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

description:
Library name: Sample 57
10x Genomics


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

status: Public on Mar 04 2025

type: SRA

city: Boston

first: Dimitra

last: Karagkouni

address: Brookline 330

country: USA

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

description:
Library name: Sample 56
10x Genomics

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

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

tag: tissue

value: PBMC

tag: treatment

value: CAR T

tag: time

value: 4wk post-CAR T


title: PBMCs, RNA, Leukapheresis, P13

description:
Library name: Sample 59
10x Genomics

library_source: transcriptomic single cell

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

value: Leukapheresis


title: PBMCs, RNA, Leukapheresis, P12

description:
Library name: Sample 53
10x Genomics


title: PBMCs, TCR, 6mo post-CAR T, P11

description:
Library name: Sample 52
10x Genomics

value: 6mo post-CAR T


title: PBMCs, TCR, Leukapheresis, P11

description:
Library name: Sample 48
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P11

description:
Library name: Sample 49
10x Genomics


title: PBMCs, TCR, 4wk post-CAR T, P11

description:
Library name: Sample 50
10x Genomics


title: PBMCs, RNA, 6mo post-CAR T, P11

description:
Library name: Sample 51
10x Genomics


title: PBMCs, RNA, Leukapheresis, P11

description:
Library name: Sample 47
10x Genomics


title: PBMCs, TCR, 6mo post-CAR T, P10

description:
Library name: Sample 44
10x Genomics


title: PBMCs, TCR, 12mo post-CAR T, P10

description:
Library name: Sample 46
10x Genomics

value: 12mo post-CAR T


title: PBMCs, RNA, 4wk post-CAR T, P10

description:
Library name: Sample 41
10x Genomics


title: PBMCs, RNA, 6mo post-CAR T, P10

description:
Library name: Sample 43
10x Genomics


title: PBMCs, TCR, Leukapheresis, P10

description:
Library name: Sample 40
10x Genomics


title: PBMCs, RNA, 12mo post-CAR T, P10

description:
Library name: Sample 45
10x Genomics


title: PBMCs, RNA, Leukapheresis, P10

description:
Library name: Sample 39
10x Genomics


title: PBMCs, TCR, 6mo post-CAR T, P9

description:
Library name: Sample 38
10x Genomics


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

description:
Library name: Sample 177
10x Genomics


title: PBMCs, TCR, 4wk post-CAR T, P9

description:
Library name: Sample 36
10x Genomics


title: PBMCs, TCR, Leukapheresis, P9

description:
Library name: Sample 34
10x Genomics


title: PBMCs, RNA, Leukapheresis, P9

description:
Library name: Sample 33
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P8

description:
Library name: Sample 31
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P9

description:
Library name: Sample 35
10x Genomics


title: PBMCs, RNA, 6mo post-CAR T, P9

description:
Library name: Sample 37
10x Genomics


title: PBMCs, TCR, Leukapheresis, P8

description:
Library name: Sample 30
10x Genomics


title: PBMCs, TCR, 4wk post-CAR T, P8

description:
Library name: Sample 32
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P6

description:
Library name: Sample 23
10x Genomics


title: PBMCs, TCR, 4wk post-CAR T, P7

description:
Library name: Sample 28
10x Genomics


title: PBMCs, TCR, 4wk post-CAR T, P6

description:
Library name: Sample 24
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P7

description:
Library name: Sample 27
10x Genomics


title: PBMCs, RNA, Leukapheresis, P7

description:
Library name: Sample 25
10x Genomics


title: PBMCs, TCR, Leukapheresis, P6

description:
Library name: Sample 22
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P5

description:
Library name: Sample 19
10x Genomics


title: PBMCs, RNA, Leukapheresis, P6

description:
Library name: Sample 21
10x Genomics


title: PBMCs, RNA, Leukapheresis, P5

description:
Library name: Sample 17
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P4

description:
Library name: Sample 15
10x Genomics


title: PBMCs, TCR, 4wk post-CAR T, P5

description:
Library name: Sample 20
10x Genomics


title: PBMCs, TCR, 4wk post-CAR T, P4

description:
Library name: Sample 16
10x Genomics


title: PBMCs, RNA, Leukapheresis, P4

description:
Library name: Sample 13
10x Genomics


title: PBMCs, TCR, Leukapheresis, P3

description:
Library name: Sample 10
10x Genomics


title: PBMCs, TCR, Leukapheresis, P4

description:
Library name: Sample 14
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P3

description:
Library name: Sample 11
10x Genomics


title: PBMCs, RNA, Leukapheresis, P8

description:
Library name: Sample 29
10x Genomics


title: PBMCs, TCR, Leukapheresis, P7

description:
Library name: Sample 26
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P2

description:
Library name: Sample 7
10x Genomics


title: PBMCs, RNA, Leukapheresis, P3

description:
Library name: Sample 9
10x Genomics


title: PBMCs, TCR, 4wk post-CAR T, P2

description:
Library name: Sample 8
10x Genomics


title: PBMCs, TCR, Leukapheresis, P2

description:
Library name: Sample 6
10x Genomics


title: PBMCs, RNA, Leukapheresis, P2

description:
Library name: Sample 5
10x Genomics


title: PBMCs, RNA, 4wk post-CAR T, P1

description:
Library name: Sample 3
10x Genomics


title: PBMCs, RNA, Leukapheresis, P1

description:
Library name: Sample 1
10x Genomics


title: PBMCs, TCR, Leukapheresis, P1

description:
Library name: Sample 2
10x Genomics


title: DFif1G2

status: Public on Feb 19 2025

city: Qingdao 266237

first: Kexuan

last: Ma

state: China

address: No. 72 Binhai Road

department: State Key Laboratory of Microbial Technology

country: China

institute: Shandong University

description: Library name: D8093_G_2

data_processing:
3' adaptor sequences were first removed from the sequencing reads to produce 50-nt long tags.
Then low quality tags, one copy tags and tags which are not 50-nt long were removed to generate clean tags.
Reference 50-nt tag databases were created from predicted Penicillium oxalicum transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Assembly: Whole Genome Shotgun project in GenBank under the accession number AGIH00000000.1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Penicillium oxalicum

source_name: strain

growth_protocol: The germination of Penicillium oxalicum were inoculated in modifeid vogel's culture medium with 2% glucose as carbon resource for 24 h at 30℃ as the pre-culture, and then mycelia were transferred and grown in the modified Mendal’s medium with 2% glucose or 1% bran + 1% microcrystalline cellulose as carbon resources for 18h. Total RNA was extracted for DGE analysis.

extract_protocol:
Total RNA was extracted, and oligo (dT) beads were used to purify mRNA and guide double-stranded cDNA synthesis. The enzyme NlaIII was used to cut the cDNA at CATG sites. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 50bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: strain

tag: genotype

value: Fif1 deletion strain

value: Modified Mendal’s medium with 2% glucose as carbon resource


title: PBMCs, TCR, 4wk post-CAR T, P1

description:
Library name: Sample 4
10x Genomics


title: DFif1G1

description: Library name: D8093_G_1


title: DFif1CW3

description: Library name: D8093_FP_3

value: Modified Mendal’s medium with 1percent bran + 1percent microcrystalline cellulose as carbon resource


title: PBMCs, TCR, Leukapheresis, P5

description:
Library name: Sample 18
10x Genomics


title: DFif1CW2

description: Library name: D8093_FP_2


title: DFif3G1

description: Library name: D4776_G_1

value: Fif3 deletion strain


title: DFif3G3

description: Library name: D4776_G_3


title: DFif3G2

description: Library name: D4776_G_2


title: DFif1CW1

description: Library name: D8093_FP_1


title: pBAT, HA-SA, replicate 4. Experiment 2

status: Public on Feb 18 2025

city: Madison

first: Andrea

last: Galmozzi

state: WI

address: 6151 WIMR, 1111 Highland Av, WIMR I, room 6151

institute: UW Madison SMPH

description: Library name: pBAT HA-SA 4

data_processing:
Libraries were sequenced using Illumina X plus platform using 150PE reads at a depth of ~20M per library.
Reads were mapped to mouse referene genome (GRCm39) using Kallisto. Unique alignments were used for downstream analysis.
Gene expression values were calculated using DESeq2, with differentially expressed genes (DEGs) calculated with 4 replicates per condition at an adjusted p-value <0.05.
Assembly: GRCm39
Supplementary files format and content: Experiment_1_Raw_Counts.xlsx is counts from Exp. 1 samples
Supplementary files format and content: Experiment_2_Raw_Counts.xlsx is counts from Exp. 2 samples
Supplementary files format and content: Experiment_3_Raw_Counts.xlsx is counts from Exp. 3 samples

organism: Mus musculus

source_name: pBAT

growth_protocol: pBAT and pWAT preadipocytes were isolated from p0-p1 pups and maintained in DMEM containing 20% FBS and antibiotic/antimycotic for ~4-6 days. B9 preadipocytes were maintained and DMEM containing 10% FBS and antibiotic/antimycotic. All cells were grown at 37C and 5% CO2 in humidified conditions.

extract_protocol:
All samples were harvested in TRIzol and RNA was isolated using the ZymoPure RNA Mini Kit. A detailed protocol and reagent information is described in the methods of the associated manuscript.
Purified RNA samples were submitted for library construction and sequencing to either BGI or Novogene. For experiments 1 and 2, libraries were prepared as DNBSEQ stranded mRNA libraries by BGI. For experiment 3, Novogene library prep was performed mRNA purification 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. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: pWAT, pBAT, and B9 cells were differentiated in DMEM containing 10% FBS and antibiotic/antimycotic. Differentiation protocol is described in the methods of the associated manuscript.

tag: cell line

value: pBAT

tag: cell type

value: Primary brown preadipocyte

value: Wild type

value: Adipogenic differentiation, 10uM HA, 1mM SA


title: pBAT, HA-SA, replicate 2. Experiment 2

description: Library name: pBAT HA-SA 2


title: pBAT, HA-SA, replicate 1. Experiment 2

description: Library name: pBAT HA-SA 1


title: pBAT, HA, replicate 3. Experiment 2

description: Library name: pBAT HA 3

value: Adipogenic differentiation, 10uM HA


title: pBAT, HA, replicate 4. Experiment 2

description: Library name: pBAT HA 4


title: pBAT, SA, replicate 4. Experiment 2

description: Library name: pBAT SA 4

value: Adipogenic differentiation, 1mM SA


title: pBAT, SA, replicate 3. Experiment 2

description: Library name: pBAT SA 3


title: pBAT, HA-SA, replicate 3. Experiment 2

description: Library name: pBAT HA-SA 3


title: DFif1G3

description: Library name: D8093_G_3


title: pBAT, SA, replicate 1. Experiment 2

description: Library name: pBAT SA 1


title: pBAT, SA, replicate 2. Experiment 2

description: Library name: pBAT SA 2


title: pBAT, Vehicle, replicate 4. Experiment 2

description: Library name: pBAT Vehicle 4

value: Adipogenic differentiation, vehicle


title: pBAT, Vehicle, replicate 3. Experiment 2

description: Library name: pBAT Vehicle 3


title: pBAT, Vehicle, replicate 2. Experiment 2

description: Library name: pBAT Vehicle 2


title: pWAT, D6 of differentiation, replicate 3. Experiment 1 differentiation time course.

description: Library name: pWAT D6 3

source_name: pWAT

value: pWAT

value: Primary white preadipocyte

value: Adipogenic differentiation


title: pBAT, Vehicle, replicate 1. Experiment 2

description: Library name: pBAT Vehicle 1


title: pWAT, D4 of differentiation, replicate 3. Experiment 1 differentiation time course.

description: Library name: pWAT D4 4


title: pWAT, D4 of differentiation, replicate 2. Experiment 1 differentiation time course.

description: Library name: pWAT D4 3


title: pWAT, D2 of differentiation, replicate 1. Experiment 1 differentiation time course.

description: Library name: pWAT D2 2


title: pWAT, D2 of differentiation, replicate 2. Experiment 1 differentiation time course.

description: Library name: pWAT D2 3


title: pWAT, D6 of differentiation, replicate 1. Experiment 1 differentiation time course.

description: Library name: pWAT D6 1


title: pWAT, D0 of differentiation, replicate 3. Experiment 1 differentiation time course.

description: Library name: pWAT D0 4


title: pWAT, D0 of differentiation, replicate 2. Experiment 1 differentiation time course.

description: Library name: pWAT D0 2


title: pBAT, HA, replicate 1. Experiment 2

description: Library name: pBAT HA 1


title: pBAT, HA, replicate 2. Experiment 2

description: Library name: pBAT HA 2


title: pWAT, D0 of differentiation, replicate 1. Experiment 1 differentiation time course.

description: Library name: pWAT D0 1


title: pWAT, D4 of differentiation, replicate 1. Experiment 1 differentiation time course.

description: Library name: pWAT D4 2


title: pWAT, D6 of differentiation, replicate 2. Experiment 1 differentiation time course.

description: Library name: pWAT D6 2


title: pBAT, D6 of differentiation, replicate 1. Experiment 1 differentiation time course.

description: Library name: pBAT D6 1


title: pWAT, D2 of differentiation, replicate 3. Experiment 1 differentiation time course.

description: Library name: pWAT D2 4


title: pBAT, D6 of differentiation, replicate 2. Experiment 1 differentiation time course.

description: Library name: pBAT D6 2


title: pBAT, D4 of differentiation, replicate 1. Experiment 1 differentiation time course.

description: Library name: pBAT D4 1


title: pBAT, D4 of differentiation, replicate 3. Experiment 1 differentiation time course.

description: Library name: pBAT D4 4


title: pBAT, D2 of differentiation, replicate 2. Experiment 1 differentiation time course.

description: Library name: pBAT D2 3


title: pBAT, D4 of differentiation, replicate 2. Experiment 1 differentiation time course.

description: Library name: pBAT D4 3


title: pBAT, D2 of differentiation, replicate 1. Experiment 1 differentiation time course.

description: Library name: pBAT D2 1


title: pBAT, D0 of differentiation, replicate 3. Experiment 1 differentiation time course.

description: Library name: pBAT D0 4


title: pBAT, D0 of differentiation, replicate 1. Experiment 1 differentiation time course.

description: Library name: pBAT D0 2


title: pBAT, D0 of differentiation, replicate 2. Experiment 1 differentiation time course.

description: Library name: pBAT D0 3


title: B9 WT, D6 of differentiation, replicate 2. Experiment 1 differentiation time course.

description: Library name: B9 D6 3

value: Immortalized brown preadipocyte


title: B9 WT, D6 of differentiation, replicate 1. Experiment 1 differentiation time course.

description: Library name: B9 D6 2


title: B9 WT, D4 of differentiation, replicate 3. Experiment 1 differentiation time course.

description: Library name: B9 D4 4


title: pBAT, D6 of differentiation, replicate 3. Experiment 1 differentiation time course.

description: Library name: pBAT D6 4


title: B9 WT, D4 of differentiation, replicate 1. Experiment 1 differentiation time course.

description: Library name: B9 D4 1


title: B9 WT, D2 of differentiation, replicate 3. Experiment 1 differentiation time course.

description: Library name: B9 D2 4


title: B9 WT, D2 of differentiation, replicate 2. Experiment 1 differentiation time course.

description: Library name: B9 D2 3


title: B9 WT, D2 of differentiation, replicate 1. Experiment 1 differentiation time course.

description: Library name: B9 D2 2


title: B9 WT, D0 of differentiation, replicate 1. Experiment 1 differentiation time course.

description: Library name: B9 D0 1


title: B9 WT, D0 of differentiation, replicate 2. Experiment 1 differentiation time course.

description: Library name: B9 D0 2


title: B9 WT, D0 of differentiation, replicate 3. Experiment 1 differentiation time course.

description: Library name: B9 D0 4


title: BAT depot from BAKO female ID 5147.

description: Library name: BAT BAKO 1

source_name: Brown adipose tissue

value: Brown adipose tissue

value: BAKO


title: BAT depot from BAKO female ID 5172.

description: Library name: BAT BAKO 3


title: pBAT, D2 of differentiation, replicate 3. Experiment 1 differentiation time course.

description: Library name: pBAT D2 4


title: BAT depot from WT female ID 5179.

description: Library name: BAT WT 5


title: BAT deport from BAKO female ID 5180.

description: Library name: BAT BAKO 5


title: BAT depot from WT female ID 5156.

description: Library name: BAT WT 1


title: BAT depot from BAKO female ID 5157.

description: Library name: BAT BAKO 2


title: B9 WT, D6 of differentiation, replicate 3. Experiment 1 differentiation time course.

description: Library name: B9 D6 4


title: DSP Mutant Cardiomyocytes - siEPAS1 replicate 3

status: Public on Feb 15 2025

city: Utrecht

first: Cornelis

middle: J.

last: Boogerd

address: Uppsalalaan 8

department: Developmental Biology and Stem Cell Research

country: Netherlands

institute: Hubrecht Institute

description: Library name: DSP.MUT.siEPAS1.3

data_processing:
mapping, readcount analysis
Assembly: GRCm38
Supplementary files format and content: EPAS1_processed_featureCounts.raw.txt: txt file - raw readcounts

source_name: iPS-derived cardiomyocytes

growth_protocol: hiPSCs were cultured on Geltrex™ LDEV-Free, hESC-Qualified, Reduced Growth Factor Basement Membrane Matrix-coated wells (GIBCO, Grand Island, NY). Cells were refreshed with Essential 8™ Medium (GIBCO, Waltham, MA) on a daily basis. hiPSCs were passaged once they reached 80-100% confluency. Briefly, medium was aspirated and TrypLE Express Enzyme (GIBCO, Waltham, MA) was added for 5 minutes at 37°C. After incubation, 4 mL of Essential 8™ Medium, supplemented with 1 mM thiazovivin (Sigma-Aldrich, Saint Louis, MI), was added to the dissociated cells and transferred to a 15 mL Falcon tube. Cells were centrifuged for 3 minutes at 200 RCF. Subsequently, cells were seeded at a density of 15,000 cells/cm2 in Essential 8™ Medium, supplemented with 1 mM thiazovivin. Medium was refreshed the next day with plain Essential 8™. For directed differentiation towards cardiomyocytes, hiPSCs were grown until a 80-90% confluency was reached (Day 0). Medium was aspirated and cells were washed once with dPBS (GIBCO, Waltham, MA). Next, cells were fed with RPMI-1640-Medium-GlutaMAX™Supplement-HEPES (GIBCO, Waltham, MA) supplemented with 0.5 mg/mL human recombinant albumin (Sigma-Aldrich, Saint Louis, MI), 0.2 mg/mL L-Ascorbic Acid 2-Phosphate (Sigma-Aldrich, Saint Louis, MI), and 4 mM CHIR99021 (Sigma-Aldrich, Saint Louis, MI). After 48 hours (Day 2), medium was aspirated and cells were washed once with RPMI-1640-Medium-GlutaMAX™Supplement-HEPES, followed by addition of RPMI-1640-Medium-GlutaMAX™Supplement-HEPES supplemented with 0.5 mg/mL human recombinant albumin (Sigma-Aldrich, Saint Louis, MI), 0.2 mg/mL L-Ascorbic Acid 2-Phosphate, and 5 mM IWP2 (Sigma-Aldrich, Saint Louis, MI). On day 4 and day 6, cells were refreshed with RPMI-1640-Medium-GlutaMAX™Supplement-HEPES supplemented with 0.5 mg/mL human recombinant albumin and 0.2 mg/mL L-Ascorbic Acid 2-Phosphate. From day 8 onwards, cells were refresh every 3-4 days with RPMI-1640-Medium-GlutaMAX™-Supplement-HEPES supplemented with B-27™Supplement (50x)-serum free (GIBCO, Waltham, MA). hiPSC-derived cardiomyocytes were subsequently dissociated with TrypLE™ Select Enzyme (10x) without phenol red (GIBCO, Waltham, MA) for a maximum of 45 minutes at 37°C. Cardiomyocytes were seeded at a density of 100,000 cells/cm2 in Geltrex-coated wells for downstream molecular applications.

extract_protocol:
RNeasy Mini Kit (Qiagen, Hilden, Germany)
Truseq RNA stranded polyA

treatment_protocol: Cells were transfected with either 10 nM scramble or siRNA oligo duplexes targeting EPAS1 (OriGene, Rockville, MD) utilizing Lipofectamine™ RNAiMAX (ThermoFisher Scientific, Waltham, MA) according to the manufacturers’ instructions. For overexpression studies, cells were transduced with AAV6-Control or AAV6-EPAS1. After 48 hours, RNA was isolated. For overexpression,

value: iPS-derived cardiomyocytes

value: Cardiomyocytes

value: DSP p.Arg1113X/WT


title: DSP Mutant Cardiomyocytes - siEPAS1 replicate 4

description: Library name: DSP.MUT.siEPAS1.4


title: DSP Mutant Cardiomyocytes - siEPAS1 replicate 1

description: Library name: DSP.MUT.siEPAS1.1


title: BAT depot from WT female ID 5174.

description: Library name: BAT WT 3


title: DSP Mutant Cardiomyocytes - siScramble replicate 3

description: Library name: DSP.MUT.scr.3

value: siScramble


title: DSP Mutant Cardiomyocytes - siScramble replicate 1

description: Library name: DSP.MUT.scr.1


title: DSP Mutant Cardiomyocytes - siScramble replicate 2

description: Library name: DSP.MUT.scr.2


title: DSP Mutant Cardiomyocytes - siEPAS1 replicate 2

description: Library name: DSP.MUT.siEPAS1.2


title: DSP Mutant Cardiomyocytes - siScramble replicate 4

description: Library name: DSP.MUT.scr.4


title: WT Cardiomyocytes - AAV-Control replicate 3

description: Library name: ATCC.AAVctr.3

value: WT


title: WT Cardiomyocytes - AAV-Control replicate 4

description: Library name: ATCC.AAVctr.4


title: B9 WT, D4 of differentiation, replicate 2. Experiment 1 differentiation time course.

description: Library name: B9 D4 2


title: WT Cardiomyocytes - AAV-EPAS1 replicate 1

description: Library name: ATCC.AAVEPAS1.1


title: BAT depot from WT female ID 5175.

description: Library name: BAT WT 4


title: WT Cardiomyocytes - AAV-EPAS1 replicate 4

description: Library name: ATCC.AAVEPAS1.4


title: WT Cardiomyocytes - AAV-Control replicate 2

description: Library name: ATCC.AAVctr.2


title: G3M14 V(D)J Sequencing

status: Public on Feb 14 2025

first: Dan

last: Barouch

state: MA

address: 3 Blackfan Cir

department: CVVR

institute: Beth Israel Deaconess Medical Center

data_processing:
Raw sequencing reads for gene expression and T cell receptor (TCR) sequencing were respectively mapped to the GRCm38 mouse reference genome (mm10, v. 2020-A) and GRCm38 V(D)J reference (version 7.0.0), using Cell Ranger multi version 7.0.0 (10X Genomics). Downstream analysis was conducted following the single-cell clustering pipeline in Seurat version 4.4.0. Quality control was applied to all 16 animals, with initial filtering to remove cells expressing fewer than 200 genes as well as genes that were expressed in three cells or fewer. Furthermore, cells whose mitochondrial reads comprised more than 5% of total reads were excluded. Raw counts for each animal were normalized using Seurat’s log-normalization function, and for exploratory purposes, the top 3,000 variable features were identified using the variance stabilizing transformation (VST) selection method. T cell metadata, including V(D)J usage and complete TCR sequence, were combined with each animal’s corresponding Seurat object metadata using scRepertoire version 1.10.1.
Assembly: GRCm38 V(D)J reference (version 7.0.0, 10X Genomics)
Assembly: GRCm38 mouse reference genome (mm10, v. 2020-A)
Supplementary files format and content: GEX and V(D)J cellranger outputs from cellrnager multi

source_name: Tumor

growth_protocol: Fifteen mice for each group (sham, peptide + adj, Ad26.VP22.7Epi) were vaccinated and implanted as previously described in the methods sections. At day 18 the five smallest tumors (6 smallest for Ad26.VP22.7Epi group) by volume in each group were selected to be harvested over the next 3 days. On day 18, two tumors of the five were harvested from each group. The same was done on day 19. On day 20, one tumor was harvested from each group except the Ad26.VP22.7Epi group which harvested two tumors. This resulted in 5 tumors for sham and peptide + adj, respectively and 6 tumors for Ad26.VP22.7Epi.

extract_protocol:
Single cell RNA-Seq library prep was provided by the Single Cell Core at Harvard Medical School, Boston, MA. For each library, cells were resuspended in DPBS with 0.04% FBS to achieve a target concentration of 200–1500 cells per microliter. Samples with more than 85% viability were processed. For each library, ~16,000 cells were loaded onto a 10× chromium controller to target a recovery of 10,000 cells.
Both gene expression and TCR libraries using the Chromium Next GEM Single Cell 5′ Reagent Kits (v2) were prepared following the 10X Genomics’ user guide. Briefly, the single cells were encapsulated and barcoded within nanoliter-sized droplets along with the reagents necessary for cell lysis and reverse transcription. Within the droplet cells are lysed and the mRNA molecules are captured and barcoded during reverse transcription.
Subsequently, full-length cDNA was made, followed by enzymatic fragmentation. P5, P7, i7 and i5 sample indexes, and TruSeq Read 2 (read 2 primer sequence) are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The libraries were sequenced at the Biopolymers Facility at Harvard Medical School using a NovaSeq 6000 V1.5 S4 full flow cell following sequencing guideline recommended by 10X Genomics protocol.

treatment_protocol: Tumors were collected and processed as discussed in the intracellular cytokine stain portion of the methods. After resuspending the tumor cells and generating a single cell suspension tumor infiltrating lymphocytes were selected for by using magnetic assisted cell sorting (MACS) for CD45+ cells. TILs were isolated following the milteny CD45 (TIL) Microbeads mouse protocol. Briefly, tumor cells were resuspended in 90 µL of MACS Buffer. After resuspension 10 µL of CD45 (TIL) Microbeads mouse were added. Cells were incubated at 4˚C for 15 minutes in the dark. Buffer was then added to the cells to reach 500 µL total volume. The cell suspension was then put through the milteny LS column on a miltenyi QuadroMACS separator and washed twice with 1 ml MACS Buffer. After washing the LS column was removed from the QuadroMACS separator and cells were flushed out using the miltenyi LS column plunger.

value: Tumor


title: G3M4 V(D)J Sequencing


title: WT Cardiomyocytes - AAV-Control replicate 1

description: Library name: ATCC.AAVctr.1


title: G3M14 Gene Expression


title: G3M5 Gene Expression


title: G3M4 Gene Expression


title: G3M13 V(D)J Sequencing


title: G3M13 Gene Expression


title: WT Cardiomyocytes - AAV-EPAS1 replicate 3

description: Library name: ATCC.AAVEPAS1.3


title: G3M11 V(D)J Sequencing


title: G3M11 Gene Expression


title: WT Cardiomyocytes - AAV-EPAS1 replicate 2

description: Library name: ATCC.AAVEPAS1.2


title: G2M4 V(D)J Sequencing

value: Peptide


title: G2M14 V(D)J Sequencing


title: G2M4 Gene Expression


title: G2M14 Gene Expression


title: G3M1 V(D)J Sequencing


title: G2M13 Gene Expression


title: G2M13 V(D)J Sequencing


title: G2M11 V(D)J Sequencing


title: G1M6 Gene Expression

value: Sham


title: G1M3 V(D)J Sequencing


title: G1M3 Gene Expression


title: G3M5 V(D)J Sequencing


title: G1M10 Gene Expression


title: G1M11 Gene Expression


title: G1M1 V(D)J Sequencing


title: TFEBKO_LLOMe_N1

status: Public on Jan 31 2025

city: Kashihara

first: Shuhei

last: Nakamura

state: Nara

address: 840 Shijo-cho

department: Department of Biochemistry

country: Japan

institute: Nara Medical University

data_processing:
Illumina package bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using TopHat (v2.1.1).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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: GRCh38
Supplementary files format and content: RPKMs

source_name: HeLa

growth_protocol: Cells were cultured in Dulbecco’s Modifed Eagle’s medium (D6046, Sigma) supplemented with 10% fetal bovine serum (10270106, Gibco) and penicillin-streptomycin (P4333, Sigma).

extract_protocol:
Isolation of total RNA was performed using RNeasy® Plus Mini Kit (74134, QIAGEN). TruSeq Stranded mRNA Library Prep Kit (Cat#RS-122-2103) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were incubated with 1mM LLOMe (L7393, Sigma) for 1 hr.

value: HeLa

value: TFEBKO

value: L-Leucyl-L-Leucine methyl ester (LLOMe)1h


title: TFEBKO_LLOMe_N2


title: G1M1 Gene Expression


title: G3M1 Gene Expression


title: G1M6 V(D)J Sequencing


title: G2M8 V(D)J Sequencing


title: G1M10 V(D)J Sequencing


title: TFEBKO_Control_N1

value: untreated


title: TFEBKO_Control_N3


title: ATG7KO_LLOMe_N2


title: G2M8 Gene Expression


title: ATG7KO_Control_N2


title: ATG7KO_Control_N1


title: ATG7KO_LLOMe_N3


title: ATG7KO_LLOMe_N1


title: TFEBKO_Control_N2


title: ATG7KO_Control_N3


title: WT_LLOMe1h_N3


title: G2M11 Gene Expression


title: WT_LLOMe1h_N2


title: G1M11 V(D)J Sequencing


title: WT_Control_N3


title: WT_Control_N2


title: WT_Control_N1


title: TFEBKO_LLOMe_N3


title: Hi-C NPC Pcgf2 KO

status: Public on Jan 28 2025

city: Hershey

first: Zhonghua

last: Gao

state: PA

address: 700 HMC Cres Rd

department: Biochemistry

institute: Pennsylvania State University

library_source: genomic

data_processing:
For Rna-seq, estimated read counts were calculated using Kallisto using mm10 as reference genome. Differential expressed genes were identified using DEseq2. STAR was used for alignment and Samtools was used for bam/sam file generation. For ChIP-seq samples, alignment was performed using BWA and mm10 was used as reference genome. Samtools was used to generate bam/sam files. Deeptools were used for bigwig file and visualization. MACS2 was used for peak calling using default parameters. For Hi-C samples, raw FASTQ files were mapped against mm10 mouse reference genome using runHiC pipeline. Briefly, bwa aligner was used for alignments and aligned reads were filtered for quality control and PCR duplication. Fragments were assembled and filtered to retain the fragments with at least 2 different restriction fragments, in order to filter out self-ligated fragments. Last, the reads were binned at multiple resolution of data and generate contract matrix using cooler tools. For each sample, Hi-C data at 10KB resolution were using for look calling, which was achieved using pyHICCUPS from HiCPeaks packages.
Assembly: mm10
Supplementary files format and content: For RNA-seq, Excel (.xlsx) file containing the list of annotated genes and their respective TPM values. For ChIP-seq, BigWig (.bw) files containing read density data of respective immunoprecipitated proteins at mapped genomic loci. For Hi-C, coolers (.cool) files containing the mapped genomic interaction matrices.

molecule: genomic DNA

growth_protocol: ESCs, EBs, and NPCs are cultured in basic stem cell media (DMEM, 15% FBS, 1 X non-essential amino acids, 0.1 mM β-mercaptoethanol, 0.5 X penicillin/streptomycin, 1X sodium pyruvate). For ESCs, 0.003 µg/mL LIF, 1 µM PD0325901 (PD), and 3 µM Chir99021 (CH) are added to the media.

extract_protocol:
Total RNA of samples were extracted with the TRIzol reagent (Invitrogen) according to the manufacturer's protocol. For ChIP-seq samples, cells were cross-linked with 1% formaldehyde for 8 minutes at room temperature. After washing, cells were sonicated with Diagenode Bioruptor in ChIP lysis buffer. For Hi-C samples, cells were cross-linked with 2% formaldehyde and incubated at room temperature for 10 minutes. Samples were sonicated using Covaris focused-ultrasonicator.
RNA samples were prepared for transcriptome sequencing using the TruSeq library preparation kit (Illumina). The ChIP-seq libraries were constructed using the sparQ DNA Library Prep kit. The Hi-C libraries were constructed using Swift Biosciences Accel-NGS 2S Plus DNA Library Kit.

treatment_protocol: NPCs are cultured in basic stem cell media with 5 µM retinoic acid (RA).

value: Mouse embryonic stem cell

value: Pcgf2 knock-out

value: Differentiation (-LIF, 2i; +RA)


title: Hi-C ESC WT

value: ESC culture (+LIF, 2i)


title: Hi-C ESC Pcgf2 KO


title: ChIP-seq ESC Pcgf2-KO Ring1b


title: ChIP-seq ESC WT Ring1b


title: ChIP-seq ESC Pcgf2-KO H2AK119ub1


title: ChIP-seq ESC WT H2AK119ub1


title: RNA-seq NPC Phc1-SAM KO 2


title: ChIP-seq ESC WT Input


title: RNA-seq NPC Phc1 KO 2

value: Phc1 knock-out


title: RNA-seq NPC Pcgf2 KO 1


title: RNA-seq NPC Phc1-SAM KO 1


title: RNA-seq EB day 8 Pcgf2 KO 2

value: Differentiation (-LIF, 2i)


title: RNA-seq EB day 8 WT 1


title: RNA-seq EB day 8 WT 2


title: RNA-seq NPC WT 2


title: RNA-seq NPC Phc1 KO 1


title: RNA-seq NPC WT 1


title: WT_LLOMe1h_N1


title: RNA-seq EB day 3 WT 1


title: RNA-seq ESC Phc1-SAM KO 1


title: RNA-seq EB day 3 Pcgf2 KO 2


title: RNA-seq ESC Phc1-SAM KO 2


title: RNA-seq EB day 3 Pcgf2 KO 1


title: RNA-seq ESC Phc1 KO 2


title: RNA-seq EB day 3 WT 2


title: RNA-seq ESC Phc1 KO 1


title: RNA-seq ESC Pcgf2 KO 2


title: ChIP-seq ESC Pcgf2-KO Input 1


title: RNA-seq ESC WT 1


title: RNA-seq NPC Pcgf2 KO 2


title: RNA-seq ESC Pcgf2 KO 1


title: Control mice1

status: Public on Jan 22 2025

city: Changzhou

first: Chao

last: Tu

state: Jiangsu

address: 185 Juqian Road

department: Department of Internal Medicine

institute: The Third Affiliated Hospital of Soochow University

description:
Control1
Fresh frozen Spatial transcriptome sequencing

data_processing:
*library strategy
Space Ranger (v1.3.1) was used for data preprocessing, gene expression quantifcation and spot identifcation. The raw reads were mapped to the reference genome (mm10) using Space Ranger (v1.3.1) with default parameters. The gene spot matrix was generated by using Visium spatial barcodes, and then spot clustering and gene expression analysis were performed.
Assembly: mm10
Supplementary files format and content: filltered expression matrices with corresponding gene names (.tsv) and barcodes (.tsv)

source_name: kidney

extract_protocol:
Samples were prepared by embedding fresh tissues in OCT Compound (PN-4583, Sakura), and stored at -80℃. To quality the samples, tissue sections were cryosectioned at 10μm by Leica CM1950 cryostat.Then, Hematoxylin & Eosin(H&E) staining, and imaging were performed following 10x Genomics Visium Spatial protocols (CG000160 Rev C, 10X Genomics). Also, some tissue sections were collected to isolate RNA with miRNeasy Mini Kit (PN-217004, QIAGEN).After quality, tissue sections were cryosectioned at 10μm and placed within pre-equilibrated Visium Spatial slide.
The libraries were prepared by Visium Spatial Gene Expression Reagent Kits (PN-1000184, 10x Genomics) according to the manufacturer’s protocol.

value: kidney

tag: Sex

value: male

tag: strain background

value: Control


title: Hyperuricemia mice1

description:
Uox_KO1
Fresh frozen Spatial transcriptome sequencing


title: 147_Vehicle 1

status: Public on Jan 23 2025

city: STANFORD

first: James

last: Brooks

address: 300 PASTEUR DR

institute: STANFORD UNIVERSITY

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. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Supplementary files format and content: Tab-delimited excel file

source_name: LuCaP 147

growth_protocol: Different Prostate cancer PDXs are implanted into the RAG2-/- mice through the intratibial injection  methods, then treated by different componds.The tumors were harvested for the RNAseq.

extract_protocol:
Total RNA was isolated from fresh frozen mouse tibial PDX tumor tissues using an Allprep DNA/RNA mini kit (Qiagen).
After RNA 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. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: LuCaP 147

value: Tumor Tissue

value: vehicle

value: 30 days


title: Hyperuricemia mice2

description:
Uox_KO2
Fresh frozen Spatial transcriptome sequencing


title: RNA-seq EB day 8 Pcgf2 KO 1


title: RNA-seq ESC WT 2

value: WT


title: eHHO_LATSi ,PY37,Female,37 yr. [R1873]

status: Public on Jan 15 2025

city: Tokyo

first: Mayumi

last: Oda

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

institute: Keio University

data_processing:
cutadapt
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt (version 1.18).
Trimmed sequence reads were mapped to hg38 using STAR (version 2.6.1b).
Assembly: Read count extraction and normalization of  the human genes in Ensembl release 81 were performed using RSEM (version 1.3.3).
Supplementary files format and content: hg38
Supplementary files format and content: comma-delimited text files include count and log2(TPM+1) values  for all samples

source_name: liver

growth_protocol: Primary human hepatocytes (PHHs) were embedded in Matrigel and maintained in EM as expanded human hepatocyte organoids (eHHOs).

extract_protocol:
PHHs, eHHOs and dHHOs were subjected to RNA extraction. The cells cultured in eHHOs minus OSM (eHHO_dOSM) and eHHOs minus OSM/WR (eHHO_dOSM_dWR) and dHHO minus Hormone-cocktail (dHHO_dHC) were also subjected to RNA extraction for comparison.
Total RNA was extracted from organoids using a Direct-zol RNA Kit micro (Zymo Research #R2063) according to the manufacturer's instructions. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit v2 (ILLUMINA) following manufacturer's protocols.

treatment_protocol: eHHOs were differentiated in DM containing DAPT and hormone cocktail as differentiated human hepatocyte organoids (dHHOs).

value: liver

value: primary human hepatocytes

value: Caucasian


title: Control mice2

description:
Control2
Fresh frozen Spatial transcriptome sequencing


title: eHHO_dOSM,PY37,Female,37 yr. [R1871]


title: eHHO_LATSi_dOSM,PY37,Female,37 yr. [R1872]


title: eHHO_LATSi_dOSM,PY31,Male,31 yr. [R1867]


title: eHHO_dOSM,PY31,Male,31 yr. [R1866]


title: eHHO_LATSi ,PY30,Male,30 yr. [R1864]


title: eHHO_LATSi ,PY31,Male,31 yr. [R1868]


title: eHHO_LATSi_dOSM,PY30,Male,30 yr. [R1863]


title: eHHO_dOSM,PY30,Male,30 yr. [R1862]


title: eHHO,PY31,Male,31 yr. [R1865]

value: eHHO


title: eHHO_2D_N,PY46,Female,46 yr. [R1471]

value: African american


title: dHHO_1Y,PY39a,Female,39 yr. [R1380]


title: dHHO_WR_GN,PY61,Female,61 yr. [R1044]

value: Latin


title: eHHO_2D_H,PY46,Female,46 yr. [R1468]


title: PHH,PY45,Female,45 yr. [R1582]

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt (version 1.18).
Trimmed sequence reads were mapped to hg38 using STAR (version 2.6.1b).
Read count extraction and normalization of  the human genes in Ensembl release 81 were performed using RSEM (version 1.3.3).
Assembly: hg38
Supplementary files format and content: comma-delimited text files include counts and log2(TPM+1) values  for all samples

growth_protocol: Primary human hepatocytes (PHHs) were embedded in Matrigel and maintained in EM as expanded human hepatocyte organoids (eHHOs).  The cells were also cultured in various expansion condition; in EM minus OSM (eHHO_dOSM) , in EM minus OSM/Wnt/RSPO (eHHO_dOSM_dWR), in EM minus OSM with LATSi (dHHO).  eHHOs  were also differentiated in varios differentiation conditions for 10-14 days; in differentiation medium (DM) (dHHO), in DM minus Hormone-cocktail (dHHO_dHC), in DM contating Wnt and RSPO (dHHO_WR), in DM and then additional starvation and reconstruction (dHHO_GN).

extract_protocol:
PHHs, eHHOs and dHHOs were subjected to RNA extraction.
Total RNA was extracted from organoids using a Direct-zol RNA Kit micro (Zymo Research #R2063) according to the manufacturer's instructions. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit v2 (ILLUMINA) following manufacturer's protocols.

value: African American

value: PHH


title: eHHO_1Y,PY39a,Female,39 yr. [R1379]


title: dHHO_GN,PY45,Female,45 yr. [R1579]


title: dHHO_WR_GN,PY53,Male,53 yr. [R1032]


title: dHHO,PY45,Female,45 yr. [R1578]

value: dHHO


title: eHHO,PY45,Female,45 yr. [R1577]


title: dHHO_GN,PY37,Female,37 yr. [R1576]


title: dHHO,PY37,Female,37 yr. [R1575]


title: dHHO,PY30,Male,30 yr. [R1572]


title: eHHO,PY30,Male,30 yr. [R1571]


title: CLiP_H,PY45,Female,45 yr. [R1470]


title: dHHO_GN,PY30,Male,30 yr. [R1573]


title: ProliHH_H,PY45,Female,45 yr. [R1469]


title: eHHO,PY37,Female,37 yr. [R1574]


title: PHH,PM11,Male,11 mo. [R1411]


title: eHHO_LATSi_dOSM,PY39a,Female,39 yr. [R1402]


title: dHHO_long,PM16,Male,16 mo. [R1378]


title: CLiP_N,PY45,Female,45 yr. [R1467]


title: eHHO_long,PM16,Male,16 mo. [R1377]


title: eHHO_long,PY51,Male,51 yr. [R1375]


title: dHHO_long,PY51,Male,51 yr. [R1376]


title: eHHO_LATSi,PY39a,Female,39 yr. [R1403]


title: eHHO_LATSi_dOSM,PY53,Male,53 yr. [R1406]


title: dHHO_eHHO_LATSi,PM16,Male,16 mo. [R1384]


title: dHHO_eHHO_LATSi,PM11,Male,11 mo. [R1388]


title: dHHO_long,PY53,Male,53 yr. [R1370]


title: eHHO_long,PY53,Male,53 yr. [R1369]


title: dHHO_long,PY61,Female,61 yr. [R1372]


title: dHHO_long,PY39b,Female,39 yr. [R1374]

value: African


title: eHHO_long,PY39b,Female,39 yr. [R1373]


title: eHHO_long,PY61,Female,61 yr. [R1371]


title: dHHO_WR,PY61,Female,61 yr. [R1163]


title: dHHO_WR,PY39b,Female,39 yr. [R1173]


title: dHHO_dHC,PY39b,Female,39 yr. [R1178]

description:
R1178
count.csv
log2TPMp1.csv

data_processing:
cutadapt
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt (version 1.18).
Trimmed sequence reads were mapped to hg38 using STAR (version 2.6.1b).
Read count extraction and normalization of  the human genes in Ensembl release 81 were performed using RSEM (version 1.3.3).
Assembly: hg38
Supplementary files format and content: comma-delimited text files include count and log2(TPM+1) values  for all samples

source_name: hepatocytes

extract_protocol:
Total RNA was extracted from organoids using a Direct-zol RNA Kit micro (Zymo Research #R2063) according to the manufacturer's instructions. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit v2 (ILLUMINA) following manufacturer's protocols.

treatment_protocol:
eHHOs were differentiated in DM containing DAPT and hormone cocktail as differentiated human hepatocyte organoids (dHHOs).
PHHs, eHHOs and dHHOs were subjected to RNA extraction. The cells cultured in eHHOs minus OSM (eHHO_dOSM) and eHHOs minus OSM/WR (eHHO_dOSM_dWR) and dHHO minus Hormone-cocktail (dHHO_dHC) were also subjected to RNA extraction for comparison.

value: hepatocytes


title: ProliHH_N,PY45,Female,45 yr. [R1466]


title: eHHO_LATSi,PY53,Male,53 yr. [R1407]


title: dHHO_dHC,PY63,Male,63 yr. [R1188]

description:
R1188
count.csv
log2TPMp1.csv


title: dHHO_dHC,PY61,Female,61 yr. [R1168]

description:
R1168
count.csv
log2TPMp1.csv


title: ICO,PY39b,Female,39 yr. [R1202]

description:
R1202
count.csv
log2TPMp1.csv

value: ICO


title: ICO,PY39a,Female,39 yr. [R1200]

description:
R1200
count.csv
log2TPMp1.csv


title: dHHO,PM16,Male,16 mo. [R1383]

description:
R1383
count.csv
log2TPMp1.csv


title: dHHO,PY51,Male,51 yr. [R1192]

description:
R1192
count.csv
log2TPMp1.csv


title: dHHO_WR,PY63,Male,63 yr. [R1183]


title: dHHO,PM11,Male,11 mo. [R1387]

description:
R1387
count.csv
log2TPMp1.csv


title: dHHO,PY63,Male,63 yr. [R1182]

description:
R1182
count.csv
log2TPMp1.csv


title: eHHO_dOSM_dWR,PY39a,Female,39 yr. [R779]

description:
R779
count.csv
log2TPMp1.csv


title: eHHO_dOSM_dWR,PY53,Male,53 yr. [R1042]

description:
R1042
count.csv
log2TPMp1.csv


title: eHHO_dOSM,PY39a,Female,39 yr. [R1400]

description:
R1400
count.csv
log2TPMp1.csv


title: dHHO,PY61,Female,61 yr. [R1162]

description:
R1162
count.csv
log2TPMp1.csv


title: eHHO_dOSM,PY53,Male,53 yr. [R1404]

description:
R1404
count.csv
log2TPMp1.csv


title: eHHO,PY53,Male,53 yr. [R1405]

description:
R1405
count.csv
log2TPMp1.csv


title: eHHO,PM11,Male,11 mo. [R1385]

description:
R1385
count.csv
log2TPMp1.csv


title: eHHO,PM16,Male,16 mo. [R1381]

description:
R1381
count.csv
log2TPMp1.csv


title: eHHO,PY39b,Female,39 yr. [R1181]

description:
R1181
count.csv
log2TPMp1.csv


title: eHHO,PY39a,Female,39 yr. [R1401]

description:
R1401
count.csv
log2TPMp1.csv


title: PHH,PM16,Male,16 mo. [R1206]

description:
R1206
count.csv
log2TPMp1.csv


title: eHHO,PY61,Female,61 yr. [R1171]

description:
R1171
count.csv
log2TPMp1.csv


title: eHHO,PY51,Male,51 yr. [R1199]

description:
R1199
count.csv
log2TPMp1.csv


title: PHH,PY51,Male,51 yr. [R1161]

description:
R1161
count.csv
log2TPMp1.csv


title: PHH,PY39b,Female,39 yr. [R1160]

description:
R1160
count.csv
log2TPMp1.csv


title: PHH,PY63,Male,63 yr. [R1159]

description:
R1159
count.csv
log2TPMp1.csv


title: ICO,PY51,Male,51 yr. [R1204]

description:
R1204
count.csv
log2TPMp1.csv


title: PHH,PY61,Female,61 yr. [R1158]

description:
R1158
count.csv
log2TPMp1.csv


title: PHH,PY61,Female,61 yr. [R1040]

description:
R1040
count.csv
log2TPMp1.csv


title: PHH,PY53,Male,53 yr. [R1029]

description:
R1029
count.csv
log2TPMp1.csv


title: dHHO,PY39b,Female,39 yr. [R1172]

description:
R1172
count.csv
log2TPMp1.csv


title: R3517

status: Public on Dec 26 2024

city: New York

first: Zeguo

last: Sun

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

description:
Risk_post-transplant
10x Genomics

data_processing:
The pre- and post-transplant PBMC sequencing data were analyzed separately as they were sequenced in different batch. The raw sequencing data was aligned to human genome hg38 and quantify gene expression with cellranger (7.1.0) count with default parameters. The gene-cell count matrix was submitted to Seurat 4.1.1 for QC, normalization and clustering.
Assembly: hg38
Supplementary files format and content: CellRanger.tar.gz: Filtered matrix from Cellranger count for each sample

extract_protocol:
The PBMC samples were retrieved from the liquid nitrogen tank and thawed for scRNAseq library generation
Briefly, the viable PBMC were loaded into chromium microfluidic chips and barcoded with a 10x Chromium Controller (10x Genomics). RNA from the barcoded cells was subjected to sequencing library generation with reagents from a Chromium Single Cell 3′ v.2 Reagent Kit (10x Genomics) according to the manufacturer's protocol.
The library was sequenced on Illumina sequencer (NovaSeq 6000) at a 150 bp paired-end  sequence length and 400 million read throughput per library.

value: PBMC

value: post-transplant


title: Mouse brain cortex, dscHi-C-multiome, HiC

status: Public on Jan 08 2025

city: Beijing

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

description: Library name: b3-month-BC-dscHiC-gDNA

library_source: other

data_processing:
dscHiCtools (https://github.com/MaoxuWang/dscHiCtools) firstly identify the true cell barcodes from index reads against whitelist (cellranger-atac-2.1.0/lib/python/atac/barcodes/737K-cratac-v1.txt.gz) barcodes that allows one mismatch. Barcodes with no or multiple hits will be discarded. Called cell barcodes are added to read name. Reads then were mapped to reference genome by bwa-mem in "5SP" mode. Hickit were used to extract and dedup contacts from sam file. Notably, we did minor modifications to Hickit (https://github.com/MaoxuWang/hickit) to adapt the single-cell features. Briefly, we extracted the cell barcode to each contact information and cell barcode was also considered in contacts duplication rather than distance (set parameters --dup-dist=100”) alone. Cells with too few contacts were considered as technique noise and were filtered.
Assembly: mm10 / hg38
Supplementary files format and content: .contacts.pairs.gz includes unique valid contact pairs for each single cell in 4DN format
Supplementary files format and content: .metadata.txt includes basic statistics for each single cell

molecule: other

source_name: Brain cortex

growth_protocol: K562 (ATCC, CCL-243) were cultured in Iscove’s Modified Dulbecco’s medium, BJ (ATCC, CRL-2522) were grown in ATCC-formulated Eagle's Minimum Essential Medium, eHAP (Cellosaurus), engineered haploid chronic myeloid leukemia cell line, were grown in Iscove’s Modified Dulbecco’s Medium, GM12878 (Coriell Institute), B lymphoblastoid cells, were grown in Roswell Park Memorial Institute 1640 Medium. These media were supplemented with 10% FBS and 1% Penicillin/Streptomycin, except for GM12878 supplemented with 15% FBS. mESC were grown in knockout DMEM medium containing 15% FBS, 1% Pen/Strep, 2 mM L-glutamine, 1 mM non-essential amino acids, 1 x nucleosides, 3 μM CHIR99021, 1 μM PD0325901, 0.1 mM 2-mercaptoethanol and 1000 U/mL LIF. The plate was pretreated with 1% gelatin. All cells were maintained at 37°C with 5% CO2 at recommended density.

extract_protocol:
Cultured cell line or isolated nuclei from primary brain cortex were processed with Hi-C 3.0 protocol. Cells were firstly double-crosslinked with PFA followed by DSG, then treated with SDS and Triton X-100 to open chromatin. Then the chromatin was digested by resuspending the nuclei in digestion mix containing DdeI and DpnII without detergent, and incubated at 37°C for 2 hours, followed by inactivating the REs. The DNA ends was filled by biotin labeled dATP, followed by proximity ligation using T4 ligase by incubating at room temperature for 2 hours. For sample prepared for dscHi-C multiome experiment, all reaction mix was supplemented 0.5 U/μL Protector RNase inhibitor.
Nuclei processed through Hi-C 3.0 procedure were bulk tagmented with Tn5 transposome, then loaded to 10x Chromium platform according to either ATAC kit or multiome kit. For dscHi-C, the DNA were barcoded by linear amplification in droplet, followed pooling droplets, further amplification and sample index were incorporated. For dscHi-C-multiome, the DNA and RNA from the same cell were barcoded in droplet, the then droplets were pooled and nuclei were decrosslinked. Genomic DNA were pull down using streptavidin beads, and cDNA were further proceeded with second time reverse transcription. Then the genomic DNA were direct subjected to library preparation. The cDNA were further fragmented and amplified for library construction.

value: Brain cortex


title: PHH,PY39a,Female,39 yr. [R901]

description:
R901
count.csv
log2TPMp1.csv


title: R1777

description:
Risk_post-transplant
10x Genomics


title: R817

description:
Ctrl_post-transplant
10x Genomics


title: PBMC-4

description:
Risk_posttransplant
10x Genomics

data_processing:
The pre- and post-transplant PBMC sequencing data were analyzed separately as they were sequenced in different batch. The raw sequencing data was aligned to human genome hg38 and quantify gene expression with cellranger (7.1.0) count with default parameters. The gene-cell count matrix was submitted to Seurat 4.1.1 for QC, normalization and clustering.
Assembly: hg38
Supplementary files format and content: Raw count expression profile of each gene in each cell

extract_protocol:
The PBMC samples were retrieved from the liquid nitrogen tank and thawed for scRNAseq library generation.
Briefly, the viable PBMC were loaded into chromium microfluidic chips and barcoded with a 10x Chromium Controller (10x Genomics). RNA from the barcoded cells was subjected to sequencing library generation with reagents from a Chromium Single Cell 3′ v.2 Reagent Kit (10x Genomics) according to the manufacturer's protocol.
The library was sequenced on Illumina sequencer (NovaSeq 6000) at a 150 bp paired-end sequence length and 400 million read throughput per library.

tag: race

value: pre-transplant


title: PBMC-3

description:
Ctrl_posttransplant
10x Genomics


title: R4697

description:
Ctrl_pretransplant
10x Genomics


title: SW480 cell,KI-CTCF-HiBiT,LgBiT-Tn5(Af-CUT&Tag),Rep1

status: Public on Dec 15 2024

city: Xiamen

first: yongyou

last: zhang

state: Fujian

address: Xiang'an South Road

institute: Xiamen University

description: Library name: SW480_CTCF-HiBiT_LgBiT-Tn5-Rep1

data_processing:
Raw reads were filtered to remove adapter sequences and low-quality sequences using fastp (version 0.20).
Clean reads were mapped to the mouse mm10 or human hg19 reference genome using Bowtie2 (version 2.4) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -l 10 -X 700.
Duplicate reads were removed using Picard MarkDuplicates (version 2.27). Mitochondrial reads, unmapped reads, and reads with mapping quality <30 were filtered out using SAMtools (version 1.15).
BigWig files were generated using deepTools bamCoverage (version 3.3.1) with options: --binSize 10 --normalizeUsing RPGC.
Peaks were called for each sample using MACS2 callpeak (version 2.2) with options: --bdg --SPMR --gsize hs --keepdup all --gvalue 0.05 --shift -75 --extsize 150 --nomodel --call-summits --nolambda.
Assembly: hg19,mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: colon

extract_protocol:
For cell samples, digestion followed by permeabilization is sufficient. For mouse liver tissue, 0.1-0.2 g of liver tissue was excised and washed with 2 mL of swelling buffer (10 mM Tric-HCl pH 7.5, 2 Mm MgCl2, 3 mM CaCl2, 1×Protease inhibitor cocktail). The liver was then dounced in 1 ml of swelling buffer (dounced 10 times, piston A) and incubated at 4°C for 20 min. Afterward, the liver was dounced again 20 times (piston B), and 1 mL of swelling buffer was added. The cells were filtered using a 100 μm cell strainer and spun at 400×g at 4°C for 10 min. The supernatant was removed, and the cells were resuspended in 0.5 ml of swelling buffer + 10% glycerol. Slowly vortex while adding drop by drop 0.5 mL of lysis buffer (Swelling buffer + 10% glycerol + 1% NP-40). Incubate for 5 min at 4°C and add 1.5 mL of lysis buffer. Spin at 600×g at 4°C for 5 min, remove the supernatant, and wash the nuclei again with 1.5 mL of lysis buffer. Spin at 600 g at 4°C for 5 min, remove the supernatant, and resuspend the nuclei in 1 mL of freezing buffer. Finally, the nuclei were stained with DAPI and counted.
Following cell or nucleus counting, permeabilization is performed without the addition of antibodies. The permeabilized samples are incubated with LgBiT-Tn5 or NbALFA-Tn5, and unbound proteins are subsequently removed. A transposition activation reaction is then conducted to fragment intracellular DNA, which is extracted for downstream library preparation. Indexed libraries are generated using universal i5 primers and unique barcoded i7 primers, with each sample assigned a distinct barcode. The libraries are amplified through 15 cycles of PCR, and the resulting DNA is purified for high-throughput sequencing.

value: colon

value: epithelial


title: eHHO,PY63,Male,63 yr. [R1191]

description:
R1191
count.csv
log2TPMp1.csv

value: primary human hepatocytes


title: R587

description:
Risk_pretransplant
10x Genomics


title: R3617

description:
Ctrl_post-transplant
10x Genomics


title: SW480 cell,KI-CTCF-ALFA,NbALFA-Tn5(Af-CUT&Tag),Rep2

description: Library name: SW480_CTCF-ALFA-NbALFA-Tn5-Rep2


title: SW480 cell,KI-CTCF-ALFA,NbALFA-Tn5(Af-CUT&Tag),Rep1

description: Library name: SW480_CTCF-ALFA-NbALFA-Tn5-Rep1


title: 8687-JF-4

status: Public on Dec 14 2024

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

data_processing:
Cellranger for alignment and seurat for data processing
Assembly: hg38
Supplementary files format and content: cellranger output format

source_name: skin

extract_protocol:
Half of a 6 mm biopsy was cryopreserved in CryoStor CS10 media (BioLife Solutions). Samples were thawed on ice, washed briefly in cold Hank’s Balanced Saline Solution (Gibco, Thermo Fisher Scientific) to remove residual CryoStor CS10 media, and bisected before being enzymatically digested in either 0.25% Trypsin-EDTA (Gibco, Thermo Fisher Scientific) with 10U/mL DNase I (Thermo Fisher Scientific) for 1 hour at 37°C, quenched with FBS (Atlanta Biologicals), or 0.2% Collagenase II (Life Technologies) and 0.2% Collagenase V (Sigma) with 10U/ml DNase I in plain medium for 1.5 hours at 37°C with rotation. The resulting cell suspensions were filtered through 70-μm cell strainers twice and re-suspended in PBS containing 0.04% BSA. Dermal and epidermal cells were combined in a 2:1 ratio.
libraries were constructed by the University of Michigan Advanced Genomics Core on the 10X Genomics Chromium system with chemistry v2 and v3

value: skin

tag: disease

value: Control

value: control


title: 8272-JF-3


title: 8272-JF-1


title: SW480 cell,KI-CTCT-HiBiT,nano-Tn5_anti-CTCF(nano-CUT&Tag),Rep1

description: Library name: SW480_CTCF-HiBiT_nano-Tn5_anti-CTCF-Rep1

value: anti-CTCF


title: reprogram_reads2

status: Public on Dec 09 2024

first: Lindsey

last: Muir

state: Michigan

address: 1600 Huron Parkway

institute: University of Michigan

description: Library name: ihsc_p2

data_processing:
Raw reads were processed with EPI2ME Labs `wf-single-cell' (https://github.com/epi2me-labs/wf-single-cell)
genome build/assembly GRCh38
processed data files format and content: Processed files are scanpy compliant AnnData objects.

molecule: polyA RNA

source_name: induced hematopoietic stem cells

growth_protocol: All cells were cultured at 37°C with 5% CO₂. Neonatal human foreskin fibroblasts (BJ, ATCC CRL-2522, RRID:CVCL_3653) were used as the initial cell type for reprogramming. Cells used for control and reprogramming cultures were at an initial passage number between 2 and 4, and were at 10 or fewer passages for endpoints. Fibroblasts were cultured in high glucose DMEM containing sodium pyruvate + 10% fetal bovine serum + 1% penicillin/streptomycin (P/S) + 1% L-glutamine. For reprogramming cultures, plates were coated with 0.1% porcine gelatin (Millipore #SF008). Primary human bone marrow CD34+ cells (ATCC PCS-800-012TM) were cultured in complete MyeloCult H5100 (STEMCELL Technologies 05150).

extract_protocol:
Adherent cells were dissociated using 1x TrypLE Express Enzyme (Gibco #12604-021)
Full-length barcoded cDNA amplicons were obtained from single cells using the 10X Genomics Next GEM Single Cell 3' Kit V3.1. Briefly, 20,000 sorted CD34+ cells and 2,000 control fibroblasts were loaded onto the 10X Genomics Chromium Controller (X) to partition single cells into Gel Beads-In Emulsion (GEMs). cDNA was generated from polyadenylated mRNA transcripts, incorporating a unique molecular identifier (UMI) and a cell-specific barcode for each transcript. Barcoded cDNA was pooled, purified with SILANE magnetic beads (10X Genomics #PN-2000048), and amplified by PCR. Barcoded cDNA libraries were prepared for sequencing according to the Oxford Nanopore Technologies (ONT) 3' cDNA protocols. Briefly, cDNA amplicons were biotin tagged by PCR with the primers shown in the ONT protocols. Biotinylated cDNA was purified with Dynabeads™ M-280 Streptavidin beads (Invitrogen #11205D), followed by secondary PCR amplification and Agencourt AMPure XP bead clean-up (Beckman Coulter #A63881). Products were assessed for quality following ONT recommendations. Long-read cDNA libraries were prepared for sequencing as in ONT protocols and sequenced on an ONT GridION or PromethION Solo 2 (P2) sequencer. Raw reads were base-called with guppy using the High Accuracy basecalling model and stored as fastq files.

treatment_protocol: Lentiviral transductions were carried out in complete medium without penicillin/streptomycin in the presence of 8 µg/mL polybrene (Millipore Sigma TR-1003-G). Integrated TF expression cassettes were induced with 1 µg/mL doxycycline hyclate (Dox, Millipore Sigma D9891) supplemented in the culture medium for 48 hours. Control fibroblasts were untransduced for single cell transcriptomics experiments. Reprogramming cells were switched to complete MyeloCult H5100 with 10e-6 M hydrocortisone (Millipore Sigma #H0888) and 1% P/S for 48 hours after the initial Dox treatment.

value: reprogrammed fibroblast

value: Doxycycline-inducible lentiviral vectors to express GATA2, GFI1B, FOS, STAT5A, and REL


title: SW480 cell,KI-CTCT-HiBiT,nano-Tn5_anti-CTCF(nano-CUT&Tag),Rep2

description: Library name: SW480_CTCF-HiBiT_nano-Tn5_anti-CTCF-Rep2


title: SW480 cell,KI-CTCF-HiBiT,LgBiT-Tn5(Af-CUT&Tag),Rep2

description: Library name: SW480_CTCF-HiBiT_LgBiT-Tn5-Rep2


title: X20181210_M-26_2-24_Group_26_EB5538-127_S1

status: Public on Dec 05 2024

data_processing:
All samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/). Raw reads were examined for quality issues using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library generation and sequencing are suitable for further analysis. Adapter sequences, other contaminant sequences such as polyA tails and low-quality sequences with PHRED quality scores less than five were trimmed from reads using atropos (https://github.com/jdidion/atropos). Trimmed reads were aligned to the mouse genome (mm10) using STAR (look to this reference STAR: ultrafast universal RNA-seq aligner). Alignments will be checked for evenness of coverage, rRNA content, genomic context of alignments (for example, alignments in known transcripts and introns), complexity and other quality checks using a combination of FastQC, Qualimap and other custom tools. Counts of reads aligning to known genes are generated by featureCounts. In parallel, Transcripts Per Million (TPM) measurements per isoform were generated using Salmon (Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference). Differential expression at the gene level were performed by DESeq2 (Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2), using counts per gene estimated from the Salmon quasialignments by tximport. A corrected p value using Benjamini-Hochberg (BH) approach and a cut-off of 0.05 was used to assess significant genes that were up-regulated or down-regulated following Ad26 vaccination. Gene set enrichment analysis (Subramanian, Tamayo, et al. (2005, PNAS 102, 15545-15550) and Mootha, Lindgren, et al. (2003, Nat Genet 34, 267-273)) and database of  biological and immunological modules (https://www.gsea-msigdb.org/gsea/index.jsp) were used to explore enriched pathways at days 3, 7 and 10 after infection. An FDR q value cut-off of 0.05 was used to selected increased or decreased pathways.
Assembly: Mm10
Supplementary files format and content: eb.raw.counts.csv (raw read counts)

source_name: Muscle

extract_protocol:
Tissue samples were collected into RNAlater (Invitrogen). Tissue samples were then transferred to QIAzol and homogenized with a TissueLyzer using 5mm steel beads (all Qiagen).
Blood was processed as outlined in the sample collection section, with cell pellets resuspended in QIAzol. Total RNA was extracted according to the QIAcube HT RNA extraction protocol (Qiagen).
Single-end 75bp libraries were barcoded for multiplexing and sequenced with 20,000 reads per sample on an Illumina NextSeq 500

tag: timepoint

value: 24 hrs

value: Muscle

tag: vaccine type


title: reprogram_reads

description: Library name: ihsc_gridion


title: fibroblast_reads

description: Library name: bj_fibroblast

source_name: neonatal foreskin

value: neonatal foreskin

value: BJ fibroblast

value: fibroblast


title: X20181129_M-26_4-6_Group_14_EB5538_S1

value: 6 hrs


title: X20181110_M-N8_Group_37_EB5538-10of10_S4

value: baseline


title: X20181129_Ill_-5_3-12_Group_23_EB5538_S4

source_name: dLN

value: 12 hrs

value: dLN


title: X20181110_M-N6_Group_37_EB5538-10of10_S3


title: X20181110_M-N4_Group_37_EB5538-10of10_S2


title: X20181110_Ill_-N9_Group_38_EB5538-10of10_S15


title: X20181110_M-N1_Group_37_EB5538-10of10_S1


title: X20181110_M-N9_Group_37_EB5538-10of10_S5


title: X20181110_Ill_-N1_Group_38_EB5538-10of10_S11


title: X20181110_Ill_-N4_Group_38_EB5538-10of10_S12


title: X20181110_Ill_-N8_Group_38_EB5538-10of10_S14


title: X20181110_Ill_-N6_Group_38_EB5538-10of10_S13


title: X20181110_Ill_-5_5-72_Group_35-9of10_S15

value: 72 hrs


title: X20181110_Ill_-26_5-72_Group_36-9of10_S20


title: X20181110_Ill_-5_3-72_Group_35-9of10_S13


title: X20181110_Ill_-5_2-72_Group_35-9of10_S12


title: X20181110_Ill_-5_1-72_Group_35-9of10_S11


title: X20181110_Ill_-5_4-72_Group_35-9of10_S14


title: X20181110_Ill_-26_3-72_Group_36-9of10_S18


title: X20181110_B-N8_Group_38_EB5538-10of10_S9

source_name: Blood

value: Blood


title: X20181110_B-N6_Group_38_EB5538-10of10_S8


title: X20181110_B-N1_Group_38_EB5538-10of10_S6


title: X20181110_Ill_-26_2-72_Group_36-9of10_S17


title: X20181110_Ill_-26_1-72_Group_36-9of10_S16


title: X20181110_B-5_3-72_Group_33-9of10_S3


title: X20181110_B-5_4-72_Group_33-9of10_S4


title: X20181110_B-N4_Group_38_EB5538-10of10_S7


title: X20181110_B-5_5-72_Group_33-9of10_S5


title: X20181110_B-5_2-72_Group_33-9of10_S2


title: X20181110_B-5_1-72_Group_33-9of10_S1


title: X20181110_B-26_4-72_Group_34-9of10_S9


title: X20181110_B-26_5-72_Group_34-9of10_S10


title: X20181110_B-26_3-72_Group_34-9of10_S8


title: X20181110_B-26_2-72_Group_34-9of10_S7


title: X20181109M-5_5-72_Group_31-8of10_S15


title: X20181110_B-26_1-72_Group_34-9of10_S6


title: X20181109M-5_1-72_Group_31-8of10_S11


title: X20181109M-5_2-72_Group_31-8of10_S12


title: X20181109M-5_4-72_Group_31-8of10_S14


title: X20181110_Ill_-26_4-72_Group_36-9of10_S19


title: X20181109M-5_3-72_Group_31-8of10_S13


title: X20181110_B-N9_Group_38_EB5538-10of10_S10


title: X20181109M-26_5-72_Group_32-8of10_S20


title: X20181109M-26_2-72_Group_32-8of10_S17


title: X20181109_M-5_5-24_Group_25_EB5538-7of10_S5


title: X20181109M-26_1-72_Group_32-8of10_S16


title: X20181109_M-5_5-12_Group_19_EB5538-5of10_S15


title: X20181109M-26_4-72_Group_32-8of10_S19


title: X20181109_M-5_4-12_Group_19_EB5538-5of10_S14


title: X20181109_M-5_2-24_Group_25_EB5538-7of10_S2


title: X20181109_M-5_4-24_Group_25_EB5538-7of10_S4


title: X20181109_M-5_3-12_Group_19_EB5538-5of10_S13


title: X20181109_M-5_1-12_Group_19_EB5538-5of10_S11


title: X20181109_M-5_1-24_Group_25_EB5538-7of10_S1


title: X20181109_M-26_5-24_Group_26_EB5538-7of10_S10


title: X20181109_M-26_4-24_Group_26_EB5538-7of10_S9


title: X20181109_M-26_4-12_Group_20_EB5538-5of10_S19


title: X20181109_M-5_2-12_Group_19_EB5538-5of10_S12


title: X20181109_M-26_3-24_Group_26_EB5538-7of10_S8


title: X20181109_M-26_5-12_Group_20_EB5538-5of10_S20


title: X20181109_M-26_2-12_Group_20_EB5538-5of10_S17


title: X20181109_M-26_3-12_Group_20_EB5538-5of10_S18


title: X20181109_M-26_1-24_Group_26_EB5538-7of10_S6


title: X20181109_M-26_1-12_Group_20_EB5538-5of10_S16


title: X20181109_Ill_-5_5-24_Group_29_EB5538-8of10_S5


title: X20181109M-26_3-72_Group_32-8of10_S18


title: X20181109_Ill_-5_4-6_Group_17_EB5538-5of10_S4


title: X20181109_Ill_-5_4-24_Group_29_EB5538-8of10_S4


title: X20181109_M-5_3-24_Group_25_EB5538-7of10_S3


title: X20181109_Ill_-5_2-24_Group_29_EB5538-8of10_S2


title: X20181109_Ill_-5_3-24_Group_29_EB5538-8of10_S3


title: X20181109_Ill_-5_2-6_Group_17_EB5538-5of10_S2


title: X20181109_Ill_-5_1-24_Group_29_EB5538-8of10_S1


title: X20181109_Ill_-5_1-6_Group_17_EB5538-5of10_S1


title: X20181109_Ill_-26_5-6_Group_18_EB5538-5of10_S10


title: X20181109_Ill_-26_5-24_Group_30_EB5538-8of10_S10


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title: X20181109_Ill_-26_4-6_Group_18_EB5538-5of10_S9


title: X20181109_Ill_-26_1-6_Group_18_EB5538-5of10_S6


title: X20181109_Ill_-26_2-24_Group_30_EB5538-8of10_S7


title: X20181109_B-5_5-24_Group_27_EB5538-7of10_S15


title: X20181109_B-5_4-24_Group_27_EB5538-7of10_S14


title: X20181109_Ill_-26_1-24_Group_30_EB5538-8of10_S6


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title: X20181109_B-26_3-24_Group_28_EB5538-7of10_S18


title: X20181109_Ill_-5_3-6_Group_17_EB5538-5of10_S3


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title: X20181105_Ill_-5_5-12_Group_23_EB5538-6of10_S15


title: X20181105_Ill_-5_2-12_Group_23_EB5538-6of10_S12


title: X20181105_Ill_-26_5-12_Group_24_EB5538-6of10_S20


title: X20181105_Ill_-26_3-12_Group_24_EB5538-6of10_S18


title: X20181105_Ill_-26_2-12_Group_24_EB5538-6of10_S17


title: X20181105_Ill_-26_1-12_Group_24_EB5538-6of10_S16


title: X20181105_B-5_5-12_Group_21_EB5538-6of10_S5


title: X20181105_B-5_4-12_Group_21_EB5538-6of10_S4


title: X20181105_B-5_2-12_Group_21_EB5538-6of10_S2


title: X20181109_B-26_1-24_Group_28_EB5538-7of10_S16


title: X20181105_B-5_1-12_Group_21_EB5538-6of10_S1


title: X20181109_B-5_2-24_Group_27_EB5538-7of10_S12


title: X20181105_B-26_5-12_Group_22_EB5538-6of10_S10


title: X20181105_B-26_4-12_Group_22_EB5538-6of10_S9


title: X20181105_B-26_2-12_Group_22_EB5538-6of10_S7


title: X20181105_B-26_3-12_Group_22_EB5538-6of10_S8


title: X20181105_Ill_-5_4-12_Group_23_EB5538-6of10_S14


title: X20181105_B-26_1-12_Group_22_EB5538-6of10_S6


title: X20181101_M-5_5-6_Group_13_EB5538-4of10_S5


title: X20181109_Ill_-26_2-6_Group_18_EB5538-5of10_S7


title: X20181101_M-5_3-6_Group_13_EB5538-4of10_S3


title: X20181101_M-5_2-6_Group_13_EB5538-4of10_S2


title: X20181101_M-5_4-6_Group_13_EB5538-4of10_S4


title: X20181101_M-5_1-6_Group_13_EB5538-4of10_S1


title: X20181101_M-26_3-6_Group_14_EB5538-4of10_S8


title: X20181101_M-26_5-6_Group_14_EB5538-4of10_S10


title: X20181105_Ill_-26_4-12_Group_24_EB5538-6of10_S19


title: X20181101_M-26_1-6_Group_14_EB5538-4of10_S6


title: X20181101_B-5_5-6_Group_15_EB5538-4of10_S15


title: X20181101_B-5_4-6_Group_15_EB5538-4of10_S14


title: X20181101_B-5_3-6_Group_15_EB5538-4of10_S13


title: X20181101_B-5_1-6_Group_15_EB5538-4of10_S11


title: X20181101_B-5_2-6_Group_15_EB5538-4of10_S12


title: X20181105_B-5_3-12_Group_21_EB5538-6of10_S3


title: X20181101_B-26_4-6_Group_16_EB5538-4of10_S19


title: X20181101_B-26_5-6_Group_16_EB5538-4of10_S20


title: X20181101_B-26_1-6_Group_16_EB5538-4of10_S16


title: X20181027_M_5_5_3_Group_7_EB5538_2of10_S15

value: 3 hrs


title: X20181027_M_5_4_3_Group_7_EB5538_2of10_S14


title: X20181027_M_5_2_3_Group_7_EB5538_2of10_S12


title: X20181027_M_5_1_3_Group_7_EB5538_2of10_S11


title: X20181027_M_26_4_3_Group_8_EB5538_2of10_S19


title: X20181027_M_26_5_3_Group_8_EB5538_2of10_S20


title: X20181027_M_26_3_3_Group_8_EB5538_2of10_S18


title: X20181101_M-26_2-6_Group_14_EB5538-4of10_S7


title: X20181027_M_26_2_3_Group_8_EB5538_2of10_S17


title: X20181027_Ill__5_5_1_Group_5_EB5538_2of10_S5

value: 1 hr


title: X20181027_Ill__5_4_3_Group_11_EB5538_3of10_S14


title: X20181027_M_26_1_3_Group_8_EB5538_2of10_S16


title: X20181027_Ill__5_3_1_Group_5_EB5538_2of10_S3


title: X20181027_Ill__5_3_3_Group_11_EB5538_3of10_S13


title: X20181027_Ill__5_2_3_Group_11_EB5538_3of10_S12


title: X20181027_Ill__5_2_1_Group_5_EB5538_2of10_S2


title: X20181027_Ill__5_1_3_Group_11_EB5538_3of10_S11


title: X20181027_Ill__5_1_1_Group_5_EB5538_2of10_S1


title: X20181101_B-26_3-6_Group_16_EB5538-4of10_S18


title: X20181027_Ill__26_5_3_Group_12_EB5538_3of10_S20


title: X20181101_B-26_2-6_Group_16_EB5538-4of10_S17


title: X20181027_Ill__26_5_1_Group_6_EB5538_2of10_S10


title: X20181027_Ill__26_3_3_Group_12_EB5538_3of10_S18


title: X20181027_M_5_3_3_Group_7_EB5538_2of10_S13


title: X20181027_Ill__26_4_1_Group_6_EB5538_2of10_S9


title: X20181027_Ill__26_2_3_Group_12_EB5538_3of10_S17


title: X20181027_Ill__26_1_3_Group_12_EB5538_3of10_S16


title: X20181027_Ill__26_1_1_Group_6_EB5538_2of10_S6


title: X20181027_Ill__5_5_3_Group_11_EB5538_3of10_S15


title: X20181027_Ill__5_4_1_Group_5_EB5538_2of10_S4


title: X20181027_B_5_3_3_Group_9_EB5538_3of10_S3


title: X20181027_B_5_4_3_Group_9_EB5538_3of10_S4


title: X20181027_B_5_2_3_Group_9_EB5538_3of10_S2


title: X20181027_B_26_5_3_Group_10_EB5538_3of10_S10


title: X20181027_B_5_1_3_Group_9_EB5538_3of10_S1


title: X20181027_B_26_3_3_Group_10_EB5538_3of10_S8


title: X20181027_B_26_4_3_Group_10_EB5538_3of10_S9


title: X20181027_B_26_2_3_Group_10_EB5538_3of10_S7


title: X20181027_B_26_1_3_Group_10_EB5538_3of10_S6


title: X20181026_M-5_5-1_Group_1_EB5538-1of10_S5


title: X20181027_Ill__26_4_3_Group_12_EB5538_3of10_S19


title: X20181026_M-5_4-1_Group_1_EB5538-1of10_S4


title: X20181026_M-5_2-1_Group_1_EB5538-1of10_S2


title: X20181026_M-5_3-1_Group_1_EB5538-1of10_S3


title: X20181026_M-26_5-1_Group_2_EB5538-1of10_S10


title: X20181027_Ill__26_3_1_Group_6_EB5538_2of10_S8


title: X20181026_M-26_3-1_Group_2_EB5538-1of10_S8


title: X20181027_Ill__26_2_1_Group_6_EB5538_2of10_S7


title: X20181026_M-5_1-1_Group_1_EB5538-1of10_S1


title: X20181026_M-26_4-1_Group_2_EB5538-1of10_S9


title: X20181026_M-26_1-1_Group_2_EB5538-1of10_S6


title: X20181026_B-5_5-1_Group_3_EB5538-1of10_S15


title: X20181026_B-5_4-1_Group_3_EB5538-1of10_S14


title: X20181026_B-5_3-1_Group_3_EB5538-1of10_S13


title: X20181026_B-5_2-1_Group_3_EB5538-1of10_S12


title: X20181027_B_5_5_3_Group_9_EB5538_3of10_S5


title: X20181026_B-26_5-1_Group4_EB5538-1of10_S20


title: X20181026_B-26_2-1_Group4_EB5538-1of10_S17


title: X20181026_B-26_1-1_Group4_EB5538-1of10_S16


title: 129_PSC_3

status: Public on Nov 27 2024

city: Berkeley

first: Rachel

middle: B

last: Brem

state: CA

address: 321 Koshland Hall

department: Plant and Microbial Biology

institute: UC Berkeley

data_processing:
Reads were mapped to either the GRCm38, CAST_EiJ, 129S1, or a concatenated CAST+129 genome using STAR
Gene counts were generated using STAR's built in quantification (--quantMode GeneCounts)
Assembly: mm10
Supplementary files format and content: tab-delimited including raw read counts for each sample

organism: Mus musculus domesticus

source_name: pluripotent stem cell

extract_protocol:
motor neurons were processed using RNAqueous™-Micro Total RNA Isolation Kit (Thermo Fisher Scientific); PSCs were processed using RNAeasy-Micro Total RNA Isolation Kit (Thermo Fisher Scientific); for both cell types samples were treated on-column with RNase-Free DNase Set (QIAGEN, Hilden, Germany)
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. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: pluripotent stem cell


title: 129_PSC_4


title: 129_PSC_1


title: X20181026_B-26_4-1_Group4_EB5538-1of10_S19


title: 129_PSC_2


title: RD18_snATACseq_miR449a340

city: Leuven

first: Maurilio

last: Sampaolesi

address: Herestraat 49, ON4 - box 804

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

description: Library name: RD18_snATACseq_miR449a340

data_processing:
Each library was sequenced separately on a NovaSeq 6000 instrument using an SP 100 cycles reagent kit (Illumina), targeting 25.000 reads/nuclei for ATAC-seq and a minimum of 20.000 reads/nuclei for gene expression.
Assembly: GRCh38
Supplementary files format and content: Cellranger output files: filtered_feature_bc_matrix.h5, barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Fragments per sample
Supplementary files format and content: bigwig file per sample
Supplementary files format and content: Bed file with atac peaks per sample
Supplementary files format and content: ATAC peak annotations per sample

extract_protocol:
Cells were processed according to the 10x Genomics Chromium Single Cell Multiome ATAC+ Gene Expression low cell number protocol conforming to protocol number CG000365_DemonstratedProtocol_NucleiIsolation_ATAC_GEX_Sequencing_RevB used for cell lysis (0.1x lysis buffer and lysed for 6.5 min) to obtain intact nuclei (10x Genomics, CA, USA).
Single cell ATAC- and RNA-seq libraries were prepared using the Chromium Single Cell Multiome ATAC + Gene Expression Platform (utilizing the 10x Genomics Single Cell Multiome Kit) .
Nuclei were prepared and counted to ensure quality and concentration. Nuclei were then transposed according to the manufacturers’ protocol. Transposed nuclei suspension was loaded onto the Next GEM Chip J (Chromium Next GEM Chip J Single Cell Kit) targeting 5000 nuclei and then ran on a Chromium Controller instrument to generate GEM emulsion (10x Genomics). Single cell gene expression libraries, as well as single cell ATAC-seq libraries, were generated according to the manufacturers’ protocol using the Chromium Next GEM Single Cell Multiome ATAC+ Gene Expression kit (10x Genomics). Final libraries were quantified using the NEBNext Library Quant Kit for Illumina (New England Biolabs, MA, USA) and High Sensitivity D1000 TapeStation (Agilent Technologies, CA, USA).

value: Human FN-RMS cell line


title: 129CAS_PSC_4

description: Mmd x Mmc F1 hybrid

organism: Mus musculus domesticus x Mus musculus castaneus


title: RD18_snATACseq_vehicle

description: Library name: RD18_snATACseq_vehicle


title: X20181026_M-26_2-1_Group_2_EB5538-1of10_S7


title: RD18_snRNAseq_vehicle

description: Library name: RD18_snRNAseq_vehicle

molecule: nuclear RNA


title: 129CAS_PSC_1

description: Mmd x Mmc F1 hybrid


title: 129CAS_PSC_2

description: Mmd x Mmc F1 hybrid


title: CAST_stem_cell_rep1

status: Public on Nov 06 2024

data_processing:
Reads were re-mapped to either the GRCm38 or CAST_EiJ genome using TopHat v 2.1.1 (parameters: -N 0 --library-type fr-unstranded)
Aligned reads were sorted with Samtools sort (parameters: -o)
Gene counts were generated using the htseq-count Python script (parameters: -s no -r pos)
Assembly: mm10
Supplementary files format and content: tab-delimited including raw read counts for each sample

organism: Mus musculus castaneus

tag: strain

value: CAST/EiJ

tag: batch info


title: CAST_stem_cell_rep2


title: p20185-s059_20-17_BH69_D28

status: Public on Oct 30 2024

data_processing:
Reads were aligned using STAR v2.7.3. Reads were aligned to M. mulatta genome. We used the macaque genome reference M. mulatta– MacaM (www.unmc.edu/rhesusgenechip/index.htm). DESeq2 was used to generate the normalized read count table based on their estimateSizeFactors() function with default parameters by calculating a pseudoreference sample of the geometric means for each gene across all samples and then using the “median ratio” of each sample to the pseudoreference as the sizeFactor for that sample.
Differential expression at the gene level was performed by DESeq2 implemented in the DESeq2 R package using counts per gene generated by a custom script that pulls out the library prep abundance estimation column into files and read those files into DESeq2 with the DESeqDataSetFromHTSeqCount() function. A corrected P value cutoff of 0.05 was used to assess genes that were significantly up-regulated or down-regulated at days 1, 7, 14, and 28 compared to baseline using the Benjamini-Hochberg (BH) method.
Assembly: MacaM
Supplementary files format and content: GSE193264_update.rawCounts.csv (raw read counts)
Supplementary files format and content: GSE193264_update.normCounts.csv (normalized read counts)

organism: Macaca mulatta

extract_protocol:
RNA was isolated from blood samples stored in PAXgene tubes at the Yerkes National Primate Center for library preparation (www.yerkes.emory.edu/nhp_genomics_core/).
NA quality was assessed using an Agilent 4200 TapeStation and concentration using the Qubit RNA HS assay (Thermo Fisher Scientific). Globin transcripts in the blood RNA were blocked with the FastSelect Globin Reagent (QIAGEN) before library preparation. Libraries were prepared using the Clontech SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio) in combination with the NexteraXT DNA Library Preparation Kit to append dual-indexed adapter sequences (Illumina). Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled at equimolar concentrations, and sequenced on an Illumina NovaSeq 6000 at 100SR, yielding 25 to 30 million reads per sample.
Raw reads were examined for quality issues using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure that library generation and sequencing are suitable for further analysis.

tag: animal id

tag: days post-prime

tag: vaccine

tag: dose


title: RD18_snRNAseq_miR449a340

description: Library name: RD18_snRNAseq_miR449a340

tag: treatment


title: p20185-s060_20-17_BS32_D28

tag: tissue


title: patient PBMCs

status: Public on Nov 05 2024

city: Seoul

first: Haeyoon

last: KWON

address: 103 Daehak-ro

country: South Korea

institute: Seoul National University College of Medicine

data_processing:
FASTQ files were aligned to the GRCh38 reference using Cell Ranger (v7.1.0). Sample demultiplexing was performed with Demuxafy, using SNP genotypes obtained from the Illumina Infinium Asian Screening Array. Ambient RNA contamination was removed using SoupX, and doublets were identified and filtered with DoubletFinder. Quality control was conducted in Seurat (v5.0.3), excluding cells with <200 or >3,000 genes, >5% mitochondrial reads, or >10% hemoglobin gene expression.
Assembly: hg38
Supplementary files format and content: rds file: Merged Seurat object containing single-cell RNA-seq data from a patient with biallelic BRF2 mutations and four pediatric healthy controls.

source_name: peripheral blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from 16 mL of blood collected from the patient using heparin CPT tubes (BD, USA). After centrifugation at 1,800 g for 20 minutes, the PBMC layer was harvested, transferred to a conical tube with culture media (RPMI with 10% FBS), cryopreserved using Cell Banker 1 (AMSBIO, UK), and stored in liquid nitrogen until library preparation.
Single-cell cDNA and library construction followed the 10X Genomics 5’ HT v2 protocol. Samples were multiplexed and pooled into a single Gel Beads-in-Emulsion (GEM), generated using the Chromium Controller, which encapsulated single cells with barcoded gel beads. Reverse transcription produced cDNA from mRNA, and GEMs were disassembled. Full-length cDNAs were purified using SILANE magnetic beads and amplified to the target cell recovery level. The resulting cDNAs were used to create gene expression libraries for sequencing.

value: peripheral blood

value: peripheral blood mononuclear cells


title: p20185-s057_20-17_16_040_D28


title: p20185-s058_20-17_BH31_D28


title: p20185-s056_20-17_15_147_D28


title: control PBMCs


title: X20181026_B-5_1-1_Group_3_EB5538-1of10_S11

tag: genotype


title: X20181026_B-26_3-1_Group4_EB5538-1of10_S18


title: p20185-s054_20-17_BE75_D28


title: p20185-s053_20-17_16_144_D28


title: p20185-s052_20-17_16_138_D28


title: p20185-s050_20-17_BS32_D14


title: p20185-s051_20-17_15_133_D28


title: p20185-s055_20-17_BE00_D28


title: p20185-s049_20-17_BH69_D14


title: p20185-s048_20-17_BH31_D14


title: p20185-s046_20-17_15_147_D14


title: 129CAS_PSC_3

description: Mmd x Mmc F1 hybrid


title: p20185-s044_20-17_BE75_D14


title: p20185-s047_20-17_16_040_D14


title: p20185-s042_20-17_16_138_D14


title: p20185-s043_20-17_16_144_D14


title: p20185-s045_20-17_BE00_D14


title: p20185-s039_20-17_BH69_D7


title: p20185-s040_20-17_BS32_D7


title: p20185-s038_20-17_BH31_D7


title: p20185-s037_20-17_16_040_D7


title: p20185-s041_20-17_15_133_D14


title: p20185-s035_20-17_BE00_D7


title: p20185-s032_20-17_16_138_D7


title: p20185-s034_20-17_BE75_D7


title: p20185-s031_20-17_15_133_D7


title: p20185-s010_20-17_BS32_D0


title: p20185-s033_20-17_16_144_D7


title: p20185-s036_20-17_15_147_D7


title: p20185-s009_20-17_BH69_D0


title: p20185-s004_20-17_BE75_D0


title: p20185-s007_20-17_16_040_D0


title: p20185-s006_20-17_15_147_D0


title: p20185-s008_20-17_BH31_D0


title: p20185-s005_20-17_BE00_D0


title: p20185-s003_20-17_16_144_D0


title: p20185-s001_20-17_15_133_D0


title: LN_3

status: Public on Oct 08 2024

city: Columbus

first: Juhi

last: Bagaitkar

address: 700 Childrens Dr

institute: Nationwide Childrens.org

data_processing:
Pair-end reads coming from bulk RNA-seq were aligned with STAR v2.7.0f. Gene counts were derived by featureCount v2.0.0.
Assembly: GRCh38.p14
Supplementary files format and content: Tab-delimited text file with raw counts

source_name: Neutrophils

extract_protocol:
RNA was collected from purified neutrophils treated with vehicle control or RgpB using RNeasy mini kit (Qiagen) according to kit instructions. Approx. 1 ug of RNA was used for construction of the sequencing library.
Takara-Clontech SMARTseq mRNA LP (according to kit instructions)

value: Neutrophils

value: Control for RgpB-treated neutrophils


title: gLN_3

value: RgpB-treated neutrophils


title: gLN_2


title: gLN_1


title: Lung, Bleomycin day 28, Rep 12

status: Public on Sep 27 2024

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

country: Denmark

institute: Gubra

description: library name: 18644

data_processing:
Reads were aligned to the GRCm38 Ensembl Mus musculus genome and counted using STAR v.2.7.0f with default settings.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file contaning raw counts from each sample

source_name: Lung

extract_protocol:
The inferior lobe was dissected, homogenised in lysis buffer and RNA was isolated using the NucleoSpin® Kit (MACHEREY-NAGEL).
cDNA libraries were prepared using the NEBNext® Ultra II Directional RNA library prep kit for illumina (New England Biolabs) and sequenced on NextSeq 500 (Illumina) with the NextSeq 500/550 High Output kit V2 (#75 CYS, Illumina)

treatment_protocol: 12–14-week-old mice received a single intratracheal instillation of bleomycin sulphate. Untreated mice served as healthy controls (CTRL). Only animals that showed a mild to moderate body weight loss (≥-5% and ≤-17%) at day 6 post-administration were randomized into study groups. Animals were terminated on day 7, 14, 21, 28, 35, or 42 after BLEO administration

value: Lung

value: Bleomycin

tag: time point

value: day 28


title: Lung, Bleomycin day 35, Rep 12

description: library name: 18645

value: day 35


title: Lung, Bleomycin day 21, Rep 12

description: library name: 18643

value: day 21


title: Lung, Bleomycin day 14, Rep 12

description: library name: 18642

value: day 14


title: Lung, Bleomycin day 28, Rep 11

description: library name: 18640


title: Lung, Bleomycin day 35, Rep 11

description: library name: 18641


title: Lung, Bleomycin day 21, Rep 11

description: library name: 18639


title: Lung, Bleomycin day 14, Rep 11

description: library name: 18638


title: Lung, Bleomycin day 35, Rep 10

description: library name: 18637


title: Lung, Bleomycin day 14, Rep 10

description: library name: 18634


title: Lung, Bleomycin day 35, Rep 9

description: library name: 18631


title: Lung, Bleomycin day 21, Rep 9

description: library name: 18629


title: Lung, Bleomycin day 28, Rep 10

description: library name: 18636


title: Lung, Bleomycin day 7, Rep 10

description: library name: 18633

value: day 7


title: Lung, Bleomycin day 21, Rep 10

description: library name: 18635


title: Lung, Saline, Rep 10

description: library name: 18632

value: Saline


title: Lung, Bleomycin day 14, Rep 9

description: library name: 18628


title: Lung, Bleomycin day 35, Rep 8

description: library name: 18625


title: p20185-s002_20-17_16_138_D0

city: Boston

value: Blood


title: LN_2

tag: cell type


title: Lung, Saline, Rep 9

description: library name: 18626


title: Lung, Bleomycin day 21, Rep 8

description: library name: 18623


title: Lung, Bleomycin day 7, Rep 9

description: library name: 18627


title: Lung, Bleomycin day 42, Rep 7

description: library name: 18619

value: day 42


title: Lung, Bleomycin day 14, Rep 8

description: library name: 18622


title: Lung, Bleomycin day 28, Rep 7

description: library name: 18617


title: Lung, Bleomycin day 7, Rep 8

description: library name: 18621


title: Lung, Bleomycin day 21, Rep 7

description: library name: 18616


title: Lung, Bleomycin day 14, Rep 7

description: library name: 18615


title: Lung, Bleomycin day 35, Rep 7

description: library name: 18618


title: Lung, Bleomycin day 7, Rep 7

description: library name: 18614


title: Lung, Bleomycin day 28, Rep 9

description: library name: 18630


title: Lung, Bleomycin day 35, Rep 6

description: library name: 18611


title: Lung, Saline, Rep 7

description: library name: 18613


title: Lung, Bleomycin day 28, Rep 6

description: library name: 18610


title: Lung, Bleomycin day 21, Rep 6

description: library name: 18609


title: Lung, Bleomycin day 14, Rep 6

description: library name: 18608


title: Lung, Saline, Rep 6

description: library name: 18606


title: Lung, Bleomycin day 7, Rep 6

description: library name: 18607


title: Lung, Bleomycin day 14, Rep 5

description: library name: 18601


title: Lung, Bleomycin day 21, Rep 5

description: library name: 18602


title: Lung, Bleomycin day 28, Rep 5

description: library name: 18603


title: Lung, Bleomycin day 35, Rep 5

description: library name: 18604


title: Lung, Saline, Rep 8

description: library name: 18620


title: Lung, Bleomycin day 7, Rep 5

description: library name: 18600


title: Lung, Bleomycin day 42, Rep 4

description: library name: 18598


title: Lung, Saline, Rep 5

description: library name: 18599


title: Lung, Bleomycin day 28, Rep 4

description: library name: 18596


title: Lung, Bleomycin day 35, Rep 4

description: library name: 18597


title: Lung, Bleomycin day 21, Rep 4

description: library name: 18595


title: Lung, Bleomycin day 28, Rep 8

description: library name: 18624


title: Lung, Saline, Rep 4

description: library name: 18592


title: Lung, Bleomycin day 14, Rep 4

description: library name: 18594


title: Lung, Bleomycin day 42, Rep 3

description: library name: 18591


title: Lung, Bleomycin day 28, Rep 3

description: library name: 18589


title: Lung, Bleomycin day 21, Rep 3

description: library name: 18588


title: Lung, Bleomycin day 7, Rep 4

description: library name: 18593


title: Lung, Bleomycin day 14, Rep 3

description: library name: 18587


title: Lung, Bleomycin day 35, Rep 3

description: library name: 18590


title: Lung, Bleomycin day 42, Rep 5

description: library name: 18605


title: Lung, Bleomycin day 35, Rep 2

description: library name: 18583


title: Lung, Saline, Rep 3

description: library name: 18585


title: Lung, Bleomycin day 42, Rep 2

description: library name: 18584


title: Lung, Bleomycin day 7, Rep 3

description: library name: 18586


title: Lung, Bleomycin day 28, Rep 2

description: library name: 18582


title: Lung, Bleomycin day 7, Rep 2

description: library name: 18579


title: Lung, Bleomycin day 14, Rep 2

description: library name: 18580


title: Lung, Bleomycin day 42, Rep 6

description: library name: 18612


title: Lung, Bleomycin day 35, Rep 1

description: library name: 18576


title: Lung, Bleomycin day 42, Rep 1

description: library name: 18577


title: Lung, Bleomycin day 28, Rep 1

description: library name: 18575


title: Lung, Bleomycin day 21, Rep 1

description: library name: 18574


title: Lung, Bleomycin day 7, Rep 1

description: library name: 18572


title: Lung, Bleomycin day 14, Rep 1

description: library name: 18573


title: UDSP-Hep, scRNA-seq

status: Public on Aug 28 2024

first: Yuanhanyu

last: Luo

address: No.7, Science Park Road, Zhongguancun Life Science Park, Beijing

institute: National Institute of Biological Sciences

description: 10x Genomics

data_processing:
Downstream pre-processing steps were performed using Cell Ranger (v.7.0.0) for sample demultiplexing, barcode processing, alignment, filtering and UMI counting.
For the first step of quality control, cells with less than 300 genes or more than 6,000 genes detected were removed. After this exclusion, cells with greater than 10% mitochondrial gene content were excluded.
scDblFinder (v.1.16.0) was utilized to detect and remove possible multiple cells captured within the same droplet (also called doublets/multiplets), yielding an expression matrix of 12,984 cells.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: annotated_Version20250711_PBS.rds: This file contains a set of repeated PBS (control) group Seurat objects, intended to help readers explore the expression of ALPK1 and TIFA across different cell lines under baseline (unstimulated) conditions.

source_name: Tumour-infiltrating immune cells

extract_protocol:
On day 19, three tumours from each experimental group were excised for further analysis. Tumour-infiltrating immune cells were isolated according to the methodology outlined in the section "Flow cytometry analysis of immune cells in tumours and dLNs". These cells were then subjected to staining with PE-anti-mouse CD45 antibody (clone 30-F11, BioLegend). The CD45+ immune cell population was subsequently enriched utilizing a BD FACSAria Fusion flow cytometer. Real-time monitoring of cell viability was conducted during the preparation of the single CD45+ immune-cell suspension.
Subsequently, ten thousand cells (approximately 1,000 single cells per microlitre) from each experimental group were barcoded and pooled using the 10x Genomics device. Sample preparation was carried out in accordance with the manufacturer's protocol, and sequencing was performed on an Illumina NextSeq sequencer.

treatment_protocol: Mice were administered subcutaneous injections of 1×106 B16F10-OVA cells, with subsequent injections of either PBS or UDSP-Hep on days 10, 12, 14, and 16 of the experimental timeline

value: Tumour-infiltrating immune cells

value: subsequent injections of UDSP-Hep


title: Lung, Saline, Rep 1

description: library name: 18571


title: Lung, Bleomycin day 21, Rep 2

description: library name: 18581