title: RNA2_4

city: Davis

first: Karol

last: Cichewicz

address: 1544 Newton Ct

department: Center for Neuroscience

institute: UC Davis

data_processing:
Alignment with STAR (version 2.5.4b)
Gene counts were generated using featureCounts
Assembly: Rn7
Supplementary files format and content: CSV gene counts

source_name: Coronal slice, 150 um thick, including hippocampus and cortical and subcortical structures

extract_protocol:
Total RNA was extracted using Ambion RNAqueous Total RNA Isolation Kit (cat# AM1912)
Illumina poly-A-enriched mRNA libraries
Illumina bulk RNA-seq, PE150

tag: condition

value: MARA

tag: autoantibody

value: F

tag: dam id

value: WT


title: 216_pre

status: Public on Jul 02 2025

type: SRA

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

description: Library name: 216_pre

library_source: transcriptomic

data_processing:
Trimming reads using fastp 0.23.4
alignment to mirbase 22.1 reference data using bowtie 1.3.0
Batch correction using ComBat-seq
Normalization and differential expression analysis using DESeq2 v1.40.2
Assembly: mirbase 22.1 human and hg38
Supplementary files format and content: Raw count data for mature miRNAs (not batch corrected)
Supplementary files format and content: Raw count data for hairpin miRNAs (not batch corrected)

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Blood samples were collected into EDTA tubes to prevent coagulation and processed within three hours to isolate peripheral blood mononuclear cells (PBMCs) using Ficoll-Paque (Cytiva) in accordance with the manufacturer’s guidelines. The PBMCs were stored in Trizol Reagent (Invitrogen) at -80°C until all samples were collected. RNA was extracted from the PBMCs following the manufacturer’s instructions, and eluted in DEPC-treated water.
RNA libraries for RNA-seq were prepared using the SMARTer smRNA-Seq Kit for Illumina (Takara) according to the manufacturer’s protocol.

tag: tissue

value: PBMC

tag: trial

value: B

tag: participant

tag: sport

value: Runner

tag: bmi

tag: Sex

value: Male

tag: timing

value: pre

tag: batch


title: Ischemic_jej_3xporcine

city: Chapel Hill

first: Yuliya

last: Pylayeva-Gupta

state: North Carolina

address: 450 West Dr

department: Genetics

country: USA

institute: University of North Carolina at Chapel Hill

library_source: transcriptomic single cell

data_processing:
Raw reads were processed and quantified using alevin v2.0.1 with Ensemble gene annotations for S. scrofa (v11.1.105), retaining all possible cell barcodes with “—keepCBFraction 1”
Data were imported into R studio using tximport and converted into a Seurat object restricting to cells with at least 100 genes detected, and genes expressed in at least 100 cells
Cells with high mitochondrial contribution were removed using MiQC, then an additional filter was applied to retain cells with at least 500 genes detected and 1000 UMIs, resulting in 1,359 cells and 13,337 genes
Counts were then log-normalized and scaled, and dimensionality was reduced using the top 50 principal components
Assembly: S. scrofa (v11.1.105)
Supplementary files format and content: files containing feature barcode matrix data

molecule: polyA RNA

organism: Sus scrofa

source_name: Jejunem Epithelium

extract_protocol:
Single cells were flow sorted to enrich for live single epithelial cells. Of the 8.3 million cells sorted, there were 147,000 cells that passed Annexin V live/dead and EpCAM parameters.
Cells were loaded onto the Chromium Next GEM Single Cell 3’ GEM, Library and Gel Bead Kit v3.1 for complementary DNA library preparation

treatment_protocol: Segments of the distal jejunum of three commercial Yorkshire cross pigs were subjected to 30 minutes of ischemic injury followed by 30 minutes of ex vivo recovery. Upon sloughing and dissociation, villus epithelial cells isolated from the jejunum of all three pigs were pooled, sorted and sequenced.

value: Jejunem Epithelium

tag: cell line

value: tissue

tag: cell type

value: epithelial

tag: genotype

tag: treatment

value: Ischemia


title: 89_M09_L5

city: HOUSTON

first: Jesus

last: Eraso

state: TX

address: 6670 Bertner

department: Pathology and Genomic Medicine

institute: Methodist Hospital

description:
Library name: Sample 71
Library obtained after processing Layer 5 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36089

data_processing:
Multiplexed single-end (SE) libraries corresponding to the in vitro and the in vivo samples were sequenced on Illumina NextSeq 500/550 and Novaseq 6000 instruments, respectively. Basecalling and demultiplexing were done on the instruments, and the RNA-Seq data was output as fastq files.
RNA-seq reads generated from the in vitro-grown samples were mapped to strains MGCS36044 (GenBank accession number CP117287.1) and MGCS36089 (GenBank accession number CP117284.1), using Edge-pro v1.3.1 (Estimated Degree of Gene Expression for Prokaryotes) which generated RPKM values by normalizing the read counts for both gene length and sequencing depth. RNA-seq reads generated from the in vivo-grown samples were first mapped to the Macaca fascicularis 6.0 assembly (GenBank accession number GCA_011100615.1) using STAR. The reads mapping to M. fascicularis were excluded, and the left-over reads were mapped to strains MGCS36044 and MGCS36089 using Edge-pro v1.3.1.
Sequencing read quality was evaluated with FASTQC software.
Adapter contamination and read quality filtering was performed with Trimmomatic.
Assembly: strains MGCS36044 (GenBank accession number CP117287.1) and MGCS36089 (GenBank accession number CP117284.1) were used for read alignment.
Supplementary files format and content: Raw reads were normalized by EDGEPro. A matrix named RPKMs_all_samples has been generated.

organism: Streptococcus dysgalactiae

source_name: NHP skeletal muscle

growth_protocol: For in vitro growth, cells were grown in Todd-Hewitt broth supplemented with yeast extract (THY media) at 37° C in atmosphere supplemented with 5% CO2. Cells were collected at mid-exponential (ME) at OD=1, and at early stationary phase (ES), at OD=2.

extract_protocol:
In vitro grown pelleted cells were mechanically disrupted using silica beads, RNA was isolated using RNeasy kit, contaminating DNA was degraded using Turbo DNA-free (Ambion), and rRNA was depleted using NEBNext rRNA depletion kit (bacteria) (NEB). The tissue (80-100 mg) corresponding to the in vivo samples was washed in PBS, homogenized, and mechanically disrupted using ZR bashing beads, 0.1 mm and 0.5 mm, (Zymo Research). RNA was extracted (MasterPure Complete DNA and RNA purification kit, Lucigen), subjected to three consecutive DNase treatments with Turbo DNA-free (Ambion), and depletion of ribosomal RNA was performed with the NEBNext rRNA depletion kit (bacteria) supplemented with human/mouse /rat depletion mix (NEB).
cDNA libraries from in vitro and in vivo samples were generated from rRNA depleted RNA using a NEBNext Ultra II Directional RNA Library Preparation kit for Illumina (NEB).

treatment_protocol: For in vitro growth, at the desired growth stage, mid-exponential (OD 600nm 1) or early-stationary (OD 600nm 2), the culture was treated with RNAprotect Bacteria Reagent and cells were harvested by centrifugation. For the in vivo growth the excised tissue sections were submerged in RNAShield and frozen at -80°C until processed.

value: NHP skeletal muscle

value: RNA extracted from HNP biopsy


title: 111_post

description: Library name: 111_post

value: A

value: post


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 024 [KBRZUSPRA_0113_S15_L001]

city: Ribeirão Preto

first: Junier

middle: Marrero

last: Gutiérrez

state: São Paulo

address: Av Bandeirantes, 3900

department: Pediatric

country: Brazil

institute: Ribeirão Preto Medical School-University of São Paulo

description:
Library name: KBRZUSPRA_0113_S15_L001
ACP_024

data_processing:
FASTQ’s were merged and aligned to GRCh387 using STAR (v2.5.3a)
All sequencing reads were converted to industry standard FASTQ files using BCL2FASTQ v1.8.4, and provided by the facility. The FASTQ files were merged and aligned to the human genome version GRCh38 using STAR v2.5.3a (40). Picard Mark Duplicates (v1.128) identified duplicate reads in the aligned BAM files and with featureCounts (v1.6.0) (41) obtained counting reads for the genomic feature of interest. We applied variance-stabilizing transformation (VST) to the read counts for downstream analysis
Assembly: GRCh38
Supplementary files format and content: raw count for each sample

source_name: microdissected tumor tissue

extract_protocol:
RNA were extracted from microdissected, fresh frozen ACP samples using Rneasy kit (QIAGEN, Hilden, Germany)
NEBNext® Ultra™ II Directional RNA Library Prep Kit (E7765)

value: microdissected tumor tissue

tag: gender

value: Female

tag: age at_diagnosis(years)

tag: tumor size_(cm)

value: not available

tag: volume (cm3)

tag: hypothalamic invasion

value: type 2


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 023 [KBRZUSPRA_0112_S14_L002]

description:
Library name: KBRZUSPRA_0112_S14_L002
ACP_023

tag: tissue


title: 89_M09_L4

description:
Library name: Sample 70
Library obtained after processing Layer 4 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36089


title: 89_M10_L1

description:
Library name: Sample 72
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 10, 24h. after infection with SDSE MGCS36089


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 023 [KBRZUSPRA_0112_S14_L001]

description:
Library name: KBRZUSPRA_0112_S14_L001
ACP_023


title: 133_pre

description: Library name: 133_pre

value: PBMC

tag: trial

value: Cyclist


title: RNA2_3

state: CA

organism: Rattus norvegicus

value: Coronal slice, 150 um thick, including hippocampus and cortical and subcortical structures

tag: condition

value: MARA

tag: autoantibody

value: F

tag: dam id

value: WT

tag: time


title: 106_pre

description: Library name: 106_pre

tag: participant

tag: sport

value: Untrained

tag: bmi

tag: Sex

tag: timing

value: pre


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 019 [KBRZUSPRA_0103_S7_L002]

description:
Library name: KBRZUSPRA_0103_S7_L002
ACP_019


title: 89_M09_L3

description:
Library name: Sample 69
Library obtained after processing Layer 3 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36089

tag: genotype

tag: treatment


title: RNA2_2

value: M


title: 89_M09_L2

description:
Library name: Sample 68
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36089

value: NHP skeletal muscle


title: RNA2_1


title: 220_post

description: Library name: 220_post

value: B

value: Runner

value: Male

tag: batch


title: RNA1_4


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 019 [KBRZUSPRA_0103_S7_L001]

description:
Library name: KBRZUSPRA_0103_S7_L001
ACP_019

value: microdissected tumor tissue

tag: gender

tag: age at_diagnosis(years)

tag: tumor size_(cm)


title: 130_post

description: Library name: 130_post

tag: tissue

value: A

value: Female

value: post


title: RNA1_3


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 015 [KBRZUSPRA_0101_S18_L001]

description:
Library name: KBRZUSPRA_0101_S18_L001
ACP_015

tag: volume (cm3)

tag: hypothalamic invasion

value: type 2


title: RNA1_2

tag: condition

tag: autoantibody


title: 230_post

description: Library name: 230_post

value: PBMC

tag: trial

value: Cyclist


title: 44_M16_L1_run3

description:
Library name: Sample 65
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 16, 24h. after infection with SDSE MGCS36044 (re-sequence-3)

value: RNA extracted from HNP biopsy


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 012 [KBRZUSPRA_0090_S12_L002]

description:
Library name: KBRZUSPRA_0090_S12_L002
ACP_012


title: 44_M16_L1_run2

description:
Library name: Sample 64
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 16, 24h. after infection with SDSE MGCS36044 (re-sequence-2)


title: RNA1_1

value: Coronal slice, 150 um thick, including hippocampus and cortical and subcortical structures

value: MARA

tag: dam id

tag: time


title: 233_post

description: Library name: 233_post

tag: participant

tag: sport

tag: bmi


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 012 [KBRZUSPRA_0090_S12_L001]

description:
Library name: KBRZUSPRA_0090_S12_L001
ACP_012


title: 44_M16_L1_run1

description:
Library name: Sample 63
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 16, 24h. after infection with SDSE MGCS36044 (re-sequence-1)

tag: genotype


title: FcRn4_4

tag: Sex

value: F

value: WT


title: 210_pre

description: Library name: 210_pre

tag: timing

value: pre

tag: batch


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 010 [KBRZUSPRA_0082_S71_L002]

description:
Library name: KBRZUSPRA_0082_S71_L002
ACP_010

tag: gender

tag: age at_diagnosis(years)


title: 44_M15_L2_run4

description:
Library name: Sample 62
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36044 (re-sequence-4)

tag: tissue

value: NHP skeletal muscle

tag: treatment


title: 44_M15_L2_run3

description:
Library name: Sample 61
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36044 (re-sequence-3)


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 010 [KBRZUSPRA_0082_S71_L001]

description:
Library name: KBRZUSPRA_0082_S71_L001
ACP_010

tag: tumor size_(cm)

tag: volume (cm3)

tag: hypothalamic invasion


title: 221_post

description: Library name: 221_post

tag: trial

value: B

value: Untrained


title: FcRn4_2

tag: condition

tag: autoantibody

value: M

tag: dam id


title: FcRn4_1

tag: time


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 015 [KBRZUSPRA_0101_S18_L002]

description:
Library name: KBRZUSPRA_0101_S18_L002
ACP_015

value: microdissected tumor tissue

value: Male


title: 89_M09_L1

description:
Library name: Sample 67
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36089


title: 116_post

description: Library name: 116_post

value: A

tag: participant

tag: sport

value: Runner

tag: bmi


title: 205_post

description: Library name: 205_post

tag: Sex

tag: timing

value: post


title: 44_M16_L1_run4

description:
Library name: Sample 66
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 16, 24h. after infection with SDSE MGCS36044 (re-sequence-4)

tag: genotype


title: 118_pre

description: Library name: 118_pre

value: PBMC

tag: batch


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 008 [KBRZUSPRA_0081_S70_L002]

description:
Library name: KBRZUSPRA_0081_S70_L002
ACP_008

tag: tissue

tag: gender

tag: age at_diagnosis(years)

value: not available


title: 44_M15_L2_run1

description:
Library name: Sample 59
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36044 (re-sequence-1)

tag: treatment

value: RNA extracted from HNP biopsy


title: IgG3_4

value: Coronal slice, 150 um thick, including hippocampus and cortical and subcortical structures


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 008 [KBRZUSPRA_0081_S70_L001]

description:
Library name: KBRZUSPRA_0081_S70_L001
ACP_008

tag: tumor size_(cm)

tag: volume (cm3)

tag: hypothalamic invasion


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 004 [KBRZUSPRA_0080_S69_L002]

description:
Library name: KBRZUSPRA_0080_S69_L002
ACP_004

value: type 2


title: IgG3_3

tag: condition

value: MARA

tag: autoantibody

value: F


title: 125_pre

description: Library name: 125_pre

tag: trial

value: Cyclist

value: Female

value: pre


title: 132_pre

description: Library name: 132_pre

tag: participant


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 004 [KBRZUSPRA_0080_S69_L001]

description:
Library name: KBRZUSPRA_0080_S69_L001
ACP_004


title: FcRn4_3

tag: dam id

value: WT

tag: time


title: IgG3_2

tag: Sex

value: M


title: 44_M15_L1_run3

description:
Library name: Sample 57
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36044 (re-sequence-3)

value: NHP skeletal muscle


title: 44_M15_L1_run4

description:
Library name: Sample 58
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36044 (re-sequence-4)


title: 44_M15_L2_run2

description:
Library name: Sample 60
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36044 (re-sequence-2)


title: IgG3_1


title: RNA4_4

value: Control


title: 112_post

description: Library name: 112_post

value: A

tag: sport

tag: bmi

tag: timing


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 003 [KBRZUSPRA_0079_S68_L002]

description:
Library name: KBRZUSPRA_0079_S68_L002
ACP_003

tag: tissue

value: microdissected tumor tissue

value: Male

value: type 0


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 003 [KBRZUSPRA_0079_S68_L001]

description:
Library name: KBRZUSPRA_0079_S68_L001
ACP_003

tag: gender


title: 231_post

description: Library name: 231_post

value: PBMC

value: B

value: post

tag: batch


title: 44_M15_L1_run2

description:
Library name: Sample 56
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36044 (re-sequence-2)

tag: genotype

tag: treatment

value: RNA extracted from HNP biopsy


title: 44_M15_L1_run1

description:
Library name: Sample 55
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36044 (re-sequence-1)


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 002 [KBRZUSPRA_0078_S67_L002]

description:
Library name: KBRZUSPRA_0078_S67_L002
ACP_002

tag: age at_diagnosis(years)

tag: tumor size_(cm)

tag: volume (cm3)

value: type 1


title: 205_pre

description: Library name: 205_pre

value: Runner


title: 44_M14_L1_run4

description:
Library name: Sample 54
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 14, 24h. after infection with SDSE MGCS36044 (re-sequence-4)


title: 232_post

description: Library name: 232_post

value: Cyclist


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 002 [KBRZUSPRA_0078_S67_L001]

description:
Library name: KBRZUSPRA_0078_S67_L001
ACP_002

tag: hypothalamic invasion


title: RNA4_3

value: Coronal slice, 150 um thick, including hippocampus and cortical and subcortical structures

tag: condition

tag: autoantibody

value: F


title: 44_M14_L1_run3

description:
Library name: Sample 53
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 14, 24h. after infection with SDSE MGCS36044 (re-sequence-3)


title: iPSC-006-1-2

city: Beijing

first: Wenpeng

last: Song

state: Beijing

address: Department of Stomatology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China

department: Department of Stomatology

country: China

institute: Capital Medical University

description: Library name: Sample 5

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. 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.
Assembly: 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.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Pluripotent stem cells

extract_protocol:
Total RNA was extracted from cells using the TRIzolTM reagent according to the manufacturer’s instructions. The RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). To construct RNA-seq libraries, mRNA was enriched using Oligo dT-attached magnetic beads, fragmented, and reverse-transcribed into cDNA.
The cDNA was then ligated to sequencing adapters, and PCR amplification was performed to enrich the libraries. After the library construction was completed, the library was initially quantified using the Qubit 2.0 Fluorometer (ThermoFisher Scientific, Massachusetts, USA) and then diluted to 1.5 ng/µL. The insert size of the library was subsequently analyzed using the Agilent 2100 Bioanalyzer. Once the insert size met the expected criteria, the effective concentration of the library was accurately determined using qRT-PCR (with the effective concentration being higher than 1.5 nM) to ensure the quality of the library. After the library passed quality control, different libraries were pooled according to their effective concentration and the required target data output for sequencing. The pooled libraries were then subjected to Illumina sequencing.

tag: cell line

value: Pluripotent stem cells


title: 112_pre

description: Library name: 112_pre

tag: trial

tag: participant

value: Female

value: pre


title: RNA4_1

value: Control

tag: Sex

value: M

tag: dam id

value: WT

tag: time


title: iPSC-006-1-1

description: Library name: Sample 4


title: 44_M14_L1_run2

description:
Library name: Sample 52
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 14, 24h. after infection with SDSE MGCS36044 (re-sequence-2)

tag: tissue

value: NHP skeletal muscle


title: 44_M14_L1_run1

description:
Library name: Sample 51
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 14, 24h. after infection with SDSE MGCS36044 (re-sequence-1)


title: IgG2_4


title: 113_post

description: Library name: 113_post

value: A

tag: sport

tag: bmi

value: Male

tag: timing


title: 202_post

description: Library name: 202_post

value: PBMC

value: B

tag: batch


title: iPSC-001-5-2

description: Library name: Sample 3


title: IgG2_3

tag: genotype


title: TB03074816-V

city: Mahasset

first: Andrew

last: Shih

state: NY

address: 350 Community Dirive

institute: Feinstein Institute - Northwell Health

description: Library name: Sample 2

data_processing:
Fastq files were demultiplexed, aligned to the human reference genome GRCh38 using 10× cellranger 7.0.0
Assembly: 10x GRCh38 2020A
Supplementary files format and content: h5 files

source_name: vehicle stimulated P3/4 endometrial stromal cells

growth_protocol: Control-eSCs (p1, from 4 participants) were plated in maintenance media at 7 × 105 cells/well in 6-well plates.

extract_protocol:
After 4 h, cells were harvested and processed for single cell RNA sequencing (scRNAseq)
10x Chromium Single cell 3’ v3 assay

treatment_protocol: Media was replaced with assay media and the following day eSCs were treated with either vehicle or quercetin (25 μM) (2 wells/condition).

tag: cell type

value: endometrial stromal cells

tag: treatment

value: vehicle


title: iPSC-001-5-1

description: Library name: Sample 2


title: 104_post

description: Library name: 104_post

value: Runner

value: post


title: IgG2_2

value: Coronal slice, 150 um thick, including hippocampus and cortical and subcortical structures


title: 44_M13_L1_run4

description:
Library name: Sample 50
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 13, 24h. after infection with SDSE MGCS36044 (re-sequence-4)

value: RNA extracted from HNP biopsy


title: EPSC-001-5

description: Library name: Sample 1

value: Pluripotent stem cells


title: 131_post

description: Library name: 131_post

value: Cyclist


title: 44_M13_L1_run2

description:
Library name: Sample 48
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 13, 24h. after infection with SDSE MGCS36044 (re-sequence-2)


title: RNA4_2


title: 209_post

description: Library name: 209_post


title: IgG2_1


title: IgG1_4

value: F


title: 44_M13_L1_run1

description:
Library name: Sample 47
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 13, 24h. after infection with SDSE MGCS36044 (re-sequence-1)


title: IgG1_3

value: Control


title: mucCRC136_RNA-seq

city: Daejeon

first: Jeewoo

last: Seo

address: 125, Gwahak-ro

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology, KRIBB

data_processing:
Reference genome sequence data from Homo sapiens were obtained from the NCBI Genome database (assembly ID: GRCh38). The reference genome indexing and read mapping of tissue samples were performed using STAR software (ver. 2.7.3a).
Then, the read counts per million fragments mapped (CPM) of each sample were estimated and were log2-transformed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text format with log2 transformed CPM values of transcripts.

source_name: mucinous colorectal cancer tissue

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, CA, USA) according to the manufacturer’s protocol. The quality and integrity of the RNA were assessed using the RNA Integrity Number (RIN).
TruSeq Stranded mRNA Library Prep Kit (Illumina, CA, USA)

tag: disease state

value: Mucinous adenocarcinoma

value: male

tag: age

tag: tumor stage

value: IIIB

value: mucinous colorectal cancer tissue


title: mucCRC137_RNA-seq


title: 117_post

description: Library name: 117_post

value: A

value: Untrained

value: Female


title: 101_pre

description: Library name: 101_pre

value: PBMC

value: Male

value: pre


title: 44_M11_L4_run3

description:
Library name: Sample 45
Library obtained after processing Layer 4 from a skeletal muscle biopsy extracted from NHP 11, 24h. after infection with SDSE MGCS36044 (re-sequence-3)

value: NHP skeletal muscle


title: 44_M13_L1_run3

description:
Library name: Sample 49
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 13, 24h. after infection with SDSE MGCS36044 (re-sequence-3)


title: IgG1_1

value: Coronal slice, 150 um thick, including hippocampus and cortical and subcortical structures

tag: condition

tag: autoantibody

value: M

value: WT


title: 44_M11_L4_run2

description:
Library name: Sample 44
Library obtained after processing Layer 4 from a skeletal muscle biopsy extracted from NHP 11, 24h. after infection with SDSE MGCS36044 (re-sequence-2)

value: RNA extracted from HNP biopsy


title: 206_pre

description: Library name: 206_pre

tag: trial

value: B

tag: participant


title: 211_pre

description: Library name: 211_pre

value: Runner

tag: Sex


title: MAR_C3_44

value: Control

tag: dam id

tag: time


title: mucCRC131_RNA-seq

value: Mucinous adenocarcinoma

value: male

value: IIA

tag: tissue


title: MAR_C3_43


title: 44_M11_L3_run4

description:
Library name: Sample 42
Library obtained after processing Layer 3 from a skeletal muscle biopsy extracted from NHP 11, 24h. after infection with SDSE MGCS36044 (re-sequence-4)


title: 208_post

description: Library name: 208_post

tag: sport

tag: bmi

value: post


title: MAR_C3_42


title: 44_M11_L3_run3

description:
Library name: Sample 41
Library obtained after processing Layer 3 from a skeletal muscle biopsy extracted from NHP 11, 24h. after infection with SDSE MGCS36044 (re-sequence-3)


title: 224_post

description: Library name: 224_post

value: Untrained

tag: timing

tag: batch


title: MAR_C3_41

tag: genotype


title: 44_M11_L4_run4

description:
Library name: Sample 46
Library obtained after processing Layer 4 from a skeletal muscle biopsy extracted from NHP 11, 24h. after infection with SDSE MGCS36044 (re-sequence-4)

tag: treatment


title: mucCRC128_RNA-seq

tag: disease state

value: mucinous colorectal cancer tissue


title: mucCRC135_RNA-seq

value: female

tag: age

value: IIIB


title: MAR_C3_40

value: MARA

value: F


title: 44_M11_L3_run2

description:
Library name: Sample 40
Library obtained after processing Layer 3 from a skeletal muscle biopsy extracted from NHP 11, 24h. after infection with SDSE MGCS36044 (re-sequence-2)

value: NHP skeletal muscle


title: mucCRC134_RNA-seq

tag: tumor stage


title: IgG1_2

value: Coronal slice, 150 um thick, including hippocampus and cortical and subcortical structures

tag: condition

value: M


title: mucCRC126_RNA-seq


title: 233_pre

description: Library name: 233_pre

value: PBMC

value: Cyclist

value: Female

value: pre


title: mucCRC132_RNA-seq

value: Mucinous adenocarcinoma


title: 223_pre

description: Library name: 223_pre

value: B

value: Runner

value: Male


title: MAR_C3_38

tag: autoantibody

value: WT


title: 201_post

description: Library name: 201_post

tag: trial

value: post


title: 44_M09_L3_run4

description:
Library name: Sample 38
Library obtained after processing Layer 3 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36044 (re-sequence-4)

value: RNA extracted from HNP biopsy


title: MAR_C3_37


title: mucCRC129_RNA-seq

value: female

value: IIIB

value: mucinous colorectal cancer tissue


title: 44_M09_L3_run3

description:
Library name: Sample 37
Library obtained after processing Layer 3 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36044 (re-sequence-3)

value: NHP skeletal muscle


title: 118_post

description: Library name: 118_post

value: A

tag: participant

value: Untrained


title: 204_pre

description: Library name: 204_pre

value: PBMC

tag: Sex


title: 44_M09_L3_run2

description:
Library name: Sample 36
Library obtained after processing Layer 3 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36044 (re-sequence-2)


title: MAR_C3_36

value: Coronal slice, 150 um thick, including hippocampus and cortical and subcortical structures

value: MARA

value: F

tag: dam id


title: MAR_C3_35

value: M

tag: time


title: 44_M09_L3_run1

description:
Library name: Sample 35
Library obtained after processing Layer 3 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36044 (re-sequence-1)

tag: tissue


title: 44_M09_L2_run4

description:
Library name: Sample 34
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36044 (re-sequence-4)


title: 114_pre

description: Library name: 114_pre

tag: sport

value: Female

value: pre


title: 110_post

description: Library name: 110_post

value: Cyclist

tag: bmi

value: Male


title: mucCRC118_RNA-seq

value: Mucinous adenocarcinoma

value: male


title: MAR_C3_34

value: WT


title: 210_post

description: Library name: 210_post

value: B

tag: timing

value: post


title: 44_M09_L2_run3

description:
Library name: Sample 33
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36044 (re-sequence-3)

value: NHP skeletal muscle

value: RNA extracted from HNP biopsy


title: mucCRC117_RNA-seq

value: IIIB

value: mucinous colorectal cancer tissue


title: mucCRC119_RNA-seq

value: IIA


title: mucCRC114_RNA-seq

value: female

value: IIC


title: MAR_C3_33

value: Coronal slice, 150 um thick, including hippocampus and cortical and subcortical structures

value: MARA

value: M


title: MAR_C3_32

value: F


title: mucCRC124_RNA-seq


title: 224_pre

description: Library name: 224_pre

value: PBMC

value: Untrained

value: Female

value: pre

tag: batch


title: 44_M11_L3_run1

description:
Library name: Sample 39
Library obtained after processing Layer 3 from a skeletal muscle biopsy extracted from NHP 11, 24h. after infection with SDSE MGCS36044 (re-sequence-1)

tag: genotype


title: mucCRC111_RNA-seq

value: Mucinous adenocarcinoma

value: male


title: 44_M09_L2_run1

description:
Library name: Sample 31
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36044 (re-sequence-1)

value: NHP skeletal muscle

tag: treatment


title: mucCRC112_RNA-seq

tag: disease state

value: IIIC


title: 225_pre

description: Library name: 225_pre

value: B

value: Cyclist


title: mucCRC122_RNA-seq

tag: age

value: I

value: mucinous colorectal cancer tissue


title: 44_M09_L2_run2

description:
Library name: Sample 32
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36044 (re-sequence-2)

value: RNA extracted from HNP biopsy


title: MAR_C3_31

value: Coronal slice, 150 um thick, including hippocampus and cortical and subcortical structures

value: WT


title: MAR_C3_30

value: Control


title: mucCRC110_RNA-seq

tag: tumor stage

value: IIIA


title: 44_M16_L5

description:
Library name: Sample 30
Library obtained after processing Layer 5 from a skeletal muscle biopsy extracted from NHP 16, 24h. after infection with SDSE MGCS36044


title: 110_pre

description: Library name: 110_pre

value: PBMC

value: A

value: Male


title: mucCRC109_RNA-seq


title: MAR_C3_29

tag: condition

value: M


title: 44_M11_L4_run1

description:
Library name: Sample 43
Library obtained after processing Layer 4 from a skeletal muscle biopsy extracted from NHP 11, 24h. after infection with SDSE MGCS36044 (re-sequence-1)


title: 44_M16_L4

description:
Library name: Sample 29
Library obtained after processing Layer 4 from a skeletal muscle biopsy extracted from NHP 16, 24h. after infection with SDSE MGCS36044


title: 44_M16_L3

description:
Library name: Sample 28
Library obtained after processing Layer 3 from a skeletal muscle biopsy extracted from NHP 16, 24h. after infection with SDSE MGCS36044


title: MAR_C3_28

value: MARA

tag: autoantibody

value: F


title: 44_M16_L2

description:
Library name: Sample 27
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 16, 24h. after infection with SDSE MGCS36044

value: NHP skeletal muscle


title: mucCRC108_RNA-seq

value: Mucinous adenocarcinoma

value: female


title: 219_post

description: Library name: 219_post

tag: trial

value: B

value: Untrained

value: post


title: mucCRC107_RNA-seq

value: male

value: IIIB

value: mucinous colorectal cancer tissue


title: mucCRC106_RNA-seq

value: IIIC


title: MAR_C3_27

value: Coronal slice, 150 um thick, including hippocampus and cortical and subcortical structures

value: WT


title: MAR_C3_26


title: 218_pre

description: Library name: 218_pre

value: PBMC

tag: participant

value: pre


title: 44_M16_L1

description:
Library name: Sample 26
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 16, 24h. after infection with SDSE MGCS36044

value: RNA extracted from HNP biopsy


title: mucCRC105_RNA-seq

tag: Sex

value: I


title: 101_post

description: Library name: 101_post

value: A

value: Runner

value: Male


title: 44_M15_L5

description:
Library name: Sample 25
Library obtained after processing Layer 5 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36044

value: NHP skeletal muscle


title: 217_post

description: Library name: 217_post

value: B

value: Female


title: mucCRC104_RNA-seq

value: Mucinous adenocarcinoma

value: IIA


title: 206_post

description: Library name: 206_post

value: Untrained

value: post


title: MAR_C3_24

value: MARA

value: F

tag: dam id


title: 44_M15_L4

description:
Library name: Sample 24
Library obtained after processing Layer 4 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36044


title: 116_pre

description: Library name: 116_pre


title: mucCRC103_RNA-seq

value: male

value: mucinous colorectal cancer tissue


title: MAR_C3_23

value: Coronal slice, 150 um thick, including hippocampus and cortical and subcortical structures

value: M

value: WT

tag: time


title: 44_M15_L3

description:
Library name: Sample 23
Library obtained after processing Layer 3 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36044

tag: tissue

value: RNA extracted from HNP biopsy


title: 104_pre

description: Library name: 104_pre

value: PBMC

value: A

tag: sport

value: Runner

value: pre


title: 119_pre

description: Library name: 119_pre

tag: bmi

value: Male


title: mucCRC102_RNA-seq

value: Mucinous adenocarcinoma

value: female

value: IIIB


title: MAR_C3_22

value: Control


title: 127_post

description: Library name: 127_post

value: not applicable

tag: timing

value: post


title: mucCRC101_RNA-seq


title: MAR_C3_21

value: F


title: MAR_C3_20


title: mucCRC099_RNA-seq

value: male

value: IIIC

value: mucinous colorectal cancer tissue


title: 44_M14_L5

description:
Library name: Sample 20
Library obtained after processing Layer 5 from a skeletal muscle biopsy extracted from NHP 14, 24h. after infection with SDSE MGCS36044

value: NHP skeletal muscle


title: 123_pre

description: Library name: 123_pre

tag: batch


title: mucCRC100_RNA-seq

value: IIB


title: 44_M15_L1

description:
Library name: Sample 21
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36044

tag: genotype

value: RNA extracted from HNP biopsy


title: MAR_C3_19

value: Coronal slice, 150 um thick, including hippocampus and cortical and subcortical structures

value: WT


title: 121_pre

description: Library name: 121_pre

value: PBMC

value: A

value: Untrained

value: pre


title: 44_M14_L4

description:
Library name: Sample 19
Library obtained after processing Layer 4 from a skeletal muscle biopsy extracted from NHP 14, 24h. after infection with SDSE MGCS36044

tag: treatment


title: MAR_C3_25

value: MARA

value: M


title: MAR_C3_18


title: 217_pre

description: Library name: 217_pre

value: B

value: Female


title: 44_M14_L3

description:
Library name: Sample 18
Library obtained after processing Layer 3 from a skeletal muscle biopsy extracted from NHP 14, 24h. after infection with SDSE MGCS36044


title: mucCRC097_RNA-seq

tag: disease state

value: Mucinous adenocarcinoma

value: female

value: IIC


title: MAR_C3_17


title: mucCRC096_RNA-seq

value: male

tag: age

value: IIA

value: mucinous colorectal cancer tissue


title: 129_post

description: Library name: 129_post

value: not applicable

value: post


title: 133_post

description: Library name: 133_post

value: Cyclist


title: MAR_C3_16

value: Coronal slice, 150 um thick, including hippocampus and cortical and subcortical structures

value: F

value: WT


title: 44_M14_L2

description:
Library name: Sample 17
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 14, 24h. after infection with SDSE MGCS36044

value: NHP skeletal muscle

value: RNA extracted from HNP biopsy


title: 44_M14_L1

description:
Library name: Sample 16
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 14, 24h. after infection with SDSE MGCS36044


title: 126_pre

description: Library name: 126_pre

value: PBMC

value: A

value: Male

value: pre


title: mucCRC092_RNA-seq

value: Mucinous adenocarcinoma

value: female

tag: tumor stage


title: mucCRC093_RNA-seq

value: IIIB


title: MAR_C3_15

tag: condition

value: MARA

value: M


title: 44_M15_L2

description:
Library name: Sample 22
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36044


title: 218_post

description: Library name: 218_post

value: B

value: Untrained


title: mucCRC091_RNA-seq

value: male

value: IIA

value: mucinous colorectal cancer tissue


title: MAR_C3_14

value: Coronal slice, 150 um thick, including hippocampus and cortical and subcortical structures

tag: autoantibody

value: F

value: WT


title: MAR_C3_13


title: 44_M13_L4

description:
Library name: Sample 14
Library obtained after processing Layer 4 from a skeletal muscle biopsy extracted from NHP 13, 24h. after infection with SDSE MGCS36044

value: NHP skeletal muscle

value: RNA extracted from HNP biopsy


title: 202_pre

description: Library name: 202_pre

value: PBMC

tag: trial

value: Runner

value: Male


title: 44_M13_L3

description:
Library name: Sample 13
Library obtained after processing Layer 3 from a skeletal muscle biopsy extracted from NHP 13, 24h. after infection with SDSE MGCS36044


title: mucCRC090_RNA-seq

value: Mucinous adenocarcinoma

value: IIB


title: 44_M13_L2

description:
Library name: Sample 12
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 13, 24h. after infection with SDSE MGCS36044


title: mucCRC089_RNA-seq

value: IIIB


title: 105_post

description: Library name: 105_post

value: A

tag: participant

value: post


title: mucCRC088_RNA-seq

tag: Sex


title: mucCRC087_RNA-seq


title: 44_M13_L1

description:
Library name: Sample 11
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 13, 24h. after infection with SDSE MGCS36044


title: 207_pre

description: Library name: 207_pre

value: B

value: pre


title: MAR_C3_10

value: Control

tag: dam id


title: 44_M11_L5

description:
Library name: Sample 10
Library obtained after processing Layer 5 from a skeletal muscle biopsy extracted from NHP 11, 24h. after infection with SDSE MGCS36044


title: 44_M13_L5

description:
Library name: Sample 15
Library obtained after processing Layer 5 from a skeletal muscle biopsy extracted from NHP 13, 24h. after infection with SDSE MGCS36044


title: 121_post

description: Library name: 121_post

value: Untrained


title: MAR_C3_9

value: Coronal slice, 150 um thick, including hippocampus and cortical and subcortical structures

value: M

tag: time


title: 44_M11_L4

description:
Library name: Sample 9
Library obtained after processing Layer 4 from a skeletal muscle biopsy extracted from NHP 11, 24h. after infection with SDSE MGCS36044

tag: tissue


title: 102_post

description: Library name: 102_post

tag: sport


title: mucCRC086_RNA-seq

value: male

value: IIA

value: mucinous colorectal cancer tissue


title: MAR_C3_8

value: MARA

value: F

value: WT


title: mucCRC085_RNA-seq

value: Mucinous adenocarcinoma

value: female

value: IIIC


title: 220_pre

description: Library name: 220_pre

value: PBMC

value: Runner

tag: bmi

value: Male


title: 103_pre

description: Library name: 103_pre

value: A

tag: timing

value: pre


title: mucCRC084_RNA-seq

value: IIIA


title: MAR_C3_7

value: Coronal slice, 150 um thick, including hippocampus and cortical and subcortical structures


title: MAR_C3_12

value: M


title: mucCRC083_RNA-seq

value: male


title: 230_pre

description: Library name: 230_pre

value: B

value: Cyclist

value: Female

tag: batch


title: 44_M11_L2

description:
Library name: Sample 7
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 11, 24h. after infection with SDSE MGCS36044

value: NHP skeletal muscle

tag: genotype

value: RNA extracted from HNP biopsy


title: 207_post

description: Library name: 207_post

value: post


title: 44_M11_L1

description:
Library name: Sample 6
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 11, 24h. after infection with SDSE MGCS36044

tag: treatment


title: mucCRC082_RNA-seq

tag: disease state

value: Mucinous adenocarcinoma

value: female

value: IIA

value: mucinous colorectal cancer tissue


title: MAR_C3_11

value: MARA

value: WT


title: 44_M09_L5

description:
Library name: Sample 5
Library obtained after processing Layer 5 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36044


title: 106_post

description: Library name: 106_post

value: PBMC

value: A

value: Untrained


title: 44_M09_L4

description:
Library name: Sample 4
Library obtained after processing Layer 4 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36044


title: MAR_C3_4

value: Coronal slice, 150 um thick, including hippocampus and cortical and subcortical structures

value: F


title: 120_pre

description: Library name: 120_pre

value: Runner

value: Male

value: pre


title: 44_M11_L3

description:
Library name: Sample 8
Library obtained after processing Layer 3 from a skeletal muscle biopsy extracted from NHP 11, 24h. after infection with SDSE MGCS36044

value: NHP skeletal muscle


title: mucCRC081_RNA-seq

value: male

tag: age

value: IIIB


title: MAR_C3_3

value: M


title: mucCRC080_RNA-seq

value: Mucinous adenocarcinoma

tag: tumor stage

value: IIIC


title: 44_M09_L3

description:
Library name: Sample 3
Library obtained after processing Layer 3 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36044

value: RNA extracted from HNP biopsy


title: MAR_C3_2

tag: condition

value: MARA


title: 44_M09_L2

description:
Library name: Sample 2
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36044


title: 127_pre

description: Library name: 127_pre

value: not applicable


title: 204_post

description: Library name: 204_post

value: PBMC

value: B

value: post


title: mucCRC078_RNA-seq

value: female

value: IIA

value: mucinous colorectal cancer tissue


title: MAR_C3_1

value: Coronal slice, 150 um thick, including hippocampus and cortical and subcortical structures

tag: autoantibody

value: WT


title: MAR_C3_6

value: F


title: 44_M09_L1

description:
Library name: Sample 1
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36044

value: NHP skeletal muscle


title: mucCRC077_RNA-seq

value: IIIB


title: 228_pre

description: Library name: 228_pre

tag: trial

value: Cyclist

value: Male

value: pre


title: RNA-seq, low input, 1day hatchling, whole

city: London

first: Ferdinand

last: Marlétaz

address: Gower Street

department: Genetics, Evolution & Environment

country: United Kingdom

institute: University College London

data_processing:
RNA-seq reads were aligned to the genome using STAR (v2.5.2b)
RNA-seq counts were obtained using featureCounts v1.6.1
Assembly: Pgot_OvL0Qm_cn.fa
Supplementary files format and content: RNA-seq: tab-delimited file containing raw counts
Supplementary files format and content: ATAC-seq: bigwig file for signal visualisation
Supplementary files format and content: EM-seq: GCmap, list of methylated bases
Supplementary files format and content: scRNA-seq: matrix files containing gene counts

organism: Paraspadella gotoi

source_name: whole hatchling

extract_protocol:
RNA was extracted using Trizol reagent (Invitrogen).
Strand-specific RNA-seq libraries were prepared using the TruSeq RNA Library (Illumina) and sequenced in a 2x150bp layout.

value: whole hatchling


title: MAR_C3_5

value: MARA


title: rat mito sedentary 32

city: Burwood

first: Jessica

last: Silver

address: 221 Burwood Highway

country: Australia

institute: Deakin University

description: GENERATE FASTQ

data_processing:
A 2nM loading pool was prepared for gel-excised isolated mitochondria pool and contained 50% gel-excised miRNA region, 25% gel-excised 190 bp region and 25% Phi-X spike-in and was sequenced on a 2x51bp run (NovaSeq 6000 XP v1.5). Following sequencing, read1 was trimmed using fastp (fastp 0.20.0) and then mapped using blast (2.9.0+) with switch -task blastn and word length set to 19nt to miRbase human mature miRNAs (mature.fa download march 12 2018, miRbase v22.1). Raw read counts for each mature miRNA  generated using short perl script. Data normalisation and differential expression analysis was performed using DEseq2 v1.36 in rstudio v4.2.1
Assembly: miRbase v22.1
Supplementary files format and content: .csv file includes raw read counts for each miRNA for each sample
Supplementary files format and content: .csv file includes normalised read counts (DEseq2) for each miRNA for each sample

source_name: skeletal muscle (red portion of the gastrocnemius)

extract_protocol:
Mitochondria were isolated from ~100mg skeletal muscle tissue with the MACS Mitochondria Isolation Kit (mouse) (Miltenyi Biotec). Following isolation, the mitochondrial fraction was resuspended in 50 μL ice-cold Storage Buffer ( Miltenyi Biotec) and incubated with 312 μg RNase-A (cat# 19101, Qiagen) for 1 h at 37°C. Following incubation, RNase-A was degraded by the addition of 5 μL proteinase-K (stock concentration 600 mAU/mL) (cat# 19131, Qiagen) and inverting the tube briefly. The solution was centrifuged at 8,000g for 10-minutes at 4C. The supernatant was aspirated, and the mitochondria pellet was washed twice with 100 μL ice-cold Storage Buffer (Miltenyi Biotec), and centrifuged at 13,000g for 2-minutes at 4C between washes. The mitochondria pellet was resuspended in 100 μL storage buffer (Miltenyi Boitec) and stored at -80°C until further analyses.  For RNA extraction from isolated mitochondria, frozen samples were suspended in 5x volumes of TriReagent (cat# R2061, Integrated Sciences), thawed on ice and then centrifuged at 16,000xg for 2 min at 4°C to pellet the mitochondria. The mitochondria pellet was first sheared 20x through a fine pipette tip. Total RNA was extracted from isolated mitochondrua using Zymo Direct-Zol Micro Prep kit (#R2061, Integrated Sciences) with on-column DNase-I digest (#E1010, Integrated Sciences) as per the manufacturer's protocol. RNA was eluted in 12ul NFW.
Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set (cat# #E7560S, New England Biolabs.) with modifications as described by our group previously (Silver and Trewin, 2022, https://doi.org/10.1101/2022.04.27.489477). (3). Briefly, the 3’ and 5’ adapters and reverse transcription primer were diluted 0.3x, and 20 end-point PCR cycles were conducted. Following PCR amplification, the cDNA library was cleaned using the Monarch PCR & DNA Cleanup Kit (5 μg) (cat# T1030L, New England Biolabs.) using the 7:1 ratio of binding buffer:sample as per the manufacturer’s instructions. Uniquely indexed libraries were placed into an equimolar pool and run on a 6% Novex TBE-polyacrylamide gel (cat# EC6265BOX, Thermo Fisher Scientific), with 5 μL Quick-Load pBR322 DNA-MspI Molecular Marker (cat#E7560S, New England Biolabs.) run in a separate lane. Bands corresponding to the 143 and 190bp molecular markers were manually excised and extracted from the gel as per the manufacturer's protocol (cat#E7560S, New England Biolabs.).

value: male

value: endurance exercise training

value: post training (sedentary)


title: rat mito sedentary 30

description: GENERATE FASTQ

value: skeletal muscle (red portion of the gastrocnemius)


title: RNA-seq, low input, gastrula, whole

source_name: whole embryo

value: whole embryo


title: 117_pre

description: Library name: 117_pre

value: PBMC

value: A

tag: participant

value: Untrained

value: Female


title: mucCRC073_RNA-seq

value: Mucinous adenocarcinoma

tag: Sex

value: IIB

value: mucinous colorectal cancer tissue


title: RNA-seq, low input, 3 days hatchling, whole


title: rat mito sedentary 29

description: GENERATE FASTQ


title: mucCRC079_RNA-seq

value: female

value: IV


title: 107_pre

description: Library name: 107_pre

value: Runner

value: Male

value: pre


title: mucCRC070_RNA-seq

value: IIA


title: RNA-seq, whole adult

source_name: whole adult

value: whole adult


title: mucCRC071_RNA-seq

value: IVB


title: rat mito sedentary 16

description: GENERATE FASTQ

value: male

value: skeletal muscle (red portion of the gastrocnemius)

value: endurance exercise training

value: post training (sedentary)


title: 114_post

description: Library name: 114_post

value: PBMC

value: A

value: post


title: mucCRC069_RNA-seq

value: Mucinous adenocarcinoma

value: I


title: Colon tumor from Fabp (Cre/+); Apc (fl/+) mouse; Kras (LSL-G12V/+) replicate 3

city: Boston

first: Bing

last: Shui

state: MA

address: 360 Longwood Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: Library name: G12VT_3

data_processing:
Quality control of RNA sequencing was using FastQC and Qualimap, and Salmon pseudo-aligner was used to map sequences and calculate transcript reads using the Ensembl mm10 mouse genome as reference. Differential gene expression was determined using DESeq2.
Assembly: mm10
Supplementary files format and content: csv file containing raw gene count for each sample

organism: Mus musculus

source_name: Colon tumor

extract_protocol:
Dissection of mice was performed immediately after cervical dislocation. Once euthanized, mice were laid on their back and their torsos were coated with 70% Ethanol. The skin was subsequently raised, a single transverse cut of ~1.2 cm was made, and the skin was pulled in opposite directions along the coronal plane. Next, the peritoneum was carefully cut along the sagittal and transverse planes and the lower gastrointestinal track was carefully placed to one side. A cut was made through the pelvic floor adjacent to the colorectum, and the entire length of the colon, from rectum to cecum, was excised and placed in ice cold PBS. Excised colon tissue was flushed with ice cold PBS to clear fecal contents, placed on bibulous paper, and cut longitudinally. For colonic epithelium, epithelial tissue was gently scraped off the lamina propria using a razor blade and flash frozen in liquid nitrogen. For colonic tumors, macroscopic tumors were then resected and flash froze in liquid nitrogen for downstream molecular characterizations. Prior to preparation of colon and tumor tissue for western blot, RNA, and DNA analysis, tissue was pulverized under cryogenic conditions using a Bessman Tissue Pulverizer. Extraction of RNA was done using the RNeasy Plus kits from QIAGEN per manufacturer’s instruction. RNA was stored at -80˚C.
RNA concentration and quality was determined using an Agilent Bioanalyzer/TapeStation. 1 µg of RNA with a RIN score greater than 7 from each sample was used as input for RNA-Seq library preparation and poly-A enrichment was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module. The RNA-seq library was prepared using the NEBNext Ultra Directional RNA Library Prep kit from Illumina and quality control of the libraries was done using the TapeStation and single read sequencing of the libraries was done on a NextSeq 500 Illumina platform in a High Output mode for 75 cycles.

value: Colon tumor

value: Fabp (Cre/+); Apc (fl/+); Kras (LSL-G12V/+)


title: ATAC-seq, hatchling, whole animal, sample 2

library_source: genomic

data_processing:
Reads obtained for each library were mapped using Bowtie2 (v2.4.1) with the parameters --very-sensitive and  -k 10 (Langmead and Salzberg, 2012) and peak calling for open chromatin region was performed using Generich (v0.6) available at https://github.com/jsh58/Genrich using ATAC model (-j), keeping unpaired alignments (-y), removing PCR duplicates (-r) and excluding reads mapped to mitochondria (-e MT). At this step, we pooled biological and technical replicates together as Generich analyses each replicate separately and then combined them by summarising p-values using Fisher’s method.
pybed tools was used to generate a set of unified peaks from the peaks called at each stage, classify peaks according to the activity during development and perform intersection with masked repetitive regions and conserved regions, as well as assigning peaks to genes
Assembly: Pgot_OvL0Qm_cn.fa
Supplementary files format and content: RNA-seq: tab-delimited file containing raw counts
Supplementary files format and content: ATAC-seq: bigwig file for signal visualisation
Supplementary files format and content: EM-seq: GCmap, list of methylated bases
Supplementary files format and content: scRNA-seq: matrix files containing gene counts

molecule: genomic DNA

extract_protocol:
ATAC-seq was performed following the Omni-ATAC protocol using Digitonin (Promega) in addition to NP40 and Tween in the cell lysis buffer  (Corces et al., 2017). Sea urchin eggs were fertilised in filtered sea water with 2 mM of Paraminobenzoic acid (Sigma) to prevent hardening of the fertilisation envelope. The fertilization envelope was then removed by repeated filtration on a nylon net (70 µM). Embryos at the appropriate stage were collected and washed in NaCl 0,55M twice then dissociated in Calcium-Magnesium artificial sea water by energetic pipetting. For each time point, different numbers of nuclei were tested, typically 50,000, 150,000 and 250,000. The integrity of the nuclei was checked on a microscope after staining the nuclei with Hoechst.
After tagmentation the libraries were purified with a Zymo DNA clean up kit then a QPCR was performed on an aliquot  of the eluted libraries using the Ad1 and Ad2.x primers and the corresponding Ct was determined for each sample (Buenrostro et al. 2013). The libraries were then amplified at Ct+ 2 cycles. The quality of the libraries was checked on a 2% agarose gel to verify the size of the fragments and the nucleosome phasing.

value: whole hatchling


title: mucCRC076_RNA-seq

value: IIIB

value: mucinous colorectal cancer tissue


title: Colon tumor from Fabp (Cre/+); Apc (fl/+) mouse; Kras (LSL-G12V/+) replicate 2

description: Library name: G12VT_2


title: mucCRC068_RNA-seq

value: IIA


title: EM-seq, whole adult

data_processing:
Reads were mapped to the reference genome, including also a phage lambda and pUC19 sequences, using BS-Seeker2 with bowtie2 as back-end. Duplicate reads were removed with Sambamba, and methylation calls were obtained using CGmapTools.
Assembly: Pgot_OvL0Qm_cn.fa
Supplementary files format and content: RNA-seq: tab-delimited file containing raw counts
Supplementary files format and content: ATAC-seq: bigwig file for signal visualisation
Supplementary files format and content: EM-seq: GCmap, list of methylated bases
Supplementary files format and content: scRNA-seq: matrix files containing gene counts
Library strategy: EM-seq

extract_protocol:
100 ng of P. gotoi gDNA were spiked in with unmethylated lambda phage and CpG methylated pUC19 control before fragmenting it to ~300 bp with a BioRuptor (Covaris).
Resulting sheared DNA was then used to prepare an Enzymatic Methyl-Seq library according to the manufacturer's instructions (NEBNext Enzymatic Methyl-seq Kit).

value: whole adult


title: Colon tumor from Fabp (Cre/+); Apc (fl/+) mouse; Kras (LSL-G12V/+) replicate 1

description: Library name: G12VT_1


title: ATAC-seq, hatchling, whole animal, sample 1


title: mucCRC067_RNA-seq

value: female

value: IIB


title: rat mito sedentary 15

description: GENERATE FASTQ

value: male

value: skeletal muscle (red portion of the gastrocnemius)


title: rat mito sedentary 12

description: GENERATE FASTQ

value: endurance exercise training

value: post training (sedentary)


title: rat mito sedentary 11

description: GENERATE FASTQ


title: ATAC-seq, adult, whole animal, sample 3


title: rat mito sedentary 8

description: GENERATE FASTQ


title: mucCRC066_RNA-seq

value: IVA


title: Colon tumor from Fabp (Cre/+); Apc (fl/+) mouse; Kras (LSL-G12C/+) replicate 2

description: Library name: G12CT_2

value: Fabp (Cre/+); Apc (fl/+); Kras (LSL-G12C/+)


title: Colon tumor from Fabp (Cre/+); Apc (fl/+) mouse; Kras (LSL-G12C/+) replicate 3

description: Library name: G12CT_3


title: mucCRC065_RNA-seq

value: Mucinous adenocarcinoma


title: ATAC-seq, adult, whole animal, sample 2


title: rat mito sedentary 7

description: GENERATE FASTQ


title: ATAC-seq, adult, whole animal, sample 1


title: Colon tumor from Fabp (Cre/+); Apc (fl/+) mouse; Kras (LSL-G12C/+) replicate 1

description: Library name: G12CT_1


title: mucCRC064_RNA-seq

value: IIIC


title: Colon tumor from Fabp (Cre/+); Apc (fl/+) mouse; Kras (LSL-G12D/+) replicate 3

description: Library name: G12DT_3

value: Colon tumor

value: Fabp (Cre/+); Apc (fl/+); Kras (LSL-G12D/+)


title: rat mito sedentary 4

description: GENERATE FASTQ


title: 10x 3' mRNA single-cell, Hatchling, sample, whole animal

data_processing:
reads were aligned using cellranger (v7/0/1)
and gene counts analysed with Seurat (v5)
Assembly: Pgot_OvL0Qm_cn.fa
Supplementary files format and content: RNA-seq: tab-delimited file containing raw counts
Supplementary files format and content: ATAC-seq: bigwig file for signal visualisation
Supplementary files format and content: EM-seq: GCmap, list of methylated bases
Supplementary files format and content: scRNA-seq: matrix files containing gene counts

extract_protocol:
animals dissociated in 1% pronase in FSW, strained in flowmis and resuspending with L15. 15k cells loaded on 10x cromium chip (v2)
constructed using 10x 3' chromium kit reagents and instructions

value: whole hatchling


title: mucCRC063_RNA-seq


title: 211_post

description: Library name: 211_post

value: PBMC

value: B

value: Runner

value: Male

value: post


title: rat mito sedentary 3

description: GENERATE FASTQ


title: Colon tumor from Fabp (Cre/+); Apc (fl/+) mouse; Kras (LSL-G12D/+) replicate 2

description: Library name: G12DT_2


title: mucCRC062_RNA-seq

value: female

value: IIA

value: mucinous colorectal cancer tissue


title: 10x 3' mRNA single-cell, Adult, sample1, whole animal

value: whole adult


title: rat mito trained 27

description: GENERATE FASTQ

value: male

value: skeletal muscle (red portion of the gastrocnemius)

value: endurance exercise training

value: post training (trained)


title: Colon tumor from Fabp (Cre/+); Apc (fl/+) mouse; Kras (LSL-G12D/+) replicate 1

description: Library name: G12DT_1


title: rat mito trained 26

description: GENERATE FASTQ


title: 10x 3' mRNA single-cell, Adult, sample22, whole animal


title: mucCRC061_RNA-seq

value: Mucinous adenocarcinoma

value: IIB


title: Colon tumor from Fabp (Cre/+); Apc (fl/+) mouse, replicate 3

description: Library name: WTT_3

value: Colon tumor

value: Fabp (Cre/+); Apc (fl/+)


title: mucCRC060_RNA-seq


title: Wild type, replicate 1

city: Qingdao

first: Yanhai

last: Gong

address: No.189 Songling Road

department: single cell center

institute: qibebt, cas

data_processing:
nfcore/rnaseq pipeline
Reads were aligned with STAR, employing modified parameters to limit intron lengths (“--alignIntronMin 20, --alignIntronMax 3000”).
Trinity was utilized to generate a gene expression matrix using the RSEM2 method, with TMM normalization implemented to account for library size variation among samples.
For the mutant samples, differentially expressed genes were identified using edgeR, applying a false discovery rate threshold of 0.001 and a minimum fold change of 2.
Assembly: NoIMET1v2
Supplementary files format and content: tab-delimited text file includes raw counts for genes in each sample
Supplementary files format and content: tab-delimited text file includes normalized TPM values for genes in each sample

organism: Nannochloropsis oceanica

growth_protocol: It is cultured in modified f/2 liquid medium containing 35 g L–1 sea salt, 1,000 mg L–1 NaNO3, 66.6 mg L–1 NaH2PO4•H2O, 3.65 mg L–1 FeCl3•6H2O, 4.37 mg L–1 Na2EDTA•2H2O, 0.0196 mg L–1 CuSO4•5H2O, 0.0126 mg L–1 Na2MoO4•2H2O, 0.044 mg L–1 ZnSO4•7H2O, 0.0109 mg L–1 CoCl2•6H2O, 0.036 mg L–1 MnCl2•4H2O, 5 mg L–1 VB12, 5 mg L–1 biotin, and 0.1 mg L–1 thiamine HCl. Cells are cultivated in liquid cultures under continuous illumination (50 μmol photons m–2 s–1) at 25 °C.

extract_protocol:
Total RNA of NoPAC4 mutants and WT cultured for 5 days was extracted using Trizol reagents (Tiangen, China). The concentration and purity of the RNA were determined spectrophotometrically (IMPLEN, USA), and RNA integrity was assessed with the RNA Nano 6000 Assay Kit on an Agilent Bioanalyzer 2100.
A total of 2 μg of RNA per sample was used as input material for RNA sample preparation. Sequencing libraries were generated using the NEBNext Ultra™ RNA Library Prep Kit for Illumina (NEB, USA), following the manufacturer’s recommendations, and index codes were added to associate sequences with each sample. The clustering of index-coded samples was performed on a cBot Cluster Generation System using the HiSeq 3000/4000 PE Cluster Kit Box 1 from Illumina.

treatment_protocol: Cells were cultured in flasks for 5 days to reach the logarithmic phase at 23 °C under continuous light (50 μmol photons m-2 sec-1).

tag: strain

value: Wild type

value: low light, 5 days


title: mucCRC059_RNA-seq


title: rat mito trained 21

description: GENERATE FASTQ

tag: time


title: N. oceanica, NoPAC4 knockout mutants 2, replicate 2

value: NoPAC4 knockout


title: Colon tumor from Fabp (Cre/+); Apc (fl/+) mouse, replicate 1

description: Library name: WTT_1

tag: tissue


title: rat mito trained 18

description: GENERATE FASTQ


title: mucCRC058_RNA-seq

value: IIIB


title: N. oceanica, NoPAC4 knockout mutants 2, replicate 1


title: rat mito trained 17

description: GENERATE FASTQ


title: mucCRC057_RNA-seq

value: I


title: rat mito sedentary 19

description: GENERATE FASTQ

value: post training (sedentary)


title: N. oceanica, NoPAC4 knockout mutants 1, replicate 2


title: Colonic epithelium from Fabp (Cre/+); Kras(LSL-G12V/+) mouse, replicate 2

description: Library name: G12VE_2

source_name: Colon epithelium

value: Colon epithelium

value: Fabp (Cre/+); Kras (LSL-G12V/+)


title: mucCRC056_RNA-seq

value: female

value: mucinous colorectal cancer tissue


title: rat mito trained 14

description: GENERATE FASTQ

value: male

value: skeletal muscle (red portion of the gastrocnemius)


title: Colonic epithelium from Fabp (Cre/+); Kras(LSL-G12V/+) mouse, replicate 1

description: Library name: G12VE_1


title: Wild type, replicate 2


title: mucCRC055_RNA-seq

value: IIA


title: N. oceanica, NoPAC4 knockout mutants 1, replicate 1


title: rat mito trained 25

description: GENERATE FASTQ

value: endurance exercise training

value: post training (trained)


title: rat mito trained 13

description: GENERATE FASTQ


title: Colonic epithelium from Fabp (Cre/+); Kras(LSL-G12C/+) mouse, replicate 3

description: Library name: G12CE_3

value: Fabp (Cre/+); Kras (LSL-G12C/+)


title: mucCRC054_RNA-seq

value: Mucinous adenocarcinoma

value: IIIC


title: TEX treatment, 48h, Replicate 2

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

country: Germany

institute: Institute for Bioinformatics and Medical Informatics

description: dRNA-Seq

data_processing:
READemption was used for quality check of the raw data, mapping and counting. It is an automated RNA-Seq processing pipeline with the purpose to process differential RNA-Seq (dRNA-Seq) data for identification of transcriptional start sites in bacteria
The pipeline encompasses: segemehl for mapping, coverage for calculation of wiggle files that serve as input for TSSpredator
TSSpredator was used to compute the transcription start sites and output a MasterTable for the two time points 33h, 48h using both replicates and default parameter settings for sensitivity/specificity of the TSS calls
Assembly: 3 scaffolds of N. terpenica IFM 0406 (NZLWGR00000000.1)
Supplementary files format and content: Master table (tsv file) of the TSS as computed using TSSpredator, with all

organism: Nocardia terpenica

source_name: bacterial cells

extract_protocol:
Firstly, the four RNA samples R1-33h, R1-48h, R2-33h and R2-48h were treated with T4 polynucleotide kinase.  The RNA samples were then split into two halves and one half was subjected to Terminator™ 5’-phosphate-dependent exonuclease treatment (+TEX), the other half was left untreated (-TEX).
For cDNA synthesis, the RNA samples were poly(A)-tailed to the 3’-end using poly(A) polymerase.  Then, the 5’-triphosphate residues were removed using RNA 5’-polyphosphatase. Accordingly, an RNA adapter was ligated to the 5’-monophosphate residue of the RNA. First strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resultant cDNAs were PCR-amplified to approximately 10-20 ng/μl using DNA polymerase. Finally, the cDNAs were purified using an Agencourt AMPure XP kit and analyzed via capillary electrophoresis. For Illumina NextSeq sequencing, the eight cDNA samples were pooled in about equimolar amounts. Subsequently, the cDNA pool was eluted from a preparative agarose gel in the size range of 200-500 bp. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina. Finally, the cDNA pool was single-end sequenced on an Illumina NextSeq 500 system using 1x75bp read length.

tag: cell type

value: bacterial cells


title: rat mito trained 10

description: GENERATE FASTQ


title: Colon tumor from Fabp (Cre/+); Apc (fl/+) mouse, replicate 2

description: Library name: WTT_2

value: Colon tumor

value: Fabp (Cre/+); Apc (fl/+)


title: mucCRC053_RNA-seq

value: IIB


title: rat mito trained 6

description: GENERATE FASTQ


title: 48h, Replicate 1

description: dRNA-Seq


title: mucCRC052_RNA-seq

value: IV


title: Colonic epithelium from Fabp (Cre/+); Kras(LSL-G12C/+) mouse, replicate 1

description: Library name: G12CE_1

value: Colon epithelium


title: Colonic epithelium from Fabp (Cre/+); Kras(LSL-G12V/+) mouse, replicate 3

description: Library name: G12VE_3

value: Fabp (Cre/+); Kras (LSL-G12V/+)


title: TEX treatment, 48h, Replicate 1

description: dRNA-Seq


title: rat mito trained 5

description: GENERATE FASTQ


title: mucCRC051_RNA-seq

value: female


title: Colonic epithelium from Fabp (Cre/+); Kras(LSL-G12D/+) mouse, replicate 3

description: Library name: G12DE_3

value: Fabp (Cre/+); Kras (LSL-G12D/+)


title: 48h, Replicate 2

description: dRNA-Seq


title: rat mito trained 2

description: GENERATE FASTQ

value: male


title: 33h, Replicate 2

description: dRNA-Seq


title: Colonic epithelium from Fabp (Cre/+); Kras(LSL-G12D/+) mouse, replicate 2

description: Library name: G12DE_2


title: TEX treatment, 33h, Replicate 2

description: dRNA-Seq


title: mucCRC050_RNA-seq

value: mucinous colorectal cancer tissue


title: rat mito trained 1

description: GENERATE FASTQ

value: skeletal muscle (red portion of the gastrocnemius)


title: Colonic epithelium from Fabp (Cre/+); Kras(LSL-G12C/+) mouse, replicate 2

description: Library name: G12CE_2


title: 33h, Replicate 1

description: dRNA-Seq


title: Colonic epithelium from Fabp (Cre/+) mouse, replicate 3

description: Library name: WTE_3

value: Fabp (Cre/+)


title: U2OS cells, GFP-MYC-U, Rep3

city: New York

first: Yang

last: Luo

address: 408 E 69th St

department: Cancer Biology and Genetics

institute: Sloan Kettering Institute

description:
Library name: U2OS_GFP-MYC-U_only_rep3
log2FC and adjusted P values from DESeq2 comparing GFP and U samples (column F-G)

data_processing:
Read count extraction and quantification were performed using Salmon (v1.10.1) and imported with tximport (v1.22.0).
Differential gene expression analysis was performed with DESeq2 in R or Galaxy.
Assembly: hg38
Supplementary files format and content: csv files include DESeq2 analysis of pairwise comparison of MYC samples and of shCtrl vs shKDM6A MCF7 samples.

growth_protocol: U2OS and MCF7 cells were maintained in DMEM high glucose media supplemented with 10% fetal bovine serum (FBS) and 1% Pen/Strep in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using TRIzol, treated with DNase I (RNase free), and precipitated with sodium acetate before submission for sequencing.
RNA libraries for RNA-seq were prepared using NEB Next Ultra II RNA library prep kit with PolyA selection following manufacturer's protocol.

treatment_protocol:
U2OS cells were transfected with the cDNA vectors containing MYC coding sequence (-NU) or MYC coding sequence and its 3′UTR (-U). The GFP+ cells were sorted by FACS 24 hours after transfection.
MCF7 cells with stable KDM6A knockdown were generated and transfected with cDNA vectors containing the KDM6A (encoding UTX) coding sequence only (-NU) or containing the KDM6A coding sequence and its 3′UTR (-U). Cells were harvested 24 hours after transfection, side by side with the control MCF7 cells that express scrambled shRNA.

tag: cell line

value: osteosarcoma cell line

value: WT

value: GFP-MYC-U transfection


title: Colonic epithelium from Fabp (Cre/+); Kras(LSL-G12D/+) mouse, replicate 1

description: Library name: G12DE_1


title: TEX treatment, 33h, Replicate 1

description: dRNA-Seq


title: U2OS cells, GFP-MYC-U, Rep2

description:
Library name: U2OS_GFP-MYC-U_only_rep2
log2FC and adjusted P values from DESeq2 comparing GFP and U samples (column F-G)


title: mucCRC049_RNA-seq

value: Mucinous adenocarcinoma

value: IIA


title: Hemispheric cerebellar tissue from subject 6, array type v2

type: other

city: Los Angeles

first: Jennifer

middle: A

last: Cotter

address: 4650 Sunset Blvd., M/S 43

department: Pathology and Laboratory Medicine

institute: Children's Hospital Los Angeles

hyb_protocol: Samples were hybridized to Infinium MethylationEPIC BeadChips and single-base extension was performed followed by staining

scan_protocol: Arrays were imaged using the iScan instrument to generate IDAT files for downstream analysis.

data_processing:
minfi R package v1.44
processed data value definition: Average Beta

label: Cy3 and Cy5

molecule: other

source_name: Cerebellum (non-tumor)

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from FFPE using the QIAamp DNA FFPE Tissue Kit.

value: Cerebellum (non-tumor)

value: 17 years


title: U2OS cells, GFP-MYC-U, Rep1

description:
Library name: U2OS_GFP-MYC-U_only_rep1
log2FC and adjusted P values from DESeq2 comparing GFP and U samples (column F-G)


title: Colonic epithelium from Fabp (Cre/+) mouse, replicate 2

description: Library name: WTE_2


title: Colonic epithelium from Fabp (Cre/+) mouse, replicate 1

description: Library name: WTE_1


title: mucCRC047_RNA-seq


title: mucCRC048_RNA-seq


title: U2OS cells, GFP-MYC-NU, Rep3

description:
Library name: U2OS_GFP-MYC-NU_only_rep3
log2FC and adjusted P values from DESeq2 comparing GFP and NU samples (column D-E)

value: GFP-MYC-NU transfection


title: mucCRC046_RNA-seq

value: IIIB


title: Hemispheric cerebellar tissue from subject 5, array type v2

source_name: cerebellum (non-tumor)

value: cerebellum (non-tumor)

value: 16 years


title: Colon tumor from Fabp (Cre/+); Apc(fl/+); Nf1(fl/fl) mouse, replicate 5

description: Library name: NF1_5

data_processing:
Quality control of RNA sequencing was using FastQC and Qualimap, and Salmon pseudo-aligner was used to map sequences and calculate transcript reads using the Ensembl mm10 mouse genome as reference. Differential gene expression was determined using DESeq2. Two separate datasets were collected and merged and underwent batch correction through DESeq2. Validation of batch correction was accomplished through principle component analysis (PCA) and UMAP.
Assembly: mm10
Supplementary files format and content: csv file containing raw gene count for each sample

extract_protocol:
Dissection of mice was performed immediately after cervical dislocation. Once euthanized, mice were laid on their back and their torsos were coated with 70% Ethanol. The skin was subsequently raised, a single transverse cut of ~1.2 cm was made, and the skin was pulled in opposite directions along the coronal plane. Next, the peritoneum was carefully cut along the sagittal and transverse planes and the lower gastrointestinal track was carefully placed to one side. A cut was made through the pelvic floor adjacent to the colorectum, and the entire length of the colon, from rectum to cecum, was excised and placed in ice cold PBS. Excised colon tissue was flushed with ice cold PBS to clear fecal contents, placed on bibulous paper, and cut longitudinally. Macroscopic tumors were then resected and flash froze in liquid nitrogen for downstream molecular characterizations. Prior to preparation of colon and tumor tissue for western blot, RNA, and DNA analysis, tissue was pulverized under cryogenic conditions using a Bessman Tissue Pulverizer. Extraction of RNA was done using the RNeasy Plus kits from QIAGEN per manufacturer’s instruction. RNA was stored at -80˚C.
RNA concentration and quality was determined using an Agilent Bioanalyzer/TapeStation. 1 µg of RNA with a RIN score greater than 7 from each sample was used as input for RNA-Seq library preparation and poly-A enrichment was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module. The RNA-seq library was prepared using the NEBNext Ultra Directional RNA Library Prep kit from Illumina and quality control of the libraries was done using the TapeStation and single read sequencing of the libraries was done on a NextSeq 500 Illumina platform in a High Output mode for 75 cycles.

value: Colon tumor

value: Fabp (Cre/+); Apc(fl/+); Nf1(fl/fl)


title: Hemispheric cerebellar tissue from subject 3, array type v2

value: 4 months


title: Hemispheric cerebellar tissue from subject 4, array type v2

value: 5 years


title: mucCRC045_RNA-seq

value: male

value: IIIC

value: mucinous colorectal cancer tissue


title: U2OS cells, GFP-MYC-NU, Rep2

description:
Library name: U2OS_GFP-MYC-NU_only_rep2
log2FC and adjusted P values from DESeq2 comparing GFP and NU samples (column D-E)

value: osteosarcoma cell line

value: WT


title: mucCRC044_RNA-seq

value: Mucinous adenocarcinoma


title: Colon tumor from Fabp (Cre/+); Apc (fl/+); Kras (LSL-G12D/+) mouse, replicate 7

description: Library name: KrasG12D_7


title: Hemispheric cerebellar tissue from subject 2, array type v2

value: 0 months


title: Colon tumor from Fabp (Cre/+); Apc(fl/+); Nf1(fl/fl) mouse, replicate 4

description: Library name: NF1_4


title: U2OS cells, GFP-MYC-NU, Rep1

description:
Library name: U2OS_GFP-MYC-NU_only_rep1
log2FC and adjusted P values from DESeq2 comparing GFP and NU samples (column D-E)


title: mucCRC043_RNA-seq

value: female


title: Hemispheric cerebellar tissue from subject 1, array type v2

value: Cerebellum (non-tumor)


title: mucCRC042_RNA-seq


title: U2OS cells, GFP only, Rep3

description:
Library name: U2OS_GFP_only_rep3
DESeq2 output with log2FC and adjusted P values comparing GFP control with the other two samples

value: GFP transfection


title: mucCRC041_RNA-seq

value: IIA


title: Colon tumor from Fabp (Cre/+); Apc(fl/+); Nf1(fl/fl) mouse, replicate 3

description: Library name: NF1_3


title: Colon tumor from Fabp (Cre/+); Apc (fl/+); Kras (LSL-A59E/+) mouse, replicate 5

description: Library name: KrasA59E_5


title: M14P_control_1

city: Detroit

first: Malathy

middle: P

last: Shekhar

state: MI

address: 421 East Canfield Avenue

department: Oncology

institute: Wayne State University

description: Library name: M14P_control_1

data_processing:
Aligned to mm10 with STAR
Tabulated to gene regions using htseq count
differential analyses in edgeR
Assembly: mm10
Supplementary files format and content: Excel file R results

growth_protocol: Parental M14 and A2058 cells were cultured in DMEM/F12 supplemented with 5% fetal bovine serum. VemR M14 and A2058 cells were maintained in same media supplemented with 100 nM or 4 mM vemurafenib, respectively. Mel-14-108 and Mel-14-089 cells were cultured in DMEM/F12 medium supplemented with 5% fetal bovine serum. All cells were grown in a humidified atmosphere with 5% CO2 at 37oC.

extract_protocol:
Total RNA was isolated from cell lines using RNA later followed by purification with RNeasy mini kit (Qiagen) using the manufacturer’s recommended in-solution DNase digestion.
Lexogen QuantSeq 3' mRNAseq

treatment_protocol: Parental M14 or A2058 cells, and their isogenic VemR counterparts were cultured in DMEM/F12 media containing 5% FBS. The VemR M14 and A2058 cells maintained in 100 nM or 4 mM vemurafenib, respectively, were rinsed three times to remove drug and incubated in drug free media prior to RNA isolation. Mel-14-108 and Mel-14-089 cells were treated overnight with 10 nM or 4 mM vemurafenib, respectively.

value: melanoma


title: BSseq MII oocytes vitro 26

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

country: Italy

institute: University of Campania "Luigi Vanvitelli"

description: Library name: vitro_46

data_processing:
We processed a total of 88 libraries (88 oocytes), adapting and quality-trimming them using Trim Galore version 0.4.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) for sequences with a Phred score of less than 20. Additionally, one negative control was sequenced to detect any technical issues. High-quality reads were aligned to the bovine reference genome (UMD3.1.1) using HiSat2 version 2.1.0 in single-end mode. For the cumulus cell samples, feature counting at the gene and transcript isoform level was done using rsem-calculate-expression (RSEM v1.3.3) (Li et al., 2011). Data processing was done in R (v4.2.2) using the edgeR (v3.38.4) package for differential gene expression analysis (Chen et al., 2016).
A total of 46 scBS-seq libraries were processed for analysis. The initial 6 base pairs, which included the N portion of the random primers, adapters, and low-quality bases (Phred score <20), were trimmed using Trim Galore version 0.4.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) in single-end mode. High-quality reads were aligned to the bovine reference genome (UMD3.1.1) using Bismark version 0.18.2 (Krueger & Andrews, 2011) in single-end and nondirectional mode, followed by deduplication and methylation calling through Bismark functions.
Assembly: Bos Taurus (UMD3.1_v91)
Supplementary files format and content: Normalized counts
Supplementary files format and content: 20CpG_windows_methylation

organism: Bos taurus

source_name: MII oocytes

growth_protocol: For the collection of in vivo matured (IVO), in vitro matured (IVM) and in vivo + in vitro mature (VV) cumulus-oocytes complexes (COCs), four non-lactating and non-pregnant Holstein heifers (15 - 18 months of age) were used. For the collection of IVO and VV COCs, animals were synchronized using an intravaginal progesterone-releasing device (CIDR, Zoetis Belgium). Eight days later, the device was removed, and heifers received 2 mL (0.5 mg) of prostaglandin (PG; Cyclix Virbac, France). Estrus (=day 0) was confirmed two days later by ultrasound. To induce ovulation, 2.5 mL (10 µg) of Gonadotropin-releasing hormone (GnRH, Receptal, Intervet, Germany) was injected on day 8 of the estrous cycle. From day 10, animals were superovulated with 180 mg of follicle-stimulating hormone (FSH, Folltropin, Vetoquinol, Canada) administered twice daily for four days in decreasing doses. On day 12, animals received 3 mL (0.75 mg) of PG, and the luteinizing hormone (LH) surge was induced with 2.5 mL GnRH administered 40 h after  PG injection. Follicles ≥ 8mm in diameter were aspirated 24h after GnRH injection, using an 18 gauge needle. A 15-20 mL/min aspiration vacuum pressure was used due to the presence of expanded and sticky cumulus cells characteristic of oocyte maturation. Before follicle aspiration, the OPU tubing system was rinsed with polyvinylpyrrolidone (PVP) medium (0.3% PVP (PVP-360; Sigma) in Ca- and Mg-free PBS + 10 IU/mL heparin (Sigma)). The follicular content was collected in a 50 mL conical tube, and COCs were recovered under a stereomicroscope and stored in EmXcell medium without BSA (IMV-technologies, France) until the end of the collection procedure. After aspiration, COCs were collected under a stereomicroscope. Oocytes with evident cumulus expansion (IVO) were immediately denuded, whereas oocytes with poor cumulus expansion were submitted to IVM for 22 h (VV group), in groups (based on the cow of origin) in 50 µL bicarbonate-buffered TCM199 medium supplemented with gentamicin (50 mg/L) and epidermal growth factor (20 µl/mL). To assess maturation status, IVO and VV COCs were denuded individually in 0.1% hyaluronidase (Sigma) in PVP medium for approximately 2 min and by pipetting with a STRIPPER pipet holder and a 135-μm capillary (Origio, Cooper Surgical, CT, US) until all cumulus cells were removed from the oocyte. Denuded oocytes were classified as mature or immature oocytes based on the presence or absence of the polar body (PB), respectively. Mature IVO oocytes (n=28) and VV oocytes (n=20) were washed individually three times in PVP medium, treated with pronase to dissolve the zona pellucida (0.1% protease from S. griseus, in TCM-199), and immediately stored in 5 µl of Buffer RLT (Qiagen) at -80 °C until further use. Cumulus cells from IVO COCs were collected and pooled based on the cow of origin, and immediately stored in a lysis buffer for further analysis. For the collection of IVM oocytes, animals received GnRH (Receptal, Intervet, Germany) injection eight days after estrus and aspiration of follicles ≤ 8 mm was performed through an OPU procedure four days later. After aspiration, immature COCs (IVM group) were collected and underwent IVM as described above. After 22h, COCs were denuded, and mature oocytes (n=32) with their respective cumulus cells were processed and stored as described in the previous paragraph.

extract_protocol:
DNA and RNA from oocyte were separated using the G&T protocol (Angermueller et al. 2016). The magnetic beads (MyOne C1, Life Technologies) were washed and then annealed to oligo dTs. These were used to capture polyadenylated mRNA from individual cell lysate. The supernatant containing the DNA was transferred to a new tube and the beads washed three times in 1xFSS buffer (Superscript II, Invitrogen), 10 mM DTT, 0.005% Tween-20 (Sigma) and 0.4 U/μl of RNAsin (Promega) to remove all DNA residue. Each washing solution was added to the DNA tube to maximise recovery. Total RNA was extracted from seven cumulus cells samples (four from in vivo matured, three from in vitro matured COCs) using RNeasy Micro Kit (Qiagen) according to the manufacturer’s instruction. The RNA samples underwent quality and concentration assessments using an RNA 6000 Pico Chip (Agilent Technologies, Carlsbad, CA, USA).
ScRNA-seq and scBSseq

value: MII oocytes

value: Wild-type


title: A2058VR_control_3

description: Library name: A2058VR_control_3


title: Colon tumor from Fabp (Cre/+); Apc(fl/+); Nf1(fl/fl) mouse, replicate 2

description: Library name: NF1_2

value: Colon tumor

value: Fabp (Cre/+); Apc(fl/+); Nf1(fl/fl)


title: mucCRC040_RNA-seq

value: IV


title: BSseq MII oocytes vitro 25

description: Library name: vitro_45


title: Colon tumor from Fabp (Cre/+); Apc(fl/+); Kras(LSL-A59E/+); Nf1(fl/fl) mouse, replicate 3

description: Library name: KrasA59E_NF1_3


title: mucCRC037_RNA-seq

value: male

value: IIIB


title: BSseq MII oocytes vitro 24

description: Library name: vitro_44


title: A2058VR_control_1

description: Library name: A2058VR_control_1


title: U2OS cells, GFP only, Rep2

description:
Library name: U2OS_GFP_only_rep2
DESeq2 output with log2FC and adjusted P values comparing GFP control with the other two samples


title: Colon tumor from Fabp (Cre/+); Apc(fl/+); Kras(LSL-A59E/+); Nf1(fl/fl) mouse, replicate 2

description: Library name: KrasA59E_NF1_2


title: BSseq MII oocytes vitro 23

description: Library name: vitro_43


title: BSseq MII oocytes vitro 22

description: Library name: vitro_42


title: Colon tumor from Fabp (Cre/+); Apc(fl/+); Kras(LSL-A59E/+); Nf1(fl/fl) mouse, replicate 4

description: Library name: KrasA59E_NF1_4


title: U2OS cells, GFP only, Rep1

description:
Library name: U2OS_GFP_only_rep1
DESeq2 output with log2FC and adjusted P values comparing GFP control with the other two samples


title: mucCRC036_RNA-seq

value: mucinous colorectal cancer tissue


title: mucCRC035_RNA-seq


title: A2058P_control_1

description: Library name: A2058P_control_1


title: Colon tumor from Fabp (Cre/+); Apc(fl/+); Kras(LSL-A59E/+); Nf1(fl/fl) mouse, replicate 1

description: Library name: KrasA59E_NF1_1


title: A2058P_control_2

description: Library name: A2058P_control_2


title: BSseq MII oocytes vitro 21

description: Library name: vitro_41


title: Colon tumor from Fabp (Cre/+); Apc (fl/+); Kras (LSL-A59E/+) mouse, replicate 4

description: Library name: KrasA59E_4


title: BSseq MII oocytes vitro 20

description: Library name: vitro_40


title: mucCRC039_RNA-seq


title: mucCRC032_RNA-seq

value: IIIC


title: A2058VR_control_2

description: Library name: A2058VR_control_2


title: R21007152-GSPMD-GSDMD-4

city: Yangling

first: Jing

last: Chen

address: Xinong road #22

institute: Northwest Agriculture & Forestry University

description:
Library name: Sample8
one sample from Gsdmd-/- mice lung tissue

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope  (https://github.com/singleron-RD/CeleScope)  pipeline.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
the lungs were resuspended with PBS containing 0.1 % Collagenase type I (SCR103, Sigma-Aldrich), 0.05 % DNase I (D5025, Sigma-Aldrich), and 5 % FBS (13011-8611, Tianhang Biotechnology). After incubation at 37 °C for 60 min, the samples were pestled and filtrated with a 200-mesh sieve, pelleted (300 g, 5 minutes), and resuspended in ACK red blood cell lysis buffer (Gibco A1049201) for 3 minutes, after which the buffer was inactivated by adding excess processing buffer. Cells were then filtered through a 70 μm strainer, pelleted again (300 g, 5 minutes), and resuspended in PBS buffer, counted, and immediately processed for single-cell RNA sequencing.
scRNA-seq libraries were constructed according to Singleron GEXSCOPE protocol by GEXSCOPE Single-Cell RNA Library Kit (Singleron Biotechnologies)

value: lung

value: Gsdmd-/-


title: R21007152-GSPMD-GSDMD-3

description:
Library name: Sample 7
one sample from Gsdmd-/- mice lung tissue


title: Colon tumor from Fabp (Cre/+); Apc (fl/+); Kras (LSL-G12D/+) mouse, replicate 6

description: Library name: KrasG12D_6


title: mucCRC031_RNA-seq

value: Mucinous adenocarcinoma


title: Colon tumor from Fabp (Cre/+); Apc(fl/+); Nf1(fl/fl) mouse, replicate 1

description: Library name: NF1_1


title: BSseq MII oocytes vivo 20

description: Library name: vivo_38


title: R21007152-GSPMD-GSDMD-2

description:
Library name: Sample 6
one sample from Gsdmd-/- mice lung tissue


title: Colon tumor from Fabp (Cre/+); Apc (fl/+) mouse, replicate 6

description: Library name: WT_6

value: Fabp (Cre/+); Apc (fl/+)


title: BSseq MII oocytes vitro 19

description: Library name: vitro_39


title: mucCRC034_RNA-seq


title: A2058P_control_3

description: Library name: A2058P_control_3


title: R21007152-GSPMD-GSDMD-1

description:
Library name: Sample 5
one sample from Gsdmd-/- mice lung tissue


title: BSseq MII oocytes vivo 19

description: Library name: vivo_37


title: mucCRC029_RNA-seq


title: Colon tumor from Fabp (Cre/+); Apc (fl/+); Kras (LSL-A59E/+) mouse, replicate 2

description: Library name: KrasA59E_2


title: R21007149-WT-WT-4

description:
Library name: Sample 4
one sample from C57 6J/BL mice lung tissue

value: WT


title: mucCRC033_RNA-seq


title: Colon tumor from Fabp (Cre/+); Apc (fl/+); Kras (LSL-A59E/+) mouse, replicate 1

description: Library name: KrasA59E_1


title: BSseq MII oocytes vivo 17

description: Library name: vivo_35


title: BSseq MII oocytes vivo 18

description: Library name: vivo_36


title: R21007149-WT-WT-2

description:
Library name: Sample 2
one sample from C57 6J/BL mice lung tissue


title: mucCRC027_RNA-seq


title: mucCRC030_RNA-seq


title: BSseq MII oocytes vivo 16

description: Library name: vivo_34


title: mucCRC026_RNA-seq

value: female


title: Colon tumor from Fabp (Cre/+); Apc (fl/+); Kras (LSL-G12D/+) mouse, replicate 4

description: Library name: KrasG12D_4


title: Colon tumor from Fabp (Cre/+); Apc (fl/+); Kras (LSL-G12D/+) mouse, replicate 5

description: Library name: KrasG12D_5


title: BSseq MII oocytes vivo 15

description: Library name: vivo_33


title: R21007149-WT-WT-3

description:
Library name: Sample 3
one sample from C57 6J/BL mice lung tissue


title: R21007149-WT-WT-1

description:
Library name: Sample 1
one sample from C57 6J/BL mice lung tissue


title: mucCRC025_RNA-seq


title: Colon tumor from Fabp (Cre/+); Apc (fl/+); Kras (LSL-A59E/+) mouse, replicate 3

description: Library name: KrasA59E_3


title: BSseq MII oocytes vivo 14

description: Library name: vivo_32


title: Colon tumor from Fabp (Cre/+); Apc (fl/+); Kras (LSL-G12D/+) mouse, replicate 3

description: Library name: KrasG12D_3


title: Colon tumor from Fabp (Cre/+); Apc (fl/+); Kras (LSL-G12D/+) mouse, replicate 2

description: Library name: KrasG12D_2


title: SI_37334_Ms#3652_R265-71del+/+; Trp53f/f PbCre+_AD_Case

city: Ann Arbor

first: Arul

last: Chinnaiyan

address: 1500 East Medical Center Dr

department: MCTP

institute: University of Michigan

data_processing:
Read demultiplexing, alignment and gene quantification are conducted with the  Cell Ranger ARC pipeline (v2.0).  Custom reference was built by adding sequences of human FOXA1 and puroR to the prebuilt mouse reference (mm10)
Assembly: mm10
Supplementary files format and content: filtered feature matrix (.h5)
Library strategy: GEM Single-cell Multiome ATAC+Gene expression

source_name: prostate

growth_protocol: Mice were aged in a pathogen-free facility in compliance with IACUC prior to tissue harvest.

extract_protocol: Single-cell multiomics was performed using the Chromium Next GEM Single-cell Multiome ATAC+Gene expression kit (10x Genomics) according to the manufacturer’s protocol20. Briefly, nuclei were isolated, followed by transposition and adapter ligation using a Tn5 transposase. Transposed nuclei were loaded onto a Chromium Next GEM microfluidic chip along with gel beads containing 10x barcoded oligonucleotides. The GEMs were incubated to produce barcoded DNA from transposed chromatin (ATAC) and barcoded full-length cDNA from polyadenylated mRNA (Gene expression) within each GEM. Following this, the GEM is broken, cDNA is amplified, and pre-amplified cDNA is used as input for both the ATAC and gene expression library preparation. For ATAC, sample indexing primers are used for further amplification while the amplified cDNA underwent fragmentation, end repair, and A-tailing, followed by adapter ligation and PCR amplification to generate final sequencing libraries. Library quality was assessed using an Agilent Bioanalyzer.

treatment_protocol: Mice were euthanized, and the distinct prostate lobes were microdissected.The lobes were then minced using a disposable scalpel into small pieces around one mm3 in a 10-cm culture dish under aseptic conditions. Subsequently, the minced tissues were transferred into 15 mL tubes containing prewarmed (37 °C) advanced DMEM F-12 +/+/+ media with 5 mg/mL of collagenase Type II (Gibco, 17101015) and incubated on a rotator for 1 hour at 37°C. Next, the tissues were digested with TrypLE (Thermo Fisher Scientific, 12605010) for 15 minutes, followed by a media wash. Single cells were strained using a 70 and 40-micron filter, followed by a 0.4% BSA in 1XPBS wash. Following this, cells were processed for single-cell RNA-sequencing using the  Chromium Next GEM Single Cell 3' kit v3.1 (10x Genomics).

value: prostate

value: mixed

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation and loss of Trp53 in the prostate epithelial cells. Pb-Cre+ mice have  expression of the transgene. Anterior and Dorsal lobes only


title: mucCRC024_RNA-seq


title: BSseq MII oocytes vivo 13

description: Library name: vivo_31

value: MII oocytes

value: Wild-type


title: Colon tumor from Fabp (Cre/+); Apc (fl/+); Kras (LSL-G12D/+) mouse, replicate 1

description: Library name: KrasG12D_1

value: Colon tumor


title: BSseq MII oocytes vivo 12

description: Library name: vivo_30


title: mucCRC028_RNA-seq

value: IIA


title: Colon tumor from Fabp (Cre/+); Apc (fl/+) mouse, replicate 5

description: Library name: WT_5


title: SI_37331_Ms#3652_R265-71del+/+; Trp53f/f PbCre+_AD_Case

molecule: nuclear RNA

value: male


title: SI_37333_Ms#3650_R265-71del+/+; Trp53f/f PbCre+_AD_Case


title: SI_37332_Ms#3651_3646_R265-71del+/+; Trp53f/f PbCre-_AD_Ctrl

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation and loss of Trp53 in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene. Anterior and Dorsal lobes only


title: Colon tumor from Fabp (Cre/+); Apc (fl/+) mouse, replicate 4

description: Library name: WT_4


title: BSseq MII oocytes vivo 11

description: Library name: vivo_29


title: mucCRC020_RNA-seq

value: mucinous colorectal cancer tissue


title: BSseq MII oocytes vivo 10

description: Library name: vivo_28


title: Colon tumor from Fabp (Cre/+); Apc (fl/+) mouse, replicate 3

description: Library name: WT_3


title: mucCRC021_RNA-seq


title: SI_37329_Ms#3651_3646_R265-71del+/+; Trp53f/f PbCre-_AD_Ctrl


title: mucCRC019_RNA-seq

value: IIIB


title: BSseq MII oocytes vivo 8

description: Library name: vivo_26


title: Colon tumor from Fabp (Cre/+); Apc (fl/+) mouse, replicate 2

description: Library name: WT_2


title: BSseq MII oocytes vivo 9

description: Library name: vivo_27


title: SI_34513_R265-71del+/+;Trp53+/+;PbCre+_Case

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation and loss of Trp53 in the prostate epithelial cells. Pb-Cre+ mice have expression of the transgene. These animals were castrated for 4 weeks.


title: mucCRC017_RNA-seq


title: BSseq MII oocytes vivo 7

description: Library name: vivo_25


title: Colon tumor from Fabp (Cre/+); Apc (fl/+) mouse, replicate 1

description: Library name: WT_1


title: SI_34512_R265-71del+/+;Trp53+/+;PbCre-_Control

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation and loss of Trp53 in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene. These animals were castrated for 4 weeks.


title: mucCRC023_RNA-seq

value: Mucinous adenocarcinoma

value: IIIC