title: MOZ-TIF2, mouse #2553, WM-1119 1 uM 1 hour, rep 2

description: MOZ-TIF2 2553 WM-1119 rep 2 mRNA


title: CDH-Good_13

status: Public on Jul 03 2024

type: SRA

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

library_source: transcriptomic

data_processing:
CLC Genomics Workbench version 9.5.3 program
Sequence reads were trimmed and mapped to the miRbase 21 database allowing up to two base mismatches.
Assembly: miRbase 21
Supplementary files format and content: txt files of raw read counts of each samples

molecule: total RNA

organism: Homo sapiens

source_name: AF-EV

extract_protocol:
Amniotic fluid was collected during cesarean delivery, and we confirmed that no blood contamination or meconium stained amniotic fluid was observed. The samples were centrifuged at 3,000 rpm for 10 min at 4℃, and the supernatant was collected and stored. Then, small EVs were collected from approximately 1 mL of each amniotic fluid sample by the ultracentrifuge method. Briefly, the samples were centrifuged at 10,000 × g for 40 min at 4°C (Kubota 3520), and the supernatant was filtered using a 0.22 µm filter (Millex-GV 33 mm, Millipore). Subseqently. the supernatant was ultracentrifuged at 110,000 × g for 70 min at 4°C using an TLA55 rotor (Beckman Coulter Inc., USA). The pellet was washed with PBS, ultracentrifuged with the same conditions, and resuspended in PBS to extract small EVs. Finally, total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany).
Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA). Then, PCR products were separated by electrophoresis (120 V, 60 min), and DNA fragments corresponding to 140–160 bp (the length of small non-coding RNA plus the adaptors) were recovered.

tag: Sex

value: male

tag: tissue

value: AF-EV

tag: disease state

value: CDH with good prognosis


title: CDH-Good_12


title: CDH-Good_11


title: MOZ-TIF2, mouse #2553, WM-1119 1 uM 1 hour, rep 1

city: Boston

first: Mitzi

middle: I

last: Kuroda

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

country: USA

institute: Brigham and Women's Hospital/Harvard Medical School

description: MOZ-TIF2 2553 WM-1119 rep 1 mRNA

data_processing:
Reads were aligned to the mm10 genome using the STAR alignment tool
BigWig files were generated using Deeptools BamCoverage 3.5.0  and normalized using 1x genome coverage
Assembly: mm10
Supplementary files format and content: bigwig

molecule: polyA RNA

organism: Mus musculus

source_name: Lin- Sca1+ cKit+ (LSK)

growth_protocol: MOZ-TIF2 and MLL-AF9 LSK cells were cultured at 37oC in IMDM media (Gibco) supplemented with 1% Pen/Strep, 20% Fetal Bovine Serum, 0.001% 2-Mercaptoethanol (BME), 6 ng/ml murine IL3, 10 ng/ml murine IL6, and 20 ng/ul murine SCF (Peprotech)

extract_protocol:
mRNA was extracted using the Monarch Total RNA Miniprep Kit (NEB). Ribosomal RNA was removed using PolyA enrichment (NEB)
Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs E7760).

treatment_protocol: Cells were treated with DMSO or 1 uM WM-1119 for 1 hour

tag: cell type

value: Lin- Sca1+ cKit+ (LSK)

tag: genotype

tag: treatment

value: 1 uM WM-1119 1 hour


title: CDH-Good_10


title: MOZ-TIF2, mouse #1, WM-1119 1 uM 1 hour, rep 3

description: MOZ-TIF2 1 WM-1119 rep 3 mRNA


title: GBM1, Patient1, Region2, Section4

city: Tianjin

first: xuejiao

last: lv

state: Tianjin

address: No.22 Qixiangtai Rd

country: China

institute: Tianjin Medical University

description:
GBM1-R2-4_D
Fresh frozen Spatial transcriptome sequencing

data_processing:
*library strategy: Spatial Transcriptomics
Raw sequencing data were processed using the 10 × Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to hg38 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding gene were quantified using Space Ranger's default settings
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_oimage.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png:low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots

source_name: WHO Grade IV GBM

extract_protocol:
For ST sequencing, 16 fresh tissue samples were extracted via surgery from 3 glioblastoma patients. The GBM tumor specimens were promptly frozen in liquid nitrogen and embedded in OCT compound. The frozen tissue specimens were then cryo-sectioned at a thickness of 10 µm and were mounted on pre-treated glass slides and incubated at 37°C for 1 minute , followed by fixation in methanol for 30 min at -20°C and washing in phosphate buffered saline. The current ST protocol was applied to all sections, resulting in both conventional hematoxylin and eosin (H&E) images that were amenable to annotation by pathologists, as well as gene expression profiles for each microarray spot.
Spatial Transcriptomome sequencing libraries were prepared with 10 × Genomics Visium Spatial Gene Expression Slides & Reagent Kit according to manufacturer's construction

value: WHO Grade IV GBM

tag: subject id


title: CDH-Good_9


title: K562_total_60min_rep1

type: RNA

first: Brendan

middle: Michael

last: Smalec

address: 77 Avenue Louis Pasteur, Rm 356

institute: Harvard Medical School

hyb_protocol: Unlabeled (unbound) RNA was hybridized with gene-specific probes at 67°C for at least 16 hours.

scan_protocol: Samples were loaded onto a nCounter Sprint Cartridge (NanoStrings) and analyzed on a nCounter SPRINT Profiler (NanoStrings)

data_processing: raw values are used as the final data set.

source_name: K562 cells

extract_protocol: RNA was extracted from subcellular fractions with Trizol LS according to the manufacturer's protocol. RNA was biotinylated with MTSEA biotin-XX and unlabeled RNA was quantified after depletion of 4sU-labeled RNA by binding to uMACS streptavidin beads.

tag: 4su pulse

tag: molecule subtype

value: Total RNA


title: CDH-Good_8

value: female


title: GBM1, Patient1, Region2, Section2

description:
GBM1-R2-2_B
Fresh frozen Spatial transcriptome sequencing


title: MOZ-TIF2, mouse #1, WM-1119 1 uM 1 hour, rep 2

description: MOZ-TIF2 1 WM-1119 rep 2 mRNA


title: CDH-Poor_2

value: CDH with poor prognosis


title: CDH-Good_6


title: CDH-Good_7


title: MOZ-TIF2, mouse #1, WM-1119 1 uM 1 hour, rep 1

description: MOZ-TIF2 1 WM-1119 rep 1 mRNA


title: GBM1, Patient1, Region2, Section3

description:
GBM1-R2-3_C
Fresh frozen Spatial transcriptome sequencing


title: MOZ-TIF2, mouse #2553, DMSO, rep 3

description: MOZ-TIF2 2553 DMSO rep 3 mRNA

value: DMSO 1 hour


title: CDH-Good_4


title: GBM1, Patient1, Region1, Section4

description:
GBM1-R1-4_D
Fresh frozen Spatial transcriptome sequencing


title: MOZ-TIF2, mouse #2553, DMSO, rep 2

description: MOZ-TIF2 2553 DMSO rep 2 mRNA


title: CDH-Good_2


title: GBM1, Patient1, Region1, Section3

description:
GBM1-R1-3_C
Fresh frozen Spatial transcriptome sequencing


title: GBM1, Patient1, Region2, Section1

description:
GBM1-R2-1_A
Fresh frozen Spatial transcriptome sequencing


title: Ctrl_24

value: healthy control


title: CDH-Good_1


title: CDH-Good_3


title: MOZ-TIF2, mouse #2553, DMSO, rep 1

description: MOZ-TIF2 2553 DMSO rep 1 mRNA


title: GBM1, Patient1, Region1, Section2

description:
GBM1-R1-2_B
Fresh frozen Spatial transcriptome sequencing


title: Ctrl_23


title: Ctrl_22


title: GBM1, Patient1, Region1, Section1

description:
GBM1-R1-1_A
Fresh frozen Spatial transcriptome sequencing


title: MOZ-TIF2, mouse #1, DMSO, rep 2

description: MOZ-TIF2 1 DMSO rep 2 mRNA


title: MOZ-TIF2, mouse #1, DMSO, rep 3

description: MOZ-TIF2 1 DMSO rep 3 mRNA


title: Ctrl_21


title: HTO files for Sa_d10

city: Hannover

first: Rodrigo

last: Gutierrez Jauregui

state: Lower saxony

address: Carl-neuberg Str. 1

department: Immunology

country: Germany

institute: Hannover Medical School

description: 10x Genomics

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software.
The R package Seurat v2.3 was used for further data trimming, unsupervised clustering, and visualization (Butler et al., 2018).
Assembly: mm10
Supplementary files format and content: Processed data include cellranger raw counts (including barcode, feature, and matrix files) before processing in Seurat package and matrices from cell hashing libraries, as determined by CITE-seq-Count protocol (https://cite-seq.com/protocol/; PMID: 30567574)

molecule: other

source_name: Dorsal Skin

extract_protocol:
Single cell suspensions from skin were generated by mechanical disruption (i.e. cut into very small pieces) followed by enzymatic digestion using DNase I (0.5 mg/ml) and collagenase VI (1 mg/ml) 60 min at 37°C in 50ml RPMI. Cells were washed twice in cold PBS and resuspended in FACS buffer (PBS, 2%v/v FCS, 5mM EDTA). They were then stained with anti-CD45 antibody  and cell sorted by FACS.
Cells were labeled with TotalSeq cell hashing antibodies (BioLegend) according to the cell hashing protocol (https://cite-seq.com/protocol/). After labeling, 5000 cells from each of 4 mice per group were pooled and used to generate single-cell gel beads in emulsions using the Chromium Single Cell 3′ Library & Gel Bead Kit v.3 following the manufacturer’s protocols. During reverse transcription, 1 µl hash tag oligo (HTO) PCRadditive primer (0.2 µM) was added to the cDNA amplification mixture to increase the yield of HTO products. After cDNA amplification, HTO-derived cDNAs were separated from mRNA-derived cDNAs using solid phase reversible immobilization (SPRI) selection and further purified, amplified, and fragmented according to the cell hashing protocol or Chromium Single Cell 3′ Reagent Kit v3 user guide (10x Genomics), respectively. For sequencing, sample indexes were added during index PCR (12 cycles), and purified libraries were sequenced on a NextSeq 550 (Illumina).

value: Dorsal Skin

value: CD45 positive

value: Staph aureus biofilm infection

tag: library type

value: Cell hashing libraries


title: MDA-MB-231 cells, siKHSRP_3

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 888 Gaoxin Avenue

institute: Nissi Biotech

data_processing:
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped.
After that, clean reads were aligned to the human genome by HISAT2 (Kim, Paggi et al. 2019) allowing maximum 4 mismatches. Uniquely mapped reads were used for gene reads number counting and FPKM calculation
The R Bioconductor package DESeq2 (Love, Huber et al. 2014) was utilized to screen out the differentially expressed genes (DEGs). The P value for correction <0.05 and fold change>2 or < 0.5 were set as the cut-off criteria for identifying DEGs.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including FPKM value for each sample

growth_protocol: MDA-MB-231 cell line (Procell, Wuhan, China) was cultured at 37℃ with 5% CO2 in Leibovitz's L-15 with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, 100 U/mL penicillin.

extract_protocol:
Total RNAs were extracted from MDA-MB-231 cells using TRIzol Reagent (NO 15596026, Invitrogen) following the canonical RNA isolation method (Chomczynski and Sacchi 1987). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies Q10210).
Total 2 μg RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.
PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

treatment_protocol: The siRNA transfection into the cells was performed using Lipofectamine™ RNAiMAX transfection reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol.

tag: cell line

value: Human breast cancer cells

value: KHSRP knockdown


title: CDH-Good_5

value: male


title: Ctrl_20

value: AF-EV


title: HTO files for Sa_d2

description: 10x Genomics


title: MOZ-TIF2, mouse #1, DMSO, rep 1

description: MOZ-TIF2 1 DMSO rep 1 mRNA


title: CD45 cells 10dpi, scRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

value: mRNA


title: MDA-MB-231 cells, siKHSRP_1


title: Ctrl_19


title: MLL-AF9, mouse 1D, WM-1119 1 uM 1 hour rep 3

description: MLL-AF9 1D WM-1119 rep 3 mRNA

value: Lin- Sca1+ cKit+ (LSK)


title: Ctrl_18


title: MDA-MB-231 cells, NC_3

value: Negative control


title: CD45 cells 2dpi, scRNAseq

description: 10x Genomics


title: MLL-AF9, mouse 1D, WM-1119 1 uM 1 hour, rep 2

description: MLL-AF9 1D WM-1119 rep 2 mRNA

value: 1 uM WM-1119 1 hour


title: MDA-MB-231 cells, NC_2


title: Ctrl_17


title: MLL-AF9, mouse 1D, WM-1119 1 uM 1 hour, rep 1

description: MLL-AF9 1D WM-1119 rep 1 mRNA


title: MDA-MB-231 cells, NC_1


title: MLL-AF9, mouse 1B, WM-1119 1 uM 1 hour rep 3

description: MLL-AF9 1B WM-1119 rep 3 mRNA


title: Ctrl_16


title: Immobilization MOTS-c, rep6

city: Los Angeles

first: Hiroshi

last: Kumagai

state: CA

address: 3715 McClintock Ave

institute: University of Southern California

description: RNA-seq

data_processing:
The quality of each fastq file was ensured using FastQC.
Sequence reads were mapped to the mouse reference genome (GRCm38.p6) using STAR.
Transcripts per million (TPM) were calculated using the RSEM.
Comparison of the gene expression levels between groups was performed using the DESeq2 package in R.
Assembly: Mouse genome (GRCm38.p6)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Gastrocnemius muscle

extract_protocol:
RNA was extracted from frozen skeletal muscle by using TRIzol (Thermo Scientific), followed by the Quick-RNA Miniprep Kit (Zymo Research).
High quality RNA was used for library preparation (mRNA-Seq Nu Quant), which captured poly-adenylated RNA.

value: Gastrocnemius muscle

tag: strain

value: Male

tag: age

value: 12 weeks old

value: MOTS-c

value: Immobilization


title: Immobilization MOTS-c, rep7

description: RNA-seq


title: MDA-MB-231 cells, siKHSRP_2


title: Ctrl_15

value: healthy control


title: MLL-AF9, mouse 1B, WM-1119 1 uM 1 hour, rep 2

description: MLL-AF9 1B WM-1119 rep 2 mRNA


title: Immobilization MOTS-c, rep5

description: RNA-seq


title: Ctrl_14

value: female


title: UCD1172CR_2

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

data_processing:
RNA-Seq data was analyzed using a hierarchical indexing for spliced alignment of transcripts 2 (HISAT2)-featureCounts pipeline. Raw sequence reads (FASTQ format) were mapped with the HISAT2 aligner to the reference human genome index (GRCh38/hg38, GENCODE release 43) and quantified with the read summarization program featureCounts.
Processed data are gene-level read counts generated from the output of HISAT2 alignment and subsequent quantification with featureCounts.
Assembly: GRCh38/hg38, GENCODE release 43
Supplementary files format and content: Single file in tab-delimited text consisting of a data matrix for all four samples. The file contains the Ensembl Gene Symbol (column 1), gene name (column 2), and gene-level counts for each gene for each sample (columns 3-6).

extract_protocol:
Total cellular RNA was isolated from the prostate cancer cell lines using the RNeasy Mini Kt (Qiagen).
Indexed, stranded mRNA-seq libraries were prepared from total RNA (100 ng) according to standarding protocols for end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

tag: phenotype

value: Enzalutamide-resistant

value: prostatic adenocarcinoma

value: untreated


title: MLL-AF9, mouse 1B, WM-1119 1 uM 1 hour, rep 1

description: MLL-AF9 1B WM-1119 rep 1 mRNA


title: Ctrl_13


title: UCD1172_2

value: Parental


title: Immobilization MOTS-c, rep3

description: RNA-seq


title: UCD1172_1


title: Immobilization MOTS-c, rep4

description: RNA-seq


title: MLL-AF9, mouse 1D, DMSO, rep 3

description: MLL-AF9 1D DMSO rep 3 mRNA

value: DMSO 1 hour


title: MLL-AF9, mouse 1D, DMSO, rep 2

description: MLL-AF9 1D DMSO rep 2 mRNA


title: Ctrl_12

value: male

value: AF-EV


title: Immobilization MOTS-c, rep2

description: RNA-seq


title: H660_231_2_5

data_processing:
RNA-Seq data was analyzed using a hierarchical indexing for spliced alignment of transcripts 2 (HISAT2). Raw sequence reads (FASTQ format) were mapped with the HISAT2 aligner to the reference human genome index (GRCh38/hg38, GENCODE release 43) and quantified to yield gene-level Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values.
Processed data are gene-level read counts generated from the output of HISAT2 alignment and subsequent quantification with featureCounts.
Assembly: GRCh38/hg38, GENCODE release 43
Supplementary files format and content: Single file in tab-delimited text consisting of a data matrix for all four samples. The file contains the Ensembl Gene Symbol (column 1), gene name (column 2), and gene-level FPKM values for each gene for each sample (columns 3-5).

extract_protocol:
Total cellular RNA was isolated from vehicle (DMSO)- or JG231-treated H660 prostate cancer cell lines using the RNeasy Mini Kt (Qiagen).
Indexed, stranded mRNA-seq libraries were prepared from total RNA (100 ng) according to standarding protocols for end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.


title: Ctrl_11


title: Immobilization MOTS-c, rep8

description: RNA-seq


title: MLL-AF9, mouse 1D, DMSO, rep 1

description: MLL-AF9 1D DMSO rep 1 mRNA

value: Lin- Sca1+ cKit+ (LSK)


title: Immobilization MOTS-c, rep1

description: RNA-seq


title: H660_231_5


title: MLL-AF9, mouse 1B, DMSO, rep 3

description: MLL-AF9 1B DMSO rep 3 mRNA


title: Immobilization control, rep8

description: RNA-seq

value: water


title: H660_DMSO

value: Vehicle-treated (DMSO)


title: Ctrl_9


title: MLL-AF9, mouse 1B, DMSO, rep 2

description: MLL-AF9 1B DMSO rep 2 mRNA


title: Immobilization control, rep7

description: RNA-seq

value: Gastrocnemius muscle


title: UCD1172CR_1


title: MLL-AF9, mouse 1B, DMSO, rep 1

description: MLL-AF9 1B DMSO rep 1 mRNA


title: EHTs, DSP+/+ biol rep3

city: Chicago,

first: Daniel

last: Selgrade

state: IL

address: 303 E. Superior Street

institute: Northwestern University

data_processing:
Raw reads were trimmed with trimmomatic (v0.36) and aligned to the human (hg19)  or rat (rn6) genome using STAR with default settings.
Uniquely aligned reads were assigned to genes using htseq-count.
Raw counts were normalized with EdgeR and used to identify differentially expressed genes.
Assembly: rn6
Assembly: hg19
Supplementary files format and content: tab-delimited text file contains CPM for each sample as well as log fold change, logCPM, likelihood ratio, p-value and FDR p-value for each gene.

source_name: Engineered Heart Tissue

growth_protocol: NRVCMs were cultured in M199 medium (Lonza) supplemented with 1% penicillin/streptomycin, heat-inactivated horse serum (Gibco), 15 µM vitamin B12 (Sigma-Aldrich), and 100 µM bromodeoxyuridine (Sigma-Aldrich). EHTs were cultured in  Dulbecco’s Modified Eagle’s Medium (DMEM) low glucose (Sigma, Cat#D5546), 10% horse serum (heat inactivated, New Zealand origin, Gibco, Cat#26050088), 1% Penicillin/Streptomycin (Thermo, Cat#15070063), and 0.1% human insulin (10 mg/mL, Sigma Cat#19278).

extract_protocol:
RNA was isolated using TRIzol™ Reagent (ThermoFisher Scientific). RNA isolation was performed with the Aurum Total RNA Mini Kit (Biorad) according to manufacturer specifications.
RNA libraries for RNA-Seq were prepared using TruSeq Stranded mRNA (Illumina) according to manufacturer's protocols.

treatment_protocol: For siRNA knockdown, constructs were cloned into the pAd/cytomegalovirus (CMV)/V5-DEST vector (Invitrogen) and used to generate virus using the ViraPower Adenoviral Expression System (Invitrogen).

value: Engineered Heart Tissue

value: DSP+/+

value: standard EHT culture


title: Immobilization control, rep6

description: RNA-seq

value: Male

value: 12 weeks old

value: Immobilization


title: Ctrl_8

value: healthy control


title: Immobilization control, rep5

description: RNA-seq


title: Ctrl_7

value: female


title: EHTs, DSP+/+ biol rep1


title: PIK3CAPodo-HET + alpelisib

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description:
Single-cell transcriptomics profiling
HTB

data_processing:
Alignment and quantification processed with CellRAnger v3.0.2 on mm10 genome with default parameters and gene annotation from Ensembl100, with the addition of eGFP and tdTomato genes
Assembly: mm10 / Ensembl 100 + eGFP tdTomato
Supplementary files format and content: csv file with raw counts from Cellranger

source_name: kidney

extract_protocol:
8-week-old PIK3CAWT and PIK3CAPod-HET (PIK3CA gain-of-function mutation specifically in podocytes) mice were treated with vehicle or alpelisib for 4 weeks. 4 mice groups, PIK3CAWT + vehicle, PIK3CAWT + alpelisib, PIK3CAPodo-HET + vehicle, and PIK3CAPodo-HET + alpelisib were processed for scRNAseq profiling to explore the transcriptional programs of PIK3CA overactivation in podocytes, as well as the effect of alpelisib in podocytes. Glomerular enrichment and single-cell suspensions were achieved by using M-450 Dynabeads (Thermofischer Scientific), Multi Tissue Dissociation Kit 1 (Miltenyi Biotec), and size filters (100 um and 70 um).
Library preparations was carried out using a Chromium Single Cell 3’ Library & Gel Bead Kit v.3 (10x Genomics) according to the manufacturer’s protocol. Note that 20,000 cells were loaded in the 10x Chromium Controller. Libraries were sequenced on an Illumina NovaSeq6000 according to the manufacturer’s instructions.
An equimolar pool of the 4 individual 10X Genomics Single Cell Expression 3' V3 libraries was prepared by the Imagine Genomic Core Facility and sequenced on an S2 FlowCell using the NovaSeq6000, Illumina (sequencing mode Paired-End 100+100 bases + indexes). A total of 2 billion reads were targeted for this pool of 4 libraries (500 million reads per library).

value: kidney

value: alpelisib


title: EHTs, DSP+/+ biol rep2


title: PIK3CAPodo-HET + vehicle

description:
Single-cell transcriptomics profiling
HTP

value: WT

value: vehicle


title: Ctrl_6

value: male

value: AF-EV


title: Immobilization control, rep4

description: RNA-seq

value: water


title: EHTs, DSP-/- biol rep2

value: DSP-/-


title: Ctrl_5


title: Ctrl_10


title: Immobilization control, rep3

description: RNA-seq

value: Gastrocnemius muscle


title: PIK3CAWT + vehicle

description:
Single-cell transcriptomics profiling
WTP


title: Immobilization control, rep2

description: RNA-seq


title: Ctrl_3


title: B30, EAECBD, Symptomatic

city: Mississippi State

first: Barbara

last: Kaplan

state: MS

address: 240 Wise Center Drive

department: Comparative Biomedical Sciences

institute: Mississippi State University

description:
EAE_CBD Asymptomatic vs EAE_CBD Symptomatic.xlsx
EAE_CBD Symptomatic  vs. EAE_CO Symptomatic.xlsx

data_processing:
CLC Genomics Workbench
Reads were trimmed for low-quality sequences using CLC Genomics Workbench using the quality limit 0.05.
Trimmed sequences were mapped to GRCm38 using CLC Genomics Workbench default parameters.
Read count extraction and normalization were performed using CLC Genomics Workbench.
Assembly: GRCm39
Supplementary files format and content: fold change between asymptomatic and symptomatic treated with CBD or CO

source_name: Brain

extract_protocol:
On D18, brains were flash-frozen in liquid nitrogen and stored in RNAlater at -80°C. RNA isolation, RNA quality evaluation, cDNA library construction, and Illumina RNA sequencing (RNA-Seq) were performed by NovoGene (Sacramento, CA). Reads were paired-end, 150 base pairs at a depth of 40 million reads. Reads were assessed for quality, trimmed, and mapped to the GRCm39 genome (NCBI), and differential expression was analyzed using CLC Genomics Workbench (Qiagen) using default parameters. Differentially expressed genes (DEGs) with a false discovery rate (FDR) ≤ 0.05 were considered significant. The CLC Differential Expression RNA-Seq workflow utilizes a multi-factorial statistical model based on a negative binomial Generalized Linear Model (GLM) to identify statistically significant genes between groups.
Reads were paired-end, 150 bp at a depth of 40 million reads.  Reads were assessed for quality, trimmed, mapped to the GRCm39 genome (NCBI), differential expression analysis in CLC Genomics Workbench (Qiagen). Differentially expressed genes (DEGs) with a false discovery rate (FDR) ≤ 0.05 were considered significant.

treatment_protocol: Mice were anesthetized using 3% isoflurane and EAE was induced by subcutaneously injecting the MOG35-55 peptide emulsion. The emulsion was prepared with vigorous mixing for 30 min of a solution containing 100 µg MOG35–55 peptide, 500 µg HKMT, and CFA. Each mouse received 100 µL emulsion delivered in 4 sites (2 at the hips, 2 at the shoulders; 25 µL per site). Control mice received 15 µL saline (SAL) at each site. Twenty-four hours after EAE induction, mice were dosed orally with 75 mg/kg CBD in 100µL of corn oil (CO) or 100µL CO for five days. Mice were observed over an 18-day period, and scores were given based on the following scale: 0-Asymptomatic; 0.5-Flaccid tail; 1-Hindlimb paresis/waddling; 1.5-Waddling gait; 2-Unable to prevent being placed in dorsal recumbency; 2.5-Hindlimb dragging; 3-Single hindlimb paralysis; 3.5-Single hindlimb paralysis with other hindlimb dragging; and 4-Complete hindlimb paralysis. Any score above 0 was considered symptomatic. Mice were never allowed to progress past a score of 4 for animal welfare purposes. Scores and samples analyzed were from two, independent cohorts. Mice (n = 3 each) were divided into three treatment groups: SAL/CO (control),  EAE/CO, and EAE/CBD. SAL/CO mice did not show any clinical signs and were not included in any downstream analyses.

value: Brain

value: EAE, CBD


title: Immobilization control, rep1

description: RNA-seq


title: MCF-7-GATA4-ChIPseq

city: Jinan

first: wenqian

last: yu

state: Shandong

address: No.105, jiefang road

department: Research Center of Translational Medicine

institute: Central Hospital Affiliated to Shandong First Medical University

library_source: genomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Clean reads were mapped to the reference genome using Bowtie2 software. And reads from organelle, mapping quality smaller then 30, PCR duplicated reads all removed. Those high quality mapping reads were subjected to further peak calling.
Macs2 software was used to call peaks.
Peaks were annotated by ChIPseeker package.
Assembly: hg38
Supplementary files format and content: bw

molecule: genomic DNA

extract_protocol:
Briefly, cells were harvested and crosslinker with 1% formaldehyde for 10 min at room temperature. After sonication, immunoprecipitation was performed with anti-GATA4. The immunoprecipitated complex was washed, and DNA was extracted and purified by Universal DNA Purification Kit (TIANGEN, #DP214).
The ChIP-Seq library was prepared using original Ultra II DNA Library Kits (NEB, #E7645) according to the manufacturer's instructions. For ChIP-seq, extracted DNA was ligated to specific adaptors followed by deep sequencing in the Illumina Novaseq 6000 using 150bp paired-end.

value: Human breast cancer cell

tag: antibody

value: untreated


title: B26, EAECBD, Asymptomatic

description:
EAE_CBD Asymptomatic vs EAE_CBD Symptomatic.xlsx
EAE_CBD Asymptomatic vs. EAE_CO Asymptomatic.xlsx


title: Ctrl_2


title: MCF-7-Input


title: Non immobilization control, rep8

description: RNA-seq

value: Male

value: 12 weeks old

value: Non-immobilization


title: B25, EAECBD, Symptomatic


title: Ctrl_1

value: healthy control


title: PIK3CAWT + alpelisib

description:
Single-cell transcriptomics profiling
WTB

value: kidney


title: Non immobilization control, rep7

description: RNA-seq


title: EHTs, DSP-/- biol rep3

value: Engineered Heart Tissue

value: standard EHT culture


title: Non immobilization control, rep6

description: RNA-seq


title: Ctrl_4

value: female


title: B21, EAECO, Symptomatic

description:
EAE_CO Asymptomatic vs EAE_CO Symptomatic.xlsx
EAE_CO Symptomatic vs. EAE_CO Asymptomatic.xlsx

value: EAE, CO


title: MDA-MB-231 cells,2DG 0mM,2

first: Kaixiang

last: Feng

address: No.169, Donghu Road

institute: Wuhan University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCh38/hg38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: Read count

source_name: breast

growth_protocol: MDA-MB-231 cells were maintained in DMEM supplemented with 10% fetal calf serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: MDA-MB-231 cells were treated with 2-deoxy-glucose (0,10mM,20mM) for 24 hours

value: breast

value: Human triple-negative breast cancer cell line

value: WT

value: 2DG 0mM 24h


title: Non immobilization control, rep5

description: RNA-seq

value: Gastrocnemius muscle

value: water


title: MDA-MB-231 cells,2DG 0mM,1


title: Non immobilization control, rep4

description: RNA-seq


title: MDA-MB-231 cells,2DG 20mM,3

value: 2DG 20mM 24h


title: ChIP-Seq Uns_iPS-CF_K27Ac_B_S5_R1_001

city: San Francisco

first: Michael

last: Alexanian

address: 1650 Owens Street

institute: Gladstone Institutes

description:
Uns_iPS-CF_K27Ac_B_S5_R1_001
H3K27-Ac ChiPseq in Human induced pluripotent stem cell derived cardiac fibroblasts

data_processing:
Illumina Casava v1.8 was used for base-calling.
Reads were demultiplexed with Illumina bcl2fastq v2.20.0.422
Demultiplexed reads were aligned, read normalized and quantified with the nfcore/chipseq pipeline v1.2.1 (https://nf-co.re/chipseq) via Nextflow and Singularity using standard settings
Assembly: GRCh38
Supplementary files format and content: Genomic coverage tracks in bigWig format

extract_protocol:
Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs) were cultured in FibroGRO Complete Medium (SCMF001; Millipore Sigma) with 2% FBS at 37°C in a humidified incubator with 5% CO2. For chromatin immuno-precipation (ChIP) sequencing experiments, 10 million iPSC-FBs were pelleted in unstimulated condition and resuspended in 10ml FibroGRO™ Basal Medium, cross-linked in 1% formalin solution (Thermo Fisher Scientific) by rocking in room temperature for 10 minutes and finally glycine (final concentration 0.125M) was added to quench the cross-link for 5 minutes. Samples were centrifuged at 1000 rcf for 5 minutes at 4C. Cells were washed twice with 10 ml of cold 1x PBS supplemented with proteinase inhibitors and phosphatase inhibitors (Roche # 4693132001) and the pellets were snap frozen in liquid nitrogen. All samples were stored at -80C until use. When ready, cell pellets were incubated in cell lysis buffer (20 mM Tris-HCl, pH 8, 85 mM KCl, 0.5% NP-40 and protease inhibitors) for 10 min on a rotator at 4C. Nuclei were isolated by centrifugation (2,500 x g, 5 min, 4C), resuspended in 1mL nuclear lysis buffer (50 mM Tris-HCl, pH 8, 10 mM EDTA, pH 8, 1% SDS, protease inhibitors) and incubated on a rotator for 30 min at 4C. Chromatin was sheared using a Covaris S2 sonicator (Covaris Inc) for 20 min (60 s cycles, 20% duty cycle, 200 cycles/burst, intensity = 5) for preparing DNA in the 200–700 base-pair range. Chromatin was diluted 3-fold in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mMEDTA, 16.7mMTris-HCl, pH 8, 167 mM NaCl, protease inhibitors) for a total volume of 3ml. 30uL of chromatin (representing 1%) was taken as input DNA. High-salt buffer (250mM Tris-HCl, pH 7.5, 32.5 mM EDTA, pH 8, 1.25M NaCl) and Proteinase K (New England Biolabs Inc (NEB)) were added and crosslinks were reversed overnight at 65C. Inputs were treated with RNase A, and DNA was purified with AMPure XP beads (Beckman Coulter cat #A63881). DNA concentration was measured with Qubit (ThermoFisher) to work out the original concentration of the sonicated chromatin. 15ug of chromatin was incubated with 4ug of anti-p65/RELA antibody (Bethyl Laboratories #A301-824A) and 3ug of chromatin was incubated with 2ul of anti-H3K27ac (Abcam #4729) for H3K27ac ChIP. All incubations were overnight at 4C under rotation. Antibody-protein complexes were immunoprecipitated using Pierce Protein A/G magnetic beads at 4C for 2 h under rotation. Beads were washed five times (2-min/wash under rotation) with cold RIPA buffer (50 mM HEPES- KOH, pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-deoxycholate), followed by one wash in cold final wash buffer (1xTE, 50 mM NaCl). Immunoprecipitated chromatin was eluted at 65C with agitation for 30 min in the elution buffer (50mMTris-HCl pH 8.0, 10mMEDTA, 1% SDS). The immunoprecipitated chromatin was then reverse-crosslinked and purified as described above for the inputs.
For subsequent sequencing, fragmented ChIP and input DNA were end-repaired, 5’-phosphorylated and dA-tailed with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645). Samples were ligated to adaptor oligos for multiplex sequencing (NEB, E7335), PCR amplified, and sequenced on a NextSeq 500 (Illumina, software 4.0.2).

tag: chip antibody

value: Abcam #4729


title: EHTs, DSP-/- biol rep1

value: DSP-/-


title: ChIP-Seq Inp_Uns_S1_R1_001_Nov2022

description:
Inp_Uns_S1_R1_001_Nov2022
Input chromatin material for ChiPseq in Human induced pluripotent stem cell derived cardiac fibroblasts

source_name: Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs)


title: MDA-MB-231 cells,2DG 0mM,3


title: Non immobilization control, rep3

description: RNA-seq

value: Male

value: 12 weeks old


title: A28, EAECBD, Symptomatic

value: Brain

value: EAE, CBD


title: ChIP-Seq Uns_iPS-CF_RELA_S10_R1_001

description:
Uns_iPS-CF_RELA_S10_R1_001
p65-RELA  ChiPseq in Human induced pluripotent stem cell derived cardiac fibroblasts

value: Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs)

value: Bethyl Laboratories #A301-824A


title: MDA-MB-231 cells,2DG 20mM,2


title: ChIP-Seq Uns_iPS-CF_K27Ac_A_S4_R1_001

description:
Uns_iPS-CF_K27Ac_A_S4_R1_001
H3K27-Ac ChiPseq in Human induced pluripotent stem cell derived cardiac fibroblasts


title: A27, EAECBD, Asymptomatic


title: Non immobilization control, rep2

description: RNA-seq

data_processing:
The quality of each fastq file was ensured using FastQC.
Sequence reads were mapped to the mouse reference genome (GRCm38.p6) using STAR.
Transcripts per million (TPM) were calculated using the RSEM.
Comparison of the gene expression levels between groups was performed using the DESeq2 package in R
Assembly: Mouse genome (GRCm38.p6)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

value: Non-immobilization


title: MDA-MB-231 cells,2DG 20mM,1


title: ChIP-Seq Uns_iPS-CF_input_S1_R1_001

description:
Uns_iPS-CF_input_S1_R1_001
Input chromatin material for ChiPseq in Human induced pluripotent stem cell derived cardiac fibroblasts


title: Non immobilization control, rep1

description: RNA-seq


title: B22, EAECO, Asymptomatic

description:
EAE_CBD Asymptomatic vs. EAE_CO Asymptomatic.xlsx
EAE_CO Asymptomatic vs EAE_CO Symptomatic.xlsx
EAE_CO Asymptomatic vs EAE_CO Symptomatic.xlsx

value: EAE, CO


title: Bulk RNA-Seq TGFB+IL1B-4

description:
TGFB+IL1B-4
Bulk RNA-seq on Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs) with IL1B and TGFB stimulation

data_processing:
Illumina Casava v1.8 was used for base-calling.
Reads were demultiplexed with Illumina bcl2fastq v2.20.0.422 and aligned to hg19 using Rsubread
Additional filtering, quality control and analysis was performed with EdgeR and LImma
Assembly: GRCh37
Supplementary files format and content: Raw Rsubread gene counts by sample matrix

extract_protocol:
Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs) were cultured in FibroGRO Complete Medium (SCMF001; Millipore Sigma) with 2% FBS at 37°C in a humidified incubator with 5% CO2. When stimulating stress in iPSC-CFs, the cells were cultured with 0.5% FBS in FibroGRO Complete Medium without supplements, with addition of either TGFB (5ng/ml; Peprotech), IL1B (10ng/ml; Sigma Aldrich), or TGFB+IL1B (10ng/ml and 5ng/ml, respectively). RNA was isolated isolated using Qiagen RNeasy spin columns following manufacturer’s directions
Bulk RNA libraries were prepared using the NEBNext Ultra II DNA Library Prep kit (NEB) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) to enrich poly-A tailed RNA molecules. Libraries were PCR’ed with single end barcodes using Illumina Multiplex Oligos (NEB).


title: A24, EAECO, Symptomatic


title: MDA-MB-231 cells,2DG 10mM,3

value: breast

value: 2DG 10mM 24h


title: ChIP-Seq Uns_AM_RelA_S11_R1_001_Nov2022

description:
Uns_AM_RelA_S11_R1_001_Nov2022
p65-RELA  ChiPseq in Human induced pluripotent stem cell derived cardiac fibroblasts


title: MDA-MB-231 cells,2DG 10mM,2

value: Human triple-negative breast cancer cell line

value: WT


title: A26, EAECBD, Asymptomatic


title: A30, EAECBD, Symptomatic


title: A23, EAECO, Asymptomatic


title: Bulk RNA-Seq TGFB+IL1B-2

description:
TGFB+IL1B-2
Bulk RNA-seq on Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs) with IL1B and TGFB stimulation


title: Bulk RNA-Seq TGFB+IL1B-3

description:
TGFB+IL1B-3
Bulk RNA-seq on Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs) with IL1B and TGFB stimulation


title: GRH_siRNA_rep14

city: Seattle

first: Research

middle: Scientific

last: Computing

state: WASHINGTON

address: 818 Stewart Street

department: Research Scientific Computing

institute: Seattle Children's Research Institute

data_processing:
Transcript abundances were estimated using Kallisto with GRCh38 transcriptome reference Ensembl version 93 , and length scaled counts were condensed to Ensembl Gene IDs using the Bioconductor TXImport package.
Assembly: GRCh38
Supplementary files format and content: abundance.tsv as tab delimited file containing transcript abundances in transcripts per million.

source_name: placenta

growth_protocol: We performed knock downs of selected TFs in primary villous trophoblast cells from placental samples collected through the OHSU placental biorepository. Cytotrophoblast cells were rapidly thawed in a 370C water bath and immediately diluted in Iscove’s modified Dulbecco’s medium (25mM glucose, 4mM glutamine and 1mM pyruvate (Gibco #12440-046) supplemented with 10% FBS (Corning #35-010-CV) and 1% penicillin/streptomycin (Gibco #15140-122) termed as complete media. Cells were centrifuged at 1000g for 10 min and suspended in fresh complete media. The cells were plated at 2x106 cells per well concentration in 12-well culture plates and cultured at 370C, 5% CO2. After 24 hours, cells were transiently transfected using the above siRNAs and Lipofectamine (Invitrogen #11668-019) as per manufacturer’s protocol and incubated for another 24 hours. At the end of 24 hours (total of 48 hours from the start of culture) the transfection media was replaced with complete media and cells were cultured for another 24 hours.

extract_protocol:
After 72 hours of total culture time (24 hours following previous complete media change) the cells were lysed in 700uL of Qiazol and RNA was isolated using the Zymo Direct-zol Mini-prep kit and reagents.
cDNA libraries were prepared from 1 μg of total RNA using the Illumina Stranded Total RNA library kit. Each library was sequenced to approximately a depth of 50 million reads on an Illumina NovaSeq 6000 S4 (2 x100 read length) sequencer by the OHSU sequencing core.

treatment_protocol: We performed knock downs of selected TFs in primary villous trophoblast cells from placental samples collected through the OHSU placental biorepository. Separate transfections were performed using the ON-Target SMARTpool siRNAs (Dharmacon) to induce silencing of four genes: CREB2L2 (Catalog # L-019357-02-0005), ESRRG (Catalog # L-003405-00-0005), GCM1 (Catalog # L-011491-00-0005) and GRHL2 (Catalog # L-014515-02-0005) with a non-targeting negative control (Catalog # D-001810-10-05). siRNAs were diluted in nuclease free water and stored at a 50 μM stock concentration.

value: placenta

value: primary villous trophoblast cells


title: S35_TBET_pos

city: Cambridge

first: Ana

last: Ferreira

address: Francis Crick Avenue, Cambridge Biomedical Campus

country: United Kingdom

institute: MRC - Laboratory of Molecular Biology

description:
S35_lib_data.csv
S35_screen_list.csv

data_processing:
Samples were sequenced using an Illumina Hiseq4000 running a single-read 50bp protocol
20 nt sgRNA sequences were trimmed from backbone sequences using Cutadapt version 1.4.1 (5' GACGAAACACCG, 3' GTTTTAGAGCTA).
sgRNA sequences were aligned to reference sgRNA libraries using Bowtie2 (version 1.2.3).
Assembly: GRCm38
Supplementary files format and content: sgRNA count files (lib data) and pool information (screen list).
Library strategy: CRISPR screen

source_name: GFP+BFP+TBET+ cells

growth_protocol: Bone marrow common lymphoid progenitors (CLPs) were sorted as live CD45+ Lin- IL-7Ra+ Flt3+ Ly6D-. For CLP expansion, purified CLPs were co-cultured with OP9 cells for 6 days in complete IMDM supplemented with 25 ng/mL rmFlt3L and 0.1 ng/mL rmIL-7 as described previously. At day 6, expanded CLPs were collected and flow sorted for viable CD45+ CD19- cells and transduced with BFP/sgRNA-expressing retroviral library. Cells were co-cultured with OP9-DL cells, in complete IMDM supplemented with 10 ng/mL rmIL-7 for the next 6 days.

extract_protocol:
Cells were flow-sorted into 50% FCS PBS and genomic DNA from sorted cells were extracted using the QIAGEN DNeasy Blood & Tissue Kits following the manufacturer's protocol, with the exception of DNA elution in water instead of buffer AE.
Illumina P7 barcodes; sgRNA-insert was first PCR-amplified using Herculase II Fusion DNA polymerase (Agilent) with primers (Forward) AATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTCG and (Reverse) CTTTAGTTTGTATGTCTGTTGCTATTATGTCTACTATTCTTTCC, using up to 2 mg genomic DNA per 50 ml reaction. Equal volumes from each reaction were pooled and used for a further PCR amplification step to attach Illumina sequencing adaptors and Illumina P7 barcodes, using Herculase II Fusion DNA polymerase. The 330 bp library was gel purified and quantified using KAPA library quantification kit (Roche).

treatment_protocol: At day 12, cells and collected and transferred to OP9 cells in complete IMDM supplemented with 25 ng/mL rmIL-7 and rmSCF  for the next 6 days. At day 18, GFP+ BFP+ cells were sorted into populations of interest discernible by reporter protein expression for genomic DNA extraction

tag: screen

value: GFP+BFP+TBET+ cells

tag: sgrna library

value: Brie

value: Rosa26Cas9EGFP x Gata3hCD2 x Tbx21hCD4 x RorcKat mice

tag: sorted phenotype

value: TBET positive


title: S35_GATA3_pos

description:
S35_lib_data.csv
S35_screen_list.csv

source_name: GFP+BFP+GATA3+ cells

value: GFP+BFP+GATA3+ cells

value: GATA3 negative


title: Bulk RNA-Seq TGFB+IL1B-1

description:
TGFB+IL1B-1
Bulk RNA-seq on Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs) with IL1B and TGFB stimulation


title: Bulk RNA-Seq TGFB-4

description:
TGFB-4
Bulk RNA-seq on Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs) with IL1B and TGFB stimulation


title: A22, EAECO, Asymptomatic

tag: tissue

value: Brain


title: GCM_siRNA_rep14

tag: cell type

tag: Sex

value: Male


title: S31_TBET_pos

description:
S31_lib_data.csv
S31_screen_list.csv

tag: genotype


title: Con_3_input

city: Fuzhou

first: Mengting

address: Fujian Medical University, 1 Xuefubei Road, Minhou, Fuzhou, Fujian province, China

institute: Fujian Medical University

data_processing:
The raw MeRIP-seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for m6A-modification peak calling and the significant methylation was identified by exomepeak2 , and the m6A peak calling can be visualized by IGV software.
The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME  was used to determine if the m6A peaks contained the consensus of m6A motif sequences.
For mRNA-seq, the mRNA expression level was analyzed by StringTie, and differentially expressed mRNAs were calculated by DEseq.
The substrates of m6A regulators were obtained from starBase v2.0.
The statistical enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for differentially expressed genes (DEGs) and differentially methylated mRNAs were applied by DAVID.
Assembly: mm10
Supplementary files format and content: The processed data files is in CSV format, containing the expression levels and m6A methylation status changes for each gene.

source_name: hippocampus

extract_protocol:
Total RNA was extracted according to manufacturer’s instruction.
The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched

value: hippocampus

value: Wild type

tag: treatment

value: Control

tag: rip antibody

value: none (input)


title: Con_2_input


title: Con_1_input


title: CRB_siRNA_rep14


title: S25_tom_pos

description:
S25_lib_data.csv
S25_screen_list.csv

source_name: GFP+BFP+TOM+ cells

value: GFP+BFP+TOM+ cells

value: Rosa26Cas9EGFP x Il13tdTom

value: Tom positive


title: Bulk RNA-Seq TGFB-2

description:
TGFB-2
Bulk RNA-seq on Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs) with IL1B and TGFB stimulation


title: Con_2_IP


title: SCR_siRNA_rep14

value: placenta

value: Scrambled siRNA


title: Bulk RNA-Seq TGFB-1

description:
TGFB-1
Bulk RNA-seq on Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs) with IL1B and TGFB stimulation


title: MDA-MB-231 cells,2DG 10mM,1

value: breast

value: Human triple-negative breast cancer cell line

value: WT

value: 2DG 10mM 24h


title: BGC823 cells, PCDNA3.1

first: Hou

address: Wenhuaxi Road 44

institute: Shandong University

hyb_protocol: Heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 1 out of 2 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

source_name: BGC823 cells, PCDNA3.1

label_protocol: total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer

growth_protocol: The gastric cancer cell line BGC823 was cultured in RPMI-1640 medium (HyClone,Logan, UT,USA) supplemented with 10% fetal bovine serum (Gibco) and incubated at 37 °C in a humidified incubator at 5% CO2.

extract_protocol: RNA was prepared using the TRIZOL. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: BGC823 cells were transfected with PCDNA3.1-HRCT1 and Negative control for 48 hours,when the gastric cancer cells state was optimal and density at about 90%, collected cells for detection and analysis of gene expression profiles.

value: gastric cancer cell

value: control

value: non-metastatic


title: Bulk RNA-Seq IL1B-4

description:
IL1B-4
Bulk RNA-seq on Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs) with IL1B and TGFB stimulation


title: Con_3_IP


title: Con_1_IP


title: GRH_siRNA_rep13

value: primary villous trophoblast cells

value: Male


title: Bulk RNA-Seq IL1B-3

description:
IL1B-3
Bulk RNA-seq on Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs) with IL1B and TGFB stimulation


title: GCM_siRNA_rep13


title: S25_tom_neg

description:
S25_lib_data.csv
S25_screen_list.csv

source_name: GFP+BFP+TOM- cells

value: GFP+BFP+TOM- cells

value: Brie

value: Tom negative


title: Me_3_input

value: hippocampus

value: Wild type

value: treat with mesaconitine

value: none (input)


title: ESR_siRNA_rep13

value: placenta

value: ESRRG


title: Me_2_input


title: Bulk RNA-Seq TGFB-3

description:
TGFB-3
Bulk RNA-seq on Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs) with IL1B and TGFB stimulation


title: Bulk RNA-Seq IL1B-1

description:
IL1B-1
Bulk RNA-seq on Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs) with IL1B and TGFB stimulation


title: ILC2_anti-Mef2d_1

data_processing:
Pooled libraries were sequenced using an Illumina NextSeq 2000 (or Hiseq4000) running a pair-end 50bp protocol
Sequenced reads were aligned to the mouse genome (GRCm38) using Bowtie2 (v2.3.5.1) with default parameters
reads that could not be uniquely mapped were removed from further analysis
Peak calling analysis was performed using Macs2 (v2.1.2)
Assembly: GRCm38
Supplementary files format and content: macs2 output files with peak calling data

source_name: mLN

growth_protocol: ILC2s Purified from MLN of IL-25 and IL-2/anti–IL-2 complex treated mice  were maintained for 7 days inRPMI-1640, 10% FCS plus penicillin/streptomycin and 2-mercaptoethanol, supplemented with IL-7 (10 ng/ml), IL-2 (10 ng/ml) and IL-33 (10 ng/ml)

extract_protocol:
Chromatin extracts from in vitro expanded ILC2 (10 million) were prepared using truChIP Chromatin Shearing kit (Covaris), with 5 min of crosslink and optimized shearing conditions (peak power 75, duty factor 10.0, cycles/burst 200, duration 300 sec) to obtain fragments of ~500bp
Chromatin-antibody-bead complexes were then subjected to tagmentation, followed by DNA elution, and libraries amplification and purification, as described previously (Schmidl et al., 2015)

value: mLN


title: CRB_siRNA_rep13


title: ESR_siRNA_rep14


title: Me_1_input


title: S31_GATA3_pos

description:
S31_lib_data.csv
S31_screen_list.csv

value: GFP+BFP+GATA3+ cells

value: Rosa26Cas9EGFP x Gata3hCD2 x Tbx21hCD4 x RorcKat mice

value: GATA3 negative


title: BGC823 cells, PCDNA3.1-HRCT1

source_name: BGC823 cells, PCDNA3.1-HRCT1

value: gastric cancer cell

value: HRCT1 overexpression

value: metastatic


title: kidney derived neutrophils, homozygous, Mm infected, rep3

city: Tampere

first: Sanna-Kaisa

middle: Emilia

last: Harjula

address: Arvo Ylpön katu 34

country: Finland

institute: University of Tampere

data_processing:
Reads were aligned to the reference genome GRz11 (grcz11_gca_000002035_4) with HISAT2.
Raw expression estimates (raw read counts) for genes (grcz11_gca_000002035_4) were counted using FeatureCounts.
Analysis of differentially expressed genes was performed with DESeq2
Assembly: GRz11
Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab-delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.

organism: Danio rerio

growth_protocol: Fish homozygous for pycardtpu4 mutation and WT controls (originally crossed to transgenic Tg(mpx:GFP)i114 (AB) to gain fluorescence in neutrophils) fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.

extract_protocol:
RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol.
Library construction was performed on the Illumina platform (paired-end sequencing, 150 bp read length) yielding > 20 million reads per sample.

treatment_protocol: Adult zebrafish were infected with 69-118 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.

value: kidney

value: neutrophils

value: homozygous for pycard (pycardtpu4 crossed to transgenic Tg(mpx:GFP)i114 (AB))

tag: infection

value: M. marinum


title: SCR_siRNA_rep13

value: primary villous trophoblast cells

value: Scrambled siRNA

value: Male


title: Bulk RNA-Seq Unstim-4

description:
Unstim-4
Bulk RNA-seq on Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs) with IL1B and TGFB stimulation


title: Me_3_IP

value: hippocampus

value: Wild type

value: treat with mesaconitine


title: Bulk RNA-Seq Unstim-3

description:
Unstim-3
Bulk RNA-seq on Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs) with IL1B and TGFB stimulation


title: kidney derived neutrophils, homozygous, Mm infected, rep1


title: GRH_siRNA_rep12

value: placenta


title: Me_2_IP


title: GCM_siRNA_rep12


title: kidney derived neutrophils, homozygous, Mm infected, rep2


title: S17_tom_neg

description:
S17_lib_data.csv
S17_screen_list.csv

value: GFP+BFP+TOM- cells

value: Brie

value: Rosa26Cas9EGFP x Il13tdTom

value: Tom negative


title: Me_1_IP


title: Bulk RNA-Seq Unstim-2

description:
Unstim-2
Bulk RNA-seq on Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs) with IL1B and TGFB stimulation


title: kidney derived neutrophils, wt, Mm infected, rep3

value: wild type for pycard (pycardtpu4 crossed to transgenic Tg(mpx:GFP)i114 (AB))


title: S17_tom_pos

description:
S17_lib_data.csv
S17_screen_list.csv

value: GFP+BFP+TOM+ cells

value: Tom positive


title: Bulk RNA-Seq IL1B-2

description:
IL1B-2
Bulk RNA-seq on Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs) with IL1B and TGFB stimulation


title: Bulk RNA-Seq Unstim-1

description:
Unstim-1
Bulk RNA-seq on Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs) with IL1B and TGFB stimulation


title: ESR_siRNA_rep12

value: ESRRG


title: DIV12 primary neurons ko, A300, CUT&TAG

city: XiaMen

first: Honghua

last: zheng

state: FuJian

address: XiaMen University xiang’an campus

institute: Institute of Neuroscience xiamen university

description: KO-Menin

data_processing:
*library strategy: CUT&Tag
Reads were aligned to mm10 using SOAP aligner (version 2.21t) software. After format conversion and sorting, duplicate reads were removed by rmdup tool from the SAM tools package. To identify significant binding site of menin, we processed the mapped sequence reads with MACS2 against their matching control samples and only peaks with P values <10−5 were kept for further analyses. A Perl script annotate Peaks.pl in HOMER package was used to associate ChIP peaks with nearby genes and visualization of the location and the shape of called peaks utilizing Integrative Genomics Viewer (IGV). Furthermore, all motifs were identified by MEME software (http://meme-suite.org/).
Assembly: mm10
Supplementary files format and content: narrowPeak(Except for IgG and KO samples)

growth_protocol: A mixture of primary cortical and hippocampal neurons were dissected from timed-pregnant females at E16.5. Men1 knockout neurons derived from Men1-NcKO (Nestin-Cre; Men1(F/F)) mice, while Control neurons derived from the litter-match Men1(F/F) mice. Briefly, brains were dissected from pups of varying genotypes. The meninges were removed, and tissue was dissociated by enzymatic digestion. Isolated primary neurons were plated on poly-D-lysine coated dishes, and cultured in Neurobasal medium supplemented with B27 (Gibco, 17504044), 1% penicillin/streptomycin (Invitrogen) and maintained in a 5% CO2 incubator at 37°C.

extract_protocol:
In brief, primary neurons were collected and bounded to Concanavalin A-coated beads. Subsequently, cells were resuspended in antibody buffer and incubated with primary antibodies against menin antibody (A300-105A; Bethyl) and secondary antibodies in order. The samples were incubated with pA-Tn5 transposase. Aftertransposon activation and tagmentation, DNA was isolated, amplified, and purified to construct library, The library for sequencing was constructed and VAHTS DNAClean Beads (N411, Vazyme Biotech) were used for purification steps.
The librarywas quantified with VAHTS Library Quantification Kit for lllumina (VazymeBiotech) and sequenced on an lllumina novaseq 150PE. The sequencing was carried out by Novogene (Novogene, Beijing, China).

value: Men1-NcKO (Nestin-Cre; Men1(F/F))

value: menin


title: CRB_siRNA_rep12

value: primary villous trophoblast cells


title: DIV12 primary neurons, A300, CUT&TAG

description: Control-Menin

source_name: primary cortical and hippocampal neurons

value: litter-match Men1(F/F)


title: DIV12 primary neurons, IgG, CUT&TAG

description: Control-IgG

value: primary cortical and hippocampal neurons

value: Rabbit IgG


title: SCR_siRNA_rep12

value: Scrambled siRNA

value: Male


title: GRH_siRNA_rep11

value: placenta


title: FKBPV12-HA-MOZ-TIF2 LSK, IgG dTAG13, rep 2

first: Mitzi

last: Kuroda

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital/Harvard Medical School

data_processing:
Adaptor read contamination was removed from fastq files with cutadapt 4.1
Reads were aligned to the mouse mm10 genome using bowtie 2.5.1
Duplicate reads were removed with samtools 1.14 using the markdup command
Deeptools was used to create bigwig files normalized to 1x genome coverage and sample matched IgG signal was subtracted
Processed IgG bigwig files were created with Deeptools and normalized to 1x genome coverage
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: Cut&Run

source_name: LSK

extract_protocol:
Cells were immobilized and permeabilized on Concanavalin A (ConA) beads and incubated with anti-HA antibody. DNA was released with pAG-Mnase
Sequencing libraries were generated using the NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: Cells were treated with DMSO or 500 nM dTAG13 for 2 hours

value: LSK

value: 500 nM dTAG13 2 hour


title: H3K4Me2_CD56Dim_rep2

city: Rotterdam

first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

country: Netherlands

institute: Erasmus Medical Center

data_processing:
Reads were aligned using bowtie 2 using default parameters.
Sorted and indexed bam files were parsed to HOMER to creat tag directories without duplicates and bedgraphs for browser visualization.
HOMER was used to identify enriched regions ('peak calling') using findPeaks with -region -size 1000 -minDist 2500 options
Genome_build: hg19
Supplementary_files_format_and_content: HOMER peak calling files

source_name: peripheral blood

extract_protocol:
Human peripheral blood mononuclear cells (PBMC) from peripheral blood were isolated by Ficoll-Paque density gradient centrifugation. Cells were isolated by FACS (viable CD45+ Lin- (CD3- CD4- CD5- TCRαβ- TCRγδ- CD14- CD19-) CD7+ CD56-high CD16- or CD56-dim CD16+ cells)
Nextera DNA library construction (as described in Schmidl et al. Nature Methods 2015).

value: FACS-purified lymphocytes

value: anti-H3K4Me2, Abcam ab32356


title: H3K4Me2_CD56Br_rep2


title: H3K4Me2_CD56Dim_rep1


title: N/TERT ZAK KO UVB #2

city: Singapore

first: Franklin

last: ZHONG

state: Singapore

address: 11 Mandalay Road

country: Singapore

institute: NTU LKC School of Medicine

data_processing:
Trimmed reads are mapped to reference genome with HISAT2
After the read mapping, Stringtie was used for transcript assembly. Expression profile was calculated for each sample and transcript/gene as read count, FPKM (Fragment per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million).
DEG (Differentially Expressed Genes) analysis was performed on 5 comparisons pairs as requested using DESeq2. The results showed 4,643 genes which satisfied |fc|>=2 & nbinomWaldTest raw p-value<0.05 conditions in at least one of comparison pairs.
Assembly: GRCh38
Supplementary files format and content: FKPM and TPM in txt

source_name: Skin

growth_protocol: HPK culture

extract_protocol:
Total RNA by Trizol
TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: DT (150ng/mL), 4hours with/without Compound 6p (1uM)

value: Skin

value: Keratinocytes

value: ZAK KO

value: UVB


title: GCM_siRNA_rep11


title: H3K4Me2_CD56Br_rep1


title: FKBPV12-HA-MOZ-TIF2 LSK, IgG dTAG13, rep 1

city: Boston


title: N/TERT ZAK KO UVB #1


title: ESR_siRNA_rep11

value: ESRRG


title: A20KO3

city: 成都

first: Hanwen

last: Li

state: 四川

address: 四川省成都市武侯区人民南路四川大学华西校区

institute: 四川大学华西口腔医学院

data_processing:
CLC GENOMICS WORKBENCH V11.0.1
Assembly: mm10
Supplementary files format and content: count and fpkm of each samples

source_name: iBMDM

extract_protocol:
RNA were harvested using TRIZOL
RNA librarys for RNA-seq were prepared using SMARTERmRNA-Seq Library Kit

value: iBMDM

value: macrophage


title: N/TERT ZAK KO Sham #3

value: Wild type

value: Sham


title: FKBPV12-HA-MOZ-TIF2 LSK, IgG DMSO, rep 2

value: DMSO


title: CRB_siRNA_rep11

value: primary villous trophoblast cells


title: N/TERT ZAK KO Sham #2


title: SCR_siRNA_rep11

value: Scrambled siRNA

value: Male


title: FKBPV12-HA-MOZ-TIF2 LSK, IgG DMSO, rep 1

value: LSK


title: A20KO2

address: 四川省成都市武侯区人民南路四川大学华西校区


title: kidney derived neutrophils, wt, Mm infected, rep1

source_name: kidney

value: kidney

value: neutrophils

value: wild type for pycard (pycardtpu4 crossed to transgenic Tg(mpx:GFP)i114 (AB))

value: M. marinum


title: FKBPV12-HA-MOZ-TIF2 LSK, HA dTAG13, rep 2

value: 500 nM dTAG13 2 hour


title: A20KO1

address: 四川省成都市武侯区人民南路四川大学华西校区


title: kidney derived neutrophils, wt, Mm infected, rep2


title: N/TERT ZAK KO UVB #3

value: Skin

value: Keratinocytes

value: ZAK KO


title: WT3

address: 四川省成都市武侯区人民南路四川大学华西校区

value: iBMDM

value: WT


title: N/TERT ZAK KO Sham #1

value: Wild type


title: GRH_siRNA_rep10

value: placenta


title: N/TERT control UVB #3

value: UVB


title: FKBPV12-HA-MOZ-TIF2 LSK, HA dTAG13, rep 1


title: WT2

address: 四川省成都市武侯区人民南路四川大学华西校区

value: macrophage


title: FKBPV12-HA-MOZ-TIF2 LSK, HA DMSO, rep 2

value: DMSO


title: N/TERT control UVB #2


title: ESR_siRNA_rep10

value: primary villous trophoblast cells

value: ESRRG

value: Male


title: FKBPV12-HA-MOZ-TIF2 LSK, HA DMSO, rep 1

value: LSK


title: N/TERT control UVB #1


title: CRB_siRNA_rep10


title: N/TERT control Sham #3

value: Sham


title: MOZ-TIF2 LSK, WM-1119, input, rep 2, ChIP

data_processing:
Adaptor contamination contamination and low quality reads were removed from fastq files with Trimmomatic 0.36
Reads were aligned to both the mouse mm10 or Drosophila dm6 genome using bowtie 2.5.1. Duplicate reads were removed with samtools 1.14 using the markdup command
Aligned mouse bam files were normalized to Counts per Million (CPM) and input reads were subtracted from IP reads using deepTools bamCompare
To normalize to Drosophila spike-in DNA, we first reversed the CPM normalization of mouse reads by scaling to the original number of uniquely aligned mouse IP reads in each samples using deepTools bigwigCompare with the –scaleFactors setting. Next, a scaling factor for each sample was calculated based on Orlando et al, 2014 using the number of S2 reads that uniquely aligned to the Drosophila genome. Mouse reads were then normalized to their appropriate scaling factor using deepTools bigwigCompare with the –scaleFactors setting to generate bigwig files that were normalized to both the input and spike-in control
Processed input files were normalized to Counts mer Million (CPM)
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Lin- Sca1+ cKit+ (LSK)

extract_protocol:
Cells were fixed in 1% formaldehyde with 5% S2 cells added as an exogenous spike-in control for 8 minutes at room temperature. Chromatin was sheared using a QSonica Probe Sonicator for 16 cycles with 15 seconds on and 45 seconds off with an amplitude of 40%.
Sequencing libraries were generated using the NEBNext Ultra II DNA Library Prep Kit (NEB Cat #E7645S).

value: Lin- Sca1+ cKit+ (LSK)

value: 1 uM WM-1119 1 hour


title: B08_43, longissimus thoracis, CON

city: São Carlos

first: Sergio

middle: A. G.

last: Pereira-Junior

state: Sao Paulo

address: Rod. Washington Luís km 235

department: Genetic and Evolution

country: Brazil

institute: Federal University of São Carlos

data_processing:
Trimgalore / cutadapt
STAR
featurecounts
DESEQ2
PCIT / CETF
Assembly: Oar_rambouillet_V1.0104
Supplementary files format and content: Raw_counts.csv file

organism: Ovis aries

source_name: Muscle thoracis

extract_protocol:
RNeasy Mini Kit, Qiagen, Hilden, Germany
TruSeq Stranded mRNA Kit (Illumina)

value: Muscle thoracis

value: CON


title: SCR_siRNA_rep10

source_name: placenta

value: Scrambled siRNA


title: N/TERT control Sham #2

value: Skin

value: Keratinocytes


title: N/TERT control Sham #1

value: Wild type


title: B28_35, longissimus thoracis, SM20


title: B36_32, longissimus thoracis, CON


title: MOZ-TIF2 LSK, WM-1119, input, rep 1, ChIP


title: GCM_siRNA_rep9

value: placenta


title: MOZ-TIF2 LSK, control, input, rep 2, ChIP


title: Granulosa cells, 123_Post-Treatment

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 42nd and Emile street

department: Genetics Cell Biology and Anatomy

institute: University of Nebraska Medical Center

data_processing:
Raw sequenced reads in FASTQ format quality assessed by FASTQC v0.11.9, trimmed using cutadapt v1.15, and aligned using STAR v2.7.3a to human reference genome hg38 guided by the corresponding transcript annotation file from ENSEMBL.
Read counts on genes were calculated using RSEM v1.3.1 and paired pre-treatment v.s. post-treatment differential expression testing and principal component analysis (PCA) was performed using DESeq2 v1.24.0. Heatmaps were produced by Java Treeview v1.1.6r4 after sorting genes by the absolute geometric mean of the fold-changes in expression across patients. Genes that possessed a consistency of >=2 FC in the absolute geometric mean were then used for over-representation analysis (ORA) using ENRICHR for Gene Ontology (GO) Molecular Function, PhenGenI, and GTEx Aging signatures.
Assembly: hg38
Supplementary files format and content: .txt files re

source_name: Ovary

growth_protocol: Primary hGCs and follicle fluid was harvested from follicular aspirates of healthy, reproductive-age women (25-35 yr old) undergoing oocyte retrieval for in vitro fertilization at the Heartland Center for Reproductive Medicine (Omaha, NE). Aspirates from a single donor were pooled and centrifuged at 1700 x G for 15 min at 10 °C with the centrifuge break off. Cells were resuspended in 2 mL of DMEM/F12, layered onto 70% Percoll (product info), and centrifuged at 2000 x G for 20 min with the centrifuge break off. hGC were collected from the interphase of the medium and Percoll and gently mixed to form a 35% Percoll gradient and centrifuged for another 20 min at 2000 x G. Cells were then resuspended in DMEM/F12 and centrifuged, followed by lysis of red blood cells using ACK Lysing Buffer (Quality Biological, USA) and two subsequent washes with Dulbecco’s Modified Eagle Medium (DMEM)/F12 (Cytiva, Fisher Scientific, USA). Cells were sustained as a monolayer culture on plates coated with collagen (0.1 mg/mL) and fibronectin (4 mg/mL) in growth medium containing DMEM/F12 supplemented with 10% FBS, 1% P/S, and 1X ITS and maintained at 37 °C in a humidified 5% CO2 incubator.

extract_protocol:
Granulosa cells (5 x 105/mL) were cultured in collagen/fibronectin coated 60 mm culture plates, detached by trypsinization (TrypLE Express, Gibco, Denmark).
Total RNA from granulosa cells was isolated using a commercial RNA extraction kit (Zymo Direct-zol Microprep Kit, Zymo Reserch Corporation, USA). The quality and concentration of RNA was determined using a NanoDrop (ND1000, Nanodrop Technologies, USA). RNA purity and integrity were tested using a 5200 Fragment Analyzer System (Agilent, USA) and scored at 10.

treatment_protocol: Cells were seeded at a density of 5 x 10^3 cells/well with five wells per treatment in a 96-well culture plate and cultured for 3 days to allow complete attachment. Cells were then exposed to PFOA, PFOS, or PFHxS mixture (2 nM PFHxS, 7 nM PFOA, 10 nM PFOS) in assay medium (DMEM/F12 supplemented with 0.5% FBS) for 96 h to collect cells.

tag: sample id

value: Ovary

value: Primary cells

value: Granulosa Cells

tag: group

value: Treatment

value: PFAS mixture (2 nM PFHxS, 7 nM PFOA, 10 nM PFOS)


title: MOZ-TIF2 LSK, control, input, rep 1, ChIP

value: DMSO


title: MOZ-TIF2 LSK, WM-1119, H3K23pr, rep 2, ChIP


title: B20_31, longissimus thoracis, SM20


title: ESR_siRNA_rep9

value: primary villous trophoblast cells

value: ESRRG

value: Male


title: Granulosa cells, 123_Pre-Treatment

tag: cell line

value: Control

value: No Treatment


title: B01_28, longissimus thoracis, CON

value: Muscle thoracis

value: CON


title: CRB_siRNA_rep9


title: GCM_siRNA_rep10


title: Granulosa cells, 114_Post-Treatment


title: B12_27, longissimus thoracis, SM20


title: WT1

address: 四川省成都市武侯区人民南路四川大学华西校区

value: iBMDM

value: macrophage

value: WT


title: B03_48, longissimus thoracis, SM20


title: MOZ-TIF2 LSK, WM-1119, H3K23pr, rep 1, ChIP

value: Lin- Sca1+ cKit+ (LSK)

value: 1 uM WM-1119 1 hour


title: SCR_siRNA_rep9

value: placenta

value: Scrambled siRNA


title: GRH_siRNA_rep8


title: Granulosa cells, 114_Pre-Treatment

value: Ovary

value: Primary cells

value: Granulosa Cells


title: MOZ-TIF2 LSK, control, H3K23pr, rep 1, ChIP

value: DMSO


title: Granulosa cells, 113_Post-Treatment

value: Treatment

value: PFAS mixture (2 nM PFHxS, 7 nM PFOA, 10 nM PFOS)


title: MOZ-TIF2 LSK, control, H3K23pr,rep 2, ChIP


title: GCM_siRNA_rep8

value: primary villous trophoblast cells

value: Male


title: Granulosa cells, 113_Pre-Treatment

value: Control

value: No Treatment


title: GRH_siRNA_rep9


title: Granulosa cells, 92_Post-Treatment


title: ESR_siRNA_rep8

value: ESRRG


title: MLL-AF9  LSK cells, WM-1119 70 nM 5 days treated, rep 2

data_processing:
Adapter contamination was removed from fastq with cutadapt 4.1
Reads were then aligned to the mouse mm10 genome using bowtie 2.5.1 and sequences that aligned to ribosomal RNA were removed.
BigWig files were generated using Deeptools BamCoverage 3.5.0  and normalized using 1x genome coverage
Assembly: mm10
Supplementary files format and content: bigwig

molecule: nuclear RNA

extract_protocol:
To extract RNA, approximately 10 million cells were harvested and nuclei were extracted with nuclear extraction buffer (10% Sucrose, 20 mM HEPES pH 7.6, 10 mM NaCl, 3 mM MgCl2, 0.5% Triton X-100) supplemented with SUPERaseIN (Invitrogen AM2696). Nuclei were resuspended in 160 uL CF buffer (10 mM Tris pH 8, 100 mM NaCl, 25 mM EDTA) supplemented with SUPERaseIN. 1 mL fresh NUN buffer (1.5 M Urea, 20 mM HEPES, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1% NP-40) was immediately added to lyse nuclei. Samples were incubated on ice for 10 minutes to precipitate genomic DNA, histones, engaged RNA PolII, and nascent transcripts. Samples were centrifuged at 20,000xg for 10 minutes and pellets were washed twice with NUN buffer. Pellets were resuspended in 700 uL CF buffer supplemented with 1 mg/ml Proteinase K and 1% SDS and incubated for 1 hour at 55oC to remove protein. Nucleic acids were isolated with phenol chloroform extraction. DNA was removed with Turbo DNAse (Invitrogen AM2238). RNA was extracted with Phenol:Chloroform:Isoamyl alcohol. To remove residual DNA, a second DNAse treatment was performed
Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs E7760).

treatment_protocol: Cells were treated with DMSO, WM-1119 at 1 uM for 1 hour or 70 nM for 5 days, or 500 nM dTAG13 for 2 hours

value: 70 nM WM-1119 5 days


title: CRB_siRNA_rep8


title: MLL-AF9  LSK cells, WM-1119 70 nM 5 days treated, rep 1


title: Neutrophils (mpx+), 8 hours post-injury, AMD3100, biol rep 1

city: Lisboa

first: Carmen

last: de Sena-Tomás

address: Av. Prof. Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

data_processing:
Libraries were paired-end sequenced on a Nextseq 500 (Illumina), high output, with a 1x75 bp Illumina Kit (Read 1: 26 cycles, index read: 6 cycles, Read 2: 60 cycles). Read 1 was used to identify the Illumina library index and CEL-Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow-Wheeler aligner (BWA-MEM). Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38
Assembly: GRCz11 (zebrafish)
Supplementary files format and content: counts table generated using the MapAndGo script

source_name: Neutrophils (mpx:GFP+)

growth_protocol: Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue

extract_protocol:
Trunks containing the lesion site and same region of age-matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV, 15 mM HEPES, 25 mM D-Glucose, 2% goat serum in HBSS without magnesium and calcium, incubated at 28.5ºC shaking at 300 rpm, and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI (1ul/ml) for 10 min at 4C. Single-cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III (BD Biosciences). All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500-4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL-seq. Samples were barcoded with CEL-seq primers during the reverse transcription and pooled after second strand synthesis
TruSeq small RNA primers (Illumina)

treatment_protocol: At 3 days post-fertilization, larvae were anesthetized in 0.5 mM tricaine. Subsequenclty, the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next, larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 hours post-injury (hpi) until 8 hpi.

value: Neutrophils (mpx:GFP+)

value: 8 hours post-injury AMD3100


title: Neutrophils (mpx+), 8 hours post-injury, AMD3100, biol rep 3


title: Granulosa cells, 92_Pre-Treatment


title: SCR_siRNA_rep8


title: Neutrophils (mpx+), 8 hours post-injury, AMD3100, biol rep 2


title: Granulosa cells, 89_Post-Treatment


title: GRH_siRNA_rep7

value: Female


title: MLL-AF9 LSK cells, control (WM-1119 70 nM 5 days control), rep 1

value: Lin- Sca1+ cKit+ (LSK)

value: DMSO 5 days


title: MLL-AF9  LSK cells, control (WM-1119 70 nM 5 days control), rep 2


title: Neutrophils (mpx+), uninjured, AMD3100, biol rep 3

value: uninjured AMD3100


title: MOZ-TIF2 LSK cells, WM-1119 70 nM 5 days treated, rep 2


title: B38_16, longissimus thoracis, CON

value: Muscle thoracis

value: CON


title: Granulosa cells, 89_Pre-Treatment

value: Ovary

value: Primary cells

value: Granulosa Cells


title: GCM_siRNA_rep7

value: placenta

value: primary villous trophoblast cells


title: Neutrophils (mpx+), uninjured, AMD3100, biol rep 1


title: MOZ-TIF2 LSK cells, WM-1119 70 nM 5 days treated, rep 1


title: Neutrophils (mpx+), 8 hours post-injury, DMSO, biol rep 3

value: 8 hours post-injury DMSO


title: Granulosa cells, 84_Post-Treatment

value: Treatment

value: PFAS mixture (2 nM PFHxS, 7 nM PFOA, 10 nM PFOS)


title: Granulosa cells, 84_Pre-Treatment

value: Control

value: No Treatment


title: CRB_siRNA_rep7


title: MOZ-TIF2 LSK cells, control (WM-1119 70 nM 5 days control), rep 2


title: ESR_siRNA_rep7

value: ESRRG


title: Neutrophils (mpx+), 8 hours post-injury, DMSO, biol rep 2

value: Neutrophils (mpx:GFP+)


title: KYSE510_siNC_1_SA09717 RNA-seq

city: Los Angeles

first: Qian

last: Yang

address: 8700 Beverly Blvd

department: Department of Surgery

institute: CEDARS SINAI MEDICAL CENTER

data_processing:
Pair-end  reads were aligned to the hg19 reference genome using Bowtie. RNA-seq reads were trimmed for adaptor sequence, and then mapped to hg19 whole genome using STAR. For Cut&Tag-Seq, Bowtie2 was applied to do the alignment based on reference genome hg38.
Adaptors were removed using Trim galore software.
PCR duplicate reads were removed using Picard MarkDuplicates in Cut&Tag -Seq.
Blacklist regions were removed using ENCODE blacklist file in Cut&Tag -Seq.
SEACR peak calling package was applied to identify peaks with defalut parameters in Cut&Tag-Seq.
Assembly: hg38 for Cut&Tag and hg19 for RNA-Seq
Supplementary files format and content: gene expression matrix and bigwig files representing signal normalized to per million reads

source_name: Esophageal Squamous Cell Carcinoma cell line

growth_protocol: KYSE510 cell line was cultured in RPMI-1640 (Corning, #10-040-CV) and FADU cell line was cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Corning, #10-013-CV). Both cell lines were supplemented with 10% of fetal bovine serum (FBS) (Omega, #FB-02), and 1% of penicillin/streptomycin (Thermofisher Scientific, #30-002-CI). Cell cultures were incubated in a 37°C incubator with 5% CO2

extract_protocol:
Total RNA was extracted by RNeasy Mini kit (QIAGEN #70106) according to the manufacturer’s instructions. DNA fragments were extracted by tagmentation reaction
Standard Illumina library preparation protocol

treatment_protocol: For RNA-Seq, KYSE510 cell line was transfected with two independent siRNA of either LAT1 or EZH2 using lipofectamine RNAiMAX (Thermofisher Scientific, 13778150) and incubated for 48 hours. Cut&Tag assay was performed according to the manufacturer’s protocols in KYSE510 and FADU cell line

value: siNC


title: SCR_siRNA_rep7

data_processing:
Transcript abundances were estimated using Kallisto with GRCh38 transcriptome reference Ensembl version 93 , and length scaled counts were condensed to Ensembl Gene IDs using the Bioconductor TXImport package.
Assembly: GRCh38
Supplementary files format and content: abundance.tsv as tab delimited file containing transcript abundances in transcripts per million.

extract_protocol:
After 72 hours of total culture time (24 hours following previous complete media change) the cells were lysed in 700uL of Qiazol and RNA was isolated using the Zymo Direct-zol Mini-prep kit and reagents.
cDNA libraries were prepared from 1 μg of total RNA using the Illumina Stranded Total RNA library kit. Each library was sequenced to approximately a depth of 50 million reads on an Illumina NovaSeq 6000 S4 (2 x100 read length) sequencer by the OHSU sequencing core.

value: Scrambled siRNA

value: Female


title: MOZ-TIF2 LSK cells, control (WM-1119 70 nM 5 days control), rep 1

value: Lin- Sca1+ cKit+ (LSK)

value: DMSO 5 days


title: MOZ-TIF2 LSK cells, WM-1119 1h 1 uM treated, rep2

value: 1 uM WM-1119 for 1 hour


title: Neutrophils (mpx+), uninjured, DMSO, biol rep 3

value: uninjured DMSO


title: GRH_siRNA_rep6


title: KYSE510_siLAT1_3_2 RNA-seq

value: Esophageal Squamous Cell Carcinoma cell line


title: Neutrophils (mpx+), uninjured, DMSO, biol rep 2


title: Neutrophils (mpx+), uninjured, AMD3100, biol rep 2

value: uninjured AMD3100


title: KYSE510_siNC_1_SA09716 RNA-seq


title: MOZ-TIF2 LSK cells, control (WM-1119 1h 1 uM control), rep2

value: DMSO 1 hour


title: KYSE510_siLAT1_3_1 RNA-seq


title: MOZ-TIF2 LSK cells, WM-1119 1h 1 uM treated, rep1


title: GCM_siRNA_rep6

value: placenta

value: primary villous trophoblast cells


title: KYSE510_siLAT1_2_2 RNA-seq


title: ESR_siRNA_rep6


title: Neutrophils (mpx+), uninjured, DMSO, biol rep 1


title: RNA-seq_N_C

first: Guoying

last: Dong

address: Jinan lixia district Wenhua west road no. 44

department: Cheeloo College of Medicine

description: Normal tissue

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads weretrimmed for adaptor sequence/low-quality sequence using CLCgeneomic benchwork(parameter-Quality limit:0.05)
Trimmed sequence reads were mapped  to GrCM38/mm10 using CLC genomic benchwork(parameters-mismath cost: 2 insertion cost: 3 deletion cost:3 length fraction:0.8 similarity fraction:0.8
Read count extraction and mormalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: pancreas

extract_protocol:
RNA was harvested using Uneasy mini plus kit(Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacture’s protocols.

value: pancreas


title: FKBPV12-HA-MOZ-TIF2 LSK cells, 500 nM dTAG 2 hour, rep 2

value: 500 nM dTAG 2 hours


title: CRB_siRNA_rep6


title: MOZ-TIF2 LSK cells, control (WM-1119 1h 1 uM control), rep1


title: SCR_siRNA_rep6


title: RNA-seq_N_B

description: Normal tissue


title: KYSE510_siLAT1_2_1 RNA-seq


title: Neutrophils (mpx+), 8 hours post-injury, DMSO, biol rep 1

value: 8 hours post-injury DMSO


title: FKBPV12-HA-MOZ-TIF2 LSK cells, 500 nM dTAG 2 hour, rep 1


title: KYSE510_siNC_2 RNA-seq


title: RNA-seq_N_A

description: Normal tissue


title: GRH_siRNA_rep5


title: FKBPV12-HA-MOZ-TIF2 LSK cells, control, rep 2

value: DMSO hours


title: KYSE510_siNC_1 RNA-seq


title: GCM_siRNA_rep5


title: ESR_siRNA_rep5

value: ESRRG


title: FKBPV12-HA-MOZ-TIF2 LSK cells, control, rep 1

value: DMSO 2 hours


title: RNA-seq_T_C

description: Tumor tissue


title: KYSE510_siEZH2_2_2 RNA-seq


title: KYSE510_siEZH2_2_1 RNA-seq


title: CRB_siRNA_rep5


title: RNA-seq_T_A

description: Tumor tissue


title: KYSE510_siEZH2_1_2 RNA-seq


title: RNA-seq_T_B

description: Tumor tissue


title: SCR_siRNA_rep5

value: Scrambled siRNA


title: NOD slet, 12W, r2 [E2]

city: BErgen

first: Simona

last: Chera

address: Haukelandsbakken 15

country: Norway

institute: University of Bergen

data_processing:
Clc Genomics Workebench 23
Trimming
Alignment
Assembly: mm10
Supplementary files format and content: Tab separated files with Raw counts per sample

source_name: Pancreatic Islet

extract_protocol:
Qiagen RNAeasy Mini Kit
polyA enrichment Library preparation, performed by Novogene (Cambridge=

value: Pancreatic Islet

value: NOD

tag: age

value: 12 Weeks


title: NOD islet, 12W, r3 [E3]


title: NOD islet, 12W, r1 [E1]


title: HS7666T-plvx-2

description: Control

value: Tumor cell

value: WT


title: GRH_siRNA_rep4

value: Female


title: GCM_siRNA_rep4


title: sgGal4 arm, day 3 time point, replicate 2, RNAseq

first: Albert

last: Xu

address: 513 Parnassus Ave, HSW 640

department: Cell and Tissue Biology

institute: University of California, San Francisco

description:
sgGal4_RNA_rep2_d3
RNA_counts.csv

data_processing:
Ribosome Profiling: Raw sequencing reads were converted from .fastq to .fasta using fastx-toolkit (v0.0.13), adapter sequences were trimmed using cutadapt (v3.4), and reads were collapsed by UMI using fastx-toolkit. Bowtie2 (v2.4.1) was used to filter out repeat RNAs (rRNA, snoRNA, miRNA). A custom Perl script was used to trim reads a second time and bbduk was used to directly remove contaminating reads mapping to the sgRNA. STAR aligner22 (v2.7.5a, GrCH38, Gencode v25) was used to align reads. RSubread was used to generate counts and the DESeq2 and Riborex packages were used for differential expression and differential translation analysis.
RNAseq: Raw sequencing reads were aligned to genome by STAR aligner (v2.7.5a, GrCH38, Gencode v25). RSubread was used to generate counts
Assembly: GrCh38, Gencode v25
Supplementary files format and content: RNA_counts.csv - counts generated by Rsubread of all the RNA samples
Supplementary files format and content: RP_counts.csv - counts generated by Rsubread of all the Ribosome Profiling samples

growth_protocol: K562 cells were grown in DMEM media supplemented with 10% Fetal Bovine Serum and 1% Pen/Strep/Glutamine

extract_protocol:
See protocol from Calviello et al 2021 (PMID: 33905506). Briefly, Direct-zol RNA Miniprep (Zymo Research) kits were used to isolate RNA from either cytosolic cell lysate (lysed in (20 mM Tris–HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2 1% (v/v) Triton X-100, 25 U/ml TurboDNase (Ambion)) or cycloheximide-fixed ribosomes (treated with RNAseI (ambion) and isolated from Illustra MicroSpin Columns S-400HR).
RNAseq libraries were prepared as per manufacturer's instructions using the NEBNext rRNA Depletion Kit V2 (NEB cat: E7400) and the NEBnext Ultra II Directional RNA Library Prep Kit (NEB cat: E7760). Ribosome Profiling libraries were prepared as previously described (PMID: 33905506). Briefly, purified RNA was ligated to 3' and 5' adapters, reverse transcribed, and PCR amplified.

treatment_protocol: 50ng/ml doxycycline to induce CRISPRi knockdown

value: immortalised myelogenous leukemia

tag: molecule

value: Cytoplasmic RNA


title: HS7666T-plvx-3

description: Control


title: NOD islet, 10W, r3 [D6]

value: 10 Weeks


title: sgGal4 arm, day 14 time point, replicate 2, RNAseq

description:
sgGal4_RNA_rep2_d14
RNA_counts.csv


title: NOD islet, 10W, r2 [D5]


title: NOD islet, 10W, r1 [D1]


title: ESR_siRNA_rep4

first: Research

value: placenta

value: primary villous trophoblast cells


title: sgGal4 arm, initial time point, replicate 2, RNAseq

description:
sgGal4_RNA_rep2_d0
RNA_counts.csv


title: CRB_siRNA_rep4


title: HS7666T-DDX18-3

description: DDX18 overexpressed

value: pancreas


title: HS7666T-DDX18-2

description: DDX18 overexpressed


title: NOD islet, 8W, r3 [C6]

value: 8 Weeks


title: sgGal4 arm, day 3 time point, replicate 1, RNAseq

description:
sgGal4_RNA_rep1_d3
RNA_counts.csv


title: sgGal4 arm, day 14 time point, replicate 1, RNAseq

description:
sgGal4_RNA_rep1_d14
RNA_counts.csv


title: NOD islet, 8W, r2 [C2]


title: SCR_siRNA_rep4


title: sgGal4 arm, initial time point, replicate 1, RNAseq

description:
sgGal4_RNA_rep1_d0
RNA_counts.csv


title: GRH_siRNA_rep3


title: HS7666T-DDX18-1

description: DDX18 overexpressed


title: GCM_siRNA_rep3


title: NOD islet, 8W, r1 [C1]


title: KYSE510_siEZH2_1_1 RNA-seq

value: Esophageal Squamous Cell Carcinoma cell line


title: T9

city: Shanghai

first: Hailong

last: Ma

address: Zhizaoju Rd

institute: Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine

data_processing:
Raw data (raw reads) were processed using Trimmomatic software. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2 software.
Raw read counts of each gene were obtained by htseq-count software.
Assembly: hg38
Supplementary files format and content: txt file contains raw counts of each gene

source_name: oral squamous cell carcinoma

extract_protocol:
extract protocol RNA was harvested using mirVanaTM miRNA ISOlation Kit (Ambion-1561).
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions

treatment_protocol: Tissue samples were collected from patients and snap frozen in liquid nitrogen within 30 min, then transfer to - 80 ℃ freezer for storage until RNA-seq detection

value: oral squamous cell carcinoma


title: T8


title: NOD islet, 6W, r2 [B3]

value: 6 Weeks


title: NOD islet, 6W, r3 [B6]


title: ESR_siRNA_rep3

address: 818 Stewart Street

institute: Seattle Children's Research Institute

value: ESRRG


title: sgDDX3 arm, day 14 time point, replicate 2, RNAseq

description:
sgDDX3_RNA_rep2_d14
RNA_counts.csv


title: HS7666T-plvx-1

city: Jinan

description: Control


title: CRB_siRNA_rep3


title: T69


title: SCR_siRNA_rep3

value: Scrambled siRNA


title: T7


title: NOD islet, 6W, r1 [B1]

value: Pancreatic Islet

value: NOD


title: NOD islet, 4W, r3 [A6]

value: 4 Weeks


title: sgDDX3 arm, day 3 time point, replicate 1, RNAseq

city: San Francisco

description:
sgDDX3_RNA_rep1_d3
RNA_counts.csv


title: sgDDX3 arm, initial time point, replicate 2, RNAseq

description:
sgDDX3_RNA_rep2_d0
RNA_counts.csv


title: GRH_siRNA_rep2

city: Seattle


title: NOD islet, 4W, r2 [A4]


title: T67


title: sgDDX3 arm, day 3 time point, replicate 2, RNAseq

description:
sgDDX3_RNA_rep2_d3
RNA_counts.csv


title: sgDDX3 arm, day 14 time point, replicate 1, RNAseq

description:
sgDDX3_RNA_rep1_d14
RNA_counts.csv


title: T66


title: sgDDX3 arm, initial time point, replicate 1, RNAseq

description:
sgDDX3_RNA_rep1_d0
RNA_counts.csv


title: NOD islet, 4W, r1 [A1]


title: T65


title: ESR_siRNA_rep2


title: GCM_siRNA_rep2


title: 26135-P, 7 months with HFD, rep5

city: Cleveland

first: Oliver

last: Wessely

state: OH

address: 9500 Euclid Avenue/NC10

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic Foundation

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore!(v0.6.10) using the default parameters
Sequence reads were aligned to mouse genome (mm10) using Salmon (v1.10.1 )
Read count extraction using Salmon (Version 1.10.1)
Read count were normalized using the DESeq2 in R (Version 1.40.2)
Assembly: mm10
Supplementary files format and content: tab-delimited text file including the normalized counts for each sample in a matrix table

extract_protocol:
miRNeasy Mini Kit (Qiagen,   74104)
TruSeq RNA Library Prep Kit (Illumina)

treatment_protocol: (i) Deoxycorticosterone acetate (DOCA) treatment: Four-month-old mice (n=9) were given two sequential subcutaneous DOCA pellet implants (50mg/pellet, 21-day release, Innnovative Research of America, Sarasota, FL) 3 weeks apart for a total of 6 weeks of sustained DOCA release. After 6 weeks, kidneys were extracted, and podocytes isolated by MACS using anti-Nephrin antibodies. (ii) High Fat Diet (HFD)-Induced Obesity Model: Four-month-old mice (n=11) were provided ad libitum HFD with 60 kcal% fat (D12492, Research Diets Inc, New Brunswick, NJ) for 12 weeks. At the end of 12 weeks, kidneys were extracted, and podocytes isolated by MACS using anti-Nephrin antibodies.

value: kidney

value: podocyte

value: wildtype

value: HFD


title: CRB_siRNA_rep2

last: Computing

value: Female


title: T63


title: T64


title: SCR_siRNA_rep2

value: placenta


title: sgGal4 arm, day 14 time point, replicate 2, ribosome footprints

description:
sgGal4_RP_rep2_d14
RP_counts.csv

data_processing:
library strategy: Ribosome profiling
Ribosome Profiling: Raw sequencing reads were converted from .fastq to .fasta using fastx-toolkit (v0.0.13), adapter sequences were trimmed using cutadapt (v3.4), and reads were collapsed by UMI using fastx-toolkit. Bowtie2 (v2.4.1) was used to filter out repeat RNAs (rRNA, snoRNA, miRNA). A custom Perl script was used to trim reads a second time and bbduk was used to directly remove contaminating reads mapping to the sgRNA. STAR aligner22 (v2.7.5a, GrCH38, Gencode v25) was used to align reads. RSubread was used to generate counts and the DESeq2 and Riborex packages were used for differential expression and differential translation analysis.
RNAseq: Raw sequencing reads were aligned to genome by STAR aligner (v2.7.5a, GrCH38, Gencode v25). RSubread was used to generate counts
Assembly: GrCh38, Gencode v25
Supplementary files format and content: RNA_counts.csv - counts generated by Rsubread of all the RNA samples
Supplementary files format and content: RP_counts.csv - counts generated by Rsubread of all the Ribosome Profiling samples

value: immortalised myelogenous leukemia

value: ribosome protected footprints


title: sgGal4 arm, day 3 time point, replicate 2, ribosome footprints

description:
sgGal4_RP_rep2_d3
RP_counts.csv


title: sgGal4 arm, initial time point, replicate 2, ribosome footprints

description:
sgGal4_RP_rep2_d0
RP_counts.csv


title: 26134-P, 7 months with HFD, rep4


title: 26132-P, 7 months with HFD, rep3


title: GRH_siRNA_rep1

value: primary villous trophoblast cells


title: T68


title: sgGal4 arm, day 3 time point, replicate 1, ribosome footprints

description:
sgGal4_RP_rep1_d3
RP_counts.csv


title: T61


title: GCM_siRNA_rep1


title: T62


title: 26106-P_HFD, 7 months with HFD, rep1


title: ESR_siRNA_rep1


title: 26460-P, 7 months, rep10

value: untreated


title: sgGal4 arm, initial time point, replicate 1, ribosome footprints

description:
sgGal4_RP_rep1_d0
RP_counts.csv


title: CRB_siRNA_rep1


title: sgDDX3 arm, day 3 time point, replicate 2, ribosome footprints

description:
sgDDX3_RP_rep2_d3
RP_counts.csv


title: 26459-P, 7 months, rep9


title: SCR_siRNA_rep1


title: T59

value: oral squamous cell carcinoma


title: FADU-EZH2 Cut&Tag-Seq

data_processing:
Pair-end  reads were aligned to the hg19 reference genome using Bowtie. RNA-seq reads were trimmed for adaptor sequence, and then mapped to hg19 whole genome using STAR. For Cut&Tag-Seq, Bowtie2 was applied to do the alignment based on reference genome hg38.
Adaptors were removed using Trim galore software.
PCR duplicate reads were removed using Picard MarkDuplicates in Cut&Tag -Seq.
Blacklist regions were removed using ENCODE blacklist file in Cut&Tag -Seq.
SEACR peak calling package was applied to identify peaks with defalut parameters in Cut&Tag-Seq.
Assembly: hg38 for Cut&Tag and hg19 for RNA-Seq
Supplementary files format and content: gene expression matrix and bigwig files representing signal normalized to per million reads
Library strategy: Cut&Tag-seq

value: FADU

value: Esophageal Squamous Cell Carcinoma cell line


title: 26458-P, 7 months, rep8


title: sgDDX3 arm, initial time point, replicate 2, ribosome footprints

description:
sgDDX3_RP_rep2_d0
RP_counts.csv


title: sgDDX3 arm, day 14 time point, replicate 2, ribosome footprints

description:
sgDDX3_RP_rep2_d14
RP_counts.csv


title: sgDDX3 arm, day 3 time point, replicate 1, ribosome footprints

description:
sgDDX3_RP_rep1_d3
RP_counts.csv


title: 26107-P, 7 months with HFD, rep2


title: T58


title: 26457-P, 7 months, rep7


title: T60


title: 26456-P, 7 months, rep6