title: HRasSn

city: Waco

first: Joe

last: Taube

state: Texas

address: One Bear Place #97388

institute: Baylor University

description: HMLERSnail ATAC DNA

data_processing:
Adapter sequences were removed using cutadapt (Galaxy version 1.16.6)
Cropped to 30 bp with Trimmomatic (Galaxy version 0.36.6)
Aligned to hg19 using Bowtie2 (v2.3.4.2)
mtDNA, unmapped and random contigs, and ChrY reads excluded using samtools (v1.9)
Tag directories, peaks, and motif enrichment generated by HOMER (version 4.10.3)
Genome_build: hg19

source_name: HMLE-Ras-Snail

growth_protocol: Cells were plated at 10,000 cells/mm2 and treated with TGFB.  Cell density was maintained every other day and media was removed and replenished with TGFB

extract_protocol:
50,000 cells were centrifuged and resuspended in 50 uL lysis buffer (10 mM Tris, 10 mM NaCl, 3 mM MgCl2, 0.01% IGEPAL) and centrifuged at 500g for 10 min at 4C.
Pellet was resuspended in transposase reaction mix (25 uL 2X TD buffer, 2.5 uL transposase, 22.5 uL H2O.  Tagmented DNA was purified and amplified using Nextera DNA Sample Preparation Kit using the following PCR conditions: 98C for 30s, then thermocycling for 98C for 10s, 63C for 30s, and 72C for 1 min for 11 cycles followed by 72C for 5 min

treatment_protocol: 5 ng/mL TGFB in 4 mM HCL with 0.01% BSA

tag: protocol

value: ATAC-seq

tag: culture conditions

value: 2D culture


title: S36 Healthy controls

status: Public on Dec 01 2021

type: RNA

city: Karachi

first: Asghar

last: Nasir

state: Sindh

address: Stadium Road

department: Pathology and Laboratory Medicine

country: Pakistan

institute: Aga Khan University

description: gene expression data

hyb_protocol: Clariom S Array Type gene expression, Affymetrix

scan_protocol: GeneChipTM Scanner 3000 7G

data_processing: CEL files were analysed using the TCAS Transcriptome Analysis Software Suite (version 2) using the Summarization Method: Gene Level - SST-RMA Pos vs Neg AUC Threshold: 0.7 against Genome Version: hg38 (Homosapiens)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: blood

growth_protocol: RNA was extracted from whole blood collected in Plasma/EDTA tube.

extract_protocol: Qiagen RNA Blood Mini Kit (Qiagen, GmbH, Germany)

treatment_protocol: no treatment

tag: disease state

value: healthy control

tag: symptons

value: Healthy controls


title: MUT3

type: SRA

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

country: USA

institute: UC Davis School of Medicine

description: Illimuna next-generation sequencing (2x150bp, paired-end)

library_source: transcriptomic

data_processing:
RNA-Seq data was analyzed using a Salmon-tximport-DEseq2 pipeline. Raw sequence reads (FASTQ format) were mapped to the reference human genome assembly (GRCh38/hg38, GENCODE release 36) and quantified with Salmon (DOI: 10.1038/nmeth.4197). Gene-level counts were imported with tximport (DOI: 10.12688/f1000research.7563.2) into DESeq2 (DOI: 10.1186/s13059-014-0550-8) and normalized.
Processed data is a data matrix of normalized read counts generated from the output of Salmon, imported wih tximport, and normalized with DESeq2. GENCODE release 36 was used for annotation. The file contains the Ensembl ID and normalized gene-level read count data for each sample.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Data matrix in tab-delimited text format. The file contains the Ensembl ID and normalized, gene-level counts for each sample.

source_name: human primary effusion lymphoma

growth_protocol: BCBL-1 xenogrft tumors were established and grown by intraperitoneal (i.p.) injection of BCBL-1 cells (2 x 10^7 cells in 200 uL PBS) into eight-week-old male NRG (NOD.Cg-Rag1tm1Mom Il2rgtm1Wjl/SzJ).

extract_protocol:
Total RNA was isolated using the TRIzol Reagent (Invitrogen).
Indexed, stranded mRNA-seq libraries were prepared from total RNA (100 ng) using the KAPA Stranded mRNA-Seq (Roche) according to the manufacturer’s standard protocol.

treatment_protocol: On day 2 (i.e., 24 hours after injection of BCBL-1 cells), mice were randomly assigned to PBS control, MBK50 (10 mg/kg), or mutant control peptide (10 mg/kg) groups. Treatments were administered by daily i.p. injection for 10 days.

tag: xenograft tumor

tag: treatment

value: mutant type peptide (10 mg/kg, i.p. injection, daily) for 10 days

tag: mouse strain for xenograft growth

value: NRG (NOD.Cg-Rag1tm1Mom Il2rgtm1Wjl/SzJ)


title: all_cells_gex

city: Baltimore

first: Christopher

last: Cherry

state: MD

address: 1800 Orleans St

institute: Johns Hopkins University

description:
RNA
Gene expression for all samples pooled

data_processing:
CellRanger with default parameters
Genome_build: CellRanger premade references; mm10
Supplementary_files_format_and_content: ZIP file containing filtered CellRanger output for hashing, BCR, TCR library

organism: Mus musculus

source_name: All samples pooled with hashing

extract_protocol:
Murine tissue samples (quadriceps femoris muscle and inguinal lymph nodes) were obtained for single cell flow cytometry and/or fluorescence activated cell-sorting. Quad tissue samples were finely diced and digested with 1.67 Wünsch U/mL Liberase TL (Roche Diagnostics) and deoxyribonuclease I (0.2 mg/ml; Roche Diagnostics) in RPMI-1640 medium (Gibco) for 45 min at 37°C. The digested quad tissues were ground through 70-µm cell strainers (Thermo Fisher Scientific), rinsed with RPMI-1640 + 5% fetal bovine serum. Percoll (GE Healthcare) density gradient centrifugation was used to remove debris from quad digestions and enrich the leukocyte fraction. Inguinal lymph node samples were ground through 70-µm cell strainers with excess RPMI-1640 + 10 mM HEPES buffer solution. The enriched single-cell suspensions were washed and stained following antibody panels, respective to the intended application. No differences in single-cell isolation from different material environments were observed.
According to 10X protocol
All samples were pooled into one after hashing. The library was split appropriately into sequencing lanes as needed for sequencing depth.

tag: strain


title: all_cells_hash

description:
Hash barcode
CITEseq hashing for all samples


title: C512 TAL1-5 iPSC p48

city: La Jolla

first: Adam

middle: Jeffrey

last: Engler

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: UC San Diego

library_source: genomic

data_processing:
All data processing was performed by UCSD Center for Epigenomics using the following pipeline: https://github.com/epigen-UCSD/atac_seq_pipeline
Additional details can be found: https://biomystery.gitbooks.io/ataq_seq/content/pipeline/overall_steps.html
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files, show peak locations across the genome, easy format to visualize on genome browsers quickly

molecule: genomic DNA

source_name: Induced Pluripotent Stem Cells

growth_protocol: Based on Bao et al protcol, varies by developmental stage, see publication

extract_protocol:
Extraction was perfomed by the UCSD Center for Epigenomics using the following protocl: https://medschool.ucsd.edu/som/cmm/research/epigenomics/Partnerships/Documents/EPIGEN_ATACseq_cells%20protocol_05102019.pdf
Libraries were constructed using a protocol adapted from Buenrostro et. al (doi: 10.1002/0471142727.mb2129s109) by the UCSD Center for Epigenomics (https://medschool.ucsd.edu/som/cmm/research/epigenomics/Partnerships/Documents/EPIGEN_ATACseq_cells%20protocol_05102019.pdf)

tag: source/clone id

value: iPSC Clone 1

tag: cell type

value: iPSC

tag: assay

value: Tn5 ATAC-Seq


title: PBS3

value: PBS (200 ul, i.p. injection, daily) for 10 days


title: HRas

description: HMLER ATAC DNA

source_name: HMLE-Ras


title: PBS2


title: 10dTGFB_24dwithdrawn_Rep2_ATAC

description: 10d +TGFB, 24d -TGFB MCF10A ATAC DNA


title: S32 Healthy controls

description: gene expression data

label_protocol: Clariom S Array Type gene expression, Affymetrix


title: S33 Healthy controls

description: gene expression data


title: 4dTGFB_10dwithdrawn_ATAC_Rep2

description: 4d +TGFB, 10d -TGFB MCF10A ATAC DNA


title: S34 Healthy controls

description: gene expression data


title: Articular chondrocytes transfected with Sephs1 siRNA, rep 3

city: Seoul

first: Jin-Hong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
Raw reads were preprocessed to remove low quality and adapter sequence before analysis and the processed reads were aligned to mm10 using HISAT v2.1.0.
Transcript assembly and abundance estimation were performed using StringTie v1.3.4d.
Genome_build: Reference gemome sequence of mm10 was downloaded from the UCSC genome browser.
Supplementary_files_format_and_content: .xlsx (raw counts and abundance measurements)

growth_protocol: Primary cultured chondrocytes were maintained in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (Gibco) and antibiotics (penicillin and streptomycin). Cultured cells were maintained in a humidified 37°C, 5% CO2, and 3% O2 atmosphere.

extract_protocol:
Total RNA was extracted using the TRI reagent (Molecular Research Center, Inc.).
One microgram of total RNA was converted into cDNA libraries using the TruSeq Stranded mRNA Sample Prep kit (Illumina). Final cDNA libraries were analyzed for size distribution, quantified by qRT-PCR using Agilent 2100 Bioanalyzer, and normalized to 2 nM for sequencing.

treatment_protocol: Mouse articular chondrocytes were transfected with 50 nM of negative control siRNA or Sephs1 siRNA for 12 h. After 12 h of transfection, the cells were incubated in fresh medium for 48 h. For efficient and long-term knockdown, transfection was carried out twice.

value: ICR

value: articular chondrocytes

value: Sephs1 siRNA transfection


title: Articular chondrocytes transfected with Sephs1 siRNA, rep 2


title: PBS1


title: Articular chondrocytes transfected with Sephs1 siRNA, rep 1


title: S31 Healthy controls

description: gene expression data


title: WT3

value: MBP50 wild type peptide (10 mg/kg, i.p. injection, daily) for 10 days


title: 4dTGFB_4dwithdrawn_ATAC_Rep2

description: 4d +TGFB, 4d -TGFB MCF10A ATAC DNA


title: C512 TAL1-5 EpiC p4

source_name: iPSC-Derived Epicardal Cells

value: Epicardial Cells from Clone 1

value: EpiC


title: Bc1_Mut_24uM_2

data_processing:
RNA-Seq data was analyzed using a Salmon-tximport pipeline. Raw sequence reads (FASTQ format) were mapped to the reference human genome assembly (GRCh38/hg38, GENCODE release 36) and quantified with Salmon (DOI: 10.1038/nmeth.4197). Gene-level counts were imported with tximport (Soneson, Love, and Robinson 2015; DOI: 10.12688/f1000research.7563.2)
Processed data is a data matrix generated from the output of Salmon and and imported wih tximport. GENCODE release 36 was used for annotation. The file contains the Ensembl ID, gene name, and gene-level read count data for each sample.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Data matrix in tab-delimited text format. The file contains include the Ensembl ID, gene name, and gene-level counts for each sample.

growth_protocol: (TREx)BCBL-1, BC-1, and BC-3 cell lines were cultured in RPMI 1640 medium supplemented with 15% FBS. The cultures were maintained at 37°C in a humidified atmosphere containing 5% CO2 (v/v). Mycoplasma contamination was routinely tested by using a PCR-based assay.

treatment_protocol: Each PEL cell line was seeded into 3 individual 25-cm^2 tissue culture flasks. After 2-3 days of growth, the cells were treated with wild type or mutant peptides at a final concentartion of 24uM for 24hrs.

tag: cell line

value: mutant peptide (24uM) for 24hrs


title: Articular chondrocytes transfected with control siRNA, rep 3

value: control siRNA transfection


title: S30 Healthy controls

description: gene expression data


title: S29 Asymptomatic

description: gene expression data

value: SARS-CoV-2 positive

value: Asymptomatic


title: 10dTGFB_10dwithdrawn_ATAC_Rep2

description: 10d +TGFB, 10d -TGFB MCF10A ATAC DNA

value: ATAC-seq

value: 2D culture


title: Articular chondrocytes transfected with control siRNA, rep 2


title: Bc1_Mut_24uM_1


title: 10dTGFB_4dwithdrawn_ATAC_Rep2

description: 10d +TGFB, 4d -TGFB MCF10A ATAC DNA


title: Articular chondrocytes transfected with control siRNA, rep 1


title: Bc1_Wt_24uM_3

value: wild type peptide (24uM) for 24hrs


title: Exp70 MC+Both Allobaculum sp. 128 and A. muciniphila-colonized PP

city: New Haven

first: Tyler

last: Rice

state: CT

address: 10 Amistad St Rm 102

department: Immunobiology

institute: Yale University

description:
single cell transcriptomes
70B_PP_MMT_S4_L002

data_processing:
base-calling: RTA3 software onboard NovaSeq instrument (Illumina)
alignment and normalized abundance measurements: cellranger 5.0 (10X Genomics)
integration of count matrices, clustering, differential expression: Seurat 3.2.1 (Satija lab)
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv: barcodes corresponding to the cells input into each library
Supplementary_files_format_and_content: features.tsv: Mus musculus transcriptome features found within library
Supplementary_files_format_and_content: matrix.mtx: normalized abundance count matrix of features measured per cell within each library

source_name: Peyer's patches

growth_protocol: Mice were colonized with specified microbiota by single oral gavage, incubated for 4 weeks to allow immune response prior to euthanasia.

extract_protocol:
10X Genomics Chromium v2 chemistry
5Prime gene expression library constructed from each sample

treatment_protocol: No additional treatments other than microbiota colonization. All responses are "endogenous" or "steady state" immune responses.

value: WT gnotobiotic C57BL/6

tag: age

value: 10 weeks

tag: microbiome + tissue abbrev

value: BP

tag: microbiome


title: S26 Asymptomatic

description: gene expression data


title: S27 Asymptomatic

description: gene expression data


title: 4dTGFB_ATAC_Rep2

description: 4d +TGFB MCF10A ATAC DNA


title: Bc1_Wt_24uM_2


title: S25 Asymptomatic

description: gene expression data


title: Exp70 MC+Both Allobaculum sp. 128 and A. muciniphila-colonized MLN

description:
single cell transcriptomes
70B_MLN_MMT_S8_L002

source_name: Mesenteric lymph nodes

value: BM


title: S24 Asymptomatic

description: gene expression data


title: Exp70 MC+A. muciniphila-colonized PP

description:
single cell transcriptomes
70K_PP_MMT_S3_L002

value: KP

value: MC+A. muciniphila


title: Untreated_ATAC_Rep2

description: Untreated MCF10A ATAC DNA


title: 2dTGFB_ATAC_Rep2

description: 2d +TGFB MCF10A ATAC DNA


title: Bc3_Mut_24uM_3


title: Bc1_Wt_24uM_1


title: Bc1_Mut_24uM_3


title: Exp70 MC+A. muciniphila-colonized MLN

description:
single cell transcriptomes
70K_MLN_MMT_S7_L002

value: KM


title: 4dTGFB_10dwithdrawn_ATAC_Rep1

description: 4d +TGFB, 10d -TGFB MCF10A ATAC DNA


title: Exp70 MC+Allobaculum sp. 128-colonized PP

description:
single cell transcriptomes
70L_PP_MMT_S2_L002

value: LP

value: MC+Allobaculum sp. 128


title: Bc3_Mut_24uM_1


title: Bc3_Mut_24uM_2


title: S28 Asymptomatic

description: gene expression data


title: S23 Asymptomatic

description: gene expression data


title: 4dTGFB_4dwithdrawn_ATAC_Rep1

description: 4d +TGFB, 4d -TGFB MCF10A ATAC DNA


title: 10dTGFB_10dwithdrawn_ATAC_Rep1

description: 10d +TGFB, 10d -TGFB MCF10A ATAC DNA


title: Bc3_Wt_24uM_3


title: Exp70 MC+Allobaculum sp. 128-colonized MLN

description:
single cell transcriptomes
70L_MLN_MMT_S6_L002

value: LM


title: S22 Asymptomatic

description: gene expression data


title: 10dTGFB_ATAC_Rep2

description: 10d +TGFB MCF10A ATAC DNA


title: Exp70 Negative control: MC-colonized PP

description:
single cell transcriptomes
70N_PP_MMT_S1_L002

value: NP

value: Negative control:Mock Community (MC)


title: S20 Asymptomatic

description: gene expression data

value: SARS-CoV-2 positive


title: S21 Asymptomatic

description: gene expression data

value: Asymptomatic


title: Bc3_Wt_24uM_2


title: 10dTGFB_4dwithdrawn_ATAC_Rep1

description: 10d +TGFB, 4d -TGFB MCF10A ATAC DNA

value: ATAC-seq


title: Exp70 Negative control: MC-colonized MLN

description:
single cell transcriptomes
70N_MLN_MMT_S5_L002

value: NM


title: Bc3_Wt_24uM_1

value: wild type peptide (24uM) for 24hrs


title: S18 Asymptomatic

description: gene expression data


title: TREx_Mut_3

value: mutant peptide (24uM) for 24hrs


title: 10dTGFB_ATAC_Rep1

description: 10d +TGFB MCF10A ATAC DNA

value: 2D culture


title: S19 Asymptomatic

description: gene expression data


title: 4dTGFB_ATAC_Rep1

description: 4d +TGFB MCF10A ATAC DNA


title: TREx_Mut_2


title: 2dTGFB_ATAC_Rep1

description: 2d +TGFB MCF10A ATAC DNA


title: Untreated_ATAC_Rep1

description: Untreated MCF10A ATAC DNA


title: iel_gex

city: Pittsburgh

first: Anthony

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

institute: University of Pittsburgh

description:
gene expression data
aom_dss_control_iel_1_gex
aom_dss_control_iel_2_gex
aom_dss_control_iel_3_gex
aom_dss_hhep_iel_1_gex
aom_dss_hhep_iel_2_gex
aom_dss_hhep_iel_3_gex

data_processing:
bcl2fastq (version 2.20.0) to demultiplex reads
cellranger (version 3.1.0) to align reads and generate gene barcode matrices, CITEseqCount (version 1.4.4) to enumerate TotalSeq-C hashtag antibodies
Genome_build: GRCm38
Supplementary_files_format_and_content: gene expression data: gene_barcode_matrix, cellranger gene barcode expression matrix consisting of features (genes), cell barcodes, and UMI counts; cell hash expression data: CITEseqCount matrix consisting of features (cell hash tags), cell barcodes, and UMI counts

molecule: polyA RNA

source_name: colonic intraepithelial immune cells

growth_protocol: Hhep 51449 was purchased from ATCC and grown in an anaerobic chamber. Hhep was grown in either supplemented Tryptic Soy Broth or on chocolate agar plates.

extract_protocol:
Colonic samples were resected from mice and dissected into small pieces, followed by incubation in RPMI with 3% fetal calf serum and 20 mM HEPES for 20 minutes at 37 degrees C with constant stirring. Tissues were then further digested with 250 mg/mL Liberase CI and 500 mg/mL DNAseq I with continuous stirring at 37 degrees C for 30 minutes. Single cell suspensions were stained with CD45/MHCI (Biolegend TotalSeq-C) for cell hashing for 10 minutes on ice. Cells from individual mice (3 per group) were pooled for single-cell RNAseq analysis from each tissue.
Libraries were contructed accoding to the manufactuerer's protocol for the 5-prime v1 kit from 10X Genomics.

treatment_protocol: Mice were injected i.p. with 10 mg/kg AOM on day 0, followed by 3 cycles of 1 week with 3% DSS in drinking water followed by 2 weeks without DSS in drinking water. Mice were gavaged with 10^8 Hhep twice, with 5 days between each gavage, 7 weeks following the beginning of tumor induction. Mice were euthanized if 25% of their bodyweight was lost over, and were weighed weekly. Mice were sacrificed at either week 9 or week 12 after AOM.

tag: tissue

value: colon

value: colonic intraepithelial immune cells

value: mixed sample (non-demultiplexed) representing control and hhep


title: lp_gex

description:
gene expression data
aom_dss_control_lp_1_gex
aom_dss_control_lp_2_gex
aom_dss_control_lp_3_gex
aom_dss_hhep_lp_1_gex
aom_dss_hhep_lp_2_gex
aom_dss_hhep_lp_3_gex

source_name: lamina proproia immune cells

value: lamina proproia immune cells


title: lp_cell_hash

description:
cell hash expression data
TotalSeq-C hashtag

molecule: protein

value: control


title: TREx_Wt_3


title: iel_cell_hash


title: TREx_Wt_2


title: S16 Asymptomatic

description: gene expression data


title: S14 Asymptomatic

description: gene expression data


title: TREx_Wt_1


title: Tpbg KO rep1

first: Dong-Wook

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Dept. of Physiol.

institute: Yonsei University College of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw FASTQ files were trimmed for adapters using bbduk, and quntified their transcripts with Salmon using the reference transcript GENCODEVM23
Normalized abundance measurements was conducted with DESeq2 (1.27.12)
Genome_build: GENCODEVM23
Supplementary_files_format_and_content: Salmon quantification file
Supplementary_files_format_and_content: Normalized abundance measurements

source_name: substantia nigra

extract_protocol:
Substantia nigra tissues were dissected out from mouse ventral midbrain slices, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA LT Sample Prep Kit was used with 200 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain-substantia nigra

value: 14 months old

tag: genotype

value: Tpbg -/-


title: S17 Asymptomatic

description: gene expression data


title: S13 Asymptomatic

description: gene expression data


title: S15 Asymptomatic

description: gene expression data


title: S12 Asymptomatic

description: gene expression data


title: WT rep2

value: wild type


title: emerin + Chk2 null replicate #2

city: Iowa City

first: Samuel

middle: Cole

last: Kitzman

state: IA

address: 3135E MERF

department: Biochemistry

institute: University of Iowa

data_processing:
fastq files were trimmed and validated as pairs use Trim-Galore! Version 0.6.6 with following conditions: --paired
transcript level counts were generated using Kallisto Version 0.46.1 with following conditions: -b 100
bam alignments to genome were made using Kallisto Version 0.46.1 with following conditions: -b 100 --genomebam -g Drosophila_melanogaster.BDGP6.28.102.gtf.gz
Genome_build: dm6 (BDGP 6.28)
Supplementary_files_format_and_content: processed data files include.tsv files of transcript counts outputed by Kallisto,  and the final gene cout table generated by tximport in R

organism: Drosophila melanogaster

source_name: newly eclosed ovary

growth_protocol: Drosophila stocks were raised on standard cornmeal/agar medium with p-hydroxybenzoic acid methyl ester as a mold inhibitor. bafKD flies were raised at 25°C, 70% humidity, all the other flies were raised at room temperature.

extract_protocol:
For each replicate, ~100 pairs of ovaries were hand dissected from newly eclosed females. RNA was extracted using TRIzol (Invitrogen) followed by purification on RNeasy spin columns (Qiagen).
mRNA is enriched using oligo(dT) beads. For library construction, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a  custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair,  A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

value: newly eclosed ovary

value: emerin Chk2 double mutant


title: emerin + Chk2 null replicate #1


title: emerin+ Chk2 null replicate #3


title: Tpbg KO rep2


title: nos_bafRNAi replicate #2

value: BAF RNAi


title: WT rep1


title: S11 Symptomatic

description: gene expression data

value: SARS-CoV-2 positive

value: Symptomatic


title: DMSO treated GBM22 orthotopic xenograft (mouse 1)

city: Washington, DC

first: Nagi

last: Ayad

state: District Of Columbia

address: 3970 Reservoir Rd NW

department: Department of Oncology

institute: Georgetown University

data_processing:
FASTQ generation was performed using CellRanger mkfastq using the default parameters. 10X index sequences available upon request.
Alignment was initially performed using CellRanger count with default parameters to mm10/hg19 dual transcriptome available from 10X genomics to identify cell species of origin (mouse vs human)
Alignments were repeated to hg39 using CellRanger count with default parameters.
The output UMI count matrix from CellRanger alignment to hg38 was then used for downstream filtering and processing.
Using dual-species alignment data and the R package Seurat, cell barcodes from cells of human origin were used to bioinformatically isolate GBM22 PDX cells for downstream processing. These data were further filtered for those with less than 10% mitochondrial transcript expression, and for those with more than 200 but less than 6000 detected genes.
Data from individual samples was integrated using scTransform and Seurat's anchor-based integration features. In the combined sample object, the raw counts assay was log-normalized with a scale factor of 10,000 and exported as a tab-separated matrix. R pipeline is available at https://github.com/AyadLab/UM002-scPerturbation
Genome_build: hg38
Supplementary_files_format_and_content: tab-separated file containing log-normalized UMI counts of human GBM22 PDX cells

source_name: PDX GBM22 orthotopic xenograft (frontal-cortex)

growth_protocol: GBM22 cells were transduced with lentiviral libraries expressing GFP. Cells were visualized to confirm GFP expression prior to intracranial implantation into mice. Cells were implanted in mice using a previously described protocol(42). Briefly, Nu/Nu mice (Charles River Laboratory) were anesthetized, and a hole was drilled through the skull (1 mm anterior and 2 mm lateral to bregma). Using a Hamilton syringe 150,000 GBM22 cells suspended in PBS were injected at a depth of 2 mm. Skin flaps were sealed using surgical glue or sutures and mice were given buprenorphine as analgesic. Procedures were approved by the University of Miami IACUC, protocol number 21-002.

extract_protocol:
Tumor-bearing mice were perfused with PBS, and their brains were removed. Tumor was isolated and dissociated using the Worthington Biochem Papain dissociation kit. Cells were washed two times using ice-cold PBS with 0.1% BSA (w/v), checked for viability using AO/PI dye and a Nexcelom K2 Cellometer, and were loaded into a 10X Chromium chip using 10x Genomics NextGEM 3’ chemistry targeting the capture of approximately 10,000 cells per sample.
10X Genomics 3' NextGEM

treatment_protocol: Following tumor implantation, mice recovered for a period of 6 days, followed by treatment with UM-002 (5 mg/kg/day) or DMSO. Drug formulation was as follows: 10% DMSO, 40% PEG400, 50% PBS. Mice were injected intraperitoneally 5 days per week for 3 weeks and monitored daily for signs of cognitive decline. Cells from tumors from three individual mice within each treatment group were isolated for single cell RNA-sequencing.

value: DMSO (IP)


title: DMSO treated GBM22 orthotopic xenograft (mouse 2 & mouse 3)

source_name: PDX GBM22 orthotopic xenografts (frontal-cortex)


title: S10 Symptomatic

description: gene expression data


title: WT_S_8

city: Piscataway

first: Premal

last: Shah

state: NJ

address: 145 Bevier Rd

department: Genetics

institute: Rutgers University

description: technical replicates

data_processing:
Adapter removal and quality control was completed using fastp v0.20.0
Transcript quantification was completed using kallisto v0.46.2
Genome_build: Gencode VM25
Supplementary_files_format_and_content: A single csv file contains the counts and TPMs for each of the samples. This file contains both the original read counts and TPMs, as well as a column for rounded read counts and TPMs generated from them. Analyses were performed using rounded read counts and the correspoinding TPMs.

source_name: amygdala

growth_protocol: Animals: Grp-/- mice were maintained on C57BL/6J background (N>10). The homozygous Grp-/- mice and their WT littermates were generated by breeding heterozygous Grp+/- mice, which in turn resulted from breeding of heterozygous mice to C57BL/6J mice (Jackson Laboratory). All mice were maintained on a 12-h light/dark cycle. Behavioral experiments were conducted during the light phase of the cycle, and mice were at least 12 weeks old at the time of training. This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. The Rutgers University Institutional Animal Care and Use Committee approved the protocol.

extract_protocol:
Mouse brains were extracted and placed on ice, bilateral punches of the amygdala were obtained and placed in Qiagen RNAlater. Total RNA was extracted from the punches using the Qiagen RNeasy mini kit.
The RNA recovered from the Qiagen RNeasy mini kit was sent to a fcility for standard illumina library preparation and 150bp paired end sequencing.

treatment_protocol: The generation of the Grp-/- mouse: Part of exon 1 of the Grp gene (77bp from translation start site) was removed, and GFP ORF and neomycin cassette were inserted. The neomycin cassette was later removed by FLP-mediated excision in vivo. SEFL paradigm: Restraint stress was performed as previously described by placing individual animals into clear 50 ml conical vials (Falcon Centrifuge Tubes) with ventilation holes for 2 hours. Tubes were placed flat in an open box in a biosafety cabinet with overhead lights on for the duration of the procedure. Mice in FC control groups were placed in a biosafety cabinet in another room during restraint stress and briefly handled in their home cages. Mice underwent the following fear conditioning protocol: two minutes of exploration followed by two CS-US pairings that co-terminated with a 0.5 mA footshock (US). Extinction training (4 days post-shock) and remote memory retrieval tests (30 days post-shock) were performed in a novel context. Post-shock freezing was used to separate the subjects to susceptible and resilient groups. Animals that froze above the mean % freezing for the stressed group were classified as stress-susceptible (SS), while those that fell below the mean were classified as stress-resilient (SR).

value: brain

value: WT

value: SEFL


title: UM002 treated GBM22 orthotopic xenograft (mouse 2 & mouse 3)

value: UM002 (5mg/kg/d for 15 days) (IP)


title: WT_S_37


title: TREx_Mut_1

value: mutant peptide (24uM) for 24hrs


title: nos driver control replicate #2


title: nos driver control replicate #1


title: UM002 treated GBM22 orthotopic xenograft (mouse 1)


title: S9 Symptomatic

description: gene expression data


title: WT_S_22


title: S8 Symptomatic

description: gene expression data


title: WT_S_18


title: S7 Symptomatic

description: gene expression data


title: G/PK replicate #2

value: emerin mutant (G/PK)


title: WT_32


title: ZKSCAN3 KO HCT116-2

first: Yong Jun

address: 26 Kyungheedaero

department: Department of Pathology

institute: Kyung Hee University

data_processing:
Illumina Real-Time Analysis 3 (RTA3) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie 2 v2.2.5 with following parameters: Seed lenth 22, Seed mismatches 0, Seed extension attempts 15, Max re-seed attempts 2, Interval between seeds S,1.0,1.25, Ambiguous character function L,0.0,0.15, Gaps per read 15, Gap end buffer 4, Ambiguous character penalty 1, Alignment score cutoff L,-0.6,-0.6, Mismatch penalty range Max6 Min2, Rad gap penalties Open5 and extend 3penalties, Reference gap penalties Open5 and extend 3penalties
Normalized by criteria Transcripts Per Million (TPM) using a protocol from Abrams et al., BMC Bioinformatics, 2019. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts, FPKM, and TPM for every gene

source_name: Colorectal carcinoma

growth_protocol: Wild type or knockout HCT116 cell lines were maintained in 10% FBS containing DMEM under the condition of 5% CO2 and 37℃.

extract_protocol:
Total RNA samples from Wild type HCT116 or ZKSCAN3 knockoout HCT116 were harvested using Trizol reagent.
The libraries were prepared for 150 bp paired-end fragments using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, CA, USA)

treatment_protocol: Genetic locus of ZKSCAN3 was targeted by CRISPR/Cas9 to delete start codon of first exon

value: ZKSCAN3 Knockout


title: G/PK replicate #1


title: WT_19


title: G/PI replicate #2

value: emerin mutant (G/PI)


title: Wild type HCT116-3

value: Wild type ZKSCAN3


title: G/PI replicate #1


title: Wild type HCT116-2


title: nos_bafRNAi replicate #1


title: Wild type HCT116-1


title: S5 Symptomatic

description: gene expression data


title: WT_11


title: yw replicate #3


title: S3 Symptomatic

description: gene expression data


title: S2 Symptomatic

description: gene expression data


title: KO_S_30

value: Grp KO


title: S4 Symptomatic

description: gene expression data


title: yw replicate #2


title: ZKSCAN3 KO HCT116-3


title: S1 Symptomatic

description: gene expression data


title: CS replicate #4


title: PBMC-TC

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Library strategy: VDJ-seq
Libraries were sequenced with 150bp paired end reads on an Illumina NovaSeq.
The reads were mapped to human T cell receptor reference genome (hg38) using cellranger vdj.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with frequencies of T cell receptor recombination segments

source_name: human T cells

growth_protocol: PBMC-Tc and PBMC-iNKT cells were isolated from healthy donor periphery mononuclear cells via MACS sorting or FACS sorting; AlloHSC-iNKT cells were cultured in C10 medium supplemented with human cytokines IL-15 and IL-17

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. The extraction weas perfrom by UCLA TCGB core
RNA libraries were prepared for sequencing using standard Illumina protocols. The library construction was perfromed by UCLA TCGB core.
single cell T cell receptor profiling

treatment_protocol: All the samples were flow sorted as single cells

value: human T cells

tag: cell subtype

value: PBMC-TC


title: yw replicate #1

value: newly eclosed ovary


title: mono-cultured TE-11 vs direct co-cultured TE-11 with macrophages

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

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

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: mono-cultured TE-11

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: To induce M2 macrophages, 1 × 10e6 cells of PBMos were seeded in the 100-mm dish with rhM-CSF (25 ng/mL) and cultured for 6days. Then, TE-11 cells (2 × 10e6) were seeded  to the 100-mm dish on which M2 macrophages were attaching and direct co-cultured for 2 days. Same amount of TE-11 cells was seeded to the 100-mm dish without M2 macrophages and mono-cultured for 2 days as a control.

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

tag: culture method

value: mono-cultured

value: direct co-cultured with the M2 macrophages


title: PBMC-iNKT

source_name: human iNKT cells

value: human iNKT cells

value: PBMC-iNKT


title: ZKSCAN3 KO HCT116-1


title: KO_S_20

value: brain


title: KO_S_16


title: AlloHSC-iNKT (CB)

source_name: HSC-engineered iNKT cells

value: HSC-engineered iNKT cells

value: AlloHSC-iNKT (CB)


title: KO_S_28

value: SEFL


title: CS replicate #3

value: WT


title: WT_15


title: mammary tumor tissue [LF2-5248]

city: San Francisco

first: Jade

last: Moore

state: California

address: 2340 Sutter St, S371

institute: University of California San Francisco

hyb_protocol: 100 ng RNA was hybridized to NanoString® PanCancer IO360™ panel code set according to the recommendations of the manufacturer (NanoString Technologies, Inc., Seattle, Washington, USA).

scan_protocol: Following hybridization, the target-probe complexes were purified and immobilized on the nCounter prep station. Digital counts for each gene-specific target RNA were then acquired on the nCounter detection analyzer and normalized to account for differences in tissue mRNA quantity as well as slight differences in assay efficiency.

data_processing: The nSolver 2.6 software was used to normalize expression values using housekeeping genes following the manufacturer's recommendations.

label: Nanostring bar coding

source_name: mammary mTDT, BALB/c host

label_protocol: Specimens were labeled with decode assignment which was linked to tumor origin.

extract_protocol: Total RNA was extracted using Trizol Reagent (Invitrogen), according to manufacturer's instructions.

value: mammary mTDT

tag: immune infiltrate

value: inflamed


title: CS replicate #2


title: mammary tumor tissue [LF2-5249]

value: excluded


title: KO_45


title: TF-1 Day 3 EPO+JQ1 rep2

city: Chicago

first: Lucy

last: Godley

state: IL

address: 5841 S. Maryland Ave. MC 2115

institute: University of Chicago

data_processing:
Sequence reads aligned to reference genome and transcriptome by HISAT2
Initial quantification by Cufflinks
Statistical test by Cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing genes and FPKM quantification

source_name: TF-1 cells

growth_protocol: TF-1 cells were cultured in RPMI 1640 with 10% FBS and 4ng/mL GM-CSF. The cells were grown at 37 degree celcius with 5% CO2.

extract_protocol:
RNA was extracted by RNAzol following manufactor's instruction.
mRNA library was prepared by KAPA mRNA HyperPrep Kit.

treatment_protocol: Cells were washed 4x with RPMI 1640 without FBS, and cultured in RPMI 1640 with 10% FBS without GM-CSF for 24 hours prior to treatment. At treatment set up, the cells were divided into 4 treatment groups: GM-CSF + DMSO, GM-CSF + JQ1, EPO + DMSO, and EPO + JQ1. Final concentrations:  4ng/mL for GM-CSF, 3u/mL for EPO, 0.002% for DMSO, and 200nM for JQ1.

tag: time point

value: Day 3

value: 200nM JQ1, 3u/mL EPO


title: KO_23

description: technical replicates

value: Grp KO


title: TF-1 Day 3 EPO+JQ1 rep1


title: CS replicate #1


title: mammary tumor tissue [GF2-2828]


title: mammary tumor tissue [GF2-2952]


title: KO_21


title: TF-1 Day 3 EPO rep2

value: 0.002% DMSO, 3u/mL EPO


title: AlloHSC-iNKT (PBSC)

value: AlloHSC-iNKT (PBSC)


title: mammary tumor tissue [FF2-2809]

value: desert


title: KO_12


title: TF-1 Day 3 JQ1 rep2

value: 200nM JQ1, 4ng/mL GM-CSF


title: d0_KO_60

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

country: Germany

institute: Institute of Clinical Molecular Biology

data_processing:
Adapters and low-quality bases from the RNA-seq reads were removed using Trim Galore
The filtered reads were mapped to the mouse genome (GRCm38) using STAR aligner
featureCounts (version 1.5.2) was used to estimate the expression counts of the genes
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene expression counts in tabular format

source_name: Intestinal epithelial cells

growth_protocol: All animal experiments were approved by the local animal safety review board of the federal ministry of Schleswig Holstein and conducted according to national and international laws and policies (V 312-72241.121-33 (95-8/11) and V242-62324/2016 (97-8/16)). Specific-pathogen free (SPF) animals were housed in the Central Animal Facility (ZTH) of the University Hospital Schleswig Holstein (UKSH, Kiel, Germany). To create the Hk2∆IEC mouse line, we crossed commercially available mice carrying a floxed Hk2 allele (EMMA #02074, 45) with mice expressing the CRE recombinase under the control of the Villin promoter. As controls we used littermate Hk2fl/fl mice, referred to as WT mice. All mice were kept under a 12-h light cycle and fed gamma-irradiated diet ad libitum. Mice were killed by cervical dislocation prior to removing tissues for histological and molecular analyses. For basal phenotyping we used 9 to 11 and 86 to 92 weeks old mice.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA concentration was measured using a NanoDrop ND-1000 spectrophotometer (PeqLab Biotechnologie). Total RNA was extracted as described from isolated IECs from Hk2∆IEC and littermate control mice under untreated conditions and after administering DSS for 3 or 7 days.
RNA libraries were prepared using TruSeq stranded mRNA Kit (Illumina) according to manufacturer’s instructions. All samples were sequenced using an Illumina NovaSeq 6000 sequencer (Illumina, San Diego,CA) with an average of 23 million paired-end reads (2x 50 bp) at IKMB NGS core facilities.

treatment_protocol: For DSS-induced colitis we used 10 to 12 weeks old male mice. Both genotypes were co-housed throughout the entire experiment. To induce colitis, mice received 1,5% (w/v) dextran sodium sulfate in autoclaved tap water.

tag: day of experiment

value: Day 0


title: TF-1 Day 3 EPO rep1

tag: treatment


title: mammary tumor tissue [CF2-2819]


title: d0_KO_54


title: mammary tumor tissue [CF2-2973]


title: TF-1 Day 3 JQ1 rep1


title: THz-3

city: xi'an

first: yang

last: caixia

address: No. 169, Changle West Road, Xi 'an

country: China

institute: fourth military medical university

description: Gene expression of 12 DIV neuron cultures irradiated from 5 DIV to 9 DIV

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression v2（8*60K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: neuron culture

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Embryonic day 16 (E16) C57/B6 mice were harvested by cesarean section from anesthetized pregnant dams. Cerebral cortices were isolated and dissociated by trituration with a fire-polished Pasteur pipette. Cultures were plated onto 35 mm confocal culture dishes with polymer coverslip (IBIDI, 81156) at high density (105 cells /cm2) for electrophysiology, RNA extraction and Western blot analyses. Lower density cultures (2X104 cells / cm2) were used for immunocytochemical studies. Tissue culture dishes were coated with poly-D-lysine. The cells were plated in Neurobasal medium supplemented with B27 plus (Thermo Fisher, A3653401), 300 µM glutamine, 25 µM β-mercaptoethanol, and streptomycin / amphotericin B. Three days after plating, half of the medium was changed and subsequently the medium was changed every 3 days.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: THz irradiation was delivered to the cultures in long duration: cultures were irradiated for 3 hr, one time a day. Neurons were irradiated from 5 day in vivo (5 DIV) to 9 DIV and collected at 12 DIV for microarray.

value: THz irradiated culture (3.1THz)

value: neuron culture


title: d0_KO_53


title: TF-1 Day 3 DMSO rep 2

value: 0.002% DMSO, 4ng/mL GM-CSF


title: mammary tumor tissue [GF2-2958]


title: mammary tumor tissue [HF2-2966]


title: THz-2


title: d0_KO_32


title: TF-1 Day 3 DMSO rep 1


title: d0_KO_24


title: mammary tumor tissue [HF2-2957]


title: mammary tumor tissue [AF2-2956]


title: Con-3

description: Gene expression of 12 DIV neuron cultures

value: Control culture


title: Con-2


title: Con-1


title: THz-1


title: JA15_LGL148_tumor

city: Rotterdam

first: Anton

middle: W

last: Langerak

state: Zuid Holland

address: Dr. Molewaterplein 40

country: Netherlands

institute: ErasmusMC

description: RNA sequencing out of sorted T-LGL cells from PBMCs from patients with T-LGL leukemia

data_processing:
After sequencing and de-multiplexing the quality of the data was assessed with fastQC (v 0.11.8).
When the RNA sequence data passed the quality check, fastq files were aligned using STAR aligner (v.2.5.3e) with GRCh38 as reference.
Read counts were obtained using FeatureCounts (v1.6.0) and Homo_sapiens GRCh38.92 as reference
The quality of the alignment and assigned reads were determined with MultiQC.
Noise reduction was applied to the count data by removing the very low read counts.
Normalized data was used for visualization and comparison purposes, which include correlation and clustering analysis generating the heatmaps and PCA plots.
For the differential expression analysis, DESeq2 (R package v1.22.2) was used.
Genome_build: GRCh38
Supplementary_files_format_and_content: .csv and .counts files containing raw RNA counts per gene

growth_protocol: Patient or healthy control PBMCs were thawed and added to 1 ml of ice-cold FCS before adding 8 ml of pre-warmed Roswell Park Memorial Institute (RPMI) 1640 Medium, GlutaMAX™ Supplement, HEPES (Sigma Aldrich, Saint Louis, MA, USA) supplemented with 10% bovine serum albumin (BSA) and 1% penicillin and streptomycin. Cells were stained and sorted based on aberrant expression levels of CD2, CD5, and/or CD7 and/or high expression of CD57. Age-matched healthy control PBMCs were stained and terminally differentiated effector memory cells (CD3+/CD8+/TCRγδ-/CD45RA+/CCR7-; TEMRA) were sorted as control populations. All sorting experiments were performed using the FACS Aria III instrument. Use of T-LGL samples was approved by the Erasmus MC Institutional Review Board (MEC2015-617). Control samples were obtained from Sanquin Blood Bank (Amsterdam, The Netherlands). All healthy blood donors were included upon informed consent and anonymized prior to use (MEC2016-202)

extract_protocol:
T-LGL and healthy control CD8 TEMRA cells were lysed in Trizol (Invitrogen) and total RNA was isolated according to manufacturer’s protocol. Quality and concentration of total RNA of the samples was determined with the RNA 6000 Nano assay on an Aligent 2100 Bioanalyzer (Agilent Technologies).
cDNA libraries were generated with 1 ng total RNA using the Smart-Seq V4 Ultra low input RNA kit (Takara-bio) in combination with the Truseq nano DNA library prep kit (Illumina).

value: Peripheral Blood Mononuclear Cells

tag: sorted cells

value: T-LGL cells

tag: disease state

value: leukemia


title: mammary tumor tissue [HF2-2968]

value: mammary mTDT

value: inflamed


title: JA16_LGL150_tumor

source_name: sorted T-LGL cells from PBMCs from patients with T-LGL leukemia


title: d0_WT_46

value: Hk2 flox/flox

tag: strain


title: mammary tumor tissue [AF2-2846]


title: d0_WT_43


title: JA13_LGL052_tumor

tag: cell type


title: d0_WT_41


title: d0_WT_31


title: JA12_LGL047_tumor


title: mammary tumor tissue [CF2-2819-2]


title: JA11_LGL037_tumor


title: mammary tumor tissue [CF2-2819-1]


title: d3_WT_487

value: Day 3


title: S6 Symptomatic

city: Karachi

first: Asghar

last: Nasir

address: Stadium Road

institute: Aga Khan University

description: gene expression data

data_processing: CEL files were analysed using the TCAS Transcriptome Analysis Software Suite (version 2) using the Summarization Method: Gene Level - SST-RMA Pos vs Neg AUC Threshold: 0.7 against Genome Version: hg38 (Homosapiens)

source_name: blood

growth_protocol: RNA was extracted from whole blood collected in Plasma/EDTA tube.

extract_protocol: Qiagen RNA Blood Mini Kit (Qiagen, GmbH, Germany)

value: SARS-CoV-2 positive

tag: symptons

value: Symptomatic


title: mammary tumor tissue [CF2-2784-2]

value: excluded


title: mammary tumor tissue [CF2-2784-1]


title: d3_WT_486


title: Adipose tissue-HFD Cont-Rep5

city: clermont ferrand

first: frederic

last: capel

address: 28 place henri dunant

department: alimentation humaine

country: France

institute: INRA

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 16 out of 24 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 40859 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 38168 rows each corresponding to a unique ProbeName (provided as processed data).

source_name: Adipose tissue

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: RNA were isolated using the Trizol reagent and washing steps with Isopropanol/Ethanol procedure before solubilization in sterile water.

tag: diet

value: HFD

value: Control fatty acid

tag: washbatch


title: JA10_LGL030_tumor


title: Adipose tissue-HFD O3-Rep7


title: Adipose tissue-STD Cont-Rep4

value: STD


title: JA9_LGL028_tumor


title: mammary tumor tissue [AF2-2797-2]


title: mammary tumor tissue [AF2-2797-1]


title: Adipose tissue-STD Cont-Rep6


title: JA14_LGL141_tumor


title: d7_KO_423

value: Day 7


title: Adipose tissue-HFD O3-Rep3


title: JA7_LGL002_tumor


title: d7_KO_422


title: mammary tumor tissue [L0]


title: Adipose tissue-STD Cont-Rep5


title: d7_KO_421


title: mammary tumor tissue [G0]

value: desert


title: Adipose tissue-HFD O3-Rep4


title: d7_KO_420


title: JA5_B95_control

description: RNA sequencing out of sorted CD8 TEMRA cells from healthy donor PBMCs

value: CD8 Effector

value: no leukemia


title: mammary tumor tissue [F0]


title: Adipose tissue-HFD Cont-Rep4


title: mammary tumor tissue [H0]


title: Adipose tissue-STD Cont-Rep7


title: Adipose tissue-HFD O3-Rep6


title: d7_WT_419


title: d7_WT_431


title: JA4_B94_control

source_name: sorted CD8 TEMRA cells from healthy donor PBMCs

value: Peripheral Blood Mononuclear Cells


title: Adipose tissue-HFD O3-Rep2


title: mammary tumor tissue [A0]


title: JA8_LGL018_tumor

value: T-LGL cells


title: Rhino-lib1: NWR iBCL2-GFP-iPSCs naïve RSet - rep1

city: Berlin

first: Jorge

last: Ruiz-Orera

state: Berlin

address: Robert-Rössle-Straße 10

institute: Max Delbruck Center for Molecular Medicine

data_processing:
RNA-seq sequencing reads were clipped for residual adapter sequences and trimmed for low-quality 3’ ends.
For mapping, we used STAR (v.2.7.1a) (Dobin et al. 2013) to align all RNA-seq datasets to the SWR genome. Maximum number of mismatches was set up to 4 to account for subspecies variability. Multiple mapping to several locations was allowed unless otherwise stated.
We quantified the gene expression by using HTSeq (Anders et al. 2015) and we filtered out genes with an average FPKM lower than 1. Read counts were normalized by sample by applying DESeq2’s median of ratios (Love et al. 2014).
Genome_build: cerSim1
Supplementary_files_format_and_content: tsv file, include raw counts per sample and gene
Supplementary_files_format_and_content: gtf file, include the transcriptome used in this study

organism: Ceratotherium simum cottoni

source_name: iPSCs

growth_protocol: Primed culturing conditions: NWR iPSCs were maintained feeder-free on Matrigel coated 6-Well plates in chemically defined mTeSR1 medium (STEMCELL technologies, #85850) supplemented with ascorbic acid (50 µg/ml, Sigma-Aldrich, #A8960-5G) at 37°C, 5% CO2 and 5% O2. Cells were split every 3 to 4 days (confluency ~80 %) using PBS 0.5 mM EDTA solution (Life technologies, #14190-250 and Thermo Fisher, #15575-020) in ratios of 1:6 and 1:12. Naive culturing conditions: To induce the naive state, cells were transitioned from primed conditions either to RSet (Stemcell Technologies, #05970) or N2B27 medium [1:1 DMEM/F12:Neurobasal medium (#11320-033 and #21103-049), 1x N2-Supplement (#17502-048), 1x B27-Supplement w/o Vit. A (#12587-010), 1x GlutaMAX (#35050-038), 1x MEM NEAA (#11140-035), 0.11 mM ß-Mercaptoethanol (#21985-023), 10 ng/ml LIF (Merck/Millipore, #LIF1010), 0.075 µM Bio (Tocris Bioscience, #3194), 5 µM XAV (Tocris Bioscience, #3748), 0.5 µM PD-0325901  (BioVision, #1643), 2 µM Gö6983 (Tocris Bioscience, #6983), 75 µg/ml ascorbic acid (Sigma-Aldrich, #A8960), 15ng/ml Activin A (#PHC9564). If not indicated otherwise, all medium components were from Life Technologies.] as follow: After TrypLE split (TrypLE 1x, Life Technologies, #12563-011, ratio 1:6 and 1:12), primed iPSCs were plated as single cells on 500.000 MEFs/6-Well (inactivated mouse embryonic fibroblasts, teBu-bio, #003MEF-MITC) with 10 µM ROCKi (ROCK Inhibitor Y-27632 2HCl; 10mM/1mL, Selleck Chemicals, #SEL-S1049-10MM) and incubated overnight in mTeSR1 (NWR iPSCs) or E8 medium (human BIHi005A). At the next day, medium was changed to N2B27 or RSet. To facilitate the conversion process, the NWR iBCL2-GFP-iPSC line was generated (see above) and ectopic expression of BCL2 was induced by 1 µg/ml Doxycycline (Clontech, #631311). Cells were maintained on MEFs in N2B27 or rather RSet medium at 37°C, 5% CO2 and 5% O2, and split using TrypLE every 3 to 4 days (confluency ~80%) in ratios varying from 1:4 to 1:10.

extract_protocol:
Total RNA was was isolated using RNeasy mini kit (Qiagen, #74104) according to the manufacturer’s instructions. 3 µg of isolated RNA were treated with TURBO DNase (Life Technologies, #AM2239) followed by clean up using RNeasy MinElute RNA cleanup kit (Qiagen, #74204). RNA purity and quality were assessed with microcapillary electrophoresis on Agilent 2100 Bioanalyzer (RNA Pico 6000 kit, Agilent, #5067-1513). Ribosomal RNA was depleted from 1 µg of total RNA using RiboZero Gold (Human/Mouse/Rat) kit (Illumina), followed by purification with RNeasy MinElute RNA cleanup kit.
Sequencing libraries were prepared from rRNA-depleted RNA using TruSeq Stranded total RNA LT kit (Illumina, #20020598) according to the manufacturer’s instructions. The final PCR amplification included 11 cycles followed by purification with Ampure XP beads (Beckman-Coulter, #A63881). Quality of final libraries was evaluated by Agilent 2100 Bioanalyzer using DNA 1000 kits (Agilent, #5067-1504). DNA concentrations were measured with Qubit (Life Technologies) and dsDNA HS Assay Kit (Thermo Fisher Scientific, #Q32854). Libraries were sequenced using Illumina NextSeq 500 instrument [75-nt single-end reads, NextSeq 500/550 High Output Kit v2.5 (75 Cycles), Illumina, #20024906].

tag: cell line

value: NWR iBCL2-GFP-iPSCs

tag: culturing conditions

value: naïve

tag: medium

value: RSet

tag: feeder

value: inactivated mouse embryonic fibroblasts (MEFs)


title: d3_KO_392

tag: genotype

value: Day 3


title: d7_WT_393

value: Hk2 flox/flox


title: JA3_B86_control


title: JA2_B81_control


title: Rhino-lib2: NWR iBCL2-GFP-iPSCs naïve RSet - rep2


title: d3_KO_388


title: d3_KO_387


title: JA6_B96_control


title: Adipose tissue-HFD Cont-Rep8


title: Rhino-lib11: NWR iBCL2-GFP-iPSCs naïve N2B27 - rep2


title: Adipose tissue-HFD O3-Rep8


title: Znf417 Znf587 WT1

city: Guangzhou

first: Bo

last: Yang

state: Guangdong

address: Guangzhou, 510150, Guangdong Province, China.

institute: The Third Affiliated Hospital of Guangzhou Medical University

data_processing:
Approximately 6Gb and Q30>90% trimmed and filtered high-quality 150-bp paired-end reads per sample were mapped to the human genome using the TopHat v2.1.1 (Galaxy toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.1) with default parameters.
Cuffdiff (Galaxy toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.5) was used for differential gene expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using bigwig

source_name: wild type 293T

growth_protocol: HEK293T cells were cultured in DMEM High Glucose (Gibco) containing 10% FBS, 2 mM L-glutamine.

extract_protocol:
RNA was prepared from cells or embryos using the Eastep Super RNA extraction kit (Peomega).
RNA-seq libraries were prepared from total RNA from cells or embryos using TruSeq stranded mRNA sample preparation kit (Illumina)

treatment_protocol: To construct the Znf417 and Znf587 knockout cell lines, pX330 and GFP vector were co-transfected into HEK293T cells by using Nucleofector. GFP positive cells were sorted by FACS after 48 hours.

value: wild type


title: Znf417 Znf587 WT2


title: d7_WT_386


title: Adipose tissue-HFD O3-Rep1


title: d3_KO_385


title: Adipose tissue-HFD Cont-Rep6


title: Znf417 Znf587 DKO2


title: Adipose tissue-HFD O3-Rep5


title: Rino-P5: NWR iPSCs primed - rep4

value: NWR iPSCs

value: primed

value: non


title: d3_WT_381


title: Adipose tissue-STD Cont-Rep3

value: STD

value: Control fatty acid


title: Rino-P4: NWR iPSCs primed - rep3


title: Znf417 Znf587 DKO1


title: Rhino-lib3: NWR iBCL2-GFP-iPSCs naïve N2B27 - rep3


title: Adipose tissue-STD Cont-Rep2


title: JA1_B80_control


title: Rhino-lib13: NWR iPSCs primed - rep2


title: Rhino-lib4: NWR iPSCs primed - rep1


title: 293T input

data_processing:
150-bp paired-end reads per ChIP-seq were mapped to the human genome using Bowtie2 (Galaxy toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0) with default parameters.
Peaks were called by model-based analysis of ChIP-seq (MACS2 Galaxy toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6) using GFP input as control and calling p value 1e-6.
Consensus target motif was derived from peak regions by using MEME-ChIP tool (http://meme-suite.org/tools/meme-ChIP).
Heatmap and profile plots then were generated by plotHeatmap or plotProfile (Galaxy toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.0.0.1, toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.1.2.0.0) using calculated matrix generated by ComputeMatrix.
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using bigwig

extract_protocol:
Crosslinked chromatin from 2-4X107 cells fragmented on a Covaris to ~100-300bp was immunoprecipitated with GFP (Invitrogen A-6455) antibodies.
library construction using the KAPA Hyper Prep Kit (Roche)

treatment_protocol: HEK293T cells  were transfected with ZNF417/587-GFP overexpression plasmids

tag: antibody

value: GFP (Invitrogen A-6455)


title: ZNF587 GFP ChIP rep2

source_name: ZNF587-GFP overexpression 293T

value: ZNF587 OE


title: Rhino-lib10: NWR iBCL2-GFP-iPSCs naïve N2B27 - rep1


title: d7_KO_366

value: Day 7


title: d7_KO_367


title: ZNF417 GFP ChIP rep2

source_name: ZNF417-GFP overexpression 293T

value: ZNF417 OE


title: SH-SY5Y ZIKV, 2dpi, rep1

city: Recife

first: Leila

last: Mendonça Vieira

state: Pernambuco

address: Av Prof. Moraes Rego, 1235 - Cidade Universitaria

department: LAVITE

country: Brazil

institute: FIOCRUZ

description: Test

data_processing:
Amount of cDNA samples added per reaction was 3.5 ng and real time qPCR reactions were performed using ABI 7500 Real-Time PCR System (Thermo Fisher Scientific, MA, USA) following the Manufacturer’s instructions (more details at shorturl.at/ckuxX).
For the normalization GUSB was used as endogenous control gene as it showed the most stable expression in our experimental conditions (standard deviation=0.26).
Fold-change calculations were performed using Microsoft Excel and GraphPad Prism 8 softwares, as follows: 1) Amplification CT values  ≤ 36 were considered as above detection limit, and CT values ≥ 36 were considered below detection limit and set to 36; 2) CT values of target genes were subtracted from CT values of endogenous control gene, resulting in ΔCT values; 3) ΔCT values from infected samples were subtracted from ΔCT values from uninfected control samples, resulting in ΔΔCT values; 4) 2^-ΔΔCT values for each condition were considered as gene expression fold-change of infected samples relative to uninfected (mock) samples.
Fold Change worksheet reports 2^-ΔΔCT values calculated as indicated in the data processing.
Matrix normalized worksheet reports normalized signal (against endogenous control gene GUSB).

label: TaqMan probe

source_name: SH-SY5Y cell line

label_protocol: cDNA synthesis was performed using High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific, MA, USA)

growth_protocol: SH-SY5Y cells (1x106 or 2.5x106) were grown in 25 cm² cell culture flasks for 24 hours before infection

extract_protocol: Total RNA extraction was performed using RNeasy Micro Kit (QIAGEN, Hilden, Germany).

treatment_protocol: SH-SY5Y cells were infected with ZIKV (MOI 0.5), and mock- and ZIKV-infected cells were harvested at 1 and 2 days post-infection

value: undifferentiated neuroblastoma cells

tag: infectious agent

value: Zika virus (MOI 0.5)

tag: time post infection

value: 2 days


title: SH-SY5Y ZIKV, 2dpi, rep2

description: Test


title: d7_KO_368

tag: day of experiment


title: d7_WT_361


title: Adipose tissue-HFD Cont-Rep1

value: HFD

tag: treatment


title: SH-SY5Y ZIKV, 1dpi, rep2

description: Test

value: 1 day


title: ZNF417 GFP ChIP rep1


title: SH-SY5Y ZIKV, 1dpi, rep1

description: Test


title: d7_WT_370


title: d3_WT_353

value: Day 3


title: d7_WT_356

value: Hk2 flox/flox


title: SH-SY5Y Mock-infected cells, rep2

description: Control

value: None (control sample)

value: Not infected


title: ZNF587 GFP ChIP rep1


title: d3_WT_352


title: SH-SY5Y Mock-infected cells, rep1

description: Control


title: wt_seedling_srna_rep3

city: Norwich

first: Jaemyung

last: Choi

address: Norwich Research Park

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

description: small RNA

data_processing:
Illumina Hiseq basecalls were performed using 'bcl2fq' at the John Innes Centre.
For bisulfite-seq, reads were mapped with bowtie and bs-sequel pipeline (https://zilbermanlab.net/tools/) allowing up to 2 mismatches.
For sRNA-seq libraries, adapter sequences were removed from reads using cutadapt (Martin, 2011). 18-28 bp, 21nt, and 24 nt fragments were isolated using following cutadapt options: -m 18 -M 28, -m 21 -M 21, -m 24 -M 24. Reads were mapped with Bowtie (Langmead et al., 2009) allowing up to 1 mismatch and up to 10 multi-mapped reads. Aligned 21 nt or 24 nt read count were normalized by reads per kilobase per million mapped reads (RPKM) of 18-28 bp fragments.
Native ChIP-seq libraries were mapped with Bowtie (Langmead et al., 2009) allowing up to 2 mismatches and up to 10 multi-mapped reads. To calculate enrichment, ChIP samples were divided by input samples and transformed into log 2 ratio values using deepTools2 bamCompare.
Genome_build: TAIR10
Supplementary_files_format_and_content: For sRNA-seq, gff files contain rpkm normalized read count of 50bp windows.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: cmt2 and cmt2 cmt3 (Stroud et al., 2014; Zemach et al., 2013) plants were crossed to h1.1 h1.2 (Zemach et al., 2013) plants to generate h1cmt2 and h1cmt2cmt3 plants. To establish h1cmt2shh1 mutant line, we crossed h1+/-cmt2 heterozygous plants with shh1  (SALK_074540C) plants first, then isolated h1cmt2shh1 homozygous siblings. met1, h1met1, ddm1, h1ddm1 plants were described previously (Choi et al., 2020; Lyons and Zilberman, 2017). Arabidopsis thaliana seedlings were germinated and grown for 4-5 weeks on soil at 20-25℃ in growth chamber (16 hr day/ 8 hr night) for all the experiments performed here.

extract_protocol: We extracted total RNA from rosette leaves of 4-5-week-old plants using Trizol (Invitrogen, cat. No. 15596026) according to manufacturer’s manual. To remove DNA from samples, 5 ug of RNA was treated with DNA-free DNA removal kit (Thermo, AM1907). 1 ug of DNA-free total RNA was subjected to sRNA library construction according to manufacturer’s protocol (Illumina, RS-200-0012 and RS-200-0024).

tag: age

value: 2-week-old seedlings

tag: tissue

value: seedlings


title: Sample 8 M0

city: Sheffiled

first: Chiara

last: Niespolo

address: Beech Hill Road

department: Infection, Immunity and Cardiovascular Disease

institute: University of Sheffield

data_processing:
Fastq files were trimmed using Cutadapt (Kechin et al., 2017).
Reads were mapped against human small RNA sequences downloaded from RNAcentral database (The RNAcentral Consortium, 2018) using bowtie2 aligner  (Langmead et al., 2012) with default parameters.
Read counts were genereated using SAMtools (Li et al., 2009)
Count Per Million values (CPM) were generated using edgeR (Robinson et al., 2010 , McCarthy et al., 2012)
Differential expression analysis was performed using DeSeq2 (Love et al., 2014)
Genome_build: RNACentral database (v15): human small non-coding RNA sequences
Supplementary_files_format_and_content: raw_counts_miRNAseq.txt

source_name: Monocyte-derived macrophages, Donor I

growth_protocol: PBMCs were isolated from 80 mL of peripheral venous blood using Ficoll centrifugation. CD14+ monocytes were positively selected using CD14+ beads. Monocytes were cultured for 7 days  (typically in a 6 well plate, 1 million cells per well) in  RPMI-1640 (Gibco) plus 10% (v/v) low–endotoxin heat–inactivated FBS (PanBiotech), 1% (v/v) L–glutamine (Gibco) and 1% (v/v) penicillin/streptomycin (Gibco). Recombinant human (rh) M–CSF (100 ng/ml, Peprotech/Immunotools) was added to the media to allow the differentiation of monocytes into macrophages.

extract_protocol:
Total RNA was extracted by using the miRNeasy Mini Kit (Qiagen) according to manufacturer instructions.
Library was constructed by Small RNA Sample Pre Kit. The final cDNA library was ready after a round of sequencing adaptor ligation, reverse transcription, PCR enrichment, purification and size selection.

treatment_protocol: In vitro polarisation: after 7 days of differentiation, monocyte-derived macrophages were polarised into pro-inflammatory macrophages for 24 hours, using 20 ng/mL IFN-γ (Human, Peprotech) and 100 ng/mL E. coli lipopolysaccharide (Serotype R515 TLR grade TM, Enzo Life Sciences).

value: Peripheral venous blood

value: Unpolarised M0

value: monocyte-derived macrophages


title: Sample 8 M1

value: Polarised M1


title: d3_KO_351

tag: strain


title: d3_KO_349


title: Sample 7 M0

source_name: Monocyte-derived macrophages, Donor H

tag: cell type


title: d3_WT_348


title: d3_KO_350


title: wt_seedling_srna_rep2

description: small RNA


title: Adipose tissue-HFD Cont-Rep7

value: Control fatty acid


title: Sample 5 M1

source_name: Monocyte-derived macrophages, Donor F


title: d3_WT_346


title: Sample 7 M1


title: Sample 6 M0

source_name: Monocyte-derived macrophages, Donor G


title: h1met1_seedling_srna

description: small RNA

value: h1 met1


title: Sample 5 M0


title: d3_KO_345


title: dendritic cell infected by EV71 rep2

city: Tianjin

middle: yue

last: jie

address: No. 7 South Sudi Road, Nankai District,

department: Infectious Diseases

institute: Tianjin Second People's Hospital

hyb_protocol: 1.5ug of Cy3-labelled cRNA (specific activity>10 pmol Cy3/ug cRNA)was fragmented to chip

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA microarray Scanner

data_processing: the scanned images were analyzed with Agilent Scanner G2505C(Agilent Technologies)

source_name: dendritic cell

label_protocol: cyanine-3(Cy3)labeled cRNA was prepared from 0.5ug RNA using the One-Color

extract_protocol: RNA was prepared using the qiagen Blood RNA kit

value: dendritic cell

tag: infection


title: Sample 4 M1

source_name: Monocyte-derived macrophages, Donor E


title: Sample 3 M1

source_name: Monocyte-derived macrophages, Donor D


title: dendritic cell not infected by EV71 rep3

value: no


title: Sample 6 M1


title: dendritic cell infected by EV71 rep1


title: WT2+5AZA

data_processing:
Approximately 6Gb and Q30>90% trimmed and filtered high-quality 150-bp paired-end reads per sample were mapped to the mouse genome (mm9) using the TopHat v2.1.1 (Galaxy toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.1) with default parameters.
Cuffdiff (Galaxy toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.5) was used for differential gene expression analysis.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using bigwig or tdf

source_name: Zfp961-GFPflox/flox ESCs

growth_protocol: Zfp961 GFPflox/flox mouse ROSA-cre-ERT2 ESCs were cultured in ESM medium containing DMEM (Gibco), 15% fetal bovine serum (FBS; Hyclone), 10mM NEAA, 100 μM β-mercaptoethanol, 2 mM L-glutamine, 10ng/mL LIF, 2i (3μM CHIR-99021, 1μM PD0325901, Selleck).

treatment_protocol: ROSA-Cre-ERT2 ESCs were treated with 5AZA for 24h or not and 4-OHT or vehicle for 48 hours, then feed with normal culture medium for another 72 hours before experiments.

value: mouse ESCs

value: Zfp961 WT


title: Sample 2 M1

source_name: Monocyte-derived macrophages, Donor C


title: dendritic cell infected by EV71 rep3


title: Sample 3 M0


title: dendritic cell not infected by EV71 rep2


title: wt_seedling_srna_rep1

description: small RNA


title: WT1+5AZA


title: KO2+5AZA

value: Zfp961 KO


title: met1_seedling_srna

description: small RNA


title: Sample 1 M1

source_name: Monocyte-derived macrophages, Donor A


title: KO1+5AZA


title: Sample 1 M0


title: dendritic cell not infected by EV71 rep1


title: WT3

value: EtOH


title: shARD_EF_1

city: Wuhan

first: Hanyang

last: Hu

state: Please Select

address: School of Basic Medical Sciences, Wuhan University

institute: Wuhan University

data_processing:
Raw reads were trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned to the hg19 build of the human genome using Subread aligner v2.0.0.
featureCounts v2.0.0 was used to count the reads numbers mapped to each gene
Genome_build: hg19
Supplementary_files_format_and_content: txt format for gene count

growth_protocol: Ishikawa cells were grown in phenol red-free DMEM media supplemented with 10% charcoal/dextran treated fetal bovine serum and 50 units/mL penicillin and 50 µg/mL streptomycin for at least 4 days before lysis

extract_protocol:
total RNA was extracted using TRIZOL Reagent (Life technologies)
Libraries were constructed usinig TruSeq mRNA LT Sample Prep Kit

treatment_protocol: Cells were treated with vehicle control (DMSO), 10 nM 17-beta-estradiol, or 10 nM 17-beta-estradiol+1OO nM fulvestrant) for 8 hour prior to trypsinization

value: Ishikawa cells

value: Endometrial Cancer Cells

value: ARID1A knockdown


title: shARD_EF_2


title: WT2


title: shARD_E2_2


title: Fgf10_neg_rep2

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

hyb_protocol: 2 Âµg of the labeled cDNA were subjected to hybridization. The cDNA was not fragmented before hybridization. Hybridization was performed following the Agilent protocol at 65Â°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 Âµm/pixel resolution and analyzed with Mapix 8.5.0

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

source_name: Primary isolated cells, Mesenchymal cells positive for Fgf10 and Axin2

label_protocol: Purified total RNA was amplified using the Ovation PicoSL WTA System V2 kit (NuGEN Technologies, Bemmel, Netherlands). Per sample, 2 Âµg amplified cDNA was Cy-labeled using the SureTag DNA labeling kit (Agilent, Waldbronn, Germany).

extract_protocol: QIAgen RNeasy macro kit

value: mesenchymal cell


title: Fgf10_neg_rep1


title: shARD_E2_1


title: KO3


title: Sample 2 M0


title: Axin2_neg_rep2


title: KO2


title: shARD_DMSO_2


title: KO1


title: Axin2_pos_rep1


title: shARD_DMSO_1


title: CTCF knockout biological replicate 3 RRBS

city: Los Angeles

first: Tom

last: Vondriska

address: 650 Charles E Young Dr, BH553

institute: UCLA

data_processing:
Single-end reads were demultiplexed into sample-specific *.fastq files using custom scripts and then aligned to the mouse genome using the BSseeker2 v2.0.10.
Briefly, we built an mm10-based reference index—simply 40-400bp MspI restriction fragments digested in silico and consistent with our enriched fragment size—using the bs_seeker2-build.py script.
We then aligned single-end reads to the reference index with bs_seeker2-align.py, using the 40-400bp fragment size range and -r flag to indicate RRBS libraries, and allowing up to 5 mismatches. We selected Bowtie2 as the aligner within BSseeker2 for this step.
Samtools was used to sort the resulting .bam files, and methylation was called using bs_seeker2-call_methylation.py, using a 10 read coverage minimum for any given cytosine, and removing all reads that did not undergo full bisulfite conversion.
From the resulting CGmaps, we retained cytosines that exist within a CpG (cytosine followed by guanine) context. These are deposited herein as processed data.
Genome_build: mm10
Supplementary_files_format_and_content: CGmap files

source_name: Isolated cardiac myocytes

extract_protocol:
DNA from left ventricular isolated adult cardiomyocytes was isolated using the QIAshredder kit (Qiagen).
Initial digestion into CpG rich regions was done by the Msp1 enzyme (NEB). The 3’ → 5’ Klenow exonuclease was used to repair sticky ends and promote poly-A tail synthesis. To facilitate multiplexing, individual TruSeq Illumina adapters were ligated to samples using the QIAseq Methyl Library Kit (Qiagen). Samples were then filtered to enrich for DNA fragments within the desired size range using magnetic AMPure XP beads (Beckman). Bisulfite conversion was performed using the Zymo EZ DNA Methylation-Lightning kit (Zymo).

treatment_protocol: DNA was isolated from mouse cardiomyocytes 3 days and 3 weeks after transverse aortic constriction (TAC) and CTCF depletion.

value: CTCF knockout


title: Exp_14_hi_rep1

hyb_protocol: 2 µg of the labeled cDNA were subjected to hybridization. The cDNA was not fragmented before hybridization. Hybridization was performed following the Agilent protocol at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 µm/pixel resolution and analyzed with Mapix 6.5.0

source_name: Primary isolated cells, Alveolar epithelial cells

label_protocol: Purified total RNA was amplified using the Ovation PicoSL WTA System V2 kit (NuGEN Technologies, Bemmel, Netherlands). Per sample, 2 µg amplified cDNA was Cy-labeled using the SureTag DNA labeling kit (Agilent, Waldbronn, Germany).

growth_protocol: 9-12 weeks mice, both genders, were maintained in a pathogen-free barrier facility with light-dark cycles and with filtered water and autoclaved chow provided ad libitum.

extract_protocol: QIAgen RNeasy Plus Micro Kit

treatment_protocol:
Control:  SftpCreERT2/+; Tomatoflox/flox (STOCK Sftpctm1(cre/ERT2,rtTA)Hap Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/sbel)
Experimental: SftpCreERT2/+; Fgfr2bflox/flox; Tomatoflox/flox (STOCK Sftpctm1(cre/ERT2,rtTA)Hap FgfR2tm1Dsn Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/sbel)
Control and Experimental groups received Tamoxifen (1mg/ml) in drinking water. The lungs were harvested at different time points after treatment with tamoxifen (d4, d7 and d14). Follwing single cell preparation and immunostaining, alveolar epithelial cells were sorted by FACS. RNA was isolated with Qiagen RNeasy micro kit from sorted cells.

tag: group

value: experimental

value: high

value: tamoxifen

tag: time

value: day 14

value: Alveolar epithelial type 2 cells (AT2)


title: shNC_EF_1

tag: cell line

value: control


title: shNC_EF_2


title: Fgf10_pos_rep1


title: CTCF knockout biological replicate 2 RRBS


title: WT1


title: CTCF knockout biological replicate 1 RRBS


title: shNC_E2_2


title: TAC 3 days biological replicate 3 RRBS

value: TAC

value: 3 days


title: TAC 3 days biological replicate 2 RRBS


title: shNC_DMSO_2


title: TAC 3 days biological replicate 1 RRBS


title: TAC 3 weeks biological replicate 3 RRBS

value: 3 weeks


title: shNC_DMSO_1


title: si-FOXM1#3

city: jinan

first: David

last: Li

address: 44 Wenhua Xi Road,Jinan

institute: Shandong University

description: B2780si-Foxm1_case_vs_B2780si-NC_ctrl_all_list

data_processing:
Sequenced reads were generated by base calling using the Illumina standard pipeline
Raw reads were first filtered to obtain clean reads using FASTX-Toolkit
High-quality reads were mapped to the human reference genome hg19 using TopHat software with default parameters
Alignment was independently performed for reads from each sample, and reads mapping to more than three genomic sites were discarded
Based on the value of reads per kilobase per million mapped reads, gene expression levels were determined using Cufflinks software

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: serous ovarian cancer cell line

tag: transfection


title: TAC 3 weeks biological replicate 2 RRBS


title: TAC 3 weeks biological replicate 1 RRBS


title: si-FOXM1#2


title: Control biological replicate 2 RRBS

value: Control


title: Axin2_pos_rep2


title: Control biological replicate 1 RRBS


title: Exp_7_hi_rep1

value: day 7


title: CTCF knockout biological replicate 3 RNA-seq

data_processing:
Paired-end 150bp reads were demultiplexed into sample-specific *_R1.fastq and *_R2.fastq files using custom scripts and then pseudoaligned to the mm10 genome using the ultra-fast pseudoalignment tool, Salmon.
Briefly, we ran salmon index to generate a mm10 (mouse) transcriptome index using the appropriate “known cDNA” FASTA file from Ensembl release 81.
Corresponding read pairs were pseudoaligned to the appropriate transcriptome using salmon quant with mm10-specific index, *_R1.fastq and *_R2.fastq files as inputs.
Salmon transcript quantifications (*.sf files) for all samples were loaded into a single R object using the tximport package, and then differential expression analysis was performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: quant.sf files

extract_protocol:
RNA from left ventricular isolated adult cardiomyocytes was isolated using the RNeasy Mini Kit (Qiagen).
Ribosomal RNA was removed using an Illumina Ribo-Zero rRNA Removal Kit and the RNA-seq libraries prepared by the Technology Center for Genomics & Bioinformatics Core (UCLA) following Illunmina standard protocols

treatment_protocol: RNA was isolated from mouse cardiomyocytes 3 days and 3 weeks after transverse aortic constriction (TAC) and CTCF depletion.


title: Exp_4_low_rep1

value: low

value: day 4


title: si-NC#3

value: si-NC


title: si-FOXM1#1


title: si-NC#1


title: si-NC#2


title: Ctrl_7_low_rep1


title: CTCF knockout biological replicate 1 RNA-seq


title: Exp_7_low_rep1


title: Fgf10_pos_rep2

value: mesenchymal cell


title: shNC_E2_1

value: Ishikawa cells

value: Endometrial Cancer Cells


title: Ctrl_7_hi_rep1

value: high


title: Exp_14_low_rep1

value: experimental

value: tamoxifen


title: TIME59

city: Halle (Saale)

first: Julia

last: Schumann

address: Franzosenweg 1a

institute: University Medicine Halle (Saale)

data_processing:
Low quality read ends as well as remaining parts of sequencing adapters were clipped off using Cutadapt (v 1.14)  with parameters -q 20 -O 7 -m 20
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters  -p 6 --dta --strandness RF -k 5
secondary alignments were filtered out using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -s 2 -M -t exon -g gene_id and Ensembl gene annotations (GRCh 38.89)
Differential gene expression was assessed using R/edgeR (v 3.18.1) using TMM normalization
Genome_build: hg38
Supplementary_files_format_and_content: tab-separated text file containing raw counts for each sample

source_name: TIME

growth_protocol: Cells were cultured according to ATCC recommendations.

extract_protocol:
Total RNA extraction was performed based on TRIZOL according to the Manufacturer`s standard protocol.
Libraries were prepared by Novogene according to Illumina's instructions accompanying the NEB Next Ultra RNA Library Prep Kit.

treatment_protocol: The fatty acids docosahexaenoic acid (DHA, C22:6n3) or arachidonic acid (AA, C20:4n6) were included in the culture medium in concentrations of 15 µmol/L using ethanol as a vehicle (0.2 % v/v final ethanol concentration). Cells were cultured in the enriched media totaling 144 h. Stimulation of cells was performed in the last 24 h of fatty acid supplementation by addition of the cytokines IL-1β, TNF-α, and IFN-γ each in a concentration of 5 ng/ml.

value: endothelial cell

tag: supplement

value: DHA supplemented

tag: stimulation

value: cytokine


title: Exp_4_hi_rep1

value: Alveolar epithelial type 2 cells (AT2)


title: TIME53


title: Axin2_neg_rep1


title: TIME56


title: iPS Cell derived RPE

city: Kobe

first: Cody

last: Kime

state: Hyogo

address: Minatojima Minamimachi, 2-2-3

department: Center for Biosystems Dynamics Research

institute: RIKEN

data_processing:
BAM files were produced with Cell Ranger (Version 3.1)
Counts were split to intron and exon counts with dropEst
Basic cell quality filtering was performed in Seurat
SkewC was performed after Seurat to remove skewed and retain typical cells, producing a final total high quality filtering of cell samples to the filteredcellbarcodes list.
Final exon, intron, and sum (exon+intron) count tables from DropEst are generated from filtered barcodes set for downstream use as R Data files (*modifiedCCM.rds).
Genome_build: hg38; GRCh38
Supplementary_files_format_and_content: List of post-filtered cell barcodes used in the study, prepared as a text file; R Data file

source_name: 253G1 Human iPS Cell Line

extract_protocol:
Cells were digested to single cell with 0.25% trypsin/EDTA, screened, and resuspended in low FBS Phosphate Buffered Saline solution, counted 16 times for cell concentration, viability, and doublet rate, and then diluted to approprate loading concentrations for the 10X Genomics Chromium Controller.
scRNA-seq libraries were prepared with 10x Genomics Chromium system using 10x Genomics 5' (v1.0 Chemistry) VDJ kit library construction with standard protocol for 5' Gene Expressoin libraries that skips Steps 4&5 and uses the i7 multipltex library Index kit following standard protocol. Libraries were diluted and submitted to Macrogen for sequencing under the library strategy.

value: iPS Cell derived RPE

tag: culture method

value: RPE Maturation Medium (SFRM-B27, 0.5uM SB431542, 10ng/mL bFGF)

tag: plate type

value: iMatrix511 coated plate

tag: sequenced molecule

value: 5' RNAs captured by template switching oligo (TSO)


title: TAC 3 days biological replicate 2 RNA-seq

state: CA

value: TAC

value: 3 days


title: TIME47

value: AA supplemented


title: TAC 3 days biological replicate 1 RNA-seq


title: iRPE reprogrammed from BJ fibroblasts with nicotinamide and chetomin.

source_name: this study; reprogrammed from BJ, ATCC CRL-2522

value: iRPE reprogrammed from BJ fibroblasts


title: TIME45


title: iRPE reprogrammed from BJ fibroblasts without nicotinamide and chetomin.


title: TIME42


title: Human Foreskin Fibroblasts (BJ, ATCC CRL-2522)

source_name: BJ, ATCC CRL-2522

value: Foreskin Fibroblasts

value: 10% Fetal Bovine Serum, High Glucose DMEM

value: Gelatin coated plate


title: TAC 3 weeks biological replicate 2 RNA-seq

value: 3 weeks


title: TAC 3 weeks biological replicate 3 RNA-seq


title: TIME190

value: unsupplemented


title: TAC 3 weeks biological replicate 1 RNA-seq


title: H82_R-3

city: Shanghai

first: Cao

last: Jy

address: Yueyang Road

institute: CAS

data_processing:
RNA-seq reads were aligned to the human reference genome hg38 using STAR version 2.6.1b with --readFilesCommand zcat.
reads counting were performed using  STAR version 2.6.1b with --sjdbGTFtagExonParentGene gene_name

source_name: small cell lung cancer cells

growth_protocol: All cell lines were incubated at 37℃ in 5% CO2 with RPMI1640 plus 10% FBS, and 10% Penicillin-Streptomycin

extract_protocol:
Total RNAs were extracted by TRIzol reagent (Life Technologies) according to the manufacturer’s instruction.
Libraries were prepared according to Illumina's instructions

treatment_protocol: Etoposide plus cisplatin

value: ATCC cell line H82

value: lung

value: etoposide plus cisplatin treated tumor


title: TIME36

value: endothelial cell

value: cytokine


title: CTCF knockout biological replicate 2 RNA-seq

tag: genotype

value: CTCF knockout


title: Control biological replicate 3 RNA-seq

value: Control


title: H82_R-1


title: TIME33


title: TAC 3 days biological replicate 3 RNA-seq


title: TIME64

value: unstimulated


title: H82_P4

data_processing:
whole exome-seq reads were aligned to the human reference genome hg38 using bwa version 0.7.17 with default parameters.
mutation calling were performed using Genome Analysis Toolkit 3.1.
Genome_build: hg38
Supplementary_files_format_and_content: VCF

extract_protocol:
Total DNAs from tumors were extracted by TRIzol reagent (Life Technologies) according to the manufacturer’s instruction.
Libraries were prepared according to Illumina's instructions

treatment_protocol: Mice were treated with etoposide plus cisplatin


title: TIME29


title: Control biological replicate 2 RNA-seq


title: H82_P3


title: Control biological replicate 1 RNA-seq


title: TIME24


title: H82_P1


title: TIME14

value: DHA supplemented


title: H82_P2


title: TIME15


title: TIME12


title: Sample 4 M0

value: Peripheral venous blood

value: Unpolarised M0

value: monocyte-derived macrophages


title: TIME98


title: TIME6


title: TIME9


title: Peripheral blood, Z360_3

city: Chengdu

first: Xuebin

last: Lv

state: SiChuan

address: Niusha Road

institute: Sichuan, Animal Science Academy

description: domestic pig

data_processing:
Illumina CASAVA ver.1.8.2 software was used for basecalling.
We removed low-quality reads including those with ≥ 10% unidentified nucleotides, > 10 nt aligned to the adapter, allowing ≤ 10% mismatches, and with > 50% of bases with phred quality < 5. Then, high-quality reads of ten strand-specific libraries were mapped to the pig reference genome (Suscrofa.11.1 from Ensemble) with Hisat2 (v.2.0.4)
Genome_build: Suscrofa.11.1 from Ensemble
Supplementary_files_format_and_content: miRNA_readcount_and_TPM.txt

organism: Sus scrofa

source_name: blood tissue

extract_protocol:
Total RNA were extracted using mirVana miRNA isolation kit (Ambion, Austin, USA) according to the manufacture’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stage

value: day 360

value: Peripheral blood


title: Peripheral blood, Z360_2

description: domestic pig


title: si2

city: Shijiazhuang

first: Xue

last: Zhang

state: Hebei

address: 12 Jiankang Road

department: Department of Medical Oncology

institute: Hebei Medical University Fourth Affiliated Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38.91
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colorectal cancer cell

tag: target sequences


title: Peripheral blood, Z360_1

description: domestic pig


title: Peripheral blood, Z180_2

description: domestic pig

value: day 180


title: Peripheral blood, Z180_1

description: domestic pig


title: H82_R-2

tag: treatment


title: si1


title: Peripheral blood, Z60_3

description: domestic pig

value: day 60

tag: tissue


title: Peripheral blood, Z60_2

description: domestic pig


title: TAT-Scr

city: shanghai

first: qiongqiong

last: hou

address: huanke road 199

institute: shanghaitech university

data_processing:
based on illumina NovaSeq 6000 sequencing platform and Paired-End was used
Raw data were filtered by FASTX-Toolkit to generate clean reads and were mapped to human GRCh38 using Hisat
Stringtie software was used to count Fragments PerKilobase Million (FPKM)
edgeR software was used to statistical quantification
Gene expression was presented with GO&KEGG annotation
Genome_build: human GRCh38
Supplementary_files_format_and_content: .xls; peak counts

source_name: cerebral organoid

extract_protocol:
Samples were washed in 1×Hank’s balanced salt solution (HBSS) and Total RNA samples were extracted with Trizol
Basaed on illumina NovaSeq 6000 platform and Base Calling was transformed to Sequenced Reads. Paired-end (PE150) was used.

tag: tat peptide treatment

value: TAT-Scrambled

value: neuroepithellum

value: cortex


title: Peripheral blood, Z60_1

description: domestic pig


title: TAT-465-481

value: TAT-465-481:inhibition of TBC1D3

tag: cell type


title: Peripheral blood, Z30_3

description: domestic pig

value: day 30


title: Peripheral blood, Z30_2

description: domestic pig


title: Peripheral blood, Z30_1

description: domestic pig


title: Tet-Express-treated ChiPSC12-M, biological rep2

city: Fukuoka

first: Sugako

last: Oka

address: 2-15-1, Tamura, Sawara-ku

institute: Fukoka Dental College

description:
normalized_counts.txt
Tet3

data_processing:
A read quality analysis of the raw data was performed using FastQC (version 0.11.7, http://bioinformatics.babraham.ac.uk/projects/fastqc/).
Quality trimming and adapter clipping were performed using Trimmomatic version 0.38 (Bolger et al., 2014), trimming trailing bases below the average quality 15, minimum length 36 and clipping Illumina adapters.
Trimmed reads were mapped to the transcript in the reference human genome (hg19) using Bowtie2 aligner within RSEM (Robinson et al., 2009) and the estimation of the abundance of genes and isoforms with RSEM generated transcripts per million (TPM) counts.
The EdgeR software program (Li et al., 2011) was used to detect the differentially expressed genes (DEGs).
The normalized count per million (CPM) value, log fold-change (logFC) and p value were obtained from the gene-level TPM count.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes normalized CPM values for each sample.

source_name: human iPS ccell line

growth_protocol: Cellartis Human iPS Cell Line 12 (ChiPSC12, Y00285) was purchased from Takara Bio Inc. (Shiga, Japan). ChiPSC12 cell lines were created by reprogramming human skin fibroblasts using defective polycistronic retrovirus technology to deliver Oct-4, SOX2, KLF4, and c-Myc. The cells were transfected with the BI SDHC (I69E) vector using X fect TM (631317, Clontech).Stable transfectants were selected in the DEF-CS culture medium (Takara Bio Inc.) containing 0.2 μg/ml puromycin, and were maintained in the presence of 0.1 μg/ml puromycin.

extract_protocol:
Total RNA from each cell was isolated using Isogen (Nippon Gene Co., Ltd, Toyama, Japan) and was subjected to RNA-Sequencing (Cell Innovator, Kyushu Univ., Fukuoka, Japan). RNA samples were quantified using an ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the quality was confirmed with a Tapestation (Agilent, Tokyo, Japan).
The sequencing libraries were prepared from 1 μg of total RNA using a TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc., Tokyo, Japan) according to the manufacturer's instructions.

treatment_protocol: ChiPSC12-M cells were cultured with Day 0 endoderm differentiation medium and the medium was replaced with Day 1 differentiation medium containing a transcriptional activator protein, Tet-Express (Takara Bio Inc.) and were cultured for 4h.

tag: parental cell line

value: ChiPSC12 cells

tag: day

value: Day 1 of differentiation


title: Tet-Express-treated ChiPSC12-M, biological rep3

description:
normalized_counts.txt
Tet4


title: Tet-Express-treated ChiPSC12-M, biological rep1

description:
normalized_counts.txt
Tet


title: Untreated ChiPSC12-M,  biological rep3

description:
normalized_counts.txt
Control2


title: NC


title: Peripheral blood, Z0_3

description: domestic pig

value: day 0


title: H82_P0

value: ATCC cell line H82

value: lung

value: untreated tumor


title: Untreated ChiPSC12-M,  biological rep2

description:
normalized_counts.txt
Control1


title: Untreated ChiPSC12-M, biological rep1

description:
normalized_counts.txt
Control


title: Peripheral blood, Z0_1

description: domestic pig


title: Peripheral blood, Z0_2

description: domestic pig