title: OCI-AML2 Day21 Venetoclax Rep2 [D21_VEN2_Ln2S8_L002]

description:
PCR library sequencing
LIB200527JT_AML2_D21_VEN2_Ln2S8_L002

value: Day 21 post puromycin selection, Venetoclax


title: OCI-AML2 Day21 Venetoclax Rep1 [D21_VEN1_Ln2S7_L002]

status: Public on Jun 30 2023

type: SRA

city: Portland

first: Daniel

last: Bottomly

address: 3181 S.W. Sam Jackson Park Rd.

country: USA

institute: Oregon Health and Science University

description:
PCR library sequencing
LIB200527JT_AML2_D21_VEN1_Ln2S7_L002

library_source: genomic

data_processing:
Read Trimming: cutadapt -j 2 -n 2 -g ACGAAACACCG -a GTTTAAGAGC  (Version 2.3)
Alignment: bowtie2 -p 1 -x yusa_library --xeq --norc -U {file}.trimmed.fastq {file}.tmp.sam (Version 2.3.5.1)
Conversion to BAM: samtools view -bS {file}.tmp.sam > {file}.bam (Version 1.9)
Filter to unique matches allowing no mismatches using bamtools (Version 2.5.1)
Counting reads for each sgRNA using MAGeCK: mageck count --norm-method none (Version: v0.5.8)
Assembly: Custom reference created from CRISPR library
Supplementary files format and content: Read counts per sgRNA for each sample

molecule: genomic DNA

organism: Homo sapiens

source_name: OCI-AML2 cells infected with library

growth_protocol: OCI-AML2 cells were grown in RPMI-1640, supplemented with 20% serum, L-glutamine, pen/strep, fungizone.

extract_protocol:
30 million cells were collected for each drug treatment in duplicate at day 14 and day 21. DNA was extracted by desalting method
50 micrograms of DNA were used to amplify sgRNA guide libraries using Herculase II enzyme following published protocols and instructions supplied by authors on Addgene  (Shalem, et al Science 2014. 343(6166): p. 84-87, Tzelepis et al, Cell Rep, 2016. 17(4): p. 1193-1205)
Shalem et al Science 2014. 343(6166): p. 84-87

treatment_protocol: After transduction, puromycin (2 mg/ml final concentration) was applied  to each flask. After 7 days, cells were collected and resuspended in fresh media with either DMSO, venetoclax (0.5 uM) or venetoclax (0.1 uM) plus ruxolitinib (1 uM)

tag: cell line

tag: genotype/variation

value: infected with CRISPR/Cas9 library

tag: treatment


title: HCC218post1

type: RNA

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

country: Japan

institute: Toray Industries, Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95%

molecule: total RNA

source_name: serum

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: Serum was collected from the blood.

extract_protocol: Total RNA from serum was extracted commercially available kit (miReasy mini kit (Qiagen)).

treatment_protocol: Blood was collected before surgical treatment.

tag: disease/diagnosis

value: hepatocellular carcinoma

tag: sample collection time

value: after operation within 14 days

tag: molecule subtype

value: miRNA


title: OCI-AML2 Day21 DMSO Rep2 [D21_DMSO2_Ln2S4_L002]

description:
PCR library sequencing
LIB200527JT_AML2_D21_DMSO2_Ln2S4_L002

value: Day 21 post puromycin selection, DMSO


title: OCI-AML2 Day21 DMSO Rep1 [D21_DMSO1_Ln2S3_L002]

description:
PCR library sequencing
LIB200527JT_AML2_D21_DMSO1_Ln2S3_L002


title: HCC218post2

value: after operation beyand 14 days


title: OCI-AML2 Day14 Venetoclax-Ruxolitinib Rep2 [D14_VENRUX2_Ln3S4_L001]

description:
PCR library sequencing
LIB200527JT_AML2_D14_VENRUX2_Ln3S4_L001

value: Day 14 post puromycin selection, Venetoclax-Ruxolitinib


title: HCC217pre

value: before operation


title: HCC217post1


title: HCC211pre


title: HCC211post1


title: OCI-AML2 Day14 Venetoclax-Ruxolitinib Rep1 [D14_VENRUX1_Ln3S3_L001]

description:
PCR library sequencing
LIB200527JT_AML2_D14_VENRUX1_Ln3S3_L001


title: HSC from steady state mouse #2 [Ctrl02]

city: Kumamoto

first: Kenichi

last: Miharada

address: 2-2-1 Honjo, Chuo-ku

institute: Kumamoto University

description: Gene expression data from CD150+ CD48- c-Kit+ Sca-I+ Lineage- cells of 10 weeks old male mouse, 24 hours after phlebotomy

hyb_protocol: 3.7 µg of fragmented and labeled ds cDNA were hybridized to Affymetrix Mouse Genome 430 PM Array Plates using an Affymetrix GeneTitan system controlled by the Affymetrix GeneChip Command Console software v4.3.3

scan_protocol: The fluorescent signals were measured with an Affymetrix GeneTitan system controlled by the Affymetrix GeneChip Command Console software v4.3.3

data_processing: Gene level summarized probe set signals in log2 scale were calculated from Affymetrix CEL files by using the RMA algorithm as implemented in the Affymetrix GeneChip Expression Console v1.4 Software

label: biotin

organism: Mus musculus

source_name: CD150+CD48-KSL cells from bone marrow of 10 weeks-old mouse

label_protocol: 300 pg of total RNA was used for reverse transcription to synthesize single-stranded (ss) cDNA with a T7 promoter sequence at the 5' end. Next a 3’ adaptor was added and the ss cDNA was converted to double-stranded cDNA, which acted as a template for a pre- in vitro transcription (IVT) amplification by a 12 cycle PCR. Afterwards antisense RNA (complimentary RNA or cRNA) was synthesized and linearly amplified by an in vitro transcription (IVT) of the double-stranded cDNA template. 20 µg of cRNA was purified and reverse transcribed into double-stranded (ds) cDNA, whereat unnatural dUTP residues were incorporated at a fixed ratio relative to dTTP. Purified ds cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the dUTP residues followed by a terminal labeling with biotin (Affymetrix GeneChip Pico Reagent Kit User Guide)

extract_protocol: Total RNA was isolated from the sorted CD150+ CD48- c-kit+ Sca-I+ lineage- cells using RNeasy® Micro Kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: Hemolytic anemia was induced by intraperitoneally injecting 60 mg/kg of phenylhydrazine (PHZ, Sigma-Aldrich). Alternatively, acute anemia was induced by phlebotomy; approximately 300 μl of peripheral blood was collected from the tail vein of the mouse for three consecutive days.

tag: strain

tag: gender

value: male

tag: age

value: 10 weeks


title: HCC210post1


title: HCC210pre


title: HSC from steady state mouse #4 [Ctrl04]

description: Gene expression data from CD244- CD48- c-Kit+ Sca-I+ Lineage- cells of 10 weeks old male mouse


title: OCI-AML2 Day14 Venetoclax Rep2 [D14_VEN2_Ln3S6_L001]

description:
PCR library sequencing
LIB200527JT_AML2_D14_VEN2_Ln3S6_L001

value: Day 14 post puromycin selection, Venetoclax


title: HSC from steady state mouse #1 [Ctrl01]


title: HSC from steady state mouse #5 [Ctrl05]


title: HCC210post2


title: HSC from steady state mouse #3 [Ctrl03]


title: HSC from phenylhydrazine injected mouse #5 [PHZ05]

source_name: CD150+CD48-KSL cells from bone marrow of 10 weeks-old mouse treated with 60 mg/kg phenylhydrazine


title: HSC from phenylhydrazine injected mouse #2 [PHZ02]

description: Gene expression data from CD150+ CD48- c-Kit+ Sca-I+ Lineage- cells of 10 weeks old male mouse, 24 hours after 60 mg/kg phenylhydrazine injection


title: HSC from phenylhydrazine injected mouse #4 [PHZ04]


title: HCC199pre


title: OCI-AML2 Day14 Venetoclax Rep1 [D14_VEN1_Ln3S5_L001]

description:
PCR library sequencing
LIB200527JT_AML2_D14_VEN1_Ln3S5_L001


title: HSC from phenylhydrazine injected mouse #1 [PHZ01]


title: HSC from phenylhydrazine injected mouse #3 [PHZ03]


title: HSC from phlebotomized mouse #4 [Phle04]

description: Gene expression data from CD150+ CD48- c-Kit+ Sca-I+ Lineage- cells of 10 weeks old male mouse, 24 hours after PBS injection

source_name: CD150+CD48-KSL cells from bone marrow of 10 weeks-old phlebotomized mouse


title: HSC from phlebotomized mouse #5 [Phle05]


title: OCI-AML2 Day14 DMSO Rep2 [D14_DMSO2_Ln3S2_L001]

description:
PCR library sequencing
LIB200527JT_AML2_D14_DMSO2_Ln3S2_L001

value: Day 14 post puromycin selection, DMSO


title: HCC199post1


title: OCI-AML2 Day14 DMSO Rep1 [D14_DMSO1_Ln3S1_L001]

description:
PCR library sequencing
LIB200527JT_AML2_D14_DMSO1_Ln3S1_L001


title: HSC from phlebotomized mouse #3 [Phle03]


title: HCC198pre


title: HSC from phlebotomized mouse #2 [Phle02]


title: Sample pool 8 of single strain transplanted or co-transplanted MDST tumors treated with or without olaparib for 20 days

first: Xi

last: Li

state: Oregon

address: 2730 SW Moody Ave

institute: Oregon Health & Science University

library_source: transcriptomic single cell

data_processing:
basecalls were done by Illumina Casava1.8 software
sequenced reads were demultiplexed by Cell Ranger v6.0.0
sequenced reads were mapped to GRCm38 whole genome with all transcripts by Cell Ranger v6.0.0 with default parameters
sequenced reads were mapped to GRCm38 whole genome with only exons by velocyto v0.17
raw reads were loaded, merged and filtered in Python using scVelo
Assembly: GRCm38
Supplementary files format and content: comma-delimited text files include CPM values of spliced RNA for each cells
Supplementary files format and content: comma-delimited text files include raw counts of spliced RNA for each cells

molecule: polyA RNA

source_name: FVB mouse/breast cancer

growth_protocol: For MDST assays female FVB mice at 6 weeks of age were purchased from the Jackson Laboratory. Animal experiments were performed by X. Li in Animal Facility, Knight cancer Institute, Oregon Health & Science University. Animal studies were performed according to IACUC approved protocol: Combination Therapy Targets Adaptive Resistance in Cancer (TR01_IP00002062) following AALAC guidelines. Mice were housed 5 to a cage with ad libitum access to food and water in 20℃ ambient temperatures, 40-50% humidity. And 12-hour light/12-hour dark cycle. 25mm3 LPA1-T22 (T22) or LPA1-T127 (T127) tumor chunks were orthotopicly transplanted into the mammary fat pad. 14 or 10 days after tumor transplanted for T22 or T127 respectively, mice were assigned to treatment groups (n>5) based on randomization of tumor size.

extract_protocol:
Tumor was harvested from FVB mouse mamary pad. Tumor tissue was dissociated with gentleMACS tissue dissociation kits (SUM149 xenograft tumors were disaggregated by gentleMACS kits (Miltenyi Biotec, #130-096-730), and incubated in cell multiplexing oligos from 10x Genomics (3' CellPlex Kit Set A 1000261) following the manufactural instructions. Live cells were isolated by EasySep Dead Cell Removal (Annexin V) Kit (STEMCELL Technologies, #17899). Single cell suspensions were processed according to 10x Genomics scRNAseq sample preparation protocol (Chromium Single Cell 3’ v3.1 Reagent Kit, 10xGenomics). 5000 cells were targeted for each sample.)
RNA libraries were prepared for sequensing using standard library construction protocol by 10x Genomics

treatment_protocol: For co-transplanted models, T22 tumor chunks were transplanted in the opposite site mammary pad 14 days prior to T127 tumors as demonstration in Figure 1A. For short term treatment assays, mice were treated with vehicle or olaparib (50mg/kg, oral galvage, daily, Selleckchem, #S7110) for 4 days, 8 days. For long-term treatment assay mice were treated with vehicle or olaparib (50mg/kg, oral galvage, daily, Selleckchem, #S7110) for 20 days.

tag: tissue

value: mamary pad

value: olaparib 50mg/kg/day


title: HCC197pre


title: HCC198post1


title: Sample pool 7 of single strain transplanted or co-transplanted MDST tumors treated with or without olaparib for 20 days


title: Sample pool 6 of single strain transplanted or co-transplanted MDST tumors treated with or without olaparib for 20 days


title: HCC197post1


title: HCC193pre


title: HSC from phlebotomized mouse #1 [Phle01]


title: Sample pool 5 of single strain transplanted or co-transplanted MDST tumors treated with or without olaparib for 20 days


title: Midbrain, transgenic

city: Hong Kong

first: Ho

last: Ko

address: 30-32 Ngan Shing Street, Shatin

department: Medicine and Therapeutics

country: China

institute: The Chinese University of Hong Kong

description:
Two brain regions from same group (3 mice)
ast_mb_barcodes.tsv.gz
ast_mb_features.tsv.gz
ast_mb_matrix.mtx.gz
mb_meta.tsv

data_processing:
The multiple fastq files were aligned to mm10 reference genome by Cellranger software (v3.0.0)
Follow the stadard Seurat (v3.1.5) process pipeline, cells were undergo quality control by following criterias: 1. Lower than 5% or higher than 95% UMI count. 2. The proportion of mitochondrial genes > 20%.
After normalization (by SCTransform function), the dimension reduction and clustering was finished by UMAP and Seurat FindNeighbors and FindClusters function on first 30 components of PCA results.
The primary cell type was identified by well-known marker genes. Any cluster with dual marker genes expression was removed.
Assembly: mm10
Supplementary files format and content: Standard 10X cellranger output files: 1. Sparse matrix (mtx), each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column). 2.The meta file contained the batch, age, sample names, clustering results and cell type identified in Seurat.

source_name: Brain midbrain

extract_protocol:
We adapted a previously described dissociation protocol using the Neural Tissue Dissociation kit (P) (130-092-628, Miltenyi Biotec) for adult mouse brain glial and vascular cell isolation
Chromium Single Cell 3′ Reagent Kit v3
Drop-seq (10X Gemonic)

value: Brain midbrain

tag: genotype

value: Transgenic

tag: mouse number

value: 6-9 months


title: Sample pool 2 of single strain transplanted or co-transplanted MDST tumors treated with or without olaparib for 20 days


title: Sample pool 4 of single strain transplanted or co-transplanted MDST tumors treated with or without olaparib for 20 days


title: Frontal cortex, transgenic

description:
Two brain regions from same group (3 mice)
ast_fc_barcodes.tsv.gz
ast_fc_features.tsv.gz
ast_fc_matrix.mtx.gz
fc_meta.tsv

source_name: Brain frontal cortex

value: Brain frontal cortex


title: HCC193post2

value: hepatocellular carcinoma


title: Sample pool 3 of single strain transplanted or co-transplanted MDST tumors treated with or without olaparib for 20 days


title: HCC192post2


title: HCC192pre


title: Midbrain, wildtype

value: Wildtype (littermate)


title: Sample pool 4 of LPA1T127 tumors treated with or without olaparib for 4 days and 8 days


title: Sample pool 1 of single strain transplanted or co-transplanted MDST tumors treated with or without olaparib for 20 days


title: HCC188pre

value: miRNA


title: Sample pool 3 of LPA1T127 tumors treated with or without olaparib for 4 days and 8 days


title: Frontal cortex, wildtype


title: HCC182pre


title: Transfection of miR-non target in GFP-SAS cells

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

institute: Ehime University Graduate School of Medicine

hyb_protocol: 7.5 µg fragmented and labeled aRNA were hybridized for 16h at 45℃ on Human Genome U219 Array Strip. Array Strip was washed and stained in the GeneAtlas fluidics station.

scan_protocol: Array Strip was scanned in the GeneAtlas imaging station.

data_processing: The robust multichip average (RMA) method was used background correction and normalization.

label: Biotin

source_name: Oral cavity

label_protocol: 10 ng of total RNA was labeled using a GeneAtlas 3'IVT Express Kit Assay (Affymetrix) according to the manufacturer's instructions.

growth_protocol: Cells were incubated in a humidified atomosphere of 95% air and 5% CO2 at 37℃

extract_protocol: Extraction of total RNA was performed with the use of ISOGEN (Nippon Gene) according to the manufacturer's instructions.

treatment_protocol: Cells were treated with 20 nM of miR-1289 mimic or miR-non target (NT) for 48 h.

tag: cell type

value: Squamous cell carcinoma cell line


title: Transfection of miR-1289 mimic in HSC2 cells


title: Transfection of miR-non target in Ca9-22 cells


title: HCC182post1

value: after operation within 14 days


title: HCC180pre


title: Transfection of miR-non target in HSC2 cells


title: Sample pool 1 of LPA1T127 tumors treated with or without olaparib for 4 days and 8 days


title: Adult lung [MY-21]

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

data_processing:
Sequenced reads were pseudoaligned to the reference mouse transcriptome (GRCm38) and quantified transcripts abundance using kallisto (v0.43.0) with parameters --single -l 380 -s 70
Genome_build: GRCm38 assembly, release 90
Supplementary_files_format_and_content: Concatenated abundances.tsv from kallisto

source_name: adult lung

extract_protocol:
For total RNA extraction of MEFs (iPUL cells), matrigel blocks containing differentiated cells and fibroblasts were digested using dispase (Corning) at 37°C for 120 minutes. The clusters of the cells were separated using 70 μm cell strainer and lysed and total RNA was harvested using RNA easy kit (Quiagen).For total RNA extraction of adult lung, lungs  were removed, flash frozen on dry ice, and total RNA was harvested using RNA easy kit (Quiagen). For total RNA extraction of SP-C+ cells in 3D culture, matrigel blocks containing differentiated cells and fibroblasts were digested using dispase (Corning) at 37°C for 120 minutes. To prepare the single cell suspension of iPUL cells, cells were incubated in 0.25% Tripsin/EDTA at 37°C for 5 min. GFP+/SP-C+ cells were sorted by flow cytometry. The sorted GFP+/SP-C+ cells were lysed and total RNA was harvested using RNA easy kit (Quiagen).
Total RNA obtained from each sample was subjected to a sequencing library construction using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, MA) with NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer’s protocols.   The quality of the libraries was assessed with an Agilent 2200 TapeStation High Sensitivity D1000 (Agilent Technologies, Santa Clara, CA).   The pooled libraries of the samples were sequenced using the illumina HiSeq 1500 system (Illumina, Inc., San Diego, CA) in 50-base-pair (bp) single-end reads.

value: mouse adult lung cells

tag: passages


title: Transfection of miR-1289 mimic in Ca9-22 cells


title: SP-C+ cells sorted from adult lungs [MY-11]

value: SP-C+ adult lung cells

value: CBA/Ca x C57BL/6


title: Adult lung [MY-20]


title: P2_E01_529_mono_37

city: Edinburgh

first: Nizar

middle: N.

last: Batada

address: Crew Road

country: United Kingdom

institute: Institute for Genetics and Molecular Medicine, University of Edinburgh

data_processing:
Smart-Seq2
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: peripheral blood

growth_protocol: Cells were isolated from B6Tg(MMTV-PyMT)634Mul/Lellj mice bearing late stage tumors (upto 24mm diameter) or from aged matched  C57BL/6JCrl controls

extract_protocol:
Cells were sorted into 96 well place containing 2 ul of lysis buffer in each well
as per Smart-seq2 protocol (Picelli et al 2013)
Nextera; 75bp + 75bp; HiSeq2500

treatment_protocol: 40µL of blood containing x µl 0.5M EDTA was lysed 400µL RBC lysis buffer (Biolegend), cells washed in excess 10% FCS/PBS, and lysis repeated. Cells were then blocked with 20 µL block and stained with antibodies in 30µL FACS buffer and individual live, single CD11b+ CD45+ CD115+ CD3- CD19-NK1.1- cells were FACS sorted into 96 well plates containing 2 ul of the lysis buffer (0.2% Triton X100 containing 1:20 RNASE inhibitor) per well.

value: monocytes

value: TUM

value: peripheral blood


title: PCHT20

city: JOUY-en-JOSAS

first: gilles

last: charpigny

state: ILe de France

address: domaine de Vilvert

department: Physiologie Animale Systeme Elevage

country: France

institute: INRAE

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Data were processed using miRDeep2 package (2.0.0.8). The raw reads were firstly trimmed against Illumina adapters, then mapped to the Btau_5.0.1 genome assembly as miRBase v22.1 with the Mapper module. Precursors and mature miRNAs were identified using the miRDeep2 core module, miRDeep2.pl. Potential miRNAs were annotated accordingly against ortholog miRNAs in goat, sheep and humans (miRBase release 22.1). We used a miRDeep2 score ≥5 as a cut-off threshold.
The normalization and differential expression analysis of the known and predicted miRNAs were conducted with the DESeq2 R package v1.26,0
Assembly: UMD3.1

organism: Bos taurus

source_name: purified small RNA

extract_protocol: Small RNA-Seq librairies were generated from 10 to 20 ng of purified small RNA fraction using TruSeq Small RNA Library Prep Kit (Illumina, San Diego, CA), according to manufacturer's instructions. The protocol takes advantage of the natural structure common to most microRNA molecules that have a 3' hydroxyl group resulting from enzymatic cleavage by Dicer or other RNA processing enzymes. Briefly, in the first step, RNA adapters were sequentially ligated to each end of the RNA, first the 3' RNA adapter that is specifically modified to target microRNAs and other small RNAs, then the 5' RNA adapter. Small RNA ligated with 3' and 5' adapters were reverse transcribed and PCR amplified (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 15 sec at 72oC] x 13 or 16cycles; 10 min at 72oC) to create cDNA constructs. Amplified cDNA constructs of 20 to 40 nt were selectively isolated by acrylamide gel purification followed by ethanol precipitation.  The final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: Healthy and Subclinical-Endometritis cows

value: blood serum

tag: animal id

tag: animal status

value: healthy

tag: sample time point

value: day 45 of sampling


title: Sample pool 3 of LPA1T22 tumors treated with or without olaparib for 4 days and 8 days

tag: cell line

value: mamary pad

value: olaparib 50mg/kg/day


title: Transfection of miR-1289 mimic in GFP-SAS cells


title: HCC188post1


title: Sample pool 4 of LPA1T22 tumors treated with or without olaparib for 4 days and 8 days


title: HCC180post1


title: HCC177post1


title: HCC177pre

value: before operation


title: Adult lung [MY-10]


title: MEFs transduced empty vector [MY-14]

source_name: embryonic fibroblast

value: mouse embryonic fibroblast (E13.5)

value: 2 to 5


title: MEFs transduced empty vector [MY-7]


title: MEFs transduced 4 foctors (Nkx2-1, Foxa1, Foxa2, Gata6) [MY-6]


title: Sample pool 2 of LPA1T127 tumors treated with or without olaparib for 4 days and 8 days


title: Sample pool 1 of LPA1T22 tumors treated with or without olaparib for 4 days and 8 days


title: HCC174pre

value: hepatocellular carcinoma

value: miRNA


title: HCC174post1

value: after operation within 14 days


title: NB4 treated with JOA_2

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: hg38
Supplementary files format and content: FPKM value

source_name: NB4 cell line treated with I13 2

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

treatment_protocol: incubating with JOA for 48 h

tag: agent

value: 1 uM JOA


title: NB4 treated with JOA_1

source_name: NB4 cell line treated with I13 1


title: Sample pool 2 of LPA1T22 tumors treated with or without olaparib for 4 days and 8 days

tag: treatment


title: NB4 treated with control_2

source_name: NB4 cell line treated with control 2

treatment_protocol: incubating with control for 48 h

value: Control


title: MEFs transduced 4 foctors (Nkx2-1, Foxa1, Foxa2, Gata6) [MY-5]

value: CBA/Ca x C57BL/6


title: HCC170pre

tag: disease/diagnosis


title: NB4 treated with control_1

source_name: NB4 cell line treated with control 1


title: HCC170post1

tag: sample collection time


title: MEFs transduced 3 foctors (Nkx2-1, Foxa1, Gata6) [MY-2]


title: tdTomato-_adult_thrb2tdTomato_rep2

city: St. Louis

first: Chi

last: Sun

state: MO

address: 4523 Clayton Ave.

department: Ophthalmology and Visual Sciences

institute: Washington University in St. Louis

data_processing:
Reads were trimmed using Trimmomatic v0.36.
Trimmed reads were processed with fastqc v0.11.5, HTStream v1.3.2.
Alignments were mapped to zebrafish reference genome GRCz11 using salmon v0.13.1.
Assembly: GRCz11
Supplementary files format and content: tsv files for raw counts
Supplementary files format and content: tsv files for DEG list

organism: Danio rerio

source_name: Retina

extract_protocol:
RNA was extracted with TRIzol LS or the Machery-Nagel RNA extraction kit.
For samples with a RIN score greater than 8.0, sequencing libraries were constructed according to the manufacturer’s protocol using the TruSeq® RNA Library Preparation Kit (Illumina) with 5µg total RNA as input.

value: Retina

value: Cone photoreceptor

value: WT

value: FACS-sorted tdTomato- retinal cells in adult zebrafish


title: Kasumi-1 treated with JOA_2

source_name: Kasumi-1 cell line treated with JOA 2


title: Kasumi-1 treated with JOA_1

source_name: Kasumi-1 cell line treated with JOA 1


title: MEFs transduced 3 foctors (Nkx2-1, Foxa2, Gata6) [MY-4]


title: tdTomato+_adult_thrb2tdTomato_rep3

value: FACS-sorted tdTomato+ cone photoreceptors in adult zebrafish


title: tdTomato-_adult_thrb2tdTomato_rep3


title: Kasumi-1 treated with JOA_3

source_name: Kasumi-1 cell line treated with JOA 3


title: tdTomato-_adult_thrb2tdTomato_rep1


title: HCC168pre

source_name: serum

tag: molecule subtype


title: HCC168post1


title: Kasumi-1 control_3

source_name: Kasumi-1 cell line treated with control 3


title: HCC169post1


title: Kasumi-1 control_2

source_name: Kasumi-1 cell line treated with control 2


title: HCC165pre


title: tdTomato+_adult_thrb2tdTomato_rep2


title: HCC165post2

value: after operation beyand 14 days


title: MEFs transduced 3 foctors (Nkx2-1, Foxa2, Gata6) [MY-13]

tag: strain


title: HCC167post1


title: HCC167pre


title: tdTomato+_adult_thrb2tdTomato_rep1


title: MEFs transduced 3 foctors (Nkx2-1, Foxa1, Gata6) [MY-12]


title: HCC169pre


title: HCC164post1


title: Kasumi-1 control_1

source_name: Kasumi-1 cell line treated with control 1


title: HCC164post2


title: lws1GFP+_adult_lwsPAC_H_rep2

value: FACS-sorted lws1 cone photoreceptors in adult zebrafish


title: lws2RFP+_adult_lwsPAC_H_rep1

value: FACS-sorted lws2 cone photoreceptors in adult zebrafish


title: HCC162post1


title: HCC162pre

value: before operation


title: lws1GFP+_adult_lwsPAC_H_rep3


title: HCC159post1


title: dnmt3aa-/-;dnmt3ab-/- replicate 4

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: Massachusetts

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

data_processing:
Raw data files were pre-processed using Trimmomatic.
Pre-processed files were mapped to the genome (GRC.z.10.90) using Bisulfite analysis tool (BAT).
BAT contains three modules for 1) Mapping reads to the genome, 2) Read Calling i.e., extraction of methylation information from the alignments, filtering for positions of interest, e.g. CG context, and conversion of methylation information for visualisation and 3) DMR calling. DMR calling includes Basic statistics of the DMRs are provided and given expression information of genes, correlating DMRs can be calculated.
Assembly: GRC.z10.90
Supplementary files format and content: vcf files of methylation at all nucleotides
Supplementary files format and content: vcf files of methylation calling at GC dinucleotides

source_name: Embryos

growth_protocol: Zebrafish embryos were obtained from pairwise breeding of fish from different genotypes.

extract_protocol:
DNA was isolated using ZymoResearch DNA isolation kit.
RRBS library preparation and sequencing were conducted by NXT-Dx, a Diagenode company (Ghent, Belgium). Briefly, libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI (New England Biolabs, Massachusetts), followed by end repair and A-tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor-ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50-bp paired-end sequencing was performed on an Illumina HiSeq2500 platform. Sequence reads from RRBS libraries were identified using standard Illumina base-calling software (Cassava v.1.8.2).

treatment_protocol: Embryos were maintained in embryo medium until 10 hpf and sampled for DNA methylation profiling.

value: Embryos

tag: developmental stage

value: 10 hours post-fertilization

value: AB strain


title: dnmt3aa-/-;dnmt3ab-/- replicate 5


title: dnmt3aa-/-;dnmt3ab-/- replicate 2


title: dnmt3aa-/-;dnmt3ab-/- replicate 3


title: HCC159pre

value: hepatocellular carcinoma

value: miRNA


title: HCC163pre


title: HCC164pre


title: HCC155post1

value: after operation within 14 days


title: HCC151pre


title: lws2RFP+_adult_lwsPAC_H_rep3


title: lws2RFP+_adult_lwsPAC_H_rep2


title: dnmt3ab-/- replicate 4


title: dnmt3ab-/- replicate 5


title: dnmt3ab-/- replicate 3


title: lws1GFP+_adult_lwsPAC_H_rep1


title: dnmt3ab-/- replicate 2


title: HCC151post2


title: HCC163post2


title: HCC150pre


title: HCC150post1


title: HCC163post1


title: dnmt3aa-/-;dnmt3ab-/- replicate 1


title: HCC155pre


title: HCC149pre


title: HCC151post1


title: dnmt3aa-/- replicate 3


title: Wildtype replicate 5

value: wild type


title: dnmt3aa-/- replicate 4


title: dnmt3aa-/- replicate 2


title: Wildtype replicate 4


title: dnmt3aa-/- replicate 5


title: dnmt3aa-/- replicate 1


title: HCC148post1


title: HCC148pre


title: dnmt3ab-/- replicate 1


title: Wildtype replicate 3


title: HCC133post1


title: HCC136pre


title: HCC136post1


title: HCC133pre


title: Wildtype replicate 1


title: YPS128_NaCl_Gen10_Rep3

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

institute: University of Wisconsin

data_processing:
Read counts generated using a script to identify samples from fastq files that are associated with each 10bp index tag
Library strategy: BAR-seq

organism: Saccharomyces cerevisiae

growth_protocol: Strains used in the study include BC187, BY4743, NCYC3290, and YPS128. Strains were grown in YPD medium containing 0.7M NaCl and G418 (200mg/L) for plasmid selection, in flasks at 30°C. Frozen library-transformed stocks were thawed and placed in 100ml of liquid YPD with 0.7M NaCl and G418 (200mg/L) at a starting OD600 of 0.05. The pooled growing cultures were transferred to fresh media after 5 generations to keep cells in log phase. Cells were harvested after 10 generations and cell pellets were stored at -80°C.

extract_protocol:
Plasmids were isolated from cell pellets using the Qiagen Spin MiniPrep Kit.
Libraries were constructed using PCR where plasmid barcodes were amplified with multiplex primers containing Illumina adapters and unique 10bp index tags to allow for sample identification after sequencing, as described in Magtanong et al., 2011 and Piotrowski et al., 2015.

treatment_protocol: Cell pellets were pretreated with 1ul Zymolyase for 1 hour at 30C prior to plasmid isolation

tag: genetic lineage

value: North American

tag: generation

tag: media

tag: stress

value: 0.7M NaCl


title: YPS128_NaCl_Gen10_Rep1


title: YPS128_NaCl_Gen10_Rep2


title: HCC133post2


title: YPS128_NaCl_Gen0_Rep3


title: HCC131post1


title: HCC131pre


title: HCC149post1


title: HCC141pre


title: YPS128_NaCl_Gen0_Rep2


title: HCC122pre


title: Wildtype replicate 2

tag: tissue

tag: genotype


title: YPS128_NaCl_Gen0_Rep1


title: HCC141post1


title: NCYC3290_NaCl_Gen10_Rep3

value: West African


title: NCYC3290_NaCl_Gen10_Rep2


title: HCC122post2


title: NCYC3290_NaCl_Gen0_Rep3


title: HCC121post2


title: HCC120post1


title: NCYC3290_NaCl_Gen0_Rep1


title: NCYC3290_NaCl_Gen0_Rep2


title: BC187_NaCl_Gen10_Rep3

value: Wine/European


title: BC187_NaCl_Gen10_Rep2


title: HCC120pre


title: HCC120post2


title: HCC118pre


title: HCC118post1


title: BC187_NaCl_Gen10_Rep1


title: HCC110pre


title: HCC110post1


title: BC187_NaCl_Gen0_Rep2


title: HCC121pre


title: BC187_NaCl_Gen0_Rep1


title: BY4743_NaCl_Gen10_Rep3

value: Laboratory


title: HCC110post2


title: NCYC3290_NaCl_Gen10_Rep1


title: HCC100pre


title: HCC121post1


title: BY4743_NaCl_Gen10_Rep1


title: BY4743_NaCl_Gen10_Rep2


title: HCC095pre


title: HCC100post1


title: HCC095post2


title: HCC094pre


title: BY4743_NaCl_Gen0_Rep3


title: BC187_NaCl_Gen0_Rep3


title: HCC095post1


title: BY4743_NaCl_Gen0_Rep1


title: BY4743_NaCl_Gen0_Rep2


title: HCC088post1


title: HCC088pre


title: HCC087pre


title: HCC094post1


title: L3 animals with lin-29 NanoDam and EGL-43::GFP, replicate 2

city: Stanford

first: Callista

last: Yee

state: California

address: 327 Campus Drive, Shen lab, Bass Biology 329

institute: Stanford University/HHMI

description:
lin-29_NanoDam_egl-43-vs-Dam.gatc.rep2.bedgraph
lin-29_NanoDam_egl-43-vs-Dam.gatc-FDR0.01.peaks.rep2.gff

data_processing:
Nanopore sequences were basecalled and demultiplexed using guppy 3.6 onboard a MinION Mk1C device, only base calling reads with a Q score higher than 8.
Fastq files were combined together using the UNIX command 'cat' and mapped to the ce10 genome using minimap2 with the options '-ax map-ont' to output .sam files.
SAM files were sorted and converted to bam using samtools.
Sorted .bam files and a file mapping all GATC sequences in C. elegans were fed into damidseq_pipeline (Marshall and Brand, 2015) to obtain bedgraph files.
Bedgraphs were analyzed for peaks using find_peaks (Owen Marshall).
Assembly: ce10
Supplementary files format and content: .bedgraphs represent the comparisons between the NanoDam alone control vs. NanoDam binding to a transcription factor
Supplementary files format and content: .gff files represent the called peaks after analysis of the .bedgraph files
Library strategy: DamID

organism: Caenorhabditis elegans

source_name: Anchor Cell

growth_protocol: Animals grown for 3 generations on Dam- bacteria (E. coli ER2925 from NEB) were bleach synchronized and L1s were grown at 25C until the L3 stage (24h after putting L1s on food). Approximately 5000 synchronized worms were harvested, washed with M9, then snap frozen in liquid nitrogen and stored at -80C.

extract_protocol:
gDNA was harvested using a Qiagen DNeasy Tissue and Blood kit (#69504) with no deviations from standard protocols.
DamID amplicons were obtained as previously described (Gomez-Saldivar et al., 2021) using 4 initial PCR cycles followed by 19 additional cycles. DamID amplicons were directly barcoded through blunt end ligation and sequenced using Oxford Nanopore library reagents (LSK-109, NBD-104, NBD-114)

value: Anchor Cell

tag: sample type

value: Specific expression of Dam in target tissue

value: bmdSi244; egl-43(bmd88)


title: L3 animals with lin-29 NanoDam and EGL-43::GFP, replicate 1

description:
lin-29_NanoDam_egl-43-vs-Dam.gatc.rep1.bedgraph
lin-29_NanoDam_egl-43-vs-Dam.gatc-FDR0.01.peaks.rep1.gff


title: L3 animals with lin-29 NanoDam and EGL-43::GFP, replicate 3

description:
lin-29_NanoDam_egl-43-vs-Dam.gatc.rep3.bedgraph
lin-29_NanoDam_egl-43-vs-Dam.gatc-FDR0.01.peaks.rep3.gff


title: vitreous humor at 7 day

city: Hsinchu

first: YIHSUN

last: CHEN

address: Rm.201, Bldg. 27, No. 321, Sec. 2,  Kuang Fu Road, Hsinchu 300, Taiwan, R.O.C

country: Taiwan

institute: Biomedical Technology and Device Research Laboratories, ITRI

description: RAT_7 day

hyb_protocol: the labelled RNA was quantified, fractionated, and hybridized to the miRNA microarray following a series of consecutive steps. First, the labelled RNA samples were heated to 99 °C for 5 min followed by heating at 45 °C for another 5 min. After this, hybridization with the RNA-array was performed with continuous agitation at 60 rpm for 16 h at 48 °C on an Affymetrix® 450 Fluidics Station. The miRNA microarray chips were then washed and stained using the Genechip Fluidics Station 450 (Affymetrix, Santa Clara, CA, USA).

scan_protocol: the miRNA microarray chips were scanned using an Affymetrix GCS 3,000 scanner (Affymetrix, Santa Clara, CA, USA)

data_processing: the signal values were evaluated using the Affymetrix® GeneChip™ Command Console software

organism: Rattus norvegicus

source_name: vitreous humor

label_protocol: Affymetrix Genechip miRNA 4.0 array was used according to the manufacturer's instructions. For each sample, 1 μg of RNA was labelled using the FlashTag™ Biotin RNA Labeling Kit (Genisphere, Hatfield, PA, USA). Following this, the labelled RNA was quantified, fractionated, and hybridized to the miRNA microarray following a series of consecutive steps.

growth_protocol: Day 0, 0.25, 1, 3, 7 vitreous humor collection after laser induced NAION model in rat.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Extravesicles were collected from vitreous humors in rat eyes through a photolabile paper based chips. And these samples were extracted for total RNA in the Trizol solution (GibcoBRL).

value: laser induced NAION

tag: time

value: 7 days after NAION

value: extracullar vesicle from rat eye


title: vitreous humor at 0 day

description: RAT_0 day

value: 0 days after NAION


title: HCC086pre

value: before operation


title: vitreous humor at 1 day

description: RAT_1 day

value: 1 days after NAION


title: L3 animals with lin-29_NanoDam control, replicate 3


title: vitreous humor at 0.25 day

description: RAT_0.25 day

value: 0.25 days after NAION


title: HCC086post1

value: hepatocellular carcinoma

value: after operation within 14 days

value: miRNA


title: HCC087post1


title: HCC085pre


title: HCC085post1


title: L3 animals with lin-29_NanoDam control, replicate 2


title: L3 animals with lin-29_NanoDam control, replicate 1


title: HCC086post2

value: after operation beyand 14 days


title: vitreous humor at 3 day

description: RAT_3 day

value: 3 days after NAION


title: HCC081pre


title: HCC081post2


title: HCC081post1


title: ATF3 knockout A549 cells with ZIKV virus infection, biological replicate 3

city: Albany

first: Morgan

middle: A

last: Sammons

address: 1400 Washington Ave, Life Sciences 2075

department: Biological Sciences

institute: University at Albany - SUNY

data_processing:
Paired end RNA-seq reads were quantified using kallisto v0.46.2 in quant mode with 100 bootstraps against the Human transcriptome (ENSEMBL Homo sapiens v104 release) was downloaded from http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz
Resulting kallisto-derived TPM counts were imported into the R statistical computing enrvironment using tximport, followed by differential gene expression analysis via DEseq2
Assembly: ENSEMBL homo sapies v104 transcriptome release
Supplementary files format and content: ab-separated value files containing standardized ENSMBL gene name, gene length, estimated tag counts, and transcripts per million (TPM) values; output from Kallisto that was imported into DEseq2 via tximport.

source_name: lung epithelial adenocarcinoma

growth_protocol: A549 cells were cultured in DMEM with 10% fetal bovine serum, 10mM nonessential amino acids, 5mM L-glutamine, and 1% final sodium pyruvate (0.055g/L).

extract_protocol:
Total RNA was isolated using TRIzol reagent, followed by clean-up with the RNA Clean and Concentrate Kit (Zymo Research), and DNAse-treated with the TURBO DNA-free kit (invitrogen)
Libraries were constructed by Azenta/Genewiz using polyA+ selection followed by standard Illumina-based RNA-seq library generation.

treatment_protocol: Cells were previously seeded to be near 80% confluency on day of infection. Control cells were trypsinized and counted to determine the multiplicity of infection (moi). Cells were infected at an moi of 10. An appropriate aliquot of viral stock was thawed at RT, diluted in PBS to a final volume of 1 ml and added to cells. For mock-infected plates, 1 ml of PBS was added. Cells were incubated at 37 oC for 1 hour, rocking every 15 minutes. An hour later, 9 ml of media was added per plate and returned to the incubator for 24 hours.

value: lung epithelial adenocarcinoma

tag: cell type

value: ZIKV Infection (10moi)


title: ATF3 knockout A549 cells with ZIKV virus infection, biological replicate 2

tag: cell line


title: Wild-type A549 cells with ZIKV virus infection, biological replicate 3

value: Parental/WT


title: HCC076pre


title: HCC076post2


title: Wild-type A549 cells with ZIKV virus infection, biological replicate 2


title: HCC085post2


title: Wild-type A549 cells with ZIKV virus infection, biological replicate 1


title: ATF3 knockout A549 cells with mock virus infection, biological replicate 3

value: Mock Infection


title: ATF3 knockout A549 cells with ZIKV virus infection, biological replicate 1


title: Wild-type A549 cells with mock virus infection, biological replicate 2


title: Wild-type A549 cells with mock virus infection, biological replicate 3


title: S120

city: Huddinge

first: Christian

middle: Günter

last: Riedel

state: Stockholm

address: Blickagången 16 (Neo Building, 6th floor)

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

data_processing:
Reads were mapped to 202,272 Ensembl transcript IDs using the Smallseq data analysis pipeline (Hagemann-Jensen et al., 2018), and to 4,121 transfer RNA fragments (tRF) using the MINTmap pipeline (Loher et al., 2017).
Only small RNA with read counts higher than 1 in more than 20% of samples were kept, resulting in a list of 4,767 small RNA.
Counts were rounded and data normalization and differential expression analysis was performed with the DESeq2 package (version 1.26.0) (Love et al. 2014). Small RNA levels were used as the dependent variable and chronological age as the explanatory variable. A local fit was used for estimating dispersions. Size factor normalized small RNA counts were obtained using the counts functions with arguments normalized = T.
After DESeq2 analysis, small RNA with unclear transcripts biotypes were removed from all analysis since they indicate potential degradation products (i.e. protein coding, lncRNA, processed transcript, retained intron, …). Transcript biotypes were defined using the biomaRt package (version 2.42.0) (Durinck et al. 2005). A total of 587 small RNA were kept after this filtering step, of which 276 were significantly associated with age at an FDR threshold of 0.2.
Assembly: hg38

source_name: plasma sample

extract_protocol:
Total RNA were extracted from plasma samples using the Qiagen miRNeasy Serum/Plasma Kit. Briefly, frozen plasma samples were thawed, vortexed and centrifuged for 16000 x g in 10 minutes and 50 µl was used for RNA extraction following the manufacturer’s protocol. Purified RNA was eluted in 50µl H2O and saved at -80C.
4 µl of purified RNA was used in a Small-seq protocol to construct the libraries (Hagemann-Jensen et al., 2018). Small RNA libraries were pooled and sequenced using an Illumina HiSeq 3000 platform for 100 bp single read.

tag: age

tag: gender

value: female

tag: status

value: healthy


title: ATF3 knockout A549 cells with mock virus infection, biological replicate 2

tag: treatment


title: S119


title: ATF3 knockout A549 cells with mock virus infection, biological replicate 1


title: Wild-type A549 cells with mock virus infection, biological replicate 1


title: HCC075post1

tag: disease/diagnosis

tag: sample collection time

tag: molecule subtype


title: HCC074post1


title: HCC075pre


title: HCC072pre


title: HCC074post2


title: S118


title: HCC074pre


title: S117


title: HCC075post2


title: HCC088post2


title: S116


title: HCC072post1


title: HCC076post1


title: HCC071pre


title: S115


title: HCC072post2


title: S114


title: HCC070post1


title: HCC070pre


title: HCC071post1


title: HCC066pre


title: S113


title: S111


title: S112


title: S50


title: HCC066post1


title: S148

data_processing:
Reads were mapped to 202,272 Ensembl transcript IDs using the Smallseq data analysis pipeline (Hagemann-Jensen et al., 2018), and to 4,121 transfer RNA fragments (tRF) using the MINTmap pipeline (Loher et al., 2017).
Only small RNA with read counts higher than 1 in more than 20% of samples were kept, resulting in a list of 4,767 small RNA.
Counts were rounded and data normalization and differential expression analysis was performed with the DESeq2 package (version 1.26.0) (Love et al. 2014). Small RNA levels were used as the dependent variable and chronological age as the explanatory variable. A local fit was used for estimating dispersions. Size factor normalized small RNA counts were obtained using the counts functions with arguments normalized = T.
After DESeq2 analysis, small RNA with unclear transcripts biotypes were removed from all analysis since they indicate potential degradation products (i.e. protein coding, lncRNA, processed transcript, retained intron, …). Transcript biotypes were defined using the biomaRt package (version 2.42.0) (Durinck et al. 2005). A total of 587 small RNA were kept after this filtering step, of which 276 were significantly associated with age at an FDR threshold of 0.2.
Genome_build: hg38
Supplementary_files_format_and_content: raw_counts_Smallseq_Ensembl.txt (raw counts)
Supplementary_files_format_and_content: raw_counts_MINTmap_tRF.txt (raw counts)
Supplementary_files_format_and_content: DESeq2_normalized_counts.xlsx (normalized counts)
Supplementary_files_format_and_content: DESeq2_small_RNA_association_with_age.xlsx (significance table)

source_name: plasma

extract_protocol:
Total RNA was extracted from plasma samples using the Qiagen miRNeasy Serum/Plasma Kit. Briefly, frozen plasma samples were thawed, vortexed and centrifuged for 16000 x g in 10 minutes and 50 µl was used for RNA extraction following the manufacturer’s protocol. Purified RNA was eluted in 50µl H2O and saved at -80C.
4 µl of purified RNA was used in a Small-seq protocol to construct the libraries (Hagemann-Jensen et al., 2018). Small RNA libraries were pooled and sequenced using an Illumina HiSeq 3000 platform for 100 bp single read.

value: plasma

value: male

tag: disease state


title: S42


title: HCC060pre-2

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95%

extract_protocol: Total RNA from serum was extracted commercially available kit (miReasy mini kit (Qiagen)).

value: before operation at 2nd recurrence


title: S150


title: S149


title: S147


title: HCC061post1


title: S146


title: S145


title: HCC061pre

value: before operation


title: HCC060post1


title: HCC060pre


title: HCC058post1


title: S144


title: HCC066post2


title: S143


title: HCC054pre


title: S142


title: S140


title: HCC054post2


title: HCC054post1


title: HCC053pre


title: HCC053post1


title: S139


title: HCC058pre


title: HCC052pre


title: S138


title: HCC058post2


title: HCC052post1


title: S137


title: HCC053post2


title: S136


title: S135


title: S134


title: HCC052post2


title: S141


title: S132


title: S131


title: S133


title: S130


title: HCC051pre


title: HCC049pre


title: HCC050pre


title: HCC051post2


title: HCC050post1


title: HCC049post2


title: S129


title: HCC051post1


title: S127


title: S128


title: HCC046pre


title: S126


title: HCC046post1


title: HCC046post2


title: S124


title: S125


title: S122


title: HCC044pre


title: S123


title: S121


title: HCC044post2


title: S100


title: S99


title: HCC043pre


title: HCC043post1


title: HCC044post1


title: S98


title: S97


title: S96


title: S93


title: HCC043post2


title: HCC041pre


title: HCC040pre


title: HCC038post1


title: HCC038pre


title: HCC040post2


title: HCC040post1


title: S91


title: S80


title: HCC041post2


title: S79


title: S92


title: S78


title: S77


title: S49


title: S48


title: HCC041post1


title: HCC037post2


title: S94


title: S47


title: HCC034pre


title: HCC034post2


title: S46


title: HCC038post2


title: HCC034post1


title: HCC037pre


title: HCC032pre


title: HCC032post2


title: S39


title: S43


title: S44


title: S40


title: S45


title: S41


title: HCC037post1


title: HCC028pre


title: HCC026post1


title: HCC028post2


title: HCC028post1


title: HCC032post1


title: HCC034pre-2


title: HCC024post1


title: Wild Type Sham3

first: Troy

last: Hornberger

address: 2015 Linden Drive

institute: University of Wisconsin - Madison

data_processing:
Raw reads contained in FASTQ files from our sequencing experiment were trimmed of adapters and poorly called bases using a Seqtk-trimfq algorithm, and were then mapped to the mouse genome (Ensemble GRCm.38) using STAR-RSEM pipeline executed in MobaXterm.
Between 137 and 444 million reads were quantified per sample. Differential gene expression analysis was performed using the EdgeR pipeline [80] implemented in R-studio using the raw reads normalized by the TMM method as the input values for each gene [81].
The differential gene expression outputs for a given comparison was FDR-corrected by EdgeR using Benjamini-Hochberg procedure.
Two-way ANOVA analysis of the data was performed in Perseus [82]
Assembly: GRCm38

source_name: plantaris muscle

growth_protocol: Mice of 9-12 weeks of age

extract_protocol:
Frozen PLT muscles were pulverized into a fine powder using an RNase-treated and liquid nitrogen-chilled mortar and pestle. The resulting powder for each sample was collected, weighed, and placed in 0.5 ml of ice-cold TRIzol. Samples were then homogenized with a Polytron (PT 1200 E) for 20 s and then centrifuged at 6,000 x G for 1 min to remove bubbles and confirm complete homogenization. Total RNA was isolated with a PureLink RNA Mini Kit according to the manufacturer’s instructions. The purity and integrity of RNA samples were checked by the ratio of A260/A280 and of 28S/18S rRNA, respectively, and then confirmed by the University of Wisconsin-Madison Biotechnology Center using the NanoDrop One Spectrophotometer and Agilent 2100 Bioanalyzer.
Total RNA libraries were prepared from samples that met the TruSeq® Stranded Total RNA Sample Preparation Guide (15031048 E) input guidelines using the Illumina® TruSeq® Stranded Total (Gold) RNA Sample Preparation kit. For each library preparation, cytoplasmic & mitochondrial ribosomal RNA was removed using biotinylated target-specific oligos combined with paramagnetic beads tagged with streptavidin. Following purification, the reduced RNA was fragmented using divalent cations under elevated temperature. Fragmented RNA was copied into first-stranded cDNA using SuperScript II Reverse Transcriptase and random primers. Second-strand cDNA was synthesized using a modified dNTP mix (dTTP replaced with dUTP), DNA Polymerase I, and RNase H. Double-stranded cDNA was cleaned up with AMPure XP Beads (1.8X). The cDNA products were incubated with Klenow DNA Polymerase to add a single ‘A’ nucleotide to the 3’ end of the blunt DNA fragments. Unique dual indexes (UDI) were ligated to the DNA fragments and cleaned up with two rounds of AMPure XP beads (0.8X). Adapter ligated DNA was amplified by PCR and cleaned up with AMPure XP beads (0.8X). Final libraries were assessed for size and quantity using an Agilent DNA1000 chip and Qubit® dsDNA HS Assay Kit, respectively. Libraries were standardized to 2 nM. Paired-end 150 bp sequencing was performed, using standard SBS chemistry on an Illumina NovaSeq6000 sequencer.

treatment_protocol: Mechanical overload via myotenectomy (MTE) or a sham surgery as the control condition

value: plantaris muscle

value: Wild Type

value: Sham


title: Wild Type MTE4

value: MTE


title: Wild Type Sham2


title: TRIM28 mKO Sham4

value: Trim28 Knockout


title: Wild Type MTE3


title: Wild Type MTE2


title: HCC024pre

first: Satoko

last: Takizawa

institute: Toray Industries, Inc.

value: hepatocellular carcinoma

value: miRNA


title: TRIM28 mKO MTE4


title: Wild Type Sham4


title: TRIM28 mKO MTE3


title: TRIM28 mKO MTE2


title: Wild Type MTE1


title: HCC019post2

value: after operation beyand 14 days


title: HCC019pre


title: HCC019post1

value: after operation within 14 days


title: HCC026pre


title: TRIM28 mKO MTE1


title: HCC018pre


title: HCC024pre-2


title: HCC024post2


title: HCC018post1


title: HCC006post2


title: Wild Type Sham1


title: HCC018post2


title: TRIM28 mKO Sham2


title: HCC003pre


title: HCC006post1


title: TRIM28 mKO Sham3


title: TRIM28 mKO Sham1


title: HCC002pre


title: HCC003post2


title: HCC002post2


title: HCC006pre


title: scRNA-seq 1

city: Xi'an

first: Yang

last: Zhao

state: Shaanxi

address: No.157, fifth west road

department: Oncology

institute: Second affiliated hospital of Xi'an Jiaotong University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung adenocarcinoma

extract_protocol:
Cancerous epithelial cells (n=3,754), as determined as those cells harboring large chromosomal aberrations from InferCNV analysis, were subset and re-clustered using the following parameters: Ngenes = 2,000, Npcs = 20, Res = 0.9, Kparam = 10 (script NI04). We found the differences in gene expression between the three treatment time points (TN, RD, and PD) using the Seurat function Find-Markers using the MAST test21 and sample_name as the latent variable. Three separate tests were used to ascertain the differences between: 1) TN and RD, 2) TN and PD and 3) RD and PD (TableS5). Resulting differential gene lists were then filtered to limit patient specific effects. This is achieved by setting a threshold for non-zero expressing cells per patient (RD = 3 of RD patients and PD = 6 of PD patients) and removing differentially expressed genes explained by less than the thresholds set. The top 100 genes from each comparison were manually curated to evaluate for pathway activation. Decreased expression could indicate lack of detection due to the stochasticity of scRNaseq and thus for analysis of activated pathways we focused on upregulated genes. Gene signatures (TableS2) were compiled using differential expressed as well as known cell marker genes. Specifically, the alveolar signature is made of differentially expressed AT1/AT2 genes among the cancer cell time point comparisons as well has additional known AT1/AT2 genes 22. The remaining signatures were identified directly from top differentially expressed genes.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: lung adenocarcinoma


title: tumor tissue, IL-33, 4

city: Nanjing

first: Keying

last: Che

address: 321 Zhongshan Road

institute: Nanjing Drum Tower Hospital

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts. Then, map the clean reads to the silva database to remove the rRNA.
Paired-end clean reads were aligned to the reference genome using Hisat2.
Featurecount was used to count the reads numbers mapped to each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: tumor tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraries.
RNA library for RNA-seq was prepared as fllows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.

value: tumor tissue

value: MFC

value: murine gastric cancer cells

value: WT


title: tumor tissue, IL-33, 8


title: tumor tissue, IL-33, 5


title: tumor tissue, IL-33, 3


title: spatial transcriptomics 2

description: 10x Genomics


title: HEK_293_Cells_Zbtb20-3XFLAG_Anti-FLAG_2

city: Lebanon

first: Edward

last: Usherwood

state: NH

address: Rubin Building, Level 7, 710-53

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth College

data_processing:
Raw reads were trimmed with Cutadapt (v2.4) and aligned to hg38 using Bowtie (v2.2.6) in “--local” mode with parameters “-no-mixed-discordant”
Unmapped & multi-mappoing reads were removed and duplicate reads were identified and removed using MarkDuplicates (Picard Tools) to create filtered BAMs
Alignments were sorted into nucleosome-free regions (fragment length <=125bp) or nucleosomal-regions (fragment length >150bp) amd processed separately in downstream analysis
Peaks were called using MACS2 (v2.2.7.1) callpeak command with parameters “-f BAMPE --keep-dup all -p 1.0E-4” and filtered against the ENCODE hg38 blacklist (H3K4me3 analysis was run in -broadPeak mode). Parameter -g was set to 2913022398 and 2652783500 for human and mouse data, respectively.
Irreproducible Discovery Rate (IDR) method was applied, using parameters --rank signal.value "--peak-merge-method avg". Peaks with an IDR threshold of 0.05 and fold change above background >4 were retained for further analysis
Normalized signal tracks (BigWig files) were generated using deepTools (v 3.3.0) command BamCoverage with parameters “–binSize 20 –smoothLength 60 –scaleFactor sfi” where sfi corresponds to the sample specific scale factor calculated using E.coli spike-in DNA
Assembly: hg38 for human samples and mm10 for mouse samples
Supplementary files format and content: peak files in BED format
Supplementary files format and content: Normalized signal tracks in BigWig format

source_name: Embryonic kidneys

extract_protocol:
CUT&RUN experiments were carried out using EpiCypher’s CUT&RUN kit version 1.0 (#14-1048) as directed by the CUTANA user manual version 1.0. Briefly, 500,000 cells (either HEK 293 or CD8 T cells) expressing Zbtb20-3XFLAG were crosslinked with 1% formaldehyde for 5 minutes and subsequently quenched with 125mM glycine. Considerations for performing CUT&RUN on crosslinked cells as described in the CUTANA user manual version 1.0 were then applied for the remainder of the procedure. The anti-FLAG (M2) antibody from Sigma-Aldrich was used for detection of Zbtb20-3XFLAG by CUT&RUN.
CUT&RUN library preparation and sequencing was performed according to the method described in the CUTANA Library Kit Manual v1.0 (EpiCypher). Briefly, 5ng of CUT&RUN DNA fragments were prepared for Illumina sequencing using the NEB Ultra II DNA kit with the following modifications: Step 3B.2 – 1.1x AmPure bead cleanup; Step 4.1.3 – PCR amplification with 45s @98C for initial denaturation followed by 14 cycles of 15s @98C, 10s @ 60C and 1m @ 72C final extension. Libraries were quantified by qubit and run on a Fragment Analyzer (Agilent) for sizing. Libraires were pooled and sequenced to a depth of 10M, 75bp paired-end reads/sample on a NextSeq500 instrument.

value: Embryonic kidneys

value: HEK 293

value: Epithelial

tag: cut&run antibody


title: scRNA-seq 2

description: 10x Genomics


title: tumor tissue, IL-33, 2


title: HEK_293_Cells_Zbtb20-3XFLAG_Anti-FLAG_1

value: anti-FLAG (M2) antibody from Sigma-Aldrich


title: HEK_293_Cells_Zbtb20-3XFLAG_Anti-H3K4me3

value: anti-H3K4me3 (Cat# 13-0041k) from EpiCypher


title: tumor tissue, control, 8

value: PBS


title: HEK_293_Cells_Zbtb20-3XFLAG_IgG

value: Rabbit IgG (Cat# 13-0042k) from EpiCypher


title: tumor tissue, control, 7


title: S12_TSC1_Dox [BD01012]

city: Vienna

first: Bianca

last: Dietrich

address: Waehringer Guertel 18-20

country: Austria

institute: Medical University of Vienna

description:
BD01012
Dietrich_12samples_raw_gene_counts_GeneSymbols_GeneTypes.tsv

data_processing:
Reads in fastq format were generated using the Illumina bcl2fastq command line tool (V2.19.1.403) inclusive trimming of the sequence adapters.
Reads were aligned to the human reference genome version GRCh38 using STAR aligner version 2.6.1a.
Raw reads pere gene were counted by STAR.
Read counts were normalized and vst-transformed using DESeq2 version 1.22.2.
TPM were generated by RSEM.
Assembly: GRCh38
Supplementary files format and content: raw counts of sequencing reads

source_name: placenta

growth_protocol: TSCs were cultivated in DMEM/F12 supplemented with 1x B-27, 1x Insulin-Transferrin-Selenium-Ethanolamine, 1 µM A83-01, 50 ng/mL recombinant human epidermal growth factor, 2 µM CHIR99021 and 5 µM Y27632.

extract_protocol:
Total RNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen).
Sequencing libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEB Next Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Pooled libraries were sequenced in 1x75bp single-read sequencing mode.

treatment_protocol: DN-MAML1 overexpression was induced by adding 1 µg/mL doxycycline for 6 consecutive days to the cell culture medium.

value: placenta

value: trophoblast stem cells

value: wild-type

value: doxycycline treated (6 days)


title: tumor tissue, IL-33, 7


title: tumor tissue, IL-33, 6


title: spatial transcriptomics 1

description: 10x Genomics


title: tumor tissue, control, 5


title: S9_TSC2 [BD01009]

description:
BD01009
Dietrich_12samples_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: non-treated


title: tumor tissue, control, 4


title: S10_TSC2_Dox [BD01010]

description:
BD01010
Dietrich_12samples_raw_gene_counts_GeneSymbols_GeneTypes.tsv


title: S8_TSC3_DN-MAML1_Dox [BD01008]

description:
BD01008
Dietrich_12samples_raw_gene_counts_GeneSymbols_GeneTypes.tsv


title: tumor tissue, control, 1


title: tumor tissue, IL-33, 1


title: S7_TSC3_DN-MAML1 [BD01007]

description:
BD01007
Dietrich_12samples_raw_gene_counts_GeneSymbols_GeneTypes.tsv


title: S3_TSC1_DN-MAML1 [BD01003]

description:
BD01003
Dietrich_12samples_raw_gene_counts_GeneSymbols_GeneTypes.tsv


title: S6_TSC2_DN-MAML1_Dox [BD01006]

description:
BD01006
Dietrich_12samples_raw_gene_counts_GeneSymbols_GeneTypes.tsv


title: KO 3

city: Nashville

first: Heather

last: Pua

state: Tennessee

address: 1161 21st Avenue South

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt Medical Center

description:
TableS4_Normalized_count_data.txt
TableS5_Deseq_results_spreadsheet.txt

data_processing:
For pipeline details please see https://github.com/parkdj1/RNASeq-Pipeline
FastQC was used to quality control data
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt
Trimmed sequence reads were mapped to mouse genome using Salmon
Read count extraction and normalization were performed using DESeq2
Assembly: mm10

source_name: primary bone marrow-derived macroaphges

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). ~0.5-1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Poly(A) selection kit by the Vanderbilt Technologies for Advanced Genomics Core

treatment_protocol:
Bone marrow isolated from control or knockout mice were differentiated into macrophages in culture for 7 days using L929 conditioned medium
Once differentiated, macrophages from both genotypes were cultured with 10nM insulin, 25mM glucose, and 250uM C16:0 to induce metabolic activation

value: primary bone marrow-derived macroaphges

value: Mirc11fl/fl  Mirc22fl/fl Lyz2Cre/Cre

value: 10 nM insulin, 25 mM glucose, 250 uM C16:0


title: KO 4


title: S5_TSC2_DN-MAML1 [BD01005]

description:
BD01005
Dietrich_12samples_raw_gene_counts_GeneSymbols_GeneTypes.tsv


title: tumor tissue, control, 6

value: tumor tissue

value: MFC

value: murine gastric cancer cells


title: S4_TSC1_DN-MAML1_Dox [BD01004]

description:
BD01004
Dietrich_12samples_raw_gene_counts_GeneSymbols_GeneTypes.tsv


title: tumor tissue, control, 3

value: WT


title: fl/fl 4

value: Mirc11fl/fl  Mirc22fl/fl Lyz2+/+


title: S11_TSC1 [BD01011]

description:
BD01011
Dietrich_12samples_raw_gene_counts_GeneSymbols_GeneTypes.tsv


title: fl/fl 2


title: fl/fl 3


title: fl/fl 1


title: Plasma, chronic trained, post acute, Female 5

city: Pittsburgh

first: Brad

last: Nindl

address: 3860 South Water

institute: University of Pittsburgh

data_processing:
Quality control completed with FASTQC from Illumina (Version 0.11.5), no trimming required
Reads were mapped to the designated reference genome (miRbase_v22) using the Qiagen GeneGlobe RNA-seq analysis portal (Version 3.0.1) with default parameters for miRNA analysis
Differential gene expression analysis was performed using the edgeR workflow
Assembly: miRbase_v22
Supplementary files format and content: Excel spreadsheet with multiple tabs that include comparisons of data and the raw counts and CPM for each sample as well as differential expression data for each comparison

source_name: Blood Plasma

extract_protocol:
RNA extraction using Norgen Biotek's Plasma/Serum Exosome Purification and RNA isolation Mini Kit, according to manufacturer's instructions
Single-end libraries constructed from 5 ng of EV RNA using QIAseq miRNA library kits from Qiagen according to manufacturer's recommendations for low yield sampels.

value: Blood Plasma

tag: Sex

value: Female

value: Chronic Exercise + Acute Exercise


title: Plasma, baseline, post acute, Female 5

value: Acute Exercise


title: Plasma, chronic trained, resting, Female 5

value: Chronic Exercise Training


title: tumor tissue, control, 2

value: PBS


title: Plasma, chronic trained, resting, Female 4


title: KO 2


title: KO 1


title: S2_TSC3_Dox [BD01002]

description:
BD01002
Dietrich_12samples_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: placenta

value: trophoblast stem cells

value: wild-type


title: S1_TSC3 [BD01001]

description:
BD01001
Dietrich_12samples_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: non-treated


title: Plasma, baseline, post acute, Female 4


title: snRNA-seq of Mut

city: Beijing

first: Dan

last: Zhang

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Using cellranger to preprocess the data.
Assembly: mm10

molecule: nuclear RNA

source_name: Spinal cord

extract_protocol:
The frozen ventral horn of L3-L5 spinal cord was used for isolation the nuclei. The spinal cord was taken from the 9-month-old male mice, and quickly placed straightly in the embedding mold. Then the spinal cord was quickly frozen with OCT in liquid nitrogen. Removed the ventral white matter in microtome until the gray matter appears and removed the white matter on both sides carefully. Then taking the gray matter at the depth of 1/2 before the confluence of the gray matter of two sides and put the gray matter into the EP tube for liquid nitrogen quick freezing again. Then the nuclei were extracted
For snRNA-seq, the single cell 3′ GEM, Library & Gel Bead Kit V3.1 (10× Genomics, 1000075) and Chromium Single Cell B Chip Kit (10× Genomics, 1000074) were used. To generate single-nuclei gel beads in emulsion, the nuclei suspension was loaded onto the Chromium single cell controller (10× Genomics). Then suspended the single nuclei in PBS (containing 0.04% BSA). Captured cells were lysed to release their RNA and barcoded through reverse transcription in individual GEMs. The reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°C for 5 min. The cDNA was kept at 4°C and then amplified for sequencing.
For snATAC-seq, incubating the nuclei with Tn5 transposase. Then the nuclei suspension was loaded into the Chromium microfluidic chip E with 10x Genomics reagents and barcoded with a 10x Genomics Chromium Controller (10x Genomics, Pleasanton, CA). DNA fragments were subsequently amplified, and the sequencing libraries were constructed with reagents from a Chromium Single Cell ATAC reagent kit (10x Genomics; PN-1000110, PN-1000156, PN-1000084) according to the manufacturer’s instructions. After preliminary quantification and quality inspection, libraries were then pooled and loaded on an Illumina NovaSeq with 2 x 50 paired-end kits.

value: Spinal cord

value: Mut

value: male


title: snATAC-seq of Mut

library_source: genomic single cell


title: snATAC-seq of WT


title: Plasma, baseline, resting, Female 4


title: snRNA-seq of WT


title: Plasma, chronic trained, post acute, Female 3


title: MOK-KO, LPS, biol rep 3

city: Seville

first: Cintia

last: Roodveldt

address: CABIMER-Av. Americo Vespucio 24, Cartuja 93

country: Spain

institute: University of Seville

description:
Stranded Total RNA
H14_LPS_3

data_processing:
Read quality check was done by using FastQC (v.0.11.9). Raw reads were processed to trim adapter sequence and remove  low quality sequence by Trimmomatic (v.0.39) with default parameters, except  “HEADCROP:1” parameter used to crop first base from all the reads at the 5’-end.
The processed reads were mapped on to the GRCm39 reference genome sequence (Ensembl  database: Mus_musculus.GRCm39.dna.primary_assembly.fa; Mus_musculus.GRCm39.104.gtf ) using  STAR aligner (v.2.7.9a) with default parameters.
Raw read counts counts were determined by featureCounts module of Rsubread package (v.2.0.1) with the help of  the alignment BAM file of each sample.
The raw read counts were normalized and further utilized in the differential expression analysis by using DESeq2 (v.1.32.0) R package.
Assembly: GRCm39 (Ensembl Mus_musculus)
Supplementary files format and content: Raw read count matrix includes raw read counts for each sample.

growth_protocol: SIM-A9 cells were maintained in DMEM-F12 that was supplemented with 10% FBS and 5% HS, 2 mM L-glutamine, 100 U/ml penicillin  and 100 ug/ml streptomycin.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen).
cDNA libraries were prepared by using the Stranded TOTAL RNA prep ligation with RIBO-ZERO PLUS kit (Illumina).
Adapters (Illumina) included a sample/library-specific index.
After library amplificationby PCR and all recommended qualiity control assays, individual libraries were pooled together at equimolar ratios and diluted to ca. 1.2 nM.

treatment_protocol: WT or H14 SIM-A9 cells in culture were treated with 1 ug/mL LPS (or medium alone) for 5 h.

value: Microglia

tag: strain

value: LPS (5 h)


title: MOK-KO, LPS, biol rep 2

description:
Stranded Total RNA
H14_LPS_2


title: Plasma, baseline, post acute, Female 3

tag: tissue


title: MOK-KO, Control, biol rep 2

description:
Stranded Total RNA
H14_2

value: Control


title: MOK-KO, LPS, biol rep 1

description:
Stranded Total RNA
H14_LPS_1


title: MOK-KO, Control, biol rep 3

description:
Stranded Total RNA
H14_3


title: Plasma, baseline, resting, Female 3


title: MOK-KO, Control, biol rep 1

description:
Stranded Total RNA
H14_1


title: WT, LPS, biol rep 3

description:
Stranded Total RNA
Wt_LPS_3


title: Plasma, chronic trained, post acute, Female 4


title: Plasma, baseline, resting, Female 5


title: WT, LPS, biol rep 2

description:
Stranded Total RNA
Wt_LPS_2


title: Plasma, chronic trained, resting, Female 2


title: Plasma, baseline, post acute, Female 2


title: WT, LPS, biol rep 1

description:
Stranded Total RNA
Wt_LPS_1


title: Total_RNA_6_S21

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description: total RNA replicate 6

data_processing:
Sequencing was performed using an Illumina HiSeq 2500 in Rapid Run mode and  employed a single-end, 50 base read length (SE50) sequencing strategy.
Files were aligned to guides using bowtie2 for each sample. Next, the barcodes for WT and mutant were  segregated for each sample.
log2 CPM values for each barcode using edgeR.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include log2 cpm  values for each Sample.
Library strategy: Polysome-Seq

source_name: PC3 cells

growth_protocol: PC3 cells were cultured in RPMI + 10% fetal bovine serum + 1x penicillin/streptomycin + 2mM L-Glutamine at 37°C with 5% CO2

extract_protocol:
~15-20 x106 cells were collected per sample and treated with 100µg of cycloheximide on ice for 10 minutes. Cells were lysed and for each sample, ~10% saved for plasmid DNA isolation, ~25% saved for total mRNA isolation, and ~65% loaded onto a sucrose gradient for polysome mRNA isolation.
Plasmid DNA was isolated using Qiagen Spin Miniprep Kit.
Total mRNA and polysome mRNA was isolated using Zymo Direct-zol RNA Miniprep Plus kit with DNase I treatment. cDNA was made using SuperScript III first-strand synthesis system and RT primer: 5’- GGTTTGTCCAAACTCATCAATGT -3’.
Library construction was performed using a two-step PCR amplicon approach.
First amplification was performed at 98°C for 30” followed by ten cycles of 98°C for 10”, 71°C for 30”, 72°C for 30”, and final elongation at 72°C for 5’ with Forward primer: 5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGgccagcgccaggatcaac -3’ and Reverse Primer: 5’- GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGcgccccgactctagctagac -3’ using Q5 Polymerase. PCR product was purified using 1.8X Ampure XP beads.
Second amplification was was performed at 98°C for 30” followed by ten cycles of 98°C for 10”, 67°C for 30”, 72°C for 30”, and final elongation at 72°C for 5’ with IDT for Illumina Nextera UDI primers using Q5 Polymerase. PCR product was purified using 0.7X Ampure XP beads.

treatment_protocol: Cells were transfected with 16 µg MPRA plasmid library DNA per 15cm plate for 16 hours, then washed and placed in fresh media for a subsequent 24 hours before collection.

value: PC3 cells

tag: fraction

value: total RNA


title: MPRA-Plasmid-Library

description: small seq on plasmid library

library_source: other

data_processing:
Sequencing was performed using an Illumina HiSeq 2500 in Rapid Run mode and  employed a single-end, 50 base read length (SE50) sequencing strategy.
Files were aligned to guides using bowtie2 for each sample. Next, the barcodes for WT and mutant were  segregated for each sample.
log2 CPM values for each barcode using edgeR.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include log2 cpm  values for each Sample.
Library strategy: DNA-seq

molecule: other

source_name: MPRA-Plasmid-Library

extract_protocol:
250ng of plasmid library DNA was used for the construction of sequencing libraries
Library construction was performed using a two-step PCR amplicon approach.
First amplification was performed at 98°C for 30” followed by ten cycles of 98°C for 10”, 71°C for 30”, 72°C for 30”, and final elongation at 72°C for 5’ with Forward primer: 5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGgccagcgccaggatcaac -3’ and Reverse Primer: 5’- GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGcgccccgactctagctagac -3’ using Q5 Polymerase. PCR product was purified using 1.8X Ampure XP beads.
Second amplification was was performed at 98°C for 30” followed by eight cycles of 98°C for 10”, 67°C for 30”, 72°C for 30”, and final elongation at 72°C for 5’ with Forward primer: 5’- aatgatacggcgaccaccgagatctacactcgtcggcagcgtc -3’ and Reverse Primer: 5’- caagcagaagacggcatacgacattcgccttagtctcgtgggctcgg -3’ using Q5 Polymerase. PCR product was purified using 1.8X Ampure XP beads.

value: small seq on plasmid library


title: Plasma, baseline, resting, Female 2

value: Blood Plasma

value: Female


title: Total_RNA_5_S17

description: total RNA replicate 5


title: Plasma, chronic trained, post acute, Female 1

value: Chronic Exercise + Acute Exercise


title: WT, Control, biol rep 3

description:
Stranded Total RNA
Wt_3


title: WT, Control, biol rep 2

description:
Stranded Total RNA
Wt_2


title: Plasma, chronic trained, resting, Female 1

value: Chronic Exercise Training


title: Total_RNA_4_S13

description: total RNA replicate 4


title: Total_RNA_3_S9

description: total RNA replicate 3


title: WT, Control, biol rep 1

description:
Stranded Total RNA
Wt_1


title: Total_RNA_2_S5

description: total RNA replicate 2


title: Plasma, chronic trained, post acute, Female 2


title: Plasma, chronic trained, post acute, Male 5

value: Male


title: Plasma, baseline, post acute, Female 1

value: Acute Exercise


title: Plasma, baseline, resting, Female 1


title: Plasma, chronic trained, resting, Male 5


title: CD4+ T cells, rmCIRP treatment, replicate 1

first: Zongsheng

last: Wu

state: Jiangsu

address: No.87 Dingjiaqiao Road

department: Department of Critical Care Medicine,

institute: Jiangsu Provincial Key Laboratory of Critical Care Medicine,  Zhongda Hospital, School of Medicine, Southeast University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Mus_musculus.GRCm38 V99
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Spleen

growth_protocol: RPMI-1640 complete medium containing 10% FBS,100 IU/ml penicillin, 100 μg/ml streptomycin, and 50 μM 2-mercaptoethanol .

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Naïve CD4+ T cells were cultured in the presence of rmCIRP（1μg/ml）or equal volume PBS.

value: Spleen

value: Primary

value: naive CD4+ T cells

tag: genotype

value: Wild type

value: PBS


title: CD4+ T cells, rmCIRP treatment, replicate 3


title: CD4+ T cells, rmCIRP treatment, replicate 2


title: Plasma, chronic trained, resting, Female 3


title: pDNA_5_S29

description: plasmid DNA replicate 5

value: plasmid DNA


title: Plasma, baseline, post acute, Male 5


title: CD4+ T cells, PBS treatment, replicate 2

value: rmCIRP


title: pDNA_4_S28

description: plasmid DNA replicate 4


title: CD4+ T cells, PBS treatment, replicate 1


title: CD4+ T cells, PBS treatment, replicate 3


title: pDNA_2_S26

description: plasmid DNA replicate 2


title: pDNA_6_S30

description: plasmid DNA replicate 6


title: Plasma, chronic trained, post acute, Male 4


title: Plasma, chronic trained, resting, Male 4


title: pDNA_3_S27

description: plasmid DNA replicate 3


title: pDNA_1_S25

description: plasmid DNA replicate 1


title: Total_RNA_1_S1

description: total RNA replicate 1


title: Plasma, baseline, post acute, Male 4


title: BS Immortalised MEF cells, subclonal population 2-6

city: Cambridge

first: Anne

last: Ferguson-Smith

address: 20 Downing Place

institute: Cambridge University

data_processing:
tcBS-seq reads were trimmed by Trim Galore (v0.6.0).
tcBS-seq reads were aligned to mm10 using Bismark.
tcBS-seq reads with map quality score less than 10 were excluded and were further filtered by M-bias: for MEF-1 and MEF-2 data, we excluded the first two bp on both paired reads and the last bp on Read 2.
tcBS-seq read data was extracted using bismark_methylation_extractor and analysed in R (v3.6.1) to combine data from all cell lines and compare with genomic annotations and other datasets.
For the all_clonal_MEF_methylation_data processed file, we used read coverage across the individual tcBS-seq libraries to look for enrichment of reads on individual chromosomes to determine coverage-based karyotypes for our immortalised MEF cell lines and find that chromosomes 12, 18, and 19 exhibit aneuploidy in at least one of the cell lines. For subsequent analyses, we removed the CpGs on the aneuploid chromosomes, as well as those on the X chromosome. Additionally, we thresholded the data for CpGs with greater than or equal to 10x coverage in all 16 sequencing libraries, retaining ~1.2 million CpGs (or ~5% of CpGs in the mouse genome) with a median coverage of 32 reads per CpG per tcBS-seq dataset.
Assembly: mm10
Supplementary files format and content: CpG_combine* files are tab delimited with the following four columns:   chromosome, genomic locus (bp), unmethylated read counts, methylated read counts
Supplementary files format and content: all_clonal_MEF_methylation_data is a tab delimited file with the following 12 columns: chromosome, start locus of CpG, end locus of CpG, read coverage, unmethylated read count, methylated read count, percentage of methylation, cell line, cell type, fidelity score, neighbour similarity score, cpg density

growth_protocol: Mouse embryonic fibroblasts (MEFs) were established from E13.5 C57BL/6J mouse embryos. MEFs were grown at 37°C and 5% CO2 in high glucose DMEM GlutaMAX™ (ThermoFisher, cat no. 31966021) supplemented with 10% FBS (Gibco, 11550356) and 1% penicillin/streptomycin solution and passaged with trypsin/EDTA. MEFs were immortalised by serial passaging the cells through crisis phase. Isolation of single immortalised MEF cells was performed by flow cytometry (MoFlo Astrios Cell Sorter) to 96-well plates. The isolated single cells were grown into clonal cell lines by successive passaging from 96-well, 48-well, 24-well, 12-well, and 6-well plates to 10cm dishes where they were grown to 75% confluency to yield 1-2 million cells per clonal line for DNA/RNA extraction. The parental lines, from which the clonal lines were derived, were also grown to 75% confluency on 10cm dishes to yield 1-2 million cells for DNA/RNA extraction.

extract_protocol:
DNA extraction was performed with the Qiagen AllPrep DNA/RNA Mini Kit (cat no. 80204).
Target capture bisulfite-sequencing (tcBS-seq) libraries were generated using the SureSelectXT Methyl-seq Library Preparation Kit with the following specifications. 1µg of DNA was sonicated to an average size of 200bp with the Covaris E220 (Duty Factor = 30%, PIP = 100, Cycles per Burst = 1000, Treatment Time = 95, Bath Temperature = 7°C, with intensifier fitted) using 50µl microTUBEs (cat no. 520166) and 24-place rack (cat no. 500308). Following end repair, dA tailing, and adaptor ligation, libraries were hybridised to single-stranded RNA probes homologous to 297,000 regions in the mouse genome (SureSelectXT Methyl-Seq Capture Probes, cat no. 931052). After purification, the libraries were bisulfite converted using Zymo Research’s Methylation-Gold Kit (cat no. D5005) and PCR amplified for 8 cycles. The PCR amplified bisulfite-treated libraries were then purified, indexed by PCR amplification (6 cycles), and purified again. All purification steps took place using Ampure XP beads (Beckman Coulter, cat no. A63881). The final libraries were then quality checked and quantified for multiplexing using the Bioanalyzer High-Sensitivity DNA kit (Agilent, 5067-4626) and Qubit dsDNA HS Assay kit (Thermo Scientific, Q32854). The multiplexed libraries were sequenced as 150 bp paired-end reads on the Illumina Novaseq 6000 SP.

value: Immortalised mouse embryonic fibroblasts (MEFs)


title: BS Immortalised MEF cells, subclonal population 2-7


title: BS Immortalised MEF cells, subclonal population 2-5


title: Low_Poly_6_S23

description: Low Polysome Fractions replicate 6

value: PC3 cells

value: Low polysome fractions


title: Low_Poly_5_S19

description: Low Polysome Fractions replicate 5


title: Plasma, baseline, resting, Male 4


title: BS Immortalised MEF cells, subclonal population 2-3


title: Plasma, chronic trained, post acute, Male 3


title: Low_Poly_4_S15

description: Low Polysome Fractions replicate 4


title: Plasma, chronic trained, resting, Male 3


title: Low_Poly_3_S11

description: Low Polysome Fractions replicate 3


title: Plasma, baseline, resting, Male 5


title: Plasma, baseline, post acute, Male 3


title: BS Immortalised MEF cells, subclonal population 2-2


title: BS Immortalised MEF cells, subclonal population 2-1


title: BS Immortalised MEF cells, parental population 2


title: Low_Poly_2_S7

description: Low Polysome Fractions replicate 2


title: Plasma, baseline, resting, Male 3


title: Low_Poly_1_S3

description: Low Polysome Fractions replicate 1


title: Plasma, chronic trained, post acute, Male 2


title: BS Immortalised MEF cells, subclonal population 1-7


title: High_Poly_6_S24

description: High Polysome Fractions replicate 6

value: High polysome fractions


title: Plasma, chronic trained, resting, Male 2

value: Blood Plasma


title: BS Immortalised MEF cells, subclonal population 1-6


title: High_Poly_5_S20

description: High Polysome Fractions replicate 5


title: Plasma, baseline, post acute, Male 2


title: BS Immortalised MEF cells, subclonal population 2-4


title: High_Poly_4_S16

description: High Polysome Fractions replicate 4


title: High_Poly_3_S12

description: High Polysome Fractions replicate 3


title: High_Poly_2_S8

description: High Polysome Fractions replicate 2


title: Plasma, baseline, resting, Male 2


title: BS Immortalised MEF cells, subclonal population 1-4


title: BS Immortalised MEF cells, subclonal population 1-3


title: BS Immortalised MEF cells, subclonal population 1-5


title: Plasma, chronic trained, post acute, Male 1


title: Plasma, chronic trained, resting, Male 1


title: BS Immortalised MEF cells, subclonal population 1-2


title: Plasma, baseline, post acute, Male 1


title: BS Immortalised MEF cells, subclonal population 1-1


title: H446 (sRNA-Seq)

city: Hefei

first: fengmei

last: chao

state: Anhui

address: East Huanhu road

institute: Anhui Provincial Cancer Hospital

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 17 nt.
Total clean reads were mapped to the human reference genome using the bwa aligner.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org) and pirnabank (www.pirnabank.ibab.ac.in) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include Normalized_Value/Count values for each Sample

source_name: Small cell lung cancer cells

growth_protocol: The cells were cultured on 10cm cell culture dish in 1640 medium supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated from cells using the Magzol Reagent (Magen, China)according to the manufacturer's protocol
Total RNAs were ligated with 3' RNA adapter, and followed by 5' adapter ligation. Subsequently, the adapter-ligated RNAs were subjected to RT-PCR and amplified with a low-cycle. Then the PCR products were size selected by PAGE gel according to instructions of NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Illumina, USA). Libraries were sequenced on the Illumina HiSeq 2500 with single-end 50bp following the manufacturer's protocols.

value: Small cell lung cancer cells

tag: cell source

value: Derived from metastatic site:pleural effusion

value: untreated

tag: phenotype

value: Chemosensitivity


title: Plasma, baseline, resting, Male 1

value: Male


title: BS Immortalised MEF cells, parental population 1

tag: cell line

tag: cell type


title: RNA-Seq BSC, Ctrl, rep12

city: Boston

first: Xingbin

last: Ai

state: MA

address: 55 Fruit St

department: Pediatrics

institute: MASSACHUSETTS GENERAL HOSPITAL

description: BSC, Ctrl, rep12

data_processing:
The paired-end 42 bp sequencing reads are mapped to the human hg38 reference genome using the STAR algorithm with default settings.
The number of fragments overlapping predefined genomic genes is counted. Only read pairs that have both ends aligned are counted.
Read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands are discarded.
The gene annotations were obtained from Subread R package. These annotations were originally from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene.
Genes with the same Entrez gene identifiers were also merged into one gene.
Assembly: hg38
Supplementary files format and content: csv

source_name: Lung

extract_protocol:
Total RNA isolation using a RNeasy kit (QIAGEN, Cat# 74104).
For each sample, 2 µg of total RNA was used in library construction using TruSeq Stranded mRNA Library kit (Illumina, Cat# 20020594).

value: Lung

value: Basal stem cell


title: Primary MEF cells, population C, DNMT3A/3B DKO (+ TAT-CRE)

data_processing:
tcBS-seq reads were trimmed by Trim Galore (v0.6.0).
tcBS-seq reads were aligned to mm10 using Bismark.
tcBS-seq reads with map quality score less than 10 were excluded and were further filtered by M-bias: for MEF DNMT3A/3B DKO and control data, we excluded the first two bp on Read 1and the first four and last two bp on Read 2.
tcBS-seq read data was extracted using bismark_methylation_extractor and analysed in R (v3.6.1).
Assembly: mm10
Supplementary files format and content: CpG_combine* files are tab delimited with the following four columns:   chromosome, genomic locus (bp), unmethylated read counts, methylated read counts

source_name: MEF-C

growth_protocol: Primary MEFs were established from Dnmt3aflox/flox3bflox/flox E13.5 embryos and grown at 37°C and 5% CO2 in high glucose DMEM GlutaMAX™ (ThermoFisher, cat no. 31966021) supplemented with 10% FBS (Gibco, 11550356) and 1% penicillin/streptomycin solution and passaged with trypsin/EDTA.

treatment_protocol: To induce the knockout of DNMT3A/3B, 1x106 cells were plated and the next day washed with PBS and media was replaced with 5ml of DMEM:PBS (1:1) with 50µl TAT-CRE recombinase (2-3µg/µl) and incubated at 37°C for 8 hours. Following the TAT-CRE recombinase treatment, cells were washed three times with PBS and the original growth media was replaced. The TAT-CRE recombinase treatment was carried out again 48 hours following the start of the initial treatment. Cells were collected for protein and DNA/RNA extraction 72 hours after the second TAT-CRE recombinase treatment.

value: MEF-C

value: Primary mouse embryonic fibroblasts (MEFs)


title: RNA-Seq BSC, Ctrl, rep11

description: BSC, Ctrl, rep11


title: Primary MEF cells, population D, DNMT3A/3B DKO (+ TAT-CRE)

source_name: MEF-D

value: MEF-D


title: RNA-Seq BSC, Ctrl, rep10

description: BSC, Ctrl, rep10


title: Primary MEF cells, population B, DNMT3A/3B DKO (+ TAT-CRE)

source_name: MEF-B

value: MEF-B


title: RNA-Seq BSC, Ctrl, rep9

description: BSC, Ctrl, rep9


title: Primary MEF cells, population A, DNMT3A/3B DKO (+ TAT-CRE)

source_name: MEF-A

value: MEF-A


title: RNA-Seq BSC, Ctrl, rep8

description: BSC, Ctrl, rep8


title: Primary MEF cells, population D, control (no TAT-CRE)


title: RNA-Seq BSC, Ctrl, rep7

description: BSC, Ctrl, rep7


title: SP-minus

city: Toulouse

first: Liliana

middle: Elisa

last: Lucca

address: 2 Avenue Hubert Curien

department: Immunology

institute: CRCT

description: single cell RNA

data_processing:
fastq files were generated from Illumina BCL files with the 'mkfastq' pipeline of cellranger v3.0.2
Assembly: mm10
Supplementary files format and content: a matrix of expression was generated by joining the outputs of the 'count' pipeline of cellranger v3.0.2, filtering cells with less than 30,000 UMIs per cell and less than 25% mitochondrial reads. Data were than transformed using the sctransform function of Seurat v3.0

source_name: Purified spleen CD137ko tomato negative CD8 T cells

extract_protocol:
At the indicated time points, CD8+ T cells were isolated from the spleen and the subcutaneous tumor using mouse CD8+ T cell isolation kit (Miltenyi Biotec) and sorted based on expression of the tomato fluorescent protein (tomato positive = Cd137 minus, tomato negative = Cd137 plus) on a FACSaria™ Fusion (BD biosciences). Cells from 7 mice were stained with hashtagging antibodies (BioLegend) in the following way: mouse 1 = ACCCACCAGTAAGAC; mouse 2 = GGTCGAGAGCATTCA; mouse 3 = CTTGCCGCATGTCAT; mouse 4 = AAAGCATTCTTCACG; mouse 5 = CTTTGTCTTTGTGAG; mouse 6 = TATGCTGCCACGGTA, mouse 7 = GAGTCTGCCAGTATC. Hashtagged cells where then pooled to yield 4 cellular suspension corresponding to spleen Cd137 minus, spleen Cd137 plus, tumor Cd137 minus, tumor Cd137 plus.
Single-cell libraries (5′ gene expression) were generated using the Chromium Controller Instrument and Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1 according to the manufacturer’s protocol (10× Genomics)
The libraries were sequenced on a NextSeq 550 (Illumina) in pair-end sequencing 28 bp (read1) × 91 bp (read2) and a single index 8 bp in length.

treatment_protocol: C57BL/6 mice are lethally irradiated (8 Gray) and reconstituted by intravenous injection of 5*10^6 BM cells from Cd4creCd137fl/flROSA26tomato and Cd137fl/flROSA26tomato. The reconstitution of the immune system of the recipient mice was verified 7 weeks after BM transplantation. B16K1 cells (10^6) were then injected subcutaneously (s.c.).

tag: tissu

value: spleen from n = 7 bone marrow chimaeric mice

value: B16K1 melanoma s.c. injection

tag: treatment kinetic

value: 21 days after tumor inoculation


title: Tum-minus

description: single cell RNA

source_name: Purified tumor-infiltrating CD137ko tomato negative CD8 T cells

value: tumor from n = 7 bone marrow chimaeric mice

tag: treatment


title: Tum-plus

description: single cell RNA

source_name: Purified tumor-infiltrating CD137wt tomato positive CD8 T cells


title: Primary MEF cells, population C, control (no TAT-CRE)


title: High_Poly_1_S4

description: High Polysome Fractions replicate 1

value: PC3 cells

value: High polysome fractions


title: SP-plus

description: single cell RNA

source_name: Purified spleen CD137wt tomato positive CD8 T cells