title: Scramble cKit Sample 5

source_name: cKit+ precursors from B16F10 scramble tumor #5


title: Hippocampus_mutant_MI_biological_rep3

status: Public on Jul 28 2022

type: RNA

city: Cologne

first: Andrea

last: Merseburg

state: North Rhine-Westphalia

address: Kerpener Str. 62

department: Institute for Molecular and Behavioral Neuroscience

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE), Bonn, and University of Cologne, Cologne, Germany

description:
HPC_357_MI
Gene expression data from hippocampus of heterozygous mutant Hcn1MI/+ mouse.

hyb_protocol: Labeled cDNA samples were hybridized to Affymetrix Clariom™ S Mouse arrays (ThermoFisher Scientific, USA, Cat# 902931) and incubated in Genechip Hybridization Oven-645 (Affymetrix, ThermoFisher Scientific, USA) rotating at 60 rpm at 45°C for 16 h. Subsequently, arrays were washed on a Genechip Fluidics Station-450 (Affymetrix, ThermoFisher Scientific, USA) and stained with the Affymetrix HWS kit according to the manufacturer’s protocol.

scan_protocol: Chips were scanned with an Affymetrix Gene-Chip Scanner-3000-7G and the Affymetrix GCOS software was used for the generation of .dat and .cel files.

data_processing: Data processing was performed with the Transcriptome Analysis Console software (TAC4.0, ThermoFisher Scientific, USA), using SST-RMA for summarization and a LIMMA Bioconductor package for differential gene expression evaluation with empirical Bayesian (eBayes) analysis and Benjamini-Hochberg method for FDR adjusted P-value calculations. All samples passed each of the QC criteria.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Hippocampus from heterozygous male Hcn1MI/+ mouse

label_protocol: 100 ng total RNA were used for reverse transcription and the resulting cDNA was fragmented and labeled via the GeneChip® WT PLUS Reagent Kit as per the manufacturer’s instructions (Affymetrix, ThermoFisher Scientific, USA).

growth_protocol: Animals were kept in type II long plastic cages under standard housing conditions (21±2°C, 50% relative humidity) with food (ssniff Spezialitäten GmbH, Soest, Germany) and water ad libitum.

extract_protocol: Total RNA was prepared from hippocampus (using material from both hemispheres) from 6-month-old male mice. Tissue from hippocampus (~40µg) was submerged in RNAprotect Tissue Reagent (Qiagen, Germany), and subsequent RNA isolation was performed with RNeasy Mini Kit (Qiagen, Germany) and RNase-free DNase Set (Qiagen, Germany).

treatment_protocol: Animals did not receive any treatment.

tag: gender

value: male

tag: genotype

value: heterozygous mutant (Hcn1MI/+)

tag: age

value: 6 months

tag: tissue

value: hippocampus from both hemispheres


title: Hippocampus_control_WT_biological_rep3

description:
HPC_354_WT
Gene expression data from hippocampus of wildtype control mouse of the Hcn1MI line.

source_name: Hippocampus from WT male mouse

value: wildtype control


title: LONP1ATF4 DmKO biological rep2

type: SRA

city: Nanjing

first: Zhenji

last: Gan

address: 12 Xuefu Road

department: Model Animal Research Center of Nanjing University

country: China

institute: Nanjing University

description: Gastrocnemius muscle from LONP1ATF4 DmKO mouse

library_source: transcriptomic

data_processing:
Illimina RTA used for base calling and converting into raw FASTQ files with Bcl2Fastq conversion software.
quality control using fastQC version 0.11.3
mRNA-seq reads were aligned to the mm10 genome assembly using TopHat2 version 2.0.14 with the default parameters.
FPKM (fragments per kilobase of exon per million fragments mapped)  were calculated using Cufflinks version 2.2.1 .
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each Sample and gene expression ratio.

source_name: Gastrocnemius muscle from 6-week-old LONP1ATF4 DmKO mouse

extract_protocol:
Gastrocnemius muscle  were harvested and flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used with 1.5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: Gastrocnemius muscle

value: 6 weeks of age

value: LONP1ATF4 DmKO mouse


title: PERK KO cKit Sample 2

city: Tampa

first: Paulo

last: Rodriguez

state: Florida

address: 3011 W. Holly Drive, MRC, 2067

country: USA

institute: H. Lee Moffitt Cancer Center

data_processing:
bcl2fastq2 is used for base-calling and demultiplexing
STAR-2.5.3a is used to align reads to reference genome
HTSeq-0.6.1 is used to count reads for gene expression
DESeq2 ver1.30.1 is used for normalization and differential expression analyses
Assembly: mm10
Supplementary files format and content: text (raw read count as expression value)
Supplementary files format and content: text (normalized read count as expression value)

source_name: cKit+ precursors from B16F10 PERK KO tumor #2

growth_protocol: Wildtype C57BL6 age and sex matched mice 6 weeks of age were injected with 150,000 B16F10 tumor cells (either Scramble B16F10 or PERK KO B16F10) as subcutaneous tumors; tumors were permitted to grow until day 17

extract_protocol:
RNA was isolated from cKit precursors via Qiagen RNEasy with the inline Qiagen DNase digestion
RNA extracted from tumor tissue was quantitated with the Qubit Fluorometer (ThermoFisher Scientific, Waltham, MA) and screened for quality on the Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA).  The samples were then processed for RNA-sequencing using the NuGEN Universal Mouse RNA-Seq Library Preparation Kit with NuQuant (Tecan Genomics, Redwood City, CA).  Briefly, 100 ng of RNA was used to generate cDNA and a strand-specific library following the manufacturer’s protocol.  Quality control steps were performed, including TapeStation size assessment and quantification using the Kapa Library Quantification Kit (Roche, Wilmington, MA).  The final libraries were normalized, denatured, and sequenced on the Illumina NextSeq 2000 sequencer with the 2-200 cycle reagent kit in order to generate approximately 50M million 105-base read pairs per sample (Illumina, Inc., San Diego, CA)

treatment_protocol: On day 17 of tumor growth, mice were humanely euthanized and tumors dissected into compelte RPMI media; after manually tissue disaggregation, tumors were treated with liberase and DNAse for 1 hour at 37C to enable generation of a single cell suspension (tumor processing); after tumor processing, red blood cells were lysed with red blood cell lysis buffer (ACK bufer) and total viable cells counted followed by magnetic bead based enrichment of ckit positive tumor infilrtating precursors- this method was chosed as it enables isolation of viable, fresh precursors which do not survive well when processed via flow sorting

tag: cell type

value: cKit+ precursors infiltrating tumor

tag: injected tumor cells

value: PERK KO B16F10 melanoma


title: Muscle Control Rep 2

city: Piscataway

first: Sohaib

last: Hassan

state: NJ

address: 145 Bevier Road

department: Department of Genetics and Human Genetics Institute of New Jersey

institute: Rutgers University

description:
Saline vehicle control
FPKM_Muscle.txt
Results_Muscle_CtrlvsMuscle_LPS.txt
Results_Muscle_CtrlvsMuscle_LPS_MIC.txt

data_processing:
Alignment: RNA-seq: Kallisto v0.46.11
RNA-seq Transcript Import: tximport 1.18.02
DESeq2 1.30.13
Assembly: RefSeq mm9
Supplementary files format and content: RNA-Seq: FPKM table outputted by DESeq2 for fragment counts normalized per kilobase of feature length per million mapped fragments and Results table outputted by DESeq2 that extracts Log2FC values, p values, adjusted p values, baseMean values, and test statistic values.

organism: Mus

source_name: Gastrocnemius

extract_protocol:
C57BL/6 mice were purchased from Charles River Laboratories (Malvern, PA). C57BL/6 male mice were randomly put into vehicle control, LPS-treated, or LPS-MIC-1-treated group as previously described in GEO (accession no. GSE155738). MIC-1 (80 mg/kg b.w.) was given by gavage daily for 3 days before LPS treatment, which was administered intraperitoneally. Gastrocnemius muscles were collected from euthanized mice after 16 h of LPS treatment. Fat and connective tissue were trimmed from muscle tissues before freezing in liquid nitrogen for further analyses. The handling and care of animals used in this study followed the standard procedures recommended by the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health, and the Rutgers University Institutional Animal Care and Use Committee approved the protocol (ID999900474)
RNA was extracted with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.

value: wild type


title: Hippocampus_mutant_GD_biological_rep3

description:
HPC_616_GD
Gene expression data from hippocampus of heterozygous mutant Hcn1GD/+ mouse.

source_name: Hippocampus from heterozygous male Hcn1GD/+ mouse

value: heterozygous mutant (Hcn1GD/+)


title: CSC LPS Treated Rep 3

description:
LPS treated (1 μg/mL)
FPKM_CSC12.txt
Results_C2C12_CtrlvsC2C12_LPS.txt
Results_C2C12_LPSvsC2C12_LPS_MIC.txt

source_name: Myoblasts


title: Hippocampus_mutant_MI_biological_rep2

description:
HPC_355_MI
Gene expression data from hippocampus of heterozygous mutant Hcn1MI/+ mouse.


title: Muscle Control Rep 1


title: Hippocampus_control_WT_biological_rep2

description:
HPC_613_WT
Gene expression data from hippocampus of wildtype control mouse of the Hcn1GD line.


title: LONP1 mKO biological rep2

description: Gastrocnemius muscle from LONP1 mKO mouse

source_name: Gastrocnemius muscle from 6-week-old LONP1 mKO mouse

value: LONP1 mKO mouse


title: Muscle LPS + MIC-1 Treated Rep 3

description:
MIC-1 (80mg/kg b.w.) gavaged group injected with LPS. Mice were pretreated (3 days) with MIC-1 in 10% DMSO (Sigma-Aldrich) via oral gavage before a LPS (10 mg/kg b.w.) intraperitoneal injection
FPKM_Muscle.txt
Results_Muscle_CtrlvsMuscle_LPS_MIC.txt
Results_Muscle_LPSvsMuscle_LPS_MIC.txt


title: Scramble cKit Sample 4

source_name: cKit+ precursors from B16F10 scramble tumor #4

value: Scramble B16F10 melanoma


title: wild-type biological rep1

description: Gastrocnemius muscle from wild-type mouse-control mouse for LONP1 mKO

source_name: Gastrocnemius muscle from 6-week-old wild-type mouse


title: CSC LPS + MIC-1 Treated Rep 3

description:
Myoblasts were treated with 10 μM MIC-1, and 1 μg/mL LPS for 24 h
FPKM_CSC12.txt
Results_C2C12_CtrlvsC2C12_LPS_MIC.txt
Results_C2C12_LPSvsC2C12_LPS_MIC.txt


title: CSC LPS + MIC-1 Treated Rep 1


title: Hippocampus_mutant_GD_biological_rep2

description:
HPC_605_GD
Gene expression data from hippocampus of heterozygous mutant Hcn1GD/+ mouse.


title: CSC12 Control Rep 3

description:
Saline vehicle control
FPKM_CSC12.txt
Results_C2C12_CtrlvsC2C12_LPS.txt
Results_C2C12_CtrlvsC2C12_LPS_MIC.txt


title: Muscle LPS + MIC-1 Treated Rep 2


title: Muscle LPS Treated Rep 2

description:
LPS treated (10 mg/kg b.w., i.p.)
FPKM_Muscle.txt
Results_Muscle_CtrlvsMuscle_LPS.txt
Results_Muscle_LPSvsMuscle_LPS_MIC.txt


title: VH1_2_mVHdel_VK1_33_SP_IgK_1

city: Boston

first: Frederick

middle: W

last: Alt

state: MA

address: 1 Blackfan Circle

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

library_source: genomic

data_processing:
HTGTS-Rep-Seq data analysis was done by the HTGTS-Rep-Seq bioinformatics pipeline (Github address: https://github.com/Yyx2626/HTGTSrep), using IgBLAST with default parameters for qualified reads mapping. Only reads with more than 98% of the sequences having a sequencing Quality Score ≥20 were kept; only joined reads (R1 and R2 had an overlap region ≥10 bp and mismatch rate ≤8%) were kept.
Assembly: mm9
Supplementary files format and content: .db.txt files were generated using HTGTS-Rep-Seq pipeline (IgBLAST)

molecule: genomic DNA

source_name: splenic B220+ B cells

extract_protocol:
Splenic B cells were purified from 5-8 weeks old mice by MACS® Microbeads according to the manufacturer’s protocol. In brief, spleens were dissected out from unimmunized mice, prepared into single cell suspensions and stained with anti-B220 Microbeads for 20 minutes at 4°C. Then, the splenic B cells were collected using the LS column and MACSTM Separater and lysed for genomic DNA extraction.
10ug of genomic DNA from purified splenic B cells was used for generating HTGTS-rep-seq libraries as previously described (Lin et al. 2016). 4 bait primers that target mouse JH1, JH2, JH3 and JH4 were mixed to capture all IgH heavy chain repertoire in one library. And 4 bait primers that target mouse Jk1, Jk2, Jk4 and Jk5 were mixed to capture all Igk light chain repertoire in one library.
OTHER: HTGTS-rep-seq

value: C57BL/6 and 129/Sv mix

value: spleen

tag: locus (ig heavy-chain or light-chain)

value: IgK

tag: conditions

value: naive

tag: primers

tag: sequencing method

value: HTGTS-Rep-Seq


title: VH1_2_mVHdel_VK1_33_SP_IgK_2


title: 129Sv_SP_IgK_3


title: Cardiomyocytes-lactate_MCT1-rep3

city: Barcelona

first: Elisabeth

last: Engel

address: C\ Baldiri Reixac 15-21, Helix Building

country: Spain

institute: Institute for Bioengineering of Catalonia

description:
6aC_S1
processe data file: edgeR_Lac6mM_MCT1i-Lac6mM

data_processing:
Clonal clusters were generated in an Illumina cBot and sequenced in an Illumina HiSeq 4000
Read quality was assessed with FASTQC
Reads were aligned using HISTAT2 and the genome assembly GRCh38
EdgeR was used for differential gene expression analysis and values were reported as counts per million (cpm) or log2(Fold change)
Genome_build: hg38

organism: Homo sapiens

growth_protocol: hiPSC were differentiated to cardiomyocytes for 15 days and cultured in RPMI 1640 supplemented with B27 with insulin on Matrigel-coated tissue culture plates.

extract_protocol: Total RNA from cell samples was extracted following the Rneasy Kit instructions (Qiagen)

treatment_protocol: Three replicates were incubated with 6mM of L-lactate supplemented in cell culture media for 7 days. Other three replicates were additionally incubated with 1mM of α-Cyano-4-hydroxycinnamic acid (α-CHC).

value: iPSC-derived cardiomyocytes

tag: treatment

value: Lactate and aCHC-treated for 7 days


title: MCK-ΔOTC biological rep2

description: Gastrocnemius muscle from MCK-ΔOTC mouse

source_name: Gastrocnemius muscle from 2-week-old MCK-ΔOTC mouse

extract_protocol:
Gastrocnemius muscle were harvested and flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used with 1.5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain background

tag: genotype/variation

value: skeletal muscle specific overexpression a deletion mutant form of ornithine transcarbamylase

value: 2 weeks of age


title: NTG biological rep2

description: Gastrocnemius muscle from NTG mouse

source_name: Gastrocnemius muscle from 2-week-old NTG mouse

value: non-transgenic (NTG)

value: Gastrocnemius muscle


title: Cardiomyocytes-lactate_MCT1-rep2

description:
6aB_S9
processe data file: edgeR_Lac6mM_MCT1i-Lac6mM


title: Cardiomyocytes-lactate_MCT1-rep1

description:
6aA_S8
processe data file: edgeR_Lac6mM_MCT1i-Lac6mM


title: CSC12 Control Rep 2


title: MCK-ΔOTC biological rep1


title: Cardiomyocytes-lactate-rep3

description:
6C_S4
processe data file: edgeR_Lac6mM-Lac0mM
processe data file: edgeR_Lac6mM_MCT1i-Lac6mM

source_name: Cardiomyocytes-lactate

value: Lactate-treated for 7 days


title: NTG biological rep1

description: Gastrocnemius muscle from NTG mouse


title: Muscle Control Rep 3

description:
Saline vehicle control
FPKM_Muscle.txt
Results_Muscle_CtrlvsMuscle_LPS.txt
Results_Muscle_CtrlvsMuscle_LPS_MIC.txt


title: 129Sv_SP_IgH_3

value: IgH

value: JH1, JH2, JH3, JH4


title: LONP1ATF4 DmKO biological rep1

description: Gastrocnemius muscle from LONP1ATF4 DmKO mouse

value: 6 weeks of age

value: LONP1ATF4 DmKO mouse


title: LONP1 mKO biological rep1

value: LONP1 mKO mouse


title: CSC LPS Treated Rep 2

description:
LPS treated (1 μg/mL)
FPKM_CSC12.txt
Results_C2C12_CtrlvsC2C12_LPS.txt
Results_C2C12_LPSvsC2C12_LPS_MIC.txt

value: wild type


title: wild-type biological rep2

value: wild-type mouse-control mouse for LONP1 mKO


title: CSC LPS Treated Rep 1


title: Cardiomyocytes-control-rep2

description:
0B_S5
processe data file: edgeR_Lac6mM-Lac0mM

source_name: Cardiomyocytes-control

value: untreated


title: 129Sv_SP_IgH_1

value: spleen

value: naive


title: Cardiomyocytes-lactate-rep2

description:
6B_S2
processe data file: edgeR_Lac6mM-Lac0mM
processe data file: edgeR_Lac6mM_MCT1i-Lac6mM

value: iPSC-derived cardiomyocytes


title: Glut1 sgRNA_2, rep3

city: Lund

first: Marcus

last: Järås

address: Universitetssjukhuset

department: Clinical Genetics

country: Sweden

institute: Lund University

data_processing:
Bcl2FastQ software was used for basecalling
Sequenced reads generated for each sample were aligned to the GRCm38 (mm10) mus musculus reference genome using STAR aligner (V2.5.0a)
Reads were quantified and normalised to FPKM (Fragments Per Kilo Million) using Cufflinks
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: Bone Marrow

extract_protocol:
RNA was isolated from leukemia cells using the ArcturusPicoPureRNA Isolation kit (Applied Biosystems).
TruSeq RNA Sample Preparation Kit V2 (Illumina) was used for library construction per manufacturer’s protocols

value: Bone Marrow

tag: cell line

value: Stem cell enriched Leukemia cells

value: MLL::AF9 rearranged leukemia cells

value: Glut1 knockdown

value: Glut1 sgRNA_2 transduction


title: Glut1 sgRNA_2, rep2


title: Glut1 sgRNA_1, rep3

value: Glut1 sgRNA_1 transduction


title: CSC12 Control Rep 1


title: Glut1 sgRNA_1, rep2


title: Glut1 sgRNA_1, rep1


title: VH1_2_mVHdel_VK1_33_SP_IgK_3

value: C57BL/6 and 129/Sv mix

value: IgK

value: HTGTS-Rep-Seq


title: CSC LPS + MIC-1 Treated Rep 2


title: 129Sv_SP_IgK_1


title: 129Sv_SP_IgK_2


title: HB-282_DMSO

city: Munich

first: Roland

last: Kappler

address: Lindwurmstr. 2a

department: Pediatric Surgery

institute: University Munich

data_processing:
The STAR aligner (v 2.4.2a) (Dobin et al., 2013) with modified parameter settings (--twopassMode=Basic) was used for split-read alignment against the human genome assembly hg19 and UCSC knownGene annotation.
Quantification of the number of mapped reads of each gene was performed using htseq-counts (v0.6.0) (Anders et al., 2015)
Differential expression analysis was done using DESeq2 (v 1.24.0) (Love et al., 2014)
Supplementary files format and content: Matrix table with raw gene counts for every gene (rows) and every sample (columns)

source_name: liver

growth_protocol: Cells were grown in advanced DMEM/F12 (Life Technologies) supplemented with 10% (v/v) fetal bovine serum, 1% (v/v) penicillin-streptomycin (Invitrogen), 1% (v/v) L-glutamine (Thermo Fisher), and the Rho-associated kinase inhibitor Y-27632 (Selleckchem) at a final concentration of 20 µM.

extract_protocol:
RNA was harvested using Trizol reagent; Illumina TruSeq_Stranded_mRNA Kit was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HB-214, HB-282 and HB-303 cells were seeded in 6-well plates and after overnight attachment exposed for 24 h  to DMSO or mebendazole at concentrations of 2 μM, 4 μM, and 2 μM.

value: liver

value: hepatoblastoma

value: DMSO


title: TM307

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
RNA quantification was performed with Cutadapt
Alignment with STAR aligner 2.4.2a to Genome GRCh38 using default parameters
Assembly: GRCh38
Supplementary files format and content: geneExp_n_114_ensembl.csv

source_name: pre-treatment endoscopic biopsies

extract_protocol:
RNA was harvested using the AllPrep DNA/RNA FFPE kit (Qiagen). 500ng of total RNA was used for the construction of sequencing libraries.
rRNA-depleted Libraries for mRNA deep sequencing was generated using an adapted version of the Illumina v1.5 protocol and optimized for reaction volume.
Paired-end 50 sequencing was done using the Illumina HiSeq 2000 Platform (Illumina).

value: pre-treatment endoscopic biopsies

tag: msi status

value: MSS

tag: response

value: CR


title: TM296

value: iCR


title: TM297


title: TM288


title: Glut1 sgRNA_2, rep4


title: Cardiomyocytes-control-rep1

description:
0A_S3
processe data file: edgeR_Lac6mM-Lac0mM

value: iPSC-derived cardiomyocytes

value: untreated


title: Glut1 sgRNA_1, rep4

value: Bone Marrow

value: Stem cell enriched Leukemia cells


title: 16wkHFD.VAT.bmal1KO.3

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: VAT.wholetissue.30wk.M.HFD.ZT0.bmal1KO#3

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: Visceral Adipose Tissue

extract_protocol:
50 to 100mg of visceral adipose tissue was excised, snap frozen and stored in trizol for RNA extraction. RNA was extracted using Qiagen's RNEasy lipid mini kit. 2ng of RNA was added to 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
Polyadenylated mRNA was selected using an anchored oligo(dT) primer and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR-amplified using barcoded primers such that each sample carried a specific combination of illumine P5 and P7 barcodes, and were pooled prior to sequencing. Sequencing was performed on an illumina NextSeq500 using 2X38bp reads.

value: Visceral Adipose Tissue

tag: diet

value: 14 weeks LFD followed by 16 weeks HFD

value: 30 weeks

value: KO

value: C57BL/6 Foxp3.Cre-YFP bmal1KO

tag: Sex

value: Male

tag: time


title: Glut1 sgRNA_2, rep1

tag: tissue

value: MLL::AF9 rearranged leukemia cells

tag: genotype

value: Glut1 knockdown

value: Glut1 sgRNA_2 transduction


title: 16wkHFD.VAT.bmal1KO.1

description: VAT.wholetissue.30wk.M.HFD.ZT0.bmal1KO#1

tag: age

tag: strain


title: Cardiomyocytes-control-rep3

description:
0C_S6
processe data file: edgeR_Lac6mM-Lac0mM

tag: cell type


title: HB-303_2µM_MBZ

value: liver

value: hepatoblastoma

value: Mebendazole 2 uM


title: Cardiomyocytes-lactate-rep1

description:
6A_S7
processe data file: edgeR_Lac6mM-Lac0mM
processe data file: edgeR_Lac6mM_MCT1i-Lac6mM

value: Lactate-treated for 7 days


title: HB-303_DMSO

value: DMSO


title: TM285

value: pre-treatment endoscopic biopsies

value: MSS

value: iCR


title: Control sgRNA, rep4

value: Bone Marrow

value: Stem cell enriched Leukemia cells

value: Glut1 WT

value: Control sgRNA transduction


title: TM274

value: CR


title: 16wkHFD.VAT.bmal1WT.1

description: VAT.wholetissue.30wk.M.HFD.ZT0.bmal1WT#1

value: Visceral Adipose Tissue

value: 14 weeks LFD followed by 16 weeks HFD

value: 30 weeks

value: WT

value: C57BL/6 Foxp3.Cre-YFP bmal1WT

value: Male


title: HB-214_2µM_MBZ

value: liver

value: hepatoblastoma

value: Mebendazole 2 uM


title: TM266

value: pre-treatment endoscopic biopsies


title: 129Sv_SP_IgH_2

value: spleen

tag: locus (ig heavy-chain or light-chain)

value: IgH

tag: conditions

value: naive

value: JH1, JH2, JH3, JH4

value: HTGTS-Rep-Seq


title: HB-282_4µM_MBZ

value: Mebendazole 4 uM


title: HB-214_DMSO

value: DMSO


title: Control sgRNA, rep3

value: Bone Marrow

value: Stem cell enriched Leukemia cells

value: MLL::AF9 rearranged leukemia cells

value: Glut1 WT

value: Control sgRNA transduction


title: 9wktransfer.VAT.Treg.bmal1KO.1

extract_protocol:
1,000 Cells were double-sorted by Aria into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
Polyadenylated mRNA was selected using an anchored oligo(dT) primer and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR-amplified using barcoded primers such that each sample carried a specific combination of illumine P5 and P7 barcodes, and were pooled prior to sequencing. Sequencing was performed on an illumina NextSeq500 using 2X38bp reads.

value: Visceral Adipose Tissue

value: Foxp3YFP+ Treg

value: 9wk adoptive transfer

value: KO

value: C57BL/6 Foxp3.Cre-YFP

value: Male


title: TM279

value: pre-treatment endoscopic biopsies

value: MSS

value: CR


title: 16wkHFD.VAT.bmal1KO.2

description: VAT.wholetissue.30wk.M.HFD.ZT0.bmal1KO#2

value: 14 weeks LFD followed by 16 weeks HFD

value: 30 weeks

value: C57BL/6 Foxp3.Cre-YFP bmal1KO


title: 16wkHFD.VAT.bmal1WT.3

description: VAT.wholetissue.30wk.M.HFD.ZT0.bmal1WT#3

value: WT

value: C57BL/6 Foxp3.Cre-YFP bmal1WT


title: TM245

value: iCR


title: TM242


title: TM239


title: Control sgRNA, rep1

value: Bone Marrow

value: Stem cell enriched Leukemia cells

value: MLL::AF9 rearranged leukemia cells

value: Glut1 WT


title: 9wktransfer.VAT.Treg.bmal1WT.2

value: Visceral Adipose Tissue

value: Foxp3YFP+ Treg

value: 9wk adoptive transfer


title: Control sgRNA, rep2

value: Control sgRNA transduction


title: TM236

value: pre-treatment endoscopic biopsies


title: 16wkHFD.VAT.bmal1WT.2

description: VAT.wholetissue.30wk.M.HFD.ZT0.bmal1WT#2

value: Male


title: 16wkHFD.VAT.Treg.bmal1WT.1

value: HFD 16 weeks

value: C57BL/6 Foxp3.Cre-YFP


title: JM205

value: MSS

value: CR


title: 4wkHFD.VAT.Treg.bmal1KO.3

value: HFD 4 weeks

value: 18 weeks

value: KO


title: TM251


title: JM204


title: 9wktransfer.VAT.Treg.bmal1KO.2


title: TM248

value: iCR


title: 9wktransfer.VAT.Treg.bmal1WT.1

value: WT


title: 16wkHFD.VAT.Treg.bmal1KO.1

value: 30 weeks


title: 4wkHFD.VAT.Treg.bmal1KO.1


title: TM240


title: JM202


title: 4wkHFD.VAT.Treg.bmal1WT.3


title: 16wkHFD.VAT.Treg.bmal1KO.2


title: TM267


title: TM237


title: JM197


title: cells extracted from mouse at steady state, biological replicate 3 of WT control group

first: Sarah

last: Warsi

address: BMC, Sölvegatan 17

description: Gene expression data from hematopoietic stem cells extracted from bone marrow from a wildtype mouse with a C57Bl/6 background, used as control data for comparison with BMPR2 knockout (littermates). Cells extracted at steady state i.e. no specific treatments given to mice prior to cell extraction.

hyb_protocol: 3,0 µg of cDNA was hybridized to Affymetrix Mouse Gene 1.0 ST arrays for 16 h at 45° C in a GeneChip hybridization oven 640. Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450. Further information in the NuGEN Ovation PicoSL WTA System V2 and NUGEN Encore Biotin Module manuals (NuGEN Technologies).

scan_protocol: GeneChips were scanned (fluorescent signals measured) with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by the Affymetrix GeneChip Command Console v4.1.3 software.

data_processing: Summarized probe set signals in log2 scale were calculated by using the RMA algorithm with the Affymetrix GeneChip Expression Console v1.3 Software. After exporting into Microsoft Excel, average signal values, comparison fold changes and significance P-values (t-test) were calculated.

source_name: bone marrow

label_protocol: Biotinylated cDNA was prepared according to a standard Affymetrix protocol from 0,5-3 ng total RNA. The process included reverse transcription of RNA in a two-step process introducing a SPIA tag sequence, bead purification, amplification by a SPIA amplification reaction, additional bead purification, fragmentation and terminal biotin-labelling.

growth_protocol: Mice on C57Bl/6 background with loxP flanking one allele of exon 4-5 of the BMPR-II gene (MMRRC, University of North Carolina, Chapel Hill) were bred to homozygosity and mated with Vav-Cre transgenic mice to generate conditional Vav-Cre;BMPR-II(fl/fl) mice. The breeding also generated littermates not containing Vav-Cre, i.e. wildtype controls. Mice were housed and bred in ventilated cages in the BMC animal facility. All experiments involving animals were approved by the regional Animal Ethical Committee.

extract_protocol: Please see associated publication. In brief, BMPR2 knockout (Vav-Cre;BMPR-II(fl/fl)) mice were sacrificed, as were littermates not containing Vav-Cre (used as controls for comparison of expression data to that of wildtype mice). Post-mortem dissection was done to retrieve femur, tibia and iliac. For sufficient cell numbers, bones from three mice of the same type (knockout or wildtype) were pooled within each sample. Bone marrow was extracted by crushing bones in PBS with 2% FCS. C-kit enrichment using microbeads and MACS columns (Miltenyi biotec). Cells were stained with fluorescently labeled antibodies and sorted on a FACS Aria, dead cells excluded using 7AAD. Cells were sorted into RLT buffer and frozen at -80 prior to shipment to KFB (Regensburg, Germany) for further processing. RNA isolation was done using the RNeasy Micro Kit (Qiagen) according to manufacturer’s protocol. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent).

treatment_protocol: No treatments were given to the mice prior to euthanization and cell extraction.

value: purified hematopoietic stem cells

tag: group

value: Wildtype control

value: Negative for Cre. 1x BMPR-II(fl/fl) and 1x BMPR-II(fl/+) and 1x BMPR-II(+/+).


title: 16wkHFD.VAT.Treg.bmal1WT.3

value: Visceral Adipose Tissue

value: Foxp3YFP+ Treg


title: LFD.VAT.Treg.bmal1KO.3

value: LFD


title: JM195

value: pre-treatment endoscopic biopsies


title: JM199


title: cells extracted from mouse at steady state, biological replicate 4 of WT control group

value: Negative for Cre. 2x BMPR-II(fl/fl) and 1x BMPR-II(fl/+).


title: JM201


title: LFD.VAT.Treg.bmal1KO.1

value: C57BL/6 Foxp3.Cre-YFP

value: Male


title: 4wkHFD.VAT.Treg.bmal1KO.2


title: 4wkHFD.VAT.Treg.bmal1WT.2


title: 16wkHFD.VAT.Treg.bmal1WT.2

value: HFD 16 weeks


title: 16wkHFD.VAT.Treg.bmal1KO.3


title: TM232

value: MSI


title: 4wkHFD.VAT.Treg.bmal1WT.1

value: HFD 4 weeks

value: 18 weeks


title: cells extracted from mouse at steady state, biological replicate 1 of KO group

description: Gene expression data from hematopoietic stem cells extracted from bone marrow from a BMPR2 knockout mouse with a C57Bl/6 background. Cells extracted at steady state i.e. no specific treatments given to mice prior to cell extraction.

value: BMPR2 knockout

value: 3x Vav-Cre;BMPR-II(fl/fl)


title: cells extracted from mouse at steady state, biological replicate 4 of KO group


title: cells extracted from mouse at steady state, biological replicate 2 of KO group


title: JM193

value: MSS

value: iCR


title: JM194


title: JM192

value: CR


title: LFD.VAT.Treg.bmal1KO.2

value: KO


title: JM191


title: LFD.VAT.Treg.bmal1WT.2

value: Visceral Adipose Tissue

value: WT


title: ZT20.sp.Treg.3

source_name: Spleen

extract_protocol:
1,000 Cells were double-sorted by Aria into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
Polyadenylated mRNA was selected using an anchored oligo(dT) primer and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR-amplified using barcoded primers such that each sample carried a specific combination of illumine P5 and P7 barcodes, and were pooled prior to sequencing. Sequencing was performed on an illumina NextSeq500 using 2X25bp reads.

value: Spleen

value: CD4+ CD25+ Treg


title: JM190

value: pre-treatment endoscopic biopsies


title: LFD.VAT.Treg.bmal1WT.1

value: Foxp3YFP+ Treg

value: LFD

value: C57BL/6 Foxp3.Cre-YFP


title: cells extracted from mouse at steady state, biological replicate 1 of WT control group

value: purified hematopoietic stem cells

value: Wildtype control

value: Negative for Cre. 1x BMPR-II(fl/fl) and 2x BMPR-II(fl/+).


title: cells extracted from mouse at steady state, biological replicate 2 of WT control group

value: Negative for Cre. 3x BMPR-II(fl/+).


title: LFD.VAT.Treg.bmal1WT.3

value: 18 weeks

value: Male


title: JM187

value: MSS


title: cells extracted from mouse at steady state, biological replicate 3 of KO group

value: BMPR2 knockout

value: 3x Vav-Cre;BMPR-II(fl/fl)


city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

institute: Uppsala University

description: Gene expression data from control cerebellar meninges (Pdgfc +/-), biological rep4

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Affymetrix raw data was normalized using the PLIER algorithms (Affymetrix Technical Note. Guide to Probe Logarithmic Intensity Error Estimation. http://affymetrix.com/support/technical/technotesmain.affx). The data from the three comparison groups were from three batches of Affymetrix experiments, and were normalized separately.

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix small sample amplification protocol from app. 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Extraction of total RNA was performed using RNeasy® Mini Kit (Qiagen)

value: cerebellar meninges

value: Pdgfc +/-


title: JM186

value: iCR


description: Gene expression data from control cerebellar meninges (Pdgfc +/-), biological rep6


description: Gene expression data from control cerebellar meninges (Pdgfc wt), biological rep5

value: Pdgfc wt


description: Gene expression data from mutant (Pdgfc-/-; Pdgfra GFP/+) cerebellar meninges, biological rep3

value: Pdgfc-/-; Pdgfra GFP/+


description: Gene expression data from control cerebellar meninges (Pdgfc +/-), biological rep7


description: Gene expression data from control cerebellar meninges (Pdgfc +/-; Pdgfra GFP/+), biological rep2

value: Pdgfc +/-; Pdgfra GFP/+


description: Gene expression data from control cerebellar meninges (Pdgfc wt), biological rep8


title: JM188

value: pre-treatment endoscopic biopsies


title: ZT20.sp.Treg.2

value: Spleen

value: CD4+ CD25+ Treg

value: WT


description: Gene expression data from control cerebellar meninges (Pdgfc -/-), biological rep3

value: Pdgfc -/-


description: Gene expression data from control cerebellar meninges (Pdgfc wt; Pdgfra GFP/+), biological rep1

value: Pdgfc wt; Pdgfra GFP/+


title: JM184

value: CR


title: ZT20.sp.Treg.1

value: Male


title: ZT20.VAT.Treg.2

value: Visceral Adipose Tissue


description: Gene expression data from mutant (Pdgfc-/-; Pdgfra GFP/+) cerebellar meninges, biological rep2


title: JM203

value: MSS


title: ZT20.VAT.Treg.1


title: ZT16.sp.Treg.3


title: JM181


description: Gene expression data from mutant (Pdgfc-/-; Pdgfra GFP/+) cerebellar meninges, biological rep4


description: Gene expression data from mutant (Pdgfc-/-; Pdgfra GFP/+) cerebellar meninges, biological rep1


title: JM176


title: ZT16.VAT.Treg.3


title: JM175


title: ZT16.sp.Treg.2


title: ZT16.sp.Treg.1


title: JM180


title: ZT16.VAT.Treg.2


title: JM173


title: ZT16.VAT.Treg.1


title: mutant (Pdgfc-/-; Pdgfra GFP/+) cerebellar tissue, biological rep5

description: Gene expression data from mutant (Pdgfc-/-; Pdgfra GFP/+) cerebellar tissue

value: cerebellar tissue

value: Embryonic day 14.5

value: mutant (Pdgfc-/-; Pdgfra GFP/+)


title: control cerebellar tissue, biological rep7

description: Gene expression data from control cerebellar tissue

source_name: control cerebellar tissue

value: control


title: control cerebellar tissue, biological rep11


title: mutant (Pdgfc-/-; Pdgfra GFP/+) cerebellar tissue, biological rep4


title: JM177


title: control cerebellar tissue, biological rep10


title: JM171

value: iCR


title: control cerebellar tissue, biological rep4

value: Embryonic day 13.5


title: control cerebellar tissue, biological rep3


title: JM170


title: ZT12.sp.Treg.2


title: control cerebellar tissue, biological rep1


title: control cerebellar tissue, biological rep2


title: control cerebellar tissue, biological rep6


title: control cerebellar tissue, biological rep8


title: control cerebellar tissue, biological rep9


title: ZT12.sp.Treg.1


title: control cerebellar tissue, biological rep5


title: JM169


title: mutant (Pdgfc-/-; Pdgfra GFP/+) cerebellar tissue, biological rep2


title: ZT12.VAT.Treg.3


title: JM168


title: JM167


title: mutant (Pdgfc-/-; Pdgfra GFP/+) cerebellar tissue, biological rep1


title: ZT12.VAT.Treg.2


title: JM166


title: ZT12.sp.Treg.3


title: JM165


title: ZT12.VAT.Treg.1


title: mutant (Pdgfc-/-; Pdgfra GFP/+) cerebellar tissue, biological rep3


title: ZT8.sp.Treg.3


title: ZT8.sp.Treg.1


title: ZT8.VAT.Treg.2


title: JM163


title: JM160


title: ZT8.VAT.Treg.3


title: ZT8.sp.Treg.2


title: JM161


title: ZT8.VAT.Treg.1


title: ZT4.sp.Treg.3


title: JM139


title: ZT4.sp.Treg.2


title: JM136


title: ZT4.VAT.Treg.3


title: JM135


title: JM130


title: JM129


title: JM128


title: JM150


title: ZT4.VAT.Treg.2


title: RPE1_siCtrl_RNAseq

city: Zhanjiang

first: Yun-Miao

last: Guo

address: 236 Yuanzhu Road

department: Zhanjiang Institute of Clinical Medicine

institute: Central People's Hospital of Zhanjiang

data_processing:
The sequencing adapters were removed from the raw RNA-seq reads, and the obtained clean data were aligned to the human reference genome (hg38) using HISAT2 software (version 2.1.0.).
To quantify gene expression, we counted the sequencing reads within each gene and normalized the counts using edgeR
Enriched GO terms were identified with MGI Gene Ontology Term Finder.| log2FC| > 1 and p value < 0.05 were used as thresholds.
Assembly: hg38
Supplementary files format and content: tab-delimited text file include RPKM values for all samples.

extract_protocol:
For total RNA analysis and data processing, the total RNA was extracted using a TRIzol reagent following a standard protocol. The RNA integrity was checked on Agilent 2100 BioAnalyzer to conduct quality control (Agilent Technologies).
Library construction and high-throughput RNA-Seq were performed with the Illumina Hiseq-PE150 platform to a depth of 1.5 × 107 reads.

value: Retinal pigment epithelial cells


title: CPY-3_RNAseq

source_name: Peripheral blood

value: Peripheral blood

value: Peripheral blood mononuclear cells


title: RPE1_siETS1-2_RNAseq

value: ETS1 knockdown


title: Ctrl-2_RNAseq

value: WT


title: ZT4.VAT.Treg.1

value: CD4+ CD25+ Treg


title: CPY-4_RNAseq


title: ZT0.sp.Treg.3

value: Spleen


title: CPY-2_RNAseq


title: JM126

value: pre-treatment endoscopic biopsies


title: ZT4.sp.Treg.1

value: Male


title: CPY-1_RNAseq


title: RPE1_siETS1-1_RNAseq


title: Ctrl-3_RNAseq


title: JM138


title: ZT0.sp.Treg.2


title: JM127


title: JM125


title: JM124


title: Ctrl-3_ATACseq

data_processing:
For ATAC-Seq data processing, FastQC (version 0.11.7) was used to evaluate the quality of the sequencing data, and Trimmomatic was explored to remove the adaptor sequences to obtain the clean data.
The clean data were subsequently aligned to the hg38 reference genome using BWA.
Multiply mapped reads were removed using SAMtools (version 1.3.1) and the MASCS2 was applied to call significant peaks with q-value < 0.05.
To identify DEGs between healthy donor and ciliopathy patients, the ATAC-seq peaks of each sample were merged to generate a consensus set of unique peaks, among which the number of peaks was further counted for each sample using bedtools v2.25.0, and CAAs and CIAs were identified by DESeq2 (v1.16.0)(50),with the thresholds of | log2FC| > 1 and p < 0.05.
Genomic features of peaks were annotated using ChIPseeker R package.
Assembly: hg38
Supplementary files format and content: bigWig files include peaks for each sample, respectively.

extract_protocol:
Fresh cells were harvested and resuspended with cold lysis buffer for 10 min on ice. 50,000 nuclei were counted using trypan blue staining and prepared for transposition reactions according to TruePrep DNA Library Prep Kit V2 for illumine (Vazyme, TD501) manufacturer’s instructions. Subsequently, nuclei were pelleted and resuspended with transposase at 37 °C for 30 min. After transposition, DNA fragments were purified with AMPure XP beads (Beckman Coulter, A63882).
DNA libraries were constructed after 8 cycles of PCR amplification using the TruePrep DNA Library Prep Kit and sequenced on the Illumina Hiseq-PE150 platform to a depth of 4.0 × 107 reads.

tag: treatment


title: RPE1_siCtrl_ATACseq

value: siRNA


title: ZT0.sp.Treg.1


title: Ctrl-1_RNAseq


title: RPE1_siETS1-2_ATACseq


title: RPE1_siETS1-1_ATACseq


title: Ctrl-2_ATACseq


title: JM123

value: MSS


title: Ctrl-1_ATACseq


title: ZT0.VAT.Treg.2

value: Visceral Adipose Tissue


title: JM116


title: RPE1_IgG_CutTag

data_processing:
For CUT&Tag data processing, FASTQC was used to measure the date quality distribution.
The clean reads were then aligned to reference genome sequences using the bwa program.
Peaks were called using MACS2 peak caller with q-value < 0.05.
Genome-wide normalized signal coverage tracks were visualized in the IGV.
Assembly: hg38
Supplementary files format and content: bigWig files include peaks for each sample, respectively.
Library strategy: CUT&Tag

growth_protocol: hTERT RPE-1 cells (ATCC, CRL-4000) were cultured in F12/DMEM (1:1) supplemented with 10% fetal bovine serum (FBS, Gemini, 900-108) and 0.01mg/ml hygromycin B under 5% CO2 at 37°C.

extract_protocol:
10,000 fresh cells were counted and processed according to Hyperactive® Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903) instructions. Briefly, ConA beads were added to the cell pellet and incubation at room temperature for 10 min. Subsequently, the mixed complexes were incubated overnight at 4°C with primary antibody. The following day, the cells were washed and incubated with diluted secondary antibody at room temperature for 2 h. Antibody-protein-DNA complexes were then linked by pA/G-Tnp by incubation at room temperature for 1 h. After washing, the eluted complexes were subsequently sheared by adding 5 × TTBL. The proteinase K and DNA extract beads were used for obtaining eluted DNA.
Sequencing libraries were established after 11 cycles of PCR amplification. Selected size-selected were proceeded using AMPure XP beads and the DNA were sequenced on the Illumina Hiseq-PE150 platform to a depth of 2.5 × 107 reads.

tag: antibody

value: IgG


title: CPY-1_ATACseq


title: JM114

value: MSI

value: CR


title: ZT0.VAT.Treg.1


title: CPY-2_ATACseq


title: CPY-4_ATACseq


title: CPY-3_ATACseq


title: JM109

value: iCR


title: ZT0.VAT.Treg.3


title: HEK293 cells, WT 2

city: Ann Arbor

first: Ming

last: Li

state: Michigan

address: Rm 3220, Biological Sciences Building, 1105 North University Ave

department: MCDB

institute: The University of Michigan

data_processing:
The raw reads were filtered using RSeQC with default parameters by removing low-quality bases (> Q30) and adapter contaminated reads
The resulting high-quality clean reads in fastq format were trimmed using Trim Galore (v 0.5.0) and aligned to the human genome (Sequence: ENSEMBL-GRCh38) using STAR (v 2.6.0)
After mapping, read counts were generated by HTSeq-count (v.0.11.3) The read counts were used for a differential expression analysis between wild-type control cells and TMEM251 knockout cells using R package DESeq2 (v.1.28.1)
Statistically significantly expressed genes were determined as having absolute log-fold change larger than 1.2 and a p-value less than 0.05 based on the Benjamini-Hochberg procedure, which controls the false discovery rate (FDR).
Principal component analysis (PCA) and heatmaps of differentially expressed genes (DEGs) were generated using ClustVis (https://biit.cs.ut.ee/clustvis/). DEGs were processed for gene ontology enrichment analyses using Metascape.
Assembly: ENSEMBL-GRCh38
Supplementary files format and content: FPKM
Supplementary files format and content: TPM
Supplementary files format and content: expected_count

growth_protocol: HEK293 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA samples were extracted from either WT or 251 KO HEK293 cells using TRIzol (Thermo Fisher Scientific) and the PureLink RNA Mini Kit (Invitrogen).
the mRNAs from total RNAs were enriched with a poly-A based selection method prior to cDNA synthesis

value: human embryonic kidney cells


title: HEK293 cells, WT 3


title: HEK293 cells, TMEM251KO sgRNAT3

value: TMEM251 KO


title: HEK293 cells, TMEM251KO sgRNAT2


title: HEK293 cells, TMEM251KO sgRNAT4


title: HEK293 cells, WT 1


title: JM108


title: JM104


title: ibm1-1-C_mRNA-seq2

city: Shanghai

first: Huiming

last: Zhang

address: No. 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

description: ibm1_mRNAseq in medium.txt

data_processing:
the raw data is preprocessed by trimmomatic (version 0.36).
The clean reads were aligned to the TAIR 10 reference genome using hisat2 (version 2.1.0) with parameters "--rna-strandness RF -p 30 --dta”.
Reads_count matrix was produced by htseq-count (version 0.9.1).
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig file
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each sample

organism: Arabidopsis thaliana

source_name: 7-day-old seedlings grown in solid MS medium

growth_protocol: For RNA-seq of plants grown in sterile medium, 7-day-old seedlings of Col-0 and ibm1-1 grown in 1/2 MS medium were collected for RNA extraction. Each sample had 2 biological replicates.

extract_protocol:
Plant RNA samples were extracted by using the RNeasy RNA extraction Plant Mini Kit (Qiagen).
An aliquot with 1 μg of total RNA per sample was used for library preparation with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7420L) following the manufacturer’s instructions. All library preparation and subsequent sequencing processes were performed at the Core Facility of Genomics at Shanghai Center for Plant Stress Biology.

value: Regular

value: ibm1-1 mutant

value: full plants


title: JM107


title: ibm1-1-C_mRNA-seq1

description: ibm1_mRNAseq in medium.txt


title: JM102


title: JM099


title: Col-0_C_mRNAseq2

description: ibm1_mRNAseq in medium.txt

value: wild type


title: Col-0_C_mRNAseq1

description: ibm1_mRNAseq in medium.txt


title: JM112


title: ibm1_mRNA_seq3

source_name: 2-week-old plants grown in soil

growth_protocol: 5-day-old seedlings of Col-0 and ibm1-1 were transferred from 1/2 MS plate into the soil, and grown for another 10 days before the whole seedlings were harvested for RNA extraction


title: JM098


title: JM091


title: PLP_BS_Tg

city: Fukuoka

first: Hiroo

last: Yamaguchi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Neurology

country: Japan

institute: Neurological Institute, Graduate School of Medical Sciences,  Kyushu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: brain, transgenic

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

tag: strain background

value: transgenic

value: brainstem/cerebellum


title: PLP_BS_Cont

source_name: brain, wild-type


title: ibm1_mRNA_seq2


title: WRN chondrocytes D4 RNA-seq-3

city: Hong Kong

first: Wai- Yee

last: Chan

state: Hong Kong

address: Shatin

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
CLC Genomics Workbench v 11.0.1
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: text files include RPKM values for each Sample

source_name: hESCs

growth_protocol: hESCs were maintained on Matrigel-coated plates (Corning) in mTesR medium (STEMCELL) before differentiation.

extract_protocol:
RNA was harvested using TRIzol™ Reagent (Invitrogen) following the manufacturer’s instructions.
The library was establised by Novogene company (Beijing, China).

treatment_protocol: hESCs differentiation was following a previously publised protocol. Briefly, the cells were cultured in basal differentiation medium including DMED/F12, 2 mM L-glutamine, 1% (vol/vol) ITS, 1% (vol/vol) nonessential amino acids, 2% (vol/vol) B27, and 90 90 µM β-mercaptoethanol supplemented with appropriate chemicals. The key growth factors and chemicals used were as follows: WNT3A, NT4 (R&D systems), BMP4, GDF5, Activin-A (Peprotech), FGF2 (Biosource, Invitrogen), and Follistatin 300 (Sigma.)

tag: cell line

value: hESCs

value: HESC-derived chondrocytes

value: WRN KD

value: Day 4


title: WRN chondrocytes D9 RNA-seq-3

value: Day 9


title: PLP_S_Cont

value: spinal cord


title: WRN chondrocytes D9 RNA-seq-2


title: WRN chondrocytes D9 RNA-seq-1


title: WRN chondrocytes D0 RNA-seq-3

value: Day 0


title: WRN chondrocytes D4 RNA-seq-1


title: JM082

value: pre-treatment endoscopic biopsies

tag: msi status

value: MSS


title: JM083

tag: response

value: iCR


title: PLP_S_Tg


title: Col-0_mRNA_seq3

value: wild type Col-0


title: ibm1_mRNA_seq1

value: Regular


title: WRN chondrocytes D0 RNA-seq-2


title: Col-0_mRNA_seq2


title: WRN chondrocytes D4 RNA-seq-2


title: WRN chondrocytes D0 RNA-seq-1


title: JM080


title: JM077


title: WT chondrocytes D9 RNA-seq-3

value: WT


title: WT chondrocytes D9 RNA-seq-2


title: WT chondrocytes D4 RNA-seq-3


title: JM076

value: CR


title: ibm1-1_BS2

data_processing:
For WGBS data analysis, the raw data were trimmed using Trimmomaticwith parameters "LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:50".
Only clean paired-end reads were mapped to TAIR10 genome using tool BSMAP with parameters "-m 0 -w 2" (other parameters were used the default value).
To remove potential PCR duplicates, the "rmdup" command of SAMtools was used. methratio.py script from BSMAP was used to extract methylation ratios from mapping results.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig file
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each sample

growth_protocol: 5-day-old seedlings of Col-0 and ibm1-1 were transferred from 1/2 MS plate into the soil, and grown for another 10 days before the whole seedlings were harvested for DNA extraction

extract_protocol:
Genomic DNA samples from Col-0 and ibm1 whole plants were extracted by using the DNeasy DNA extraction Plant Mini Kit (Qiagen).
An aliquot with 1 μg of DNA per sample was used for library preparation with NEBNext Ultra II DNA Library Prep Kit for Illumina® (New England BioLabs, E7645L) and Epitect Plus DNA Bisulfite Kit (Qiagen, Cat. No. 59124). All library preparation and subsequent sequencing processes were performed at the Core Facility of Genomics at Shanghai Center for Plant Stress Biology.

value: ibm1-1 mutant

value: full plants


title: Col-0_mRNA_seq1


title: JM064


title: WT chondrocytes D0 RNA-seq-2


title: JM084


title: WT chondrocytes D9 RNA-seq-1


title: Col-0_BS1


title: WT chondrocytes D0 RNA-seq-1


title: hESCs, Input3

data_processing:
Callpeaks performed using MACS2 software.
ChIP-seq reads were aligned to the hg38 genome assembly.
Motif prediction, peak annotation and data visualization were generated using MACS2 software.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated and followed by the instruction of a Pierce Magnetic ChIP kit (Thermo, 26157).
The library was establised by Novogene company (Beijing, China).

tag: chip antibody


title: hESCs, WRN2, SIGMA

value: WRN (Sigma, W0393)


title: Col-0_BS2


title: hESCs, WRN3, SIGMA

value: hESCs


title: hESCs, WRN1, SIGMA

value: HESC-derived chondrocytes


title: WT chondrocytes D4 RNA-seq-1


title: ibm1-1_BS1


title: JM058


title: CHL1 cell, PRMT5 inhibition,72 hours, 2

city: Melbourne

first: David

last: Goode

state: Victoria

address: 305 Grattan Street

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Read quality was assessed using FastQC v0.11.6.
Reads were aligned to the GRCh37.73 (hg19) version of the human genome using Hisat 2.0.4.
Bam files were sorted and index using Picard v2.17.3 and samtools v1.18.
Aligned reads in the BAM files and the GRCh37 GTF annotation file from Ensembl were input to HTSeq v0.11.2 with default settings for read quantification of genes.
Gene counts from HTSeq were normalised with the Trimmed Mean of M-values (TMM) method using edgeR.
Differential alternative splicing analysis was performed with rMATS (v.4.1.0) to detect five categories of splicing events including skipped exon (SE), intron retention (RI), mutually exclusive exons (MXE), alternative 5’ splice site (A5SS) and alternative 3’ splice site (A3SS).
Assembly: hg19
Supplementary files format and content: Single combined csv file containing gene counts of all samples.
Supplementary files format and content: csv file containing normalised gene counts from edgeR

growth_protocol: CHL1 cell lines were obtained from American Type Culture Collection. and grown in DMEM (Gibco) supplemented with 10% (vol/vol) fetal bovine serum (FBS) (Gibco), 2 mM GlutaMAX-I L-alanyl-L-glutamine dipeptide (Gibco), 100 μg/mL penicillin/streptomycin (Gibco), and buffered with 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES).

extract_protocol:
total RNA was isolated using the RNeasy Mini kit (QIAGEN) following the manufacturer’s instructions.
Approximately 1 μg of RNA was used for library preparation according to standard protocols (TruSeq RNA; Illumina).

treatment_protocol: Four different culture conditions with two replicates each were grown: (i) DMSO alone added for 72 hours (control), (ii) 1µM of palbociclib added for 72 hours (CDK4/6i_72hr), (iii) 1µM of palbociclib added for 6 days (CDK4/6i_6d) and (iv) 500nM of GSK3326595 added for 72 hours (PRMT5i_72hr).

tag: time point

value: 72 hours

value: melanoma cell

value: PRMT5 inhibition


title: CHL1 cell, CDK4/6 inhibition,6 days, 2

value: 6 days

value: CDK4/6 inhibition


title: JM065

value: pre-treatment endoscopic biopsies


title: JM062

value: MSI


title: WT chondrocytes D4 RNA-seq-2

tag: time

value: Day 4


title: CHL1 cell, CDK4/6 inhibition,6 days, 1


title: JM059

tag: tissue

value: MSS

value: iCR


title: hESCs, Input2


title: JM035


title: CHL1 cell, CDK4/6 inhibition,72 hours, 1

tag: genotype

value: WT


title: JM061


title: CHL1 cell, control,72 hours, 2

value: Control


title: JM034

value: CR


title: JM032


title: CHL1 cell, control,72 hours, 1


title: CHL1 cell, CDK4/6 inhibition,72 hours, 2


title: WT chondrocytes D0 RNA-seq-3

value: Day 0


title: JM056


title: JM030


title: CHL1 cell, PRMT5 inhibition,72 hours, 1


title: JM036


title: JM029


title: JM028


title: IMR32_H3K27me1

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

institute: Saitama Cancer Center

data_processing:
Short reads were trimmed by trimmomatic.
Reads were mapped by bowtie2-2.3.1
Duplicated reads were removed by MarkDuplicates of Picard.
Peak call were performed by  Danpos2 for with option “-q 40 -kw 750 -kd 1500”.
Bigwig files were generated by bamCompare with “--binSize 200”.
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: Human NB cell line IMR32 were cultured in RPMI1640 (Wako) supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen) and 50 μg/ml penicillin/streptomycin (Sigma–Aldrich) in an incubator with humidified air at 37 °C with 5% CO2

extract_protocol:
ChIP assays were performed as previous papers (Orlando V et al., 1997, Methods, Fujimura Y et al., 2006, Development). Cross-linked chromatin prepared from the indicated cells was precipitated by each antibodies.
NEBNext Ultra DNA Library Kit for Illumina (NEB) was used to generate libraries from samples. All procedures were performed according to the protocols suggested by the manufacturers. The concentration of libraries was measured by Qubit 2.0 Fluorometer with Qubit dsDNA HS Assay Kit (Invitrogen).
Average length of libraries was analyzed on TapeStation with High Sensitivity D1000 ScreenTape (Agilent Technologies) according to the manufacturer's protocol. Finally, the molar concentration of each library was quantified by Library Quantification Kit (Takara). Single-read sequencing of libraries with a read length of 75 was performed with NextSeq 500 Sequencing System (Illumina)

treatment_protocol: without treatment

value: neuroblastoma cell line

value: H3K27me1, Active Motif MABI 0321


title: JM026

extract_protocol:
RNA was harvested using the AllPrep DNA/RNA FFPE kit (Qiagen). 500ng of total RNA was used for the construction of sequencing libraries.
rRNA-depleted Libraries for mRNA deep sequencing was generated using an adapted version of the Illumina v1.5 protocol and optimized for reaction volume.
Paired-end 50 sequencing was done using the Illumina HiSeq 2000 Platform (Illumina).


title: Sam68_si_3

city: Tsukuba

first: takehito

last: sugasawa

state: Select State

address: Ibaraki

institute: University of tsukuba

data_processing:
RNA-seq reads were aligned to the hg38 genome assembly using CLC genomics workbench 21.0.3 with the default settings.
A statistical differential expression test was used "Differential Expression for RNA-Seq tool" in the CLC software.
Supplementary files format and content: Excel file of statistic test and expression data.

molecule: polyA RNA

source_name: Oral squamous cell carcinoma

growth_protocol: HO-1-N-1 cells were cultured at 37℃ in a 5% CO2 atmosphere in Dulbecco’s Modified Eagle Medium (DMEM) (Nacalai Tesque, Kyoto, Japan) containing 10% fetal bovine serum (Nichirei Biosciences).

extract_protocol:
Total cellular RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s protocol.
Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina, and NEBNext Poly(A) mRNA Magnetic Isolation Module (Cat# E7770 and E7490; New England Biolabs).

treatment_protocol: Sam68 or control siRNA were transfected into cells (60–70% confluence) using HilyMax (Dojindo Laboratories, Kumamoto, Japan) transfection reagent according to the manufacturer’s instructions.

value: Sam68 siRNA transfection


title: JM027


title: Control_5

value: Control siRNA transfection


title: JM024


title: JM025


title: Sam68_si_1


title: Control_1


title: Control_3


title: IMR32_EZH1

value: EZH1, Millipore ABE281


title: JM023


title: JM022


title: JM020


title: Healthy 6 [Sample17H]

first: Mattias

last: Magnusson

address: BMC A12

department: Molecular Medicine and Gene Therapy

institute: Lund university

data_processing:
Data sequenced on illumina  Nextseq 500
data procesing and analysis using Kallisto, version 0.46.0)
scvelo==0.2.4, loompy==3.0.6, scanpy==1.8.2, igraph==0.9.9, phate==1.0.7,  pandas==1.5.0.dev0+268.gbe8d1ec88,  re==2.2.1, numpy==1.19.5, matplotlib==3.5.1. We removed mitochondrial and ribosomal genes. data = adata[ adata.obs['geneSum'] > 1000]. scanpy.pp.filter_cells(adata, min_genes=100 ). scanpy.pp.downsample_counts(adata, counts_per_cell= 1000 ). scanpy.pp.filter_genes(adata, min_counts=1 )
read alignment via kallisto version 0.46.0
Assembly: Genome sequence, primary assembly (GRCh38)” file named GRCh38.primary_assembly.genome.fa.gz was attained from "https://notebook.community/linnarsson-lab/loompy/notebooks/build_index"
Assembly: the comprehensive PRI gene annotation on the primary assembly GTF file named gencode.v31.primary_assembly.annotation.gtf  was attained from "https://notebook.community/linnarsson-lab/loompy/notebooks/build_index"
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: the CellRanger matrix files and therefore can be loaded by e.g. scanpy.read_10x_mtx( "untar path" )

source_name: proximall lung cells

extract_protocol:
Total RNA was extracted from 160546 cells in from all samples, of which only 148 were deemed to be mast cells that were used for thie analysis. This was after red blood cell lysis (and CD45 depletion for sample 1)
cDNA Library constructed using Chromium system (10x Genomics)

treatment_protocol: Freshly isolated human lung cells from proximal tissue

tag: subject status

value: Healthy never smoker

value: Biopsy

value: proximall lung cells


title: Healthy 8 [sample21]


title: Sam68_si_2


title: JM017

data_processing:
RNA quantification was performed with Cutadapt
Alignment with STAR aligner 2.4.2a to Genome GRCh38 using default parameters
Assembly: GRCh38
Supplementary files format and content: geneExp_n_114_ensembl.csv

value: pre-treatment endoscopic biopsies


title: Healthy 4 [NovaSeq6.Pavan1]


title: Tumefactive demyelinating lesion, scRNAseq

city: Fuzhou

first: Xiaoyong

last: Chen

address: Taijiang district

institute: The First Affiliated Hospital of Fujian Medical University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumefactive demyelinating lesion

extract_protocol:
The fresh samples of Tumefactive demyelinating lesion and glioma were harvested from the center of lesion and immediately preserved in tissue preservation solution waiting for further processing. Then, the sample was taken out and washed by phosphate-buffered saline (PBS). After that, the sample was minced into small pieces by scissors on ice and enzymatically digested by brain dissociation kit, which contains 1.25 mL of Enzyme N, 2×50 mL of Buffer X (sterile), 1.5 mL of Buffer Y (sterile), 1 vial of Enzyme A (lyophilized powder), and 1 mL of Buffer A. The mixture consisted of sample and enzyme hydrolysate was subjected to the next step for mechanical dissociation via the gentleMACS™ Dissociators. Then, cell clumps and large fragments were strained by a MACS® SmartStrainer (70 μm). After centrifuging cell suspension and resuspending cells with buffer, the final single-cell suspension was generated.
According to the manufacturer’s protocol, the single-cell suspension was loaded into the Chromium single-cell controller (10X Genomics) for single-cell capturing and downstream library constructions with the Single Cell 3′v2 reagent kit (10x Genomics). Briefly, single cells were suspended and recovered, aiming for 6000 cells. Cells were partitioned into Gel Bead-In-EMulsions (GEMs) with barcoded gel beads. Following cell capture and lysis, complementary DNA was generated and amplified via a S1000TM Touch Thermal Cycler (Bio-Rad).

value: Tumefactive demyelinating lesion


title: Glioma, scRNAseq

description: 10x Genomics

source_name: Glioma

value: Glioma


title: JM018

value: MSS


title: JM008

value: iCR


title: JM011


title: Healthy 2 [nextseq5.s11]


title: Healthy 3 [NextSeq7.Sample15]

value: Healthy smoker

value: Proximal lung donor tissue


title: JM015


title: Healthy 7 [Sample18H]


title: hmec, GNAQ Q209R, rep 3

city: Durham

first: Daniel

last: Snellings

state: NC

address: 213 Research Drive

institute: Duke University

data_processing:
nf-core/rnaseq v3.6
Assembly: hg19
Supplementary files format and content: merged.gene_tpm.tsv provides the per-gene count in tmp for each sample in the experiment
Supplementary files format and content: merged.gene_counts_length_scaled.tsv provides the normalized per-gene counts for each sample in the experiment scaled by transcript size

source_name: microvasculature

extract_protocol:
Qiagen Rneasy
Illumina dual index

value: microvasculature

value: HMEC

value: endothelial cell line

value: GNAQ Q209R


title: JM004


title: hmec, GNAQ Q209R, rep 2


title: Healthy 1 [nextseq3.Sample2]

source_name: Proximall lung cells after CD45 depletion


title: hmec, GNAQ Q209L, rep 2

value: GNAQ Q209L


title: hmec, GNAQ Q209L, rep 1


title: hmec, GNAQ Q209R, rep 1


title: JM006

source_name: pre-treatment endoscopic biopsies


title: JM001


title: JM007

value: MSI


title: JM003

value: CR


title: JM002


title: hmec, GNAQ Q209L, rep 3


title: hmec, GNAQ R183Q, rep 3

value: GNAQ R183Q


title: Healthy 5 [nextseq5.S10]

value: Healthy never smoker

value: Biopsy


title: hmec, GNAQ C9X, rep 3

value: GNAQ C9X


title: hmec, GNAQ R183Q, rep 1


title: hmec, GNAQ C9X, rep 2


title: A549_siDDX17_3rd

city: Wuhan

first: Dong

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
Raw reads were first discarded if containing more than 2-N bases. The adaptors were removed from raw reads, and low-quality bases were trimmed using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also discarded.
Subsequently, clean reads were aligned to the GRch38 genome by Tophat2 allowing no more than mismatches. Only the uniquely mapped reads were applied to calculate gene reads number and fragments per kilobase of transcript per million fragments mapped (FPKM) value .
The R Bioconductor package edgeR  was utilized to screen out the differentially expressed genes (DEGs). The cut-off criteria for identifying DEGs was set as P value <0.01 and fold change>1.5 or < 2/3
The ABLas pipeline was applied to define and quantify the alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples according to previously described methods
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: A549 cells (Human lung adenocarcinoma cell line)

growth_protocol: A549 cells (Human lung adenocarcinoma cell line ) obtained from China Center for Type Culture Collection (CCTCC, Wuhan, China) were cultured in MEM supplemented with 10% fetal bovine serum (FBS), 100 μg/mL streptomycin and 100 U/mL penicillin at 37°C in 5% CO2. Transfection of A549 cells with siRNA was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instruction. After 48 h transfection, the cells were harvested for RT-qPCR analysis.

extract_protocol:
Total RNA was extracted with TRIZOL (Ambion).  RQ1 DNase (Promega) was used to remove any remaining DNA form the total RNA.  RNA quality and quantity were assessed by measuring the absorbance at 260nm/280nm (A260/A280) using Nanodrop One (Thermo).  RNA integrity was further verified by electrophoresis through a 1.5% agarose gel.
After ligation, the cDNAs were fragmented into 300–500bp fragments. Finally, the DNA fragments were amplified, purified, quantified, and stored at -80℃ until used for sequencing. The dUTP marked second strand was not amplified, allowing strand specificity.

treatment_protocol: Cell proliferation was examined using a Cell Counting kit-8 (CCK-8;  dojindo, Co., Shanghai, China).  Briefly, A549 cells were seeded at a density of 6,000 cells/well in 96-well culture plates.  Wells without cells were used as blank controls and cells treated with an equal volume of phosphate-buffered saline (PBS) were used as controls.  After siRNA transfection at 24, 48 and 72 h, a solution of CCK-8 (20 μl ) was added to the culture medium and incubated for a further 3 h. At last, stop solution 50 μl was then added to each well and the OD450 values was measured with a PerkinElmer/envision.  The cell proliferation rate was calculated according to the following formula: proliferation rate = (experimental OD value − blank OD value) / (control OD value − blank OD value) × 100%.

value: Human lung adenocarcinoma

tag: genotype/variation

value: DDX17 knockdown


title: A549_siDDX17_1st

tag: cell type


title: Ribo-seq miRNA inhibitors_1

city: Tokorozawa

first: Hiroaki

last: Sako

institute: Waseda University

data_processing:
library strategy: Ribosome profiling
Adapter sequences were removed with Cutadapt
rRNA contmaination was removed from sequenced reads with Bowtie and converted to fastq files which were deposited as raw files
Sequences were aligned to Ensembl canonical transcript sequences with Bowtie
Assembly: GRCh38
Supplementary files format and content: txt, raw counts

growth_protocol: DMEM high glucose with 10% FBS, streptomycin, and penicillin

extract_protocol:
Cells were lysed with polysome lysis buffer with cycloheximide (100ug/ml)
TruSeq Ribo Profile (Mammalian) Kit (illumina) was used with some modifications.

value: miRNA inhibitors


title: Ribo-seq non-cleaving shNBD1_1

value: non-cleaving shRNA


title: Ribo-seq NC control2

value: control for inhibitors


title: Ribo-seq miRNA inhibitors_2


title: Ribo-seq non-cleaving shNBD1_2


title: Ribo-seq NC control1


title: A549_siDDX17_2nd


title: JM005

first: Bic

value: pre-treatment endoscopic biopsies

value: MSS


title: A549_siCtrl_3rd

value: control plasmid


title: hmec, GNAQ R183Q, rep 2

value: microvasculature

value: HMEC

value: endothelial cell line


title: Ribo-seq Scr2

value: control for shRNA


title: A549_siCtrl_1st


title: Ribo-seq Scr1


title: hmec, wild type GNAQ, rep 3

value: GNAQ WT


title: A549_siCtrl_2nd


title: hmec, GNAQ C9X, rep 1


title: H216-vN

city: Madison

first: Sushmita

last: Roy

state: WI

address: 330 N. Orchard St.

department: Dept. of Biostatistics and Medical Informatics

institute: University of Wisconsin-Madison

description: HOX PROPAGATION + Cells were sub-cultured at a 2:3 ratio. Briefly, cells were washed once with PBS, incubated in Accutase for 1.5-2 mins, and removed from the surface by gentle pipetting. After centrifugation, cells were gently resuspended in NMP Medium containing 10 μM Y27632 and seeded on 35 mm Matrigel-coated plates. Media was replenished on Day 4. Cells were sub-cultured again at a 2:3 ratio on Day 5. The media was replenished daily on Days 7-10 with NMP media containing 30 ng/mL GDF11 (Peprotech) and 1 μM dorsomorphin (Tocris) to stimulate caudal NMP development. Cells were sub-culture on Day 9 at a 1:1 ratio, and NMPs were differentiated after 216hrs + DIFFERENTIATION of H168 and H216

data_processing:
Cell Ranger v2.0.2 and bcl2fastq v2.20.0.422 were used to perform demultiplexing, alignment, filtering, barcode counting, UMI counting, and gene expression estimation for each sample according to the 10x Genomics documentation. The gene expression estimates from each sample were then aggregated using Cellranger (cellranger aggr).
Genes that appeared in fewer than 5 cells and cells with fewer than 5000 UMIs from the dataset were filtered out from each sample.
Each cell’s expression value was depth normalized to a depth of 5000 followed by variance stabilizing normalization as implemented AdjustVariance in the pagoda2 package with default parameters except gam.k=10
Genome_build: hg19
Supplementary_files_format_and_content: MatrixMarket format matrix files include normalized (depth, variance stabilization) values, tar packed and gzipped for each sample
Supplementary_files_format_and_content: text files include barcode IDs, tar packed and gzipped for each sample
Supplementary_files_format_and_content: tab-delimited text files include HUGO symbol IDs of genes, tar packed and gzipped for each sample

source_name: hESC-derived neurons (WA09)

growth_protocol: hESCs were maintained at 37°C in 5% CO2 in Essential 8 (E8) medium on 35 mm Matrigel (WiCell) coated tissue culture-treated plates and were passaged when 70-80% confluent. Briefly, cells were washed once with phosphate buffered saline (PBS, Invitrogen), then incubated at 37°C in Versene (Invitrogen) for 5 minutes. Versene was aspirated, the cells were gently dissociated from the well with fresh E8, and re-plated at a  1:12 seeding ratio. Media was replenished daily (Lippmann et. al. 2014).

extract_protocol:
Cells were singularized for scRNAseq by dissociation with Papain (Worthington). Briefly, cells were washed once with PBS and incubated in papain at 37°C for 1hr on an orbital shaker, then triturated vigorously with a wide-bore pipette. The cell suspension was centrifuged at 300g for 5 minutes, then quenched with ovomucoid solution for 10 minutes at room temperature. Quenched cells were centrifuged, gently resuspended in PBS containing 0.2% BSA and 10 μM Y27632, then passed through a 40 mm cell strainer (Mitenyi Biotec) to remove debris. Cells were kept on ice before being quantified and diluted for sequencing.
RNA libraries were prepared for sequencing according to the manufacturer’s recommendations using the Single Cell 30 Reagent v2/v3  kits (10X Genomics).

treatment_protocol:
HOX PROPAGATION: To initiate neuromesodermal progenitor (NMP) differentiation, hESCs were washed once with PBS, incubated at 37°C in Accutase (Invitrogen) for 5 mins, singularized by gentle trituration, and quenched with 1 volume E8 media. Following centrifugation for 5 mins at 300g, hESCs were replated onto 35 mm Matrigel-coated plates at a density of 1.5 x 105 cells/cm2 in E8 medium with 10 μM ROCK inhibitor (Y27632, Tocris). The media was replaced with Essential 6 (E6) medium (Lippmann et al., 2014) on the following day (Day 0), and then changed to E6 supplemented with 200 ng/mL FGF8b (Peprotech) 24 hours later (Day 1). On Day 2, Hox propagation was initiated by activation of Wnt signaling using NMP media comprised of E6 medium supplemented with 200 ng/mL FGF8b and 3 μM CHIR99021 (Tocris). This constitutes the “Hox timepoint” of 0hrs.
pCNSP DIFFERENTIATION: NMPs were cultured for 1 day in pCNSP media, comprising of E6 media supplemented with 1 µM retinoic acid (RA; Sigma), 10 µM SB-431542 (Abcam), and 100 nM µL LDN-193189 (Stemgent). Cells were singularized and replated at 5 x 105 cells/cm2 in pCNSP media containing 10 μM Y27632 for an additional 2 days. Media was replenished daily.
VENTRAL DIFFERENTIATION: Ventral progenitors were generated by culturing in E6 media containing 100 nM RA, 10 µM SB-431542, 100 nM LDN-193189, 0.5 μM Pur, and 0.5 μM SAG for 4 days. Progenitors were cryopreserved to synchronize cultures.
NEURONAL DIFFERENTIATION: For neuronal differentiation and maturation prior to sequencing, cells were thawed in maturation media containing 10 μM Y27632 at 5 x 105 cells/cm2 overnight, with daily media changes for 6 days. Maturation media consisted of E6 containing 1x N2 Supplement (Thermofisher), 50x B27 Supplement (Thermofisher), 1 µM cAMP (Sigma), 10 ng/mL GDNF, 10 ng/mL BDNF, 10 ng/mL NT-3 (Peprotech), and 10 µM DAPT (Tocris). Media was switched to Neurobasal media (Gibco) containing 1x N2 Supplement, 50x B27 Supplement, 1x Glutamax (Thermofisher), 1x PenStrep (Invitrogen), 1 ng/mL laminin (Thermofisher), 1 µM cAMP, 10 ng/mL GDNF, 10 ng/mL BDNF, and 10 ng/mL NT-3 for 14 days. 2 days prior to sequencing, the media was supplemented with 10 µM AraC (Sigma) to eliminate proliferating cells.
DIFFERENTIATION of H168 and H216: Cultures were then switched to E6 media containing 1 μM RA, 2 μM SAG, and 2 μM purmorphamine for 3 days. Progenitors were sub-cultured at a 1:3 ratio and gently resuspended in E6 medium supplemented with 1 μM RA, 100 nM SAG, 100 nM purmorphamine, and 10 μM Y27632 and plated on 35mm Matrigel-coated well-plates for an additional 3 days. Then, the media was switched to E6 medium supplemented with 1 μM RA, 100 nM SAG, 100 nM purmorphamine, and 5 μM DAPT for an additional 5 days, then cryopreserved. Media was replenished daily.

value: hESC-derived neurons

value: HUES3-Hb9-GFP (Di Giorgio et al. 2008)

value: 216 hrs of HOX propagation (11 days), followed by 5 days of RA/SAG/Pur treatment. Cultures were matured for 5 days with DAPT prior to sequencing.


title: DN6_snATACseq

city: SAINT LOUIS

first: Parker

middle: C

last: Wilson

state: MO

address: 660. S Euclid Ave., CB 8118

institute: Washington University in St. Louis

data_processing:
Fastq files was processed with cellranger-atac v2.0 count using refdata-cellranger-arc-GRCh38-2020-A-2.0.0
Filtered barcode-peak matrix and fragment file
snRNA-seq: cellranger count v4.0
snATAC-seq: cellranger-atac count v2.0
Genome_build: snRNA-seq: GRCh38-2020-A.premrna
Genome_build: snATAC-seq: refdata-cellranger-arc-GRCh38-2020-A-2.0.0
Supplementary_files_format_and_content: A total of 11 snRNA-seq libraries from this repository (1 control, 2 DKD), GSE13188213 (3 control, 3 DKD), and GSE151302 (2 control; samples 4 and 5) were counted with cellranger count v4.0 and a custom pre-mrna reference on GRCh38. A total of 13 snATAC-seq libraries from this repository (1 control, 7 dkd) and GSE151302 (5 control) were counted with cellranger-atac count v2.0 and refdata-cellranger-arc-GRCh38-2020-A-2.0.0.

source_name: Human Kidney Cortex - DN6

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche). Samples were cut into < 2 mm pieces, homogenized using a Dounce homogenizer (885302–0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer, and incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. The homogenate was filtered through a 40-μm cell strainer (43–50040–51; pluriSelect) and centrifuged at 500g for 5 minutes at 4°C. The pellet was resuspended, washed with 4 ml of buffer, and incubated on ice for 5 minutes. Following centrifugation, the pellet was resuspended in Nuclei Buffer (10× Genomics, PN-2000153), filtered through a 5-μm cell strainer (43–50020–50; pluriSelect)
10xGenomics snATAC-seq library(v1 chemistry)
snATAC-seq
Nuclear isolation from bulk kidney cortex https://www.protocols.io/view/nuclei-isolation-from-human-kidney-for-single-nucl-nahdab6
10X genomics single cell gene expression OR single cell ATAC
snRNA-seq and snATAC-seq

tag: Sex

value: F

tag: age

tag: race

tag: egfr

tag: global glomerulosclerosis

value: Severe, >50%

tag: ifta


title: DN7_snATACseq

source_name: Human Kidney Cortex - DN7

value: M

value: Moderate, 26 - 50%


title: manL mutant, Glucose, rep 2

city: Gainesville

first: Alejandro

last: Riveros Walker

state: Fl

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

data_processing:
Fastq groomer
Fastq quality trimmer
Cutadapt
Map with Bowtie for Illumina
Htseq-count
Assembly: NC_009009.1
Supplementary files format and content: Excel file, normalized output from edgeR

organism: Streptococcus sanguinis SK36

source_name: planktonic culture

growth_protocol: Overnight BHI cultures (n = 3) of each bacterial strain were diluted 20-fold into TY medium supplemented with 20 mM glucose and incubated at 37 degree in ambient air supplemented with 5% CO2. After the optical density OD600 reached 0.5, cells were harvested by centrifugation and treated with RNAprotect reagent.

extract_protocol:
Bacterial cells were resuspended in a lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, and 0.4% SDS) and disrupted by vigorous shaking for 1 min together with an equal volume of acidic phenol: chloroform (1:1, v/v) and similar amount of glass beads. After 10 min of centrifugation at 15,000× g at room temperature, the clarified aqueous layer was removed and processed using an RNeasy mini kit (Qiagen, Germantown, MD) for extraction of total RNA. Genomic DNA contamination was removed in column using an RNase-free DNase I solution (Qiagen).
Total RNA is treated with RiboZero Plus rRNA depletion kit to remove rRNA, followed by standard procedure for Illumina cDNA library preparation and sequencing

value: planktonic culture

value: mid-exponential phase

value: manL mutant

tag: treatment

value: 37 degree, ambient air with 5% CO2


title: manL mutant, Glucose, rep 1


title: manL mutant, Glucose, rep 3


title: DN3_snATACseq

source_name: Human Kidney Cortex - DN3


title: H72-vN

description: HOX PROPAGATION + Cells were sub-cultured at a 2:3 ratio. Briefly, cells were washed once with PBS, incubated in Accutase for 1.5-2 mins, and removed from the surface by gentle pipetting. After centrifugation, cells were gently resuspended in NMP Medium containing 10 μM Y27632 and seeded on 35 mm Matrigel-coated plates. Media was replenished on Day 4. pCNSPs were differentiated after 72hrs + pCNSP DIFFERENTIATION + VENTRAL DIFFERENTIATION + NEURONAL DIFFERENTIATION

tag: cell line

value: 72 hrs of HOX propagation (5 days), followed by 5 days of RA/SAG/Pur treatment. Cultures were matured for 5 days with DAPT prior to sequencing.


title: H168-vN

description: HOX PROPAGATION + Cells were sub-cultured at a 2:3 ratio. Briefly, cells were washed once with PBS, incubated in Accutase for 1.5-2 mins, and removed from the surface by gentle pipetting. After centrifugation, cells were gently resuspended in NMP Medium containing 10 μM Y27632 and seeded on 35 mm Matrigel-coated plates. Media was replenished on Day 4. Cells were sub-cultured again at a 2:3 ratio on Day 5. The media was replenished daily on Days 7-9 with NMP media containing 30 ng/mL GDF11 (Peprotech) and 1 μM dorsomorphin (Tocris) to stimulate caudal NMP development. NMPs were differentiated after 168hrs. + DIFFERENTIATION of H168 and H216

value: 168 hrs of HOX propagation (9 days), followed by 5 days of RA/SAG/Pur treatment. Cultures were matured for 5 days with DAPT prior to sequencing.


title: WT, Glucose, rep 1

value: Wild type


title: DN5_snATACseq

source_name: Human Kidney Cortex - DN5

value: Non-hispanic White


title: WT, Glucose, rep 3


title: hmec, wild type GNAQ, rep 2

value: microvasculature

value: HMEC

value: endothelial cell line


title: WT, Glucose, rep 2


title: H120-vN

description: HOX PROPAGATION + Cells were sub-cultured at a 2:3 ratio. Briefly, cells were washed once with PBS, incubated in Accutase for 1.5-2 mins, and removed from the surface by gentle pipetting. After centrifugation, cells were gently resuspended in NMP Medium containing 10 μM Y27632 and seeded on 35 mm Matrigel-coated plates. Media was replenished on Day 4. Cells were sub-cultured again at a 2:3 ratio on Day 5. pCNSPs were differentiated after 120hrs. + pCNSP DIFFERENTIATION + VENTRAL DIFFERENTIATION + NEURONAL DIFFERENTIATION

value: hESC-derived neurons

value: HUES3-Hb9-GFP (Di Giorgio et al. 2008)

value: 120 hrs of HOX propagation (7 days), followed by 5 days of RA/SAG/Pur treatment. Cultures were matured for 5 days with DAPT prior to sequencing.


title: DN4_snATACseq

source_name: Human Kidney Cortex - DN4


title: hmec, wild type GNAQ, rep 1

value: GNAQ WT


title: H48-vN

description: HOX PROPAGATION + Cells were sub-cultured at a 2:3 ratio. Briefly, cells were washed once with PBS, incubated in Accutase for 1.5-2 mins, and removed from the surface by gentle pipetting. After centrifugation, cells were gently resuspended in NMP Medium containing 10 μM Y27632 and seeded on 35 mm Matrigel-coated plates. pCNSPs were differentiated after 48hrs. + pCNSP DIFFERENTIATION + VENTRAL DIFFERENTIATION + NEURONAL DIFFERENTIATION

value: 48 hrs of HOX propagation (4 days), followed by 5 days of RA/SAG/Pur treatment. Cultures were matured for 5 days with DAPT prior to sequencing.


title: Control6_snRNAseq

data_processing:
Fastq files was processed with cellranger v4.0 count using a custom pre-mrna reference GRCh38-2020-A.premrna
Filtered barcode-feaure matrix
snRNA-seq: cellranger count v4.0
snATAC-seq: cellranger-atac count v2.0
Genome_build: snRNA-seq: GRCh38-2020-A.premrna
Genome_build: snATAC-seq: refdata-cellranger-arc-GRCh38-2020-A-2.0.0
Supplementary_files_format_and_content: A total of 11 snRNA-seq libraries from this repository (1 control, 2 DKD), GSE13188213 (3 control, 3 DKD), and GSE151302 (2 control; samples 4 and 5) were counted with cellranger count v4.0 and a custom pre-mrna reference on GRCh38. A total of 13 snATAC-seq libraries from this repository (1 control, 7 dkd) and GSE151302 (5 control) were counted with cellranger-atac count v2.0 and refdata-cellranger-arc-GRCh38-2020-A-2.0.0.

source_name: Human Kidney Cortex - Control6

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche) and RNase inhibitors (Promega, N2615 and Life Technologies, AM2696). Samples were cut into < 2 mm pieces, homogenized using a Dounce homogenizer (885302–0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer, and incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. The homogenate was filtered through a 40-μm cell strainer (43–50040–51; pluriSelect) and centrifuged at 500g for 5 minutes at 4°C. The pellet was resuspended, washed with 4 ml of buffer, and incubated on ice for 5 minutes. Following centrifugation, the pellet was resuspended in nuclei suspension buffer (1x PBS, 1% BSA, 0.1% RNase inhibitor), filtered through a 5-μm cell strainer (43–50020–50; pluriSelect)
10xGenomics snRNA-seq library(3' kit v3)
snRNA-seq
Nuclear isolation from bulk kidney cortex https://www.protocols.io/view/nuclei-isolation-from-human-kidney-for-single-nucl-nahdab6
10X genomics single cell gene expression OR single cell ATAC
snRNA-seq and snATAC-seq

value: F


title: H24-vN

description: HOX PROPAGATION + pCNSP DIFFERENTIATION (after 24hr of HOX PROPAGATION) + VENTRAL DIFFERENTIATION + NEURONAL DIFFERENTIATION

value: 24 hrs of HOX propagation (3 days), followed by 5 days of RA/SAG/Pur treatment. Cultures were matured for 5 days with DAPT prior to sequencing.


title: Osteoblast-hPTH-3

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

hyb_protocol: Fragmented and Labeled ss-DNA (3.5 ug) was hybridized to Affymetrix Mouse Gene 2.0 ST GeneChips overnight at 45oC. Hybridized GeneChips were washed and stained in an Affymetrix Fluidics Station 450

scan_protocol: Microarrays were scanned using an Affymetrix 7G Scanner

data_processing: CEL files were imported into Affymetrix Expression Console software and data were anayzed by RMA (Gene Level Default RMA sketch) to obtain probe set expression values

source_name: osteoblast, human parathyroid hormone (1-34) 4hr

label_protocol: Total RNA (100 ng) converted to fragmented and biotin-labeled ssDNA by WT Plus kit (Affymetrix)

growth_protocol: Dissected strips of calvaria from 7-10 day old C57BL/6J mice were incubated at 37oC with shaking for 20 min in a solution of 0.1% collagenase II (Worthington) and 0.05% trypsin (Invitrogen) in αMEM (Invitrogen). Supernatants were neutralized with 25% heat-inactivated fetal bovine serum (FBS, Invitrogen), and the digestion of calvarial strips was repeated twice. Supernatants from the three digestions were combined and centrifuged, and pellets were reconstituted in growth medium consisting of αMEM containing 10% heat-inactivated FBS and 0.1% Primocin (Invivogen). After 24 hours in culture, Primocin was reduced to 0.05%. Cells were sub-cultured at 90% confluency and at passage 2 differentiated post-confluence (Day 3). Cells were differentiated starting on Day 3 in αMEM containing 10% heat-inactivated FBS and 0.05% Primocin supplemented with 5 mM β-glycerophosphate (Millipore Sigma) and 50mg/L ascorbic acid (Millipore Sigma). On Day 10 cells were serum deprived in medium containing 0.5% BSA (Millipore Sigma) for 24 hrs before experimental treatment.

extract_protocol: RNA was prepared with the RNeasy Plus Mini Kit (Qiagen).  RNA quality was assessed by Bioanalyzer 2100 (Agilent).

treatment_protocol: Cells were treated with vehicle or hormone for 4 hours in serum-free medium containing 0.5% BSA. Following treatment, cells were washed with PBS prior to RNA isolation

tag: strain

value: Osteoblast

value: human parathyroid hormone


title: DN2_snATACseq

source_name: Human Kidney Cortex - DN2

value: M

value: Moderate, 26 - 50%


title: DN1_snATACseq

source_name: Human Kidney Cortex - DN1


title: Osteoblast-bPTH-1

source_name: osteoblast, bovine parathyroid hormone (7-34) 4hr

value: bovine parathyroid hormone


title: Osteoblast-bPTH-3


title: Osteoblast-bPTH-2


title: Treated AntagomiR experiment 2 [R2223P]

city: Clemson

first: Susan

last: Duckett

state: South Carolina

address: 105 Collings ST, RM 112 BRC

department: Animal and Veterinary Science

institute: Clemson University

data_processing:
fastqc/0.11.8
trimgalore/0.6.5
rsem/1.3.3
subread's feature Counts/2.0.2
edgeR/3.34.1
Assembly: Ovis aries (TEXEL) ensembl release 96
Supplementary files format and content: tab-delimited text of raw gene counts

organism: Ovis aries

source_name: Ovine primary cells

growth_protocol: Satellite cells were cultured in high glucose (4.5g/L) DMEM with 20% fetal bovine serum (FBS), 1% penecilline/ streptomycin, and 0.1% gentamicin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was harvested using Trizol, and then shipped on dry ice to Novogene for sequencing.
mRNA was isolated from total RNA using poly-T oligo-attached magnetic beads. Purified mRNA was fragmented, and first strand cDNA was synthesized with random hexamer primers and followed by second strand cDNA synthesis. Libraries then had end repair, A-tailing, adapter ligation, size selection, amplification, and purification and were then ready for quality control. Libraries were checked for quality, quantity, and size distribution with Qubit and RT-PCR. Libraries were then pooled and sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol:
miRNA treatments (mimiic miR-127 or AntagomiR-22-3p) were andministered using RNAiMAX lipofectamine when cells reached 60% confluence at 100nM or 500nM concentration, respectively, according to manufacturer specifictions.
Cells were transfected on d 0 and RNA was harvested 4 d following transfection.

value: Ovine primary cells

value: skeletal muscle satellite cells

value: SuffolkxTexel

value: AntagomiR-22-3p at 500 nM

value: 4 d after transfection


title: VH1-2, mVHdel, VK1-33-CS, SP, IgH3

city: Boston

first: Frederick

last: Alt

address: 1 Blackfan Circle

institute: Boston Children's Hospital

data_processing:
Library strategy: HTGTS-rep-seq
HTGTS-Rep-Seq data analysis was done by the HTGTS-Rep-Seq bioinformatics pipeline (Github address: https://github.com/Yyx2626/HTGTSrep), using IgBLAST with default parameters for qualified reads mapping. Only reads with more than 98% of the sequences having a sequencing Quality Score ≥20 were kept; only joined reads (R1 and R2 had an overlap region ≥10 bp and mismatch rate ≤8%) were kept.
Genome_build: mm9
Supplementary_files_format_and_content: .db.txt files were generated using HTGTS-Rep-Seq pipeline (IgBLAST)

source_name: splenic B220+ B cells

extract_protocol:
Splenic B cells were purified from 5-8 weeks old mice by MACS® Microbeads according to the manufacturer’s protocol. In brief, spleens were dissected out from unimmunized mice, prepared into single cell suspensions and stained with anti-B220 Microbeads for 20 minutes at 4°C. Then, the splenic B cells were collected using the LS column and MACSTM Separater and lysed for genomic DNA extraction.
10ug of genomic DNA from purified splenic B cells was used for generating HTGTS-rep-seq libraries as previously described (Lin et al. 2016). 4 bait primers that target mouse JH1, JH2, JH3 and JH4 were mixed to capture all IgH heavy chain repertoire in one library. And 4 bait primers that target mouse Jk1, Jk2, Jk4 and Jk5 were mixed to capture all Igk light chain repertoire in one library.

value: C57BL/6 and 129/Sv mix

value: spleen

value: B220+ B cells

tag: locus (ig heavy-chain or light-chain)

value: IgH

tag: conditions

value: naïve

tag: primers

value: JH1, JH2, JH3, JH4

tag: sequencing method

value: HTGTS-Rep-Seq


title: Osteoblast-Vehicle-3

source_name: osteoblast, vehicle 4 hr

value: Osteoblast

value: Vehicle


title: VH1-2, mVHdel, VK1-33-CS, SP, IgH2

tag: tissue


title: Osteoblast-hPTH-1

value: human parathyroid hormone


title: VH1-2, mVHdel, VK1-33-CS, SP, IgH1


title: hTERT-RPTEC_bulkATAC_1

city: St. Louis

first: Yoshiharu

last: Muto

department: Medicine / Nephrology

data_processing:
Fastq files were trimmed with Trim Galore and aligned with Bowtie2 with --very-sensitive -X 2000 using hg38. PCR duplicates were removed with Picard's MarkDuplicates function.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig format

source_name: hTERT-RPTEC (ATCC, P8)

extract_protocol:
Adherent cells were scraped from culture dishes and centrifuged at 500 × g for 5 min.
50,000 cells were suspended in 50 μL of ice-cold lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 0.01% Digitonin), followed by incubation on ice for 4 min. Subsequently, 450 μL of ice-cold wash buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20) was added and centrifuged at 600 × g for 6 min. Pellets were resuspended in 25 μL of ATAC-seq transposition mix [12.5 μL 2× Illumina Tagment DNA (TD) buffer; 10.5 μL nuclease-free water; 2.0 μL Tn5 transposase (Illumina/Nextera, FC-121-1030)] and incubated at 37°C for 1 h on a thermomixer. The transposed DNA was purified with QIAGEN MinElute kit and amplified with dual indexes.

value: hTERT-RPTEC