title: PBMC RNA, sri 2, 2nd visit

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

data_processing:
Raw sequencing data were trimmed using fastp 0.19.6, filtered using RNA-QC-Chain, then aligned to the GRCh38 assembly using STAR 2.7.1a
Batch correction was performed using SVA 3.36.0
Differential gene expression was analyzed using DESeq 1.24.0
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include gene counts for each sample

source_name: peripheral blood mononuclear cells

extract_protocol:
Samples underwent RNA purification using phenol-chloroform extraction.
Libraries were prepared using TrueSeq stranded total RNA LT sample prep kit.

treatment_protocol:
ECT: was administered with hand-held electrodes using propofol (1.20–2.69 mg/kg) for anesthesia and succinylcholine (0.45–1.09 mg/kg) as a muscle relaxant. ECT was applied unilaterally twice a week.
Ketamine: participants were randomized to one of two (double-) blinded groups: 1. Active intravenous (i.v): i.v 0.2 mg/kg ketamine and intranasal placebo (saline 0.9%), 2. Active intranasal inhalation (INH): intranasal 50 mg ketamine and i.v placebo (saline 0.9%). Treatments were administered twice weekly for three weeks.
Antidepressants drugs alone:were personalized (i.e.type and dose) for patients by their psychiatrists.
Pharmacotherapy for the ECT and ketamine groups included antipsychotics and antidepressants. In the ECT group, 10/17 (59%) received antipsychotics: 6/10 (60%) of the responders and 4/7 (57%) of the non-responders. In the ketamine group, 10/14 (71%) received antipsychotics: 2/4 (50%) of the responders and 8/10 (80%) of the non-responders. The antideoressants types were - SSRI, SNRI or other types. In the ECT group, 5/17 (29%) received SSRIs: 3/10 (30%) of the responders and 2/7 (29%) of the non-responders. In the ketamine group, 5/14 (36%) received SSRIs: 2/4 (50%) of the responders and 3/10 (30%) of the non-responders. SNRIs were administered to 7/17 (41%) in the ECT group: 4/10 (40%) of the responders and 3/7 (43%) of the non-responders; and to 5/14 (36%) in the ketamine group: 1/4 (25%) of the responders and 4/10 (40%) of the non-responders. Other antidepressants were administered to 5/17 (29%) in the ECT group: 3/10 (30%) of the responders and 2/7 (29%) of the non-responders; and to 4/14 (29%) in the ketamine group: 1/4 (25%) of the responders and 3/10 (30%) of the non-responders.
Blood samples collection: The first blood samples were collected from the study and control arms upon recruitment, at the start of treatment (i.e. 1st visit). Blood samples were collected again (i.e. 2nd visit) from the study arm, 8–10 weeks following ECT or TAU, or 10 days following ketamine. A second set of control blood samples were taken from the same control volunteers within six months following their first blood sample collection.
Blood samples separation: were separated to plasma and PMBC. PMBC washed with 7ml PBS, centrifuged and re-suspended in 3 ml PBS before storing.

value: peripheral blood mononuclear cells

value: ssri

value: after treatment


title: RNA108 Endometrium, advanced maternal age

status: Public on Jun 30 2024

type: SRA

city: Maastricht

first: Darina

last: Obukhova

state: Limburg

address: P. Debyelaan 25

department: Department of Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center +

description:
RNA108
raw_counts.csv
batch_corrected_filtered_counts.csv

library_source: transcriptomic

data_processing:
Reads were mapped to the Homo sapiens reference genome (UCSC release GRCh37/hg19),  using STAR (v.2.7.9) in “Basic” two-pass mode and in “GeneCounts” quantification mode..
The mapped reads were estimated at gene level using the Ensembl database for annotation. The raw expression count matrix was produced using FeatureCounts (v.2.0.1).
Batch effect of the sequencing run was corrected for  using the ‘Combat-Seq2’ method from the sva R package (v.3.42.0)
Genes in which the number of mapped reads was <5 in more than 75% of samples were filtered out.
Assembly: GRCh37/hg19
Supplementary files format and content: comma-separated values text file includes raw counts for each sample
Supplementary files format and content: comma-separated values text file includes batch-corrected counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: endometrium

extract_protocol:
Total RNA was extracted from all samples using miRNeasy kit (Qiagen, cat.no. 217084), followed by DNase treatment (DNase Free, Life Technologies, cat.no. EN0521), RNA integrity was assessed with Qubit RNA IQ Assay kit (Thermo Fisher, cat.no. Q33221)
cDNA libraries were randomly assigned into two sequencing batches  and prepared using the TruSeq Stranded mRNA Sample Preparation Guide (Illumina, cat.no. 20020595).

tag: tissue

value: endometrium

tag: age

value: advanced


title: Breast tumor 01_001 from Combination Arm sample type B

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

country: USA

institute: University of Colorado Anschutz Medical Campus

data_processing:
Raw gene read counts were generated by BioSpyder.  Genes with multiple probes were summed to unique genes. Samples with <40% mapping rate were discarded.  Lowly expressed genes were discarded by removing those expressed in less than 10 samples or with less than 1 count per million across all samples.
Assembly: Human transcriptome
Supplementary files format and content: Text file containing filtered sample and gene counts

source_name: Breast tumor

extract_protocol:
The TempO-Seq Human Whole Transcriptome kit from BioSpyder was used to lyse and prepare the samples.
TempO-Seq Human Whole Transcriptome kit from BioSpyder (Carlsbad, CA)

value: Breast tumor

tag: treatment

value: Combination Arm

tag: study id

tag: sample type

value: B

tag: paired

value: FALSE


title: PMSCs,rep3

city: Chang chun

first: huixin

last: Lv

address: 1500 Tsinghua Road

country: China

institute: School and Hospital of Stomatology, Jilin University

data_processing:
Fastp software was used to process raw reads in fastq format, and clean reads were obtained after removing low-quality reads for subsequent data analysis.
The clean reads were mapped to the reference genome using HISAT2.
Fragments Per Kilobase of exon model per Million fragments mapped (FPKM) of each gene was calculated.
The read counts of each gene were obtained through HTSeq-count.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: human maxillary sinus membrane

growth_protocol: Mesenchymal stem cells were maintained in MEM α supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using RNAiso reagent (TAKARA, USA). RNA purity and quantification were evaluated using the NanoDrop2000 Spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The transcriptome libraries were constructed using VAHTS Universal V5 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol:
Osteogenic differentiation was induced by treatment of hLMSCs and hPMSCs with Osteogenic Differentiation Kits (Oricell).
The control group was cultured in normal complete medium (NCM). For osteogenic induction group, the cells were cultured in NCM overnight and the medium was replaced by differentiation induction medium on the next day. The renewing time of the medium was 3 days.

value: human maxillary sinus membrane

tag: cell type

value: mesenchymal stem cells

value: non


title: Media control HEKa RNA rep 3

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

description:
XL15
Column "XL15_L001" in counts.matrix

data_processing:
STAR 2.4.2a for alignment
subread 1.5.0.post3 (featureCount) for quantification of genes
Assembly: GRCh37
Supplementary files format and content: Tab delimited text file consisting raw gene counts of each sample

source_name: Skin

growth_protocol: HEKa cells were grown in EpiLife media supplemented with EDGS, antibiotic and antimycotic

extract_protocol: RNA were harvested using Qiagen miRNeasy

treatment_protocol: keratinocytes were treated with 2*10^9 bacteria/ml for 3 hours

value: Skin

tag: cell line

value: HEKa

value: Keratinocyte

value: no treatment


title: RNA382 Endometrium, young maternal age

description:
RNA382
raw_counts.csv
batch_corrected_filtered_counts.csv

value: young


title: PBMC RNA, sri 3, 2nd visit

value: peripheral blood mononuclear cells

tag: time


title: RNA70 Endometrium, young maternal age

description:
RNA70
raw_counts.csv
batch_corrected_filtered_counts.csv


title: Media control HEKa RNA rep 2

description:
XL14
Column "XL14_L001" in counts.matrix


title: Breast tumor 01_002 from Fulvestrant Arm sample type W

value: Fulvestrant Arm

value: W


title: Media control HEKa RNA rep 1

description:
XL13
Column "XL13_L001" in counts.matrix


title: LMSCs,rep2


title: Ozone Exposed 2

city: Albuquerque

first: Matthew

last: Campen

state: NM

address: 2502 Marble Ave NE

department: Pharmaceutical Sciences

institute: University of New Mexico Health Sciences Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Illumina NovaSEQ 6000 at University of Colorado Anschutz Medical Campus Genomics Shared Resource Cancer Center, demultiplexed with bcl2fastq v2.20.0.422 with “--barcode-mismatches” set to 1
Aligned and counted with CellRanger v3.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: Placenta

growth_protocol: Standard housing, 12hr light,dark, food ad libitum

extract_protocol:
Pregnant mice were anesthetized via isoflurane and euthanized via cardiac exsanguination. Placentas were removed (n=7 per mouse), and excess decidual tissue was excised. Placentas were placed in a conical tube containing 10mL warmed RPMI media containing Collagenase B at a concentration of 2.4mg/mL. Tissue was minced via surgical scissors to increase surface area of sample. Tubes were then places on a rocker in an incubator at 37C for 2 hours. Following incubation, 20 mL DPBS was added to the mixture and resuspended through the pipettor to further break down the tissue. Tubes were centrifuged at 1200rpm for 7 minutes and the supernatant was decanted. The tissue pellet was resuspended in 6mL of fresh RPMI with DNase added. This solution was returned to the incubator for 20 minutes. The tube was next centrifuged as described previously and the supernatant decanted. and the pellet was resuspended in 10mL of 1mM EDTA and pipetted through a pipettor to mix. This solution was poured through a 70μm cell strainer into a fresh 50mL conicle tube. This tube was centrifuged as described and the supernatant was decanted and the pellet resuspended in 2mL fresh RPMI media for library preparation.
Cell concentrations and viability were determined using the Cell Countess II FL (ThermoFisher) prior to calculating cell counts and loading the suspension into the Next GEM Chip G and Chromium Controller (10x Genomics) per the manufacturer’s protocol for GEM formation. The 10x Chromium Next GEM 3’ protocol was used to create 3’ libraries; briefly, cells were lysed and barcoded within each GEM prior to first strand cDNA synthesis, also within each GEM. After GEM’s are broken, cells are pooled prior to library completion as described in the manufacture’s protocol. Library quality was assess after cDNA synthesis and after completion on the BioAnalyzer using a DNA High Sensitivity Chip (Agilent). Prior to sequencing, Agilent Tape Station 4200 and Invitrogen Qubit 4.0 reagents were used determine final library concentrations prior to dilution, normalization and pooling at 4nM. qPCR was used to determine cluster efficiency.

treatment_protocol: 4hr exposure to 1Ppm ozone or filtered air

value: Placenta

value: Dissociated tissue

value: 17 unique clusters

tag: genotype

value: Maternal Ozone exposure on GD 10


title: PBMC RNA, sri 4, 2nd visit

value: ssri

value: after treatment


title: Ozone Exposed 3

description: 10x Genomics


title: PBMC RNA, sri 2, 1st visit

value: before treatment


title: Staph epidermidis exposed HEKa RNA rep 3

description:
XL12
Column "XL12_L001" in counts.matrix

value: Staphylococcus epidermidis


title: PBMC RNA, sri 1, 2nd visit


title: Staph epidermidis exposed HEKa RNA rep 1

description:
XL10
Column "XL10_L001" in counts.matrix


title: RNA83 Endometrium, young maternal age

description:
RNA83
raw_counts.csv
batch_corrected_filtered_counts.csv

value: endometrium


title: MCF10A_JUN_KO_JUN_M14, IgG, rep3

city: Jena

first: Bjoern

last: von Eyss

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute on Aging

library_source: genomic

data_processing:
Adapter removal and quality trimming was performed by Cutadapt. Since the carry-over DNA of pAG-MNase purification from E. coli was used as spike-in control, mapping was performed to hg19 and a human repeat-masked E. coli genome by Bowtie2. Paired-end reads mapped to hg19 with inserts <120 bp were extracted using alignment Sieve (deepTools). A scaling factor was inferred by: scaling factor= (mapped reads < 120 bp to hg19)⁄(mapped reads to E.coli).
The scaling factor was used to generate spike-in normalized bigWig files by bamCoverage (deepTools).
Assembly: hg19
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: MCF10A JUN KO

growth_protocol: MCF10A cells  were cultured in DMEM/F12 (Thermo Fisher Scientific) supplemented with 5 % horse serum (Thermo Fisher Scientific), 1 % penicillin-streptomycin (Sigma-Aldrich), 10 µg/ml human insulin (Sigma-Aldrich), 0.5 µg/ml hydrocortisone (Sigma-Aldrich), 0.1 µg/ml cholera toxin (Sigma-Aldrich) and 20 ng/ml human EGF (Biomol).

extract_protocol:
CUT and RUN experiments were performed as described previously (Kim et al., Nat. Commun., 2022). Briefly, for each CUT and RUN reaction 200,000 cells were trypsinized, washed, resuspended in 100 µl wash buffer (20 mM HEPES, pH7.5, 150 mM NaCl, 0.5 mM Spermidine) and bound to 10 µl activated BioMag®Plus Concanavalin A magnetic beads (Polysciences) for 10 min at room temperature. The cells were then incubated with antibodies diluted in 100 µl antibody buffer (wash buffer + 0.01% digitonine and 2 mM EDTA) overnight at 4°C. IgG rabbit antibody was used as negative control. After incubation with antibodies, the beads were washed in digitonin wash buffer (wash buffer + 0.01% digitonin) and incubated 1h at 4°C with 1 µg/ml protein A/G Micrococcal Nuclease fusion protein (pA/G MNase). After washing with digitonin wash buffer, beads were rinsed with low salt buffer (20 mM HEPES, pH7.5, 0.5 mM Spermidine, 0.01% digitonine), resuspended in 200 µl incubation buffer (20 mM HEPES, pH7.5, 10 mM CaCl2, 0.01% digitonin) and placed at 0°C to initiate cleavage. After 30 min, reactions were stopped by adding 200 µl STOP buffer (170 mM NaCl, 20 mM EGTA, 0.01% digitonin, 50 µg/ml RNAse A) and the samples were incubated 30 min at 37°C to digest the RNA and release the DNA fragments. The samples were then treated with proteinase K for 1 h at 50°C and the DNA was purified using Phenol/Chloroform/Isoamyl alcohol. After precipitation with glycogen and Ethanol, the DNA pellet was resuspended in 0.1 X TE and used for library preparation.
For DNA library generation, the NEBNext®Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs) was used. Adaptor ligation was performed with 1:25 diluted adaptor and 15 cycles were used for library amplification using dual indices (NEB dual index kit). Paired-end 2x25 bp sequencing was performed.

treatment_protocol: MCF10A JUN KO cells were either reconstituted with JUN WT, JUN M14 or an empty vector control.

tag: antibody

value: MCF10A JUN KO

value: breast epithelial

value: JUN M14


title: PBMC RNA, sri 1, 1st visit


title: RNA138 Endometrium, young maternal age

description:
RNA138
raw_counts.csv
batch_corrected_filtered_counts.csv


title: Staph epidermidis exposed HEKa RNA rep 2

description:
XL11
Column "XL11_L001" in counts.matrix

value: Skin

value: HEKa

value: Keratinocyte


title: Ozone Exposed 1

description: 10x Genomics


title: P melaninogenica exposed HEKa RNA rep 3

description:
XL09
Column "XL09_L001" in counts.matrix

value: Prevotella melaninogenica


title: MCF10A_JUN_KO_JUN_M14, JUN, rep3


title: Filtered Air 3

description: 10x Genomics

value: Maternal filtered air exposure on GD 10


title: MCF10A_JUN_KO_JUN_WT, IgG, rep3

value: JUN WT


title: Filtered Air 2

description: 10x Genomics

value: Placenta

value: Dissociated tissue


title: Filtered Air 1

description: 10x Genomics

value: 17 unique clusters


title: PBMC RNA, kat 3, 2nd visit

value: peripheral blood mononuclear cells

value: ketamine


title: P melaninogenica exposed HEKa RNA rep 1

description:
XL07
Column "XL07_L001" in counts.matrix


title: F nucleatum exposed Heka RNA rep 3

description:
XL06
Column "XL06_L001" in counts.matrix

value: Fusobacterium nucleatum


title: MCF10A_JUN_KO_JUN_WT, JUN, rep3


title: PBMC RNA, kat 2, 2nd visit

value: after treatment


title: MCF10A_JUN_KO_ev, IgG, rep3

value: empty vector


title: F nucleatum exposed Heka RNA rep 2

description:
XL05
Column "XL05_L001" in counts.matrix


title: MCF10A_JUN_KO_ev, JUN, rep3

value: MCF10A JUN KO


title: F nucleatum exposed HEKa RNA rep 1

description:
XL04
Column "XL04_L001" in counts.matrix


title: P nigrescens exposed Heka RNA rep 3

description:
XL03
Column "XL03_L001" in counts.matrix

value: Prevotella nigrescens


title: PBMC RNA, kat 4, 1st visit

value: before treatment


title: MCF10A_JUN_KO_JUN_M14, JUN, rep2

value: breast epithelial

value: JUN M14


title: MCF10A_JUN_KO_JUN_WT, IgG, rep2


title: P nigrescens exposed Heka RNA rep 2

description:
XL02
Column "XL02_L001" in counts.matrix

value: Skin

value: HEKa

value: Keratinocyte


title: PBMC RNA, kat 2, 1st visit


title: PBMC RNA, ecf 5, 2nd visit

value: electroconvulsive therapy


title: PBMC RNA, kat 4, 2nd visit


title: PBMC RNA, ecf 4, 2nd visit


title: MCF10A_JUN_KO_JUN_WT, JUN, rep2

value: JUN WT


title: P melaninogenica exposed HEKa RNA rep 2

description:
XL08
Column "XL08_L001" in counts.matrix

value: Prevotella melaninogenica


title: MCF10A_JUN_KO_ev, IgG, rep2


title: P nigrescens exposed HEKa RNA rep 1

description:
XL01
Column "XL01_L001" in counts.matrix


title: SPT2

city: Nanjing

first: Shu

last: Xu

state: Jiangsu Province

address: China Pharmaceutical University

institute: China Pharmaceutical University

data_processing:
Illumina Casava1.7 software used for basecalling.
After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (HyClone), 100 U/mL penicillin, and 100 µg/mL streptomycin at 37 °C with 5% CO2 incubation. Cells were seeded into 6-well plates (Corning) 24 h prior to transfection at a density of 200,000 cells per well.

extract_protocol:
Total RNA was prepared from transfection experiments after 72 h using a RNA Isolation Reagent (R701-01, Vazyme). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

treatment_protocol: Cells were transfected by using TransIntro EL Transfection Reagent following the manufacturer’s recommended protocol. For each well of a 6-well plate, 4 μg plasmids were transfected and 500 pmoL of DNA probes were transfected 24 h later.

value: human liver carcinoma cells

value: siRNA-PPIB knockdown-control

value: TransIntro EL Transfection Reagent


title: SPT1

value: siRNA-PPIB knockdown-test


title: PBMC RNA, kat 1, 2nd visit

value: peripheral blood mononuclear cells

value: ketamine

value: after treatment


title: MCF10A_JUN_KO_ev, JUN, rep2

value: MCF10A JUN KO

value: empty vector


title: MCF10A_JUN_KO_JUN_M14, IgG, rep2

value: breast epithelial


title: PBMC RNA, ecf 3, 2nd visit


title: PBMC RNA, ecf 2, 2nd visit


title: MCF10A_JUN_KO_JUN_M14, IgG, rep1

value: JUN M14


title: PT1

value: TaqTth-PPIB knockdown-test


title: MCF10A_JUN_KO_JUN_M14, JUN, rep1


title: PT2

value: TaqTth-PPIB knockdown-control


title: PBMC RNA, ecf 1, 2nd visit


title: MCF10A_JUN_KO_JUN_WT, IgG, rep1


title: PBMC RNA, kat 3, 1st visit

value: before treatment


title: PC2


title: PBMC RNA, kat 1, 1st visit


title: MCF10A_JUN_KO_JUN_WT, JUN, rep1


title: PBMC RNA, ecf 4, 1st visit

value: electroconvulsive therapy


title: PC1


title: 4T1 DAC replicate 3 [RNA-seq]

city: Boston

first: Eric

last: Greer

state: MA

address: 320 Longwood Avenue

department: Newborn Medicine/Department of Pediatrics

institute: Boston Children's Hospital/Harvard Medical School

data_processing:
Real-Time Analysis (RTA) software
sequencing reads were aligned to the mm10 genombe in RSEM pipeline
Differential analysis were conducted in EdgeR. The significant genes were deducted by computing NB exact genewise tests with corrected p < 0.05.
P-values of differential expression were adjusted for multiple-hypothesis testing using False Discovery Rate (FDR) method.
Assembly: mm10
Supplementary files format and content: Data matrix was generated by RSEM

growth_protocol: B16F10  cell line was a kind gift of Gordon Freeman (Dana-Farber Cancer Institute). 4T1 cells were provided by Fred Miller (Wayne State University). Cells were cultured with Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS, VWR), 6 mM HEPES, 1.6 mM L-glutamine, 50 mM 2-mercaptoethanol, 100 U/ml penicillin G and 100 mg/ml streptomycin sulfate (Sigma-Aldrich). All cell lines were verified to be free of mycoplasma by PCR and were authenticated by morphology.

extract_protocol:
genomic DNA was isolated with Quick-DNA Microprep Kit (ZYMO RESEARCH).
12 groups were prepared for RNA-seq libraries using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific)

treatment_protocol: B16F10 and 4T1 cells (2x10^4/well in 24 well plates) were treated with 0.1 uM or 1 uM of DAC for 48 hours, respectively. Dead cells were removed with dead cell removal microbeads and live cells were used for RNAseq

value: DAC for 48 h


title: MCF10A_JUN_KO_ev, IgG, rep1


title: SKC2

value: siRNA-KRAS knockdown-control


title: 4T1 DAC replicate 2 [RNA-seq]


title: MCF10A_JUN_KO_ev, JUN, rep1


title: 4T1 DAC replicate 1 [RNA-seq]


title: SKC1

value: human liver carcinoma cells


title: PBMC RNA, ecf 1, 1st visit


title: PBMC RNA, control 12

value: 1 visit


title: iPSC-derived thyroid follicular cells (day 16) cultured with Retinoic Acid

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

data_processing:
The sample was processed using the standard Cellranger v.3 pipeline
Reads were mapped to GRCh38 supplemented with sequences for tdTomato reporter and lentiviral BFP
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCh38
Supplementary files format and content: the processed files are the standard output from the cellranger count pipeline: count matrices compressed in the HDF5  format

source_name: BU3 NGP8T

growth_protocol: Directed differentiation toward thyroid follicular cell progenitors, cultured with Retinoic Acid

extract_protocol:
Cells were resuspended in buffer at a concentration of 1000 cells/ul and captured using a 10X chromium instrument (10X Chromium, Pleasanton, CA), following standard Chromium 10x guidelines.
Libraries were prepared using a Chromium Single-Cell 3' v3 kit (10X Genomics) and loaded on a NovaSeq 6000 system (Illumina) aiming for sequencing depth of approximately 100,000 reads/cell

value: BU3 NGP8T

value: iPSC-derived thyroid follicular cell progenitor

value: culture medium with Retinoic Acid


title: 4T1 control replicate 3 [RNA-seq]


title: PBMC RNA, control 11

value: peripheral blood mononuclear cells


title: iPSC-derived thyroid follicular cells (day 16) cultured without Retinoic Acid

growth_protocol: Directed differentiation toward thyroid follicular cell progenitors, cultured without Retinoic Acid

value: culture medium without Retinoic Acid


title: 4T1 control replicate 2 [RNA-seq]


title: 10A_JUNoe_dox,TEAD1, replicate2

treatment_protocol: MCF10A cells expressing a doxycycline-inducible YAP5SA allele were infected with a JUN overexpression vector or an empty vector control. YAP induction was induced by doxycycline addition (100 ng/ml) and control cells were treated with solvent control (EtOH).

value: JUN overexpression

value: doxycycline


title: PBMC RNA, control 10


title: 10A_JUNoe_dox, YAP1, replicate2

value: breast epithelial


title: PBMC RNA, ecf 3, 1st visit


title: MDA-MB-231, NOb, Day 10, m6A

city: Chicago

first: Douglas

middle: D

last: Thomas

state: IL

address: 833 S. Wood Street, MC 781

institute: University of Illinois at Chicago

data_processing:
Basic assessment of Illumina output reads quality (FastQ) including GC bias were checked by FastQC (v0.11.9) program. Poor quality reads were eliminated before mapping based on default quality flag by Illumina pipeline in FastQ file. FastQC quality analysis results were summarized using MultiQC (v1.14)
Paired-end reads were mapped to human GRCh38 genome reference genome using TopHat (version: 2.1.1) and Bowtie (version 2.5.0.0). Identified average 150bp short reads were uniquely aligned allowing at best two mismatches, 0 splice-mismatches, with no-duplicates nor multimapping allowed (-N 2 -M -g 1).
Read depth and coverage were assessed using RseQC (version 2.6.4) tool.
Mapping quality, duplicate removal, and indexing were performed using samtools (version 1.13).
Normalized BedGraph and BigWig count files as well as read density plots were generates using deepTools (version 3.5.1).
Assembly: GRCh38
Supplementary files format and content: big wig file
Library strategy: meRIP-Seq

molecule: polyA RNA

source_name: breast

growth_protocol: MDA-MB-231 cells were cultured in Dulbecco's modified Eagle's medium (DMEM; Gibco) supplemented with 10% qualified fetal bovine serum (FBS; Gibco) and 1% penicillin/streptomycin (P/S; Gibco). All cells were cultured at 37°C in 5% CO2.

extract_protocol:
The m6A immunoprecipitation procedure was modified from previously reported methods (Dominissini 2013). mRNA was isolated following three rounds of NEB Magnetic mRNA Isolation (New England Biolabs) and treated with DNase I (Ambion) to avoid genomic DNA contaminations.
Libraries were prepared with KAPA RNA Hyper Prep kit (Roche).

treatment_protocol: For experiments studying chronic exposure to NO (10 days), cells were first plated with a density of 1.5x106 cells into 100 mm dishes. After 4h of cell adherence, 100 M of DETA/NO was added to the media and grown for 48h. At this time, cells were collected with trypsin (Gibco), pooled according to each replicate, counted, and re-plated at the same starting density of 1.5x106 cells into new 100mm dishes. This was repeated every 48 h for a total of 10 days of DETA/NO treatment.

value: breast

value: epithelial

value: DETA/NO


title: MDA-MB-231, NOb, Day 10, INP


title: 10A_JUNoe_etoh, IgG, replicate2

value: etoh


title: MDA-MB-231, NOa, Day 10, m6A


title: PBMC RNA, control 9


title: MDA-MB-231, NOa, Day 10, INP


title: PBMC RNA, control 7


title: PBMC RNA, control 8


title: PBMC RNA, ecf 2, 1st visit

value: electroconvulsive therapy

value: before treatment


title: 10A_JUNoe_dox, IgG, replicate2


title: 10A_JUNoe_etoh, YAP1, replicate2


title: 10A_JUNoe_etoh,TEAD1, replicate2


title: MDA-MB-231, Utb, Day 10, m6A

value: untreated


title: PBMC RNA, control 5


title: 4T1 control replicate 1 [RNA-seq]


title: 10A_ev_dox, JUN, replicate2

value: empty vector


title: PBMC RNA, control 6

value: 1 visit


title: MDA-MB-231, Uta, Day 10, m6A


title: 10A_ev_dox, IgG, replicate2


title: 10A_JUNoe_dox, JUN, replicate2


title: MDA-MB-231, Utb, Day 10, INP


title: 10A_ev_dox, YAP1, replicate2


title: 10A_JUNoe_etoh, JUN, replicate2


title: CONTROL4

city: Beijing

first: jinhua

last: jin

state: Beijing

address: 33 Ba-Da-Chu Road, Shi-Jing-Shan District

institute: Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample …

source_name: dorsal root ganglion cells

growth_protocol: Mice were killed under deep anesthesia with sevoflurane and placed under  ice and DRG were extraced with the aid of a microscope

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit following manufacturer's protocols.

value: dorsal root ganglion cells

value: female

value: Primary Cell

value: wt

value: untreated mice


title: CONTROL5


title: PBMC RNA, control 4

value: peripheral blood mononuclear cells


title: 10A_ev_dox,TEAD1, replicate2

value: doxycycline


title: MDA-MB-231, Uta, Day 10, INP


title: MDA-MB-231, NOa, Day 10, 2

data_processing:
Basic assessment of Illumina output reads quality (FastQ) including GC bias were checked by FastQC (v0.11.9) program. Poor quality reads were eliminated before mapping based on default quality flag by Illumina pipeline in FastQ file. FastQC quality analysis results were summarized using MultiQC (v1.14)
Single-end reads were mapped to human reference genome GRCh38 with TopHat (version 2.1.1) and Bowtie (version 2.5.0.0). Identified average 150bp short reads were uniquely aligned allowing at best two mismatches, 0 splice-mismatches and no-duplicates  (-N 2 -M -g 1). Sequences aligned to more than one location with equal quality were discarded to avoid bias.
EnsEMBL version 109 gene model was used for this process. Normalized BedGraph and BigWig count files, read density plots were generates using deepTools (version 3.5.1)
SubRead package featureCount (version 2.0.3) to calculate absolute read abundance for each transcript/gene associated with EnsEMBL (v109) genes of Homo sapiens.
For differential expression (DE) analysis, we used Bioconductor78 package DESeq2 (version 1.38.3) with R version 4.2.2 (2022-10-31)
Assembly: GRCh38
Supplementary files format and content: normalized big wig file

extract_protocol:
Total RNAs were isolated using the RNAqueous™-4PCR kit (Ambion) and treated with DNase I (Ambion) to avoid genomic DNA contaminations.
Libraries were prepared with KAPA RNA Hyper Prep kit (Roche).


title: PBMC RNA, control 3


title: CONTROL1


title: CONTROL3


title: CONTROL2


title: MDA-MB-231, Uta, Day 10, 3


title: Stromal cells, HC.6

city: Milan

first: Mattia

last: Chiesa

address: Via Parea 4

department: Bioinformatics and Artificial Intelligence facility

country: Italy

institute: Centro Cardiologico Monzino IRCCS

data_processing:
The Bismark tool was used to 1) align reads against the GRCh38 Human Genome reference (version 99), 2) identify the methylation sites and 3) assess the methyla-tion level.
Assembly: HG38/GRCh38.99
Supplementary files format and content: Tab-delimited text file includes raw counts values for each Sample. The header of the files reports Meth_Site and Sample identifiers.

source_name: cardiac mesenchymal stromal cells

growth_protocol: Cells were obtained through the digestion of endomyocardial biopsies and they were characterized as previously described. The culture medium for CMSC maintenance was Iscove’s Modified Dulbecco’s Medium (Thermo Fisher Scientific), supplemented with 20% Fetal Bovine Serum (EuroClone), 10 ng/mL basic fibroblast growth factor (Peprotech), 10,000 U/mL Penicillin (EuroClone), 10,000 µg/mL Streptomycin (EuroClone), and 0.02 M L-Glutamine (EuroClone). All the assays were performed on CMSC cultured in these conditions.

extract_protocol:
Patients' DNA was extracted 6 ACM and 6 control CMSC through QIAamp DNA Kit Mini (QIAGEN) following the recommended instructions.
Methylome analyses were performed by bisulfite conversion of DNA combined with next generation sequencing (NGS), using the Ovation Ultralow Methyl-Seq DR Multiplex system method (performed by GenomeScan, based on Agilent Technologies). Briefly, after sodium bisulfite treatment, unmethylated cytosines in single-stranded DNA were deaminated to give uracil while leaving methylated cytosine intact. Next, bisulfite-converted DNA were analyzed by NGS. The depth of sequencing necessary were obtained using the Illumina HiSeq4000 platform.

value: cardiac mesenchymal stromal cells

value: unknown

tag: Sex

value: M

tag: condition

value: Healthy Control


title: 10A_ev_etoh, IgG, replicate2

value: breast epithelial

value: etoh


title: MDA-MB-231, NOa, Day 10, 3

value: breast

value: epithelial

value: DETA/NO


title: PBMC RNA, control 2

value: 1 visit


title: 10A_ev_etoh, JUN, replicate2

value: empty vector


title: PBMC RNA, control 1


title: 10A_ev_etoh, YAP1, replicate2


title: MDA-MB-231, Uta, Day 10, 1

value: untreated


title: O4

value: dorsal root ganglion cells

value: female

value: Primary Cell

value: old mice


title: Stromal cells, HC.5


title: 10A_JUNoe_dox, IgG, replicate1

value: JUN overexpression

value: doxycycline


title: 10A_ev_etoh,TEAD1, replicate2


title: MDA-MB-231, NOa, Day 10, 1


title: MDA-MB-231, Uta, Day 10, 2


title: MDA-MB-468, NOa, Day 10, 3

data_processing:
Basic assessment of Illumina output reads quality (FastQ) including GC bias were checked by FastQC (v0.11.9) program. Poor quality reads were eliminated before mapping based on default quality flag by Illumina pipeline in FastQ file. FastQC quality analysis results were summarized using MultiQC (v1.14)
Single-end reads were mapped to human reference genome GRCh38 with TopHat (version 2.1.1) and Bowtie (version 2.5.0.0). Identified average 150bp short reads were uniquely aligned allowing at best two mismatches, 0 splice-mismatches and no-duplicates  (-N 2 -M -g 1). Sequences aligned to more than one location with equal quality were discarded to avoid bias.
EnsEMBL version 109 gene model was used for this process. Normalized BedGraph and BigWig count files, read density plots were generates using deepTools (version 3.5.1)
SubRead package featureCount (version 2.0.3) to calculate absolute read abundance for each transcript/gene associated with EnsEMBL (v109) genes of Homo sapiens.
For differential expression (DE) analysis, we used Bioconductor78 package DESeq2 (version 1.38.3) with R version 4.2.2 (2022-10-31)
Assembly: GRCh38
Supplementary files format and content: tab delimited txt file of normalized counts

growth_protocol: MDA-MB-468 cells were cultured in Dulbecco's modified Eagle's medium (DMEM; Gibco) supplemented with 10% qualified fetal bovine serum (FBS; Gibco) and 1% penicillin/streptomycin (P/S; Gibco). All cells were cultured at 37°C in 5% CO2.


title: 10A_JUNoe_dox, JUN, replicate1


title: Stromal cells, HC.4

value: cardiac mesenchymal stromal cells

value: unknown

value: F


title: O5

value: wt


title: Stromal cells, HC.3

value: M

value: Healthy Control


title: O2


title: Stromal cells, HC.2


title: Stromal cells, HC.1


title: MDA-MB-468, NOa, Day 10, 2

value: breast


title: 10A_JUNoe_dox,TEAD1, replicate1

value: breast epithelial


title: A_04

value: old mice+AEW treated


title: MDA-MB-468, NOa, Day 10, 1

value: DETA/NO


title: Stromal cells, ACM.5

value: ACM


title: MDA-MB-468, Uta, Day 10, 3

value: untreated


title: Stromal cells, ACM.6


title: A_01

value: dorsal root ganglion cells

value: female


title: A_02

value: Primary Cell


title: 10A_JUNoe_dox, YAP1, replicate1

value: JUN overexpression


title: Stromal cells, ACM.4


title: MDA-MB-468, Uta, Day 10, 2


title: H4

value: ovariectomized+placebo


title: H5

value: ovariectomized+estrogen


title: 10A_JUNoe_etoh, JUN, replicate1

value: etoh


title: H3


title: Stromal cells, ACM.3

value: cardiac mesenchymal stromal cells

value: F


title: 10A_ev_dox, IgG, replicate1

value: empty vector

value: doxycycline


title: Expression_aPR_4

city: shanghai

first: panpan

last: liu

address: No219,MiaoPU Road

institute: shanghai pudong new area gongli hospital

description:
FPKM_allsamples.txt
counts_allsamples.txt

data_processing:
Data preprocessing and genomic alignment
Transcript splicing、lncRNA prediction、and Gene quantification
Differential screening analysis and Functional Analysis
CircRNA prediction, Expression analysis and Interaction research,Gene structure optimization and New transcript prediction
Alternative splicing Analysis and SNP、INDEL Analysis
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: peripheral blood

extract_protocol:
A. Add 600 μL Lysis/Binding Buffer to the cell or tissue lysate. Then add 30 μL miRNA Homogenate Additive to homogenate, and mix well by vortexing or inverting the tube several times. Leave the mixture on ice for 10 min. B. Add a volume of Acid-Phenol: Chloroform that is equal to the lysate volume before addition of the miRNA Homogenate Additive. Centrifuge for 5 min at maximum speed (10,000 x g) to separate the aqueous and organic phases. Carefully remove the aqueous (upper) phase without disturbing the lower phase, and transfer it to a fresh tube. C. Add 1.25 volumes of room temperature 100% ethanol to the aqueous phase. D. Pipet the lysate/ethanol mixture (from the previous step) onto the Filter Cartridge (Note: Up to 700 μL can be applied to a Filter Cartridge at a time.). Centrifuge for 30 sec at 13,000 rpm to pass the mixture through the filter. Discard the flow-through. E. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube. F. The 10 μL DNase I and 70 μL Buffer RDD QIAGEN (#79254) were mixed. Then the mixture was added to the Filter Cartridge. Leave it at the room temperature for 15 minG. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at  13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into  5 the same Collection Tube. H. Apply 500 μL Wash Solution 2/3 and centrifuge for 30 sec at 13,000 rpm. Draw it through  the Filter Cartridge as in the previous step. Repeat with a second 500 μL aliquot of Wash Solution 2/3. I. Spin the assembly for 1 min to remove residual fluid from the filter. Transfer the Filter  Cartridge into a fresh Collection Tube. Apply 100 μL of pre-heated (95°C) Elution Solution to the  center of the filter. Leave it at the room temperature for 2 min. Spin for 20–30 sec at maximum speed  to recover the RNA. Collect the eluate (which contains the RNA) and store it at -70°C
RNA libraries for RNA-seq were prepared using smarter mTotal RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the  manufacturer’s protocol

value: peripheral blood

value: after 12weeks aerobic exercises


title: MDA-MB-468, Uta, Day 10, 1

value: breast


title: Expression_aPR_3


title: Stromal cells, ACM.2

value: M


title: 10A_JUNoe_etoh,TEAD1, replicate1

value: breast epithelial


title: Stromal cells, ACM.1

value: ACM


title: Expression_aPR_2


title: H2

value: dorsal root ganglion cells

value: wt


title: 10A_JUNoe_etoh, YAP1, replicate1


title: HC.6

data_processing:
Sequential aligning of raw reads was performed against the GRCh38 Human Genome reference (release 99) with the “Spliced Transcripts Alignment to a Reference” (STAR v. 2.7.5c) software, and with “Bowtie2” (v. 2.4.1) to align locally any reads not mapped by STAR. We excluded 'haplotypes' and 'patches' sequences from the reference, in order to focus on primary assembly and to avoid under-estimation of gene expression.
Gene expression quantification were computed by “featureCounts” (v.2.0.1) grouping meta-features by 'gene name'.
Assembly: HG38/GRCh38.99
Supplementary files format and content: Tab-delimited text files include raw counts values for each Sample. The header of the files reports gene name and sample identifiers.

extract_protocol:
We extracted total RNA of CMSC, using the total RNA purification kit (Norgen Biotek Corp.) and following the recom-mended protocol.
High-quality libraries were prepared using the PrepXTM RNA-Seq Library Kit for Illumina platforms.

value: unknown

value: Healthy Control


title: 10A_ev_dox, JUN, replicate1


title: H1

value: female

value: Primary Cell


title: 10A_JUNoe_etoh, IgG, replicate1

value: JUN overexpression

value: etoh


title: V4

value: ovariectomized+placebo


title: HC.5

value: cardiac mesenchymal stromal cells


title: Expression_aPR_1


title: Expression_bPR_4

value: NC


title: 10A_ev_dox, YAP1, replicate1

value: empty vector

value: doxycycline


title: 10A_ev_dox,TEAD1, replicate1


title: HC.4

value: F


title: V3


title: HC.3

value: M


title: V1


title: Expression_bPR_2

value: peripheral blood


title: Expression_bPR_3


title: 10A_ev_etoh, IgG, replicate1

value: breast epithelial


title: HC.2


title: A4

value: dorsal root ganglion cells

value: AEW  treated


title: 10A_ev_etoh, JUN, replicate1


title: Expression_bPR_1


title: HC.1

value: unknown


title: Hypertonic-1

city: WuHan

first: chenchao

last: yan

state: Hubei Province

address: Donghu Road, No. 115

institute: WuHan university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, the clean data were mapped to human genome (hg38) using HISAT2 (v2.1.0)
Raw reads were counted using FeatureCounts (v1.6.4)
Assembly: GRCh38

growth_protocol: human ESC lines, H9, were cultured in mTeSR1 medium (STEMCELL Technologies, #AB217641) on Matrigel-coated plates. The endoderm differentiation protocol of human ESCs was based on the previous reports. IMDM (Gibco, #C12440500BT) and F12 (Gibco, #C11765500BT) mixed at the ratio of 1:1 (IMDM/F12), was used as basal medium, supplemented with 0.2% BSA (YEASEN, #36106ES76), 1% B27 (without Vitamin A, Shanghai BasalMedia Technologies, S441J7), 1% penicillin-streptomycin and Activin A (100 ng/ml, PeproTech, #120-14P) was added for 4 days for endoderm differentiation. When indicated, 10μM Blebbistatin and 2% sucrose was added for 4 days for endoderm differentiation.

extract_protocol:
ThecellswerewashedbyDPBSandharvestedbybufferRL.TheHiPureTotalRNAMiniKit(Magen,Cat#R4111-03)wasusedtoextracttotalRNAfollowingthemanufacturer’sinstructionsandtheRNAwasquantitatedwithnanodrop2000(ThermoFisher).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: humandefinitiveendoderm

value: WT

value: 2% sucrose treated humandefinitiveendodermdifferentiation


title: A2

value: female

value: Primary Cell

value: wt


title: Hypertonic-2


title: ACM.6

value: cardiac mesenchymal stromal cells

value: ACM


title: 10A_ev_etoh,TEAD1, replicate1

value: empty vector

value: etoh


title: 10A YAP5SA, IgG,rep2

treatment_protocol: MCF10A cells overexpressing YAP 5SA were subjected to CU&RUN.

value: YAP5SA epxression


title: A1


title: Ble-hypertonic-2

value: 10uM Blebbistatin and 2% sucrose treated humandefinitiveendodermdifferentiation


title: ACM.4

value: M


title: 10A_ev_etoh, YAP1, replicate1

value: breast epithelial


title: ACM.5


title: Ble-hypertonic-1


title: 10A YAP5SA, cFOS,rep2


title: Cyp2e1 -/-, EtOH-fed, brain #1

city: Charleston

first: Je-Hyun

last: Yoon

state: SC

address: 173 Ashley Avenue BSB 512B, MSC 509

institute: Medical University of South Carolina

description: Circular RNA expression of Cyp2e1 KO mice upon EtOH treatment

data_processing:
Analyses were performed on two paired-ends samples.
Reads were mapped to the mouse genome (mm9) with Hisat2 (Ver. 2.2.1)
Transcripts were assembled by Stringtie (Ver. 2.2.0)
The expression profile was calculated for each sample and transcript/gene  as  a read  count  and  FPKM.
To analyze circular RNA expression, we profile mouse circular RNA junctions.
The raw data of total RNA-seq was filtered using the Trimmomatic trimmer tool (Ver. 0.32) to eliminate the 5’ and 3’ adaptor sequences
The resulting sequences were aligned to the mouse Reference Sequence (mm10) using the STAR aligner (Ver. 2.7.10a).
FKPM of the junction sequences was calculated using the DCC algorithm
Assembly: mm9, and mm10
Supplementary files format and content: FPKM

source_name: Brain

extract_protocol:
Each mouse was sacrificed for total RNA extraction and total RNA was isolated with Trizol reagent (Invitrogen).
Library was prpared using the TruSeq Stranded Total RNA kit with Ribo-Zero (Part#15031048 Rev. E) according to the standard protocol of Illumina sequencing.

value: Brain

tag: agent

value: Ethanol


title: ACM.3

value: F


title: Cyp2e1 -/-, EtOH-fed, brain #2


title: 10A YAP5SA, JUN,rep2


title: ACM.2


title: A3

value: dorsal root ganglion cells

value: AEW  treated


title: 10A YAP5SA, TEAD1,rep2


title: Isotonic-2

value: humandefinitiveendoderm

value: WT


title: ACM.1


title: Cyp2e1 -/-, pair-fed, brain #3

value: Maltose dextrin


title: 10A YAP5SA, YAP1,rep2


title: Isotonic-1


title: PACE_300

city: New York City

last: Muller

address: 550 First Avenue

department: Department of Medicine

institute: New York University

data_processing:
Fastq qualtiy assessed via FastQC 0.11.7
Sample contamination assessed via fastqscreen v0.13.0
Fastq files trimmed via Trimmomatic v0.36
Fastq files aligned to the HG38 human genome via STAR v2.7.3a
Reads counted via featurecounts v1.6.3
Assembly: hg38
Supplementary files format and content: Raw count table as a .txt file.

source_name: whole blood

extract_protocol:
18mLs of whole blood was drawn into 3.2% sodium citrate tubes (BD Vacutainer). Blood was centrifuged to obtain platelet rich plasma, and then depleted of leukocytes and RBCs using StemCell EasySep CD45 and RBC magnetic depletion kits. Purified platelets were pelleted and lysed with 500uL of Qiazol lysis buffer and stored at -80 until ready for RNA extraction. RNA extraction was done by utilizing Zymo Microprep kits (R2062), and stored again at -80 until ready for sequencing.
Sequencing libraries were barcoded and prepared using the Clontech SMART-Seq HT with Nxt HT kit (Takara Bio USA), and libraries sequenced single end on an Illumina NovaSeq 6000

value: whole blood

value: platelet

value: Male


title: Cyp2e1 +/+, EtOH-fed, brain #3

description:
Circular RNA expression of Cyp2e1 KO mice upon EtOH treatment
Total RNA expression of EtOH fed mice


title: Cyp2e1 +/+, EtOH-fed, brain #2


title: 10A YAP5SA, IgG, rep1


title: DMD-CD56neg_4V Day 25 post transduction n2

city: La Jolla

first: Jimmy

last: Massenet

state: CA

address: 10901 N Torrey Pines Rd, Building 12

institute: Sanford Burnham Prebys Medical Discovery Institute, Puri laboratory

data_processing:
The adapter sequences were trimmed using Cutadapt 2.6. Next, the reads were aligned to the reference hg38 genome using Bowtie 2 v2.3.4.1. The files were sorted and indexed with Samtools v1.10 and mitochondrial reads were removed. Peak calling was performed using MACS2 2.1.2 with the default q-value cut-off of 0.05 and keep-dup 1. Functional annotation of peaks was done with ChIPseeker 3.1.1.
Assembly: hg38

source_name: muscle

growth_protocol: Primary cells were cultured in growth medium, which includes Skeletal Muscle Cell Growth Medium (Promocell #C23260) containing skeletal muscle supplemental mix (Promocell #C39365), 10% of Fetal Bovine Serum (FBS) (Abcys #S1810-500), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco #15140).

extract_protocol:
The ATAC-seq libraries were generated using 50,000 cells from two technical replicates of 1 DMD sample. The samples were used as detailed in (Corces et al. 2017). In brief, nuclei were isolated and were incubated with a transposase solution (with a final concentration of transposase buffer 1X, 100 nM of transposase, 0.01% of digitonin, 0.1% of Tween-20 and PBS 0.33X) and incubated in a thermomixer with shaking at 1000 rpm for 30 min at 37°C. The mixture was cleaned using DNA Clean & Concentrator-TM-5 kit (Zymo #D4003).
Transpose DNA was amplified by 12 cycles of PCR using SureSelectQXT Library Prep for WGS (Agilent #9684). The library quality and fragment size were quantified using an Agilent bioanalyzer 2100 before to be sequenced on Illumina HiSeq 4000 platform with paired-end sequencing.

treatment_protocol: Cells were seeded at 3,000 cells per cm2 in 6-well plates in growth medium and 6 h later, medium was replaced by growth medium supplemented with 6 µg/ml polybren and shControl or the 4 shCBX3, shH2AZ2, shH3F3B and shSMC3 together to a final MOI of 1. After 36 h, medium was replaced by selection medium (growth medium containing 1 µg/ml puromycin). After 3 days of puromycin selection, MuSCs were cultured in growth medium for 5-10 divisions for further analysis.

value: muscle

value: Primary fibroblasts

value: DMD


title: 10A YAP5SA, cFOS, rep1

value: YAP5SA epxression


title: PACE_293

value: Female


title: PACE_295


title: DMD-CD56pos_4V Day 25 post transduction n2

value: Primary myoblasts


title: Cyp2e1 +/+, pair-fed, brain #3

value: Brain


title: DMD-CD56neg_4V Day 25 post transduction n1


title: 10A YAP5SA, JUN, rep1

value: breast epithelial


title: Cyp2e1 +/+, pair-fed, brain #2


title: PACE_289


title: PACE_284


title: Cyp2e1 +/+, pair-fed, brain #1


title: DMD-CD56neg_empty Day 25 post transduction n2


title: DMD-CD56pos_4V Day 25 post transduction n1


title: PACE_282


title: 10A YAP5SA, YAP1, rep1


title: DMD-CD56pos_empty Day 25 post transduction n2


title: 10A_JUNoe_etoh, IgG, rep2

value: JUN overexpression

value: etoh


title: Cyp2e1 +/+, EtOH-fed, brain #1

value: Ethanol


title: DMD-CD56neg_empty Day 25 post transduction n1


title: Cyp2e1 -/-, EtOH-fed, liver #1

source_name: Liver

value: Liver


title: PACE_279


title: Cyp2e1 -/-, EtOH-fed, liver #2


title: 10A_JUNoe_etoh, ARID1A, rep2


title: PACE_275


title: Cyp2e1 -/-, pair-fed, liver #3


title: Cyp2e1 -/-, pair-fed, liver #2


title: DMD-CD56pos_empty Day 25 post transduction n1


title: DMD-4V Day 20 post transduction n2

value: shCBX3, H2AZ2, H3F3B,SMC3_20Days


title: 10A_JUNoe_etoh, NCOR1, rep2


title: PACE_263


title: 10A_JUNoe_etoh, cFOS, rep2


title: DMD-4V Day 20 post transduction n1


title: 10A YAP5SA, TEAD1, rep1


title: Cyp2e1 +/+, EtOH-fed, liver #2

value: WT


title: PACE_246

value: whole blood


title: DMD-Empty Day 20 post transduction n1


title: 10A_JUNoe_etoh, YAP1, rep2


title: PACE_241

value: platelet


title: Cyp2e1 +/+, EtOH-fed, liver #1


title: Cyp2e1 -/-, pair-fed, liver #1

value: Maltose dextrin


title: DMD-4V Day 15 post transduction n2

value: muscle

value: shCBX3, H2AZ2, H3F3B,SMC3_15Days


title: Cyp2e1 +/+, pair-fed, liver #3


title: 10A_ev_dox, ARID1A, rep2

value: empty vector

value: doxycycline


title: PACE_269

value: Female


title: PACE_236

value: Male


title: Cyp2e1 +/+, pair-fed, liver #2


title: PACE_235


title: DMD-4V Day 15 post transduction n1

value: Primary myoblasts

value: Primary fibroblasts

value: DMD


title: 10A_ev_dox, NCOR1, rep2

value: breast epithelial


title: DMD-Empty Day 15 post transduction n2


title: 10A_ev_dox, cFOS, rep2


title: PACE_230


title: 10A_JUNoe_etoh, JUN, rep2

value: JUN overexpression

value: etoh


title: Cyp2e1 -/-, EtOH-fed, intestine #2

source_name: Intestine

value: Intestine

value: Ethanol


title: DMD-Empty Day 15 post transduction n1


title: PACE_248

value: whole blood


title: 10A_ev_dox, JUN, rep2


title: DMD-Empty Day 20 post transduction n2


title: DMD-CD56pos Day 0 n2

value: Control


title: Cyp2e1 -/-, EtOH-fed, intestine #1


title: 10A_ev_dox, IgG, rep2


title: 10A_ev_dox, YAP1, rep2


title: DMD-CD56pos Day 0 n1


title: PACE_212

value: platelet


title: 10A_ev_etoh, IgG, rep2


title: PACE_211


title: Cyp2e1 -/-, pair-fed, intestine #2

value: Maltose dextrin


title: SGBS adipocytes day 8, miR-27a-5p mimic transfected #2

city: Ulm

first: Julian

last: Roos

department: Department of Pediatrics and Adolescent Medicine

institute: Ulm University Medical Center

data_processing:
analysis was performed by the Core Unit Bioinformatics and Datamanagement of Ulm University
Assembly: hg38
Supplementary files format and content: .csv, ensembl_gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, normalized read counts, ensembl_gene_id_version, refseq_ids, hgnc_symbols

source_name: cell strain

growth_protocol: The preadipocyte cell strains Simpson-Golabi-Behmel syndrome (SGBS) was cultured as described [Wabitsch M, Brenner RE, Melzner I, Braun M, Möller P, Heinze E, et al. Characterization of a human preadipocyte cell strain with high capacity for adipose differentiation. Int J Obes [Internet]. 2001 Jan [cited 2018 Aug 1];25(1):8–15. Available from: http://www.ncbi.nlm.nih.gov/pubmed/11244452].

extract_protocol:
Total RNA was isolated with Direct-zol RNA mini Prep Kit (Zymo Research, Freiburg im Breisgau, Germany) according to the manufacturer’s protocol after cells were harvested with Tri-Reagent (Zymo Research)).
performed by Eurofins Genomics

treatment_protocol: To study the effect of miR-27a-3p/-3p on SGBS or hMADS cells, they were either transfected with 20 nM miR-27a-5p mimic (Syn-hsa-miR-27a-5p, Qiagen, Hilden, Germany), miR-27a-3p mimic (Syn-hsa-miR-27a-3p, Qiagen) or non-target control (AllStars Negative Control siRNA, Qiagen) mixed with 0.66 μl/cm2 Lipofectamine 2000 (Thermo Fisher Scientific, Germering, Germany) according to the manufacturer’s protocol. Adipogenesis was induced using an adipogenic induction cocktail containing FBS-free DMEM-F12 (Thermo Fisher Scientific, Germering, Germany) supplemented with 10 μg/ml transferrin, 20 nM insulin, 100 nM cortisol, 200 pM T3, 25 nM dexamethasone, 250 μM IBMX and 2 μM rosiglitazone (all from Sigma-Aldrich, Taufkirchen, Germany) as described (2). On day 4, medium was changed into FBS-free DMEM-F12 supplemented with 10 μg/ml transferrin, 20 nM insulin, 100 nM cortisol, 200 pM T3.

value: cell strain

value: Simpson Golabi Behmel Syndrome (SGBS) cell strain

value: adipocyte

value: miR-27a-5p mimic transfected


title: Cyp2e1 -/-, pair-fed, intestine #3


title: Cyp2e1 +/+, pair-fed, liver #1

value: Liver

value: WT


title: PACE_199

value: Male


title: PACE_202


title: SGBS adipocytes day 8, miR-27a-5p mimic transfected #3


title: Cyp2e1 +/+, EtOH-fed, intestine #3


title: 10A_ev_etoh, ARID1A, rep2

value: empty vector


title: SGBS adipocytes day 8, control (NT) transfected #3

value: control


title: SGBS adipocytes day 8, miR-27a-5p mimic transfected #1


title: SGBS adipocytes day 8, control (NT) transfected #2


title: PACE_188


title: 10A_ev_etoh, JUN, rep2

value: breast epithelial


title: 10A_ev_etoh, cFOS, rep2

value: etoh


title: 10A_ev_etoh, YAP1, rep2


title: Cyp2e1 +/+, EtOH-fed, intestine #1

value: Intestine


title: PACE_227


title: Cyp2e1 +/+, pair-fed, intestine #3


title: PACE_187


title: SGBS adipocytes day 8, control (NT) transfected #1


title: 10A_JUNoe_etoh, IgG, rep1

value: JUN overexpression


title: Cyp2e1 +/+, pair-fed, intestine #2


title: PACE_186

value: whole blood


title: Cyp2e1 -/-, pair-fed, intestine #1


title: VCaPaa_2

city: Göttingen

first: Oliver

last: Hahn

address: Robert-Koch-Str. 40

department: Department of Urology

institute: University Medical Center Göttingen

data_processing:
Base calling was done using the BaseCaller to bcl files function in the Illumina software.
De-multiplexing was done using bcl2fastq (version 2.17.1.14).
Fastq files were then mapped to the human transcriptome (UCSC HG19) using TopHat2 (version 2.1.0) with very sensitive Bowtie2 settings
Differential gene expression was assessed with the Cuffdiff function of the Cufflinks package (version 2.2.1).
Genome_build: hg19
Supplementary_files_format_and_content: Normalized abundance measurements resulting from cuffdiff analysis of VCaP samples vs. VCaPrev samples

source_name: prostate cancer

growth_protocol: Cells were cultured in phenol-red free DMEM with 10% fetal bovine serum (both Sigma Aldrich, Taufkirchen, Germany), 1% L-Glutamine and 2% Sodium-Pyruvate (both Gibco, Thermo Fisher Scientific, Waltham, USA). For the experiments, cells were kept under 35 passages and confluence was kept under 80%.

extract_protocol:
Total RNA was extracted using Trizol extraction and quantified with a Qubit 3 fluorometer. RNA quality was checked on a 1.5% agarose gel. 1 µg of total RNA was then used for library preparation.
Library preparation was done with a total amount of 1 µg RNA per sample using the TruSeq RNA Library Prep Kit v2 (Illumina Inc., San Diego, CA, USA). Size range was verified to be around 280 bp using BioAnalyzer 2100 (Agilent Technologies. Santa Clara, CA, USA). Sequencing was done at the NGS core facility (NIG) at the University Medical Center Göttingen on an Illumina HiSeq 4000 platform

treatment_protocol: VCaP AA cells were kept with 5 µmol/l abiraterone acetate over 20 passages. Control cells were grown in normal DMEM media.

value: VCaP

value: 5 uM abiraterone

tag: disease

value: prostate cancer


title: 10A_ev_etoh, NCOR1, rep2

data_processing:
Adapter removal and quality trimming was performed by Cutadapt. Since the carry-over DNA of pAG-MNase purification from E. coli was used as spike-in control, mapping was performed to hg19 and a human repeat-masked E. coli genome by Bowtie2. Paired-end reads mapped to hg19 with inserts <120 bp were extracted using alignment Sieve (deepTools). A scaling factor was inferred by: scaling factor= (mapped reads < 120 bp to hg19)⁄(mapped reads to E.coli).
The scaling factor was used to generate spike-in normalized bigWig files by bamCoverage (deepTools).
Assembly: hg19
Library strategy: CUT&RUN


title: Cyp2e1 +/+, pair-fed, intestine #1

value: Maltose dextrin


title: 10A_JUNoe_etoh, ARID1A, rep1


title: 10A_JUNoe_etoh, NCOR1, rep1


title: PACE_193

value: platelet


title: VCaPaa_1


title: bone, Het_HOM_F, rep3 (L002)

city: Clayton

first: Patrick

middle: S

last: Western

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

country: Australia

institute: Hudson Institute of Medical Research

description:
bone_growth_plate_reference_gene_raw_count.txt
2243_2_S6_L002

data_processing:
For oocyte dataset, adaptor and low quality sequences of raw sequencing reads were trimmed using AdaptorRemovel (v2.2.1) with following parameters: --trimns --trimqualities --minquality 20 --minlength 35. For bone growth plate and placenta datasets, adaptor and low quality sequences of raw reads were trimmed using trimmomatic (v0.39) with following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20.
Clean reads were mapped to mouse reference genome (GRCm38) using either STAR (v2.5.3a) for oocyte dataset with default settings, or STAR (v2.7.5c) for bone growth plate and placenta datasets with following settings: --outFilterMismatchNoverLmax 0.03 --alignIntronMax 10000.
For oocyte dataset, raw counts for mouse reference genes (ensembl-release-93) were calculated using featureCounts (v1.5.2) based on mapped bam files with following parameters: -Q 10 -s 2. For bone growth plate and placenta datasets, raw counts for mouse reference genes (ensembl-release-101) were calculated using STAR (v2.7.5c) with parameter "--quantMode GeneCounts" whening doing genome alignment.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text file including raw reads counts for mouse reference genes in all samples

source_name: bone Het HOM F

growth_protocol: For oocyte sample collection, wild type and Eed deleted oocytes grown in vivo in C57bl6 mice. Eedfl/fl mice were crossed with ZP3Cre transgenic mice, facilitating oocyte specific deletion from the primary follicle oocyte stage. For production of placental and bone growth plate samples, females producing wild type (Eedfl/fl), heterozygous (Eedwt/del) of homozygous (Eeddel/del) oocytes were mated to isogenic wild type C57bl6 males to produce wild type or heterozygous offspring from oocytes that developed with wild type, heterozygous or homozygous null EED function. These offspring were produced from females producing Eed-wt, Eed-het or Eed-hom oocytes to generate wild type or heterozygous offspring as previously described by Prokopuk, L. et al. Clinical Epigenetics 10, 95 (2018). Heterozygous offspring generated from Eed heterozygous oocytes (HET-het offspring) or from Eed homozygous null oocytes (HET-hom offspring) are isogenic. However, the HET-hom offspring were generated from oocytes that completely lacked functional EED. In contrast, the HET-het offspring were generated from oocytes that had one functional copy of EED. As they are isogenic and heterozygous, comparison of HET-hom with HET-het offspring allowed the identification of differences that resulted from a loss of EED-dependent oocyte programming in the absence of confounding genetic differences. In addition, wild type offspring generated from Eed-het and Eed-wt oocytes allowing the comparison of WT-wt and WT-het offspring with HET-het and HET-hom offspring. This provided controls for differences generated as a result of Eed heterozygosity in offspring. The mouse lines used were obtained from the following sources: Zp3Cre mice (C57BL/6-Tg 93knw/J; Jackson Labs line 003651, constructed and shared by Prof Barabara Knowles), Eed floxed mice (Eedfl/fl) (B6; 129S1-Eedtm1Sho/J; Jackson Labs line 0022727; constructed and shared by Xie, H. et al. Cell Stem Cell 14, 68-80 (2014). The Eed line was backcrossed to a pure C57BL6/J and shared with us by Associate Professor Rhys Allen and Professor Marnie Blewitt, Walter and Eliza Hall Institute for Medical Research, Melbourne. All subsequent breeding and oocyte collection was performed by the authors at the Hudson Institute of Medical Research / Monash Medical Centre, Clayton, Victoria, Australia. Mice were housed at Monash Medical Centre Animal Facility using a 12-hour light-dark cycle as previously reported by Prokopuk, L. et al. Clinical Epigenetics 10, 95 (2018). Food and water were available ad libitum with room temperature maintained at 21-23°C with controlled humidity. All animal work was undertaken in accordance with Monash University Animal Ethics Committee (AEC) approvals.

extract_protocol:
Oocytes: Cumulus-Oocyte Complexes (COCs) were collected from eight-twelve week old female mice and transferred to M2 media. Oocytes were denuded mechanically with a narrow-bore glass pipette and incubated with M2 media containing 5 μg/mL Hoechst 33342 for 10 minutes at 37°C. GV oocytes were then scored as either surrounded nucleolus (SN), or non-surrounded nucleolus (NSN) based on Hoechst staining. SN oocytes were then collected, frozen on dry ice and stored at -80°C until RNA extraction. Ten to fifteen oocytes isolated from each female were pooled and total RNA isolated using the Agencourt RNAdvance Cell V2 extraction kit. High quality RNA (RIN >7.5) was used for library preparation (>1.2ng total RNA) using the Nugen Trio Library protocol, MU01440V2; 2017. 75bp single end sequencing was carried out on 4-6 libraries / genotype using Illumina NextSeq500 High output mode and v2.5 chemistry (Illumina Protocol 15046563 v02, Mar 2016) to collect >25M reads per sample. Bone growth plate tissue was isolated at E17.5 and snap frozen as described in the associated manuscript (Jarred et al. In prep). Femoral growth plates were isolated from E17.5 offspring and growth plates were extracted from the distal end on both the left and right femurs, washed in PBS, digested in 3mg/ml collagenase for 15 min at 37°C in a 5% CO2 incubator. Growth plates were then washed in PBS, agitated in 0.5mg/ml collagenase in PBS to remove soft tissue, washed in PBS, frozen on dry ice and stored at -80°C. Placentas were isolated at E17.5, weighed and bisected. Half of the placenta was rinsed in PBS, snap-frozen on dry ice and stored at -80°C for RNA analysis. Growth plate and placental RNA was extracted from 4-5 samples / genotype using NucleoSpin RNA XS (bone growth plate) or NucleoSpin RNA Plus columns (Placenta). RNA quality was assessed on an Agilent Bioanalyzer and samples with RIN >7.5 used for library preparation and sequencing either on the Illumina NovaSeq 6000 S1 collecting >25M 150b PE reads (bone growth plates; Ramaciotti Centre for Genomics) or on the BGI Genomics platform (placentae, BGI Genomics, Hong Kong).
Oocyte libraries were constructed using Nugen Trio Library prep using protocol M01440v2; 2017 followed by 75bp SR sequencing using Illumina NextSeq500 High output mode and v2.5 chemistry. Illumina Protocol 15046563 v02, Mar 2016. Bone Growth Plate libraries were constructed using Illumina RNAseq chemistry followed by sequencing on an Illumina NovaSeq 6000 S1 2x150bp flowcell (Ramaciotti Centre for Genomics). Placental libraries were constructed using the BGI DNBseq protocol followed by 150bp PE sequencing on the BGI DNBSeq Eukaryotic Transcriptome Resequencing platform (Beijing Genomics)

treatment_protocol: Refer to growth protocol for mouse strain information. Mice were crossed to produce genotypes described for each sample.

value: bone growth plate

value: E17.5 Left and right distal femural growth plates

tag: strain

value: Eed.fl.Zp3Cre on C57BL/6 background


title: PACE_185


title: PACE_184

value: Female


title: PACE_178


title: 10A_JUNoe_etoh, cFOS, rep1

extract_protocol:
CUT and RUN experiments were performed as described previously (Kim et al., Nat. Commun., 2022). Briefly, for each CUT and RUN reaction 200,000 cells were trypsinized, washed, resuspended in 100 µl wash buffer (20 mM HEPES, pH7.5, 150 mM NaCl, 0.5 mM Spermidine) and bound to 10 µl activated BioMag®Plus Concanavalin A magnetic beads (Polysciences) for 10 min at room temperature. The cells were then incubated with antibodies diluted in 100 µl antibody buffer (wash buffer + 0.01% digitonine and 2 mM EDTA) overnight at 4°C. IgG rabbit antibody was used as negative control. After incubation with antibodies, the beads were washed in digitonin wash buffer (wash buffer + 0.01% digitonin) and incubated 1h at 4°C with 1 µg/ml protein A/G Micrococcal Nuclease fusion protein (pA/G MNase). After washing with digitonin wash buffer, beads were rinsed with low salt buffer (20 mM HEPES, pH7.5, 0.5 mM Spermidine, 0.01% digitonine), resuspended in 200 µl incubation buffer (20 mM HEPES, pH7.5, 10 mM CaCl2, 0.01% digitonin) and placed at 0°C to initiate cleavage. After 30 min, reactions were stopped by adding 200 µl STOP buffer (170 mM NaCl, 20 mM EGTA, 0.01% digitonin, 50 µg/ml RNAse A) and the samples were incubated 30 min at 37°C to digest the RNA and release the DNA fragments. The samples were then treated with proteinase K for 1 h at 50°C and the DNA was purified using Phenol/Chloroform/Isoamyl alcohol. After precipitation with glycogen and Ethanol, the DNA pellet was resuspended in 0.1 X TE and used for library preparation.
For DNA library generation, the NEBNext®Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs) was used. Adaptor ligation was performed with 1:25 diluted adaptor and 15 cycles were used for library amplification using dual indices (NEB dual index kit). Paired-end 2x25 bp sequencing was performed.


title: PACE_176

value: Male


title: 10A_JUNoe_etoh, JUN, rep1


title: bone, Het_HOM_F, rep2 (L002)

description:
bone_growth_plate_reference_gene_raw_count.txt
2243_1_S24_L002


title: bone, Het_HOM_F, rep1 (L002)

description:
bone_growth_plate_reference_gene_raw_count.txt
2216_1_S19_L002


title: M2c Macrophages, donor 3, TAFA4-treated

city: Marseille

first: Bertrand

last: Escaliere

address: 163 avenue de Luminy

country: France

institute: CIML

description: tableCount.csv

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment was performed using STAR 2.5.3a
Count table was generated using featureCounts v1.6.0 on GRCh38.98 gtf
Genome_build: hg38

source_name: monocyte-derived macrophages

growth_protocol: Monocytes were isolated from peripheral blood of three independant donors and generated different polarisations. Monocytes were cultured with M-CSF for six days to induce their differentiation in macrophages (Mφ).

extract_protocol:
Total RNA was then extracted with the RNeasy Plus Micro Kit (Qiagen) and stored at -80°C until use
Full length cDNA were generated from 5 ng of total RNA  using Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 9 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, CA) followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

treatment_protocol: On day six, the cells were left untreated or were treated for two days with specific factors to induce their polarization. Untreated cells remained M0 Mφ, whereas cells treated with dexamethasone polarized into M2c Mφ. During the two days of polarization, cells were TAFA4-treated or left untreated.

tag: polarization

value: Yes

tag: donor


title: VCaP_2_control

value: control media


title: M2c Macrophages, donor 2, TAFA4-treated

description: tableCount.csv


title: 10A_JUNoe_etoh, YAP1, rep1

value: breast epithelial


title: PACE_170

tag: tissue

tag: age


title: 10A_ev_dox, IgG, rep1

tag: treatment

value: empty vector

value: doxycycline


title: PACE_167


title: bone, Het_HOM_F, rep4 (L002)

description:
bone_growth_plate_reference_gene_raw_count.txt
2185_1_S3_L002


title: PACE_165


title: M2c Macrophages, donor 1, TAFA4-treated

description: tableCount.csv


title: bone, Het_HET_F, rep3 (L002)

description:
bone_growth_plate_reference_gene_raw_count.txt
2167_8_S18_L002

source_name: bone Het HET F


title: bone, Het_HET_F, rep2 (L002)

description:
bone_growth_plate_reference_gene_raw_count.txt
2178_3_S12_L002


title: 10A_ev_dox, ARID1A, rep1


title: 10A_ev_dox, NCOR1, rep1


title: VCaP_1_control


title: bone, Het_HET_F, rep4 (L002)

description:
bone_growth_plate_reference_gene_raw_count.txt
2221_4_S14_L002


title: 10A_ev_dox, cFOS, rep1


title: M2c Macrophages, donor 3

description: tableCount.csv

value: No


title: bone, Het_HET_F, rep1 (L002)

description:
bone_growth_plate_reference_gene_raw_count.txt
2178_2_S15_L002


title: M2c Macrophages, donor 1

description: tableCount.csv


title: PACE_161

value: whole blood


title: 10A_ev_dox, JUN, rep1


title: PACE_157


title: M2c Macrophages, donor 2

description: tableCount.csv


title: bone, Wt_WT_F, rep2 (L002)

description:
bone_growth_plate_reference_gene_raw_count.txt
2220_4_S8_L002

source_name: bone Wt WT F

value: Eedfl/fl


title: PACE_155


title: 10A_ev_etoh, IgG, rep1

value: etoh


title: M0 Macrophages, donor 3

description: tableCount.csv


title: M0 Macrophages, donor 1

description: tableCount.csv


title: 10A_ev_dox, YAP1, rep1


title: PACE_156


title: bone, Wt_WT_F, rep3 (L002)

description:
bone_growth_plate_reference_gene_raw_count.txt
2220_5_S10_L002


title: KLE_A2

city: Wuhan

first: Fang

last: Fang

address: 1277 Jiefang Avenue

department: Department of Obstetrics and Gynecology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
The raw reads were filtered with SOAPnuke (v1.5.2) to remove sequencing adaptor and low-quality reads.
The clean reads were mapped to reference genome using Bowtie2 (v2.2.5).
The expression levels of genes were calculated by RSEM (v1.2.12).
Genome_build: GCF_000001405.38_GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Endometrial carcinoma

growth_protocol: Human endometrial carcinoma cell lines, AN3CA and KLE, were purchased from the China Center for Type Culture Collection (Wuhan, China). AN3CA cells were maintained in MEM medium (Life Technologies, Grand Island, NY, USA) supplemented with 10% (v/v) fetal bovine serum (Life Technologies, Grand Island, NY, USA) while KLE cells were cultured in DMEM/F12 medium supplemented with 10% (v/v) fetal bovine serum (Life Technologies, Grand Island, NY, USA). All cell lines were incubated at 37 °C with 5% CO2 in a humidified atmosphere.

extract_protocol:
Total RNA was extracted from the cultured cells using Trizol (Invitrogen, Carlsbad, CA, USA) according to manufacturer’s instructions.
The cDNA libraries were established using the TruSeq® RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) according to Illumina’s instructions.

treatment_protocol: Cells were seeded in 6-well plates and cultured in serum free medium for 24 h to synchronize populations into G0. The next day, the medium was replaced with complete media containing 10% FBS and the cells were treated with Apcin (0 and 75 μM) for 72 h.

value: KLE

value: Apcin


title: 10A_ev_etoh, NCOR1, rep1

last: von Eyss

institute: Leibniz Institute on Aging


title: PACE_154

first: Matthew

value: platelet


title: PACE_149


title: bone, Wt_WT_F, rep1 (L002)

description:
bone_growth_plate_reference_gene_raw_count.txt
2123_1_S1_L002

value: bone growth plate


title: 10A_ev_etoh, cFOS, rep1

first: Bjoern


title: 10A_ev_etoh, ARID1A, rep1


title: KLE_2

value: Control


title: bone, Het_HOM_F, rep2 (L001)

description:
bone_growth_plate_reference_gene_raw_count.txt
2243_1_S24_L001

value: E17.5 Left and right distal femural growth plates

value: Eed.fl.Zp3Cre on C57BL/6 background


title: bone, Het_HOM_F, rep4 (L001)

description:
bone_growth_plate_reference_gene_raw_count.txt
2185_1_S3_L001


title: M0 Macrophages, donor 2

description: tableCount.csv


title: bone, Wt_WT_F, rep4 (L002)

description:
bone_growth_plate_reference_gene_raw_count.txt
2229_2_S23_L002


title: 10A_ev_etoh, JUN, rep1


title: PACE_147

value: Male


title: bone, Het_HOM_F, rep1 (L001)

description:
bone_growth_plate_reference_gene_raw_count.txt
2216_1_S19_L001


title: PACE_136


title: bone, Het_HET_F, rep4 (L001)

description:
bone_growth_plate_reference_gene_raw_count.txt
2221_4_S14_L001


title: PACE_129


title: bone, Het_HET_F, rep3 (L001)

description:
bone_growth_plate_reference_gene_raw_count.txt
2167_8_S18_L001


title: AN3CA_A2


title: AN3CA_A1


title: MDA-MB231 cells, Capsule 3

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

data_processing:
RNA-seq libraries were prepared using Illumina’s TruSeq protocol and were sequenced on an Illumina NextSeq 500. Reads were aligned to the hg38 genome using Rsubread v1.5.3. Gene counts were quantified by Entrez Gene IDs using featureCounts and Rsubread’s built-in annotation. Gene symbols were provided by NCBI gene annotation. Genes with count-per-million above 0.5 in at least 3 samples were kept in the analysis. Differential expression analysis was performed using limma-voom
Assembly: hg38
Supplementary files format and content: CSV files containing read counts values for each Sample

growth_protocol: MDA cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol extraction method
RNA-seq libraries were prepared using Illumina’s TruSeq protocol

treatment_protocol: liquid overlay + 5% matrigel following trastuzumab treatment, 96 hours incubation prior to rna extraction

value: epithelium

value: WT


title: MDA-MB231 cells, Capsule 2

value: 5% matrigel following trastuzumab treatment, 96 hours incubation prior to rna extraction


title: PACE_128

value: Female


title: KLE_A1


title: bone, Het_HOM_F, rep3 (L001)

description:
bone_growth_plate_reference_gene_raw_count.txt
2243_2_S6_L001


title: bone, Het_HET_F, rep2 (L001)

description:
bone_growth_plate_reference_gene_raw_count.txt
2178_3_S12_L001


title: PACE_127


title: 10A_ev_etoh, YAP1, rep1

city: Jena

address: Beutenbergstr. 11

growth_protocol: MCF10A cells  were cultured in DMEM/F12 (Thermo Fisher Scientific) supplemented with 5 % horse serum (Thermo Fisher Scientific), 1 % penicillin-streptomycin (Sigma-Aldrich), 10 µg/ml human insulin (Sigma-Aldrich), 0.5 µg/ml hydrocortisone (Sigma-Aldrich), 0.1 µg/ml cholera toxin (Sigma-Aldrich) and 20 ng/ml human EGF (Biomol).

value: breast epithelial

value: empty vector


title: bone, Het_HET_F, rep1 (L001)

description:
bone_growth_plate_reference_gene_raw_count.txt
2178_2_S15_L001


title: PACE_145

value: whole blood


title: AN3CA_2


title: KLE_1


title: MDA-MB231 cells, Capsule 1


title: PACE_138


title: MDA-MB231 cells, liquid overlay spheroid large 3


title: PACE_125


title: bone, Wt_WT_F, rep4 (L001)

description:
bone_growth_plate_reference_gene_raw_count.txt
2229_2_S23_L001

value: Eedfl/fl


title: PACE_121


title: bone, Wt_WT_F, rep3 (L001)

description:
bone_growth_plate_reference_gene_raw_count.txt
2220_5_S10_L001


title: MDA-MB231 cells, liquid overlay spheroid large 1


title: MDA-MB231 cells, liquid overlay spheroid large 2


title: PACE_119


title: A14_non-respond

city: Guangzhou

first: jiang

last: li

address: 651 Dongfeng East Road, Yuexiu District, Guangzhou

institute: Sun yat-sen university

data_processing:
The gene expression data was mapped to human genome reference sequence (GRCh38) using the programe PISA. Then the gene expression matrices for 4 TIL samples were combined in R software (version 4.0.3) and analyzed using the R package Seurat (version 4.0.0).Doublets were removed predicted by the R package DoubletFinder, with an expected doublet rate of 0.04 and other default parameters. Quality filtering was performed to remove cells with < 300 expressed genes or > 10% of detected genes linked to mitochondrial genes. The processed gene expression matrix with remaining cells was fed to the R package Seurat for downstream analyses. Firstly, the gene expression matrix was log normalized by using ‘NormalizeData’ function and generated with linear regression by using ‘ScaleData” function of the R package Seurat. Then, top 2000 variable genes were identified by suing ‘FindVariableFeatures’ function of the R package Seurat. Next, we clustered and visualized the cells using a graph-based clustering approach.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files containing gene/barcode matrices for each Sample

source_name: TIL infusion product

growth_protocol: Fresh tumor tissue from the nasopharyngeal biopsy specimens obtained before treatment will be collected and placed in 15- or 50-mL sterile test tubes containing 10 mL serum-free RPMI1640. After cutting the tumor tissue under normal working conditions at a clean bench, the tumor tissue will be digested with serum-free RPMI1640 and type IV collagenase (0.1 mg/ml) at 37°C for 2–3 hours (depending on the size of the tumor).After digestion, centrifugation, and discarding of the supernatant, the cell sediment will be washed 1–2 times with serum-free RPMI1640. The cells will be suspended in VIVO supplemented with 500 IU/mL recombinant human interleukin-2 and cultured in 12-well cell culture plates. The medium and wells will be changed whenever necessary. The cells will be cultivated for 2–3 weeks (14–22 days, as different tumors and patients may have differences in time to culture growth), until the tumor cells are all dead and the TIL count is >107. Subsequently, the "Young TILs" will be harvested for large-scale amplification or cell cryopreservation.Amplification of young TILs: 0·5–1 × 106 TILs will be co-cultured with irradiated (40 Gy, X-ray) allogeneic PBMCs (50–200-fold) in a 175-mm2 flask with VIVO containing IL-2 1500 IU/mL, OKT-3 30 ng/mL, and anti-CD28 antibody 30 ng/mL. The liquid will be changed on the 5th and 8th day and the culture of cells will be expanded when necessary every day after the 8th day. Once the number of cells increases, the cells can be transferred to culture bags. After 15 days of rapid amplification, the number of cells could reach 109–1010 (the number of cells will vary among tumors and patients). The total cell culture time will be approximately 35 days (from tumor biopsy to cell transfusion).The TIL samples will be inspected 1 day before expansion and 2 days before transfusion, and 1 mL will be extracted per bottle. After the details are described in an inspection sheet, the detection of bacterial and fungal organisms will be performed in the Bacteriology Room of the Laboratory Department.On day 15, we will assess the laboratory results of the bacterial and fungal test. After observing the state of the cell growth, 5 mL of the culture will be randomly and uniformly sampled, and a phenol blue staining method would be used to count the total number of living and dead cells. After ensuring that the cell suspension is negative for endotoxin, the cells will be subsequently collected in a sterile 250-mL centrifuge cup after centrifugation at 2500 rpm for 8 min. The supernatant will be discarded, and the cells will subsequently be washed twice with 0·9% sterile saline and centrifuged at 2000 rpm for 8 min. The supernatant will be discarded, and the cells will be collected in approximately 150 mL 0·9% sterile saline. Subsequently, 5 mL of 20% human serum albumin will be extracted with a 5-mL syringe into the cell suspension, and 1 mL of cell suspension will be sampled with a graduated pipette and sealed in a glass ampoule. The sample will be stored at 4°C for 3 months. Finally, the finished cell suspension will be sealed in a bottle labeled with the patient's ward, name, hospital number, sex, age, cell count, endotoxin, test results of sterility, and other items to ensure correct labeling; the detailed experimental records and signatures will be completed; and the suspension will be reinfused back into the patients.

extract_protocol:
Single Cell 3′ mRNA transcriptome profiling was  constructed with a negative pressure orchestrated DNBelab C4 system according to manufacturer’s instructions. Libraries were sequenced at the MGISEQ2000 platforms.
RNA libraries were prepared for sequencing using standard MGISEQ2000 protocols

treatment_protocol: Patients were screened and randomly assigned to receive either CCRT plus TIL infusion or CCRT alone. Both groups of patients received radiotherapy and concurrent chemotherapy regimen consisted of 100 mg/m2 cisplatin for three cycles. Patients assigned to the TIL group received TIL infusion within 1 week after CCRT.

tag: cancer type

value: nasopharyngeal carcinoma

tag: patient id

tag: response

value: non-responder


title: AN3CA_1

tag: cell line


title: A5_non-respond


title: MDA-MB231 cells, liquid overlay spheroid small 2

tag: cell type


title: PACE_113


title: A4_respond

value: responder


title: bone, Wt_WT_F, rep1 (L001)

description:
bone_growth_plate_reference_gene_raw_count.txt
2123_1_S1_L001

tag: genotype


title: PACE_109

value: platelet


title: MDA-MB231 cells, liquid overlay spheroid small 1


title: MoMs -Alk1 fl/fl Vav1-Cre repeat-4

first: Dianyuan

last: Zhao

address: 38 Life Science Park Road

institute: National Center for Protein Sciences

description: MoMs from Alk1 ff mice VS MoMs from Alk1 ff Vav1-Cre mice.xlsx

data_processing:
Sequencing reads were mapped to the mouse reference genome (Version mm10 from the University of California Santa Cruz (UCSC)) using Bowtie 2 (version 2.3.4.1) with default parameters.
Expression values of each gene were quantified as TPM using the RSEM program (version 1.3.1).
Differentially expressed genes were determined with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files containing normalized abundance measurements for each sample.

source_name: MoMs

extract_protocol:
Total RNA was isolated with RNeasy plus Mini Kit (Qiagen) according the manufacturer's protocol.
Library preparation was performed with UltraTM RNA Library Prep Kit (Illumina) according the manufacturer's protocol.

value: Liver

value: MoMs

value: Alk1 fl/fl Vav1-Cre

tag: infection

value: Listeria monocytogenes 3d post infection


title: A1_respond


title: PACE_106

tag: Sex

value: Male


title: IAA 4sU rep3

data_processing:
The data were processed using the Nextflow pipeline (https://nf-co.re/slamseq).
Assembly: hg19
Supplementary files format and content: ConversionRate and CPM

source_name: MCF10A cells

growth_protocol: MCF10A JUN KO cells  were cultured in DMEM/F12 (Thermo Fisher Scientific) supplemented with 5 % horse serum (Thermo Fisher Scientific), 1 % penicillin-streptomycin (Sigma-Aldrich), 10 µg/ml human insulin (Sigma-Aldrich), 0.5 µg/ml hydrocortisone (Sigma-Aldrich), 0.1 µg/ml cholera toxin (Sigma-Aldrich) and 20 ng/ml human EGF (Biomol).

extract_protocol:
RNA was extracted using TRIzol(Thermo) with the following modifications of the manufacturer protocol. After the transfer of the aqueous solution, 1% vol/vol 100 mM DTT was added to keep the RNA in an unoxidized state. After dissolving the RNA pellet in 1x PBS, 5 µg of RNA in a vloume of 90 µl were ued for Iodacetamide treatment.  90 µlof 20 mM Iodacetamide were added and incubated at 50°C for 15 min. The reaction was quenched by the addition of 20 μl of 1 M DTT, and the RNA was precipitated by NaAc/EtOH. The RNA was then used for QuantSeq library prep.
3'Seq libraries were generated using the QuantSeq 3'-mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) according to the manufacturer's protocol.

treatment_protocol: MCF10A JUN KO cells were infected with a JUN-AID fusion protein and a TIR1-expression vector. The cells were then either treated with 100 µM IAA or DMSO control to induce acute JUN degradation. After 1 hour, 100 µM 4sU (Sigma) was  added for another hour to label nascent RNA transcripts or an untreated control was kept.

value: MCF10A cells

value: Mammary breast epithelial

value: IAA 4sU


title: MoMs -Alk1 fl/fl Vav1-Cre repeat-3


title: DMSO 4sU rep3

value: DMSO 4sU


title: CKsdd rep3

city: Shenzhen

first: Yan

last: wei

address: shenzhenxueyuanroad

institute: Southern University of Science and Technology

data_processing:
Bowtie for alignment, v2, default parameter
Cufflink for expression profiling, V2.1.0, default parameter
Assembly: TAIR11
Supplementary files format and content: pyj_raw_data.xlsx represents FPKMs

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Surface sterilized seeds were imbibed in water at 4 °C for 3 days and germinated on 1/2 MS agar at standard condition (16h ligth/8h dark, 22 °C) for 7 days

extract_protocol:
Total RNA extracted using Trizol (Invitrogen)
stander Illumina mRNA-seq protocol

treatment_protocol: HS was imposed by submersion of parafilm-sealed plates into a temperature_x0002_controlled water bath

value: ski2 dcl4 dcl2

tag: stress

value: 0 min with heat stress


title: PACE_096

value: whole blood

value: Female


title: CKsdd rep1


title: PACE_104


title: PACE_095


title: MoMs -Alk1 fl/fl Vav1-Cre repeat-2


title: GF8_sc

city: Norwich

first: Wenbo

last: Ma

address: Norwich Research Park

country: United Kingdom

institute: The Sainsbury Laboratory

description: Biological replicate 4

data_processing:
The quality of the raw sequencing data was checked with FastQC v0.11.9
reads were aligned with the indexed CLas-Psy62 isolate genome assembly (NC_012985.3) and parsed to it using HISAT2 v2.2.1
The number of reads mapped to each gene was counted using the feature counts function of the Rsubread package
Read counts were normalized for each sample for differential expression analysis using DESeq2 v1.30.1
Assembly: NC_012985.3
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with normalized read counts for every genes and every sample

organism: Citrus x paradisi

source_name: Citrus paradisi Macfadyenand (Ri Red grapefruit)

extract_protocol:
100 mg of frozen seed coat vasculature samples were ground under freezing conditions using a GenoGrinder and tungsten beads at 1500 rpm for 30 seconds twice. The RNA was extracted from the homogenized tissue for untreated samples using the Qiagen RNeasy Plant Mini Kit according to the handbook instructions which included an on column Dnase I treatment. Samples were eluted with 50 uL of RNase-free water. The RNA was extracted from the bacterial pellet obtained after the above bacterial isolation resusepndedn in 1 mL of TLE extraction buffer. Then, 60 µL of 500 mM CaCl2 was added, mixed thoroughly, and placed on ice for 10 min. Centrifugation at 12,000 x g for 10 min at 4 °C was performed, followed by two rounds of separation with 500 µl of phenol:Chloroform:isoamyl alcohol (25:25:1) and centrifugation at 15,000 x g for 10 min at 4 °C. The supernatant was mixed with 2 M LiCl and incubated overnight at -20 °C. RNA was precipitated by centrifugation at 15,000 x g for 30 min, washed twice with ice-cold 75% ethanol, centrifuged at 15,000 x g for 15 min and re-suspended in 20 µl of RNAse-free water.
RNA was converted into sequencing-ready libraries for sequencing using TruSeq Stranded Total RNA Library Prep Kit (Illumina) for the bacterial isolation sample or Meta-transcriptome Library (Novogene) for untreated samples.  cDNA libraries were subjected to RNASeq, using an Illumina HiSeq-4000 system  with 100-bp strand-specific single-end reads for the bacterial isolation sample or Illumina NovaSeq-6000 system with 150-bp strand-specific paired-end reads for untreated samples.

treatment_protocol: pre-enrichment (bacterial isolation) performed according to De Francesco et al. 2022. All samples underwent ribodepletion using Illumina Ribo-Zero Plus kit

value: seed coat

value: bacterial isolation pre-enrichment


title: bone, Wt_WT_F, rep2 (L001)

description:
bone_growth_plate_reference_gene_raw_count.txt
2220_4_S8_L001

value: bone growth plate

value: E17.5 Left and right distal femural growth plates

value: Eed.fl.Zp3Cre on C57BL/6 background

value: Eedfl/fl


title: no 4sU Ctrl rep3

value: no 4sU


title: MoMs -Alk1 fl/fl repeat-4

city: Beijing

value: Liver

value: MoMs

value: Alk1 fl/fl

value: Listeria monocytogenes 3d post infection


title: MoMs -Alk1 fl/fl Vav1-Cre repeat-1

value: Alk1 fl/fl Vav1-Cre


title: IAA 4sU rep2

value: MCF10A cells

value: Mammary breast epithelial

value: IAA 4sU


title: MDA-MB231 cells, liquid overlay spheroid small 3

value: epithelium

value: WT

value: 5% matrigel following trastuzumab treatment, 96 hours incubation prior to rna extraction


title: PACE_094

value: whole blood

value: platelet

value: Female


title: PACE_093

value: Male


title: MoMs -Alk1 fl/fl repeat-2


title: DMSO 4sU rep2

value: DMSO 4sU


title: CKsd rep1

value: ski2 dcl4

value: 0 min with heat stress


title: no 4sU Ctrl rep2

value: no 4sU


title: PACE_092


title: CKsdd rep2

value: ski2 dcl4 dcl2


title: CKs678 rep3

value: smxl6 smxl7 smxl8


title: MoMs -Alk1 fl/fl repeat-1

value: Liver

value: MoMs

value: Alk1 fl/fl

value: Listeria monocytogenes 3d post infection


title: IAA 4sU rep1

value: MCF10A cells

value: Mammary breast epithelial

value: IAA 4sU


title: CKs678 rep2


title: PACE_088

value: whole blood


title: KCs from Smad4 fl/fl Vav1-Cre repeat-3

description: KCs from Smad4 ff mice VS KCs from Smad4 ff Vav1-Cre mice.xlsx

source_name: Kupffer cells

value: Kupffer cells

value: Smad4 fl/fl Vav1-Cre


title: CKs678 rep1


title: PACE_085

source_name: whole blood

value: platelet

value: Female


title: CKsd rep3

value: ski2 dcl4


title: KCs from Smad4 fl/fl Vav1-Cre repeat-2


title: no 4sU Ctrl rep1


title: CKsd rep2

value: 0 min with heat stress


title: PACE_080


title: MoMs -Alk1 fl/fl repeat-3


title: JUN Dox rep3

data_processing:
Reads containing adapters/ with low quality were trimmed using cutadapt (v4.2), -m 30
Trimmed sequence reads were mapped against hg19 using bowtie2 (2.3.5.1)
Read count extraction was performed in R using countOverlaps (GenomicRanges)
Assembly: hg19

extract_protocol:
RNA was extracted using Rneasy columns (Qiagen). 1 µg of RNA was used for library prep.
RNA-Seq libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770/E7775) according to the manufacturer's protocol.

value: JUN Dox


title: CKs45 rep3

value: smxl4 smxl5


title: PACE_082

value: Male


title: KCs from Smad4 fl/fl repeat-3

value: Liver

value: Smad4 fl/fl


title: KCs from Smad4 fl/fl Vav1-Cre repeat-1


title: CKs45 rep2


title: JUN EtOH rep3

value: JUN EtOH


title: PACE_076


title: CKs45 rep1


title: vector Dox rep3

value: vector Dox


title: KCs from Smad4 fl/fl repeat-2


title: CKco rep3


title: PACE_073


title: vector EtOH rep3

value: MCF10A cells

value: vector EtOH


title: KCs from Smad4 fl/fl repeat-1


title: CKco rep2


title: DMSO 4sU rep1

value: Mammary breast epithelial

value: DMSO 4sU


title: PACE_072

value: whole blood


title: Clec4F- Tim4+ KCs repeat-3

description: Clec4F+Tim4+ VS Clec4F-Tim4+ KCs from Alk1 ff Cx3cr1-Cre.xlsx

source_name: Clec4F- Tim4+ Kupffer cells

value: Clec4F- Tim4+ Kupffer cells

value: Alk1 fl/fl Cx3cr1-Cre


title: Clec4F- Tim4+ KCs repeat-2


title: PACE_071

value: platelet


title: JUN Dox rep2


title: CKco rep1


title: PACE_069


title: JUN EtOH rep2


title: 85sdd rep3

value: ski2 dcl4 dcl2

value: 85 min with heat stress


title: vector Dox rep2


title: Clec4F+ Tim4+ KCs repeat-3

source_name: Clec4F+ Tim4+ Kupffer cells

value: Clec4F+ Tim4+ Kupffer cells


title: vector EtOH rep2


title: 85sdd rep2


title: Clec4F- Tim4+ KCs repeat-1


title: PACE_065


title: PACE_067

value: Female


title: Clec4F+ Tim4+ KCs repeat-2


title: PACE_059

value: Male


title: 85sd rep3

value: ski2 dcl4


title: 85sdd rep1


title: Clec4F+ Tim4+ KCs repeat-1

value: Liver


title: JUN EtOH rep1

value: JUN EtOH


title: 85sd rep2


title: PACE_051


title: PACE_048


title: vector Dox rep1

value: vector Dox


title: 85sd rep1


title: vector EtOH rep1

value: MCF10A cells


title: PACE_041


title: siYAP/TAZ rep3

extract_protocol:
RNA was extracted using Rneasy columns (Qiagen). 0.5 µg of RNA were used for library prep.
3'Seq libraries were generated using the QuantSeq 3'-mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) according to the manufacturer's protocol.

treatment_protocol: MCF10A cells were transfected with siRNAs (20 nM, Dharmacon) using the Lipofectamine RNAiMAX reagent (Thermo) according to the manufacturer's recommendations.

value: siYAP/TAZ


title: PACE_036


title: 85s678 rep3

value: smxl6 smxl7 smxl8


title: 85s678 rep2


title: PACE_032


title: siYAP/TAZ rep2

value: Mammary breast epithelial


title: JUN Dox rep1

value: JUN Dox


title: 85s678 rep1


title: 85s45 rep3

value: smxl4 smxl5


title: siCtrl rep3

value: Non-targeting control


title: siCtrl rep2


title: PACE_029

value: whole blood

value: platelet


title: 85s45 rep2

value: 85 min with heat stress


title: PACE_028


title: siYAP/TAZ rep1


title: 85s45 rep1