title: RNA-seq of resting Treg "wannabe" Rep1

city: New York

first: Michail

last: Schizas

address: 1275 York ave

institute: Memorial sloan Kettering

data_processing:
Bulk RNA-seq alignment: STAR v2.7.3a
Bulk RNA-seq local alignment adjustment: Genome Analysis Toolkit v4.1.4.1
Bulk RNA-seq differential gene expression analysis: DESeq2 v1.28.1
Genome_build: GRCm38

source_name: T cell

extract_protocol:
Trizol extraction
SMART-Seq v4 Ultra Low Input RNA Kit KAPA Hyper Prep Kit

treatment_protocol: Male mice were treated with a single dose of 4-hydroxytamoxifen on postnatal day 14 and 8-10-week-old female mice were treated with diphtheria toxin 1, 3, 5, and 7 days prior to analysis.

value: Spleen and lymph node

value: T cell

tag: age

value: 9-11 weeks

value: diphtheria toxin

tag: fraction

value: mRNA


title: RNA-seq of activated Treg "wannabe" Rep1

status: Public on Jul 09 2021

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: RNA-seq of activated Treg "wannabe" Rep2


title: RNA-seq of resting Treg "wannabe" Rep2


title: RNA-seq of resting Treg "wannabe" Rep3


title: RNA-seq of rescued Treg rep3

value: Day 21


title: RNA-seq of rescued Treg rep2


title: RNA-seq of rescued Treg rep1


title: RNA-seq of Treg "wannabe" rep2


title: RNA-seq of Treg "wannabe" rep1


title: RNA-seq of control Treg Rep3


title: Vitamin D3 treated macrophages

city: Tucson

first: Kellen

last: Chen

state: AZ

address: 1501 N Campbell Ave

department: Surgery

institute: University of Arizona

data_processing:
Base calls were converted to reads using the Cell Ranger (10X Genomics; version 3.1) implementation of mkfastq
Then aligned against the mm9 (mouse) genome using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample
Cell barcodes representative of quality cells were delineated from barcodes of apoptotic cells or background RNA based on a threshold of having at least 200 unique transcripts profiled, less than 10,000 total transcripts, and less than 10% of their transcriptome of mitochondrial origin.
Unique molecular identifiers (UMIs) from each cell barcode were retained for all downstream analysis.
Raw UMI counts were normalized with a scale factor of 10,000 UMIs per cell and subsequently natural log transformed with a pseudocount of 1 using the R package Seurat (version 3.1.1).
Highly variable genes were identified, and cells were scaled by regression to the fraction of mitochondrial transcripts. Aggregated data was then evaluated using uniform manifold approximation and projection (UMAP) analysis
Genome_build: mm9 (mouse)

source_name: bone marrow

growth_protocol: Femurs and tibias were removed from C57/BL6 mice after euthanasia. The epiphyses on both ends of the long bones were removed. The bones were flushed with 5 ml RPMI to collect the bone marrow. The epiphyses were crushed using a pestle and mortar to isolate the bone marrow. Red blood cells were lysed with ACK lysis buffer. Cells were strained and washing in complete media 2x106 per 100 mm dish in 10 ml RPMI containing 10% fetal bovine serum (FBS), 100 U/ml penicillin, 0.1 mg/ml streptomycin, 2 mM glutamine, 50 μM 2-mercaptoethanol, and 200 murine granulocyte-macrophage colony-stimulating factor (GM-CSF, Peprotech, Frankfurt, Germany). On day 3 10 ml complete media were added to the cultures and on day 6 10 ml of media were collected, cells were spun down and re-suspended in fresh media. On day 7, half of the cultures were stimulated with 10-6M 1,25 dihydroxy-cholecalciferol (Sigma-Aldrich) for 24 h.

extract_protocol:
The cellular suspension was then submitted for droplet-based microfluidic single cell RNA sequencing (scRNA-seq) at the Stanford Functional Genomics Facility (SFGF) using the 10x Chromium Single Cell platform (Single Cell 3’ v3, 10x Genomics, USA). For the in vivo study, skin grafts were explanted after 14 days of in vivo subcutaneous implantation. Tissue was minced and enzymatically digested using collagenase IV. The cellular suspension was then submitted for droplet-based microfluidic single cell RNA sequencing (scRNA-seq) at the Stanford Functional Genomics Facility (SFGF) using the 10x Chromium Single Cell platform (Single Cell 3’ v3, 10x Genomics, USA).
cDNA was fragmented followed by end repair and A-tailing at 65°C for 30min. cDNA were double-sided size selected using SpriSelect beats. Sequencing adaptors were ligated to the cDNA at 20°C for 15min. cDNA was amplified using a sample-specific index oligo as primer, followed by another round of double-sided size selection using SpriSelect beads.
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. cDNA libraries were sequenced on a HiSeq 4000 Illumina platform aiming for 50,000 reads per cell.

treatment_protocol: On day 7, half of the cultures were stimulated with 10-6M 1,25 dihydroxy-cholecalciferol (Sigma-Aldrich) for 24 h, the second group was left untreated

tag: passages

value: no passage

value: bone marrow derived cells


title: Control (untreated) macrophages


title: RNA-seq of control Treg Rep1


title: STSG

source_name: STSG implanted into mice

value: skin


title: PKS5-3

city: Beijing

first: Jingrui

last: Li

address: Yuanmingyuan West Road No.2

country: China

institute: China Agricultural Universtiy

library_source: genomic

data_processing:
library strategy: amplicon-seq
Basecalls performed using CASAVA
The 29 bp vector sequence was determined and removed from the 5’ end of the Read_1 by using the Cutadapt 1.18.
The trimmed reads were then mapped to genomic DNA, cDNA and CDS by using HISAT2.1.0 with default parameters.
The in-frame reads were collected into a new SAM file by using a home-made python script.
The number of gene mapped reads and unique read were calculated by using a home-made python script.
Genome_build: Arabidopsis_tair10
Supplementary_files_format_and_content: Tab-delimited text file includes reads count and number of unique read for each samples.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: cDNA library for Y2H screening

extract_protocol:
Plasmids were extracted according to the manual of TIANprep yeast plasmid kit (TIANGEN, China). The prey inserts were amplified by PCR.
The PCR products were sheared into 200-300 bp DNA fragments by Bioruptor Plus (Diagenode). End repair and adaptor ligation were performed by using NEBNext Ultra II End Repair/dA-Tailing Module and NEBNext Ultra II Ligation Module (NEB). The sequencing libraries were constructed by using PCR.

value: selected by SD-Trp-Leu-His medium with 1 mM 3-AT

tag: recovery time

value: 4 hours

tag: sample info

value: Interacting partners of PKS5

tag: molecule subtype

value: amplified DNA


title: K7M2_lung

city: Columbus

first: Ryan

last: Roberts

state: OH

address: Research Building II, 5th Floor WA5108, 700 Children's Drive,

department: Center for Childhood Cancers and Blood Disorders

institute: Nationwide Children's Hospital

data_processing:
Cell Ranger
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw UMI counts for every gene and every single cell in the specific sample

source_name: Cell line - murine

growth_protocol: OS17 cells in culture were infected with a barcoded lentivirus library synthesized from CloneTracker XP™ 10M Barcode-3' Library with Venus-Puro (plasmid) (Cellecta, BCXP10M3VP-P) as described in Wang and McManus 2009 45 with PEI as the transfection reagent. The barcoded plasmids contain ~10M 38-bp semi-random oligonucleotide sequence that is captured on the Chromium Single Cell 3′RNA-sequencing system. 48 h post-infection, barcoded OS17 cells were used to inoculate mice intra-tibially and intra-venously to generate primary and metastatic lesions.

extract_protocol:
Tumor harvested from mice were processed using the human tumor dissociation kit (Miltenyi Biotec, 130-095-929) with a GentleMacs Octo Dissociator with Heaters (Miltenyi Biotec, 130-096-427). Single cell suspensions in 0.04% BSA-PBS of cell lines, and dissociated tumor tissues were generated and run on Chromium Single Cell 3′RNA-sequencing system (10x Genomics) with the Reagent Kit v3 according to the manufacturer's instructions.
Libraries were constructed according to Chromium Single Cell 3′RNA-sequencing system (10x Genomics) with the Reagent Kit v3 according to the manufacturer's instructions. Briefly, cells were loaded into Chromium Single Cell Chip v3 (10x Genomics) with a targeted cell recovery of 5,000 cells per sample. After performing cDNA purification, amplification, and library construction (sample index PCR 14 cycles) as instructed, we sequenced sample libraries on a half lane of HS4000 (Illumina) to yield (after QA) about 65,000 paired-end reads per cell.

treatment_protocol: Cell lines/mice did not receive any treatment

tag: disease

value: osteosarcoma

value: Balb/c

tag: condition

value: lung metastasis


title: F420_lung_Rep1


title: K7M2_tibia

value: bone tumor


title: F420_tibia


title: NCH-OS-2_metastatic

source_name: PDX - human


title: F420_lung_Rep2


title: NCH-OS-7_primary


title: NCH-OS-7_flank

value: subcutaneous flank


title: NCH-OS-7_metastatic


title: NCH-OS-2_primary


title: 143B_primary

source_name: Cell line - human


title: 143B_metastatic


title: NCH-OS-2_flank


title: RNA-seq of control Treg Rep2

value: Spleen and lymph node

value: T cell


title: OS17_primary


title: OS17 metastatic_Rep2


title: 180_jejunum_PN-sens_PN_60min

city: Chapel Hill

first: Erin

middle: C

last: Steinbach

state: NC

address: 111 Mason Farm Road, 7314 MBRB

department: Medicine

institute: University of North Carolina at Chapel Hill

description: 151bp paired-end sequences aligned and quantified using Salmon

data_processing:
Trim adapter sequences:
cutadapt version 1.18
cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCG  TCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT --quality-cutoff 10 --cores 4 --len  gth 150 --minimum-length 20 -o
Align and quantify:
salmon version 1.2.1
salmon quant --libType A --seqBias --gcBias --validateMappings --writeUnmappedNames --numBootstraps=10 --threads 8
Genome_build: mm10
Supplementary_files_format_and_content: salmon quant.sf text file - quantification

molecule: polyA RNA

extract_protocol:
Murine jejuna (starting 6 cm from pyloric junction and continuing for 4 cm) were obtained by sterile dissection, flushed with cold sterile PBS, and cut open longitudinally. Tissue was incubated in Isolation Buffer with freshly added 2 mM EDTA and 0.5 mM DTT at room temperature for 75 minutes, washed in PBS twice, and shaken vigorously in Isolation Buffer to release the epithelial cells.
Preparation of RNA library and transcriptome sequencing was conducted by Novogene Co., LTD (Beijing, China).

treatment_protocol: CC027/GeniUnc mice were given intragastric (i.g.) 2 mg crude peanut extract ("peanut") or PBS once weekly for 3 weeks, then i.g. 5 mg peanut or PBS once in Week 4 to establish sensitization. A subset of mice were challenged with i.g. 12 mg peanut and sacrificed at indicated time points (30, 60, 120 minutes) for isolation of jejunal epithelial cells. Unchallenged mice were sacrificed for isolation of jejunal epithelial cells at the same time.

value: Dissociated jejunal epithelial cells

value: Peanut-sensitized & challenged

tag: time point

value: 60 min


title: 186_jejunum_PN-sens_NA_0min

value: Peanut-sensitized & unchallenged

value: 0 min


title: 175_jejunum_PN-sens_PN_60min


title: 183_jejunum_PN-sens_PN_30min

value: 30 min


title: 179_jejunum_PN-sens_PN_60min


title: 188_jejunum_PN-sens_PN_30min


title: 182_jejunum_PN-sens_NA_0min


title: 181_jejunum_PN-sens_PN_120min

value: 120 min


title: 184_jejunum_PN-sens_PN_120min


title: 173_jejunum_PN-sens_NA_0min


title: OS17_metastatic_Rep1


title: 172_jejunum_PBS-sens_NA_0min

value: PBS-sensitized & unchallenged


title: 170_jejunum_PBS-sens_NA_0min


title: 169_jejunum_PBS-sens_NA_0min


title: Dicer+/+aviD+/+ 1

city: London

first: Enzo

last: Poirer

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

data_processing:
Reads were trimmed to 40bp using Cutadapt (version 0.1.9) and  mapped to the genome of interest using Bowtie (version 1.2.0) with default parameters with one mismatch (-v 1).
Coverage over ZIKV or SARS-CoV-2 genome was determined using mapped 22 bp reads only, using BEDTools's genome CoverageBed function. version 2.27.1
Genome_build: GenBankID: MK105975.1 [ZIKV] ; MT0795851.1 [SARS]
Supplementary_files_format_and_content: Read coverage (per basepair) over the Zika genome (MK105975.1) or SARS genome (MT0779851.1)

source_name: Brain organoids

extract_protocol:
RNA extraction was performed from organoids grinded in 2 ml Eppendorf tube containing 500 ul TRIzol reagent and one Stainless Steel 5 mm bead (Qiagen) using a TissuLyser LT (Qiagen) at 50 oscillations/s for 1 min. 400 ng of RNA was process for next-generation sequencing using the HiSeq 4000 platform (Illumina).
NEBNext_small_RNA

treatment_protocol: Individual Dicer+/+aviD+/+, Dicer+/+aviD—/— and Dicer—/—aviD+/+ brain organoids were infected with ZIKV or SARS, and collected after 4 days

value: Brain organoids

tag: variation

value: Dicer+/+aviD+/+

tag: infection

value: ZIKV


title: Dicer+/+aviD+/+ 2


title: Dicer-/-aviD+/+ 1

value: Dicer-/-aviD+/+


title: Dicer+/+aviD-/- 1

value: Dicer+/+aviD-/-


title: 185_jejunum_PN-sens_PN_120min


title: Control Rep2 S-Medium Reversion

city: Newark

first: Irem

last: Celen

state: DE

address: 15 Innovation Way

institute: University of Delaware

data_processing:
Quality control was implemented on the raw sequence data with FastQC software (version 0.11.2).
The raw reads were then mapped to the reference genome (WBCel235), obtained from Ensembl along with the annotation file, with Burrows-Wheel Aligner (BWA; version 0.7.4)
The peaks were called separately for replicates with Model-based Analysis for ChIP-Seq (MACS; version 2.0). For H3K27me3, broad peaks were called with parameters --broad --nomodel -B -p 0.00001 -m 10 35.
The corresponding annotations to peaks were acquired by using Hypergeometric Optimization of Motif EnRichment (HOMER; version 4.9)
Integrative genomics viewer was used to visualize the data.
Genome_build: WBCel235
Supplementary_files_format_and_content: format: bed; output: Peaks called for each of the ChIP-seq libraries for the histone modifications and RNA Pol II.

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: P0 generation animals were grown in bacteria-seeded agar plates (OP50 NGM), F1 generation animals of both the N2 and AB1 strain were cultured in CeHR. F1 generation of the N2 strain was also cultured in S-Medium. F2 generation animals were placed back to OP50 NGM. All animals were grown at 21°C

extract_protocol:
ChIP-seq for the histone marks were performed as described previously (Doh et al., 2016) with additional antibodies. Five micrograms of each anti-H3K27me3 (MBL MABI0323), anti-H3K4me3 (MBL MABI0304), anti-H3K9me3 (MBL MABI0318), anti-RNA Polymerase II (MBL MABI0601), anti-H4K20me1 (abcam ab9051), and anti-H3K36me1 (abcam ab9048) antibodies and 300 µg of extracts were used.
Sequencing libraries were prepared using 5 ng of DNA with the TruSeq® ChIP Sample Preparation Kit A (Illumina®) according to the manufacturer’s protocol.

tag: chip antibody

tag: generation

tag: developmental stage

value: Young adult


title: Control Rep1 S-Medium


title: Control Rep1 CeHR Reversion


title: Control Rep2 CeHR


title: Control Rep2 S-Medium


title: Control Rep1 S-Medium Reversion


title: Control Rep2 CeHR Reversion


title: 174_jejunum_PN-sens_PN_30min

tag: strain


title: Control Rep1 CeHR


title: Control Rep2 OP50 NGM


title: Control Rep1 OP50 NGM


title: H3K36me1 Rep2 S-Medium Reversion


title: RNA Pol II Rep1 S-Medium Reversion


title: H4K20me1 Rep2 S-Medium Reversion


title: H4K20me1 Rep1 S-Medium Reversion


title: H3K27me3 Rep2 S-Medium Reversion


title: RNA Pol II Rep2 S-Medium Reversion


title: H3K27me3 Rep1 S-Medium Reversion


title: H3K9me3 Rep2 S-Medium Reversion


title: H3K4me3 Rep1 S-Medium Reversion


title: H3K4me3 Rep2 S-Medium Reversion


title: RNA Pol II Rep1 CeHR Reversion


title: H3K36me1 Rep1 CeHR Reversion


title: RNA Pol II Rep2 CeHR Reversion


title: H3K27me3 Rep2 CeHR Reversion


title: H3K4me3 Rep2 CeHR Reversion


title: H4K20me1 Rep2 CeHR Reversion


title: H3K9me3 Rep1 CeHR Reversion


title: RNA Pol II Rep2 S-Medium


title: H3K4me3 Rep1 CeHR Reversion


title: H3K9me3 Rep2 CeHR Reversion


title: RNA Pol II Rep1 S-Medium


title: H3K27me3 Rep2 S-Medium


title: H3K36me1 Rep1 S-Medium Reversion


title: H3K36me1 Rep1 S-Medium


title: H3K9me3 Rep1 S-Medium Reversion


title: H4K20me1 Rep1 S-Medium


title: H3K27me3 Rep1 S-Medium


title: H4K20me1 Rep2 S-Medium


title: H3K36me1 Rep2 S-Medium


title: H3K9me3 Rep1 S-Medium


title: H3K9me3 Rep2 S-Medium


title: H3K36me1 Rep2 CeHR


title: H3K4me3 Rep1 S-Medium


title: RNA Pol II Rep2 CeHR


title: H3K4me3 Rep2 S-Medium


title: H3K36me1 Rep1 CeHR


title: RNA Pol II Rep1 CeHR


title: H3K36me1 Rep2 CeHR Reversion


title: H3K27me3 Rep1 CeHR Reversion


title: H3K27me3 Rep2 CeHR


title: H4K20me1 Rep1 CeHR Reversion


title: H3K9me3 Rep1 CeHR


title: H3K4me3 Rep2 CeHR


title: H3K9me3 Rep2 CeHR


title: RNA Pol II Rep1 OP50 NGM


title: H4K20me1 Rep1 CeHR


title: RNA Pol II Rep2 OP50 NGM


title: H3K4me3 Rep1 CeHR


title: H4K20me1 Rep2 OP50 NGM


title: H3K36me1 Rep1 OP50 NGM


title: H3K36me1 Rep2 OP50 NGM


title: H3K27me3 Rep1 OP50 NGM


title: H3K27me3 Rep2 OP50 NGM


title: H3K9me3 Rep1 OP50 NGM


title: H3K9me3 Rep2 OP50 NGM


title: H4K20me1 Rep1 OP50 NGM


title: H3K4me3 Rep2 OP50 NGM


title: H3K4me3 Rep1 OP50 NGM


title: H4K20me1 Rep2 CeHR


title: ATAC_PANC1_1

city: Göttingen

first: Shiv K.

last: Singh

address: Robert-Koch-Str. 40

department: Gastroenterology and Gastrointestinal Oncology

country: Germany

institute: Univeristy Medical Center

description: ATAC-seq in PANC1 cell line

data_processing:
Raw reads were quality-checked using FastQC
For ATAC-seq, adapters were trimmed, unmapped reads, those mapping at low quality (MAPQ < 30), mapping to chrM, and unpaired were removed, as were PCR duplicates using the Picard tool
Alignment against hg19 human reference genome using BWA v0.7.17 (ChIP-seq) or Bowtie2 (ATAC-seq)
Peaks were called using MACS2; for ChIP-seq against input; for ATAC-seq using parameters: -p 0.01 --shift -100 --extsize 200 -B --SPMR --keep-dup all --call-summits
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak

organism: Homo sapiens

source_name: Pancreatic cancer

extract_protocol: none provided by the submitter

tag: cell line


title: ATAC_PANC1_3

description: ATAC-seq in PANC1 cell line


title: ATAC_CAPAN1_1

description: ATAC-seq in CAPAN1 cell line


title: ATAC_PANC1_2

description: ATAC-seq in PANC1 cell line


title: ATAC_CAPAN2_1

description: ATAC-seq in CAPAN2 cell line


title: ATAC_CAPAN2_3

description: ATAC-seq in CAPAN2 cell line


title: H3K27me3 Rep1 CeHR


title: ATAC_CAPAN1_3

description: ATAC-seq in CAPAN1 cell line


title: ATAC_MiaPaCa2_2

description: ATAC-seq in MiaPaCa2 cell line


title: ATAC_CAPAN2_2

description: ATAC-seq in CAPAN2 cell line


title: ChIP_JUNB_CAPAN1_2

description: JUNB ChIP-seq in CAPAN1 cell line

value: JUNB


title: ChIP_input_PANC1

description: input for cJUN ChIP-seq in PANC1 cell line


title: ATAC_MiaPaCa2_1

description: ATAC-seq in MiaPaCa2 cell line


title: ATAC_CAPAN1_2

description: ATAC-seq in CAPAN1 cell line


title: ChIP_input_CAPAN1

description: input for JUNB ChIP-seq in CAPAN1 cell line


title: ChIP_cJUN_PANC1_1

description: cJUN ChIP-seq in PANC1 cell line

value: cJUN


title: ChIP_cJUN_PANC1_2

description: cJUN ChIP-seq in PANC1 cell line


title: ChIP_JUNB_CAPAN1_1

description: JUNB ChIP-seq in CAPAN1 cell line


title: miRNA IGROV1-LIN28A positive-TUT4/7-mutant_2-rep1

city: cambridge

first: Jonathan

middle: Lewis

last: Price

address: The Sanger Building Tennis Court Road

department: Biochemistry

institute: University of Cambridge

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
iko21

data_processing:
Trim low quality reads and apapters: Trimmomatic V0.39 - ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36
Remove ribosomal RNA: SortmeRNA
map to the reference genome: HISAT2 V2.1.0.
Count reads on features: htseq-count
Genome_build: hg38
Supplementary_files_format_and_content: HTSeq-count files, mirDeep2 matrix and chimera output

source_name: IGROV1 ovarian cancer cell line

growth_protocol: DU145 was routinely cultured in EMEM complete media (EMEM,10%FBS,1X NEAA, 1X antibiotics (Penicillin-streptomycin) and 1X sodium pyruvate) and IGROV1 was  routinely cultured in RPMI complete media (RPMI-1640 ,10%FBS,1X NEAA and 1X antibiotics)

extract_protocol:
TRIsure (BIO-38033) followed by phenol-chloroform RNA extraction.
mRNA libraries were prepared after poly(A) selection using NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads kit (NEB E7765S) and miRNA libraries were prepared from total RNA using NextFlex Small RNA-seq v3 kit (BIOO Scientific).

treatment_protocol: TUT4 (exon12) and TUT7 (exon 14) were targeted using CRISPR

value: ovarian cancer

value: LIN28A+; TUT4-; TUT7-

tag: type

value: CRISPR Clone 14.1.17

tag: passage number


title: RNA IGROV1-LIN28A positive-TUT4/7-mutant_2-rep4

description: TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR

tag: genotype

value: CRISPR Clone 14.1.20


title: miRNA IGROV1-LIN28A positive-TUT4/7-mutant_2-rep4

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
iko24


title: RNA IGROV1-LIN28A positive-TUT4/7-mutant_2-rep2

value: CRISPR Clone 14.1.18


title: miRNA IGROV1-LIN28A positive-TUT4/7-mutant_2-rep2

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
iko22


title: miRNA IGROV1-LIN28A positive-TUT4/7-mutant_2-rep3

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
iko23

value: CRISPR Clone 14.1.19


title: RNA IGROV1-LIN28A positive-TUT4/7-mutant_1-rep4

value: CRISPR Clone 12.1.10


title: miRNA IGROV1-LIN28A positive-TUT4/7-mutant_1-rep3

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
iko13

value: CRISPR Clone 12.1.9


title: RNA IGROV1-LIN28A positive-TUT4/7-mutant_2-rep1


title: miRNA IGROV1-LIN28A positive-TUT4/7-mutant_1-rep4

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
iko14


title: miRNA IGROV1-LIN28A positive-TUT4/7-mutant_1-rep1

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
iko11

value: CRISPR Clone 12.1.7


title: RNA IGROV1-LIN28A positive-TUT4/7-mutant_1-rep3


title: miRNA IGROV1-LIN28A positive-TUT4/7-mutant_1-rep2

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
iko12

value: CRISPR Clone 12.1.8


title: miRNA IGROV1-LIN28A positive-wildtype-rep2

description:
not targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
i2

value: LIN28A+; TUT4+; TUT7+

value: parental


title: RNA IGROV1-LIN28A positive-wildtype-rep3

description: not targeted using CRISPR


title: RNA DU145-LIN28A negative-TUT4/7-mutant_2-rep4

source_name: DU145 prostate cancer cell line

value: prostate cancer

value: LIN28A-; TUT4-; TUT7-

value: CRISPR Clone 163.4.26.8


title: RNA IGROV1-LIN28A positive-TUT4/7-mutant_1-rep1


title: miRNA DU145-LIN28A negative-TUT4/7-mutant_2-rep4

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
dko24


title: miRNA IGROV1-LIN28A positive-wildtype-rep3

description:
not targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
i3


title: RNA IGROV1-LIN28A positive-wildtype-rep2

description: not targeted using CRISPR


title: F3_SLUDGE

city: Barcelona

first: Claudia

middle: Sanz

last: Lanzas

state: Barcelona

address: Carrer Jordi Girona, 20

department: Environmental Toxicology

country: Spain

institute: IDAEA-CSIC

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
F3

data_processing:
Library strategy: 16S rDNA metagenome-seq
Paired-end reads was assigned to samples based on their unique barcodes and truncated by cutting off the barcode and primer sequences. Paired-end reads were merged using FLASH (V1.2.7)[21] (see details http://ccb.jhu.edu/software/FLASH/), a very fast and accurate analysis tool, which was designed to merge paired-end reads when at least some of the reads overlap the read generated from the opposite end of the same DNA fragment, and the splicing sequences were called raw tags. Quality filtering on the raw tags were performed under specific filtering conditions to obtain the high-quality clean tags[22] according to the Qiime (V1.7.0)[23] (see details http://qiime.org/scripts/split_libraries_fastq.html) quality controlled process.
The tags were compared with the reference database (Gold database, see details http://drive5.com/uchime/uchime_download.html) using UCHIME algorithm (UCHIME Algorithm, see details http://www.drive5.com/usearch/manual/uchime_algo.html)[24] to detect chimera sequences (see details https://drive5.com/usearch/manual/chimeras.html). And then the chimera sequences were removed[25]. Then the Effective Tags finally obtained.
OTU cluster and Taxonomic annotation: Sequences analysis were performed by Uparse software (Uparse v7.0.1001, see details http://drive5.com/uparse/)[26] using all the effective tags. Sequences with ≥97% similarity were assigned to the same OTUs. Representative sequence for each OTU was screened for further annotation.
OTU cluster and Taxonomic annotation: For each representative sequence, Mothur software was performed against the SSUrRNA database of SILVA Database (see details http://www.arb-silva.de/)[27]for species annotation at each taxonomic rank (Threshold:0.8~1)[28] (kingdom, phylum, class, order, family, genus, species).
OTU cluster and Taxonomic annotation: To obtain the phylogenetic relationship of all OTUs representative sequences, the MUSCLE[29] (Version 3.8.31, see details http://www.drive5.com/muscle/) can compare multiple sequences rapidly.
OTU cluster and Taxonomic annotation: OTUs abundance information were normalized using a standard of sequence number corresponding to the sample with the least sequences. Subsequent analysis of alpha diversity and beta diversity were all performed basing on this output normalized data.
Genome_build: SILVA database
Supplementary_files_format_and_content: tab-delimited text files include normalized reads values (normalized counts) for each sample.

organism: sludge metagenome

source_name: AMENDMENT

growth_protocol: Soils were freezed at -20ºC prior to DNA extraction

extract_protocol:
DNeasy PowerSoil Kit (Qiagen Laboratories, Inc.)
Sequencing libraries were generated using NEBNext Ultra DNA Library Pre ®Kit for Illumina, following manufacturer's recommendations. Sequencing was carried out on an Illumina platform and 250 bp paired-end reads were generated

treatment_protocol: Soil directly added to the kit at a total amount of 0,25g following manufacturer´s indications

tag: treatment

value: SLUDGE

tag: geographic location

tag: sampling date

tag: soil type

value: Soil type not applicable. Sample is Raw Sludge


title: miRNA IGROV1-LIN28A positive-wildtype-rep4

description:
not targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
i4

tag: disease

value: ovarian cancer


title: miRNA IGROV1-LIN28A positive-wildtype-rep1

description:
not targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
i1


title: RNA IGROV1-LIN28A positive-wildtype-rep1

description: not targeted using CRISPR


title: miRNA DU145-LIN28A negative-TUT4/7-mutant_2-rep3

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
dko23

value: CRISPR Clone 163.4.26.7


title: RNA IGROV1-LIN28A positive-TUT4/7-mutant_2-rep3

value: LIN28A+; TUT4-; TUT7-


title: RNA IGROV1-LIN28A positive-TUT4/7-mutant_1-rep2


title: RNA DU145-LIN28A negative-TUT4/7-mutant_2-rep2

value: CRISPR Clone 163.4.26.6


title: RNA DU145-LIN28A negative-TUT4/7-mutant_2-rep3


title: RNA IGROV1-LIN28A positive-wildtype-rep4

description: not targeted using CRISPR


title: miRNA DU145-LIN28A negative-TUT4/7-mutant_2-rep2

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
dko22


title: RNA DU145-LIN28A negative-TUT4/7-mutant_2-rep1

value: CRISPR Clone 163.4.26.5


title: miRNA DU145-LIN28A negative-TUT4/7-mutant_1-rep4

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
dko14

value: CRISPR Clone 8.1.3.4


title: miRNA DU145-LIN28A negative-TUT4/7-mutant_2-rep1

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
dko21


title: RNA DU145-LIN28A negative-TUT4/7-mutant_1-rep4

description: TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR


title: miRNA DU145-LIN28A negative-TUT4/7-mutant_1-rep3

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
dko13


title: TCR-seq of rescued Treg 7 months post-treatment, rep4

data_processing:
TCR-seq alignment: MiXCR v3.0.13
TCR-seq clonotype pre-processing: VDJTools v1.2.1
Genome_build: GRCm38

extract_protocol:
RNeasy plus micro kit
reverse transcription of polyA RNA and 5'RACE of Trac transcripts
RNA-seq (5'RACE)

tag: tissue

value: Spleen and lymph node

tag: cell type

value: T cell

tag: age

value: 7.5 months

tag: fraction

value: Trac mRNA


title: TCR-seq of rescued Treg 7 months post-treatment, rep5


title: RNA DU145-LIN28A negative-TUT4/7-mutant_1-rep3


title: miRNA DU145-LIN28A negative-TUT4/7-mutant_1-rep1

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
dko11


title: miRNA DU145-LIN28A negative-TUT4/7-mutant_1-rep2

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
dko12


title: TCR-seq of rescued Treg 7 months post-treatment, rep3


title: RNA DU145-LIN28A negative-TUT4/7-mutant_1-rep1


title: TCR-seq of rescued Treg 7 months post-treatment, rep2


title: Young_2

type: RNA

city: Seoul

first: Sun-Hee

last: Hwang

address: Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu

country: South Korea

institute: The Rheumatism Research Center

description: 6-week-old NOD/shiLtJ mice2

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Mouse   2.0 ST Array at 45°C for 16hour

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

data_processing: The data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Power Tools(APT)

label: biotin

source_name: 6-week-old NOD/shiLtJ mice2

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Isolation of salivary gland cells and RNA preparation in Ex vivo.

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

treatment_protocol: Salivary gland tissue was cut into 1U/ml dispase II solution (Stemcell) + 2mg/ml collagenase IV (Gibco) solution and incubated at 37°C. The cells were transferred to a tube, rinsed with PBS, and filtered to isolate salivary gland cells.

value: NOD/shiLtJ

tag: disease state

value: no diabetes

value: Salivary gland

tag: gender

value: Female


title: TCR-seq of rescued Treg 7 months post-treatment, rep1


title: miRNA DU145-LIN28A negative-wildtype-rep4

description:
not targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
d4

value: prostate cancer

value: LIN28A-; TUT4+; TUT7+

value: parental


title: TCR-seq of rescued Treg 5 months post-treatment, rep1

value: 5.5 months


title: SS_2

description: 21-week-old NOD/shiLtJ mice2

source_name: 21-week-old NOD/shiLtJ mice2


title: SS_3

description: 21-week-old NOD/shiLtJ mice3

source_name: 21-week-old NOD/shiLtJ mice3


title: SS_1

description: 21-week-old NOD/shiLtJ mice1

source_name: 21-week-old NOD/shiLtJ mice1


title: Young_1

description: 6-week-old NOD/shiLtJ mice1

source_name: 6-week-old NOD/shiLtJ mice1


title: T_S_4

description: 21-week-old NOD/shiLtJ mice with type 1 diabetes4

value: type 1 diabetes


title: Young_3

description: 6-week-old NOD/shiLtJ mice3

source_name: 6-week-old NOD/shiLtJ mice3


title: T_S_2

description: 21-week-old NOD/shiLtJ mice with type 1 diabetes2


title: RNA DU145-LIN28A negative-wildtype-rep4

description: not targeted using CRISPR


title: TCR-seq of rescued Treg 5 months post-treatment, rep2

source_name: T cell


title: T_S_1

description: 21-week-old NOD/shiLtJ mice with type 1 diabetes1


title: T_S_3

description: 21-week-old NOD/shiLtJ mice with type 1 diabetes3


title: RNA DU145-LIN28A negative-TUT4/7-mutant_1-rep2

value: LIN28A-; TUT4-; TUT7-


title: TCR-seq of rescued Treg 3 months post-treatment, rep4

value: 3.5 months


title: RNA DU145-LIN28A negative-wildtype-rep3

description: not targeted using CRISPR


title: miRNA DU145-LIN28A negative-wildtype-rep2

description:
not targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
d2


title: TCR-seq of rescued Treg 3 months post-treatment, rep3


title: miRNA DU145-LIN28A negative-wildtype-rep1

description:
not targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
d1


title: TCR-seq of rescued Treg 1.5 months post-treatment, rep2

value: 8 weeks


title: TCR-seq of rescued Treg 3 months post-treatment, rep1


title: TCR-seq of rescued Treg 3 months post-treatment, rep2


title: TCR-seq of rescued Treg 1.5 months post-treatment, rep1


title: RNA DU145-LIN28A negative-wildtype-rep1

description: not targeted using CRISPR


title: miRNA DU145-LIN28A overexpressing-TUT4/7-mutant_2-rep4

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
ako24

value: LIN28A+; TUT4-; TUT7-

value: CRISPR Clone 163.4.26.8


title: e22ne

city: Redwood City

first: Kavita

last: Sarin

address: 450 Broadway St, Pavilion C 2nd Fl MC 5334

department: Dermatology

institute: Stanford University

data_processing:
Total RNA sample quality control, including RNA concentration, RIN value, 28S/18S, and fragment length distribution were conducted on Agilent 2100 Bio (Agilent RNA 6000 Nano Kit).
mRNAs were isolated from total RNA using oligo(dT) and fragmented, cDNA were synthesized and ends repaired, adenine was added to the tail, cDNA fragments were linked with adapters, and cDNA fragments were then amplified using PCR.
After filtering out low quality reads, reads with adaptors, and reads with unknown bases, clean reads were converted to a FASTQ format then mapped onto the reference genome using HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts)(55) and Bowtie2.
Gene expression levels were calculated using RSEM.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM data in .csv files

source_name: EBS epidermis_nonblister

extract_protocol:
Skin samples were obtained from 11 EBS patients with 4mm punch biopsies. 9 biopsies were taken from a site of an acute blister (occurrence within 1 week of biopsy), and 11 biopsies were taken from a site without any blistering. All samples were taken from the flank or upper arm for ease of wound care. In blisters, the dermis and epidermis self-separated without need for additional manipulation. In non-blistered skin, the dermis and epidermis were processed via one freeze-thaw cycle of liquid nitrogen.
RNA preparation, library construction, and sequencing were performed by the Beijing Genomics Institute.

tag: blister status

value: nonblister

value: Epidermolysis Bullosa Simplex (EBS)

value: epidermis


title: miRNA DU145-LIN28A negative-wildtype-rep3

description:
not targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
d3


title: RNA DU145-LIN28A overexpressing-TUT4/7-mutant_2-rep4


title: miRNA DU145-LIN28A overexpressing-TUT4/7-mutant_2-rep3

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
ako23

value: CRISPR Clone 163.4.26.7


title: e22be

source_name: EBS epidermis_blister

value: blister


title: e21ne


title: e21be


title: RNA DU145-LIN28A overexpressing-TUT4/7-mutant_2-rep3


title: e13ne


title: RNA DU145-LIN28A overexpressing-TUT4/7-mutant_2-rep1

value: CRISPR Clone 163.4.26.5


title: RNA DU145-LIN28A negative-wildtype-rep2

description: not targeted using CRISPR


title: RNA DU145-LIN28A overexpressing-TUT4/7-mutant_2-rep2

value: CRISPR Clone 163.4.26.6


title: miRNA DU145-LIN28A overexpressing-TUT4/7-mutant_2-rep2

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
ako22

value: prostate cancer


title: RNA DU145-LIN28A overexpressing-TUT4/7-mutant_1-rep4

value: CRISPR Clone 8.1.3.4


title: e11ne


title: e11be


title: e13be


title: miRNA DU145-LIN28A overexpressing-TUT4/7-mutant_2-rep1

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
ako21


title: e9ne


title: e10ne


title: e9be


title: miRNA DU145-LIN28A overexpressing-TUT4/7-mutant_1-rep4

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
ako14


title: e10be


title: miRNA DU145-LIN28A overexpressing-TUT4/7-mutant_1-rep2

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
ako12


title: miRNA DU145-LIN28A overexpressing-TUT4/7-mutant_1-rep3

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
ako13


title: e8ne


title: RNA DU145-LIN28A overexpressing-TUT4/7-mutant_1-rep3

description: TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR


title: RNA DU145-LIN28A overexpressing-TUT4/7-mutant_1-rep2


title: e8be


title: P1_SLURRY

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
P1

organism: feces metagenome

value: SLURRY

value: Soil type not applicable. Sample is Raw Slurry


title: e6ne


title: e3ne


title: RNA DU145-LIN28A overexpressing-TUT4/7-mutant_1-rep1


title: miRNA DU145-LIN28A overexpressing-wildtype-rep4

description:
not targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
a4

value: LIN28A+; TUT4+; TUT7+

value: parental


title: RNA DU145-LIN28A overexpressing-wildtype-rep4

description: not targeted using CRISPR


title: e2be


title: PDLSCs Control

first: Yunfei

last: Zheng

state: Beijing

address: 22 Zhongguancun Avenue South, Haidian District

department: Oral and Maxillofacial Surgery

institute: Peking University School and Hospital of Stomatology

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: periodontal ligament

growth_protocol: The cells were cultured in α-Modified Eagle’s Medium supplemented with 10% (v/v) fetal bovine serum and 1% penicillin/streptomycin in a humidified atmosphere at 37°C under 5% (v/v) CO2.

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

treatment_protocol: PDLSCs were subjected to static compressive stress

value: periodontal ligament stem cells

value: periodontal ligament

value: control

value: wild type


title: miRNA DU145-LIN28A overexpressing-wildtype-rep3

description:
not targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
a3


title: e1ne

value: nonblister


title: PDLSCs Force

value: static compressive stress


title: miRNA DU145-LIN28A overexpressing-TUT4/7-mutant_1-rep1

description:
TUT4 (exon12) and TUT7 (exon 14) targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
ako11

value: LIN28A+; TUT4-; TUT7-


title: RNA DU145-LIN28A overexpressing-wildtype-rep3

description: not targeted using CRISPR


title: e1be

value: Epidermolysis Bullosa Simplex (EBS)

value: epidermis


title: Control_100088

city: Pittsburgh

first: Ramon

last: Bataller

state: Pennsylvania

address: 200 Lothrop St

department: Gastroenterology Hepatology And Nutrition

institute: University of Pittsburgh

description:
Control
RB_N9

data_processing:
Short read alignment was performed using STAR alignment algorithm with default parameters
Genome_build: Hg19
Supplementary_files_format_and_content: comma separated file with count values for all samples

source_name: Liver biopsy

extract_protocol:
Total RNA was extracted from human liver tissues using the Qiagen AllPrep DNA/RNA/Protein Mini kit following manufacturer’s instructions (Qiagen, Valencia, CA).
Extracted RNA was analyzed with the Agilent 2100 Bioanalyzer system (Agilent Biotechnologies, Palo Alto, CA). High quality RNA was used for library construction using the Illumina TruSeq Stranded Total RNA Ribo-Zero Gold kit (Illumina, San Diego, CA). Multiplexed samples were sequenced using Illumina HiSeq2000 platform (Illumina, San Diego, CA) using a read length of 2 x 50 bases.

value: liver

value: Normal


title: RNA DU145-LIN28A overexpressing-wildtype-rep2

description: not targeted using CRISPR

value: prostate cancer


title: e2ne


title: Control_100733

description:
Control
RB_N8


title: miRNA DU145-LIN28A overexpressing-wildtype-rep2

description:
not targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
a2


title: Low altitude basal  PBMC Sahiwal_6

city: Karnal

first: Preeti

last: Verma

state: Haryana

address: GT Road

department: Division of Animal Biotechnology

country: India

institute: National Bureau of Animal Genetics Resources

description: Gene expression of low altitude adapted Sahiwal basal PBMCs

hyb_protocol: For hybridization, 1.65 μg of linearly amplified and cyanine 3-labeled cRNA were fragmented using fragmentation mix (10X Blocking Agent and 25X Fragmentation Buffer) and incubated at 60°C for exactly 30 min. The fragmented RNA samples were immediately transferred on ice for one minute and 55μl of 2x GEx Hybridization Buffer HI-RPM was added to stop the fragmentation reaction. The fragmented samples (110μl volume) were loaded to the array placed in slide chamber. The assembled slide chamber placed in rotisserie was put in a hybridization oven set to rotate at 10 rpm and 65°C. The hybridization was allowed for 17 hours.

scan_protocol: Immediately after washing, the slides were scanned on GenePix-4000B (Molecular Device) microarray scanner using one colour scan setting with 5μm resolution at wavelength of 532 nm (Cy3). After scanning, the images were collected as 16 bit images and finally stored as tif image files.

data_processing: These files were further subjected to feature extraction using Agilent Feature Extractor Software Version 9.5 (Agilent Technologies) software. The data was normalized using GeneSpring GX 13.1 (Agilent Technologies). Genespring GX 13.1 (Agilent technologies) was used to perform the analysis of raw data obtained from feature extraction software.

organism: Bos taurus

source_name: PBMCs

label_protocol: For One-Color Microarray-Based Gene Expression Analysis using Low Input Quick Amp Labelling kit (Agilent Technologies, Santa Clara, CA), the RNA samples of Ladakhi cattle and Sahiwal cattle were labelled with T7 promoter primer (65°C for 10 min followed by incubation in ice for 5 min). cDNA was constructed from labelled RNA samples after adding cDNA master mix (5X First Strand Buffer, 0.1 M DTT, 10 MmdNTP mix and AffinityScriptRNase Block Mix) followed by incubation at 40°C for 2 h, 70°C for 15 min and final incubation on ice for 5 min. The cRNA synthesis and amplification was performed by adding transcription master mix (5X Transcription Buffer, 0.1 M DTT, NTP mix, T7 RNA Polymerase Blend and Cyanine 3-CTP) followed by incubation at 40°C for 2 h. The amplified labelled cRNA was purified (RNeasy mini column kit, Qiagen, Germany), quantified [μgcRNA yield = (Concentration of cRNA) x 30 µL (elution volume)/ 1000] and checked for specific activity [pmol Cy3 per µg cRNA = (Concentration of Cy3/ Concentration of cRNA) x 1000]. All the samples exhibited yield and specific activity values higher than the minimum value of 1.65 and 6, respectively using four pack microarray format.

extract_protocol: Total RNA was extracted from PBMCs using Trizol reagent (Invitrogen, USA) according to the manufacturer’s protocol. After extraction, RNA was purified using RNeasy Mini kit (Qiagen, Germany) and followed by on-column digestion with the RNase-free DNase (Qiagen, Germany). RNA was quantified using Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA integrity was confirmed by denaturing agarose gel electrophoresis and experion bioanalyser (BioRad, USA,).

tag: cells

value: PBMCs

value: Female


title: Low altitude basal  PBMC Sahiwal_5


title: 2-cell embryos with anti-COPS3 antibody rep1

city: Muenster

first: Michele

last: Boiani

address: Roentgenstrasse 20

institute: Max Planck Institute Muenster

description: Pool of 100 embryos was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water

hyb_protocol: The GeneChip Hybridization, Wash and Stain Kit was used, for 16 h (+/- 1h) at 45°C with 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The GeneChips were scanned using the Affymetrix 3000 7G scanner.

data_processing: The robust multiarray averaging method was applied for background correction, normalization, and probe summarization using the Affymetrix Expression Console.

source_name: preimplantation mouse embryo

label_protocol: Biotinylated cDNA was prepared using GeneChip WT Pico kit, reverse-transcribing and amplifying (8 cycles) 20 micrograms cRNA and, of these, subjecting 5.5 micrograms to labeling

growth_protocol: Zygotes from B6C3F1 x CD1 mating (stimulated cycle, 10 IU each PMSG + hCG given 48 hours apart) were collected from the oviducts and cultured in KSOM(aa) medium using a 4-well plate under 5% CO2 in air at 37 degrees C.

extract_protocol: 28 hours post-injection, pools of 100 embryos were lysed in in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water according to the manufacturer's instructions.

treatment_protocol: At the mid-pronuclear stage (9-11 am) the zygotes were transferred from KSOM(aa) to Hepes-buffered CZB medium in a micromanipulation chamber, where the ooplasm was injected: with Trim21 mRNA (named 'group 2'), or Trim21 mRNA+COPS3 antibody (named 'group 3'; antibody 79698 from AbCam), using a piezo-driven needle coupled to a Gilmont micrometer syringe. Control group (named 'group 1') was left unmanipulated and undisturbed in the incubator. 15 minutes after injection the zygotes were returned to KSOM(aa) in a 4-well plate and all three groups were cultured for additional 28 hours.

tag: genetic background

value: B6C3F1 x CD1

value: Theiler stage 2; 1 dpc (24h IVC)

tag: formation of blastocyst cavity

value: 2-cell formation stunted, many zygotes remained undivided


title: 2-cell embryos with anti-COPS3 antibody rep2


title: 2-cell embryos with Trim21 mRNA and anti-COPS3 antibody rep2


title: Control_120396

description:
Control
RB_N6


title: 2-cell embryos with Trim21 mRNA and anti-COPS3 antibody rep1


title: 2-cell embryos with Trim21 mRNA rep1

value: 2-cell formation normal


title: E17Merkel_WT_RNAseq_rep1

city: Los Angeles

first: Neil

last: Segil

state: CA

address: 1425 san pablo st, BCC 503K

department: BCC

institute: University of Southern California

data_processing:
For RNAseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using STAR. Reads were quantified against genes using RSEM, and differential gene expression analysis was conducted using DESeq2.
For ATACseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using bowtie2. PCR-duplicates were removed by Sambamba, and then peaks were called by MACS2 from individual replicate using filter p value < 0.01.
For Cut&Run, reads were trimmed based on quality score and then aligned to referene mouse genome (mm10) using STAR. PCR duplicates were removed based on UMI by umi_tools,  and then peaks were called by MACS2 for individual replicate using filter p value < 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: read count for genes in text format for RNAseq; peak regions in narrowPeak format for ATACseq and CUT&RUN

source_name: epidermis

extract_protocol:
Merkel cells (Atoh1-GFP+) were purified from the skin of E17 wildtype animals by FACS sorting. RNA was extracted using Quick RNA micro-kit (zymo).
Libraries were prepared using using QIAseq FX Single Cell RNA Library Kit (Qiagen).

tag: developmental stage

value: embryonic day 17.5

value: Merkel cells

value: Wildtype


title: E17Merkel_WT_RNAseq_rep2

tag: genotype


title: Control_111089

description:
Control
RB_N5


title: E17Merkel_Pou4f3KO_RNAseq_rep2

extract_protocol:
Merkel cells (Atoh1-GFP+) were purified from the skin of E17 Pou4f3 mutant animals by FACS sorting. RNA was extracted using Quick RNA micro-kit (zymo).
Libraries were prepared using using QIAseq FX Single Cell RNA Library Kit (Qiagen).

value: Pou4f3 KO


title: Low altitude basal  PBMC Sahiwal_3


title: Low altitude basal  PBMC Sahiwal_2


title: Low altitude basal  PBMC Sahiwal_1


title: Low altitude basal  PBMC Sahiwal_4


title: Control_100630

description:
Control
RB_N7


title: OS17_culture_Rep2

source_name: Cell line - human

value: osteosarcoma

tag: strain

tag: condition

value: cell culture (In vitro)


title: miRNA DU145-LIN28A overexpressing-wildtype-rep1

description:
not targeted using CRISPR
miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv
a1

source_name: DU145 prostate cancer cell line

value: LIN28A+; TUT4+; TUT7+

tag: type

value: parental

tag: passage number


title: High altitude PBMC  Ladakhi_3

description: Gene expression of high altitude adapted Ladakhi PBMCS


title: RNA DU145-LIN28A overexpressing-wildtype-rep1

description: not targeted using CRISPR

tag: disease


title: High altitude PBMC_ Ladakhi_5


title: High altitude PBMC Ladakhi_4


title: 2-cell embryos with Trim21 mRNA rep2


title: non-manipulated 2-cell embryos rep2


title: High altitude PBMC Ladakhi_2


title: non-manipulated 2-cell embryos rep1


title: 143B_culture


title: Control_400

description:
Control
RB_N4

tag: tissue

value: liver


title: E17Merkel_Pou4f3KO_RNAseq_rep1

tag: cell type


title: E17HC_WT_RNAseq_rep1

source_name: Cochlea

extract_protocol:
Hair cells (Atoh1-GFP+) were purified from wildtype mutant cochlea  by FACS sorting. RNA was extracted using Quick RNA micro-kit (Zymo).
Libraries were prepared using using QIAseq FX Single Cell RNA Library Kit (Qiagen).

value: hair cells

value: WT


title: E17HC_WT_RNAseq_rep2


title: Control_399

description:
Control
RB_N3

value: Normal


title: OS17_culture_Rep1

extract_protocol:
Tumor harvested from mice were processed using the human tumor dissociation kit (Miltenyi Biotec, 130-095-929) with a GentleMacs Octo Dissociator with Heaters (Miltenyi Biotec, 130-096-427). Single cell suspensions in 0.04% BSA-PBS of cell lines, and dissociated tumor tissues were generated and run on Chromium Single Cell 3′RNA-sequencing system (10x Genomics) with the Reagent Kit v3 according to the manufacturer's instructions.
Libraries were constructed according to Chromium Single Cell 3′RNA-sequencing system (10x Genomics) with the Reagent Kit v3 according to the manufacturer's instructions. Briefly, cells were loaded into Chromium Single Cell Chip v3 (10x Genomics) with a targeted cell recovery of 5,000 cells per sample. After performing cDNA purification, amplification, and library construction (sample index PCR 14 cycles) as instructed, we sequenced sample libraries on a half lane of HS4000 (Illumina) to yield (after QA) about 65,000 paired-end reads per cell.


title: E17HC_Pou4f3KO_RNAseq_rep2

extract_protocol:
Hair cells (Atoh1-GFP+) were purified from E17 Pou4f3 mutant cochlea  by FACS sorting. RNA was extracted using Quick RNA micro-kit (Zymo).
Libraries were prepared using using QIAseq FX Single Cell RNA Library Kit (Qiagen).


title: E17HC_Pou4f3KO_RNAseq_rep1


title: Control_396

description:
Control
RB_N2


title: P1SC_permissive_48h_RNAseq_3

data_processing:
For RNAseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using STAR. Reads were quantified against genes using RSEM, and differential gene expression analysis was conducted using DESeq2.
For ATACseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using bowtie2. PCR-duplicates were removed by Sambamba, and then peaks were called by MACS2 from individual replicate using filter p value < 0.01.
For Cut&Run, reads were trimmed based on quality score and then aligned to referene mouse genome (mm10) using STAR. PCR duplicates were removed based on UMI by umi_tools,  and then peaks were called by MACS2 for individual replicate using filter p value < 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts for RNAseq in text files, peak regions for ATACseq and H3K27ac CutnRun in narrowPeak files.

growth_protocol: P1 cochleae were cultured on SPI black filter membrane (SPI Supplies) in L15 Leibovitz media (Hyclone) supplemented with N2 (Invitrogen, 1:100), B27 (Gibco, 1:50), Penicillin G (Sigma, 100U/ml), EGF(Shenandoah Biotechnology, 5ng/ml), FGF (Shenandoah Biotechnology,2.5ng/ml) and HEPES (Invitrogen, 10mM).

extract_protocol:
Cultured organs were diggested were digested with Trypsin (Invitrogen, 0.125%) at 37°C for 8 minutes, and then dissociated by trituation with P200 pipettes. Lfng-CreER/TdT and Atoh1-GFP double positive supporting cells were FACS purified into 300μL RNA lysis buffer (Zymo), and RNA was extracted with Quick-RNA Micro-prep kit (Zymo).
Libraries were prepared using QIAseq FX Single Cell RNA Library Kit (Qiagen).

treatment_protocol: Cultured cochlear organs were treated with 10μ DAPT or equivalent amount of DMSO (VWR) for 24 hours or 48 hours

value: postnatal day 1

tag: treatment

value: DAPT

tag: timepoint

tag: marker

value: Lfng-CreET/TdT, Atoh1-GFP

value: supporting cells


title: P1SC_permissive_48h_RNAseq_2


title: P1SC_nonpermissive_48h_RNAseq_3

extract_protocol:
Cultured organs were diggested were digested with Trypsin (Invitrogen, 0.125%) at 37°C for 8 minutes, and then dissociated by trituation with P200 pipettes. Lfng-CreER/TdT+ supporting cells were FACS purified into 300μL RNA lysis buffer (Zymo), and RNA was extracted with Quick-RNA Micro-prep kit (Zymo).
Libraries were prepared using QIAseq FX Single Cell RNA Library Kit (Qiagen).

value: Lfng-CreET/TdT


title: Control_091119

description:
Control
RB_N12

tag: disease state


title: Control_111330

description:
Control
RB_N11


title: P1SC_permissive_48h_RNAseq_1


title: High altitude PBMC Ladakhi_1

value: PBMCs

tag: gender

value: Female


title: P1SC_nonpermissive_48h_RNAseq_2


title: Control_111484

description:
Control
RB_N10


title: RNA-Seq of  HEPG2 treated with DECANOYL-L-CARNITINE at 100uM concentration H_26_02

first: Brunilda

last: Balliu

address: 621 Charles Young Drive South

department: Computational Medicine

institute: UCLA

data_processing:
Reference genome (hg19) and gene model annotation files were downloaded from the UCSC genome browser website directly.
Indexes of the reference genome were built using STAR3 and paired-end clean reads were aligned to the reference genome using STAR (v2.6.0; with default option mismatch = 10).
Bam files were filtered for uniquely mapped reads, sorted, and indexed using SAMtools4 (v1.4.1).
HTSeq5 (v0.11.0) was used to count the read numbers mapped to each gene (with option -m union).
Genome_build: hg19

source_name: liver

growth_protocol: HepG2, terminally differentiated SGBS, and HCML-7304 cells were starved for 6 hours in EMEA with no FBS (HepG2), DMEM/F12 supplemented with pan/bio and penicillin/streptomycin but no FBS (SGBS adipocytes) or HCML growth medium (PromoCell) without supplements. For the glucose condition DMEM no glucose medium (Thermo) was used.

extract_protocol: none provided by the submitter

treatment_protocol: After starvation and washing with PBS, the cells were exposed for 2 hours to the different compounds or the respective control media.

value: hepatocyte

tag: cell line

value: DECANOYL-L-CARNITINE


title: RNA-Seq of  HEPG2 treated with DECANOYL-L-CARNITINE at 100uM concentration H_26_01


title: RNA-Seq of  HEPG2 CONTROL  H_25_03

description: RNA-Seq of  HEPG2 CONTROL

value: CONTROL (EMPTY EMEM MEDIUM) 4


title: P1SC_control_48h_RNAseq_2

value: DMSO


title: RNA-Seq of  HEPG2 treated with DECANOYL-L-CARNITINE at 100uM concentration H_26_03


title: P1SC_control_48h_RNAseq_1


title: RNA-Seq of  HEPG2 CONTROL  H_25_02

description: RNA-Seq of  HEPG2 CONTROL


title: Control_389

description:
Control
RB_N1


title: RNA-Seq of  HEPG2 CONTROL  H_25_01

description: RNA-Seq of  HEPG2 CONTROL


title: P1SC_TSA_48h_RNAseq_2

data_processing:
Reads were trimmed based on quality score, and then aligned to reference mouse genome (mm10) using STAR aligner.
Aligned reads were counted against genes using RSEM package.
Read counts for genes were used for differential gene expression analysis by DESeq2 package. Only protein coding genes were analyzed.
Genome_build: mm10
Supplementary_files_format_and_content: Read counts for genes delimited by tab in text file

extract_protocol:
Cultured organs were diggested were digested with Trypsin (Invitrogen, 0.125%) at 37°C for 8 minutes, and then dissociated by trituation with P200 pipettes. GFP positive supporting cells were FACS purified into 300μL RNA lysis buffer (Zymo), and RNA was extracted with Quick-RNA Micro-prep kit (Zymo).
Libraries were prepared using QIAseq FX Single Cell RNA Library Kit (Qiagen).

treatment_protocol: Cultured cochlear organs were treated with 200nM TSA (Sigma), 10μM GSK-343 (GSK) or equivalent amount of DMSO (VWR) for 48 hours

value: TSA


title: P1SC_TSA_48h_RNAseq_1


title: Cirrhosis without AH_420

description:
Cirrhosis
RB_EC6

value: Alcohol-related Cirrhosis


title: P1SC_GSK343_48h_RNAseq_3


title: RNA-Seq of  HEPG2 treated with RETINOIC ACID at 1uM concentration H_24_03

value: liver

value: RETINOIC ACID


title: Cirrhosis without AH_419

description:
Cirrhosis
RB_EC5


title: P1SC_GSK343_48h_RNAseq_2


title: RNA-Seq of  HEPG2 treated with RETINOIC ACID at 1uM concentration H_24_02


title: P1SC_GSK343_48h_RNAseq_1


title: Cirrhosis without AH_398

description:
Cirrhosis
RB_EC3


title: RNA-Seq of  HEPG2 treated with RETINOIC ACID at 1uM concentration H_24_01


title: P1SC_DMSO_48h_RNAseq_2


title: leg skin 3

city: Vienna

first: Julia

last: Lachner

address: Waehringer Guertel 18-20

country: Austria

institute: Medical University of Vienna

data_processing:
Initial analysis was performed using the 10xGenomics software cellranger version 3.0.2
In the beginning the raw feature barcode matrix of each leg sample was used and distinguished between background noise and droplets containing cells using empty Drops. Briefly, this method (Lun et al. 2019) models ambient RNA background in the data set and tests for deviations from the background RNA. A false discovery rate of 0.05 and a threshold of 15% of mitochondrial RNA content was used to call cells to be included into further analysis. On the other end of the spectrum, the scran package to remove droplets containing more than one cell was used (Lun et al. 2016). The applied approach simulates thousands of doublets by adding together two randomly chosen single cell profiles. For the doublet score calculation cell clustering including the set randomly generated doublets is performed. Then for each cell of the original dataset the number of simulated doublets in their neighborhood is recoded and used as input for score calculation. 200 nearest neighbors for each cell were used and a threshold of doublet score > 4 to identify doublets in each dataset separately applied. Doublet score was log10 of the ratio between simulated doublet cells and total number of neighbors taken into consideration for each cell. Following the “R” based package Seurat Version 3 from Satija Lab was used (Butler et al. 2018; Stuart et al. 2019), a Seurat object created and a SCTransform performed, within the regression of mitochondrial RNA and cell-cycle depended RNA. For further procedure 15 principal components were used and a clustering based on the Louvain algorithm at a resolution of 0.2.
Subsequent to individual quality control of each leg samples raw read counts of across datasets were combined to one count matrix. Pearson residuals derived from a generalized negative binomial model of UMI counts were used as input for principal component analysis and differential gene expression analysis. This approach is implemented in R package Seurat as SCTransform (Hafemeister and Satija 2019). Apart from cellular sequencing depth, which is added by default to the regression model, it was also adjusted for mitochondrial RNA content, batch, and cell cycle score. Calculation of cell cycle scores was performed as implemented in Seurat package where gene expression of cell cycle marker genes are combined to score. The score consisted of 43 genes primarily expressed in G1/S and 55 primarily expressed in G2/M (Triosh et al. 2016). Batch correction between individual datasets was done as part of the Principal Component Analysis using Harmony algorithm (Korsunsky et al. 2019). Harmony starts off with user supplied information about batch then uses fuzzy clustering to assign each cell to multiple clusters in a way that batch diversity in each cluster was maximized. To get a correction factor for each cell, global and batch specific centroids were calculated for each cluster. Data were corrected for batch and the procedure was repeated until convergence of global and batch specific centroids (Korsunsky et al. 2019).
Genome_build: ggal5, ensembl 91 annotations plus custom annotations described in this paper
Supplementary_files_format_and_content: Tab-separated plain text file and matrix data file

organism: Gallus gallus

source_name: leg skin 3

extract_protocol:
One day old chicks (strain Lohmann) were obtained from Schropper GmbH, Gloggnitz, Austria. Skin was excised from the leg of sacrificed animals and incubated in thermolysin (0.5 mg/ml) (Sigma-Aldrich) at 37°C for 45 minutes. The lower dermis was removed using forceps and the remaining tissue, including the epidermis and parts of the upper dermis, was processed further according to protocols established for human skin (Vorstandlechner et al. 2020; Kalinina et al. 2020). For the isolation of cells, the tissue was split into two fractions that were incubated either in buffer-enzyme mix of the Whole Skin Dissociation Kit human (MACS Milteny Biotech) for 2.5 h at 37°C or with 0.05% trypsin/EDTA (Thermo Fisher Scientific) and DNase 1 (10 µg/ml) (Roche Diagnostics) at 37°C for 15 minutes. Afterwards the samples were combined and processed according to the manufacturer’s protocol (Whole Skin Dissociation Kit human, MACS Milteny Biotech). In brief, the epidermis-enzyme mix was diluted in 0.5 ml medium and dissociated with the gentleMACS Dissociator. The ground tissue was filtered through 100-micron (Falcon) and 40-micron (Falcon) meshes. Subsequently, cells were stained with DAPI and viable cells were purified by fluorescence-activated cell sorting at the Core Facility Flow Cytometry, Medical University of Vienna. Sequencing libraries of viable cells were prepared using Cell Ranger (10x Genomics) version 3.0.2 at the Center for Molecular Medicine, Vienna, Austria.
10x Genomics Chromium Single Cell 3' Reagent Kit v2

value: skin

value: Lohmann

tag: age

value: 1 day old


title: RNA-Seq of  HEPG2 treated with WORTMANIN at 100nM concentration H_23_03

value: WORTMANIN


title: leg skin 2

source_name: leg skin 2


title: P1SC_nonpermissive_48h_RNAseq_1

value: postnatal day 1

value: DAPT


title: Cirrhosis without AH_394

description:
Cirrhosis
RB_EC2


title: Treat_3

city: Shanghai

first: Jinchao

last: Jia

address: No. 197 Ruijin Second Road

institute: New Markers for Adult-Onset Still's Disease

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12)
Differentially expressed genes (DEGs) with a fold change >2 and p value< 0.05 were determined using DEGseq analysis package
Genome_build: Genome Reference Consortium Human Build 38 patch release 12 (GRCh38.p12)
Supplementary_files_format_and_content: text files include read count values for each Sample

source_name: bone marrow-derived neutrophils

growth_protocol: freshly isolated

extract_protocol:
Mouse BMDNs were isolated by density gradient centrifugation using Histopaque 1119 (Sigma-Aldrich) and Histopaque 1077 (Sigma-Aldrich)
Oligo(dT)-attached magnetic beads-purified mRNA was fragmented into pieces at appropriate temperature. cDNA was generated by random hexamer-primed reverse transcription. Afterwards, RNA Index Adapters and A-Tailing Mix were added to end repair. The cDNA fragments were amplified by polymerase chain reaction (PCR), and products were purified using Ampure XP Beads. The products were qualified on Agilent Technologies 2100 bioanalyzer. The double-strand PCR products were denatured and circularized by the splint oligo sequence to construct the final library. Then the single-strand circle DNA was formatted as the final library. The final library was amplified by phi29 to produce DNA nanoball (DNB) with more than 300 copies of one molecule. DNBs were loaded into patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: Neutrophils

value: ferritin


title: Cirrhosis without AH_392

description:
Cirrhosis
RB_EC1


title: P1SC_DMSO_48h_RNAseq_1

value: supporting cells


title: RNA-Seq of  HEPG2 treated with WORTMANIN at 100nM concentration H_23_01

value: hepatocyte


title: Severe AH_AH2

description:
AH
RB_AH9

value: Alcoholic Hepatitis


title: Treat_1


title: Treat_2


title: PBS_3

value: PBS


title: PBS_2


title: RNA-Seq of  HEPG2 treated with U0126 at 5uM concentration H_22_03


title: RNA-Seq of  HEPG2 treated with U0126 at 5uM concentration H_22_02


title: Cirrhosis without AH_418

description:
Cirrhosis
RB_EC4


title: RNA-Seq of  HEPG2 treated with U0126 at 5uM concentration H_22_01


title: Severe AH_AH1

description:
AH
RB_AH8


title: IL4c injection Rα knockout mouse sample 12

city: Riverside

first: Meera

middle: G

last: Nair

address: 3401 Watkins Drive

department: Division of Biomedical Sciences

institute: University of California Riverside

description:
6-8 week old Female RαΤd/Td mouse, IL4c i.p day 0 and 2
IL4c RαTd/Td_12

hyb_protocol: Hybridization was performed according to manufacturer's instructions.

scan_protocol: Scanning and image acquisition using the nanoString Digital Analyzer.

data_processing: nanoString data were analyzed in the Advanced Analysis Nanostring software. Raw counts were normalized using NanoStringNorm (using the positive control, negative control, and Eef1g, Gusb, Oaz1 and Rpl19 housekeeping probes), n>30 counts were included for analysis.

source_name: IL4c treated peritoneal macropgage

label_protocol: Labeling was performed according to manufacturer's instructions.

extract_protocol: Cells was lysed by RLT buffer and keep in -80'C.

treatment_protocol: PBS or IL4c  i.p at day 0 and day 2. Macrophage was sorted at day 4.

value: RalphaTd/Td (KO)

tag: Sex

value: Female

value: 6-8 week


title: IL4c injection Rα knockout mouse sample 10

description:
6-8 week old Female RαΤd/Td mouse, IL4c i.p day 0 and 2
IL4c RαTd/Td_10


title: Severe AH_414

description:
AH
RB_AH6

value: liver


title: Severe AH_415

description:
AH
RB_AH7


title: IL4c injection Rα knockout mouse sample 11

description:
6-8 week old Female RαΤd/Td mouse, IL4c i.p day 0 and 2
IL4c RαTd/Td_11


title: PBS_1


title: IL4c injection Rα knockout mouse sample 09

description:
6-8 week old Female RαΤd/Td mouse, IL4c i.p day 0 and 2
IL4c RαTd/Td_09


title: RNA-Seq of  HEPG2 treated with SP600125 at 5uM concentration H_21_03


title: leg skin 1

source_name: leg skin 1


title: Severe AH_413

description:
AH
RB_AH5


title: IL4c injection wild-type mouse sample 07

description:
6-8 week old Female C57BI/6 mouse, IL4c i.p day 0 and 2
IL4c Rα+/+_07

value: Ralpha+/+(Wt)


title: Igf2 KO EB day6 RNA-seq-2

city: Hong Kong

first: Wuming

last: Wang

address: Sha Tin

institute: The Chinese University of Hong Kong

data_processing:
The raw reads were cleaned using internal software SOAPnuke (Version v1.5.2, Website: https://github.com/BGI-flexlab/SOAPnuke) by removing adapter sequences, reads in which unknown bases are more than 10%, and low quality reads.
The clean reads were stored in FASTAQ format.
We used HISAT (Version v2.0.4, Website: http://www.ccb.jhu.edu/software/hisat) to do the mapping step, and calculated gene expression with a software package called RSEM (Version v1.2.12, Website: http://deweylab.biostat.wisc.edu/ RSEM).
FPKM method was used in calculated expression level, and the calculated gene expression can be directly used for comparing the difference of gene expression among sample.
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: embryoid bodies

growth_protocol: Mouse ESCs were cultured in DMEM/F12 containing GlutaMAX and sodium pyruvate (Life Technologies, 10565) with 15% fetal bovine serum (Hyclone, SH30071), nonessential amino acid solution (Life Technologies, 11140), b-mercaptoethanol (Life Technologies, 31350) with 1000 units/ml LIF (Millipore, ESG1106), 1  mM PD0325901 (Sigma, PZ0162), and 2.5 mM CHIR99021 (Sigma, SML1046). The mouse ESCs were grown on gelatin-coated plates and the medium was replaced every other day. The ESC cultures were passaged every 2 days.

extract_protocol:
ESCs and embryoid bodies were collected at different time points, and RNA was harvested using Trizol reagent. The quality of the isolated RNA was determined with Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit). The RNA was converted into a template molecules library for sequencing on the BGISEQ-500.
Briefly, total RNA samples were ribo-depleted and then fragmented. The fragmented samples were reversed transcribed to cDNA, end-repaired and 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. The ligation products were purified, and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer. Denature the PCR products by heat, and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: The Igf2-/- ESCs were generated by the CRISPR-Cas9 system. ESCs were cultured in 6-well plates and transfected with donor plasmid and constructs containing Cas9 and target sequences using lipofectamine 3000, and these were then subjected to cell sorting of GFP-positive cells after transfection for 48 h. The enriched gene-modified cell populations were cultured in 60-mm dishes for 4-5 days, and each cell clone was passaged into 24-well plates. Finally, the Igf2-/- cell lines were identified by sequencing, and the cells were stored in liquid nitrogen.

value: ESC-derived embryoid bodies

tag: time

value: day 6

value: cell line


title: Igf2 KO EB day6 RNA-seq-3

tag: genotype


title: IL4c injection wild-type mouse sample 06

description:
6-8 week old Female C57BI/6 mouse, IL4c i.p day 0 and 2
IL4c Rα+/+_06

tag: strain


title: Severe AH_412

description:
AH
RB_AH4


title: Severe AH_410

description:
AH
RB_AH3


title: RNA-Seq of  HEPG2 treated with SP600125 at 5uM concentration H_21_01


title: Igf2 KO EB day6 RNA-seq-1


title: WT EB day6 RNA-seq-3

value: wild type


title: IL4c injection wild-type mouse sample 05

description:
6-8 week old Female C57BI/6 mouse, IL4c i.p day 0 and 2
IL4c Rα+/+_05


title: RNA-Seq of  HEPG2 treated with SB203580 at 5uM concentration H_20_03


title: PBS injection Rα knockout mouse sample 04

description:
6-8 week old Female RαΤd/Td mouse, PBS i.p day 0 and 2
PBS RαΤd/Td_04

source_name: PBS treated peritoneal macrophage


title: Severe AH_409

description:
AH
RB_AH2


title: WT EB day6 RNA-seq-2


title: RNA-Seq of  HEPG2 treated with SB203580 at 5uM concentration H_20_02


title: Severe AH_AH3

description:
AH
RB_AH10


title: Severe AH_406

description:
AH
RB_AH1


title: PBS injection Rα knockout mouse sample 03

description:
6-8 week old Female RαΤd/Td mouse, PBS i.p day 0 and 2
PBS RαΤd/Td_03


title: sRNA_HepG2

first: Daehyun

last: Baek

address: Rm 402, Bldg 504, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul

department: School of Biological Sciences

institute: Seoul National University

description:
Small RNA
sRNA-seq in HepG2

data_processing:
1. Base-calling by RTA(Real Time Analaysis) software within HiSeq 2500 (mRNA-Seq) or HiSeq 2000 (sRNA-Seq)
2. Quality trimming by the highest scoring path algorithm (hsptrim-1.2.6)
3. Adapter trimming by cutadapt-1.2.1
4. Remove tRNA, rRNA-derived reads by Bowtie2 alignment
5. Remove sequencing artifacts by fastx_artifacts_filter of fastx_toolkit
6. Alignment of filtered reads to human reference genome by Tophat2 (mRNA-Seq) or Bowtie2 (sRNA-Seq)
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Tab-delimited text file (*.quants.txt) contains expression levels for individual genes. Columns: (1) id: Gene identifier (e.g. NM_000000), (2) symbol: Gene symbol (e.g. GAPDH), (3) readcount: Number of mapped reads, (4) exlev: Expression level (RPM or RPKM), (5) expct: Expression percentile rank
Supplementary_files_format_and_content: BED file (*.dmscount.{plus,minus}.txt) contains RT truncation counts by DMS treatment in single nucleotide resolution

source_name: liver hepatocellular carcinoma

extract_protocol:
For sRNA-seq, total microRNA was extracted with PureLink™ miRNA Isolation Kit (Invitrogen) according to the manufacturer’s protocols
sRNA-seq
Both of the library preparations (mRNA-Seq and sRNA-Seq) were done based on the Illumina Truseq small RNA library preparation protocol (TruSeq Small RNA Library Prep Guide, Part # 15004197 Rev. G). DMS-seq libraries were prepared using adaptors from a previous study (PMID: 30605524) following procedures from Rouskin et al., 2014 (PMID: 24336214).
mRNA-seq, sRNA-seq, DMS-seq


title: RNA-Seq of  HEPG2 treated with LEPTIN at 100ng/ml concentration H_19_03

value: LEPTIN


title: WT EB day6 RNA-seq-1


title: Igf2 KO EB day4 RNA-seq-3

value: day 4


title: PBS injection wild-type mouse sample 02

description:
6-8 week old Female C57BI/6 mouse, PBS i.p day 0 and 2
PBS Rα+/+_02

value: Ralpha+/+ (Wt)


title: RNA-Seq of  HEPG2 treated with LEPTIN at 100ng/ml concentration H_19_02


title: sRNA_HCT116

description:
Small RNA
sRNA-seq in HCT116

source_name: human colorectal carcinoma


title: RNA-Seq of  HEPG2 treated with SP600125 at 5uM concentration H_21_02


title: Igf2 KO EB day4 RNA-seq-2


title: RNA-Seq of  HEPG2 treated with LEPTIN at 100ng/ml concentration H_19_01


title: sRNA_HeLa

description:
Small RNA
sRNA-seq in HeLa

source_name: human cervical carcinoma

value: HeLa


title: Igf2 KO EB day4 RNA-seq-1


title: sRNA_HEK293T

description:
Small RNA
sRNA-seq in HEK293T

source_name: human embryonic kidney


title: WT EB day4 RNA-seq-3


title: RNA-Seq of  HEPG2 treated with ADIPONECTIN at 1nM concentration H_18_02

value: ADIPONECTIN


title: RNA-Seq of  HEPG2 treated with ADIPONECTIN at 1nM concentration H_18_03

value: hepatocyte


title: RNA-Seq of  HEPG2 treated with SB203580 at 5uM concentration H_20_01


title: RNA-Seq of  HEPG2 treated with ADIPONECTIN at 1nM concentration H_18_01


title: WT EB day4 RNA-seq-2


title: RBE cells, HDM201+GSK2830371_24H

city: Taoyuan

first: Chiao-Ping

last: Chen

address: No.259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The raw output file of each individual library was > 3GB. The sequence of each read was trimmed based on the quality score (Q30), and read lengths less than 45 bp were discarded prior to further analysis.
The differentially expressed genes were selected for more than 2-fold changes and p-values for differences in ex-pression of less than 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include fold change (log2) and p-values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Cell lysate

growth_protocol: RBE and SK-Hep-1 were authenticated and cultured in RPMI medium 1640 (Gibco) and DMEM (Gibco) containing 10% FBS, respectively.

extract_protocol:
Total RNA 200ng from each cell line sample was prepared for sequencing using Illumina TruSeq Stranded mRNA Sample Preparation Kit.
Fifteen-cycle-PCR was performed, and the libraries were quantified using the LC480 qPCR system (Roche). Then, all libraries were pooled into a new 1.5 ml tube as a 10 nM pooled DNA library. The final pool was used for sequencing (illumina NextSeq sequencer, 2×150bp).

treatment_protocol: HDM201 and/or GSK2830371 were initially dissolved in DMSO and used to dose cells at a final concentration of 0.5% DMSO for 6 or 24 hours.

value: RBE

value: cholangiocarcinoma cell

value: 24 hours


title: control_diet_rep10

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from liver of mice treated with control diet for 22 weeks, biological replicate 10

hyb_protocol: According to the Thermo Fisher Scientific expression protocol (HWS kit)

scan_protocol: According to the Thermo Fisher Scientific expression protocol, Scanner 3000 7G

data_processing: SST-RMA gene-level probeset summary with standard settings of the Thermo Fisher Scientific Expression Console software (v.1.4.1.46). The provided SST-RMA data was obtained by including samples from an additional dataset (GSE137924)

source_name: liver_control chow

label_protocol: Total RNA (150 ng) was amplified using the WT PLUS Reagent Kit (Thermo Fisher Scientific Inc., Waltham, USA).

growth_protocol: All experiments were performed in adult male C57BL/6J mice purchased from Janvier Labs (Saint-Berthevin, Cedex, France). Mice were maintained on a 12-h light-dark cycle with free access to water and standard chow diet (Altromin, #1314) or 58% high fat diet (HFD) (Research Diets, D12331).

extract_protocol: Total RNA was isolated from liver tissue employing a commercially available kit (NucleoSpin RNA, #740955, Macherey-Nagel, Düren, Germany)

treatment_protocol: To promote diet-induced obesity (DIO), mice were ad-libitum fed with 58% high-fat diet (HFD) (Research Diets, D12331) for 22 weeks. Control mice were kept with normal chow. Mice were fasted for 4 hours and then sacrificed by cervical dislocation for organ withdrawal. Livers were removed immediately, flash frozen in liquid nitrogen and stored at -80°C until further analysis.

tag: genotype/variation

value: male

value: 30 weeks

tag: diet

value: control chow


title: control_diet_rep9

description: Gene expression data from liver of mice treated with control diet for 22 weeks, biological replicate 9

value: liver


title: RBE cells, HDM201+GSK2830371_6H

value: 6 hours


title: RBE cells, HDM201_24H

value: HDM201 (MDM2i)


title: RNA-Seq of  HEPG2 CONTROL  H_17_03

description: RNA-Seq of  HEPG2 CONTROL

value: CONTROL (EMPTY EMEM MEDIUM) 3


title: RNA-Seq of  HEPG2 CONTROL  H_17_025

description: RNA-Seq of  HEPG2 CONTROL


title: WT EB day4 RNA-seq-1

value: ESC-derived embryoid bodies

tag: type

value: cell line

value: wild type


title: Igf2 KO EB day3 RNA-seq-2

value: day 3


title: PBS injection wild-type mouse sample 01

description:
6-8 week old Female C57BI/6 mouse, PBS i.p day 0 and 2
PBS Rα+/+_01

value: PBS

value: Ralpha+/+ (Wt)

value: Female

value: 6-8 week


title: RBE cells, HDM201_6H

value: RBE

value: cholangiocarcinoma cell


title: Igf2 KO EB day3 RNA-seq-3


title: control_diet_rep7

description: Gene expression data from liver of mice treated with control diet for 22 weeks, biological replicate 7

value: male


title: RNA-Seq of  HEPG2 CONTROL  H_17_024

description: RNA-Seq of  HEPG2 CONTROL

value: hepatocyte


title: control_diet_rep6

description: Gene expression data from liver of mice treated with control diet for 22 weeks, biological replicate 6

value: 30 weeks

value: control chow


title: Igf2 KO EB day3 RNA-seq-1


title: RBE cells, DMSO 24H

value: DMSO

value: 24 hours


title: RNA-Seq of  HEPG2 CONTROL  H_17_023

description: RNA-Seq of  HEPG2 CONTROL

value: liver

value: CONTROL (EMPTY EMEM MEDIUM) 3


title: WT EB day3 RNA-seq-3

value: ESC-derived embryoid bodies

value: cell line


title: RNA-Seq of  HEPG2 CONTROL  H_17_022

description: RNA-Seq of  HEPG2 CONTROL


title: RNA-Seq of  HEPG2 CONTROL  H_17_021

description: RNA-Seq of  HEPG2 CONTROL


title: control_diet_rep4

description: Gene expression data from liver of mice treated with control diet for 22 weeks, biological replicate 4

value: wild type


title: control_diet_rep3

description: Gene expression data from liver of mice treated with control diet for 22 weeks, biological replicate 3


title: control_diet_rep8

description: Gene expression data from liver of mice treated with control diet for 22 weeks, biological replicate 8


title: control_diet_rep5

description: Gene expression data from liver of mice treated with control diet for 22 weeks, biological replicate 5


title: RNA-Seq of  HEPG2 CONTROL  H_17_02

description: RNA-Seq of  HEPG2 CONTROL


title: control_diet_rep2

description: Gene expression data from liver of mice treated with control diet for 22 weeks, biological replicate 2


title: Igf2 KO ESC RNA-seq-3

source_name: embryonic stem cells

value: embryonic stem cells


title: KO_Rep2

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

data_processing:
Reads were aligned to human transcriptome (GENCODE v26) using Salmon and to human genome (hg38) using HISAT2. Gene expression levels were quantified with Salmon using  transcriptome alignments.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file of normalized read counts per gene/samples.

source_name: Breast cancer cell line

growth_protocol: MCF12A cells were cultivated in a special medium containing DMEM/F12 (Thermo Fisher Scientific, USA), 5% heat inactivated horse serum (Gibco, USA), 20 ng/mL recombinant human EGF (AF100-15 Peprotech, USA), 0.5 µg/mL hydrocortisone, 100 ng/mL cholera toxin (Vibrio cholerae C8052, Sigma, USA), 10 µg/mL human recombinant insulin (Zinc solution 12585-014, Gibco, USA), and 1% penicillin/streptomycin and incubated at 37 °C with 5% humified CO2.

extract_protocol:
Total RNA was extracted by using TRIzol reagent (Invitrogen), according to manufacturer’s protocol.
Quantity and quality of the starting RNA were checked by Qubit and Bioanalyzer (Agilent). 1 μg of total RNA was subjected to poly(A) selection, and libraries were prepared using the TruSeq RNA Sample Prep Kit (Illumina) following the manufacturer’s instructions. Libraries were sequenced on Illumina NextSeq 500 System (single-end 75 bp reads).

value: C1orf132 KO


title: KO_Rep1


title: RNA-Seq of  HEPG2 treated with ATORVASTATIN at 1uM concentration H_16_03

value: ATORVASTATIN


title: WT EB day3 RNA-seq-1

value: day 3


title: WT_Rep2

value: Wild type (WT)


title: RNA-Seq of  HEPG2 CONTROL  H_17_01

description: RNA-Seq of  HEPG2 CONTROL


title: Igf2 KO ESC RNA-seq-2


title: Igf2 KO ESC RNA-seq-1


title: WT ESC RNA-seq-3


title: RNA-Seq of  HEPG2 treated with ATORVASTATIN at 1uM concentration H_16_02


title: WT EB day3 RNA-seq-2


title: WT_Rep1


title: IgG ChIP-seq rep2

city: Lausanne

first: Guido

last: van Mierlo

address: Route Cantonale

country: Switzerland

institute: EPFL

description: ISB_4_Elution_GFP-V5-FLYWCH1_anti-IgG_repl2_Z14_S1

data_processing:
Biotin chip reads were mapped against the hg38 genome build using bwa with parameters mem -t 32, duplicate reads were identified and filtered using picard tools (versions 1.129 or higher) and peaks were called using macs2
Flywch1 and IgG ChIP-seq were processed using the seq2science pipeline (https://github.com/vanheeringen-lab/seq2science). Parameters were fastp as trimmer, bwa-mem2 as alingers, minimal map quality of 30 and peak calling using macs2
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files

source_name: IgG ChIP-seq

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% FBS and pen/strep. Cells were routinely passaged every 3-4 days.

extract_protocol:
For biotin ChIP-seq, cells were crosslinked with 1% PFA, permeabilized and incubated with an a-H3K9me3 or a-IgG antibody, followed by binding of protA-Turbo, biotinylation for 10 minutes, lysis and IP with magnetic streptavidin beads. For flywch1 and IgG ChIP-seq, cells were crosslinked in 1% PFA and chromatin was sonicated to 300-800 bp fragments and IPs were performed with antibodies against V5 (present in the flywch1-V5-GFP fusion protein) or IgG.
Libraries were prepared using the KAPA HyperPrep Kit (Kapa Biosystems) according to the manufacturer’s instructions, which some minor modifications. There include 2 ng DNA as input material for the library preparation, 12 PCR cycles for the library amplification, and a 0.65x reverse phase size selection followed by a double 1.0x bead-based clean up after library amplification. Library concentrations were determined using the DeNovix dsDNA High Sensitivity Assay (DeNovix), and fragment distribution using a High Sensitivity DNA Chip on a Bioanalyzer 2100 system (Aligent Technologies).

value: HeLa

tag: chip antibody

value: Rabbit IgG (Millipore, #Cat:12-370)


title: IgG ChIP-seq rep1

description: ISB_3_Elution_GFP-V5-FLYWCH1_anti-IgG_repl1_Z13_S2


title: high_fat_diet_rep10

description: Gene expression data from liver of mice treated with high fat diet for 22 weeks, biological replicate 10

source_name: liver_high fat diet treatment for 22 weeks

value: male

value: high fat diet treatment for 22 weeks

tag: tissue


title: high_fat_diet_rep7

description: Gene expression data from liver of mice treated with high fat diet for 22 weeks, biological replicate 7

value: 30 weeks


title: high_fat_diet_rep8

description: Gene expression data from liver of mice treated with high fat diet for 22 weeks, biological replicate 8


title: control_diet_rep1

description: Gene expression data from liver of mice treated with control diet for 22 weeks, biological replicate 1

value: control chow


title: RNA-Seq of  HEPG2 treated with ATORVASTATIN at 1uM concentration H_16_01

source_name: liver

tag: cell type

value: hepatocyte


title: high_fat_diet_rep6

description: Gene expression data from liver of mice treated with high fat diet for 22 weeks, biological replicate 6

value: liver


title: WT ESC RNA-seq-2


title: WT ESC RNA-seq-1


title: RNA-Seq of  HEPG2 treated with METFORMIN at 1mM concentration H_15_03

tag: treatment

value: METFORMIN


title: Flywch1 ChIP-seq rep2

description: ISB_2_Elution_GFP-V5-FLYWCH1_anti-V5_repl2_Z12_S3

source_name: Flywch1 ChIP-seq

value: a-V5 (Invitrogen, #Cat:P/N46-0705)


title: RNA-Seq of  HEPG2 treated with METFORMIN at 1mM concentration H_15_02


title: Flywch1 ChIP-seq rep1

description: ISB_1_Elution_GFP-V5-FLYWCH1_anti-V5_repl1_Z11_S4


title: pA-Turbo targeted IgG biotin ChIP rep 2

source_name: pA-Turbo targeted IgG biotin ChIP

value: Wildtype

value: Targeting Ab:Rabbit IgG (Millipore, #Cat:12-370). ChIP with Dynabeads M280 Strepatividin 11205D


title: RNA-Seq of  HEPG2 treated with METFORMIN at 1mM concentration H_15_01


title: pA-Turbo targeted IgG biotin ChIP rep 1


title: high_fat_diet_rep9

description: Gene expression data from liver of mice treated with high fat diet for 22 weeks, biological replicate 9

value: wild type


title: pA-Turbo targeted H3K9me3 biotin ChIP rep 2

source_name: pA-Turbo targeted H3K9me3 biotin ChIP

value: Targeting Ab:a-H3K9me3 (Abcam, #Cat:ab8898). ChIP with Dynabeads M280 Strepatividin 11205D


title: RNA-Seq of  HEPG2 treated with TGF-B1 at 10ng/ml concentration H_14_02


title: high_fat_diet_rep4

description: Gene expression data from liver of mice treated with high fat diet for 22 weeks, biological replicate 4


title: NCC-IT-A3 DMSO_1

city: Tokushima

first: Takaaki

last: Tsunematsu

address: 3-18-15 Kuramoto

department: Oral Molecular Pathology

country: Japan

institute: Tokushima University

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads’ quality, total bases, total reads, GC (%) and basic statistics are calculated.
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner.
Transcript is assembled by StringTie with aligned reads.
Genome_build: hg19
Supplementary_files_format_and_content: Expression profiles are represented as read count and normalization value which is based on transcript length and depth of coverage. The FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) value or the RPKM (Reads Per Kilobase of transcript per Million mapped reads) is used as a normalization value.

growth_protocol: Cells were maintained by RPMI with 10%FBS

extract_protocol:
Culture supernatant were removed and cells were washed by PBS twice. Then, the total RNAs were extracted by using Rneasy mini kit (Qiagen, #74106). TruSeq Standard mRNA LT Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

treatment_protocol: DMSO or 100nM Barasertib for 4days

value: Embryonal carcinoma

value: DMSO


title: pA-Turbo targeted H3K9me3 biotin ChIP rep 1


title: NCC-IT-A3 DMSO_2


title: WT Cardiomyocyte (Sample_C1)

description:
Whole-Genome Bisulfite Seq
MGI2000- PE100
DMR_info.tar.gz

data_processing:
The raw data was filtered first to remove those low-quality data and get clean data.
The clean data was mapped to the reference genome when we made sure the data quantity of clean data was sufficient. Meanwhile, we needed to make a quality test about the alignment.
We used those mapped data to get methylation information of the cytosine through the whole genome after we made sure that the alignment result was qualified.
We used the cytosine information for standard bioinformatics analysis and personalized bioinformatics analysis.
Genome_build: NA
Supplementary_files_format_and_content: Count format and DMR format.

source_name: cardiomyocytes

growth_protocol: ESCs were cultured in ESC culture medium withdraw of 2iL (2i, PD0325901 and CHIR99021; L, LIF) to form EBs for 5 days. EBs were formed using the hanging drop method with 250 cells/drop in DMEM/F12 media containing GlutaMAX and sodium pyruvate with 15% fetal bovine serum, nonessential amino acid solution, and b-mercaptoethanol. Then EBs were collected and transferred to petri dishes with NM medium containing DMEM/F12 (Life Technologies, 10565), nonessential amino acid solution (Life Technologies, 11140), Heparin (Sigma, H3149), and N2 (Life Technologies, 17502). After 2 days suspension culture in NM medium, EBs could be collected and transferred to tissue culture plate with NM medium. At about 9 days, the beating cardiomyocytes will be generated and could be collected to perform the downstream experiments.

extract_protocol:
Genomic DNA from WT and Pten-/- embryoid bodies and cardiomyocytes were extracted by the genomic DNA extraction Kit.
The DNA was fragmented by sonication using a Bioruptor (Diagenode, Belgium) to a mean size of approximately 250 bp, followed by the blunt-ending, dA addition to 3'-end, finally, adaptor ligation (in this case of methylated adaptors to protect from bisulfite conversion), essentially according to the manufacturer’s instructions. Ligated DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (ZYMO). Different Insert size fragments were excised from the same lane of a 2% TAE agarose gel. Products were purified by using QIAquick Gel Extraction kit (Qiagen) and amplified by PCR. At last, Sequencing was performed using the DNBseq platforms.

treatment_protocol: The Pten-/- ESCs were generated by the CRISPR-Cas9 system. ESCs were cultured in 6-well plates and transfected with donor plasmid and constructs containing Cas9 and target sequences using lipofectamine 3000, and these were then subjected to cell sorting of GFP-positive cells after transfection for 48 h. The enriched gene-modified cell populations were cultured in 60-mm dishes for 4-5 days, and each cell clone was passaged into 24-well plates. Finally, the Pten-/- cell lines were identified by sequencing, and the cells were stored in liquid nitrogen.

value: ES-derived cardiomyocytes

value: cell line


title: high_fat_diet_rep3

description: Gene expression data from liver of mice treated with high fat diet for 22 weeks, biological replicate 3


title: Pten KO Cardiomyocyte (Sample_K1)

value: Pten-/-


title: Pten KO EB (Sample_K2)

source_name: embryoid bodies

value: ES-derived embryoid bodies


title: high_fat_diet_rep1

description: Gene expression data from liver of mice treated with high fat diet for 22 weeks, biological replicate 1

value: male

value: high fat diet treatment for 22 weeks


title: WT EB (Sample_C2)


title: NCC-IT-A3 Barasetib_2

value: Barasertib


title: NCC-IT-A3 Barasetib_1


title: Pten KO Cardiomyocyte RNA-seq-3

extract_protocol:
Cardiomyocytes were collected, and RNA was harvested using Trizol reagent. The quality of the isolated RNA was determined with Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit). The RNA was converted into a template molecules library for sequencing on the BGISEQ-500.
For RNA-seq, total RNA samples were ribo-depleted and then fragmented. The fragmented samples were reversed transcribed to cDNA, end-repaired and 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. The ligation products were purified, and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer. Denature the PCR products by heat, and the single strand DNA is cyclized by splint oligo and DNA ligase.


title: RNA-Seq of  HEPG2 treated with LAUROYL-L-CARNITINE at 100uM concentration H_13_03

value: hepatocyte

value: LAUROYL-L-CARNITINE


title: RNA-Seq of  HEPG2 treated with TGF-B1 at 10ng/ml concentration H_14_01

value: liver