title: 15-00807 Ava+ORY rep 3

description:
C3
counts_table.txt

data_processing:
[RNA-seq]
Sequencing from Bulk RNA seq was aligned using STAR.
Differential Expression was determined using DESeq2.
[CUT&Tag]
Sequencing from CUT&Tag was aligned using Bowtie2.
Peaks were called using gopeaks.
CPM normalized bigwigs merged with UCSC bigWigMerge.
Bedgraphs converted to bigwigs with UCSC bedGraphToBigWig.
Differential enrichment was assessed using DESeq2.
[CUT&RUN]
Sequencing from CUT&RUN was aligned using Bowtie2.
Peaks were called using gopeaks.
CPM normalized bigwigs merged with UCSC bigWigMerge.
Bedgraphs converted to bigwigs with UCSC bedGraphToBigWig.
[ATAC-seq]
Sequencing from ATAC was aligned using BWA-MEM.
Peaks were called using MACS2.
[scRNA-seq]
Sequencing from scRNAseq libraries was aligned using Cell Ranger.
Expression matrices were processed using Seurat.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bed: peak files, bw: bigWig files, peaks.tsv: peak files.
Supplementary_files_format_and_content: barcodes.tsv: barcodes files, features.tsv: features files, matrix.mtx: matrix files.

source_name: 15-00807 ex vivo culture

extract_protocol: Libraries were prepared according to published protocol Buenrostro et al. 2015.

value: 50 nM avapritinib + 50 nM ORY-1001

value: 24 hours


title: H3K27me3p21_2

status: Public on May 29 2022

type: SRA

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

country: USA

institute: NIH

library_source: genomic

data_processing:
Raw reads were filtered by cutadpt v1.8.1,-m 20 --trim-n --max-n 0.7 -q 20
Contaminants were filtered by fastq_screen (v0.5.1. 4)
Clean reads were mapped to UCSC mm9/mm10/rn6 genome via STAR v2.5.2b
Reads were assigned to Ensembl genes by featureCounts (subread-1.4.6-p1 command line)
Genome_build: mm10 for mouse
Genome_build: rn6 for rat
Supplementary_files_format_and_content: txt,raw counts of RNA-seq
Supplementary_files_format_and_content: xlsx,log fold change of RNA-seq
Supplementary_files_format_and_content: bedGraph, read intensity of ChIPSeq samples

molecule: genomic DNA

organism: Mus musculus

source_name: cardiomyocytes

extract_protocol:
Mouse CMs were fixed using 1% formaldehyde for 10 min, and 0.125 M glycine was added to stop fixation. Cells were harvested, and DNA was fragmented to 300–500 bp by sonication with Covaris S220 sonicator. Immunoprecipitation was performed with antibodies conjugated to Dynabeads Protein G beads (Life Technology). ChIP DNA was eluted, reverse cross-linked, extracted by phenol/chloroform, and precipitated.
Cell suspension was centrifuge (100 x g, 2min) three times to separate the cardiomyocytes and non-cardiomyocytes

tag: strain

tag: cell type

value: cardiomyocytes

tag: time point

tag: chip antibody


title: P.aeruginosa-infected lungs, Day 4, biological rep 2

city: Singapore

first: Hong Sheng

last: Cheng

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine,

country: Singapore

institute: Nanyang Technological University

library_source: transcriptomic

data_processing:
Sequencing reads were mapped to the mouse genome (GRCm39) retrieved from Ensembl using Hisat2.
Gene counts of each sample were performed using featureCounts.
Assembly: GRCm39
Supplementary files format and content: A .csv file of raw gene counts of each sample.

molecule: total RNA

source_name: Lung

extract_protocol:
Total RNA was extracted from frozen mouse lung tissues using TRIzol (Thermo Fisher). The integrity of the total RNA and level of DNA contamination was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies) and Qubit 2.0 fluorometer (Invitrogen).
Library preparation was performed according to the mRNA-seq sample preparation kit (Illumina).

treatment_protocol: For intratracheal mouse infection experiments, 6-10 week old C57BL/6 mice were anesthetized using 80 mg/kg body weight ketamine and 10 mg/kg body weight xylazine and infected via intratracheal delivery with the Neisseria subflava (isolate SG-KL01) and Pseudomonas aeruginosa at 2 x 107 CFU in sterile phosphate-buffered saline (PBS). Mice were euthanized on Day 0, 2, 4, 7 , and 14 and the lung tissues were harvested and snap frozen in liquid nitrogen for total RNA extraction.

tag: tissue

value: Lung

tag: time

value: Day 4

tag: genotype

value: Wild type

tag: treatment

value: Pseudomonas aeruginosa


title: Donor2_TCR_Stim3 [FB3D_S95_L004_R1_001]

city: San Francisco

first: Eric

last: Shifrut

state: CA

address: 513 Parnassus Ave, HSW 1033

institute: University of California, San Franscisco

data_processing:
To analyze the gene expression, reads were mapped to the human reference transcriptome (GRCh38 Ensembl release 96) using Kallisto v0.46.1 with default parameters. Genes with zero counts in more than 80% of the samples were filtered out.
Assembly: GRCh38 Ensembl release 96
Supplementary files format and content: Count matrix file with named columns as listed in "description" field.

organism: Homo sapiens

source_name: Blood

extract_protocol:
T cells were subjected to the repeated stimulation assay in 24-well plates, transferring T cells to freshly seeded cancer cells every 48 hours. Cultured T cells were sorted after each stimulation using BD FACSAria Fusion to obtain a pure population of NY-ESO-1 multimer positive cells T cells from the co-cultures with target cancer cells, and resuspended in TRI Reagent (Sigma, Cat.# T9424). Total RNA was extracted using Direct-zol RNA MicroPrep kit (Zymo research, Cat.# R2061)
For paired-end samples, RNA-seq libraries were prepared by Oligo dT enrichment followed by a stranded Illumina library prep protocol with the KAPA mRNA HyperPrep kit (Kapa Biosystems, KK8580). Libraries were checked for quality on an AATI Fragment analyzer (Agilent, DNF-935–1000), quantified using the Illumina Quant Universal qPCR Mix (Kapa Biosystems, KK4824), and pooled evenly at 3nM. For single read samples (RASA2KO and CTRL Stim5), batch-Tag-seq protocol was used (PMID 27037501).

value: Blood

value: T cells

tag: subject id

value: TCR


title: Donor4_TCR_Stim2 [FB2G_S90_L004_R1_001]


title: 15-00807 Ava+ORY rep 2

city: Portland

first: Theodore

middle: P

last: Braun

state: Oregon

address: 2720 S Moody Ave

institute: Oregon Health and Science University

description:
C2
counts_table.txt

tag: cell line


title: P.aeruginosa-infected lungs, Day 4, biological rep 1


title: H3K27me3p21_1


title: 15-00807 Ava+ORY rep 1

description:
C1
counts_table.txt


title: P.aeruginosa-infected lungs, Day 2, biological rep 5

value: Day 2


title: Donor1_TCR_Stim2 [FB2E_S88_L004_R1_001]


title: H3K27me3p1_3


title: Donor2_TCR_Stim2 [FB2F_S89_L004_R1_001]


title: P.aeruginosa-infected lungs, Day 2, biological rep 4


title: H3K27me3p1_2


title: 15-00807 ORY rep 2

description:
O2
counts_table.txt


title: 15-00807 ORY rep 3

description:
O3
counts_table.txt


title: 15-00807 ORY rep 1

description:
O1
counts_table.txt


title: P.aeruginosa-infected lungs, Day 2, biological rep 3


title: Donor2_CAR_Stim1 [FB2C_S86_L004_R1_001]

value: CAR


title: Donor1_CAR_Stim1 [FB2B_S85_L004_R1_001]


title: P.aeruginosa-infected lungs, Day 2, biological rep 2


title: 15-00807 Ava rep 3

description:
A3
counts_table.txt

value: 50 nM avapritinib


title: H3K27acp7_4


title: Donor4_TCR_Stim1 [FB2A_S84_L004_R1_001]


title: P.aeruginosa-infected lungs, Day 2, biological rep 1


title: 15-00807 Ava rep 1

description:
A1
counts_table.txt


title: 15-00807 Ava rep 2

description:
A2
counts_table.txt


title: P.aeruginosa-infected lungs, Day 0, biological rep 4

value: Day 0


title: H3K27acp7_3


title: 15-00807 DMSO rep 3

description:
D3
counts_table.txt

value: DMSO


title: Donor4_CAR_Stim1 [FB2D_S87_L004_R1_001]


title: Donor2_TCR_Stim1 [FB1H_S83_L004_R1_001]


title: H3K27acp56_4


title: P.aeruginosa-infected lungs, Day 0, biological rep 1


title: 15-00807 DMSO rep 2

description:
D2
counts_table.txt


title: H3K27me3p1_1


title: P.aeruginosa-infected lungs, Day 0, biological rep 3


title: H3K27acp7_5


title: Donor1_TCR_Stim1 [FB1G_S82_L004_R1_001]


title: H3K27acp7_1


title: Donor4_CAR_Input [FB1F_S81_L004_R1_001]


title: N. subclava-infected lungs, Day 14, biological rep 5

value: Day 14

value: Neisseria subclava


title: Donor1_CAR_Input [FB1D_S79_L004_R1_001]


title: P.aeruginosa-infected lungs, Day 0, biological rep 2


title: H3K27acp56_3


title: Donor2_CAR_Input [FB1E_S80_L004_R1_001]


title: N. subclava-infected lungs, Day 14, biological rep 4


title: H3K27acp56_2


title: p5: SCLS , replicate 4, RNAseq

city: Bethesda

first: Katherine

middle: M

last: Hornick

state: MD

address: 10 Center Dr, Building 29B

department: Integrated Data Sciences Section (IDSS)

institute: NIAID

data_processing:
Raw fastq files were trimmed for quality and adapter contamination using Cutadapt v1.18 (Martin 2011). Trimmed reads were mapped to the hg38 reference genome and Gencode GRCh38 v.39 tran-scriptome using STAR v2.7.6a (Dobin et al. 2013) in two-pass mode. Gene-level expression quantifi-cation was performed using RSEM v.1.3.0 (Li and Dewey 2011).
Genes not expressed at a level greater than one count per million (CPM) reads in at least three of the samples were excluded from further analysis. The gene-level read counts were normalized using the trimmed means of M-values (TMM) in edgeR (Robinson et al. 2010) to adjust samples for differences in library size. Differential expression analysis was performed using the quasi-likelihood F-test with the generalized linear model (GLM) approach in edgeR (Robinson et al., 2010).
Assembly: hg38
Supplementary files format and content: raw expression (expected counts) text file generated from RSEM

source_name: Blood outgrowth endothelial cells

extract_protocol:
Whole blood was collected from SCLS subjects during an asymptomatic interval or from age, sex, and ethnicity-matched healthy controls. Age-, sex-, and ethnicity-matched blood samples from anonymous donors were obtained from the NIH Blood Bank. We prepared buffy coat mononuclear cells from blood using Lymphocyte separation medium (MP Biomedicals). Cells were re-suspended in Endothelial Growth Medium (EGM-2, Lonza), and plated into culture wells coated with collagen I. The culture medium was changed every other day for several weeks until the colonies formed, and BOEC were expanded according to published protocols. RNA was extracted from BOECs using Direct-zol RNA Kit (Zymo Research).
RNA libraries were prepared using the Illumina TruSeq® Stranded Total RNA Sample Preparation kit (Illumina) according to the manufacturer's instructions.

tag: disease state

value: systemic capillary leak syndrome (SCLS)

value: Blood outgrowth endothelial cells


title: H3K27acp56_1

value: cardiomyocytes


title: Donor4_TCR_Input [FB1C_S78_L004_R1_001]


title: N. subclava-infected lungs, Day 14, biological rep 2

value: Lung


title: H3K27acp7_2


title: p6: SCLS, replicate 5, RNAseq


title: N. subclava-infected lungs, Day 14, biological rep 3


title: Donor2_TCR_Input [FB1B_S77_L004_R1_001]


title: p2: SCLS, replicate 2, RNAseq


title: H3K27acp21_4


title: p4: SCLS, replicate 3, RNAseq


title: 15-00807 DMSO rep 1

description:
D1
counts_table.txt

value: 24 hours


title: Trophoblast, normal placenta, case 4

city: VANCOUVER

first: Jefferson

last: Terry

state: British Columbia

address: 4480 Oak Street, Room 2H60

country: Canada

institute: Anatomical Pathology

description:
N4-T
CIUE DSP Processed Data NS.xslx

data_processing:
Data processing is performed with GeoMX-NGS Data Analysis Software, v. 2.2
Quality control is performed by excluding AOIs with <1000 raw reads, <80% aligned raw reads, sequencing saturation <50%, negative probe count geomean <10, and no template PCR control count >1000 (Sample G2-M failed QC).
Outlier probes with ≤10% of the counts for all probes to a particular gene and/or that fail the Grubbs outlier test in ≥20% of samples are expunged from all samples.
Targets with ≥10% segments and segments with ≥10% targets above the threshold of 2 or the limit of quantitation, whichever is higher, are retained.
The data is scaled to area (geometric mean) and normalized using the upper quartile (Q3) method. Background correction is performed using signal to noise ratio of the geometric mean of negative targets.
Assembly: Whole transcriptome atlas probes target 99.5% of the protein-coding genes defined in the HUGO database (23 highly expressed genes are omitted).
Supplementary files format and content: CIUE DSP JT Processed Data Matrix NS.xlsx
Library strategy: GeoMx Seq

source_name: Placenta

extract_protocol:
A 5 micron formalin fixed paraffin embedded tissue microarray section is labeled with fluorescently labeled cytokeratin and CD68 antibodies to highlight the trophoblast, stroma, and macrophage components. GeoMX human whole transciptome atlas is hydridized and bound probe barcode oligomers cleaved and collected for further analysis using the GeoMX digital spatial profiler.
NanoString's GeoMX Human Whole Transcriptome Atlas

value: normal control

value: Placenta

value: Trophoblast


title: N. subclava-infected lungs, Day 14, biological rep 1

value: Wild type


title: H3K27acp21_2


title: Donor1_TCR_Input [FB1A_S76_L004_R1_001]

value: Blood

value: T cells

value: TCR


title: H3K27acp21_3


title: Villus stroma, normal placenta, case 4

description:
N4-S
CIUE DSP Processed Data NS.xslx

value: Placental villus stroma


title: p1: SCLS, replicate 1, RNAseq


title: H3K27acp21_1


title: N. subclava-infected lungs, Day 7, biological rep 3

value: Day 7


title: N. subclava-infected lungs, Day 7, biological rep 5


title: N. subclava-infected lungs, Day 7, biological rep 4


title: H3K27acp1_5


title: Villus stroma, normal placenta, case 3

description:
N3-S
CIUE DSP Processed Data NS.xslx


title: D5: control, replicate 5, RNAseq

value: control


title: Trophoblast, normal placenta, case 3

description:
N3-T
CIUE DSP Processed Data NS.xslx


title: D4: control, replicate 4, RNAseq


title: Trophoblast, normal placenta, case 2

description:
N2-T
CIUE DSP Processed Data NS.xslx


title: H3K27acp1_4


title: D3: control, replicate 3, RNAseq


title: D2: control, replicate 2, RNAseq


title: H3K27acp1_3


title: Villus stroma, normal placenta, case 2

description:
N2-S
CIUE DSP Processed Data NS.xslx


title: N. subclava-infected lungs, Day 4, biological rep 5

value: Day 4


title: H3K27acp1_2


title: D6: control, replicate 6, RNAseq


title: D1: control, replicate 1, RNAseq


title: N. subclava-infected lungs, Day 4, biological rep 4

value: Neisseria subclava


title: H3K27acp1_1


title: Villus stroma, normal placenta, case 1

description:
N1-S
CIUE DSP Processed Data NS.xslx


title: T8ML1-WT

city: Omaha

first: Chengfeng

last: Bi

state: Nebarska

address: 42nd and, Emile St

institute: University of Nebraska Medical Center

data_processing:
Quality of the raw reads were assessed by FASTQC (v 0.11.7)
Reads were then aligned to the hg19 genome using STAR (v 2.5.3)
Gene expression quantification was done using HTSeq (v.0.9.1
Gene expression normalization was done with the R package DESeq2 (1.24.0)
Assembly: hg19
Supplementary files format and content: tab-delimited text files include normalised DESeq2 counts

extract_protocol:
RNA was extracted with Qiagen All-Prep DNA/RNA mini kit  (cat# 80284)
Library was contructed with the KAPA mRNA HyperPrep kit per the manufacturer's protocol.

value: Peripheral T-cell lymphoma derived cell line

value: WT


title: Trophoblast, normal placenta, case 1

description:
N1-T
CIUE DSP Processed Data NS.xslx


title: N. subclava-infected lungs, Day 4, biological rep 3


title: Macrophages, granulomatous lymphadenitis, case 4

description:
G4-M
CIUE DSP Processed Data NS.xslx

source_name: Lymph node

value: granulomatous lymphadenitis

value: Lymph node

value: Macrophage


title: N. subclava-infected lungs, Day 7, biological rep 2

value: Lung


title: T8ML1-886, DNMT3A-mutant-Q886


title: NIH_p7_2

description:
RNAseq_NIH_DEG.xlsx
RNAseq_genecountsraw_NIH.txt

extract_protocol:
RNA was extracted from cells using the GeneJet RNA Purification Kit (Thermo Scientific). One µg of RNA was used for generation of sequencing library using the TruSeq RNA Library Prep Kit V2 (Illumina) according to the manufacturer’s instructions.
Cell suspension was centrifuge (100 x g, 2min) three times to separate the cardiomyocytes and non-cardiomyocytes

value: NIH

value: cardiomyocytes


title: NIH_p21_1


title: N. subclava-infected lungs, Day 4, biological rep 2

value: Wild type


title: T8ML1-882, DNMT3A-mutant-R882


title: NIH_p21_2


title: N. subclava-infected lungs, Day 2, biological rep 5

value: Day 2


title: N. subclava-infected lungs, Day 7, biological rep 1


title: Macrophages, granulomatous lymphadenitis, case 2

description:
G2-M
No Processed Data Available


title: N. subclava-infected lungs, Day 4, biological rep 1


title: Macrophages, granulomatous lymphadenitis, case 1

description:
G1-M
CIUE DSP Processed Data NS.xslx


title: NIH_p7_1


title: T8ML1-716, DNMT3A-mutant-V716


title: Macrophages, granulomatous lymphadenitis, case 3

description:
G3-M
CIUE DSP Processed Data NS.xslx


title: Trophoblast, CIUE, case 4

description:
C4-T
CIUE DSP Processed Data NS.xslx

value: chronic intervillositis of unknown etiology (CIUE)

value: Placenta

value: Trophoblast


title: N. subclava-infected lungs, Day 2, biological rep 4


title: NIH_p1_2


title: 14-00613 Ava+ORY

description: single cell RNAseq

source_name: 14-00613 ex vivo culture

extract_protocol: 10X scRNAseq libraries were prepared using the NextGem 3' V3.0 kit according to the manufacturer's instructions.

value: 12 nM avapritinib + 12 nM ORY-1001

value: 24 hours


title: N. subclava-infected lungs, Day 2, biological rep 3


title: N. subclava-infected lungs, Day 2, biological rep 2


title: T8ML1, Empty Vector

value: Empty Vector


title: 14-00613 Ava

description: single cell RNAseq

value: 12 nM avapritinib


title: KM_p21_2

description:
RNAseq_KM_DEG.xlsx
RNAseq_genecountsraw_KM.txt

value: KM


title: Villus stroma, CIUE, case 4

description:
C4-S
CIUE DSP Processed Data NS.xslx

value: Placental villus stroma


title: NIH_p1_1


title: 14-00613 ORY

description: single cell RNAseq


title: KM_p21_1


title: Trophoblast, CIUE, case 3

description:
C3-T
CIUE DSP Processed Data NS.xslx


title: 14-00613 DMSO

description: single cell RNAseq

value: DMSO


title: N. subclava-infected lungs, Day 2, biological rep 1

value: Neisseria subclava


title: SD_p7_2

description:
RNAseq_SD_DEG.xlsx
RNAseq_genecountsraw_SD.txt

organism: Rattus rattus

value: Sprague Dawley


title: Intervillus macrophages, CIUE, case 4

description:
C4-M
CIUE DSP Processed Data NS.xslx

value: Macrophage


title: Intervillus macrophages, CIUE, case 3

description:
C3-M
CIUE DSP Processed Data NS.xslx


title: N. subclava-infected lungs, Day 0, biological rep 5

value: Lung

value: Day 0


title: Villus stroma, CIUE, case 3

description:
C3-S
CIUE DSP Processed Data NS.xslx


title: N. subclava-infected lungs, Day 0, biological rep 4

value: Wild type


title: KM_p7_1

value: cardiomyocytes


title: KM_p1_2


title: KM_p1_1


title: SD_p4_2


title: N. subclava-infected lungs, Day 0, biological rep 2


title: N. subclava-infected lungs, Day 0, biological rep 3


title: SD_p4_1


title: Villus stroma, CIUE, case 2

description:
C2-S
CIUE DSP Processed Data NS.xslx

value: chronic intervillositis of unknown etiology (CIUE)


title: N. subclava-infected lungs, Day 0, biological rep 1


title: C57_p56_2

description:
RNAseq_logFC.xlsx
RNAseq_genecountsraw.txt


title: SD_p1_2


title: Intervillus macrophages, CIUE, case 2

description:
C2-M
CIUE DSP Processed Data NS.xslx

value: Placenta


title: Vehicle Sham 5

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

data_processing:
RNA-seq analyses were performed using Partek® Flow® software, v10.0. Pre-alignment quality control was completed using the default QA/QC tool.
Alignment of sequencing reads to the mouse genome using the splice-aware program STAR (v2.7.8a).
Gene counts were quantified using Partek E/M against transcriptome release 103.
Genome_build: GRCm39
Supplementary_files_format_and_content: raw counts

source_name: Plantaris Muscle

growth_protocol: Animals were subjected to bilateral synergist ablation surgery to induce hypertrophy of the plantaris muscle. Following anesthetization with 5% isoflurane, 1/4-1/3 of the soleus and the gastrocnemius muscles were surgically excised via an incision on the dorsal aspect of the hind limb. Particular attention was made to ensure neural and vascular supply to the plantaris muscle remained intact and undamaged. Sham surgeries were performed as controls, in which the skin was opened without removal of the gastrocnemius and soleus muscles. Plantaris muscle was collected at 14 days after the surgery.

extract_protocol:
Each muscle was homogenized in 700 uL Qiazol. Muscle homogenate was then transfered into Phase Lock Gel Heavy tubes with 150 uL of BCP and were mixed for one minute followed by 3 minutes on the benchtop. Samples were then centrifuged at 12,000xg for 15 minutes at 4C and then RNA was isolated using the Qiagen miRNeasy Mini Kit. RNA concentration was assessed via Nanodrop and the RIN was determined using an Agilent 2100 bioanalyzer.
Standard Eukaryotic RNA-Seq (cDNA library) prep from Novogene

treatment_protocol: Mice were administered a vehicle or senolytic cocktail containing 5 mg/kg dasatinib and 50 mg/kg quercetin through gavage on days 7 and 10 of the 14-day mechanical overload using 20-gauge disposable polypropylene feeding tubes.

value: Plantaris Muscle

value: Vehicle

tag: surgery

value: Sham

tag: age

value: 2 years


title: SD_p1_1


title: C57_p21_2


title: C57_p56_1


title: KM_p7_2


title: Villus stroma, CIUE, case 1

description:
C1-S
CIUE DSP Processed Data NS.xslx


title: Vehicle Sham 4


title: Wistar_p7_2

description:
RNAseq_Wistar_DEG.xlsx
RNAseq_genecountsraw_Wistar.txt

value: Wistar


title: Trophoblast, CIUE, case 1

description:
C1-T
CIUE DSP Processed Data NS.xslx

value: Trophoblast


title: C57_p21_1


title: Vehicle Sham 3


title: SD_p7_1


title: C57_p7_2


title: Vehicle Sham 2


title: Trophoblast, CIUE, case 2

description:
C2-T
CIUE DSP Processed Data NS.xslx


title: Vehicle Sham 1


title: Wistar_p7_1


title: Vehicle 14d Overload 5

value: Overload


title: Wistar_p4_1


title: Wistar_p4_2


title: C57_p1_2


title: Wistar_p1_2


title: C57_p1_1


title: Vehicle 14d Overload 4


title: Vehicle 14d Overload 3


title: Kasumi-1 ORY LSD1 rep 3

data_processing:
Library strategy: CUT&RUN
[RNA-seq]
Sequencing from Bulk RNA seq was aligned using STAR.
Differential Expression was determined using DESeq2.
[CUT&Tag]
Sequencing from CUT&Tag was aligned using Bowtie2.
Peaks were called using gopeaks.
CPM normalized bigwigs merged with UCSC bigWigMerge.
Bedgraphs converted to bigwigs with UCSC bedGraphToBigWig.
Differential enrichment was assessed using DESeq2.
[CUT&RUN]
Sequencing from CUT&RUN was aligned using Bowtie2.
Peaks were called using gopeaks.
CPM normalized bigwigs merged with UCSC bigWigMerge.
Bedgraphs converted to bigwigs with UCSC bedGraphToBigWig.
[ATAC-seq]
Sequencing from ATAC was aligned using BWA-MEM.
Peaks were called using MACS2.
[scRNA-seq]
Sequencing from scRNAseq libraries was aligned using Cell Ranger.
Expression matrices were processed using Seurat.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bed: peak files, bw: bigWig files, peaks.tsv: peak files.
Supplementary_files_format_and_content: barcodes.tsv: barcodes files, features.tsv: features files, matrix.mtx: matrix files.

source_name: Kasumi-1 cells

extract_protocol: Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB).

value: 12 hours

tag: antibody


title: Wistar_p1_1


title: MI_Myh6_RFP_P7

data_processing:
Raw reads were processed by the perl pipeline script developed by Takara Bio
Read pairs were filtered by cutadapt (v1.8.1). The parameters were: -m 20 --trim-n --max-n 0.7 –q 20.Contaminants were filtered by fastq screen (v0.5.1. 4)
Clean reads were mapped to UCSC mm10 genome via STAR v2.5.2b
Reads were assigned to Ensembl genes by featureCounts (subread-1.4.6-p1 command line)
Genome_build: mm10 for mouse RNASeq
Supplementary_files_format_and_content: csv,gene expression matrix for single cell RNASeq

source_name: Cardiomyocyte

extract_protocol:
Cells were sorted by flow cytomentry to get RFP positive cells and MI mouse injected with PBS as negtive control.
The libraries were generated with the Nextera XT Library Preparation Kit (Illumina, 15032350) following the manufacturer's instructions, and were purified using Agencourt AMPure XP magnetic beads (Beckman, A63880)
scRNA-Seq

treatment_protocol: For Single cell RNA-Seq, ventricles close to auricle and far away auricle and cardiac apex were chopped into small pieces respectively and digested with Pierce™ Primary Cardiomyocyte Isolation Kit (Thermo, 88281).

tag: sample type

value: Cardiomyocyte


title: Kasumi-1 ORY LSD1 rep 2


title: Intervillus macrophages, CIUE, case 1

description:
C1-M
CIUE DSP Processed Data NS.xslx


title: Vehicle 14d Overload 2


title: Kasumi-1 Ava+ORY LSD1 rep 3

value: 12 nM avapritinib + 12 nM ORY-1001


title: C57_p7_1


title: MI_Myh6_RFP_P1


title: Kasumi-1 Ava+ORY LSD1 rep 2


title: Kasumi-1 ORY LSD1 rep 1


title: T8ML1-EV, IP

data_processing:
350ng was sheared in a Covaris S220 focused ultra-sonicator and 150bp fragments were used in library preparatio
Samples were sequenced on a NextSeq500 (75bp paired-end). An average of 24.5 million paired end reads were generated from the MeDIP libraries (range 13-50 million) and 30 million for the input control libraries (range 18-46 million)
Raw reads were aligned to hg19 with BWA-mem (v0.7.15). Duplicate removal was performed with Picard5 (v2.9.0). Reads mapping to multiple regions or present in the ENCODE blacklisted regions6 were excluded and only autosomal chromosomes were used for subsequent analysis to avoid gender related differences
Homer (v4.11.1) was used to create tag directories from the bam files, identify methylated "peaks" in comparison to input control (style=histone, fold enrichment over input=4), annotate the type of genomic region the methylated peaks are associated with (e.g. transcription start site, transcription termination site, Exon , 5' UTR , 3' UTR, Intronic, or Intergenic, etc) and create metagene profiles. Association of genes with each peak was based on the nearest TSS
Association of genes with each peak was based on the nearest TSS. Differentially methylated regions were identified with Homer using the getDifferentialPeaksReplicates.pl function with a fold difference setting of 1.5.
To identify hypermethylated regions associated with DNMT3A mutation, DNMT3A mutant samples were, used for the IP directory and DNMT3A wild-type sample directories were used as the background directories. To identify hypomethylated regions associated with DNMT3A mutation, the wild-type tag directories were used as the IP directories with the DNMT3A mutant samples serving as background. We then integrated our gene expression data and identified differentially methylated regions (DMRs) annotated to have the strongest influence on changes to gene expression (i.e., promoter, intergenic (e.g. CpG)8,9, and intron-110 regions) which were concurrent with changes in gene expression (i.e., hypomethylation and increased expression, hypermethylation and decreased expression)

growth_protocol: Cells were cultured in 2.05mM L-Glutamine RPMI 1640 (HyClone) supplemented with 10% fetal bovine serum (FBS), penicillin G (199 U/ml), streptomycin (100 μg/ml), and IL-2 (10 ng/ml)

extract_protocol:
DNA was extracted with Qiagen All-Prep DNA/RNA mini kit  (cat# 80284)
MeDIP-seq libraries were prepared using Diageneode MagMeDIP-seq Package (C02010040) per the manufacuter's protocol.

value: Peripheral T-cell lymphoma derived cell line


title: Kasumi-1 Ava LSD1 rep 2

value: 12 nM avapritinib


title: Kasumi-1 Ava+ORY LSD1 rep 1


title: Kasumi-1 Ava LSD1 rep 3


title: T8ML1-EV, INPUT


title: Olaparib+ADUS100 tumor #1539

type: RNA

city: Boston

first: Geoffrey

middle: I

last: Shapiro

state: MA

address: Dana Farber Cancer Inst 450 Brookline Avenue Mayer 446

department: Medical Oncology

institute: Dana-Farber Cancer Institute

hyb_protocol: 5ul hybridization buffer was added to the mix, then 2ul nCounter Mouse Cancer Immune Capture ProbeSet (XT formulation, nanoString) was added and hybridization was performed at 65 degress Celsius for 16 hours.

scan_protocol: Post-hybridazation processing and data collection was performed uisng nanoString nCounter instrument.

data_processing: Raw mRNA counts were analyzed using the Advanced Analysis Module of the nSolver analysis software 4.0 (NanoString Technologies). Data were automatically subjected to quality control, background correction (based on negative controls) and normalization to positive controls (normalization of experimental variables). geNorm algorithm was used to determine the most stable reference (housekeeping) genes, and 8 reference genes were chosen for normalization. Normalized mRNA counts were then plotted.

source_name: breast tumor, treated, 3 days

label_protocol: For each reaction 100ng RNA was mixed with 3ul nCounter Mouse Cancer Immune Reporter CodeSet (XT formulation, nanoString).

growth_protocol: K14-Cre;Brcaf/fTrp53f/f tumors were transplanted into the mammary fat pad of syngeneic FVB/129P2 female recipients. When tumors reached 150-300 mm3 in volume mice were randomized in treatment groups, so that the average tumor volume in each group was the same.

extract_protocol: RNA isolation from snap-frozen tumor chunks excised from mice, was performed at the Center for AdvancedMolecular Diagnostics (CAMD; Brigham and Women’s Hospital) using the Maxwell RSC Tissue kit. 100ng RNA was used.

treatment_protocol: Mice received DMSO or DMSO-reconstituted olaparib, each diluted in saline immediately before intraperitoneal injection, with olaparib administered at 50 mg/kg daily for 3 days. Vehicle (saline) or ADU-S100 was administered intratumorally once on the first day in a single 40 μl injection with ADU-S100 injections containing 50 μg compound. Mice were sacrifised 3 days after treatment start, tumors were extracted and snap-frozen.

tag: agent

value: Murine breast tumor

tag: tumor type

value: Triple negative breast cancer

tag: model

value: K14-Cre;Brcaf/fTrp53f/f syngeneic


title: Olaparib+ADUS100 tumor #1270


title: Kasumi-1 Ava LSD1 rep 1


title: Olaparib+ADUS100 tumor #1251


title: T8ML1-DNMT3A-WT, IP

tag: cell type


title: Senolytic Sham 3

value: Senolytic


title: Kasumi-1 DMSO LSD1 rep 3

value: DMSO

tag: time point


title: Senolytic Sham 5

value: Plantaris Muscle


title: Vehicle 14d Overload 1

value: Vehicle


title: T8ML1-DNMT3A-WT, INPUT


title: T8ML1-DNMT3A-mutant-Q886, IP


title: Senolytic Sham 2

value: Sham


title: Olaparib tumor #1521

value: Olaparib


title: Senolytic 14d Overload 5

value: 2 years


title: Kasumi-1 RUN Ava+ORY 12hr IgG

value: IgG (CST, cat 2729, lot 9)


title: Olaparib tumor #1517


title: Kasumi-1 DMSO LSD1 rep 1


title: Senolytic Sham 1


title: Olaparib tumor #1510


title: Kasumi-1 DMSO LSD1 rep 2


title: T8ML1-DNMT3A-mutant-Q886, INPUT


title: Senolytic 14d Overload 3

value: Overload


title: T8ML1,  DNMT3A-mutant-R882, INPUT


title: Senolytic 14d Overload 4


title: Kasumi-1 RUN Ava 12hr IgG

value: 12 hours


title: Senolytic Sham 4


title: T8ML1,  DNMT3A-mutant-V716, IP


title: ADUS100 tumor #1512


title: Kasumi-1 RUN ORY 12hr IgG


title: T8ML1,  DNMT3A-mutant-R882, IP


title: ADUS100 tumor #1506


title: Vehicle tumor #1269


title: Vehicle tumor #1536


title: RNA-seq of WT_3

status: Public on May 28 2022

city: qingdao

first: yang

last: zhao

address: binhai road72#

country: China

institute: shandong university

data_processing:
Clean reads were then aligned to the Medicago truncatula reference transcriptome (version 4.0) using Bowtie, and differential gene expression was analyzed
Genome_build: Medicago truncatula reference transcriptome (version 4.0)
Supplementary_files_format_and_content: XLS file for two sample comparison testing if a gene is differentially expressed

organism: Medicago truncatula

source_name: Medicago truncatula nodules

growth_protocol: The seeds of wild-type and mtbzr1-1 were germinated at 4°C for one week and then transferred into plastic trays filled with pearlite/sand (in a 3:1 ratio).

extract_protocol:
Total RNA was extracted with Trizaol RNA extraction kit (Transgene)
the mRNA sequencing libraries construction and sequencing on the BGISEQ-500 platform were performed at Beijing Geonomics institute(BGI)

treatment_protocol: Five-day-old seedling of wild-type, mtbzr1-1, and were inoculated with 5 mL with Sinorhizobium meliloti 1021

value: 28 days after inoculation

tag: genotype/variation

value: wild type


title: Senolytic 14d Overload 2

tag: tissue


title: RNA-seq of bzr1_1


title: Kasumi-1 RUN DMSO 12hr IgG


title: T8ML1,  DNMT3A-mutant-V716, INPUT

value: Peripheral T-cell lymphoma derived cell line


title: RNA-seq of WT_2


title: Senolytic 14d Overload 1


title: AMB198

city: Stanford

first: Avin

last: Veerakumar

address: 279 Campus Drive, Beckman Center B400

institute: Stanford University

data_processing:
cDNA sequencing reads were pruned for low nucleotide quality scores and adapter sequences using Skewer48 (version 0.2.2).
Reads were aligned to the mm10 genome using STAR (version 2.6.1d) in two-pass mapping mode and read counts were generated.
Assembly: mm10
Supplementary files format and content: "AMB_Cell_IDs.csv": Table with cell IDs, Target (retrograde label origin), and Assigned Cluster (transcriptomic cluster cell was assigned to in Veerakumar et al., 2022)
Supplementary files format and content: "AMB_CPM.csv": Table with cell IDs, genes, and counts per million (CPM) (read count per million reads for given cell)

source_name: Nucleus ambiguus neuron

extract_protocol:
Acute live brainstem slices were generated from the medulla at postnatal day 2 to 4. Cells retrogradely labeled with cholera toxin B fluorescent conjugate were visualized on a fluorescent microscope, aspirated using pulled glass micropipettes, and placed in lysis buffer.
The Smart-seq2 protocol was used to prepare cDNA libraries. Sequencing library was prepared using the Nextera XT Library Sample Preparation kit.
Libraries were sequenced on a NextSeq 500 (Illumina) using 75bp paired-end sequencing and de-multiplexed to generate fastq files

tag: strain

value: Nucleus ambiguus

value: Postnatal day 2 to 4


title: Vehicle tumor #1529

value: Murine breast tumor

value: Triple negative breast cancer


title: ADUS100 tumor #1513

value: K14-Cre;Brcaf/fTrp53f/f syngeneic


title: RNA-seq of bzr1_3


title: AMB203


title: RNA-seq of bzr1_2


title: AMB199


title: AMB202


title: AMB191


title: AMB192


title: AMB201


title: AMB193


title: AMB190


title: AMB186


title: AMB200


title: AMB196


title: AMB195


title: AMB197


title: AMB194


title: RNA-seq of WT_1


title: AMB181


title: AMB180


title: AMB177


title: AMB179


title: AMB189


title: AMB187


title: AMB172


title: AMB170


title: AMB174


title: AMB173


title: AMB185


title: AMB184


title: AMB183


title: AMB182


title: AMB160


title: AMB159


title: AMB178


title: AMB155


title: AMB176


title: AMB171


title: AMB188


title: AMB175


title: AMB152


title: AMB162


title: AMB147


title: AMB168


title: AMB149


title: AMB165


title: AMB166


title: AMB167


title: AMB164


title: AMB156


title: AMB163


title: AMB157


title: AMB161


title: AMB154


title: AMB158


title: AMB169


title: AMB140


title: AMB151


title: AMB153


title: AMB139


title: AMB138


title: AMB137


title: AMB136


title: AMB146


title: AMB150


title: AMB129


title: AMB148


title: AMB130


title: AMB128


title: AMB124


title: AMB132


title: AMB145


title: AMB144


title: AMB121


title: AMB120


title: AMB143


title: AMB142


title: AMB141


title: AMB117


title: AMB135


title: AMB113


title: AMB112


title: AMB109


title: AMB108


title: AMB134


title: AMB133


title: AMB127


title: AMB131


title: AMB104


title: AMB125


title: AMB105


title: AMB126


title: AMB123


title: AMB114


title: AMB102


title: AMB100


title: AMB101


title: AMB119


title: AMB118


title: AMB116


title: AMB095


title: AMB115


title: AMB092


title: AMB094


title: AMB093


title: AMB110


title: AMB090


title: AMB111


title: AMB106


title: AMB122


title: AMB107


title: AMB103


title: AMB087


title: AMB097


title: AMB098


title: AMB099


title: AMB081


title: AMB096


title: AMB077


title: AMB089


title: AMB076


title: AMB085


title: AMB082


title: AMB088


title: AMB083


title: AMB080


title: Sample 11_WT: Placenta from Rgs2-WT sire and wildtype dam

city: Iowa City

first: Justin

middle: L

last: Grobe

state: IA

address: 2-300 Bowen Science Building, Iowa City, IA 52242

department: Pharmacology

institute: University of Iowa

description: GD12.5 Placenta from Rgs2-WT sire and wildtype dam

data_processing:
Kallisto v0.43.1 was used for alignment and quantifying the abundance of transcripts using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include TPM values for each sample

growth_protocol: Animals were maintained in conventional housing, including a standard 12 hour light-dark cycle and an ambient temperature of 25°C, with ad libitum access to tap water and chow (Teklad 7013).

extract_protocol:
Total RNA from placentas of pregnant GD12.5 mice was isolated using mirVanaTM RNA isolation kit (ThemoFisher Scientific: AM1560) per manufacturer’s instructions.
Indexed sequencing libraries were generated from total RNA according to the manufacturer’s (Illumina) suggested protocol.

treatment_protocol: A selective breeding strategy in which wildtype C57BL/6J dams were mated with Rgs2-deficient (Rgs20KO) sires or with wildtype male littermates of these Rgs2-KO sires. These matings resulted in pregnant wildtype C57BL/6J dams carrying feto-placental units that were either heterozygous for Rgs2 or wildtype, respectively. Total RNA from whole placenta at GD 12.5 was isolated, and transcriptomes were assessed by RNAsequencing.

value: Gestation Day 12.5


title: AMB091


title: Sample 8_WT: Placenta from Rgs2-WT sire and wildtype dam


title: AMB079


title: AMB072


title: AMB084


title: AMB078


title: Sample 7_WT: Placenta from Rgs2-WT sire and wildtype dam


title: AMB086


title: Control , Clone-3

city: Taipi

first: Shao-Chin

last: Wu

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: National Yang Ming Chiao Tung University

hyb_protocol: Following fragmentation, 5.2 ug of ss-cDNA were hybridized for 16 hr at 45C on GeneChip™ Mouse Transcriptome Array 1.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G System .

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) Software (version 4.0) using Affymetrix default analysis settings .

label: biotin

source_name: 3T3-L1 Cells infected by the vector only lentivirus

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (GeneChip™WT PLUS Reagent Kit USER GUIDE, 2013, Affymetrix).

growth_protocol: 3T3-Ll murine fibroblasts were maintained in high-glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10 % bovine calf serum and 1% sodium pyruvate. To induce differentiation into adipocyte-like cells, gene modified 3T3-Ll cells were first grown to confluence. Two days after reaching confluence, the medium was replaced with DMEM supplemented with 10 % fetal bovine serum (FBS) containing MDI cocktail, including 0.5 mM IBMX, 0.25 µM dexamethasone, and 10 g/ml bovine insulin. After 72 hours, the medium was replaced with DMEM supplemented with 10 % FBS and 10 µg/ ml bovine insulin. The medium was refreshed every other day. The cells were harvested on day7 of differentiation.

extract_protocol: Total RNA was extracted from cells using TRIzol® reagent

treatment_protocol: shRNA for Stom Lenti-Vector (11,shSTOM-1), Plas4w Lenti-Vector (V, Control), packaging plasmids pCMV delta R8.91 and PMD.G were obtained from the National RNAi Core Facility Platform (Academic Sinica, Taiwan). HEK-293T cells were co-transfected with Lenti-Vector and packaging plasmids using NTR II Non-liposome transfection reagent II (T-Pro-Biotechnology, Taiwan). The supernatants containing lentivirus were harvested after 24- and 48-hour and centrifuged at 1,250 rpm for 5 minutes to exclude any remaining HEK-293T packaging cells. Subsequently, 3T3-L1 cells were transduced with the lentivirus-containing supernatants for 24 hours, followed by 3 µg/mL puromycin selection for 3 days.

value: D7 of adipogenesis

value: adipocyte-like 3T3-L1


title: Sample 12_WT: Placenta from Rgs2-WT sire and wildtype dam


title: AMB074


title: shSTOM-1, Clone-1

source_name: 3T3-L1 Cells infected by the lentivirus containing the shRNA of stomatin


title: shSTOM-1, Clone-3


title: Sample 10_WT: Placenta from Rgs2-WT sire and wildtype dam


title: Control , Clone-1


title: Sample 9_WT: Placenta from Rgs2-WT sire and wildtype dam


title: Sample 6_KO: Placenta from Rgs2-KO sire and wildtype dam

description: GD12.5 Placenta from Rgs2-KO sire and wildtype dam


title: shSTOM-1, Clone-2


title: AMB075


title: AMB066


title: AMB071


title: AMB068


title: AMB069


title: Sample 4_KO: Placenta from Rgs2-KO sire and wildtype dam


title: AMB067


title: AMB064


title: Sample 2_KO: Placenta from Rgs2-KO sire and wildtype dam


title: Sample 5_KO: Placenta from Rgs2-KO sire and wildtype dam


title: Sample 1_KO: Placenta from Rgs2-KO sire and wildtype dam


title: Sample 3_KO: Placenta from Rgs2-KO sire and wildtype dam


title: AMB063


title: AMB070


title: AMB062


title: AMB065


title: AMB060


title: AMB061


title: AMB059


title: AMB058


title: Placenta from AVP-infused pregnant mouse replicate 4

description: Placenta from  GD 12.5 pregnant mouse infused with AVP (24 ng/hr)

extract_protocol:
RNA from placentas of pregnant GD12.5 mice were isolated using mirVanaTM RNA isolation kit (ThemoFisher Scientific: AM1560) per manufacturer’s instructions.
500 ng of RNA was fragmented, converted to cDNA and ligated to sequencing adaptors containing indexes using the Illumina TruSeq stranded mRNA sample preparation kit (Cat. #RS-122-2101, Illumina, Inc., San Diego, CA).  The molar concentrations of the indexed libraries were measured using the 2100 Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA) and combined equally into pools for sequencing.  The concentration of the pools were measured using the Illumina Library Quantification Kit (KAPA Biosystems, Wilmington, MA)

treatment_protocol: Pregnant C57BL/6J mice were infused with arginine vasopressin (AVP, 24ng/hr, sc) or saline via osmotic pumps (Alzet model 1004) from three days before mating until tissues were collected on gestational day 12.5.

tag: gestation day


title: Placenta from AVP-infused pregnant mouse replicate 6


title: AMB057


title: Placenta from saline-infused pregnant mouse replicate 3

description: Placenta from  GD 12.5 pregnant mouse infused with saline


title: Placenta from AVP-infused pregnant mouse replicate 5


title: Placenta from saline-infused pregnant mouse replicate 4


title: Placenta from saline-infused pregnant mouse replicate 1


title: Placenta from saline-infused pregnant mouse replicate 2


title: Placenta from AVP-infused pregnant mouse replicate 3


title: AMB056


title: AMB054


title: AMB053


title: AMB055


title: FL020 VDJ (BCR seq)

city: Houston

first: Michael

middle: R

last: Green

state: TX

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

description:
10x Genomics
FL_meta_bcr.csv

data_processing:
The raw scRNA-seq data were pre-processed (demultiplex cellular barcodes, read alignment and generation of feature-barcode matrix) using Cell Ranger (10× Genomics, v2.1.1)
Detailed QC metrics were generated and evaluated. Genes detected in fewer than three cells and cells where fewer than 200 genes had nonzero counts were filtered out and excluded from subsequent analysis. Low-quality cells where more than 15% of the read counts derived from the mitochondrial genome were also discarded. In addition, cells with more than 7,000 detected genes were discarded to remove likely doublet or multiplet captures.
Assembly: hg19
Supplementary files format and content: Comma-separated values files and matrix files
Library strategy: scVDJ-seq

source_name: lymph node

extract_protocol:
Tissues were processed fresh by physical disaggregation through a metal screen followed by a 40µM filter and loaded onto a 10X Chromium with 5’GEX chemistry to obtain a goal of 10,000 cells per sample.
scRNAseq: Cell lysis and barcoded reverse transcription of RNAs from single cells were finished inside each GEM. Barcoded complementary DNA (cDNA) product was recovered through post GEM-RT cleanup and PCR amplification. cDNA QC and quantification were determined by High Sensitivity D5000 DNA ScreenTape analysis (Agilent Technologies) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). Fifty nanograms of cDNA was used for 5′ Gene Expression library construction, and each sample was indexed by a Chromium i7 Sample Index Kit. scTCR/BCR seq: TCR α/β sequencing was performed with 10× Genomics Single Cell V(D)J Immune Profiling Solution (10× Genomics). Briefly, full-length V, D and J gene segments were amplified from barcoded cDNA using a Chromium Single Cell V(D)J Enrichment Kit (human T cells) to generate enrichment products. Enriched product was measured by D5000 DNA ScreenTape analysis and Qubit dsDNA HS Assay Kit, and then 50 ng of enrichment TCR product was used for library construction. Single Cell V(D)J enriched libraries were pooled for sequencing on HiSeq4000 to produce paired 2 × 150 bp reads, taking into account depth requirement (5,000 read pairs per cell) between the pooled libraries.

value: B cell

value: lymph node


title: RLT2 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: RLT1 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: FL019 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: AMB051


title: AMB073


title: AMB052


title: Placenta from AVP-infused pregnant mouse replicate 1


title: Placenta from AVP-infused pregnant mouse replicate 2


title: AMB049


title: Control , Clone-2

tag: treatment


title: FL017 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: AMB048


title: FL018 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: AMB050


title: FL016 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: AMB047


title: FL014 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: FL015 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: AMB046


title: FL012 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: FL013 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: AMB044


title: AMB045


title: AMB042


title: FL009 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: FL011 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: FL007 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: FL010 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: AMB041


title: AMB040


title: FL008 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: AMB039


title: AMB038


title: FL006 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: FL005 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: FL002 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: AMB036


title: AMB037


title: AMB034


title: AMB035


title: FL004 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: AMB033


title: AMB043


title: AMB032


title: FL001 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: FL019 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv

value: T cell


title: FL003 VDJ (BCR seq)

description:
10x Genomics
FL_meta_bcr.csv


title: AMB026


title: FL020 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: AMB031


title: AMB029


title: AMB030


title: FL017 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: AMB027


title: FL018 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: AMB028


title: FL015 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: AMB023


title: AMB022


title: FL014 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: AMB024


title: FL013 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: FL010 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: FL009 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: FL011 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: AMB025


title: FL012 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: AMB021


title: AMB020


title: AMB019


title: RLT1 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: RLT2 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: FL008 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: AMB018


title: FL016 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: AMB017


title: FL007 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: FL006 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: AMB016


title: FL005 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: FL004 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: AMB012


title: AMB013


title: FL002 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: AMB009


title: AMB011


title: AMB008


title: AMB010


title: FL001 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: FL003 VDJ seq (TCR)

description:
10x Genomics
FL_meta_tcr.csv


title: RLT3 GEX

description:
10x Genomics
FL-gex-meta.csv
FL-matrix.mtx.gz

data_processing:
The raw scRNA-seq data were pre-processed (demultiplex cellular barcodes, read alignment and generation of feature-barcode matrix) using Cell Ranger (10× Genomics, v2.1.1)
Detailed QC metrics were generated and evaluated. Genes detected in fewer than three cells and cells where fewer than 200 genes had nonzero counts were filtered out and excluded from subsequent analysis. Low-quality cells where more than 15% of the read counts derived from the mitochondrial genome were also discarded. In addition, cells with more than 7,000 detected genes were discarded to remove likely doublet or multiplet captures.
Assembly: hg19
Supplementary files format and content: Comma-separated values files and matrix files


title: AMB007


title: FL020 GEX


title: RLT1 GEX


title: FL018 GEX


title: FL019 GEX


title: AMB005


title: AMB015


title: FL016 GEX


title: AMB004


title: AMB003


title: AMB006


title: AMB014


title: FL017 GEX


title: FL014 GEX


title: FL015 GEX


title: FL012 GEX


title: AMB002


title: RLT2 GEX


title: AMB001


title: FL013 GEX


title: FL011 GEX


title: mock rep 2

city: Milano

first: gabriele

last: bucci

state: MI

address: via olgettina 58

department: CTGB

country: Italy

institute: IRCCS Ospedale San Raffaele

data_processing:
Image analysis and base calling were performed using the IlluminaNextSeq Control Software (NCS) version 4.
demultiplexing: bcl2fastq v2.20.0.422
trimming: with BBDuk v38.49 from BBTools suite (sourceforge.net/projects/bbmap/).
alignment: STAR v2.5.3a
R v3.5.1 and Bioconductor v3.8 were used for secondary analysis
counts: featureCounts function from Rsubread v1.6.4 package was used to assign read counts to the genes of the Ensembl GRCm38.97
Genome_build: mm10
Supplementary_files_format_and_content: bigWig signal

source_name: 4T1 mouse mammary gland cancer cells

growth_protocol: 4T1 mouse mammary gland cancer cells (obtained from ATCC, no. CRL-2539) were cultured in DMEM/F12 plus 10% FBS

extract_protocol:
High-quality RNA was extracted from either mock or METTL7A1-overexpressing 4T1 cells (biological triplicates for each experimental condition), and a total of six libraries were prepared using standard Illumina Stranded Total RNA Prep with Ribo-Zero Plus protocol and sequenced on Illumina NovaSeq 6000
Illumina Stranded Total RNA Prep with Ribo-Zero Plus

treatment_protocol: 4T1 cells were stably transfected with full-length Mettl7a1 cDNA cloned into pBICEP-CMV-2 vector using Lipofectamie 3000 (Thermo-Fisher)  and were maintained in selective medium containing  350 μg/ml G418 (SigmaAldrich)

tag: genotype

value: mock


title: mock rep 1


title: mock rep 3


title: FL009 GEX


title: FL007 GEX


title: Mettl7a1 rep 3


title: FL006 GEX


title: FL008 GEX


title: Mettl7a1 polysomal fraction D

description: rybosome-bound RNA

data_processing:
demultiplexing: bcl2fastq v2.20.0.422
trimming: with BBDuk v38.49 from BBTools suite (sourceforge.net/projects/bbmap/).
alignment: STAR v2.5.3a
R v3.5.1 and Bioconductor v3.8 were used for secondary analysis
counts: featureCounts function from Rsubread v1.6.4 package was used to assign read counts to the genes of the Ensembl GRCm38.97
Genome_build: mm10
Supplementary_files_format_and_content: bigWig signal

extract_protocol:
One milliliter fraction was collected monitoring the absorbance at 260 nm using a Density Gradient Fractionation System by Teledyne ISCO with sensitivity set to 0.2. Using the proﬁle of the 260 nm absorbance, fractions corresponding to free ribosomal subunits (40S and 60S) and monosomes (80S, considered as not translating), separately from fractions corresponding to light polysomes (2–5 ribosomes) and heavy polysomes (>6 ribosomes) were pooled together for RNA extraction (see below). Proteins were isolated from each fraction through TCA/acetone precipitation. The same volume of 100% ice-cold acetone and 1/10th of TCA were added to each fraction. The samples were placed at -80°C overnight and then centrifuged at 16000 g for 10 min at 4°C. Pellets were washed three times with 1 ml of 100% ice-cold acetone, dried at RT for 5 min and resuspended in SDS-PAGE loading buffer.
Illumina Stranded Total RNA Prep with Ribo-Zero Plus

treatment_protocol: Either 4T1 mock or 4T1-METTL7A1 cells (~70% conﬂuence) were treated with cycloheximide (0.1 mg/ml) for 5 min at 37 °C, washed twice with PBS supplemented by 0.01 mg/ml cycloheximide, scraped in PBS 1× with 0.01 mg/ml cycloheximide, pelleted by centrifugation, lysed in 500 μl of ice-cold Lysis Buffer (Salt Solution 1X, 1% Triton-X100, 1% NaDeoxycholate, 0.2 U/μl RNase Inhibitor, 1 mM DTT, 0.01 mg ml −1 cycloheximide), centrifuged for 5 min at 16,000 × g at 4 °C, and supernatants were loaded onto sucrose gradients

tag: fraction


title: Mettl7a1 polysomal fraction F

description: rybosome-bound RNA


title: FL005 GEX


title: Mettl7a1 rep 2


title: FL010 GEX


title: Mettl7a1 rep 1


title: Gossypol, 100 µg/ml SAMPLE 24

city: New Orleans

first: Heping

last: Cao

state: LA

address: 1100 Robert E. Lee Blvd

department: Southern Regional Research Center

institute: USDA-ARS

description: Test

hyb_protocol: SYBR Green qPCR reaction mixtures contained 5 ng of total RNA-derived cDNAs, forward primer, reverse primer and 1X iQ SYBR Green Supermix (Bio-Rad Laboratories, Hercules, CA). The thermal cycle conditions were as follows: 3 min at 95°C, followed by 40 cycles at 95°C for 10 s, 65°C for 30 s and 72°C for 30 s. The qPCR reactions were performed in 96-well clear plates sealed by adhesives with a CFX96 real-time system-C1000 Thermal Cycler (Bio-Rad Laboratories).

data_processing:
BCL2 mRNA was selected as the internal reference for qPCR analysis for this cell type (HKG).
1% DMSO treatment was used as sample control
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
"GOS normalized to Bcl2 worksheet" reports normalized signal (against housekeeping genes), where deltaCt = (Ct_Target − Ct_Bcl2)
"GOS normalized to Bcl2 and DMSO worksheet" reports normalized signal (against housekeeping genes and smaple control), where deltadeltaCt = delta(Ct_Target )− delta(Ct_DMSO)
"GOS fold Change worksheet" reports test/control (i.e., test/DMSO control) ratios. The 2-ΔΔCT method of relative quantification was used to determine the fold change in expression.

label: SYBR Green

source_name: COLO 225

label_protocol: The cDNAs were synthesized from total RNA using SuperScript II reverse transcriptase (Life Technologies). The cDNA synthesis mixture (20 μl) contained 2.5 μg total RNA, 2.4 μg oligo(dT)12-18 primer, 0.1 μg random primers, 500 μM dNTPs, 10 mM DTT, 40 units RNaseOUT and 200 units SuperScript II reverse transcriptase in 1X first-strand synthesis buffer (Life Technologies). The cDNA synthesis reactions were incubated at 42°C for 50 min. The cDNA samples were stored in -80°C freezer and diluted with water to 1 ng/µl before qPCR analyses.

extract_protocol: Total RNA was extracted from the human colon cancer cells with Trozol reagent followed by DNase I treatment.

value: epithelial cells isolated in 1975 from ascitic fluid derived from a 70-year-old, Caucasian man with colon cancer.

tag: activation agent

value: Gossypol, 100 µg/ml

tag: time

value: 8 h


title: Gossypol, 100 µg/ml SAMPLE 23

description: Test


title: Mettl7a1 sub polysomal fraction E

description: rybosome-bound RNA


title: Gossypol, 100 µg/ml SAMPLE 22

description: Test


title: FL003 GEX


title: FL004 GEX


title: Mettl7a1 sub polysomal fraction F

description: rybosome-bound RNA


title: KO_IMQ_3

city: Ningbo

first: Liang

last: Yong

state: Zhejiang

address: No. 59, Liuting Street

institute: The First Affiliated Hospital of Ningbo University

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/, version 1.9) was used to remove the reads that contained adaptor contamination.
After removing the low quality bases and undetermined bases, we used HISAT2 software (https://daehwankimlab.github.io/hisat2/, version 2.0.4) to map reads to the genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version 1.3.4d) with default parameters.
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version 0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM.
Assembly: mm10 (GRCm38)
Supplementary files format and content: genes_fpkm_expression.txt: Tab-delimited text file includes FPKM values for each sample.

source_name: skin

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen) following the manufacturer's procedure. The RNA amount and purity of each sample were quantified using NanoDrop 1000 (NanoDrop). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent) with RIN number > 7.0, and confirmed by electrophoresis with denaturing agarose gel. 1 μg of total RNA was used for the construction of sequencing libraries.
Poly (A) RNA was purified from 1 μg total RNA using Dynabeads Oligo (dT) (Thermo Fisher) by two rounds of purification. Then the poly (A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module kit (NEB) at 94℃ for 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript II Reverse Transcriptase (Invitrogen), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB), RNase H (NEB), and dUTP Solution (Thermo Fisher). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 ± 50 bp.

treatment_protocol: For establishment of psoriasis mouse model, WT and KO mice were topically treated with 62.5 mg commercially available 5% IMQ cream on shaved 2.5 cm × 2.5 cm back skin daily for 5 consecutive days. At day 5, mice were euthanized and skin samples were harvested for RNA sequencing.

value: skin

value: Camk4 KO

value: imiquimod


title: KO_IMQ_1


title: KO_IMQ_2


title: WT_IMQ_3

value: WT


title: 11- Control groul  from patient number 4

city: Tehran

first: Pooria

last: Safarzadeh Kozani

state: Tehran

address: Jalaal st.

department: Medical Biotechnology

country: Iran

institute: Tarbiat Modares University

hyb_protocol: Gene Expression Hybridization Kit (5188-5242), Lot: 0006236519

scan_protocol: Project Run Summary: FE_Project1  Project started on Fri, Dec 19, 2014 at 10:08:14.    D:\ScanData\Eng Chee Heng\Year 2014\Mohadese_UPM_8GE(H)_19122014\US83503546_253949429191_S01.tif Fri Dec 19 10:08:14 2014           Processing 8 arrays in single scan.   INFO:     Grid Template in use : 039494_D_F_20120628   INFO:     Protocol in use: GE1_107_Sep09   INFO:     multiple extractions   INFO:     MetricSet in use: GE1_QCMT_Sep09.   INFO:     FE automatically determined that ArrayFormat is 30 micron feature size   INFO:     FE automatically determined that GridFormat is 30 micron feature size   INFO:     FE automatically determined that SpotFormat is 30 micron feature size   INFO:     FE automatically determined that Scanner is Agilent Scanner   INFO:     FE automatically determined that GridTestFormat is 30 micron feature size   INFO:     (Array_1_1) There are 7581 (Green) negative features (Non-Controls).    INFO:     (Array_1_1) 0 (Green) saturated features   INFO:     (Array_1_1) 26 (Green) feature non-uniformity outliers   INFO:     (Array_1_1) 549 (Green) feature population outliers   INFO:     (Array_1_1) 348 (Green) background non-uniformity outliers   INFO:     (Array_1_1) 1648 (Green) background population outliers   INFO:     (Array_1_1) QCMetrics Totals:  Found 10 Metrics In Good Range   INFO:     (Array_1_2) There are 8238 (Green) negative features (Non-Controls).    INFO:     (Array_1_2) 0 (Green) saturated features   INFO:     (Array_1_2) 12 (Green) feature non-uniformity outliers   INFO:     (Array_1_2) 503 (Green) feature population outliers   INFO:     (Array_1_2) 42 (Green) background non-uniformity outliers   INFO:     (Array_1_2) 1478 (Green) background population outliers   INFO:     (Array_1_2) QCMetrics Totals:  Found 10 Metrics In Good Range   INFO:     (Array_1_3) There are 8620 (Green) negative features (Non-Controls).    INFO:     (Array_1_3) 1770 (Green) background population outliers   INFO:     (Array_1_3) QCMetrics Totals:  Found 10 Metrics In Good Range   INFO:     (Array_1_3) 0 (Green) saturated features   INFO:     (Array_1_3) 4 (Green) feature non-uniformity outliers   INFO:     (Array_1_3) 494 (Green) feature population outliers   INFO:     (Array_1_3) 21 (Green) background non-uniformity outliers   INFO:     (Array_1_4) There are 8613 (Green) negative features (Non-Controls).    INFO:     (Array_1_4) 0 (Green) saturated features   INFO:     (Array_1_4) 5 (Green) feature non-uniformity outliers   INFO:     (Array_1_4) 542 (Green) feature population outliers   INFO:     (Array_1_4) 70 (Green) background non-uniformity outliers   INFO:     (Array_1_4) 4453 (Green) background population outliers   INFO:     (Array_1_4) QCMetrics Totals:  Found 10 Metrics In Good Range   INFO:     (Array_2_1) There are 12044 (Green) negative features (Non-Controls).    INFO:     (Array_2_1) QCMetrics Totals:  Found 10 Metrics In Good Range   INFO:     (Array_2_1) 0 (Green) saturated features   INFO:     (Array_2_1) 8 (Green) feature non-uniformity outliers   INFO:     (Array_2_1) 786 (Green) feature population outliers   INFO:     (Array_2_1) 219 (Green) background non-uniformity outliers   INFO:     (Array_2_1) 2170 (Green) background population outliers   INFO:     (Array_2_2) There are 12142 (Green) negative features (Non-Controls).    INFO:     (Array_2_2) QCMetrics Totals:  Found 10 Metrics In Good Range   INFO:     (Array_2_2) 0 (Green) saturated features   INFO:     (Array_2_2) 14 (Green) feature non-uniformity outliers   INFO:     (Array_2_2) 767 (Green) feature population outliers   INFO:     (Array_2_2) 2107 (Green) background population outliers   INFO:     (Array_2_2) 57 (Green) background non-uniformity outliers   INFO:     (Array_2_3) 1637 (Green) background population outliers   INFO:     (Array_2_3) 34 (Green) background non-uniformity outliers   INFO:     (Array_2_3) 747 (Green) feature population outliers   INFO:     (Array_2_3) QCMetrics Totals:  Found 10 Metrics In Good Range   INFO:     (Array_2_3) 6 (Green) feature non-uniformity outliers   INFO:     (Array_2_3) 0 (Green) saturated features   INFO:     (Array_2_3) There are 14138 (Green) negative features (Non-Controls).    INFO:     (Array_2_4) QCMetrics Totals:  Found 9 Metrics In Good Range, Found 1 Metrics In Evaluate Range   INFO:     (Array_2_4) There are 11503 (Green) negative features (Non-Controls).    INFO:     (Array_2_4) 2436 (Green) background population outliers   INFO:     (Array_2_4) 268 (Green) background non-uniformity outliers   INFO:     (Array_2_4) 700 (Green) feature population outliers   INFO:     (Array_2_4) 7 (Green) feature non-uniformity outliers   INFO:     (Array_2_4) 0 (Green) saturated features   QCREPORT: D:\ScanData\Eng Chee Heng\Year 2014\Mohadese_UPM_8GE(H)_19122014\US83503546_253949429191_S01_GE1_107_Sep09_1_1.pdf  QCREPORT: D:\ScanData\Eng Chee Heng\Year 2014\Mohadese_UPM_8GE(H)_19122014\US83503546_253949429191_S01_GE1_107_Sep09_1_2.pdf  QCREPORT: D:\ScanData\Eng Chee Heng\Year 2014\Mohadese_UPM_8GE(H)_19122014\US83503546_253949429191_S01_GE1_107_Sep09_1_3.pdf  QCREPORT: D:\ScanData\Eng Chee Heng\Year 2014\Mohadese_UPM_8GE(H)_19122014\US83503546_253949429191_S01_GE1_107_Sep09_1_4.pdf  QCREPORT: D:\ScanData\Eng Chee Heng\Year 2014\Mohadese_UPM_8GE(H)_19122014\US83503546_253949429191_S01_GE1_107_Sep09_2_1.pdf  QCREPORT: D:\ScanData\Eng Chee Heng\Year 2014\Mohadese_UPM_8GE(H)_19122014\US83503546_253949429191_S01_GE1_107_Sep09_2_2.pdf  QCREPORT: D:\ScanData\Eng Chee Heng\Year 2014\Mohadese_UPM_8GE(H)_19122014\US83503546_253949429191_S01_GE1_107_Sep09_2_3.pdf  QCREPORT: D:\ScanData\Eng Chee Heng\Year 2014\Mohadese_UPM_8GE(H)_19122014\US83503546_253949429191_S01_GE1_107_Sep09_2_4.pdf  INFO:     Extraction completed successfully.   QCChart: D:\ScanData\Eng Chee Heng\Year 2014\Mohadese_UPM_8GE(H)_19122014\FE_Project1.pdf    Project finished on Fri, Dec 19, 2014 at 10:14:45.

data_processing:
Normalizing Agilent One-Color Microarray Data  When comparing data across a set of one-color microarrays, a simple linear  scaling of the data is usually sufficient for most experimental applications.  Agilent has determined that the signal value of the 75th percentile of all of  non-control probes on the microarray is a more robust and representative  value of the overall microarray signal as compared to the median or 50th  percentile signal. Therefore, use the 75th percentile signal value to normalize  Agilent one-color microarray signals for inter-array comparisons.  To do downstream analysis of Agilent microarray data  •Use GeneSpring GX 9.0 or later.  Note that the default normalization scheme for Agilent one-color data in the  GeneSpring GX 9 (or later) program is 75th percentile normalization.  For more information on the GeneSpring GX program, go to  http://www.agilent.com/chem/genespring.To use Feature Extraction  To normalize Agilent one-color microarray data without the GeneSpring  program, use the 75th percentile value for each microarray assay in the  Agilent Feature Extraction text file.  1Generate a Feature Extraction text file.  2Find the “STATS Table” in the middle section of the text file. This section describes the results from the array-wide statistical calculations.  3Find the 75th percentile value of the non-control signals under the column with the heading gPercentileIntensityProcessedSignal.  4Divide each of the green processed signals (gProcessedSignal) by the 75th percentile signal (gPercentileIntensityProcessedSignal) to generate the 75th percentile normalized microarray processed signals.  You can further scale the resulting 75th percentile-normalized signals by a  constant, such as the average of the 75th percentile signals of the arrays in the  experiment.  For more information on the output from the Agilent Feature Extraction  program, please refer to the Agilent G2567AA Feature Extraction Software  Reference Guide. You can download this guide from the Agilent Web site at  www.agilent.com/chem/dnamanuals-protocols.
A total of 927 dysregulated genes were detected by micro array and 712 genes were identified as DEGs (differentially expressed genes). The inclusion criteria were p value of less than 0.05 and, more than two fold changes in expression. Filtered genes were categorized by DAVID software based on gene ontology (GO). Genes involved in controlling the proliferation of HSC such as self-renewal related signaling pathway regulators (e.g. Wnt , MAPK, Hedgehog, FGF, P53, JAK-STAT , TGF-beta),  cytokine-cytokine receptor interaction regulators, cell cycle regulators, and apoptosis regulators which were obtained through micro array analysis were categorized by DAVID software. Figure 4-30 shows categorization of differentially expressed genes (DEGs) in HSC after co-culture with MSC based on pathways and Gene Ontology (GO).

source_name: Hematopoietic stem cells culturing alone

label_protocol: 100 ng of total RNA was labeled with Low Input Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-2305) following manufacturer instruction (One-Color Microarray-Based Gene Expression, Analysis Low Input Quick Amp Labeling, version 6.5). Briefly, 100 ng of total RNA was converted into double-stranded cDNA by priming with an oligo-dT primer containing the recognition site for T7 RNA polymerase. In vitro transcription with T7 RNA polymerase was used to produce cyanine 3-CTP labeled cRNA. 600ng of labeled cRNA was hybridized onto Agilent SurePrint G3 Human GE 8x60K Microarray for 17 hours at 65oC, 10 rpm in Agilent hybridization oven. After hybridization, the microarray slide was washed in gene expression wash buffer 1 for one minute at room temperature and another minute in gene expression wash buffer 2 at 37oC before scanning on Agilent High Resolution Microarray Scanner (C-model). Raw signal data were extracted from the TIFF image with Agilent Feature Extraction Software (V10.7.1.1).Low Input Quick Amp Labeling Kit (Agilent: 5190-2331), Lot: 0006223633 (8 samples)

growth_protocol: Suspended Hematopoietic stem cell were seeded in 24-well tissue culture plates at a density of 2×104 cells/ well on top of the mitomycin-C treated feeder layer made of mesenchymal stem cell  , in DMEM-F12 [supplemented with 10% fetal bovine serum combined with growth factors (SCF (100 ng/mL), IL-3 (50 ng/mL), and GM-CSF (25 ng/mL). Cells were incubated at 37°C with 5% CO2 in a humidified incubator for 7 days without media change.

extract_protocol: Total RNA from HSC (from 4 different individuals) that were cultured with MSC (Test Group) and were cultured alone (Control Group) were extracted after 7 days with RNeasy Plus Mini Kit (Qiagen GmbH, Hilden, Germany), based on the protocol that was recommended by manufacturer (APPENDIX 2). RNA quantity was checked by Nano-Drop ND-1000 (Thermo Scientific, Wilmington, DC, USA).  RNA samples with 260/280 ratio in the range of 2–2.3 and a 260/230 ratio in the range of 2.3–2.6 were used for subsequent analyses. The integrity of the RNA samples was also verified by Genomax in-house facility (Genomax Technologies Sdn Bhd, Molecular Genomics Pte Ltd, Southeast Asia, Singapore). Samples were sent to Genomax for micro array analysis.

value: Hematopoietic stem cell were isolated Human cord blood

tag: label (cy3 conc pmol/ul)


title: 9- Control groul  from patient number 3

treatment_protocol: Suspended Hematopoietic stem cell were seeded in 24-well tissue culture plates at a density of 2×104 cells/ well on top of the mitomycin-C treated feeder layer made of mesenchymal stem cell  , in DMEM-F12 [supplemented with 10% fetal bovine serum combined with growth factors (SCF (100 ng/mL), IL-3 (50 ng/mL), and GM-CSF (25 ng/mL). Cells were incubated at 37°C with 5% CO2 in a humidified incubator for 7 days without media change.


title: Mettl7a1 polysomal fraction E

description: rybosome-bound RNA


title: 2-Experimental group  from patient number 1

source_name: Hematopoietic stem cells culturing in the presence of Mesenchymal stem cells

value: Mesenchymal stem cell were isolated from human umblical cord tissue


title: WT_IMQ_1


title: 7- Control groul  from patient number 2


title: 8-Experimental group  from patient number 2


title: Mettl7a1 sub polysomal fraction D

description: rybosome-bound RNA


title: 12-Experimental group  from patient number 4


title: 10-Experimental group  from patient number 3


title: FL001 GEX


title: mock polysomal fraction C

description: rybosome-bound RNA


title: Gossypol, 50 µg/ml SAMPLE 20

description: Test

value: Gossypol, 50 µg/ml


title: Gossypol, 50 µg/ml SAMPLE 21

description: Test


title: WT_IMQ_2


title: dissociated bulk-seq control testes - rep 3 (compared to intact control testes)

city: Gainesville

first: Tracie

last: Baker

state: FL

institute: University of Florida

data_processing:
Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01
Count data was imported to Seurat (version 4.0.4) for quality control (QC) filtering, clustering, dimensionality reduction, visualization, and differential gene expression
Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.
Samples were merged prior to normalization and clustering (resolution 0.3).
Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function
Genome_build: Zebrafish May 2017 (GRCz11/danRer11) Assembly
Supplementary_files_format_and_content: xlsx; read counts and DEGs; Cell Ranger output matrices
10X SC TCDD DEG clusters: 10X Single cell cluster DEGs
GEO_CDxCI read counts_DEGs: Control dissociated cells compared to Control intact cells
GEO_CPxCB read counts_DEGs: Control psuedo bulk-seq compared to Control dissociated cells for bulk-seq
GEO_TBxCB read counts_DEGs: TCDD dissociated cells compared to Control dissociated cells
GEO_TPxCP read counts_DEGs: TCDD psuedo bulk-seq compared to Control psuedo bulk-seq
GEO_TPxTB read counts_DEGs: TCDD psuedo bulk-seq compared to TCDD dissociated cells bulk -seq

molecule: polyA RNA

organism: Danio rerio

source_name: testes

growth_protocol: Zebrafish were maintained on a 14:10h light/dark cycle, with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin-Madison, according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals (Protocol No. M00489).

extract_protocol:
Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5,000-cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate.
cDNA libraries of mRNA from 25,000 cells were constructed using the 10x Genomics platform, and sequenced on a NovaSeq.

treatment_protocol: Experimental fish (Sample 4 and 5) were exposed to 1 hour of TCDD at 3 and 7 weeks post-fertilization, allowed to mature, and testes were harvested as adults.

value: AB

value: 50 pg/mL 0.1% DMSO

tag: sample preparation

value: dissociated cell suspension


title: mock polysomal fraction B

description: rybosome-bound RNA


title: Gossypol, 50 µg/ml SAMPLE 19

description: Test


title: 1- Control groul  from patient number 1


title: FL002 GEX


title: Gossypol, 10 µg/ml SAMPLE 17

description: Test

value: Gossypol, 10 µg/ml


title: Gossypol, 10 µg/ml SAMPLE 18

description: Test


title: dissociated bulk-seq control testes - rep 2 (compared to intact control testes)


title: Gossypol, 10 µg/ml SAMPLE 16

description: Test


title: mock polysomal fraction A

description: rybosome-bound RNA


title: bulk-seq intact control testes - rep 3

value: non-dissociated (intact) testes


title: mock sub polysomal fraction B

description: rybosome-bound RNA


title: mock sub polysomal fraction A

description: rybosome-bound RNA


title: mock sub polysomal fraction C

description: rybosome-bound RNA


title: Gossypol, 5 µg/ml SAMPLE 15

description: Test

value: Gossypol, 5 µg/ml


title: batch 2 AMP-3

city: Hong Kong

first: Lifang

last: HAN

address: 6202D, Clear Water Bay

department: LIFS

institute: HKUST

data_processing:
fastq files were generated on basespace
Low quality reads and adaptor sequences were trimmed from the raw reads file using Trim Galore
Trimmed sequencing reads were mapped to the mouse mm10 genome assembly using the STAR RNA-seq aligner
Gene count table was generated using FeatureCounts from Subread package with following parameters: -p -t exon -g gene_id
Differential analysis was done using DEseq2 package in R
Genome_build: mm10 (Mus musculus)
Supplementary_files_format_and_content: tab-delimited text file containing raw counts for each sample
Supplementary_files_format_and_content: tab-delimited text file containing fpkm values for each sample

source_name: hindlimb muscle

growth_protocol: Muscle satellite cells were cultured in groeth medium (F10 plus 10% Horse Serum)

extract_protocol:
Total RNA was extracted with the NucleoSpin RNA XS kit (MACHEREY-NAGEL) following manufacture’s instruction
cDNA was then synthesized and amplified according to the Smart-Seq2 protocol. Purified cDNA was then fragmented using Tn5 followed by library construction using TruePrep® DNA Library Prep Kit V2 for Illumina.

treatment_protocol: One triplicate was treated with 0.1 mM Adenosine,another one was treated 0.25 mM AMP for 24 hours, while the DMSO treated group served as control


title: Gossypol, 5 µg/ml SAMPLE 14

description: Test


title: Gossypol, 1 µg/ml SAMPLE 12

description: Test

value: Gossypol, 1 µg/ml


title: bulk-seq TCDD testes-rep 2(to be compared  to scRNA-seq TCDD testes)

value: 50 pg/mL TCDD in 0.1% DMSO


title: mock

data_processing:
Image analysis and base calling were performed using the IlluminaNextSeq Control Software (NCS) version 4.
demultiplexing: bcl2fastq v2.20.0.422
pipe4C v1.0
chr15:100,302,780 as viewpoint; and CAGCAACCACATGGTGGCTCA sequence as primer
Peaks were then called using PeakC v0.2 R package with a window size of 10 (wSize=10)
Genome_build: mm10
Supplementary_files_format_and_content: wiggle variable step signal

source_name: NMuMG mouse mammary gland cancer cells

growth_protocol: Trypsinized cells were cross-linked in suspension with 2% formaldehyde for 10 min at room temperature in culture medium

extract_protocol:
DNA was then extracted with Phenol–chloroform–isoamyl alcohol mixture (Sigma Aldrich) and Ethanol precipitated
3C-Seq libraries construction with Illumina primers was performed
3C-Seq

treatment_protocol: Formaldehyde was then quenched with 200 mM of glycine for 5 min at 4ºC. Cells were then washed in ice-cold PBS, pelleted, and lysed with lysis buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 0.2% NP40, 1X cOmplete [Roche]) for 10 min at 4ºC. The nuclear pellets were washed once with PBS, snap-frozen, and stored at -80ºC. Nuclei were incubated with 0.5% SDS in ultrapure H2O at 62ºC for 10 min in a Thermomixer (600 rpm, Eppendorf) then SDS was quenched with Triton X-100 for 15 min at 37ºC with shaking (600 rpm). Restriction Enzyme buffer (NEBuffer, New England Biolabs) was added to reach 1X ﬁnal concentration. DNA was then digested with 600U DpnII restriction endonuclease (New England Biolabs) overnight at 37ºC at 900 rpm. Inactivation of DpnII was performed by incubating the samples at 62ºC for 20 min at 900 rpm. Digestion was checked by agarose gel electrophoresis and ligation with T4 DNA Ligase (New England Biolabs) was carried out for 4 hours at 20ºC at 900 rpm.

value: mock

value: NMuMG


title: NMuMG-EPR

value: NMuMG-EPR


title: bulk-seq intact control testes - rep 1


title: batch 2 AMP-1


title: batch 2 Adenosine-3


title: RENCA_B4_R2

city: Los Angeles

first: Paul

last: Boutros

address: 10833 Le Conte Ave

department: Human Genetics

institute: University of California, Los Angeles

data_processing:
The identification of differentially methylated regions was performed using SeqMonk (The Babraham Institute).
To identify locus-specific differences in methylation, we performed 12 Chi-square test with FDR adjusted p-values less than 0.05 as well as a logistic regression under the same constraints. We then applied a threshold of 25% absolute difference in methylation between parental and KO cells.
Assembly: NOT PROVIDED
Supplementary files format and content: NOT PROVIDED

source_name: Kidney

extract_protocol: DNA was obtained from cultured cells using Maxwell RSC (Promega); BIOO NEXTflex Bisulfite-Seq Kit

value: Kidney

tag: cell line

value: RENCA

value: renal cell carcinoma

value: Bisulphite sequencing


title: batch 2 Adenosine-2


title: bulk-seq TCDD testes-rep 1 (to be compared to scRNA-seq TCDD testes)


title: RENCA_B4_R1


title: Gossypol, 1 µg/ml SAMPLE 11

description: Test

value: epithelial cells isolated in 1975 from ascitic fluid derived from a 70-year-old, Caucasian man with colon cancer.

value: 8 h


title: bulk-seq control testes-rep 3 ( to be compared to  scRNA-seq control testes)

value: AB


title: dissociated bulk-seq control testes - rep 1 (compared to intact control testes)

value: 50 pg/mL 0.1% DMSO


title: bulk-seq intact control testes - rep 2


title: Gossypol, 1 µg/ml SAMPLE 10

description: Test


title: RENCA_JL1_R2

value: Sdhb-KO


title: batch 2 AMP-2


title: batch 2 DMSO-3


title: bulk-seq control testes-rep 2 ( to be compared to  scRNA-seq control testes)

value: dissociated cell suspension


title: bulk-seq control testes-rep 1 (to be compared to scRNA-seq control testes)


title: Gossypol, 0.5 µg/ml SAMPLE 9

description: Test

value: Gossypol, 0.5 µg/ml


title: RENCA_JL1_R1


title: Gossypol, 0.5 µg/ml SAMPLE 8

description: Test


title: Gossypol, 5 µg/ml SAMPLE 13

description: Test

value: Gossypol, 5 µg/ml


title: batch 2 DMSO-2


title: RENCA_parental_R2

value: WT


title: RENCA_parental_R1


title: scRNA-seq TCDD testes - rep 2

value: 50 pg/mL TCDD in 0.1% DMSO


title: Gossypol, 0.5 µg/ml SAMPLE 7

description: Test


title: Adenosine 3

growth_protocol: Muscle satellite cells were cultured in growth medium (F10 plus 10% Horse Serum)

treatment_protocol: One triplicate was treated with 0.05mM Adenosine while another one with DMSO as control for 24 hours

value: hindlimb muscle

value: satellite cells

value: Adenosine


title: Gossypol, 0.1 µg/ml SAMPLE 6

description: Test

value: Gossypol, 0.1 µg/ml


title: batch 2 DMSO_1


title: scRNA-seq TCDD testes - rep 1


title: Gossypol, 0.1 µg/ml SAMPLE 5

description: Test


title: scRNA-seq control testes - rep 2


title: scRNA-seq control testes - rep 3


title: Adenosine 1


title: Adenosine 2


title: Gossypol, 0.1 µg/ml SAMPLE 4

description: Test


title: LPS-induced sepsis HUVECs, LPS2, 12h

city: Beijing

first: Haiyan

last: Liao

state: Beijing

address: 168 Litang Road Changping District, Beijing, China

institute: Tsinghua University

data_processing:
Illumina PE150
Raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts.
Clean reads for each sample were first mapped to a reference genome with the software HISAT2. Reads alignment results were transferred to the program StringTie for transcript assembly.
Quantification of the transcripts and genes was performed using StringTie software.
analysis
Assembly: mm9
Supplementary files format and content: tab-delimited text files include readcount and TPM  values for each Sample

source_name: Human umbilical vein endothelial

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

extract_protocol:
Total RNA was extracted using total RNA kit (TAKARA, Japan)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sepsis was induced by treatment of 12h with 1000ng/ml LPS (Sigma),

value: endothelial cells

value: LPS-induced

value: Sepsis


title: LPS-induced sepsis HUVECs, LPS1, 12h


title: Human umbilical vein endothelial cells (HUVECs), Control2, 12h


title: batch 2 Adenosine-1


title: DMSO, 1% SAMPLE 2

description: Control

value: epithelial cells isolated in 1975 from ascitic fluid derived from a 70-year-old, Caucasian man with colon cancer.

value: DMSO, 1%


title: DMSO2

value: DMSO


title: DMSO3


title: DMSO, 1% SAMPLE 1

description: Control

value: 8 h


title: Human umbilical vein endothelial cells (HUVECs), Control1, 12h


title: LPS-induced sepsis HUVECs, LPS3, 12h


title: DMSO1


title: HNF4A-5ugml-rep1

status: Public on May 27 2022

city: St. Louis

first: Barak

last: Cohen

state: MO

address: 4515 McKinley Ave

department: Genetics

institute: Washington University in St. Louis

data_processing:
We aligned transcripts with bowtie2 using recommended parameters (Kaya-Okur et al. 2020): --very-sensitive --end-to-end --no-mixed --no-discordant -I 10 -X700.
We used DeepTools bamCoverage (Ramirez et al. 2016) to generate RPKM normalized bigwig coverage files.
We called peaks with macs2 with p=1e-5.
We combined overlapping peaks from replicate samples with bedtools intersect.
Assembly: hg19
Supplementary files format and content: Peak files from macs2 are in .narrowPeak format.
Library strategy: CUT&Tag

growth_protocol: We used clonal FOXA1 and HNF4A lines derived from K562 blood cells (ATCC CCL-243) that were previously transduced with doxycycline-inducible FOXA1 or HNF4A lentiviral constructs. We cultured lines in IMDM supplemented with 10% FBS, 1% penicillin-streptomycin, and 1% non-essential amino acids at 37C.

extract_protocol:
We isolated 1e5 cells/sample and then followed the CUTANA Direct-to-PCR CUT&Tag protocol (Epicypher).
We generated libraries by following the CUTANA Direct-to-PCR CUT&Tag protocol (Epicypher) and then size selected the libraries with AmpureXP beads.

treatment_protocol: We induced transgene expression by treating cells for 24 hours with a range of doxycycline concentrations.

tag: cell line background

value: Immortalized lymphoblast

value: HNF4A doxycycline-inducible clonal line

value: 5ug/ml doxycycline for 24 hours

tag: primary antibody

value: Mouse anti-human Hnf4a monoclonal (Invitrogen #MA1-199)

tag: secondary antibody

value: Goat anti-mouse (Epicypher #13-0048)


title: HNF4A-0.25ugml-rep2

tag: cell type

value: 0.25ug/ml doxycycline for 24 hours


title: HNF4A-0.05ugml-rep1

value: 0.05ug/ml doxycycline for 24 hours


title: DMSO, 1% SAMPLE 3

description: Control


title: HNF4A-0.05ugml-rep2


title: HNF4A-0.1ugml-rep2

value: 0.1ug/ml doxycycline for 24 hours


title: HNF4A-0.25ugml-rep1


title: HNF4A-0.1ugml-rep1


title: HNF4A-5ugml-rep2


title: HNF4A-0.5ugml-rep1

value: 0.5ug/ml doxycycline for 24 hours


title: Human umbilical vein endothelial cells (HUVECs), Control3, 12h

value: WT


title: FOXA1-5ugml-rep1

value: FoxA1 doxycycline-inducible clonal line

value: Rabbit anti-human FoxA1 monoclonal (Cell Signaling #53528)

value: Goat anti-rabbit (Epicypher #13-0047)


title: HNF4A-0.005ugml-rep2

value: 0.005ug/ml doxycycline for 24 hours


title: FOXA1-5ugml-rep2


title: FOXA1-0.5ugml-rep1


title: FOXA1-0.1ugml-rep2


title: FOXA1-0.25ugml-rep1


title: FOXA1-0.5ugml-rep2


title: FOXA1-0.1ugml-rep1


title: FOXA1-0.25ugml-rep2


title: HNF4A-0.005ugml-rep1


title: HNF4A-0.5ugml-rep2


title: FOXA1-0.05ugml-rep1


title: FOXA1-0.005ugml-rep2


title: FOXA1-0.005ugml-rep1


title: MET delta 14 exon 6h HGF NCIH596S6skp146hHGF1

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

description: MET delta 14 exon 6h HGF

data_processing:
Read were trimmed with skewer v 1.0
Mapping was performed using STAR v 2.5.0
Counts were generated unsing RSEM 1.3.2
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited

source_name: cell line

growth_protocol: Cell were purchased from ATCC and  cultured according to manufacturer's instructions

extract_protocol:
QIAGEN RNeasy® Mini Kit. Extraction was performed following the manufacture's instruction
Illumina TrueSeq kit was used, following the manufacture's instruction

treatment_protocol: After serum deprivation for 12 hours HGF was added

value: lung adenosquamous carcinoma cell line


title: MET delta 14 exon 3h HGF NCIH596S3skp143hHGF2

description: MET delta 14 exon 3h HGF


title: MET delta 14 exon 6h HGF NCIH596S6skp146hHGF2

description: MET delta 14 exon 6h HGF


title: FOXA1-0.05ugml-rep2


title: MET delta 14 exon no HGF NCIH596Sskp140h1

description: MET delta 14 exon no HGF


title: MET delta 14 exon 12 h HGF NCIH596S12skp1412hHGF2

description: MET delta 14 exon 12 h HGF


title: MET delta 14 exon no HGF NCIH596Sskp140h2

description: MET delta 14 exon no HGF


title: MET delta 14 exon 3h HGF NCIH596S3skp143hHGF1

description: MET delta 14 exon 3h HGF


title: ATAC_Follicle_Fresh_D3

city: Dallas

first: Laura

last: Banaszynski

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

data_processing:
The ATAC-seq reads were aligned to the hg19 human reference genome using the BWA aligner (Li and Durbin, 2010) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).This is the raw bigwigs.
AtacWorks was used to denoise and improve the signal-to-noise ratio. The bigwigs are the denoised tracks obtained from Atacworks.
The seqeunce length was 33 for R1 and 33 for R2 for paired-end data.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: ovarian cortex

extract_protocol:
Ovarian follicles were isolated after liberase digestion and subjected to the Omni-ATAC protocol (Corces 2017).
Libraries were constructed according to the Illumina Nextera protocol.

treatment_protocol: Tissue vitrification and thaw (Kagawa 2009).

tag: individual

value: donor 3

value: follicles derived from ovarian cortex

tag: tissue state

value: Fresh


title: ATAC_Follicle_Fresh_D4

value: donor 4

tag: tissue


title: MET wt 6h HGF A549S6wt6hHGF1

description: MET wt 6h HGF

value: lung cancer cell line


title: MET wt 12h HGF A549S12wt12hHGF1

description: MET wt 12h HGF


title: MET wt 3h HGF A549S3wt3hHGF1

description: MET wt 3h HGF


title: MCF-7_siControl

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

country: Japan

institute: Saitama Medical University

description: Gene expression data from MCF-7 cells treated with control siRNA

hyb_protocol: Approximately 5.5 micro g of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45 degrees centigrade for 16 hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix GeneChip Command Console Software (AGCC).

source_name: MCF-7 cells treated with siControl

label_protocol: cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: Human breast cancer MCF-7cells were maintained in Dulbecco's modified Eagle's medium (DMEM).

extract_protocol: Total RNA was extracted using ISOGEN reagent (Nippon Gene, Japan).

treatment_protocol: MCF-7 cells were transfected with siRNAs targeting SCFD2 (siSCFD2 #A and #B) or control siRNA (siControl) for 48 hours.

value: breast cancer MCF-7 cells

value: siControl


title: ATAC_Follicle_Cryo_D2

data_processing:
The ATAC-seq reads were aligned to the hg19 human reference genome using the BWA aligner (Li and Durbin, 2010) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).This is the raw bigwigs.
AtacWorks was used to denoise and improve the signal-to-noise ratio. The bigwigs are the denoised tracks obtained from Atacworks.
The sequence length was 33 for R1 and 33 for R2 for paired-end data.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

value: donor 2

value: Cryo


title: MET wt 6h HGF A549S6wt6hHGF2

description: MET wt 6h HGF


title: ATAC_Follicle_Cryo_D1

value: donor 1


title: MET wt no HGF A549Swt0h2

description: MET wt no HGF


title: ATAC_Follicle_Fresh_D2


title: MET wt no HGF A549Swt0h1

description: MET wt no HGF


title: scRNA-seq control testes - rep 1

tag: strain

value: AB

value: 50 pg/mL 0.1% DMSO

value: dissociated cell suspension


title: IPS_BAMS9_3

city: Marseille

first: Frederique

last: Magdinier

address: 27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone

country: France

institute: Aix-Marseille Université - Marseille Medical Genetics

data_processing:
We assessed fastq sequence data quality using FastQC v0.11.5 (Andrews, 2010) and trimmed the reads to remove adapter sequences and low quality bases using Trimmomatic v0.36
Paired end reads were aligned using STAR v2.5.3a  to the GRCh38 human genome release
BAMS index were generated using Sambamba v0.6.6
DEGs and abundance measurements were identified using StringTie v1.3.1c and R package DESeq2 v1.30.1 (median of ratio)
Genome_build: GRCh38 human genome
Supplementary_files_format_and_content: tab-delimited text files (.xlsx) include TPM values for each Sample and DEGs

source_name: hIPSCs

growth_protocol: Fibroblasts were cultivated in DMEM + 10% FBS + 1% penicilline/streptomycine. hiPSCs were grown in mTESR1.

extract_protocol:
Total RNA was extracted using the RNAeasy kit (Qiagen) following manufacturer’s instructions. Quality, quantitation and sizing of total RNA was evaluated using the RNA 6000 Pico assay.  (Agilent Technologies Ref. 5067-1513) on an Agilent 2100 Bioanalyzer system.
RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: disease

value: BAMS (bosma arhinia microphthalmia syndrome)


title: IPS_BAMS9_4


title: MET delta 14 exon 12 h HGF NCIH596S12skp1412hHGF1

description: MET delta 14 exon 12 h HGF


title: ATAC_Follicle_Cryo_D5

value: donor 5


title: MET wt 3h HGF A549S3wt3hHGF2

description: MET wt 3h HGF


title: MCF-7_siSCFD2_#A

description: Gene expression data from MCF-7 cells treated with siRNA targeting SCFD2 (siSCFD2 #A)

source_name: MCF-7 cells treated with siSCFD2 #A

tag: treatment

value: siSCFD2 #A


title: MCF-7_siSCFD2_#B

description: Gene expression data from MCF-7 cells treated with siRNA targeting SCFD2 (siSCFD2 #B)

source_name: MCF-7 cells treated with siSCFD2 #B

value: siSCFD2 #B


title: IPS_AG09_4

value: CT


title: IPS_BAMS9_1


title: IPS_AG09_2


title: IPS_AG09_3


title: IPS_AG09_1


title: IPS_BAMS9_2


title: IPS_14586_5


title: IPS_14586_6


title: MET wt 12h HGF A549S12wt12hHGF2

description: MET wt 12h HGF


title: ATAC_Follicle_Fresh_D1

value: follicles derived from ovarian cortex


title: Fb_BAMS9_2

source_name: Fibroblasts


title: Fb_AG08C5_3


title: Fb_AG08C5_5


title: Fb_14586_4


title: IPS_14586_2


title: Fb_BAMS9_4


title: BAMS1_IPS_5


title: IPS_14586_4


title: Fb_14586_3


title: Fb_BAMS9_3


title: BAMS1_IPS_4


title: Fb_AG08C5_2


title: Fb_AG08C5_1


title: Fb_14586_2


title: BAMS1_Fb4


title: BAMS1_IPS1


title: BAMS1_IPS_3


title: BAMS1_Fb3


title: BAMS1_Fb2


title: Fb_BAMS9_1


title: AG09_Fb4


title: AG09_Fb3


title: BAMS1_Fb1


title: AG09_Fb2


title: AG09_Fb1


title: AG08C5_IPS_4


title: 11491_IPS_2


title: 11491_IPS_3


title: 11491_IPS_4


title: 11491_Fb1


title: 11491_Fb4


title: AG08C5_IPS_1


title: AG08C5_IPS_3


title: 11491_Fb3


title: 11491_IPS_1