CA-Tumor-4

description: Library name: 8_D4_S10


title: kidney biopsy N270


title: sh2


title: PDAC-CA-Tumor-3

description: Library name: 6_C8_2_S4


title: kidney biopsy N11


title: primary tumor, discovery cohort, YCC-194, 5' scRNA-seq

description: 10X Genomics 5'

value: wild

value: NEG


title: PDAC-CA-Tumor-2

description: Library name: 5_E8_S9

value: Pancreas


title: primary tumor, discovery cohort, YCC-192, 5' scRNA-seq

description: 10X Genomics 5'


title: primary tumor, discovery cohort, YCC-191, 5' scRNA-seq

description: 10X Genomics 5'


title: PDAC-CA-Tumor-1

description: Library name: 3_B5_S7

value: Caucasian


title: C3

value: shNC


title: kidney biopsy N106

value: NR


title: kidney biopsy N115


title: C2


title: PDAC-CA-Normal-5

description: Library name: 51_B3_N_S9

value: Normal


title: primary tumor, discovery cohort, YCC-190, 5' scRNA-seq

description: 10X Genomics 5'

value: colorectal adenocarcinoma

value: Female

value: sigmoid


title: primary tumor, discovery cohort, YCC-189, 5' scRNA-seq

description: 10X Genomics 5'

value: Male

value: rectum

value: MSS


title: kidney biopsy N260

value: pABMR


title: PDAC-CA-Tumor-5

description: Library name: 11_E4_S5

value: Tumor


title: sh1


title: Germ-free C57BL/6 mice, Fn group

description:
Library name: GF mice validation Fn group
10X Genomics 5'

data_processing:
Sequencing reads were aligned to the mouse reference genome (GRCm39) using Cell Ranger software (v9.0.0).
Assembly: GRCm39
Assembly: Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Supplementary files format and content: CellRanger output .h5 file containing filtered gene by cell count data

organism:
Mus musculus
Fusobacterium nucleatum subsp. nucleatum ATCC 25586

source_name: normal colon tissue

growth_protocol: Six-week-old female germ-free (GF) mice with a C57BL/6 background were used in all experiments. Ten mice were randomly divided into two groups (5 mice per group) including control group and Fn group. All animal experiments were conducted in accordance with the Public Health Service Policy on Humane Care and Use of Laboratory Animals and approved by the IACUC (2022-0286) of the Department of Laboratory Animal Resources of Yonsei University College of Medicine, accredited by AAALAC International (#001071). GF mice were housed in individually ventilated caging (IVC) systems under controlled temperature (22–23°C) and light (12 h light/12 h dark) conditions. Food and water were sterile and provided to mice and were available ad libitum.

extract_protocol:
All colon tissues, from proximal to distal, were cut open longitudinally and washed in ice-cold PBS twice. The colon tissues were then immersed in ice-cold RPMI-1640 media and processed for tissue dissociation. Cecum was isolated from the gastrointestinal tract by performing a horizontal dissection at the junction between the cecum and the ileum, and between the cecum and proximal region of colon. The weight of the cecum in each group was measured. Dissected colon tissues from PBS control (n=5) and Fn-treated (n=5) GF mice were pooled for each group. Colon tissues were cut into approximately 5 mm pieces and washed three times with ice-cold PBS. The tissue fragments were pre-digested twice for 20 min in Hanks' Balanced Salt Solution (HBSS, Gibco, USA) without Ca2+ and Mg2+ containing 5 mM EDTA, 5% fetal bovine serum (FBS), 1 mM DTT at 37°C using a rotator mixer (Miltenyi Biotec, USA). The fragments were further transferred into a C-tube (Cat# 130-096-334, Miltenyi Biotec, USA) containing HBSS with Ca2+ and Mg2+ (Gibco, USA) and an enzyme mix (enzyme D, enzyme R, enzyme A) prepared from the mouse Lamina Propria Dissociation Kit (Cat# 130-097-410, Miltenyi Biotec, USA). The mixture was churned by gentleMACS Octo Dissociator (Cat# 130-134-029, Miltenyi Biotec, USA) with heaters for 30 min at 37°C. After incubation, ice-cold PB buffer (PBS containing 0.5% bovine serum albumin) was added to the C-tubes and the samples were passed through the 100 μm strainer. The samples were centrifugated at 300 x g for 10 min at 4°C and the pellet was resuspended in ice-cold PB buffer. The samples were filtered through a 70 μm strainer, and rinsed once with ice-cold PB buffer.
Viable cells were subsequently purified using the Dead Cell Removal Kit (Cat# 130-090-101, Miltenyi Biotec). Single-cell suspensions were processed using 10X Chromium Next GEM Single Cell 5’ RNA library v2 and 10X Chromium Next GEM Single Cell VDJ library v2 kit.

treatment_protocol: GF mice were fasted for 2 hours prior to oral gavage. Fn group received an oral administration of 1 × 10⁹ colony-forming units (CFU) in 200 µL of PBS, while the control group received an equivalent volume of PBS alone, three times per week for 5 weeks. The body weight of each mouse was measured three times weekly until the point of sacrifice. At the end of the experiment, the GF mice were sacrificed, and colon tissues were collected from control (n=5) and Fn (n=5) groups.

value: normal colon tissue

value: female

value: POS

tag: age

value: 6 weeks

tag: host strain

tag: bacterial strain


title: primary tumor, discovery cohort, YCC-187, 5' scRNA-seq

description: 10X Genomics 5'

value: wild

value: NEG


title: kidney biopsy N89


title: DH55-Leaf-rep3

city: Saskatoon

first: Isobel

last: Parkin

address: 107 Science Pl

institute: Agriculture and Agri-Food Canada

data_processing:
Raw RNA-seq data were filtered using Trimmomatic (version 0.32) with the following settings (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10; SLIDINGWINDOW:4:15; LEADING:15; TRAILING:15; MINLEN:55) to remove adapter and low-quality sequences. For expression profiling, clean reads were aligned to reference transcriptome using salmon (v1.10.0) and gene expression levels were summarized by tximport (version 1.30.0).
Assembly: Camelina sative (GCF_000633955.1); Brassica napus (DH12075 v3.1); Thlaspi arvense (GCA_911865555)
Supplementary files format and content: TPM_N99.csv, TPM_DH12075.csv, TPM_DH55.csv, and TPM_pennycress.csv, all files contain the TPM values summarized by tximport

organism: Camelina sativa

source_name: Leaves

extract_protocol:
We collected the fully expanded cotyledons and true leaves from the young seedlings to extract their total RNA using the RNeasy plant mini kit (Qiagen) according to the manufacturer’s protocol.
The concentration and integrity of total RNA were examined by BioAnalyzer with RNA 6000 Nano Kit (Agilent). cDNA sequencing libraries were constructed according to the standard TruSeq RNA library preparation guide

value: Leaves

value: plant cell

tag: genotype


title: primary tumor, discovery cohort, YCC-186, 5' scRNA-seq

description: 10X Genomics 5'


title: PDAC-CA-Normal-3

description: Library name: 31_A8_N_S5

value: Pancreas

value: Caucasian

value: Normal


title: PDAC-CA-Normal-2

description: Library name: 30_C12_N_S4


title: kidney biopsy N186

value: NR


title: PDAC-CA-Normal-4

description: Library name: 48_A3_N_S7


title: kidney biopsy N293


title: kidney biopsy N248


title: kidney biopsy N212


title: kidney biopsy N236

value: ABMR


title: primary tumor, discovery cohort, YCC-180, 5' scRNA-seq

description: 10X Genomics 5'

value: colorectal adenocarcinoma

value: Female

value: rectum


title: PDAC-CA-Normal-1

description: Library name: 11_E4_N_S2


title: DH55-Leaf-rep2


title: PDAC-AA-Tumor-9

description: Library name: 49_A11_S2

value: African American

value: Tumor


title: DH55-Leaf-rep1


title: primary tumor, discovery cohort, YCC-175, 5' scRNA-seq

description: 10X Genomics 5'

value: Male

value: cecum

value: MSS


title: DH55-COT-rep3

source_name: Cotyledons

value: Cotyledons


title: PDAC-AA-Tumor-8

description: Library name: 44_C14_S11


title: primary tumor, discovery cohort, YCC-172, 5' scRNA-seq

description: 10X Genomics 5'

value: ascending

value: POS


title: primary tumor, discovery cohort, YCC-166, 5' scRNA-seq

description: 10X Genomics 5'

value: sigmoid


title: DH55-COT-rep2

value: plant cell


title: DH55-COT-rep1


title: PDAC-AA-Tumor-7

description: Library name: 40_G4_T_S9

value: Pancreas


title: primary tumor, discovery cohort, YCC-162, 5' scRNA-seq

description: 10X Genomics 5'

value: wild


title: PDAC-AA-Tumor-6

description: Library name: 39_B7_2_S9


title: SP1, 32, 3

city: Jinan

first: Wenqiang

state: Shandong

address: No. 44 West Wenhua Road

institute: Shandong University

data_processing:
Illumina Casava 2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GCF_000182965.3 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GCF_000182965.3
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Candida albicans

source_name: SC5314 was treated 32μg/ml SP1

extract_protocol:
RNA was extracted using a RiboPure-Yeast kit (Ambion) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Overnight grown C. albicans SC5314 was diluted to 5E6 cells per milliliter using RPMI1640 medium, and treated with 32μg/ml SP1 for 3h at 30℃.   The same volume of dimethyl sulfoxide-treated cells were set as control group.

tag: strain

value: yeast cell


title: primary tumor, discovery cohort, YCC-155, 5' scRNA-seq

description: 10X Genomics 5'

value: trans


title: kidney biopsy N42

value: NR


title: PDAC-AA-Tumor-5

description: Library name: 38_D8_S8


title: SP1, 32, 2

tag: cell type


title: PDAC-AA-Tumor-4

description: Library name: 34_A3_T_S1


title: primary tumor, discovery cohort, YCC-151, 5' scRNA-seq

description: 10X Genomics 5'

value: colorectal adenocarcinoma

value: NEG


title: SP1, 32, 1

tag: treatment


title: PDAC-AA-Tumor-3

description: Library name: 32_C12_S7

value: African American


title: DOHH2_D40_100521

city: Rennes

first: Simon

last: Leonard

address: 2 avenue du Prof Léon Bernard

country: France

institute: Université Rennes

data_processing:
RNA was sequenced on a NovaSeq 6000 (Illumina). Raw sequencing read data was checked and visualized for quality using FastQC (v0.11.5).
Reads were aligned to the reference genome Hg38_R90 using STAR (v2.5.2a).
Read summarization, gene and transcript counts were performed using the featureCounts (v1.4.6).
Analysis of differentially expressed genes (DEGs) was performed using DESeq2 (v1.40.1) R package33. P values were adjusted with FDR Benjamini-Hochberg procedure. Log2 fold changes (Log2FC) were moderated using Lfcshrink method. Genes were ranked according to the Log2FC.
Assembly: Hg38_R90
Supplementary files format and content: tab-delimited text files include counts values from featureCounts

extract_protocol:
Mouse femurs of steady-state (control), PBS-injected (Sham), and DOHH2-injected (grafted) mice were harvested at D19 and D40. BM was flushed and dissociated in PBS containing DNase I (10 U/ml, Pulmozyme, Roche) and Liberase DH (0.025 mg/ml, 5401089001, Roche). Bones were cut into small fragments using scissors in a dissociating media containing 10 U/ml DNase I and Collagenase P (1.2 mg/ml, 11213865001, Roche). Bones and BM were digested at 37°C for 20 min under agitation. PBS supplemented with 5% FBS and 15% sodium citrate was added to neutralize the digestion solution, followed by a centrifugation at 450 g for 5 min. After filtration on 100 µM cell strainer, depletion of red blood cells was carried out with RBC lysis buffer (00-4333-57, Thermo Fisher), stromal cell enrichment was performed using anti-Cd45 (clone 30-F11, 103102, Biolegend) and anti-Ter119 (116202, Biolegend) Abs and using magnetic beads (Dynabeads) according to manufacturer’s instructions. After depletion, cells were stained for sorting with the following antibodies: anti-Cd31 BUV395 (clone MEC13.3, BD Biosciences), anti-Cd51 BV650 (clone RMV-7, BD Biosciences), anti-Sca1 PECy7 (clone D7, Biolegend), anti-Cd200 APC (clone OX-90, Biolegend), anti-Cd45 APC-Cy7 (clone 30F11, BD Biosciences), anti-Ter119 APC-Cy7 (116223, Biolegend), anti-hCD45 APC-Cy7 (clone 2D1, BD Biosciences) and anti-hCD20 FITC (clone 2H7, 555622, BD Biosciences) and with live dead reagent (L34959, Thermo). Cells were then sorted using a FACSAria II (BD Biosciences) as Cd45/Ter119negCd31negCd51posCd200pos stromal cells, Cd45/Ter119negCd31posSca1pos endothelial cells31,32, and hCD20pos human lymphoma B cells. After cell sorting, BM DOHH2 were resuspended in RA1 buffer and tris(2-carboxyethyl)phosphine (TCEP) from Macherey-Nagel and stored at -80°C for less than 3 months. RNA was extracted using NucleoSpin RNA kit (Macherey-Nagel) and RNA integrity number (RIN) was assessed using an RNA 6000 Nano kit (5067-1511, Agilent) on a 2100 Bioanalyzer from Agilent. All RIN were above 7.
RNA libraries were prepared (500ng of total RNA) for sequencing using standard Illumina Protocols

tag: cell line


title: primary tumor, discovery cohort, YCC-150, 5' scRNA-seq

description: 10X Genomics 5'


title: contr, 3

source_name: SC5314 without compound

value: control


title: PDAC-AA-Tumor-2

description: Library name: 14_C5_S12

value: Tumor


title: kidney biopsy N111

tag: mmdx (abmr, mixed, nr[no rejection], pabmr, ptcmr, tcmr)


title: contr, 2


title: kidney biopsy N239


title: C1

value: shNC


title: kidney biopsy N101


title: DOHH2_D19_200421


title: kidney biopsy N47

value: ABMR


title: DOHH2_D0_010421


title: kidney biopsy N105


title: PDAC-AA-Normal-3

description: Library name: 49_A11_N_S8

tag: tissue

value: Normal


title: kidney biopsy N133


title: kidney biopsy N158


title: liver, knockdown, dex rep3

city: Berkeley

first: Jen-Chywan

last: Wang

address: 315 Morgan Hall, UC Berkeley

department: Nutritional Sciences & Toxicology

institute: UC Berkeley

description: Library name: shS1PR2Dex16

data_processing:
Samples sequenced using DNBSEQ platform with sequencing length PE150
Final clean data is QC'd by the software SOPAnuke to remove low quality sequencing reads and adaptor sequencing reads
Final clean data amount is about 20 million read pars per sample
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: excel open XML spreadsheet (.xlsx) file containing fpkm, tpm, read count, norm read count per sample

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA was extracted from liver tissue using Direct-zol RNA Miniprep Kit from Zymo Research
Library prep is performed using Optimal Dual-mode mRNA library prep kit (BGI - Shenzhen, China). 200 ng of RNA is denatured and mRNA is enriched by oligo (dT) magnetic beads. The final library is strand specific with only the first strand of cDNA amplified.

treatment_protocol: Mice were given standard chow diet food and treated with or without 4 mg/kg Dexamethasone via drinking water for two weeks

value: Liver

value: S1PR2 knockdown

value: Dexamethasone


title: DOHH2_D40_120121


title: PDAC-AA-Normal-2

description: Library name: 38_D8_N_S6

tag: race


title: kidney biopsy N85


title: kidney biopsy N147


title: DOHH2__D19_050121


title: DOHH2_D0_171220


title: PDAC-AA-Normal-1

description: Library name: 14_C5_N_S3

tag: condition


title: liver, knockdown, dex rep1

description: Library name: shS1PR2Dex13


title: kidney biopsy N282


title: liver, knockdown, dex rep2

description: Library name: shS1PR2Dex15


title: liver, control dex, rep3

description: Library name: shScrDex11


title: kidney biopsy N16


title: DOHH2_D40_280920


title: kidney biopsy N275

value: TCMR


title: PDAC-AA-Tumor-1

description: Library name: 10_E3_S1

value: Pancreas


title: ProTcell CB3

city: Milan

first: Monah

last: Abou Alezz

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

description:
Library name: MLA008_HTLP_CB3
10x Genomics

data_processing:
Preliminary analysis using the 10X Genomics pipeline relying on cellranger (base calling, alignment, feature count) using default parameters
Filtering, Normalization, Scaling using the R package Seurat
Identification of clusters using the Louvain algorithm privded by the R package Seurat
Identification of differentially expressed genes using the MAST algorithm provided by the R package Saurat
Assembly: GRCh38
Supplementary files format and content: Sparse Cellranger matrix

source_name: Cord blood

growth_protocol: ProTcell were produced as previously described (Moirangthem RD et al., 2021). Plating CD34+ HSPCs for 7 days on a DLL4- and Retronectin-coated culture flask, in presence of SCF, TPO, FLT3L, IL7 and TNFa, in alpha-MEM.

extract_protocol:
Progenitors were harvested after 7 day of culture, washed and frozen in 10% DMSO. After thawing, they were washed and the whole cell product was used for transcriptomic analysis.
Libraries were generated with Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit (v3.1), following manufacturer’s instruction. Quality control was performed by High Sensitivity DNA assay, analyzed by Agilent 2100 Expert software. Sequencing was made using Illumina technology (Illumina NextSeq 500) with libraries embedded in NovaSeq S2 FlowCell.

value: Cord blood

value: T lymphoid progenitor

tag: batch


title: ProTcell mPB3

description:
Library name: MLA007_HTLP_Largescale02
10x Genomics

source_name: Mobilized peripheral blood

value: Mobilized peripheral blood


title: contr, 1

value: yeast cell


title: liver, control dex, rep2

description: Library name: shScrDex10


title: DOHH2_D19_051020


title: ProTcell CB1

description:
Library name: MLA006_HTLP_CB1
10x Genomics


title: liver, control dex, rep1

description: Library name: shScrDex9


title: kidney biopsy N110


title: kidney biopsy N171


title: kidney biopsy N122


title: ProTcell mPB2

description:
Library name: MLA005_HTLP_testLTCGFullcoating
10x Genomics


title: kidney biopsy N288


title: liver, knockdown, no dex rep3

description: Library name: sS1PR2NoDex7

value: Vehicle control


title: Tregs, CEACAM1 knockout, biol repl 2

city: Miami

first: Ying

last: Ding

address: 1600 NW 14th st

department: Microbiology and Immunology

institute: University of Miami

data_processing:
Raw data of FASTQ format were firstly processed through fastq. In this step, clean data were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
Clean sequence reads were mapped to the Homo sapiens (human) genome GRCh38 using the Spliced Transcripts Alignment to a Reference (STAR) software.
Differential expression analysis was performed using the edgeR R package.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for all 4 samples
Supplementary files format and content: tab-delimited text file includes edgeR results comparing the fold change and p value between CEACAM1KO and control cells

source_name: blood

growth_protocol: FACS-purified human regulatory T cells (5 x 105/well/ml) were cultured in 24 well plates with anti-CD3/CD28 dynabeads and human IL-2 (500 U/ml) in OpTmizer CTSTM T cell expansion medium (designated as SFM) for 3 days and  electorporated with guide RNAs and Cas9. Cells were then seeded at 5 x 105/well/ml in SFM with IL-2 (500 U/ml) in 24 well plates and were sub-cultured with IL-2 (500 U/ml) in SFM for 7 days.

extract_protocol:
RNA was isolated using the Rneasy Micro Kit (Qiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

value: blood

value: regulatory T cells

value: CEACAM1 knockout

value: culture with IL-2 for 7 days


title: ProTcell CB2

description:
Library name: MLA004_HTLP_CB2
10x Genomics


title: liver, knockdown, no dex rep2

description: Library name: sS1PR2NoDex6


title: Tregs, CEACAM1 knockout, biol repl 1


title: KO IMQ 2

city: Taipei City

first: Yeh Fong

last: Tan

state: Taipei

address: No. 128, Section 2, Academia Rd, Nangang District

department: Institute of BioMedical Sciences

country: Taiwan

institute: Academia Sinica

data_processing:
Combination of Ubuntu 22.04.1 LTS, Trimmomatic, Hisat2, SAMtools, StringTie and prepDE python package.
Separate fastq files are merged using Terminal of Ubuntu.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (MinLen: 36, Phred33).
Trimmed sequence reads were mapped to GrCM38.dna.toplevel.fa.gz using Hisat2.
Aligned sequence were converted from SAM to BAM using SAMtools. Read count extraction was performed using StringTie. Files are then converted into CSV format using prepDE.py3 package.
Assembly: GrCM38.dna.toplevel.fa.gz
Supplementary files format and content: tab delimited text file. Sum of raw counts for each sample.

source_name: Ear

extract_protocol:
RNA from isolated Langerhans cells was extracted using R2060 DirectZol RNA MicroPrep kit (Zymo Research). 10 to 70 ng of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq Kit v2- Pico Input Mammalian according to manufacturer's protocols.

treatment_protocol: We excised mice ears, digested the ears with dispase, collagenase IV and Dnase I, and stained the cells for Langerhans cells (CD207+ and MHC II+). We then performed sorting to isolate Langerhans cells and the cells were then treated with Imiquimod and a-CD40L for 24 hours before collecting the cells for RNA extraction.

value: Ear

value: Langerhans cell

value: Imiquimod treated


title: liver, knockdown, no dex rep1

description: Library name: sS1PR2NoDex5

value: Liver


title: ProTcell mPB1

description:
Library name: MLA003_HTLP_SmallScale
10x Genomics


title: Tregs, scramble control, biol repl 2

value: WT


title: KO IMQ 1


title: liver, control no dex, rep 3

description: Library name: shScrNoDex4

value: control


title: kidney biopsy N143

value: ABMR


title: Tregs, scramble control, biol repl 1


title: liver, control no dex, rep 2

description: Library name: shScrNoDex3


title: DOHH2_D0_170920


title: shCopa-3

city: Shanghai

first: Li

last: Zhang

address: Dongchuan road 800

institute: Shanghai Cancer Institute

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and trimming low qulity base with Trimmomatic
paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
Htseq-count was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCm39
Supplementary files format and content: The processed count data is provided as a tab-delimited text file (.txt) containing gene IDs as rows, sample names as columns, and the corresponding gene expression values. The counts were generated using featureCounts and normalized using DESeq2

source_name: AY-mICC

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

extract_protocol:
Total RNA was extracted by TRIzol and subjected to RNA-seq analysis. 1ug of total RNA was used for the construction of sequencing libraries.
Total RNA samples in each experiment were submitted to Shanghai Majorbio Corporation (Shanghai, China) for sequencing. Standard mRNA library preparation kit was used for library preparation. Paired-end sequencing was performed on Illumina HiSeq 2500.

value: AY-mICC

value: Copa knockdown


title: Transcriptional profiling of LPS-stimulated THP-1 macrophages with control miRNA transfection, duplication 06

city: Beijing

first: Wenjie

last: Zheng

address: No1 ShuaiFuYuan，Dong Cheng District ，Beijing, Beijing, CN

institute: Peking Union Medical College Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: hg38
Supplementary files format and content: count_matrix.csv concludes combined csv file of matrix table with raw gene counts for every gene and every sample

source_name: cell line

extract_protocol:
RNA was harvested using Trizol reagent.A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To gain insight into the mechanism of immunoregulatory effects of exosomal miR-122-5p, we transfected 30nM miR-122-5p mimics or control miRNA mimics (n=6 for each group) into THP-1 macrophages using RNAimax. After 24-hour transfection, THP-1 macrophages were rested and then stimulated with LPS for 4 hours

value: cell line

value: THP-1 macrophage

value: control miRNA mimic transfection and LPS stimulation


title: liver, control no dex, rep 1

description: Library name: shScrNoDex2

value: Vehicle control


title: Transcriptional profiling of LPS-stimulated THP-1 macrophages with control miRNA transfection, duplication 05


title: shCopa-2


title: NAV

description: BD Rhapsody

data_processing:
Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification workflow. In brief, second strand cDNA was synthesized, followed by ligation of the WTA adaptor for universal amplification. Eighteen cycles of PCR were used to amplify the adaptor-ligated cDNA products. Sequencing libraries were prepared using random priming PCR of the whole-transcriptome amplification products to enrich the 3′ end of the transcripts linked with the cell label and UMI. The final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific) and the size distribution of the libraries were determined using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent).
All libraries were sequenced by DNBSEQ-T7 Sequencer (MGI, Shenzhen, China) on a 150 bp paired-end run.scRNA-seq data analysis was performed by NovelBio Co.,Ltd. with NovelBrain Cloud Analysis Platform. We applied fastp with default parameter filtering the adaptor sequence and removed the low-quality reads to achieve the clean data. To quantify the gene expression of the single-cell data, we used STARsolo (version 2.7.10a) along with mouse genome mm10 (ensemble annotation version 100).
Multiple samples were aggregated by cellranger aggr.
Assembly: mm10_Ensembl100
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: iCCA

extract_protocol:
The C57BL/6 mice were hydrodynamic co-injected transposon-based vectors expressing Myr-AKT  and YAPS127A. 7 days later,mice were treated with or without NAV2729(NAV,30mg/kg) every other day for another 7days.aline-perfused mouse livers were sheared into small pieces with scissors and digested in a digest buffer (RPMI 1640 supplemented with 5% FBS, 0.05 mg/mL collagenase type I, 0.05 mg/mL collagenase type IV, 0.025 mg/mL hyaluronidase, and 0.01 mg/mL DNase I) at 37 °C for 30 min. After filtrating through 100 μm strainer, red blood cells (RBCs) were lysed with RBC lysis buffer (420301, BioLegend, San Diego, USA) for 5 min. The single-cell suspensions were blocked with purified rat anti-mouse CD16/CD32 (553140, BD Biosciences, San Jose, USA) for 30 min and incubated with the corresponding antibodies for 30 min at 4 °C.  The immune cells were isolated from 3 paired Myr-AKT/YAPS127A-driven iCCA by Fluorescence-activated cell sorting (FACS) according to expression of CD45 and sujected to scRNAseq.
RNA libraries were generated by BD Rhapsody™ Express System  using standard Illumina protocols

value: iCCA

value: CD45+ immune cells

value: NAV-treatment


title: shCopa-1


title: Transcriptional profiling of LPS-stimulated THP-1 macrophages with control miRNA transfection, duplication 04


title: kidney biopsy N146


title: shCon-3


title: MOCK

description: BD Rhapsody

value: MOCK-treatment


title: Transcriptional profiling of LPS-stimulated THP-1 macrophages with control miRNA transfection, duplication 03


title: kidney biopsy N135

value: NR


title: PBS_2

type: protein

city: Dallas

first: Chengsong

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

description:
Slide2_532.gpr/Slide2_635.gpr
Negative control

hyb_protocol: Mouse serum samples were first treated with DNAse I to remove free-DNA and then applied onto antoantigen arrays with 1:50 dilution. The autoantibodies binding to the antigens on the array were detected with cy3-labeled anti-Mouse IgG  and the array slides were scanned with Genepix 4400A scanner with laser wavelengths 532nm for cy3 and 635nm for cy5 to generate Tiff images.  Genepix Pro 7.0 software is used to analyze the image and generate the Genepix report (GPR) files (Molecular Devices, Sunnyvale, California, USA). The net fluorescent intensity (NFI) of each antigen was generated by subtracting the local background and negative control (Phosphate buffered saline or simplified as PBS) signal.

data_processing: NFI were normalized by robust linear model using build-in Ig control with various dilutions

molecule: protein

organism: blank sample

extract_protocol: Serum samples from all mice were collected as described above. Sera from all strains were stored at -20ºC.

treatment_protocol: 8 positive controls (anti-IgG and IgG control) were also imprinted on the arrays as positive controls.

tag: slide

tag: block


title: kidney biopsy N182

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

value: pABMR


title: DKO_5M

description:
Slide2_532.gpr/Slide2_635.gpr
The sample will be incubated with autoantigen array and the autoantibodies binding to the antigens on the array will be detected with laser wavelengths 532nm (cy3 labeled anti-IgG) and 635nm (cy5 labeled anti-IgM)

scan_protocol: Mouse serum samples were first treated with DNAse I to remove free-DNA and then applied onto antoantigen arrays with 1:50 dilution. The autoantibodies binding to the antigens on the array were detected with cy3-labeled anti-Mouse IgG  and the array slides were scanned with Genepix 4400A scanner with laser wavelengths 532nm for cy3 and 635nm for cy5 to generate Tiff images.  Genepix Pro 7.0 software is used to analyze the image and generate the Genepix report (GPR) files (Molecular Devices, Sunnyvale, California, USA). The net fluorescent intensity (NFI) of each antigen was generated by subtracting the local background and negative control (Phosphate buffered saline or simplified as PBS) signal.

value: Tlr-DKO

tag: gender

value: Male


title: kidney biopsy N65


title: shCon-2


title: Transcriptional profiling of LPS-stimulated THP-1 macrophages with control miRNA transfection, duplication 02


title: shCon-1


title: DKO_4M

label_protocol: Mouse serum samples were first treated with DNAse I to remove free-DNA and then applied onto antoantigen arrays with 1:50 dilution. The autoantibodies binding to the antigens on the array were detected with cy3-labeled anti-Mouse IgG  and the array slides were scanned with Genepix 4400A scanner with laser wavelengths 532nm for cy3 and 635nm for cy5 to generate Tiff images.  Genepix Pro 7.0 software is used to analyze the image and generate the Genepix report (GPR) files (Molecular Devices, Sunnyvale, California, USA). The net fluorescent intensity (NFI) of each antigen was generated by subtracting the local background and negative control (Phosphate buffered saline or simplified as PBS) signal.


title: kidney biopsy N295


title: kidney biopsy N193


title: kidney biopsy N183

value: TCMR


title: kidney biopsy N71


title: kidney biopsy N286


title: Transcriptional profiling of LPS-stimulated THP-1 macrophages with miR-122-5p transfection, duplication 06

value: miR-122-5p mimic transfection and LPS stimulation


title: DKO_3M


title: Transcriptional profiling of LPS-stimulated THP-1 macrophages with miR-122-5p transfection, duplication 05


title: kidney biopsy N1

value: ABMR


title: DKO_5F

value: Female


title: Transcriptional profiling of LPS-stimulated THP-1 macrophages with miR-122-5p transfection, duplication 04


title: DKO_4F


title: Transcriptional profiling of LPS-stimulated THP-1 macrophages with control miRNA transfection, duplication 01


title: Transcriptional profiling of LPS-stimulated THP-1 macrophages with miR-122-5p transfection, duplication 03


title: SW480 HD, high-dose cell line, 80 uM oxaliplatin, 10 cycles, replicate 2

city: Singapore

first: Mohua

last: Das

country: Singapore

institute: Genome Institute of Singapore

description: Library name: SHS014

data_processing:
RNA sequencing was done at the Next Generation Sequencing Platform in the Genome Institute of Singapore, A*STAR. All pre and post processing steps, including bioinformatics analyses were performed by the sequencing platform. A list of read counts was provided as the final output of the sequencing. Differentially expressed genes were obtained using the DESeq2 package. Subsequently, GSEA using hallmark gene sets from the Molecular Signatures Database (MSigDB) was done using the fgsea package. All packages and pipelines were processed using R on RStudio
Assembly: hg38
Supplementary files format and content: One excel sheet (.xlsx) containing counts for all samples is provided

source_name: colorectal carcinoma

growth_protocol: HCT116 and SW480 cells are cultured in McCoy supplemented with 10% FBS, 1% Pen-Stre and 1% Sodium Pyruvate.

extract_protocol:
Cells were washed twice with ice-cold PBS before being scrapped and transferred to eppendorf tube. RNA was extracted using Qiagen RNA extraction kit. RNA was sent to GIS sequencing core.
RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN) following manufacturer’s protocol. Yield and integrity of RNA were determined using the Agilent 2100 Bioanalyzer (Agilent Technologies) following manufacturer’s protocol. Sample preparation for the Bioanalyzer was done using the Agilent RNA 6000 Nano Kit (Agilent Technologies, USA) following manufacturer’s protocol.

treatment_protocol: HCT116 and SW480 cells were treated with 0.5 uM (low dose; LD), 5 uM (mid dose; MD) or 80 uM (high dose; HD) for 72 hours before changing to drug free media. Cells were then subcultured and treated again with the same dose for 72 hours. Cells were treated for 10 cycles. Cells were subsequently cultured in drug free media and used for downstream experiments.

value: colorectal carcinoma

value: epithelial


title: Transcriptional profiling of LPS-stimulated THP-1 macrophages with miR-122-5p transfection, duplication 02

value: cell line

value: THP-1 macrophage


title: TLR9.KO_5M

value: Tlr9 KO


title: Transcriptional profiling of LPS-stimulated THP-1 macrophages with miR-122-5p transfection, duplication 01


title: TLR9.KO_4M


title: Input-2

data_processing:
The fragment distribution and concentration of RNAs（after immunoprecipitation） were detected using an Agilent 2100 bioanalyzer (Agilent) and simpliNano spectrophotometer (GE Healthcare). Then, immunoprecipitated RNA or Input was used for library construction with NEB Next® Ultra™ RNA Library Prep Kit (New England Biolabs). Library quality was assessed on the Agilent Bioanalyzer 2100 system. The libraries were sequenced on an Illumina Novaseq platform with a paired-end read length of 150 bp according to the standard protocols. The sequencing was carried out with XX independent biological replicates.
Raw data (raw reads) of fastq format were firstly processed using fastp software[1]. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low- quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem (v 0.7.12).
After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak calling software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
Assembly: ensembl_homo_sapiens_grch38_106
Supplementary files format and content: Text Document  include Raw read counts for each Sample

extract_protocol:
Total RNA was obtained from IP used HA antibody according to the instructions of RIP Immunoprecipitation Kit, then ribominus rRNA were depleted
RNA libraries were prepared for sequencing using standard Illumina protocols

value: empty vector


title: SW480 MD, mid-dose cell line, 5 uM oxaliplatin, 10 cycles, replicate 3

description: Library name: SHS019


title: SW480 HD, high-dose cell line, 80 uM oxaliplatin, 10 cycles, replicate 1

description: Library name: SHS007


title: TLR9.KO_5F


title: Input-1


title: SW480 MD, mid-dose cell line, 5 uM oxaliplatin, 10 cycles, replicate 1

description: Library name: SHS005


title: SW480 HD, high-dose cell line, 80 uM oxaliplatin, 10 cycles, replicate 3

description: Library name: SHS021


title: kidney biopsy N20

source_name: kidney biopsy


title: kidney biopsy N181


title: kidney biopsy N14


title: Pooled control pancreas RNA

city: Tokyo

first: Xuguang

last: Li

address: 1-1-1 Yayoi, Bunkyo-ku

country: Japan

institute: Tokyo University

description: RNA pooled from pancreas of 10-week-old male control offspring

hyb_protocol: Hybridisation was performed at 45 °C for 16 hours using Affymetrix protocol. Chips were then washed and stained automatically.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed and normalized using R. Rank products were used for intergroup comparison. Significance was set at -log(P) > 1.5 or < 0.67. Pathway analysis was done in IPA.

source_name: pancreas

label_protocol: Biotin-labeled cRNA was prepared using the GeneChip 3′ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Female C57BL/6J mice were fed control or methionine-deficient diet during pregnancy. Male offspring were weaned at 3 weeks and provided control diet until 10 weeks.

extract_protocol: Total RNA was extracted from pancreas using Trizol reagent (Invitrogen) following manufacturer’s protocol.

treatment_protocol: Control and MD groups were defined by the maternal diet during pregnancy. Offspring were not directly treated after birth.

tag: sample tgroup

value: control group

value: pancreas


title: DKO_3F


title: TLR9.KO_4F


title: IP-2

value: HA tagged PLEK2


title: SW480 LD, low-dose cell line, 0.5 uM oxaliplatin, 10 cycles, replicate 3

description: Library name: SHS017


title: TLR9.KO_3F


title: kidney biopsy N9

value: NR


title: IP-1


title: SW480 LD, low-dose cell line, 0.5 uM oxaliplatin, 10 cycles, replicate 2

description: Library name: SHS010


title: NOD.B10_5M


title: SW480 MD, mid-dose cell line, 5 uM oxaliplatin, 10 cycles, replicate 2

description: Library name: SHS012


title: kidney biopsy N289


title: kidney biopsy N292

value: Mixed


title: kidney biopsy N36


title: kidney biopsy N84


title: NOD.B10_4M


title: SW480 LD, low-dose cell line, 0.5 uM oxaliplatin, 10 cycles, replicate 1

description: Library name: SHS003


title: input HUVEC

city: London

first: Hannah

middle: Louise Hoskins

last: Green

address: 125 Coldharbour Lane

country: United Kingdom

institute: King's College London

library_source: genomic

data_processing:
base calling were performed using Off- Line Basecaller software (OLB V1.8).
Solexa CHASTITY quality filter
the clean reads were aligned to human genome (UCSC hg19) using Hisat2 software
Aligned reads were used for peak calling, long ncRNA, mRNA and small ncRNA associated hMeDIP enriched regions (peaks) with statistically significant were identified for each sample, using a q-value threshold of 10−4 by MACS2 software.
Long ncRNA, mRNA and small ncRNA associated hMeDIP enriched regions (peaks) were annotated by the nearest gene using the newest UCSC RefSeq database.
Long ncRNA, mRNA and small ncRNA associated differentially hydroxymethylated regions (DhMRs) within promoter between two samples/groups with statistically significant were identified by diffReps software (Cut-off: log2FC≥0.585, p-value≤0.001).
Assembly: hg19
Supplementary files format and content: Peak files in .wig.gz format
Supplementary files format and content: Differentially hydroxymethylated regions and their normalised tag counts in .xlsx format
Library strategy: hMeDIP-seq

molecule: genomic DNA

source_name: HUVEC

extract_protocol:
Monarch Genomic DNA Purification Kit
1) End repair of DNA samples; 2) A single ‘A’ base was added to the 3’ ends; 3) Ligation of Illumina’s genomic adapters to DNA fragments; 4) hMeDIP to enrich hydroxymethylated DNA by anti-5-hydroxymethylcytosine antibody; 5) PCR amplification to enrich precipitated fragments; 6) Size selection of ∼300-900bp DNA fragments using AMPure XP beads.

value: HUVEC

tag: ip antibody

value: anti-5-hydroxymethylcytosine antibody


title: IFN

description:
IFN_Count
Enhancer associated Intergenic Differentially Hydroxymethylated Regions.xlsx
LncRNA-associated Differentially Hydroxymethylated Regions(Promoter).xlsx
mRNA-associated Differentially Hydroxymethylated Regions(Promoter).xlsx
Small_ncRNA-associated Differentially Hydroxymethylated Regions(Promoter).xlsx
SuperEnhancer associated Intergenic Differentially Hydroxymethylated Regions.xlsx

value: 10ng/ml IFNg

tag: time


title: kidney biopsy N235

city: Edmonton

first: Jessica

institute: University of Alberta


title: SW480 PAR, control cell line, 0 uM oxaliplatin, 10 cycles, replicate 3

description: Library name: SHS015


title: Pooled methionine-deficient pancreas RNA

description: RNA pooled from pancreas of 10-week-old male methionine-deficient offspring

value: methionine-deficient group


title: NOD.B10_4F


title: Mann

description:
Mann_Count
Enhancer associated Intergenic Differentially Hydroxymethylated Regions.xlsx
LncRNA-associated Differentially Hydroxymethylated Regions(Promoter).xlsx
mRNA-associated Differentially Hydroxymethylated Regions(Promoter).xlsx
Small_ncRNA-associated Differentially Hydroxymethylated Regions(Promoter).xlsx
SuperEnhancer associated Intergenic Differentially Hydroxymethylated Regions.xlsx

value: 5mM D-glucose + 20mM mannitol

value: 2 weeks


title: SW480 PAR, control cell line, 0 uM oxaliplatin, 10 cycles, replicate 2

description: Library name: SHS008

value: colorectal carcinoma


title: kidney biopsy N278


title: Glu

description:
Glu_Count
Enhancer associated Intergenic Differentially Hydroxymethylated Regions.xlsx
LncRNA-associated Differentially Hydroxymethylated Regions(Promoter).xlsx
mRNA-associated Differentially Hydroxymethylated Regions(Promoter).xlsx
Small_ncRNA-associated Differentially Hydroxymethylated Regions(Promoter).xlsx
SuperEnhancer associated Intergenic Differentially Hydroxymethylated Regions.xlsx

value: 25mM D-glucose


title: kidney biopsy N148


title: PBS_1

description:
Slide1_532.gpr/Slide1_635.gpr
Negative control


title: kidney biopsy N41


title: HCT116 HD, high-dose cell line, 80 uM oxaliplatin, 10 cycles, replicate 3

description: Library name: RHH6814

value: epithelial


title: ctl

description:
ctl_Count
Enhancer associated Intergenic Differentially Hydroxymethylated Regions.xlsx
LncRNA-associated Differentially Hydroxymethylated Regions(Promoter).xlsx
mRNA-associated Differentially Hydroxymethylated Regions(Promoter).xlsx
Small_ncRNA-associated Differentially Hydroxymethylated Regions(Promoter).xlsx
SuperEnhancer associated Intergenic Differentially Hydroxymethylated Regions.xlsx


title: HCT116 HD, high-dose cell line, 80 uM oxaliplatin, 10 cycles, replicate 2

description: Library name: RHH6813


title: Tregs, PRDM1 knockout, biol rep 4

description:
PRDM1ko_vs_ctrl_counts.txt
PRDM1ko_vs_ctrl_PW_results.txt

data_processing:
50 bp reads aligned to Hg19 with tophat2, assembled with cufflinks and gene-level counts compiled with htseq-count.
Genes failing to reach an empirically defined count threshold were purged using htsfilter. 10,000-12,000 were typically recovered post filtering.
Filtered genes were normalized and differentially expressed genes (DEG) called by quasi- likelihood F testing using edgeR.
Assembly: Hg19
Supplementary files format and content: tab-delimited text file includes raw counts for all 8 samples
Supplementary files format and content: tab-delimited text file includes edgeR results comparing the fold change and p value between PRDM1KO and control cells

growth_protocol: FACS-purified human regulatory T cells (5 x 10^5/well/ml) were cultured in 24 well plates with anti-CD3/CD28 dynabeads and human IL-2 (500 U/ml) in OpTmizer CTSTM T cell expansion medium (designated as SFM) for 3 days and  electorporated with guide RNAs and Cas9. Cells were then seeded at 5 x 10^5/well/ml in SFM with IL-2 (500 U/ml) in 24 well plates and were sub-cultured with IL-2 (500 U/ml) in SFM for 7 days.

extract_protocol:
RNA was isolated using the Rneasy Micro Kit (Qiagen)
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep kit for Illumina (NEB) following manufacturer's protocols.

treatment_protocol: 7 days after electroporation, anti-CD3/CD28 dynabeads were removed and cells were washed 3 times with PBS. Cells were rested in SFM overnight and stimulated with anti-CD3/CD28 dynabeads and IL-2 for 16 hr.

value: blood

value: regulatory T cells

value: PRDM1 knockout

value: TCR and IL2R stimulation


title: DKO_1M

description:
Slide1_532.gpr/Slide1_635.gpr
The sample will be incubated with autoantigen array and the autoantibodies binding to the antigens on the array will be detected with laser wavelengths 532nm (cy3 labeled anti-IgG) and 635nm (cy5 labeled anti-IgM)

value: Tlr-DKO

value: Male


title: DKO_2F

value: Female


title: kidney biopsy N57

value: NR


title: HCT116 MD, mid-dose cell line, 5 uM oxaliplatin, 10 cycles, replicate 3

description: Library name: RHH6808


title: Tregs, PRDM1 knockout, biol rep 2


title: NOD.B10_5F


title: SW480 PAR, control cell line, 0 uM oxaliplatin, 10 cycles, replicate 1

description: Library name: SHS001


title: HCT116 MD, mid-dose cell line, 5 uM oxaliplatin, 10 cycles, replicate 2

description: Library name: RHH6807


title: Tregs, PRDM1 knockout, biol rep 1


title: kidney biopsy N60


title: kidney biopsy N244


title: DKO_1F


title: kidney biopsy N280


title: HCT116 MD, mid-dose cell line, 5 uM oxaliplatin, 10 cycles, replicate 1

description: Library name: RHH6806


title: DKO_2M


title: kidney biopsy N240


title: kidney biopsy N117


title: kidney biopsy N40

value: ABMR


title: TLR9.KO_2M

value: Tlr9 KO


title: Tregs, PRDM1 knockout, biol rep 3


title: Tregs, scramble control, biol rep 3

value: WT


title: HCT116 HD, high-dose cell line, 80 uM oxaliplatin, 10 cycles, replicate 1

description: Library name: RHH6812


title: kidney biopsy N157


title: kidney biopsy N168


title: Tregs, scramble control, biol rep 2


title: TLR9.KO_2F


title: TLR9.KO_3M


title: Tregs, scramble control, biol rep 1


title: HCT116 LD, low-dose cell line, 0.5 uM oxaliplatin, 10 cycles, replicate 2

description: Library name: RHH6801


title: HCT116 LD, low-dose cell line, 0.5 uM oxaliplatin, 10 cycles, replicate 1

description: Library name: RHH6800


title: TLR9.KO_1M


title: TLR9.KO_1F


title: Tregs, scramble control, biol rep 4


title: HCT116 PAR, control cell line, 0 uM oxaliplatin, 10 cycles, replicate 3

description: Library name: RHH6796


title: NOD.B10_3M


title: HCT116 LD, low-dose cell line, 0.5 uM oxaliplatin, 10 cycles, replicate 3

description: Library name: RHH6802


title: NOD.B10_2M


title: HS578T HSF2oe TGFb rep2

city: Turku

first: Lea

last: Sistonen

address: Tykistökatu 6 A

department: Cell Biology

country: Finland

institute: Åbo Akademi University

data_processing:
Basecalling and adapter trimming was performed by bcl2fastq conversion software (NovaSeq 6000)
Reads were mapped to the human genome (GRCh38) using STAR v2.7.9a with the default parameters
Read pairs aligned to each genomic feature in the GENCODE annotation v38 (primary assembly) were counted with featureCounts from subread v2.0.1 with the parameter -isPairedEnd
The raw read counts were processed with edgeR v3.34.1 to filter out lowly expressed genes with filterByExpr() and were normalized using the TMM method.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file containing the raw read counts per feature for each sample
Supplementary files format and content: Tab-delimited text file containing the normalized logCPM values for each sample

source_name: breast cancer-derived epithelial cells

growth_protocol: HS578T cells were grown in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 100 µg/mL penicillin-streptomycin and 10 µg/mL insulin, and maintained at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol:
After treatments, the cells were collected and total RNA was purified with the AllPrep DNA/RNA/miRNA Universal Kit (80224, QIAGEN) according to manufacturer’s instructions.
RNA libraries were prepared according to the Illumina stranded mRNA preparation guide (1000000124518).

treatment_protocol: HS578T cells were transfected with 25 µg of the corresponding DNA (GFP or HSF2oe). 24 h after transfections, cell were treated with assay medium only (DMEM with 2%) or with assay medium supplemented with 10 ng/ml TGF-β1 (240-B-002, R&D Systems) for 24 h.

tag: transfection

tag: disease

value: Carcinoma


title: HS578T HSF2oe TGFb rep1


title: HCT116 PAR, control cell line, 0 uM oxaliplatin, 10 cycles, replicate 2

description: Library name: RHH6795


title: HS578T HSF2oe Control rep2


title: NOD.B10_1M


title: kidney biopsy N163

last: Chang

address: 250 Heritage Medical Research Centre

value: Mixed


title: HCT116 PAR, control cell line, 0 uM oxaliplatin, 10 cycles, replicate 1

description: Library name: RHH6794


title: NOD.B10_3F


title: HS578T HSF2oe Control rep1


title: HCT116 HD, high-dose cell line, 80 uM oxaliplatin, 10 cycles

description: Library name: Project_MUX9350

data_processing:
In-house generated single-cell datasets from HCT116 PAR/LD/MD/HD cell were aligned to the human reference genome (GrCh38). Cellranger count was used to generate raw barcode matrices from the fastq files through the Cellranger 6.0.1 pipeline. The raw feature-barcode matrix was loaded into Seurat (v4.3.0). Cells of low quality (fewer than 200 genes per cell) and cells expressing rare genes (those expressed in fewer than 30 cells) were excluded from the analysis. Cells with over 20% mitochondrial gene content were also removed. Potential cell doublets were filtered out by first setting an upper limit of 6000 genes detected per cell and then consequently by using the DoubletFinder package. The data was normalized with ScaleData() using a scaling factor of 10000, and gene expression was scaled to unit variance and a mean of 0. Principal component analysis was performed using the RunPCA function for dimensionality reduction, with an elbow plot determining the inflection point where variance changes became insignificant. The neighborhood graph for clustering was calculated using FindNeighbors, and cell clustering was done with the FindClusters function using louvain clustering. UMAP of the clusters were made using RunUMAP() function and split UMAPs were used to compare the differences in clusters across different conditions. Proportions of cell clusters across different conditions were visualized using ggplot2. Signature scores were calculated using the UCell package. Lastly, the expression of RESIST-M signatures was verified across the different LD/MD/HD conditions using DotPlot() or VlnPlt() function.
Assembly: hg38
Supplementary files format and content: Two rds objects are provided- a) Unannotated HCT116.rds, nd b) Annotated hct116_md.rds

source_name: Colorectal

extract_protocol:
Cells were processed according to protocol using the 10x universal 3' gene expression kit.
According to 10x 3' gene expression kit protocol.

value: Colorectal

value: Cancer cell ATCC

value: Epithelial adherent

value: 80 uM Oxaliplatin


title: HS578T Mock TGFb rep2

value: GFP

value: DMSO


title: kidney biopsy N142


title: NOD.B10_2F


title: HCT116 MD, mid-dose cell line, 5 uM oxaliplatin, 10 cycles

description: Library name: Project_MUX9349

value: 5 uM Oxaliplatin


title: kidney biopsy N266


title: kidney biopsy N59


title: HCT116 LD, low-dose cell line, 0.5 uM oxaliplatin, 10 cycles

description: Library name: Project_MUX9348

value: 0.5 uM Oxaliplatin


title: kidney biopsy N285


title: NOD.B10_1F


title: HS578T Mock Control rep2


title: kidney biopsy N113


title: kidney biopsy N141


title: HS578T Mock TGFb rep1


title: HCT116 PAR, control cell line, 0 uM oxaliplatin, 10 cycles

description: Library name: Project_MUX9347

value: No treatment


title: kidney biopsy N214


title: Weight-cycling, B2

city: Nagoya

first: Eri

last: Wada

state: Aichi

address: Furo-cho, Chikusa-ku

department: Research Institute of Environmental Medicine

institute: Nagoya University

description: Library name: Sample4

data_processing:
Low-quality reads and adapter sequences were trimmed using fastp software (doi: 10.1093/bioinformatics/bty560). The reads were mapped to the mm10 reference genome using HISAT2 (doi: 10.1038/s41587-019-0201-4) followed by transcript assembly and quantification using StringTie (doi:10.1038/nbt.3122).
Assembly: mm10
Supplementary files format and content: tab-delimited txt file includes CPM values for each sample
Supplementary files format and content: tab-delimited txt file includes TPM values for each sample

source_name: Epididymal adipose tissue

extract_protocol:
Total RNA was purified using RNeasy MiniElute Cleanup Kit (QIAGEN, Hilden, Germany).
RNA-seq libraries were constructed by NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB) and MGIEasy RNA Directional Library Prep Set (MGI), according to the manufacturer’s instructions.

treatment_protocol: We fed high-fat fed (HFD) or standard diet (SD) to eight-week-old male C57BL/6J mice to establish a Weight Cycling (WC) protocol. The WC group was fed HFD for 8 weeks, followed by SD for 2 weeks for weight loss, then HFD again for an additional 6 weeks.The control group was fed HFD continuously for 14 weeks from 10 weeks of age.

value: Epididymal adipose tissue

tag: genotype

value: Weight-cycling


title: HS578T Mock Control rep1


title: HeLa cells, EMC2 knockdown Tg_24h, rep1

last: Zhou

address: ChengFu Road

department: College of Chemistry and Molecular Engineering

institute: Peking University

description:
Library name: 24h_EMC2_1
Column name in EMC2_raw_counts_1.csv: 24h-EMC2

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).
Assembly: Reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL.
Supplementary files format and content: two fpkm_anno files including all raw counts and fpkm values for each sample in two biological replicates

source_name: HeLa

growth_protocol: HeLa cells were cultured in DMEM (Gibco) with 10% FBS (v/v., Gibco), 100 IU/mL penicillin and 100 mg/mL streptomycin (Thermo Fisher) at 37℃ under 5% CO2 condition in cell incubators.

extract_protocol:
Each group of cells were lysed in 1000 μL Vezol Reagent (Vazyme, R411-02) by pipetting or vortexing. To the lysate, 200 μL of CHCl3 was added, mixed thoroughly, and the mixture was centrifuged at 12,000 rpm, 4 °C for 15 minutes to transfer the upper clear aqueous phase to a new RNase-free tube. Total RNA was extracted using RNA clean & concentrator kits (Zymo, R1015).
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

treatment_protocol: Wildtype HeLa cells and EMC2 knockdown HeLa cells were treated with 500 nM thapsigargin (TargetMol, TQ0302) for both 0 hours and 24 hours

value: HeLa

value: EMC2 knockdown

tag: cell type

value: cervical cancer cell line

value: thapsigargin-treated

value: 24 hours


title: HeLa cells, EMC2 knockdown Tg_24h, rep2

description:
Library name: 24h_EMC2_2
Column name in EMC2_raw_counts_2.csv: 24h-EMC2

tag: treatment


title: kidney biopsy N144

value: NR


title: Weight-cycling, B1

description: Library name: Sample3

value: WT


title: KO MET/CAT_3

city: Maywood

first: wei

last: Qiu

state: IL

department: Surgery

institute: Loyola University Chicago

data_processing:
The original reads were mapped tomouse genome (GRCm38) using HISAT2 (version 2.0.4), and then the number of reads unambiguously mapped to each gene was counted using HTSeq (version 0.11.2).
Assembly: GRCm38
Supplementary files format and content: Normalized counts are included in a csv file named dat.norm.

extract_protocol:
Total RNA were extracted by the RNA isolation kit.
The library was prepared by Novogene.

treatment_protocol: 50 µg of total plasmids, encoding the sleeping beauty transposase and transposons with oncogenes MET and CAT (22.5 µg pT3-EF1a-c-MET + 22.5 µg pT3-EF1a-DN90- β-Catenin + 5 µg HSB2) were prepared.  the plasmid cocktails were diluted in 2 mL saline (0.9% NaCl) and injected into the lateral tail vein of 6 to 8-week-old mice in 5 to 7 seconds by means of a hydrodynamic injection. Mice were age- and gender-matched and maintained on the standard diet. The liver and body weight of each mouse was measured, and mice were euthanized 8 weeks after injection.

value: Liver

value: whole liver cells

value: Sirt2 liver KO

value: MET/CAT OE


title: High-fat control, A2

description: Library name: Sample2

value: High-fat control


title: HeLa cells, wildtype, Tg_24h, rep2

description:
Library name: 24h_NC_2
Column name in EMC2_raw_counts_2.csv: 24h-NC

tag: cell line

value: wildtype


title: KO MET/CAT_2


title: KO MET/CAT_1


title: High-fat control, A1

description: Library name: Sample1


title: kidney biopsy N91

tag: mmdx (abmr, mixed, nr[no rejection], pabmr, ptcmr, tcmr)

value: pABMR


title: kidney biopsy N160

value: Mixed


title: HeLa cells, wildtype, Tg_24h, rep1

description:
Library name: 24h_NC_1
Column name in EMC2_raw_counts_1.csv: 24h-NC


title: kidney biopsy N25


title: HeLa cells, EMC2 knockdown Tg_0h, rep1

description:
Library name: 0h_EMC2_1
Column name in EMC2_raw_counts_1.csv: 0h-EMC2

value: 0 hours


title: WT MET/CAT_1

tag: tissue

value: GFP overxpression


title: Donor 3_2 Run 1

city: Chicago

first: Alexander

middle: V

last: Misharin

state: Illinois

address: 303 E Superior St

department: Pulmonary and Critical Care

institute: Northwestern University

hyb_protocol: 383 unique genes were included in the analysis of this dataset. 289 genes came from the 10x base human lung panel and 94 genes from a custom designed panel (J2A6YV). The custom panel was curated based on human lung single cell analysis data, selecting for genes useful in cell type identification and/or with suspected involvement in SSc. Panel and slide preparation followed 10x Xenium guidelines as found in 10X Genomics Demonstrated Protocol CG000578. Slides were stained for H&E immediately following Xenium run completion.

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

data_processing: Cells were separated into transcript based niches (stored in counts matrix meta data for each sample) using Cellcharter.   Information about output files can be found here:  https://www.10xgenomics.com/support/in-situ-gene-expression/documentation/steps/onboard-analysis/understanding-xenium-outputs

source_name: Lung, donor

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

extract_protocol: Lung tissue was obtained at the time of transplant and stored on ice until processing. An approximately 10x10x10 mm piece of lung tissue was fixed in 10% neutral buffered formalin for 48 hours at 4 °C, followed by storage in 70% EhOH at room temperature, followed by series of ehanol and xylene dehydration steps and embedding in paraffin using Sakura Tissue-Tek VIP 5 instrument at 60 °C. Tissue blocks were rehydrated in an ice bath for 30 min and sectioned on Leica HistoCore Biocut microtome at 5 um thickness using the “Easy Does It” mode.

tag: run

tag: timepoint

tag: location

value: RML

tag: disease status

value: Donor

tag: diagnosis

tag: age

tag: race

value: White

value: Female


title: HeLa cells, wildtype, Tg_0h, rep1

description:
Library name: 0h_NC_1
Column name in EMC2_raw_counts_1.csv: 0h-NC

value: HeLa

value: cervical cancer cell line

value: thapsigargin-treated


title: KO GFP_3

source_name: Liver

value: Liver


title: HeLa cells, EMC2 knockdown Tg_0h, rep2

description:
Library name: 0h_EMC2_2
Column name in EMC2_raw_counts_2.csv: 0h-EMC2

value: EMC2 knockdown


title: WT MET/CAT_2

value: whole liver cells

value: WT


title: Donor 3_2 Run 2

tag: gender


title: HeLa cells, wildtype, Tg_0h, rep2

description:
Library name: 0h_NC_2
Column name in EMC2_raw_counts_2.csv: 0h-NC

tag: time


title: Donor 3_1 Run 1

value: Donor in situ

value: RLL


title: KO GFP_2

value: Sirt2 liver KO

value: MET/CAT OE


title: WT MET/CAT_3


title: Anther, Lyc-B3

city: yinchuan

first: ru

middle: ya

last: wei

address: helanshanxilu

institute: NingxiaUniversity

data_processing:
The Sequenced original sequence (Sequenced Reads) , or raw Reads, contains low-quality Reads with linkers, as shown in Figure 3. In order to guarantee the quality of information analysis, it is necessary to filter raw reads to get clean reads.
The transcriptome from Trinity splicing was used as a reference sequence (ref-RRB- , and the clean reads of each sample were mappedRef ref. We used the RSEM software (Li et al. , 2011) , which uses the bowtie parameter mismatch 2, the bowtie default parameter.
RSEM counted Bowtie's alignment results, further obtaining the number of readcounts per sample aligned to each gene and performing FPKM conversions on them to analyze gene expression levels.
Assembly: parameter-free
Supplementary files format and content: tab-delimited text files include readcount and FPKM values for each Sample

organism: Lycium barbarum

source_name: anther

extract_protocol:
Peel off the anthers and place quickly on ice,RNA was havested using Trial reagent,Illumina HiSeq/MiSeq sequencing.
After the samples were eligible for detection, eukaryote mRNA was enriched with magnetic beads bearing Oligo (DT)(in the case of prokaryotes, the mRNA was enriched by kit removal of rRNA) . Fragmentation buffer was then added to break up the mRNA into short fragments and use the mRNA as a template to synthesize one-stranded cDNA using six-base random primers (random hexamers) . Then buffer, dNTPs and DNA polymerase I and RNase H were added to synthesize two-stranded cDNA, the double-stranded cDNA was purified with AMPure XP beads. The purified double-stranded cDNA was repaired, a-tailed and connected with sequencing linker, then the fragment size was selected with AMPure XP beads. The PCR products were purified with AMPure XP beads and the final library was obtained.
After the library was built, Qubit2.0 was used for initial quantification, diluting the library to 1.5 ng/ul, and then Agilent 2100 was used for insert size detection of the library

value: anther

tag: phenotype

value: sterile


title: Anther, Lyc-B2


title: Donor 2_2 Run 2

value: RML

value: Black


title: Donor 2_2 Run 1

value: Donor


title: HeLa cells, Tg_10h, rep1

description:
Library name: Tg_10h_1
Column name in Tg_raw_counts_1.csv: Tg-10h

treatment_protocol: HeLa cells were treated with DMSO or 500 nM thapsigargin (TargetMol, TQ0302) for both 2 hours and 10 hours

value: 10 hours


title: KO GFP_1


title: Anther, Lyc-B1


title: Donor 2_1 Run 2

value: LUL

value: Female


title: Donor 3_1 Run 2

value: White


title: HeLa cells, DMSO_10h, rep2

description:
Library name: DMSO_10h_2
Column name in Tg_raw_counts_2.csv: DMSO10h

value: HeLa

value: cervical cancer cell line

value: DMSO-treated


title: kidney biopsy N100

value: pTCMR


title: kidney biopsy N126

value: ABMR


title: kidney biopsy N7

value: NR


title: kidney biopsy N185


title: kidney biopsy N155

value: Mixed


title: kidney biopsy N140


title: HeLa cells, Tg_10h, rep2

description:
Library name: Tg_10h_2
Column name in Tg_raw_counts_2.csv: Tg10h

value: thapsigargin-treated


title: Donor 1_2 Run 2


title: WT GFP_2

value: Liver

value: whole liver cells

value: WT

value: GFP overxpression


title: Anther, Lyc-K4

value: anther

value: fertile


title: HeLa cells, Tg_2h, rep2

description:
Library name: Tg_2h_2
Column name in Tg_raw_counts_2.csv: Tg2h

value: 2 hours


title: HeLa cells, DMSO_10h, rep1

description:
Library name: DMSO_10h_1
Column name in Tg_raw_counts_1.csv: DMSO-10h

value: 10 hours


title: Anther, Lyc-K3


title: Anther, Lyc-K5


title: Donor 1_2 Run 1

value: LUL

value: Donor

value: White

value: Female


title: Anther, Lyc-K6


title: WT GFP_1

value: GFP overxpression (OE)


title: Donor 1_1 Run 1

value: Donor in situ


title: dog6_control_left

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

description: Library name: 12L

data_processing:
Raw fastq was aligned to canine reference genome with hisat2 v2.1.0; gene counts were quantified by using featureCounts software.
Assembly: CanFam3.1
Supplementary files format and content: gene expression matrix

organism: Canis lupus familiaris

source_name: Dorsal Root Ganglion

growth_protocol: All animal experiments were approved by The Ohio State University Institutional Animal Care and Use Committee (IACUC). Female beagles (3-4 y.o. N=6) were obtained from Marshall BioResources and group housed according to federal regulations and institutional policies.

extract_protocol:
DRGs from L4/5 (internal control) and T12/L1 (puncture) were dissected and RNA isolated using the TRIzol Plus RNA Purification Kit (Cat#12183555). RNA-seq was performed at The Ohio State University Genomics Core with library generation using a NEBNext rRNA Depletion and Prep Kit.
cDNA libraries were sequenced on Novaseq SP system (Illumina, USA).

treatment_protocol: Following a dorsolateral approach to the thoracolumbar vertebral column, the thoracolumbar fascia was incised and epaxial muscles reflected laterally on one side to reveal the dorsolateral aspect of the intervertebral disc spaces from T11 to L1. The T11/T12, T12/T13, and T13/LI IVDs were identified and punctured with a 26G needle containing either 10 µL of 1x phosphate buffered saline (PBS) (injury control; N=3) or 100 µM PAR2A and 25 µM CS (treatment; N=3).

value: Dorsal Root Ganglion

tag: Sex


title: WT GFP_3

tag: genotype


title: HeLa cells, DMSO_2h, rep1

description:
Library name: DMSO_2h_1
Column name in Tg_raw_counts_1.csv: DMSO-2h

value: HeLa

tag: cell type

value: cervical cancer cell line

value: DMSO-treated


title: dog6_punctured_pbs_right

description: Library name: 11R


title: HeLa cells, DMSO_2h, rep2

description:
Library name: DMSO_2h_2
Column name in Tg_raw_counts_2.csv: DMSO2h

tag: treatment


title: HeLa cells, Tg_2h, rep1

description:
Library name: Tg_2h_1
Column name in Tg_raw_counts_1.csv: Tg-2h

tag: cell line

value: thapsigargin-treated


title: dog6_control_right

description: Library name: 12R


title: Anther, Lyc-K1


title: SSc 4_2 Run 2

source_name: Lung, SSc

value: Explant

value: SSc

value: SSc-ILD


title: dog6_punctured_pbs_left

description: Library name: 11L


title: Donor 2_1 Run 1

value: Black


title: PIM110

city: Houston

first: Jeffrey

address: 6431 Fannin St

institute: University of Texas

description: Library name: PIM110

data_processing:
The gene expression data was sequenced in six separate batches and preprocessed using the same pipeline.
We processed the data using the BETSY system, which aligned the reads to the hg19 genome with STAR estimated the transcript abundance as transcripts per million (TPM) with RSEM.
We applied ComBat to log_2 TPM values for batch effect normalization.
Assembly: hg19
Supplementary files format and content: expression.counts.txt.  Read counts for each gene and sample.  Tab-delimited text file.
Supplementary files format and content: expression.tpm.txt.  Transcripts per million for each gene and sample.  Tab-delimited text file.
Supplementary files format and content: expression.combat.txt.  ComBat normalized transcripts per million.  Includes only genes with positive variance in all batches before correction.  Tab-delimited text file.

source_name: patient-derived xenograft (PDX) model of TNBC from tumor

growth_protocol: The fourth mammary fat pads of 4-to-8-week-old female NOD/SCID mice were implanted with 500,000 PDX tumor cells suspended in 30 µL of a 50:50 mixture of DMEM/F12 media and Matrigel. Cells in Matrigel were maintained on ice until engraftment.

extract_protocol:
The RNA was extracted using PicoPure RNA isolation kit and RNA concentration was quantified by Nanodrop.
Whole transcriptome RNA-seq libraries were prepared using RNA HyperPrep kit with RiboErase following the manufacturer's instructions. Paired-end sequencing was performed on Illumina instruments, which varied across batches.

treatment_protocol: Patients were treated with neoadjuvant chemotherapy.  Tumors were extracted and engrafted into xenograft mouse models before (pre), during (mid), and after (post) treatment.

value: tumor

value: doxorubicin + cyclophosphamide

tag: time point

value: mid

tag: batch


title: SSc 4_2 Run 1

tag: run

value: LUL


title: PIM077

description: Library name: PIM077

tag: tissue

value: pre


title: Graft_D40

city: Rennes

first: Simon

last: Leonard

address: 2 avenue du Prof Léon Bernard

institute: Université Rennes

description: 10X Genomics

data_processing:
Raw data processed with Cellranger v3.1.0 (10X Genomics)
Assembly: mm10
Supplementary files format and content: Sparse matrix of raw UMI counts

source_name: Bone marrow

extract_protocol:
Mouse femurs of steady-state (control), PBS-injected (Sham), and DOHH2-injected (grafted) mice were harvested at D19 and D40. BM was flushed and dissociated in PBS containing DNase I (10 U/ml, PulmozymeÒ, Roche) and Liberase DH (0.025 mg/ml, 5401089001, Roche). Bones were cut into small fragments using scissors in a dissociating media containing 10 U/ml DNase I and Collagenase P (1.2 mg/ml, 11213865001, Roche). Bones and BM were digested at 37°C for 20 min under agitation. PBS supplemented with 5% FBS and 15% sodium citrate was added to neutralize the digestion solution, followed by a centrifugation at 450 g for 5 min. After filtration on 100 µM cell strainer, depletion of red blood cells was carried out with RBC lysis buffer (00-4333-57, Thermo Fisher), stromal cell enrichment was performed using anti-Cd45 (clone 30-F11, 103102, Biolegend) and anti-Ter119 (116202, Biolegend) Abs and using magnetic beads (Dynabeads) according to manufacturer’s instructions. After depletion, cells were stained for sorting with the following antibodies: anti-Cd31 BUV395 (clone MEC13.3, BD Biosciences), anti-Cd51 BV650 (clone RMV-7, BD Biosciences), anti-Sca1 PECy7 (clone D7, Biolegend), anti-Cd200 APC (clone OX-90, Biolegend), anti-Cd45 APC-Cy7 (clone 30F11, BD Biosciences), anti-Ter119 APC-Cy7 (116223, Biolegend), anti-hCD45 APC-Cy7 (clone 2D1, BD Biosciences) and anti-hCD20 FITC (clone 2H7, 555622, BD Biosciences) and with live dead reagent (L34959, Thermo). Cells were then sorted using a FACSAria II (BD Biosciences) as Cd45/Ter119negCd31negCd51posCd200pos stromal cells, Cd45/Ter119negCd31posSca1pos endothelial cells31,32, and hCD20pos human lymphoma B cells
RNA libraries were prepared according to manufacter's intructions (single cell 3' v3.1 protocol, 10x Genomics)

treatment_protocol: We extracted stromal and endothelial cells from ungrafted RAGγc KO mice (control), PBS-grafted mice (SHAM) and DOHH2-grafted mice at D19 and D40 femurs.

value: Bone marrow

tag: strain

value: stromal and endothelial cells

tag: tumor stage

value: Late

value: Graft

tag: developmental stage


title: Donor 1_1 Run 2

tag: timepoint

value: Donor in situ

tag: location

tag: disease status

value: Donor

tag: diagnosis

tag: age

value: White

value: Female


title: SSc 4_1 Run 2

value: Explant

value: RML

tag: race

tag: gender


title: Graft_D19

description: 10X Genomics

tag: cell type

tag: genotype

value: Early


title: PIM051

description: Library name: PIM051

tag: treatment

value: post


title: dog5_control_left

description: Library name: 10L

value: Dorsal Root Ganglion

tag: Sex


title: SSc 4_1 Run 1

value: SSc

value: SSc-ILD


title: dog5_punctured_pbs_right

description: Library name: 9R


title: Anther, Lyc-K2

value: anther

tag: phenotype

value: fertile


title: Sham_D40

description: 10X Genomics

value: Bone marrow

value: SHAM


title: PIM046

description: Library name: PIM046

value: tumor

tag: time point

value: pre

tag: batch


title: PIM040

description: Library name: PIM040

tag: tissue


title: SSc 3_1 Run 2

tag: run

value: RUL

value: American Indian or Alaska Native


title: dog4_control_right

description: Library name: 8R


title: dog5_punctured_pbs_left

description: Library name: 9L


title: PIM042

description: Library name: PIM042


title: VC_snRNAseq-13_Animal5_Central_Nucleus__AP3_

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

data_processing:
FASTQ files were pre-processed with the 10x CellRanger pipeline
Human reads were aligned to reference genome GRCh38, rhesus macaque reads were aligned to reference genome Mmul_10, and Olive Baboon reads with aligned to refernce genome Panubis1.0.
Assembly: GRCh38, Mmul_10, and Panubis1.0
Supplementary files format and content: Raw FASTQ files and data processed with the 10x CellRanger pipeline with barcode, feature, and matrix files for each sample.

organism: Macaca mulatta

source_name: brain (amygdala)

extract_protocol:
For human samples, the amygdala was dissected from fresh frozen postmortem human tissue and 100 micron coronal sections of amygdala from fresh frozen postmortem human tissue were obtained by cryosectioning. For nonhuman primates, coronal brain blocks were flash-frozen immediately prior to tissue punches localized to specific amygdala subregions. All nuclei were isolated and barcoded with 10x Genomics Chromium.
Libraries were prepared using 10x Chromium Next GEM Single Cell 3’ v3.1 (dual-index) kit according to manufacturer's instructions.
single-nucleus RNA-sequencing

value: brain (amygdala)


title: Ctrl

description: 10X Genomics

tag: strain

value: stromal and endothelial cells

value: Control


title: dog4_control_left

description: Library name: 8L

value: Female


title: SSc 3_1 Run 1

tag: timepoint

value: Explant


title: SSc 2_1 Run 2

tag: location

value: SSc-ILD, PH

value: White


title: PIM038

description: Library name: PIM038

value: doxorubicin + cyclophosphamide

value: mid


title: dog5_control_right

description: Library name: 10R

value: Dorsal Root Ganglion


title: SSc 2_1 Run 1

tag: disease status

value: SSc


title: VC_snRNAseq-12_Animal5_Lateral__AP1_


title: PIM025

description: Library name: PIM025


title: dog4_punctured_par2acs_right

description: Library name: 7R


title: SSc 1_1 Run 2

tag: diagnosis

value: SSc-ILD


title: PIM024

description: Library name: PIM024


title: VC_snRNAseq-12_Animal5_Basal__AP2_


title: dog4_punctured_par2acs_left

description: Library name: 7L


title: SSc 1_1 Run 1

tag: age


title: VC_snRNAseq-12_Animal5_Basal__AP1_


title: dog3_control_right

description: Library name: 6R


title: PIM013

description: Library name: PIM013


title: VC_snRNAseq-12_Animal5_Lateral__AP2_


title: dog3_control_left

description: Library name: 6L


title: VC_snRNAseq-12_Animal4_Central_Nucleus