title: Memory CD8 T cells_S308_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta

value: blood PBMCs

value: T-cells

tag: Sex


title: Hi-TrAC_K562_cas9-ZNF234-promoter_rep1

status: Public on Oct 02 2022

type: SRA

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

country: USA

institute: NHLBI

library_source: genomic

data_processing:
Hi-TrAC data raw paired-end reads in FASTQ files were first trimmed of linker sequence CTGTCTCTTATACACATCT for both ends. Only PETs with both ends length >=10bp were kept. Trimmed PETs were mapped to hg38 using Bowtie2 with key parameters of --end-to-end --very-sensitive. Mapped PETs with MAPQ >=10 were converted to BEDPE files. Mapped PETs with distance shorter than 1kb without linker sequence in any end were further filtered. PCR replicates of PETs were filtered if both ends locations were identical.  Unique intra-chromosomal PETs (cis PETs) as BEDPE files were mainly used for downstream analysis. All described processing steps were summarized as tracPre2.py in the cLoops2 package. Raw RNA-seq data reads were mapped to human reference genome hg38 by STAR (v2.7.3a). Gene annotation file (v30) downloaded from GENCODE 89 were used to quantify gene expression level by Cufflinks (v2.2.1). Raw ChIP-seq and ATAC-seq data reads were mapped to human reference genome hg38 by Bowtie2 with key parameters of --local --very-sensitive --no-unal --no-mixed --no-discordant. Mapped PETs with MAPQ >=10 were converted to normalized signals (reads per million) as bigWig files by deepTools for visualization.  Raw Hi-C data reads were processed to human reference genome hg38 by HiC-Pro (v2.11.1). Only intra-chromosomal PETs from the files with a suffix of allValidPairs output by HiC-Pro were used for all following analysis.
Assembly: hg38
Supplementary files format and content: BEDPE files contain the high quality and unique processed interaction paired-end tags.
Library strategy: Hi-TrAC

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: GM12878 cells were cultured in RPMI 1640 medium supplied with 15% fetal bovine serum and 2mM L-glutamine. K562 cells were cultured in RPMI 1640 mudium supplied with 10% fetal bovine serum  and antibiotics ( 100 units/mL Penicillin, 100 µg/mL Streptomycin). Mouse ES cells were cultured with PMEF as feeder cells on gelatin coated plates in ES medium ( MEM, 15% FBS, 2 mM GlutaMAX, 1 mM Sodium Pyruvate, 100 µM Non-essential amino acids, 0.1 mM 2-mercaptoethanol, 10 ng/mL LIF, Penicillin-Streptomycin).

extract_protocol:
For Hi-TrAC and Hi-C, genomic DNA was purified by Phenol-Chloroform extraction. RNA was extracted with QIAzol lysis reagent (QIAGEN) and RNeasy mini kit (QIAGEN). For ChIP-seq and ATAC-seq, genomic DNA was purified with QIAGEN MinElute Reaction Cleanup Kit.
For Hi-TrAC, repair DNA gaps with T4 DNA polymerase. Remove free bridging linker by AMPure XP beads. Then, Digest purified DNA with restriction enzymes MluCI/NlaIII, and enrich biotin-labeled DNA fragments with streptavidin beads. Perform adapter ligation on beads. After washing the beads, run PCR with illumina multiplexing indexed primers. For RNA-seq, libraries were constructed following Smart-seq2 protocol (Picelli et al., 2014). For ChIP-seq, DNA was purified, then end-repaired using End-It DNA End-Repair kit (Epicentre). A-tailing was performed with Klenow Fragment (3'->5' exo-) with the presence of dATP. Universal adapters were then ligated. The libraries were then amplified by PCR using indexed primers. For ATAC-seq, purified genomic DNA was amplified by PCR with indexed primers to construct the libraries. For Hi-C, purified genomic DNA was treated with T4 DNA polymerase to remove biotin labels at DNA ends. Fragment the DNA by sonication to 300-500 bp. Fragmentated DNA was end-repaired, followed with A-tailing. Biotin labeled DNA was enriched with MyOne Streptavidin C1 beads (Invitrogen). PCR adapters were then ligated to the enriched DNA on beads. Perform PCR with indexed primers to amplify the libraries.

treatment_protocol: Cells for Hi-TrAC were fixed with 1% Formaldehyde in culture medium at room temperature for 10 minutes. Wash cells with ice-cold PBS twice, then resuspend cells  with 100 µL reaction buffer (50mM Tris-acetate, pH 7.5, 150mM potassium acetate, 10mM magnesium acetate, 4mM spermidine, 0.5% NP-40). Incubate at 37 ℃ for 4 hours. To extract RNA for RNA-seq, add 700 µL QIAzol to 5,000 cells. Cells for ChIP-seq were fixed with 1% Formaldehyde in culture medium at room temperature for 10 minutes. Wash cells with ice-cold PBS twice. Then perform sonication to break chromatins. Sheared chromatin was immunoprecipitated with anti-CTCF, anti-RAD21, anti-HCFC1, anti-ZNF143 antibodies. After washing, perform Portease K digestion and reverse cross-linking at 65 ℃ overnight. For ATAC-seq, cells were lysed in 100 µL lysis buffer (10 mM Tris-HCl, 10 mM sodium chloride, 3 mM manesium chloride, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin) on ice for 3 minutes. Add 1 mL wash buffer (10 mM Tris-HCl, 10 mM sodium chloride, 3 mM manesium chloride, 0.1% Tween-20), then collect the nuclei by spinning at 500 xg for 10 minutes. Resuspend the nuclei in transposition reaction buffer, and add Tnp complex to perform transposition at 37 ℃ for 30 minutes.  For Hi-C, 1% Formaldehyde fixed cells were permeabilized with lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% NP-40, 1 X protease inhibitor). Chromatin was decondensed with the presence of 0.1% SDS in 1 x restriction enzyme digestion buffer at 65 ℃ for 10 minutes. Add 1% Triton X-100, and incubate at 37 ℃ for 1 hour to quench SDS. Digest the chromatin with restriction enzymes CviQ I, CviA II and BfaI. Wash cells twice with wash buffer (1 x PBS, 1 mM EDTA, 0.1% Triton X-100). The DNA ends of digested chromatin were blunted and labeled with biotin by Klenow enzyme with the presence of dCTP, dGTP, dTTP and biotin-14-dATP, followed by ligation using T4 DNA ligase. Reverse cross-linking at 65 ℃ overnight.

tag: cell line

tag: tissue

tag: genotype/variation

value: ZNF234 gene promoter deletion


title: Hi-TrAC_K562_cas9-ZNF225-promoter_rep2

value: ZNF225 gene promoter deletion


title: Hi-TrAC_K562_cas9-ZNF225-promoter_rep1


title: Naïve CD4 T cells_S308_D0 IR-Seq

city: Seoul

first: Sojeong

last: Kim

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

department: Blood Cancer Research Institute

country: South Korea

institute: Yonsei University College of Medicine

description:
IR-Seq
iReperoire human TCR beta

library_source: transcriptomic

data_processing:
Raw reads were assembled and low-quality reads were filtered using Cutadapt (version 2.8).
Filtered reads were aligned on a reference genome downloaded from Ensembl (GRCh38.p13, Accession number: GCA_000001405.28) using STAR (version 2.7.1a).
Assembly: Ensembl (GRCh38.p13, Accession number: GCA_000001405.28) for RNAseq, human reference V, D, J and C genes of TCRs for IR-Seq
Supplementary files format and content: gene expression files of RNAseq contains raw gene counts IR-Seq processed data consists of raw read counts of each CDR3

molecule: total RNA

source_name: blood PBMCs

extract_protocol:
TRIzol reagent (Invitrogen) and QIAgen_RLT_buffer were used for isolation of total RNA for RNAseq, and IR-seq, respectively
Extracted RNAs were processed using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer‟s instructions.
RNA-seq/ IR-seq

tag: cell type

tag: il-7 administration

value: Before

tag: age

value: Male


title: S203_D7_CD8_ME RNAseq

description:
RNAseq
RNAseq

value: Female


title: Naïve CD8 T cells_S306_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta

value: Post


title: S203_Post_CD8_NA RNAseq

description:
RNAseq
RNAseq


title: Hi-TrAC_K562_cas9-CEMIP2-E5_rep2

value: CEMIP2 gene enhancer E5 deleiton


title: Hi-TrAC_K562_cas9-CEMIP2-E5_rep1


title: Memory CD8 T cells_S306_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Memory CD4 T cells_S308_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Hi-TrAC_K562_cas9-ZNF234-promoter_rep2


title: Hi-TrAC_K562_cas9-CEMIP2-E3_rep2

value: CEMIP2 gene enhancer E3 deleiton


title: Hi-TrAC_K562_cas9-CEMIP2-E3_rep1


title: Hi-TrAC_K562_cas9-CEMIP2-E2_rep2

value: CEMIP2 gene enhancer E2 deleiton


title: Control IFN Rep 3

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were aligned to the human genome (G1k V37) using HiSAT2 and reads were assigned to genes using htseq-count.
Differential expression was calculated using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Raw gene counts from htseq

molecule: polyA RNA

source_name: AML

growth_protocol: Cells were cultured in RPMI-1640 supplemented with 2 mM Glutamax, 100 IU/mL Penicillin, 100 μg/mL Streptomycin and 10% HI-FCS in 5% CO2 at 37°C.

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit. RNA concentration was quantified with a Qubit Fluorometer (Thermo Fisher Scientific).
Libraries were prepared using QuantSeq 3’ mRNA-seq Library Prep kit (Lexogen).

treatment_protocol: CRISPR/Cas9 KOs +/- IFN-gamma 25 ng/mL for 48 hours as outlined above.

tag: crispr ko

value: safe

tag: ifn-gamma

value: IFN

tag: replicate


title: Hi-TrAC_K562_cas9-CEMIP2-E2_rep1


title: Naïve CD4 T cells_S306_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Control IFN Rep 2


title: HiC_K562_shHCFC1shZNF143_rep1

data_processing:
Hi-TrAC data raw paired-end reads in FASTQ files were first trimmed of linker sequence CTGTCTCTTATACACATCT for both ends. Only PETs with both ends length >=10bp were kept. Trimmed PETs were mapped to hg38 using Bowtie2 with key parameters of --end-to-end --very-sensitive. Mapped PETs with MAPQ >=10 were converted to BEDPE files. Mapped PETs with distance shorter than 1kb without linker sequence in any end were further filtered. PCR replicates of PETs were filtered if both ends locations were identical.  Unique intra-chromosomal PETs (cis PETs) as BEDPE files were mainly used for downstream analysis. All described processing steps were summarized as tracPre2.py in the cLoops2 package. Raw RNA-seq data reads were mapped to human reference genome hg38 by STAR (v2.7.3a). Gene annotation file (v30) downloaded from GENCODE 89 were used to quantify gene expression level by Cufflinks (v2.2.1). Raw ChIP-seq and ATAC-seq data reads were mapped to human reference genome hg38 by Bowtie2 with key parameters of --local --very-sensitive --no-unal --no-mixed --no-discordant. Mapped PETs with MAPQ >=10 were converted to normalized signals (reads per million) as bigWig files by deepTools for visualization.  Raw Hi-C data reads were processed to human reference genome hg38 by HiC-Pro (v2.11.1). Only intra-chromosomal PETs from the files with a suffix of allValidPairs output by HiC-Pro were used for all following analysis.
Assembly: hg38
Supplementary files format and content: BEDPE files contain the high quality and unique processed interaction paired-end tags.

value: ZNF143 HCFC1 double knockdown


title: RNA-seq_K562_cas9-ZNF225-promoter


title: HiC_K562_shHCFC1shZNF143_rep2


title: Memory CD4 T cells_S306_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: HiC_K562_shControl_rep2

value: shRNA control


title: Control IFN Rep 1


title: Control noIFN Rep 3

value: noIFN


title: HiC_K562_shCTCFshRAD21_rep1

value: CTCF RAD21 double knockdown


title: Naïve CD8 T cells_S306_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta

value: blood PBMCs


title: HiC_K562_shCTCFshRAD21_rep2


title: HiC_K562_shControl_rep1


title: ATAC-seq_GC5382_K562_shCTCFshRAD21_rep2


title: HiC_K562_shCTCF_rep2

value: CTCF knockdown


title: Control noIFN Rep 2


title: HiC_K562_shCTCF_rep1


title: Control noIFN Rep 1


title: Memory CD4 T cells_S306_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta

value: T-cells


title: ATAC-seq_GC5381_K562_shZNF143shHCFC1_rep2


title: Naïve CD4 T cells_S306_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Naïve CD8 T cells_S302_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: ATAC-seq_GC5380_K562_shRAD21_rep2

value: RAD21 knockdown


title: RREB1KO IFN Rep 3


title: ATAC-seq_GC5379_K562_shCTCF_rep2


title: RREB1KO IFN Rep 2


title: Memory CD8 T cells_S302_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: ATAC-seq_GC5377_K562_shZNF143_rep2

value: ZNF143 knockdown


title: ATAC-seq_GC5378_K562_shHCFC1_rep2

value: HCFC1 knockdown


title: RREB1KO IFN Rep 1


title: ATAC-seq_GC5267_K562_shCTCFshRAD21_rep1


title: Naïve CD4 T cells_S302_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta

value: Female


title: ATAC-seq_GC5266_K562_shZNF143shHCFC1_rep1


title: RREB1KO noIFN Rep 3


title: Memory CD8 T cells_S306_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta

value: Before


title: ATAC-seq_GC5265_K562_shRAD21_rep1


title: Memory CD4 T cells_S302_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta

value: Post


title: RREB1KO noIFN Rep 2


title: Naïve CD8 T cells_S302_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: RREB1KO noIFN Rep 1


title: ATAC-seq_GC5263_K562_shHCFC1_rep1


title: Memory CD8 T cells_S302_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: FBXO11KO IFN Rep 3


title: ATAC-seq_GC5261_K562_shControl_rep1


title: ChIP-seq_GC4281_K562_HZdKD_ZNF143_rep2

tag: antibody

value: ZNF143 antibody


title: Naïve CD4 T cells_S302_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: ATAC-seq_GC5376_K562_shControl_rep2


title: ChIP-seq_GC4279_K562_HZdKD_HCFC1_rep2

value: HCFC1 antibody


title: ChIP-seq_GC4280_K562_HZdKD_RAD21_rep2

value: RAD21 antibody


title: ChIP-seq_GC4277_K562_CRdKD_ZNF143_rep2


title: FBXO11KO IFN Rep 1

value: IFN


title: Memory CD4 T cells_S302_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Heart, TOF-1_1

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

data_processing:
Adapter Trimming and HQ reads filtering
Size calculation and Alignment against miRBase (Release 22.1) mature miRNA
Known miRNA discovery using MiRDeep2
Analysis of differential expressed miRNAs using iGEAK
Genome_build: miRBase
Supplementary_files_format_and_content: All_Expressed_miRNA_CPM.xlsx (CPM of all expressed miRNAs), All_Expressed_miRNAs_Log2CPM.xlsx (Log2CPM of all expressed miRNAs)

source_name: Heart

extract_protocol:
The total RNA was extracted from the cardiac muscle tissue biospy using mirVana miRNA isolation kit. 1 μg of total RNA was used to generate the small RNA sequencing library.
Libraries were prepared using TruSeq Small RNA Library Prep Kit as per Illumina Recommeded Protocol
Small RNA sequencing

tag: site of cardiac muscle tissue

value: Right atrium of heart

tag: study group

value: CHD (Tetralogy of Fallot)


title: ChIP-seq_GC4276_K562_CRdKD_RAD21_rep2


title: ChIP-seq_GC4274_K562_CRdKD_CTCF_rep2

value: CTCF antibody


title: ChIP-seq_GC4275_K562_CRdKD_HCFC1_rep2

value: CTCF RAD21 double knockdown


title: Heart, TOF-2_1


title: ChIP-seq_GC4271_K562_control_HCFC1_rep2

value: shRNA control


title: ATAC-seq_GC5262_K562_shZNF143_rep1


title: ChIP-seq_GC4270_K562_control_CTCF_rep2


title: FBXO11KO noIFN Rep 1

value: noIFN


title: ChIP-seq_GC4272_K562_control_RAD21_rep2


title: ChIP-seq_GC4273_K562_control_ZNF143_rep2


title: ChIP-seq_GC4256_K562_HZdKD_ZNF143

data_processing:
Hi-TrAC data raw paired-end reads in FASTQ files were first trimmed of linker sequence CTGTCTCTTATACACATCT for both ends. Only PETs with both ends length >=10bp were kept. Trimmed PETs were mapped to hg38 using Bowtie2 6 with key parameters of --end-to-end --very-sensitive. Mapped PETs with MAPQ >=10 were converted to BEDPE files. Mapped PETs with distance shorter than 1kb without linker sequence in any end were further filtered. PCR replicates of PETs were filtered if both ends locations were identical.  Unique intra-chromosomal PETs (cis PETs) as BEDPE files were mainly used for downstream analysis. All described processing steps were summarized as tracPre2.py in the cLoops2 package. Raw RNA-seq data reads were mapped to human reference genome hg38 by STAR (v2.7.3a). Gene annotation file (v30) downloaded from GENCODE 89 were used to quantify gene expression level by Cufflinks (v2.2.1). Raw ChIP-seq data reads were mapped to human reference genome hg38 by Bowtie2 90 with key parameters of --local --very-sensitive --no-unal --no-mixed --no-discordant. Mapped PETs with MAPQ >=10 were converted to normalized signals (reads per million) as bigWig files by deepTools for visualization.
Genome_build: hg38
Supplementary_files_format_and_content: BEDPE files contain the high quality and unique processed interaction paired-end tags.

growth_protocol: GM12878 cells were cultured in RPMI 1640 medium supplied with 15% fetal bovine serum and 2mM L-glutamine. K562 cells were cultured in RPMI 1640 mudium supplied with 10% fetal bovine serum  and antibiotics ( 100 units/mL Penicillin, 100 µg/mL Streptomycin).

extract_protocol:
Genomic DNA was purified by Phenol-Chloroform extraction. RNA was extracted with QIAzol lysis reagent (QIAGEN) and RNeasy mini kit (QIAGEN).
For Hi-TrAC, repair DNA gaps with T4 DNA polymerase. Remove free bridging linker by AMPure XP beads. Then, Digest purified DNA with restriction enzymes MluCI/NlaIII, and enrich biotin-labeled DNA fragments with streptavidin beads. Perform adapter ligation on beads. After washing the beads, run PCR with illumina multiplexing indexed primers. For RNA-seq, libraries were constructed following Smart-seq2 protocol (Picelli et al., 2014). For ChIP-seq, sheared chromatins were immunoprecipitated with anti-CTCF, anti-RAD21, anti-HCFC1, anti-ZNF143 antibodies. DNA was purified, then end-repaired using End-It DNA End-Repair kit (Epicentre). A-tailing was performed with Klenow Fragment (3'->5' exo-) with the presence of dATP. Universal adapters were then ligated. The libraries were then amplified by PCR using indexed primers.

treatment_protocol: Cells for Hi-TrAC were fixed with 1% Formaldehyde in culture medium at room temperature for 10 minutes. Wash cells with ice-cold PBS twice, then resuspend cells  with 100 µL reaction buffer (50mM Tris-acetate, pH 7.5, 150mM potassium acetate, 10mM magnesium acetate, 4mM spermidine, 0.5% NP-40). Incubate at 37℃ for 4 hours. To extract RNA for RNA-seq, add 700 µL QIAzol to 5,000 cells. Cells for ChIP-seq were fixed with 1% Formaldehyde in culture medium at room temperature for 10 minutes. Wash cells with ice-cold PBS twice. Then perform sonication to break chromatins.

tag: genotype

value: ZNF143 HCFC1 double knockdown

tag: chip antibody


title: ATAC-seq_GC5264_K562_shCTCF_rep1

value: CTCF knockdown


title: ChIP-seq_GC4254_K562_HZdKD_RAD21


title: Heart, VSD-2_1

value: CHD (Ventricular Septal Defect)


title: FBXO11KO IFN Rep 2


title: ChIP-seq_GC4278_K562_HZdKD_CTCF_rep2


title: ChIP-seq_GC4252_K562_HZdKD_HCFC1


title: FBXO11KO noIFN Rep 2


title: MV411-A366-H3K27me3

data_processing:
Library strategy: CUT&Tag
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were aligned to the human genome (GRCh37) with BWA-mem
Peak calling was performed with MACS2 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: bed files of peaks called by MACS2

extract_protocol:
Cells were serially washed with PBS and wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1 x protease inhibitor cocktail) at room temperature.  Concanavalin A beads were activated by washing twice with binding buffer (20 mM HEPES pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2), after which 10 μL of activated beads were added to each sample and incubated for 10 minutes at room temperature.  Bead-bound cells were then resuspended in 150 μL of antibody buffer (wash buffer plus 0.05% digitonin, 2 mM EDTA, 0.1% BSA) with a 1:50 dilution of primary antibody and incubated for 2 hours at room temperature.  The supernatant was then removed and the beads were washed twice with digitonin buffer (wash buffer plus 0.1% digitonin) prior to re-suspension in 50 μL of Dig-300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1 x protease inhibitor cocktail, 0.01% digitonin) with pAG-Tn5 enzyme for 1 hour at room temperature.  The supernatant was again aspirated and the beads washed twice with Dig-300 buffer, followed by re-suspension in 50 μL Tagmentation buffer (Dig-300 buffer plus 10 mM MgCl2) and incubation for 1 hour at 37°C.  An equal volume of 2X stop buffer (Dig-300 buffer plus 40 mM EDTA, 0.2% SDS, 400 μg/mL proteinase K) was then added and the samples were incubated at 55°C for 2 hours, then held at 4°C overnight.  The following day, the supernatant was taken and purified using the MinElute PCR purification kit (Qiagen), with each sample eluted in 25 μL of elution buffer.
21 μL of eluted DNA was mixed with 2 μL of a universal i5 primer and 2 μL of a unique barcoded i7 primer, as well as 25 μL of NEBNext HiFi 2X PCR Master Mix.  Following 14 cycles of PCR amplification, cleanup was performed using 1.1 x volume of AMPure XP beads (Beckman Coulter), analyzed on the Agilent 4200 TapeStation to determine size distribution of libraries and then sequenced on the NextSeq500 using 75 bp paired end chemistry.

treatment_protocol: A-366 1uM or vehicle control for 7 days as outlined above.

tag: treatment

value: A-366 1uM for 7 days

tag: ko

value: Cell Signaling H3K27me3 (cat# 9733S)


title: Heart, ASD-1_1

value: CHD (Atrial Septal Defect)


title: Heart, VSD-3_1

value: Infundibular muscle of heart


title: MV411-A366-H3K9me2

value: Active Motif H3K9me2 (cat# 39239)


title: ChIP-seq_GC4249_K562_HZdKD_CTCF


title: ChIP-seq_GC4245_K562_CRdKD_RAD21


title: FBXO11KO noIFN Rep 3


title: Heart, VSD-1_1


title: ChIP-seq_GC4248_K562_CRdKD_ZNF143

value: ZNF143 antibody


title: ChIP-seq_GC4242_K562_CRdKD_CTCF


title: Heart, CONT-1_1

value: Non-CHD (No Congenital Heart Disease)


title: ChIP-seq_GC4232_K562_control_RAD21

value: RAD21 antibody


title: EB2 treatment 2h 3

city: Daejeon

first: bomin

state: Yuseong

address: 141, Gajeong-ro

institute: Korea reserch institute of chemical technology

data_processing:
To check the quality of data before processing with analysis on raw data, FastQC (v0.11.7) was used.
Trimming was performed with various parameters for illumina paired-end or single-end using trimmomatic 0.38.
HISAT2 (ver 2.1.0) was used as a tool to map high throughput sequencing data to the reference genome, and graph FM index (GFM) was implemented based on the BWT extension of the graph.
Using StringTie (ver 2.1.3b), the potential transcript was assembled using the sequencing information mapped to the reference.
Assembly: ASM24013v3
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Fusarium graminearum

growth_protocol: Spores of PH1 were incubated with potato dextrose broth (PDB) with agitation at 25℃ for 1day.

extract_protocol:
RNA was harvested using easy-spinTM Total RNA Extraction Kit (Intron biotechnology)
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA LT Sample Prep Kit (Gold) following manufacturer's protocols.

treatment_protocol: Edeine B1 was treated at 10 μg/mL on hyphae, and incubated 1 h,2 h, and 4 h.

value: Hyphae

value: WT

value: Edeine B1


title: EB2 treatment 4h 3


title: OCI-AML3 screen control.

data_processing:
Library strategy: CRISPR-seq
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were trimmed to remove adapter with fastx clipper or cutadapt
Trimmed reads were aligned to the reference sgRNA library with bowtie2
After filtering to remove multi-aligning reads, the read counts were computed for each sgRNA.
The RSA algorithm was used to rank the genes for which targeting sgRNA were significantly enriched in the sorted populations compared to the control unsorted populations grown in parallel.
Supplementary_files_format_and_content: Guide Counts file

extract_protocol:
Genomic DNA was extracted using Puregene Core Kit A, Qiagen
Two rounds of PCR, with the second round primers containing adaptors for Illumina sequencing.

treatment_protocol: MOLM13 and OCI-AML3 Cas9 cells (300 x 10^6 per cell line) were infected with the pooled lentiviral sgRNA libraries at a multiplicity of infection of 0.3.  Infected cells were selected with 2 μg/mL puromycin for 72 hours, commencing 48 hours after transduction.  Cells were pulsed with 25 ng/mL IFN-γ for 48 hours prior to FACS sorting and enriched for MHC-II+ cells by 3 rounds of sorting at approximately days 12, 21 and 28 following transduction with the sgRNA libraries.

tag: crispr library

value: Bassik Human CRISPR KO Library

tag: facs antibody

value: control


title: MV411-ETOH-H3K27me3

tag: cell line

value: ETOH (vehicle control) for 7 days


title: LNM(+)-5

city: Jinan

first: Zhaohua

last: Xiao

state: Shandong

address: The second Hosiptal of Shandong University, 247Beiyuan Avenue, Jinan, Shandong 250033,P.R. China

country: China

institute: Shandong University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw dataswere calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou  et al., 2010):Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
For the samples with biological replicates:Differential expression analysis of two conditions/groups was  performed using the DESeq R package (3.0.3). The P-values was adjusted using the Benjamini& Hochberg  method. Corrected P-value of 0.05 was set as the threshold for significantly differential expression by default
Assembly: homo_sapiens_Ensembl_97
Supplementary files format and content: Excel files include FPKM value, readcount and difference significance analysis for each gene in all comparison combinations for each Sample.

source_name: plasma exosomes

extract_protocol:
The isolation of plasma exosomes was conducted using an exosome isolation kit (System Biosciences) according to the manufacturer’s instructions. Then, total RNA was isolated from  plasma exosomes by a miRcute miRNA Isolation Kit
3 μg of RNA was used as input material for the generation of a small RNA library. Then, the small RNA library was sequenced on an Illumina HiSeq 2500 platform. Differential expression analysis was performed using the DESeq R package (3.0.3).

tag: tissue

value: plasma exosomes

value: ESCC patients with LNM


title: Heart, VSD-4_1

value: CHD (Ventricular Septal Defect)


title: MOLM13 MHC-II+, IFN, sort 3.

value: Alexa Fluor 647 mouse anti-human HLA-DR, DP, DQ antibody (BioLegend cat# 361704)


title: EB2 treatment 4h 2

tag: cell type


title: MV411-ETOH-H3K9me2


title: ChIP-seq_GC4244_K562_CRdKD_HCFC1

value: CTCF RAD21 double knockdown

value: HCFC1 antibody


title: Heart, ASD-2_1

value: Right atrium of heart

value: CHD (Atrial Septal Defect)


title: OCI-AML3 MHC-II+, IFN, sort 2.


title: EB2 treatment 4h 1


title: EB2 treatment 2h 1


title: LNM(+)-3


title: MOLM13 screen control.


title: OCI-AML3 MHC-II+, no IFN, sort 3.


title: Heart, CONT-2_1


title: ChIP-seq_GC4230_K562_control_HCFC1

value: shRNA control


title: OCI-AML3 MHC-II+, no IFN, sort 3

extract_protocol:
Genomic DNA was extracted using Puregene Core Kit A, Qiagen.
One-step PCR was performed, containing adaptors for Illumina sequencing.

treatment_protocol: MOLM13 and OCI-AML3 Cas9 cells (100 x 10^6 per cell line) were infected with the pooled lentiviral sgRNA libraries at a multiplicity of infection of 0.3.  Infected cells were selected with 2 μg/mL puromycin for 72 hours, commencing 48 hours after transduction.  Cells were pulsed with 25 ng/mL IFN-γ for 48 hours prior to FACS sorting and enriched for MHC-II+ cells by 3 rounds of sorting at approximately days 12, 21 and 28 following transduction with the sgRNA libraries.

value: Custom targeted epigenetic library


title: EB2 treatment 1h 2


title: EB2 treatment 2h 2


title: ChIP-seq_GC4233_K562_control_ZNF143

value: ZNF143 antibody


title: Control (Mock) 3

value: Hyphae


title: Control (Mock) 2

value: WT


title: LNM(-)-4

value: ESCC patients without LNM


title: LNM(+)-4


title: RNA-seq_GC4205_K562_CTCF_RAD21_rep2


title: MOLM13 MHC-II+, IFN, sort 3


title: Control (Mock) 1

value: Edeine B1


title: MOLM13 MHC-II+, no IFN, sort 3.

value: Bassik Human CRISPR KO Library


title: MOLM13 MHC-II+, no IFN, sort 3


title: ChIP-seq_GC4228_K562_control_CTCF

value: CTCF antibody


title: EB2 treatment 1h 3


title: ChIP-seq_GC4226_K562_HZdKD_input

value: ZNF143 HCFC1 double knockdown

value: input DNA


title: LNM(+)-2

value: plasma exosomes

value: ESCC patients with LNM


title: LNM(-)-2


title: OCI-AML3 screen control

value: control


title: OCI-AML3 MHC-II+, IFN, sort 3

value: Alexa Fluor 647 mouse anti-human HLA-DR, DP, DQ antibody (BioLegend cat# 361704)


title: RNA-seq_GC4202_K562_ZNF143_HCFC1_rep1


title: ChIP-seq_GC4225_K562_CRdKD_input

value: CTCF RAD21 double knockdown


title: LNM(-)-1


title: LNM(+)-1


title: EB2 treatment 1h 1


title: ChIP-seq_GC4224_K562_control_input


title: LNM(-)-5


title: RNA-seq_GC4204_K562_CTCF_RAD21_rep1


title: Ecsit WT skeletal progenitors [wt2]

city: Worcester

first: Rui

last: Li

state: Massachusetts

address: 364 Plantation Street, LRB

department: MCCB

institute: University of Massachusetts Medical School

description: txt file has the count of total RNA-seq first column has the name and second column has the count

data_processing:
mapped to the human reference genome (GCF_000001405.38_GRCh38.p12) with STAR aligner (v.2.6.1b)
read counts were generated by using HTSeq-count (v.0.11.3)
The read counts were used for a differential expression analysis between control and A9 group, and control and A10 group using DESeq2 (v.1.28.1) with the ashr shrinkage estimator (v.2.2.47)
Assembly: mm10GCF_000001405.38_GRCh38.p12
Supplementary files format and content: excel format, raw counts for each gene

organism: Mus musculus

source_name: WT skeletal progenitors

growth_protocol: Freshiy isolated skeletal progenitors were used for RNAseq.

extract_protocol:
Total RNA was extracted using QIAzol lysis reagent (QIAGEN).
Isolate polyA RNA using dynabeads mRNA purification kit (Life Technologies).
Fragmentation/The first cDNA systhesis (SuperScript II reverse transcription kit)/The second-strand synthesis (Rnase H (Life Techonologies)/DNA polymerase (Enzymatics)/ Short double-stranded cDNA fragments purification: QIA quick PCR purification kit and Agencourt AMPure beads/end-repair with klenow polymerase (T4 DNA polymerase and T4 polynucleotide kinase)/ A single 3' A adding to the double-stranded cDNA (Kelnow (Enzymatics) and dATP (GE Healthcare)/The illumina PE Adapter oligo mix ligation/library amplification/denaturation of library with sodium hydroxide and diluted to 2.5 pM in hybridization buffer for loading into a HiSeq flowell.

treatment_protocol: No treatment

value: skeletal progenitors


title: LNM(-)-3


title: Ecsit WT skeletal progenitors [wt3]


title: RNA-seq_GC4203_K562_ZNF143_HCFC1_rep2


title: RNA-seq_GC4198_K562_CTCF_rep2

value: CTCF knockdown


title: Ecsit cKO skeletal progenitors [ko3]

source_name: cKO skeletal progenitors


title: MOLM13 screen control

value: Custom targeted epigenetic library


title: RNA-seq_GC4197_K562_CTCF_rep1


title: Ecsit cKO skeletal progenitors [ko2]


title: RNA-seq_GC4201_K562_RAD21_rep2

value: RAD21 knockdown


title: liver HSCF-1 [LHSCF1]

city: Qingdao

first: Yong

last: Zhao

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: gene expression

source_name: Liver

extract_protocol:
Liver were removed, quikly frozen in luquid nitrogen, and RNA was harvested using Trizol reagent. PurelinkTM RNA Mini Kit (Cat#12183018A) was used tp abtain 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: ICR

value: liver

value: 10 weeks

value: High fat diet & STZ+control-FMT


title: RNA-seq_GC4199_K562_RAD21_rep1


title: RNA-seq_GC4195_K562_HCFC1_rep1

value: HCFC1 knockdown


title: liver HSAF-3 [LHSAF3]

tag: age

value: High fat diet & STZ+AOS10mg/kg-FMT


title: liver HSCF-3 [LHSCF3]


title: epithelial colon cells replicate-4

type: RNA

city: Bronx

first: Elena

last: Tosti

address: 1301 Morris park avenue

institute: Albert Einstein College of Medicine

description: gene expression data from epithelial cells from CRC model with  Msh2 and Tgfbr2inactivaton

hyb_protocol: hybridization was perfromed  by the Genomics Core at Einstein according to the standard Affymetrix protocol

scan_protocol: GeneChips were scanned using the Genechip scanner 7G

data_processing: Microarray data were pre-processed and analyzed using R-Bioconductor software.Raw data were background-corrected and RMA-normalized, expression values calculated (oligo package) followed by annotation with the pd.mogene.1.0.st.v1 package

label: biotin

source_name: matched colon mucisa epithelial cellsfrom Mus musculus model

label_protocol: labeling was perfromed  by the Genomics Core at Einstein according to the standard Affymetrix protocol

growth_protocol: tissue was collected from sacrfied mice

extract_protocol: RNA extraction from sorted epithelial intestinal cells was performed using the RNA plus micro kit (Qiagen).RNA quantity was determined using a 2100 Bioanalyzer (Agilent).

treatment_protocol: intestinal tissues collected from Msh2 and Tgfbr2 intestinal epithelium inactivated mouse model

value: colon cancer free mucosa  (epithelial cells)


title: epithelial colon cells replicate-6


title: epithelial colon cells replicate-5


title: HYS_5 C-section delivery

city: Caldes de Montbui

first: Yuliaxis

last: Ramayo Caldas

state: Barcelona

address: Torre Marimon

country: Spain

institute: IRTA

description: C-section delivery

hyb_protocol: Mouse transcriptomics was performed using SurePrint G3 Mouse GE 8x60K Microarray (Design ID: 028005, Agilent Technologies), according to manufacturer's instructions

scan_protocol: Standard Agilent Protocol

data_processing: Probe intensities were corrected, log2 scaled and quantile normalized using the limma R package version 3.38.[43]. In order to remove noise from expression patterns associated with very weakly expressed genes, the probes with values higher than the lowest 5%-quantile of each sample, in at least 4 samples, were retained. Other probes were filtered out and controls were discarded. Subsequently, we averaged expression of probes representing the same gene

source_name: intestine

extract_protocol: Total RNA was isolated from the colon samples using RNeasy Mini Kit, according to manufacturer's instructions. The RNA integrity was verified in Bioanalyzer 2100 with RNA 6000 Nano chips (Agilent Technologies).

treatment_protocol: Experiments with ex germ free (GF) mice were conducted on the ANAXEM platform (INRAE, Jouy-en-Josas). We used a murine model of CSD in conventional and ex germ-free animals with a special focus on gut barrier structure and permeability. Further, we performed a diferentially abundance analysis to identify the differential expressed genes between CSD and VD samples.

tag: Sex

value: F

tag: delivery

value: HYS

tag: mother

tag: animal


title: epithelial colon cells replicate-2


title: liver HSAF-1 [LHSAF1]


title: liver HSCF-2 [LHSCF2]


title: HYS_6 C-section delivery

description: C-section delivery

value: M


title: HYS_9 C-section delivery

description: C-section delivery


title: epithelial colon cells replicate-1


title: epithelial colon cells replicate-3


title: VD_6 Vaginal delivery

description: Vaginal delivery

value: VD


title: epithelial colon cancer cells replicate-5

source_name: colon cancer epithelial cellsfrom Mus musculus model

value: colon cancer (epithelial cells)


title: RNA-seq_GC4192_K562_Control_rep2

value: shRNA control


title: VD_11 Vaginal delivery

description: Vaginal delivery


title: RNA-seq_GC4196_K562_HCFC1_rep2


title: HYS_2 C-section delivery

description: C-section delivery


title: VD_4 Vaginal delivery

description: Vaginal delivery


title: liver HSA10-3 [LHSA3]

value: High fat diet & STZ+AOS10mg/kg


title: RNA-seq_GC4191_K562_Control_rep1


title: liver HSAF-2 [LHSAF2]


title: RNA-seq_GC4193_K562_ZNF143_rep1

value: ZNF143 knockdown


title: liver HSA10-1 [LHSA1]


title: VD_7 Vaginal delivery

description: Vaginal delivery


title: RNA-seq_GC4194_K562_ZNF143_rep2


title: Hi-TrAC_GC4060_GC4084_K562_CTCF_RAD21_KD_rep1

data_processing:
Library strategy: Hi-TrAC
Hi-TrAC data raw paired-end reads in FASTQ files were first trimmed of linker sequence CTGTCTCTTATACACATCT for both ends. Only PETs with both ends length >=10bp were kept. Trimmed PETs were mapped to hg38 using Bowtie2 6 with key parameters of --end-to-end --very-sensitive. Mapped PETs with MAPQ >=10 were converted to BEDPE files. Mapped PETs with distance shorter than 1kb without linker sequence in any end were further filtered. PCR replicates of PETs were filtered if both ends locations were identical.  Unique intra-chromosomal PETs (cis PETs) as BEDPE files were mainly used for downstream analysis. All described processing steps were summarized as tracPre2.py in the cLoops2 package. Raw RNA-seq data reads were mapped to human reference genome hg38 by STAR (v2.7.3a). Gene annotation file (v30) downloaded from GENCODE 89 were used to quantify gene expression level by Cufflinks (v2.2.1). Raw ChIP-seq data reads were mapped to human reference genome hg38 by Bowtie2 90 with key parameters of --local --very-sensitive --no-unal --no-mixed --no-discordant. Mapped PETs with MAPQ >=10 were converted to normalized signals (reads per million) as bigWig files by deepTools for visualization.
Genome_build: hg38
Supplementary_files_format_and_content: BEDPE files contain the high quality and unique processed interaction paired-end tags.

value: CTCF RAD21 double knockdown


title: VD_8 Vaginal delivery

description: Vaginal delivery


title: epithelial colon cancer cells replicate-4


title: liver HSA10-2 [LHSA2]


title: Hi-TrAC_GC4059_GC4083_K562_ZNF143_HCFC1_KD_rep2

value: ZNF143 HCFC1 double knockdown


title: epithelial colon cancer cells replicate-2


title: HYS_1 C-section delivery

description: C-section delivery


title: liver HS-2 [LHS2]

value: ICR

value: High fat diet & STZ


title: Memory CD8 T cells_S214_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta

value: blood PBMCs

value: T-cells

tag: il-7 administration

value: Post

value: Male


title: Memory CD8 T cells_S208_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta

value: Female


title: epithelial colon cancer cells replicate-6


title: liver HS-1 [LHS1]

value: liver

value: 10 weeks


title: Hi-TrAC_GC4061_GC4085_K562_CTCF_RAD21_KD_rep2


title: Hi-TrAC_GC4056_GC4080_K562_RAD21_shRNA2_KD_rep1

value: RAD21 knockdown


title: epithelial colon cancer cells replicate-3


title: liver con-3 [Lcon3]

value: control


title: Hi-TrAC_GC4058_GC4082_K562_ZNF143_HCFC1_KD_rep1


title: Memory CD8 T cells_S111_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: HYS_3 C-section delivery

description: C-section delivery

value: F

value: HYS


title: Memory CD8 T cells_S103_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Naïve CD8 T cells_S214_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Hi-TrAC_GC4055_GC4079_K562_RAD21_shRNA1_KD_rep2


title: HYS_7 C-section delivery

description: C-section delivery

value: M


title: VD_10 Vaginal delivery

description: Vaginal delivery

value: VD


title: VD_9 Vaginal delivery

description: Vaginal delivery


title: epithelial colon cancer cells replicate-1

value: colon cancer (epithelial cells)


title: VD_5 Vaginal delivery

description: Vaginal delivery


title: liver HS-3 [LHS3]


title: Naïve CD8 T cells_S208_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: liver con-2 [Lcon2]


title: Hi-TrAC_GC4054_GC4078_K562_RAD21_shRNA1_KD_rep1


title: liver con-1 [Lcon1]


title: Naïve CD8 T cells_S103_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: ctrl2-Fib-MYOD-day8-biolrep3

city: Ankara

first: Pervin

last: Dinçer

address: Hacettepe, Merkez Kampüs, A kapısı, 4. kat

department: Dept. of Medical Biology

country: Turkey

institute: Hacettepe University

data_processing:
Raw reads were cleaned by discarding all reads less than 31 bp. For the remaining reads the first 8 bp were trimmed, and reads longer than 300 bp after trimmming were truncated to 300 bp using cutadapt (V1.18) (i.e. cutadapt -j 6 -m31 -l300).
The cleaned reads were mapped to the human transcriptome using Salmon (V0.8.1). The mapping index was created based on the GRCh38 cdna library (Homo_sapiens.GRCh38.cdna.all.fa). Salmon was run with GC and sequence specific bias correction ( i.e. --gcBias --seqBias).
Assembly: GRCh38
Supplementary files format and content: Salmon quant.sf files.

growth_protocol: Primary fibroblasts at passage 2 were immortalized by transduction with a lentiviral vector encoding the catalytic subunit of human telomerase reverse transcriptase. In addition, cells were transduced with a lentiviral vector expressing MYOD1 under the control of a doxycycline-inducible Tet-On promoter. Proliferating cells were cultured in a proliferative medium consisting of high-glucose (4500 mg/mL) Dulbecco’s MEM (DMEM) with stable L-glutamine supplemented with 10% fetal bovine serum (FBS), 50 µg/mL of gentamycin and 2.5 µg/mL of amphotericin B and maintained in 5% CO2 at 37 °C.

extract_protocol:
Control and LAP1B-deficient immortalized MyoD-converted fibroblasts were seeded as triplicates on three independent culture plates and differentiation was induced as described above. Total RNA was extracted from 1 million cells at day 0, day 2, day 5 and day 8 after induction of differentiation using Hybrid-R total RNA isolation kit (GeneAll Biotechnology, Seoul, Korea) according to the manufacturer’s instructions.
Total mRNA libraries were constructed using SENSE mRNA-seq Library Prep Kit for Ion Torrent (Lexogen).

treatment_protocol: For induction of MyoD expression, growth medium was replaced at 90% confluence by a serum-free differentiation medium made with high glucose DMEM supplemented with 2 µg/mL of doxycycline (Sigma-Aldrich) and 10 µg/mL of insulin (Sigma-Aldrich). For myogenic differentiation, cells were differentiated for 8 days at 37 °C in 5% CO2 by refreshing the differentiation medium every two days.

value: Cultured fibroblasts

value: MyoD induction, differentiation day 8


title: ctrl2-Fib-MYOD-day8-biolrep2


title: Hi-TrAC_GC4057_GC4081_K562_RAD21_shRNA2_KD_rep2


title: liver A10-3 [LA3]

value: ICR

value: AOS 10mg/kg


title: Memory CD4 T cells_S214_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta

value: blood PBMCs

value: T-cells


title: ctrl2-Fib-MYOD-day8-biolrep1


title: Hi-TrAC_GC4053_GC4077_K562_CTCF_shRNA2_KD_rep2

value: CTCF knockdown


title: liver A10-1 [LA1]


title: Hi-TrAC_GC4052_GC4076_K562_CTCF_shRNA2_KD_rep1


title: Hi-TrAC_GC4051_GC4075_K562_CTCF_shRNA1_KD_rep2


title: ctrl1-Fib-MYOD-day8-biolrep2


title: liver A10-2 [LA2]


title: ctrl1-Fib-MYOD-day8-biolrep3


title: Nes:F/F 4044CKO T80C

city: Raleigh

first: Troy

last: Ghashghaei

state: North Carolina

address: 1060 William Moore Drive

department: Molecular Biomedical Sciences

institute: North Carolina State University

data_processing:
Sequenced reads were adapter trimmed with BBDuk v. 38.94 (parameters> ref=adapters.fa t=10 ktrim=r minlength=60 entropy=0.01 maq=10 tpe tbo)
Trimmed reads were aligned to the GENCODE GRCm39 primary genome using STAR v. 2.7.8a (parameters> --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMax 1000000 --outFilterMultimapNmax 20 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outSAMmultNmax 1 --sjdbOverhang 75
Reads were quantified with featureCounts v. 2.0.3 (parameters> -s 2 -M -O --fraction --countReadPairs)
Assembly: GRCm39
Supplementary files format and content: tab-deliminated files include read counts per sample

source_name: Caudal cerebral cortex

extract_protocol: P5 Nestin-EgfrF/F and control (EgfrF/+) pups were obtained from pregnant females. The morning when the litter appeared in the cage was considered P0.  The cortices and the hippocampal formation were dissected away from the ventral forebrain using microforceps in ice cold HBSS, and split into rostral and caudal halves. Samples were collected and Total RNA was extracted using the RNeasy Mini kit (Qiagen, catalog no. 74104). 700 ng of total RNA per sample underwent mRNA capture and was then fragmented at 94 °C for 6 min. Sequencing libraries were prepared according to the manufacturer’s protocol using KAPA mRNA HyperPrep Kit (catalog no. KK8580). Indexes used: NEXTFLEX® Unique Dual Index Barcodes, catalog no. NOVA-512921. Next-generation sequencing was performed on a Novaseq 6000 (catalog no. 20012850) using NovaSeq 6000 SP Reagent Kit v1.5 (100 cycles), catalog no. 20028401 for the 50x8x8x50 cycle configuration.

value: Caudal cerebral cortex

value: NcreEGFRFF

tag: developmental stage


title: Nes:F/F 4044CKO T80R

source_name: Rostral cerebral cortex

value: Rostral cerebral cortex

tag: genotype


title: Memory CD4 T cells_S208_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta

value: Post

value: Female


title: ctrl1-Fib-MYOD-day8-biolrep1

value: control


title: Memory CD4 T cells_S103_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta

value: Male


title: Memory CD4 T cells_S111_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: LAP1BFib-MYOD-day8-biolrep3


title: Naïve CD4 T cells_S214_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Hi-TrAC_GC4050_GC4074_K562_CTCF_shRNA1_KD_rep1


title: Hi-TrAC_GC4049_GC4073_K562_HCFC1_shRNA2_KD_rep2

value: HCFC1 knockdown


title: Nes:F/F 4044CKO T6C


title: LAP1BFib-MYOD-day8-biolrep2


title: Hi-TrAC_GC4048_GC4072_K562_HCFC1_shRNA2_KD_rep1


title: Naïve CD4 T cells_S208_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Hi-TrAC_GC4047_GC4071_K562_HCFC1_shRNA1_KD_rep2


title: Nes:F/F 4044CKO T3C


title: LAP1BFib-MYOD-day8-biolrep1


title: Nes:F/F 4044CKO T6R


title: Naïve CD4 T cells_S111_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Naïve CD4 T cells_S103_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Hi-TrAC_GC4046_GC4070_K562_HCFC1_shRNA1_KD_rep1


title: ctrl2-Fib-MYOD-day5-biolrep3

value: MyoD induction, differentiation day 5


title: HYS_8 C-section delivery

description: C-section delivery

value: M

value: HYS


title: Memory CD8 T cells_S214_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta

value: Before


title: Hi-TrAC_GC4045_GC4069_K562_ZNF143_shRNA2_KD_rep2

value: ZNF143 knockdown


title: ctrl2-Fib-MYOD-day5-biolrep2

value: Cultured fibroblasts


title: Control 4044F+ T70C

value: WT


title: Nes:F/F 4044CKO T3R


title: ctrl2-Fib-MYOD-day5-biolrep1


title: Hi-TrAC_GC4044_GC4068_K562_ZNF143_shRNA2_KD_rep1


title: Memory CD8 T cells_S208_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta

value: blood PBMCs

value: T-cells


title: Memory CD8 T cells_S111_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Hi-TrAC_GC4043_GC4067_K562_ZNF143_shRNA1_KD_rep2


title: Control 4044F+ T70R


title: ctrl1-Fib-MYOD-day5-biolrep3


title: Control 4044F+ T8C

value: Caudal cerebral cortex


title: Memory CD8 T cells_S103_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Hi-TrAC_GC4041_GC4065_K562_shRNA2_Control_rep2

value: shRNA control


title: Control 4044F+ T8R

value: Rostral cerebral cortex


title: Hi-TrAC_GC4042_GC4066_K562_ZNF143_shRNA1_KD_rep1


title: Control 4044F+ T4C


title: ctrl1-Fib-MYOD-day5-biolrep1


title: ctrl1-Fib-MYOD-day5-biolrep2


title: Naïve CD8 T cells_S214_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Hi-TrAC_GC4040_GC4064_K562_shRNA2_Control_rep1


title: LAP1BFib-MYOD-day5-biolrep2


title: Hi-TrAC_GC5112_5212_mESC-E14_10K_tech4

data_processing:
Hi-TrAC data raw paired-end reads in FASTQ files were first trimmed of linker sequence CTGTCTCTTATACACATCT for both ends. Only PETs with both ends length >=10bp were kept. Trimmed PETs were mapped to hg38 using Bowtie2 with key parameters of --end-to-end --very-sensitive. Mapped PETs with MAPQ >=10 were converted to BEDPE files. Mapped PETs with distance shorter than 1kb without linker sequence in any end were further filtered. PCR replicates of PETs were filtered if both ends locations were identical.  Unique intra-chromosomal PETs (cis PETs) as BEDPE files were mainly used for downstream analysis. All described processing steps were summarized as tracPre2.py in the cLoops2 package. Raw RNA-seq data reads were mapped to human reference genome hg38 by STAR (v2.7.3a). Gene annotation file (v30) downloaded from GENCODE 89 were used to quantify gene expression level by Cufflinks (v2.2.1). Raw ChIP-seq and ATAC-seq data reads were mapped to human reference genome hg38 by Bowtie2 with key parameters of --local --very-sensitive --no-unal --no-mixed --no-discordant. Mapped PETs with MAPQ >=10 were converted to normalized signals (reads per million) as bigWig files by deepTools for visualization.  Raw Hi-C data reads were processed to human reference genome hg38 by HiC-Pro (v2.11.1). Only intra-chromosomal PETs from the files with a suffix of allValidPairs output by HiC-Pro were used for all following analysis.
Assembly: hg38
Supplementary files format and content: BEDPE files contain the high quality and unique processed interaction paired-end tags.
Library strategy: Hi-TrAC

tag: development stage

value: mESC

tag: genotype/variation


title: Hi-TrAC_GC4039_GC4063_K562_shRNA1_Control_rep2


title: LAP1BFib-MYOD-day5-biolrep3

tag: treatment


title: Hi-TrAC_GC4038_GC4062_K562_shRNA1_Control_rep1


title: LAP1BFib-MYOD-day5-biolrep1


title: Hi-TrAC_GC5111_5211_mESC-E14_10K_tech3


title: Naïve CD8 T cells_S208_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta

data_processing:
Raw reads were assembled and low-quality reads were filtered using Cutadapt (version 2.8).
Filtered reads were aligned on a reference genome downloaded from Ensembl (GRCh38.p13, Accession number: GCA_000001405.28) using STAR (version 2.7.1a).
Assembly: Ensembl (GRCh38.p13, Accession number: GCA_000001405.28) for RNAseq, human reference V, D, J and C genes of TCRs for IR-Seq
Supplementary files format and content: gene expression files of RNAseq contains raw gene counts IR-Seq processed data consists of raw read counts of each CDR3

value: Female


title: Memory CD4 T cells_S214_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: ctrl2-Fib-MYOD-day2-biolrep3

value: control

value: MyoD induction, differentiation day 2


title: Hi-TrAC_GC2286_4150_K562_bio2_tech3


title: Hi-TrAC_GC5110_5210_mESC-E14_10K_tech2


title: Memory CD4 T cells_S208_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Hi-TrAC_GC2285_4149_K562_bio2_tech2


title: Memory CD4 T cells_S111_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta

value: Male


title: Hi-TrAC_GC5109_5209_mESC-E14_10K_tech1


title: Hi-TrAC_GC2284_4148_K562_bio2_tech1


title: ctrl2-Fib-MYOD-day2-biolrep1


title: Control 4044F+ T4R


title: ctrl1-Fib-MYOD-day2-biolrep3


title: Hi-TrAC_GC2262_GM12878_linker50bp


title: Hi-TrAC_GC5108_5208_mESC-E14_100K_tech4


title: Hi-TrAC_GC2261_GM12878_linker40bp


title: Naïve CD8 T cells_S103_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Memory CD4 T cells_S103_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Naïve CD4 T cells_S214_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Naïve CD4 T cells_S208_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: ctrl1-Fib-MYOD-day2-biolrep1


title: Hi-TrAC_GC5106_5206_mESC-E14_100K_tech2


title: Naïve CD4 T cells_S111_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Hi-TrAC_GC2259_GM12878_linker20bp


title: Hi-TrAC_GC5105_5205_mESC-E14_100K_tech1


title: Hi-TrAC_GC2258_GM12878_linker10bp


title: Hi-TrAC_GC2260_GM12878_linker30bp


title: LAP1BFib-MYOD-day2-biolrep3


title: LAP1BFib-MYOD-day2-biolrep2


title: Naïve CD4 T cells_S103_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Hi-TrAC_GC5103_5203_mESC-E14_1M_tech3


title: ctrl2-Fib-MYOD-day2-biolrep2


title: Meningeal Endothelial cells, WT, Batch5

city: Milano

first: Stefano

last: de Pretis

address: Via Olgettina, 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Institute

data_processing:
Sequence reads were trimmed for adaptor sequence using Trimmomatic (version 0.39)
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR aligner (STAR_2.5.3a)
Read count extraction was performed using featureCounts (v1.6.4) on the Gencode release vM22
Read count normalization and differential expression analysis were performed using the R/Bioconductor package DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Meninges Spinal Cord

extract_protocol:
The spinal cord and surrounding meninges were dissected, pooled according to genotype, and dissociated with Papain Dissociation System (Worthington Biochemical). GFP+ motor neurons and Cherry+ endothelial cells were isolated on a BD Influx Cell Sorter and collected in RLT lysis buffer (Qiagen) containing β-mercaptoethanol. RNA was extracted with RNeasy Mini Kit and on-column DNase digestion (Qiagen).
Stranded mRNA libraries prepared with Illumina TruSeq RNA Library Preparation Kit (v2)

value: Meninges Spinal Cord

value: Endothelial cells

value: FACS-sorted

tag: cell sorting

value: Kdr-Cherry+ sorted endothelial cells


title: Hi-TrAC_GC2257_GM12878_linker5bp


title: Hi-TrAC_GC5104_5204_mESC-E14_1M_tech4

extract_protocol:
For Hi-TrAC and Hi-C, genomic DNA was purified by Phenol-Chloroform extraction. RNA was extracted with QIAzol lysis reagent (QIAGEN) and RNeasy mini kit (QIAGEN). For ChIP-seq and ATAC-seq, genomic DNA was purified with QIAGEN MinElute Reaction Cleanup Kit.
For Hi-TrAC, repair DNA gaps with T4 DNA polymerase. Remove free bridging linker by AMPure XP beads. Then, Digest purified DNA with restriction enzymes MluCI/NlaIII, and enrich biotin-labeled DNA fragments with streptavidin beads. Perform adapter ligation on beads. After washing the beads, run PCR with illumina multiplexing indexed primers. For RNA-seq, libraries were constructed following Smart-seq2 protocol (Picelli et al., 2014). For ChIP-seq, DNA was purified, then end-repaired using End-It DNA End-Repair kit (Epicentre). A-tailing was performed with Klenow Fragment (3'->5' exo-) with the presence of dATP. Universal adapters were then ligated. The libraries were then amplified by PCR using indexed primers. For ATAC-seq, purified genomic DNA was amplified by PCR with indexed primers to construct the libraries. For Hi-C, purified genomic DNA was treated with T4 DNA polymerase to remove biotin labels at DNA ends. Fragment the DNA by sonication to 300-500 bp. Fragmentated DNA was end-repaired, followed with A-tailing. Biotin labeled DNA was enriched with MyOne Streptavidin C1 beads (Invitrogen). PCR adapters were then ligated to the enriched DNA on beads. Perform PCR with indexed primers to amplify the libraries.


title: Hi-TrAC_GC5107_5207_mESC-E14_100K_tech3


title: ctrl1-Fib-MYOD-day2-biolrep2


title: Meningeal Endothelial cells, WT, Batch4


title: Hi-TrAC_GC2256_4147_K562_bio1_tech3


title: Hi-TrAC_GC2255_4146_K562_bio1_tech2


title: Meningeal Endothelial cells, WT, Batch3


title: ctrl2-Fib-MYOD-day0-biolrep3

value: No treatment


title: Hi-TrAC_GC5101_5201_mESC-E14_1M_tech1


title: Meningeal Endothelial cells, WT, Batch2


title: Hi-TrAC_GC2254_4145_K562_bio1_tech1


title: Hi-TrAC_GC4383_5004_mESC-R1_10K_tech2


title: ctrl2-Fib-MYOD-day0-biolrep2

value: Cultured fibroblasts


title: ctrl2-Fib-MYOD-day0-biolrep1


title: Hi-TrAC_GC4382_5003_mESC-R1_10K_tech1

value: WT


title: Hi-TrAC_GC4381_5002_mESC-R1_100K_tech2


title: Meningeal Endothelial cells, WT, Batch1


title: Hi-TrAC_GC2202_2252_GM12878_bio2_tech2


title: Hi-TrAC_GC2203_2253_GM12878_bio2_tech3


title: Hi-TrAC_GC4380_5001_mESC-R1_100K_tech1


title: ctrl1-Fib-MYOD-day0-biolrep3


title: RAW CT26 rep1

city: Beijing

first: Xuefei

last: Guo

state: Bejing

address: Xueyuan road, haidian district

department: Institute of Systems Biomedicine

institute: Peking university health science center

description: fpkm rep1.csv

data_processing:
The raw fastq files was trimmed to clean data by trim-galore software.
The clean data were aligned to human hg38 genome using subread, which produced the BAM type file directly.
The featureCounts command line tool was used to calculate the gene count matrix.
Then the count matrix was normalized with FPKM formula.
The GFOLD software was used to identify the differantially expressed genes.
Assembly: UCSC hg38 genome was used as reference genome.
Supplementary files format and content: FPKM value for each sample.

growth_protocol: RAW264.7 cells were grown in DMEM, CT26 cells were grown in RPMI1640.

extract_protocol: The transcriptome library for sequencing was generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme Biotech Co.,Ltd, Nanjing, China) following the manufacturer’s recommendations.

treatment_protocol: Coculture

value: ct26 coculture


title: Spinal Endothelial cells, WT, Batch5

source_name: whole Spinal Cord (parenchyma)

value: whole Spinal Cord (parenchyma)


title: ctrl1-Fib-MYOD-day0-biolrep2


title: Spinal Endothelial cells, WT, Batch4


title: RAW CT26 rep2

description: fpkm rep2.csv


title: Hi-TrAC_GC5102_5202_mESC-E14_1M_tech2


title: LAP1BFib-MYOD-day0-biolrep1


title: RAW MOCK rep1

description: fpkm rep1.csv

value: mock


title: ctrl1-Fib-MYOD-day0-biolrep1


title: Hi-TrAC_GC1477_1496_2248_GM12878_bio1_tech1


title: Spinal Endothelial cells, WT, Batch3

source_name: venral Spinal Cord (parenchyma)

value: venral Spinal Cord (parenchyma)


title: RAW MOCK rep2

description: fpkm rep2.csv


title: LAP1BFib-MYOD-day0-biolrep3


title: Spinal Endothelial cells, WT, Batch1

source_name: ventral Spinal Cord (parenchyma)

value: ventral Spinal Cord (parenchyma)


title: Hi-TrAC_GC1479_1498_2250_GM12878_bio1_tech3


title: TGCT3, ISO-seq

status: Public on Oct 01 2022

city: Stanford

first: Matt

last: van de Rijn

state: California

address: 300 Pasteur Drive

institute: Stanford University

description: IsoSeq

data_processing:
scRNA-Seq: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.
IsoSeq: alignment using pbmm2.
IsoSeq: Other than the aligned Bam files there is no processed data. The paper contains some text and a screen capture regarding the aligned reads.
Assembly: GRCh38
Supplementary files format and content: scRNA-Seq: Raw feature bc matrix for downstream analysis.
Library strategy: Iso-Seq

source_name: Tenosynovial Giant Cell Tumor

extract_protocol:
scRNA-seq: dissociation with Miltenyi tumor dissociation kit. IsoSeq: Qiagen Rnease Kit RNA extraction.
scRNA-seq: 10x v3.1 3' library according to protocol. IsoSeq: PacBio IsoSeq protocol.

value: Tumor

value: Tenosynovial Giant Cell Tumor


title: 99KS76A-1, germinated spores

city: Manhattan

first: Eduard

last: Akhunov

state: Kansas

address: 1712 Claflin Road

department: Plant Pathology

institute: Kansas State University

data_processing:
Assembly was performed using Canu v1.7 followed by correcting assembly errors by aligning MiSeq reads (2 x 300 bp) to the assembled contigs using Pilon v1.22.
Bin-assignment strategy: gene models predicted in our 99KS76A-1 assembly were aligned against the assembled contigs using BLASTN v2.9.0. In Puccinia spp., somatic cells are dikaryotic, consisting of two physically distinct haploid nuclei. If two contigs shared at least 25 genes, they were considered to represent haplotypes from distinct Pgt nuclei. These homologous contigs were grouped into distinct bins.
This step is based on ALLHiC assembler v0.9.8 that started with raw Hi-C reads mapped to the Canu contigs using BWA-MEM v0.7.17. The resulting alignments were split into 18 homologous groups (HGs) defined by aligning gene models from the Canu assembly to the assembled chromosomes of the Pgt21-0 isolate. For each HG, noisy inter-allelic and weak Hi-C signals were removed. The scaffolds connected by Hi-C reads were built using binned contigs from the first step of assembly and partitioned into two haplotypes.
The haplotype assignment for the 99KS76A-1 genome scaffolds was performed by counting Hi-C links between the scaffolds. Hi-C reads were processed with HiCUP pipeline v0.8.2 to filter out non-unique alignments and experimental artefacts, using Bowtie2 as aligner and the 99KS76A-1 assembly as a reference. The resulting haplotypes correspond to genomes of individual nuclei in a dikaryotic fungus.
Processed hic file was generated by Juicer Tools v2.13.07.
Assembly: PGFY00000000.2
Supplementary files format and content: .hic file

organism: Puccinia graminis f. sp. tritici

source_name: germinated spores

growth_protocol: Spores of Pgt race RKQQC were sprayed onto wheat cultivar “Morocco”. After drying for 30 minutes, plants were kept in dew chambers (with settings of 9C wall, 43C water, and 18-22C air temperature) for 12-16 hours. Afterwards, plants were immediately transferred to a controlled setting growth chamber, treated with Miracle-Gro (Home Depot) fertilizer for spores grow-up (about 2 weeks).

extract_protocol:
High Molecular Weight (HMW) DNA exaction was done by Dovetail Genomics.
Dovetail Hi-C library construction, followed by sequecning with HiSeqX 2x150bp.

treatment_protocol: To promote the germination of urediniospores, urediniospores collected from plants were dusted in a fine layer over the diluted germination solution (nonyl alcohol or nonanol, Tween 20, ethanol, Milli Q water) to form a spore mat, which was sent to Dovetail Genomics for Hi-C library preparation and sequencing.

value: germinated spores

tag: isolate


title: Spinal Endothelial cells, WT, Batch2


title: TGCT1, ISO-seq

description: IsoSeq


title: Hi-TrAC_GC2201_2251_GM12878_bio2_tech1

extract_protocol:
Genomic DNA was purified by Phenol-Chloroform extraction. RNA was extracted with QIAzol lysis reagent (QIAGEN) and RNeasy mini kit (QIAGEN).
For Hi-TrAC, repair DNA gaps with T4 DNA polymerase. Remove free bridging linker by AMPure XP beads. Then, Digest purified DNA with restriction enzymes MluCI/NlaIII, and enrich biotin-labeled DNA fragments with streptavidin beads. Perform adapter ligation on beads. After washing the beads, run PCR with illumina multiplexing indexed primers. For RNA-seq, libraries were constructed following Smart-seq2 protocol (Picelli et al., 2014). For ChIP-seq, sheared chromatins were immunoprecipitated with anti-CTCF, anti-RAD21, anti-HCFC1, anti-ZNF143 antibodies. DNA was purified, then end-repaired using End-It DNA End-Repair kit (Epicentre). A-tailing was performed with Klenow Fragment (3'->5' exo-) with the presence of dATP. Universal adapters were then ligated. The libraries were then amplified by PCR using indexed primers.

tag: cell line


title: 33.3 µg EE2/g, rep4 [QE1-H4]

city: Sainte-Anne-de-bellevue

first: Yeon-Seon

last: Jeon

state: Quebec

address: 21111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

data_processing:
Processed using the Kallisto workflow on Galaxy.ecotoxxplorer.ca and manually formatted to be used for NetworkAnalyst.ca
Assembly: Coturnix japonica 2.0 genome from Ensemble (GCA_001577835.1)
Supplementary files format and content: Count table in a tab-delimited text file format with Entrez IDs in rows and samples in columns

organism: Coturnix japonica

source_name: Left-lobe liver

growth_protocol: Incubation at 37°C and 60% humidity

extract_protocol:
Liver tissue was homogenized in buffer RLT using a TissueLyser II (Qiagen, Toronto, ON, CA), and RNA was extracted using the RNeasy® Mini QIAcube Kit (Qiagen) following the manufacturer’s protocol. An extra DNase I digestion step was included to eliminate genomic DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Aircell injection of 10 µl dosing solution prior to incubation

tag: tissue

value: Left-lobe liver

value: embryonic day 9

value: 33.3 µg EE2/g egg weight


title: 33.3 µg EE2/g, rep5 [QE1-H5]


title: TGCT2, ISO-seq

description: IsoSeq

tag: cell type


title: 33.3 µg EE2/g, rep3 [QE1-H3]


title: Hi-TrAC_GC1478_1497_2249_GM12878_bio1_tech2

city: Bethesda

first: Yaqiang

address: 9000 Rockville Pike

institute: NHLBI


title: 33.3 µg EE2/g, rep2 [QE1-H2]


title: LAP1BFib-MYOD-day0-biolrep2


title: 3.33 µg EE2/g, rep4 [QE1-M4]

value: 3.33 µg EE2/g egg weight


title: 33.3 µg EE2/g, rep1 [QE1-H1]


title: 3.33 µg EE2/g, rep2 [QE1-M2]


title: 3.33 µg EE2/g, rep3 [QE1-M3]


title: 3.33 µg EE2/g, rep1 [QE1-M1]


title: 3.33 µg EE2/g, rep5 [QE1-M5]


title: Solvent, rep5 [QE1-S5]

value: DMSO (solvent)


title: Solvent, rep4 [QE1-S4]


title: Solvent, rep3 [QE1-S3]


title: Solvent, rep2 [QE1-S2]


title: Solvent, rep1 [QE1-S1]


title: LAP1BFib-MYOD-day2-biolrep1

value: MyoD induction, differentiation day 2


title: Mouse vessels, WT, suppl_rep1

city: Stockholm

first: Michael

last: Vanlandewijck

address: Blickagången 6

department: Department of Medicine

country: Sweden

institute: Karolinska Institute

description:
dual index
151966

library_source: transcriptomic single cell

data_processing:
Demultiplexing with Cellranger mkfastq
Alignment with Cellranger count
Loading of the samples into the R Seurat package
Seurat object with min.cells=3 and min.features=200
subset cells with nFeature_RNA > 200 & nFeature_RNA < 7500 & percent.mt < 10
FindVariableFeatures(bind, selection.method = "vst", nfeatures = 2000)
FindNeighbors(cells, dims = 1:17) for main and 1:20 for suppl
FindClusters(cells, resolution = 0.8) and 0´.6 for suppl
Assembly: mm10
Supplementary files format and content: Cellranger output folder with barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz

source_name: Brain microvessels

growth_protocol: Standard protocol

extract_protocol:
Mice were euthanized by cervical dislocation and the head was immediately removed and placed in ice cold primary washing medium (Dulbecco's Modified Eagle Medium (DMEM) with 1% Penicillin/Streptomycin (P/S), both from Gibco. Once in the lab, the brain was carefully dissected from the skull and the brain stem and olfactory bulbs were removed. For scRNAseq, the cerebellum was also removed and only one hemisphere was used for further analysis. The brain was then placed in a 100 mm petri dish and minced by cutting with a pair of scissors parallel to the petri dish plane to avoid cutting into the plastic surface (<1 mm3 pieces). Once homogenous, the tissue was dissolved in 3 ml freshly prepared primary dissociation buffer (collagenase 1 mg/ml, Sigma C6885, in DMEM w/o phenol red, Gibco) and passed through a cut p1000 pipet tip ten times or until smooth passing. The solution was transferred to a 5 ml Eppendorf tube and placed in a rotating incubator (speed 20 rev/min) at 37 °C for 10 minutes. Samples were then passed through an uncut p1000 pipet tip 10 times or until smooth passing. Samples were placed back in the rotating incubator for 10 minutes at 37 °C. The samples were filtered through a 70 µm mesh strainer (Falcon) into a 50 µl tube (Falcon) to remove large undigested tissue fragments. The filter was washed with 10 ml of primary washing medium, and samples were spun at 300 g for 5 minutes at RT. The supernatant was removed, and the pellet was resuspended in 4.5 ml secondary washing medium (DMEM with 1% PS (Gibco), 0.5 mg/mL heparin (Sigma)) and divided into three 2 ml Eppendorf tubes. 15 µl Rat anti-mouse CD31 antibody (BD, 10 µl/brain) coupled Dynabeads® Sheep Anti-Rat IgG (Invitrogen, 50 µl/ brain, prepared according to manufacturer’s instructions) were added to each subsample and placed in a rotating incubator for 30 minutes at room temperature. After antibody incubation, the tubes were placed on a DynaMag 2 magnet (Invitrogen), and the supernatant was removed. Beads were washed twice by resuspension and magnetic capture in secondary washing medium, after which the three samples were pooled in one 2 ml Eppendorf tube. The resuspended beads coupled with microvasculature were visualized using an inverted microscope at 20x magnification.
Libraries were constructed as per manufacurers' recommendation (10x Genomics Gene expression v3.1)

value: Brain microvessels

value: 3 months

value: Multiple


title: Mouse vessels, WT, main_rep3

description:
single index
WT_12m_07_1

value: 12 months


title: Mouse vessels, WT, suppl_rep3

description:
dual index
153449


title: Mouse vessels, WT, main_rep1

description:
single index
WT_12m_04_1


title: Mouse vessels, WT, suppl_rep4

description:
dual index
152611


title: Mouse vessels, WT, suppl_rep2

description:
dual index
153443


title: 1dpi-L4

city: Nanjing

first: jie

last: Huang

address: NO.1 Weigang

institute: NJAU

description: infection sample-1dpi

data_processing:
The RNA-seq reads were aligned to the tomato genome (ITAG2.4) using tophat-2.0.11 with anchor length more than 8nt for spliced alignments. Only uniquely mapped reads were retained for subsequent analysis.
Genome_build: ITAG2.4
Supplementary_files_format_and_content: bigWig

organism: Solanum lycopersicum

source_name: leaves

growth_protocol: Solanum lycopersicum (Heinz 1706) plants were grown in a greenhouse for 8-10 weeks under a 14 h day at 24°C and 10 h night at 22°C

extract_protocol:
The total RNA was extracted using the Invitrogen PureLink RNA Mini kit (Cat no. 12183018A)
These libraries were sequenced using Illumina HiSeq 2X150 in paired-end mode with a read length of 150 bp.

treatment_protocol: The detached tomato leaves were inoculated with four 20 µl (200 zoospores per microliter) droplets of the zoospore solution

tag: infection

value: leaves

tag: cultivar

value: Heinz 1706


title: 2dpi-L1

description: infection sample-2dpi


title: 1dpi-L3

description: infection sample-1dpi


title: Cre, replicate 1

city: Sydney

first: Martyn

last: Bullock

state: NSW

address: Cnr Reserve Rd  and Westbourne St, Royal North Shore Hospital, St Leonards

department: Kolling Institute

institute: Univeristy of Sydney

hyb_protocol: Hybridization was performed as part of automated array processing using the GeneTitan Multi-Channel Instrument (Applied Biosystems).

scan_protocol: Imaging was performed as part of automated array processing using the GeneTitan Multi-Channel Instrument.

data_processing: Raw CEL data was background adjusted, normalized and converted into summarized expression values by the RMA (Robust Multi-array Average) algorithm implemented using Affymetrix Expression Console Software with standard settings.

source_name: Cre thyroid harvested two weeks post-treatment

label_protocol: 250 ng total RNA was reverse transcribed into cDNA, then transcribed into cRNA and labeled into biotinylated cRNA using GeneChip WT (whole transcriptome) PLUS Reagent Kit (Applied Biosystems) according to the manufacturer’s protocol.

growth_protocol: Mice were housed in Allentown 30 × 20 × 18 cm individually ventilated cages (5 per cage) with cellulose bedding under Specific Pathogen Free conditions. Rooms were maintained at 21-22°C and kept on 12 hr light/dark cycle (7:00/19:00 hr). Mice received acidified water and a commercial complete pelleted food ad libitum, and enrichment was provided in the form of autoclaved ice block sticks or straws.

extract_protocol: Total RNA was isolated from frozen mouse thyroid tissue (one lobe per animal) using Tri-Reagent (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s protocol, with the homogenization step being performed using a Qiagen (Hilden, Germany) TissueLyser II set at 30 Hz (1800 oscillations per min) for 2 mins. Contaminating genomic DNA was eliminated by in-solution digestion with RNase-Free DNAse I, followed by clean-up with the RNeasy Plus mini kit (All reagents from Qiagen). The purified RNA was quantified using a Qubit 4 Fluorometer with RNA HS Assay Kit (Thermo Scientific), and the integrity assessed with a Bioanalyzer 2100 system using the RNA Nano 6000 Assay Kit (Agilent Technologies, Santa Clara, CA, United States). Samples with an RNA integrity number ≥ 7, 260/280 ratio 1.8-2.2 and 260/230 ratio >1.7 were selected for analysis.

treatment_protocol: Tamoxifen (0.05g/kg) was administered intraperitoneally (into the lower abdominal quadrant) to mice aged 6-8 weeks, once daily for five consecutive days.

tag: strain background

value: Cre control

value: thyroid


title: Foxe1/Cre, replicate 3

source_name: Foxe1/Cre thyroid harvested two weeks post-treatment


title: Cre, replicate 2


title: Foxe1/Cre, replicate 1


title: 2dpi-L4

description: infection sample-2dpi


title: 3dpi-L2

description: infection sample-3dpi


title: 3dpi-L4

description: infection sample-3dpi


title: 3dpi-L3

description: infection sample-3dpi


title: 3dpi-L1

description: infection sample-3dpi


title: SerumLCEVs_ASD2_rep1

city: Xi'an

first: Yannan

last: Qin

address: West Road Yanta

institute: Xi'an Jiaotong University

description: Expression of mRNA and lncRNA in serum LCEVs

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human lncRNA Microarray 4×180 K for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The slide was then scanned with the Agilent Microarray Scanner G5761A.

data_processing: Data were extracted with Feature Extraction software 12.0.3.1 (Agilent Technologies), and raw data were normalized by Quantile algorithm. Genes with a p value less than 0.05 and a fold change of at least 2 were selected for further analysis.

source_name: Serum LCEVs, ASD-2 subgroup, rep1

label_protocol: Equal amount of RNA from each subgroup was reversely transcribed into cDNA, which was then labeled with Cy3.

extract_protocol: 0.5 ml serum was incubated with 0.15 ml of thromboplastin-D (Fisher Scientific, Inc., Hanover Park, IL) at room temperature for 60 min. Then, 0.5 ml calcium- and magnesium-free Dulbecco’s balanced salt solution (DBS−2) with protease inhibitor cocktail (Roche Applied Sciences, Inc., Indianapolis, IN) and phosphatase inhibitor cocktail (Pierce Halt, Thermo Scientific, Inc., Rockford, IL) was added and the mixture was centrifuged at 1,500×gfor 20 min. The supernatant was mixed with 252 μL ExoQuick exosome precipitation solution (EXOQ; System Biosciences, Inc., Mountainview, CA), and incubated for 1 hr at 4°C. The resultant EVs suspension was centrifuged at 1,500×g for 30 min at 4°C and the pellet was re-suspended in 150 μl DBS−2 with the inhibitor cocktails before immunochemical enrichment of LCEVs. Each sample received 100 μL 3% BSA (1:3.33 dilution of Blocker BSA 10% solution in DBS−2 [Thermo Scientific, Inc.]) and was incubated with 1 μg mouse anti-L1CAM biotinylated antibody (clone 5G3, eBioscience, San Diego, CA) for 1 hr at 4°C. Following that, 25 μL streptavidin-agarose resin (Thermo Scientific, Inc.) plus 50 μL 3% BSA was added and the sample was incubated at 4°C for 30 min. After centrifugation at 200×g for 10 min at 4°C and removal of the supernate, 3% BSA was added again, and centrifugation and supernatant removal were repeated. Each pellet was suspended in 50 μL 0.05 M glycine-HCl (pH 3.0), incubated at 4°C for 10 min, and re-centrifuged at 4,000×g for 10 min at 4°C. The obtained supernatant was transferred to a new Eppendorf tube containing 5μL of 1 M Tris-HCl (pH 8.0) and stored at −80°C.

treatment_protocol: Venous blood samples were collected by a pediatric nurse. The blood was allowed to clot at room temperature for 30 min, and the clot was then removed by centrifuging at 1,500×g for 10 minutes. The resulting supernatant is immediately transferred to a clean polypropylene tube, and EDTA-free inhibitor cocktail (Halt protease inhibitor; Thermo Scientific Pierce Protein Research Products, Rockford, IL, USA) was added at a concentration of 10 μL/mL serum.

value: Serum

tag: age

value: 2-6 years


title: 2dpi-L3

description: infection sample-2dpi


title: Cre, replicate 3


title: Foxe1/Cre, replicate 2


title: SerumLCEVs_ASD5_rep1

source_name: Serum LCEVs, ASD-5 subgroup, rep1


title: SerumLCEVs_TD1_rep1

source_name: Serum LCEVs, TD-1 subgroup,rep1


title: 1dpi-L2

description: infection sample-1dpi


title: 0dpi-L3

description: control sample

value: Mock control


title: SerumLCEVs_ASD3_rep1

source_name: Serum LCEVs, ASD-3 subgroup, rep1


title: SerumLCEVs_ASD1_rep1

source_name: Serum LCEVs, ASD-1 subgroup, rep1


title: 1dpi-L1

description: infection sample-1dpi


title: SerumLCEVs_TD3_rep1

source_name: Serum LCEVs, TD-3  subgroup,rep1


title: 2dpi-L2

description: infection sample-2dpi


title: SerumLCEVs_ASD4_rep1

source_name: Serum LCEVs, ASD-4 subgroup, rep1


title: SerumLCEVs_TD2_rep1

source_name: Serum LCEVs, TD-2  subgroup,rep1


title: 0dpi-L2

description: control sample


title: 0dpi-L4

description: control sample


title: REV2.0

city: Tianjin

first: Xinna

last: Zhu

state: Tianjin

address: 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academic Sciences

description: AM1 medium, 5%w/v glucose,5% w/v xylose pH=7.0

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli ATCC 8739 genome using Bowtie 2 (version 2.2.5)
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated
Detailed parameters for reads mapping: bowtie2 -x ATCC 8739 -1 X_1.fq -2 X_2.fq --no-mixed -p 2 -S X.sam
Genome_build: Escherichia coli ATCC 8739
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

organism: Escherichia coli ATCC 8739

source_name: Reverse engineered strain REV2.0

growth_protocol: Co-utilization were assessed using AM1 mineral salt media supplemented with glucose and xylose at each concentration of 50 g·L-1. Seed culture were grown overnight (16 h) in AM1 medium supplemented with 2% sugar. For each experiment, E. coli was grown at 37 ℃ in a pH-controlled fermentation vessel with the initial cell density at OD550nm of 0.1

extract_protocol:
Total RNA was isolated by the Trizol-Phenol-Chloroform method. An additional clean-up including the on-column DNase I treatment was performed by using the RNeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were collected at the mid-log phase. Cultures were fixed with 2:1 volume of RNAprotect Bacteria (Qiagen) and harvested. RNA was isolated from the pellet using RNeasy Mini kit (Qiagen). Genomic DNA was removed using DNAse I (Qiagen). RNA quality was determined using Agilent 2100 Bioanalyser (Agilent) and quantified using the ND-1000 (NanoDrop Technologies).The 150-nt paired-end RNA-seq libraries were generated commercially at Novogene Biotechnology Co. Ltd (Tianjin, China) by using Illumina’s Hiseq X Ten platform (Illumina, San Diego, USA).

tag: strain

value: ATCC 8739


title: REV1.0

source_name: Reverse engineered strain REV1.0


title: AE2.0

source_name: Adaptively evolved strain AE2.0


title: PS1.0

source_name: Precursor strain PS1.0


title: IRI_t30

city: Firenze

first: Roberto

last: Semeraro

address: Viale Pieraccini, 6

department: Medicina Sperimentale e Clinica

institute: Università degli studi di Firenze

data_processing:
Basecall performed with cellranger mkfastq v3.0.1.
Single cell feature counts performed with cellranger count v.3.0.1.
Assembly: mm10
Supplementary files format and content: matrix.mtx (filtered count matrix), barcodes.tsv, and features.tsv files generated through cellranger count.

source_name: kidney

extract_protocol:
The single cell suspension with 95% viability was run on a 10x Chromium Single Cell instrument (10x Genomics, Pleasanton, CA) following Manufacturer’s instructions
3’ gene expression libraries were constructed following 10x Genomics's instructions

treatment_protocol: Male mice were subjected to unilateral ischemia reperfusion injury for 30 minutes by clamping the left renal artery. Mice were then sacrificed at different days after ischemia (2 days after ischemia, n=2 performed in 2 times; 30 days after ischemia, n=3, performed by pulling together 3 mice) or without undergoing ischemia reperfusion injury (healthy n=1)

value: Total cells from mouse kidney

value: 12 weeks

value: 30 days after unilateral ischemia reperfusion injury


title: DSS mouse 1718

city: Marseille

first: Quentin

last: Da Costa

address: 232 boulevard de Sainte Marguerite

country: France

institute: Institut Paoli-Calmettes

data_processing:
The quantification of the gene transcripts was performed using the program Kallisto, which is based on pseudo-alignment principle, with default settings.
GRCm38 NCBI RefSeq was used to annotate the transcripts.
Assembly: mm10
Supplementary files format and content: A tab-delimited text file include raw transcript counts for each sample.

source_name: Colonic Fibroblasts

extract_protocol:
Total RNA was extracted from each sample using the Maxwell® RSC Instrument (Promega, Madison, WI, USA) and Maxwell RSC simplyRNA Blood Kit (AS1380, Promega).
RNA-seq libraries were prepared using the NEBNext rRNA Depletion Kit (NEB #E6310, New England Biolabs, Ipswich, MA, USA) and NEBNext Ultra II Directional RNA Library Prep Kit (NEB #E776) for Illumina, following the manufacturer’s instructions.

value: Colon

value: 6 weeks

value: DSS


title: Ctrl mouse 1718

value: control


title: Healthy

value: 8 weeks

value: healthy control


title: Ctrl mouse 1717


title: DSS mouse 1716


title: DSS mouse 1717


title: IRI_t2_1

value: 2 days after unilateral ischemia reperfusion injury


title: Ctrl mouse 1716


title: AE1.0

source_name: Adaptively evolved strain AE1.0


title: R688-49-CTL-2

city: Houston

first: Khandan

last: Keyomarsi

state: TX

address: 1515 Holcombe Blvd

department: Experimental Radiation Onc

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Paired-end reads in fastq format were initially checked for read quality using FastQC 0.11.8
Sequence reads were mapped to the mouse reference genome (Gencode GRCm38) using TopHat 2.1.1 (parameter: --library-type=fr-firststrand)
The BAM file with mapped reads for each sample was sorted and then used as an input for HTSeq 0.11.0 in order to generate read count data on gene level (parameters: -s reverse  -m union)
Assembly: GRCm38
Supplementary files format and content: raw read count data generated by htseq-count 0.11.0 for each sample

source_name: enriched epithelia from mammary glands

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using TruSeq stranded protocol.

value: enriched epithelia from mammary glands

value: WT

value: C57BL/6J X BALB/cJ F1 hybrid

tag: gender

value: Female


title: R688-48-CTL-1


title: Control

city: Tokyo

first: Yasutaka

last: Hayashi

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Cellular Therapy, Advanced Clinical Research Center

country: Japan

institute: Institute of Medical Science, The University of Tokyo

data_processing:
The sequence data were processed using Cell Ranger (version 3.1.0) to align reads and generate feature-barcode matrices.
Subsequent detailed analysis was performed using Seurat (version 3.2.3)(Satija et al., 2015).

source_name: mesenchymal stromal cell

extract_protocol:
To sort CD45-TER119-CD31-CD140a+CD51+MSCs, bones (femora and tibiae) were crushed, digested with 2 mg/mL collagenase (Wako) in Dulbecco's Modified Eagle Medium for 60 min at 37℃ and sorted using the FACS AriaⅡ.
The libraries were constructed using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 according to the manufacturer’s protocol. Reverse transcription and library preparation were performed on a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad). Amplified cDNA and final libraries were evaluated on an Agilent BioAnalyzer using a High Sensitivity DNA Kit (Agilent Technologies). The libraries were sequenced on a NextSeq Illumina 500 platform using NextSeq 500/550 High Output v2.5 Kit (150 cycles).
scRNA-seq

value: bone marrow mesenchymal stromal cell


title: Tg_A2


title: WT_A1


title: Abcg2


title: R688-50-CTL-3


title: 0dpi-L1

description: control sample

source_name: leaves

value: Mock control

value: leaves

value: Heinz 1706


title: nLRC 2y_3

city: Tsukuba

first: Hiromi

last: Yanagisawa

address: 1-1-1 Tennodai

department: TARA center

institute: University of Tsukuba

description: other name: non-Label retaining cells (nLRCs)

data_processing:
Sequencing was done in Illumina NextSeq500 generating 8 gz fastq files per samples
Fastq files were imported to CLC GW as paired-end reads and mapped to mouse mm10 genome (ENSEMBL but provided by CLC)
Mapped reads exported, converted into bedgraph for visualization in UCSC browser
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 12.0 (Qiagen).
Differentially expressed genes were filtered using fold change and p value < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM and RPKM values for each gene in every sample

source_name: tail epidermis

extract_protocol:
Tail skin was incubated overnight at 4 °C in 0.25% trypsin/EDTA and the next day at 37 °C for 30 minutes. Single-cell suspensions were then filtered, stained with antibodies and sorted by flow cytometry directly into Trizol (Ambion, 10296028) for RNA extraction. RNA quality was measured by Agilent Bioanalyzer RNA 6000 pico kit (5067-1513) and quantity using nanodrop.
Library was synthesized using low input protocol (≤50ng RNA) by SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara) and the library quality was checked by Agilent Bioanalyzer DNA high-sensitivity kit (5067-4626).

treatment_protocol: Doxycycline was mixed in the chow (cat no) for 2 weeks, fresh chow was given every week.

value: fast-cycling epidermal stem cells

value: K5-tTA/pTRE H2B-GFP

value: 2 years old

value: doxycycline 2 weeks


title: HFSC 2y_3

description: other name: bulge

value: hair follicle stem cells


title: HFSC 2y_2

description: other name: bulge


title: LRC 2y_3

description: other name: Label retaining cells (LRCs)

value: slow-cycling epidermal stem cells


title: nLRC 2y_2


title: LRC 2y_2


title: PS2.0

source_name: Precursor strain PS2.0

value: ATCC 8739


title: HFSC 2y_1

description: other name: bulge


title: IRI_t2_2

value: Total cells from mouse kidney

value: 8 weeks


title: nLRC 2y_1


title: Mouse vessels, WT, main_rep2

description:
single index
WT_12m_06_2

source_name: Brain microvessels

value: Brain microvessels

value: 12 months

value: Multiple


title: LRC 2y_1


title: nLRC 1.5y_2

value: 1.5 years old


title: HFSC 1.5y_2

description: other name: bulge


title: HFSC 2m_3

description: other name: bulge

value: 2 months old


title: LRC 1.5y_2


title: nLRC 1.5y_1


title: HFSC 1.5y_1

description: other name: bulge


title: LRC 1.5y_1


title: nLRC 2m_3


title: 1y_KO_2

source_name: back skin epidermis

extract_protocol:
Back skin was incubated overnight at 4 °C in 0.25% trypsin/EDTA and the next day at 37 °C for 30 minutes. Single-cell suspensions were then filtered, stained with antibodies and sorted by flow cytometry directly into Trizol (Ambion, 10296028) for RNA extraction. RNA quality was measured by Agilent Bioanalyzer RNA 6000 pico kit (5067-1513) and quantity using nanodrop.
Library was synthesized using low input protocol (≤50ng RNA) by SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara) and the library quality was checked by Agilent Bioanalyzer DNA high-sensitivity kit (5067-4626).

value: epidermal stem cells

value: Fbln7 KO

value: 1 year old


title: HFSC 2m_1

description: other name: bulge


title: 1y_KO_3


title: LRC 2m_1


title: nLRC 2m_1

value: fast-cycling epidermal stem cells


title: 1y_KO_4


title: LRC 2m_3

value: K5-tTA/pTRE H2B-GFP


title: nLRC 2m_2


title: HFSC 2m_2

description: other name: bulge


title: LRC 2m_2


title: 1y_WT_3

value: Fbln7 WT


title: 1y_KO_1


title: 1y_WT_1


title: 1y_WT_2


title: 2mths_KO_3


title: 2mths_KO_1


title: 2mths_KO_2


title: 2mths_WT_2


title: 2mths_WT_1


title: 2mths_WT_3


title: BMDM_LPS_8h_1

city: Warsaw

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute Of Molecular And Cell Biology In Warsaw

data_processing:
Illumina bcl2fastq 2.20 software used for basecalling.
Sequence reads from C. elegans experiments were mapped to the WBCel235 genome build (ENSEMBL, release 94) using STAR v. 2.6.1b
Sequence reads from M. musculus were mapped to the GRCm38 mouse genome build (ENSEMBL, release 94) using STAR v. 2.7.6a
Counts for each transcript in C. elegans experiments were collected using featureCounts from Subread package (v. 1.6.3),  with options options -Q 10 -p -B -C -s 2 -g gene_id -t exon and respective annotation gtf file (WBCel235; ENSEMBL; release 94)
Counts for each transcript in M. musculus experiments were collected using featureCounts from Subread package (v. 2.0.1),  with options options -Q 10 -p -B -C -s 2 -g gene_id -t exon and respective annotation gtf file (Gencode, vM25)
Differential expression analysis was performed using DESeq2, with default settings
Genome_build: GRCm38
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 normalized counts for each sample.

source_name: bone marrow-derived macrophages

extract_protocol:
Total RNA from C. elegans and BMDM cells was isolated with TRI Reagent (Sigma-Aldrich) according to the manufacturer’s instructions. Before RNA-seq library preparation, total RNA samples were treated with TURBO DNase (Thermo Fisher Scientific) to remove DNA contamination. RNA was then purified by phenol/chloroform extraction and ethanol precipitation.
Ribosomal RNA was removed from samples using a Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat, Epicentre). Strand-specific libraries were prepared using a dUTP protocol (KAPA Stranded RNA-Seq Library Preparation Kit), according to the manufacturer. Library quality was assessed using chip electrophoresis performed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).

treatment_protocol: The primary BMDM cell cultures were established from the bone marrow monocytes from wild-type mice and cultured in IMDM medium (Thermo Fisher Scientific) supplemented with macrophage colony-stimulating factor (M-CSF, Preprotech) at 37°C in 5% CO2 as described previously (Graczyk et al., 2015). For BMDM stimulation with lipopolysaccharide (LPS), cells were treated with 100 ng/ml LPS (Santa Cruz Biotechnology) for 8 h. Cells were scratched from the plates, pelleted by centrifugation for 3 min at 350 x g, and resuspended in TRI Reagent.

value: wild type

value: LPS-activated for 8h

value: bone marrow-derived macrophages

tag: replicate


title: BMDM_LPS_0h_3

treatment_protocol: The primary BMDM cell cultures were established from the bone marrow monocytes from wild-type mice and cultured in IMDM medium (Thermo Fisher Scientific) supplemented with macrophage colony-stimulating factor (M-CSF, Preprotech) at 37°C in 5% CO2 as described previously (Graczyk et al., 2015). Cells were scratched from the plates, pelleted by centrifugation for 3 min at 350 x g, and resuspended in TRI Reagent.

value: untreated


title: BMDM_LPS_8h_3


title: BMDM_LPS_0h_2


title: BMDM_LPS_8h_2


title: BMDM_LPS_0h_1


title: Maize inbred line Q8-56DAP-Grain-rep2

city: Yangling

first: Zhou

middle: Jian

last: Qu

state: Shaanxi

address: No.3 Taicheng Road

institute: Northwest A&F University

data_processing:
RNA sequencing was performed on an Illumina NovaSeq-PE150 system
Sequencing reads were quality trimmed using Trimmomatic (v0.38; http://www.usadellab.org/cms/?page=trimmomatic)
Sequencing reads were aligned to the maize B73 reference genome (RefGen_v4; ftp://ftp.ensemblgenomes.org/pub/plants/release-41/fasta/zea_mays/dna/) sequences assembly using HISAT2 (version 2.0.5)
The stringtie (version 1.3.5; https://ccb.jhu.edu/software/stringtie/) was used to normalization and estimation of gene expression level in terms of FPKM (fragments per kilobase per million)
Differentially expressed genes in time-series samples were identified using edgeR (Robinson et al., 2010)
Genome_build: Zea mays v4
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample

organism: Zea mays

source_name: Maize grain

growth_protocol: Eight maize inbred lines were planted during the summer of 2018 at the maize breeding testing ground of the Northwest A&F University in Yangling, Shaanxi Province (NT, 108°02', 34°16'). The field experiment was conducted using a completely randomized design with two replications. Each inbred lines were planted in a 4 m row, with 4.5 m long and a distance of 0.6 m between adjacent rows. The planting density was 75,000 plants/ha, and following standard irrigation and fertilization management throughout the whole developmental period. The ears were bagged prior to silk emergence and then subjected to manual self-pollination.

extract_protocol:
The RNA of three biological replicates of the samples was extracted separately from each sample using the TRIzol reagent (Invitrogen) following the manufacturer’s instructions.
A total of 2 μg RNA was used for library construction with an Illumina NEBNext® UltraTM RNA Library Prep Kit (Illumina Co, Ltd), according to the manufacturer’s instructions.

value: Grain

tag: Stage

value: 56 day after pollination (DAP)

tag: inbred line


title: Maize inbred line Q8-56DAP-Grain-rep3


title: Maize inbred line Q8-49DAP-Grain-rep3

value: 49 day after pollination (DAP)


title: Maize inbred line Q8-42DAP-Grain-rep3

value: 42 day after pollination (DAP)


title: Maize inbred line Q8-49DAP-Grain-rep2


title: Maize inbred line Q8-49DAP-Grain-rep1


title: Maize inbred line Q8-42DAP-Grain-rep1


title: Maize inbred line Q8-42DAP-Grain-rep2


title: Maize inbred line Q8-28DAP-Grain-rep2

value: 28 day after pollination (DAP)


title: Maize inbred line Q8-35DAP-Grain-rep1

value: 35 day after pollination (DAP)


title: Maize inbred line Q8-35DAP-Grain-rep3


title: Maize inbred line Q8-21DAP-Grain-rep3

value: 21 day after pollination (DAP)


title: Maize inbred line Q8-21DAP-Grain-rep2


title: Maize inbred line Q8-28DAP-Grain-rep1


title: Maize inbred line Q8-28DAP-Grain-rep3


title: Maize inbred line Q8-21DAP-Grain-rep1


title: Maize inbred line Q7-56DAP-Grain-rep1


title: Maize inbred line Q7-56DAP-Grain-rep2


title: Maize inbred line Q7-56DAP-Grain-rep3


title: Maize inbred line Q7-49DAP-Grain-rep2


title: Maize inbred line Q7-49DAP-Grain-rep3


title: Maize inbred line Q8-56DAP-Grain-rep1


title: Maize inbred line Q7-42DAP-Grain-rep2


title: Maize inbred line Q8-35DAP-Grain-rep2


title: Maize inbred line Q6-35DAP-Grain-rep3


title: Maize inbred line Q6-35DAP-Grain-rep1


title: Maize inbred line Q6-35DAP-Grain-rep2


title: Maize inbred line Q7-49DAP-Grain-rep1


title: Maize inbred line Q6-28DAP-Grain-rep3


title: Maize inbred line Q7-42DAP-Grain-rep1


title: Maize inbred line Q6-42DAP-Grain-rep2


title: Maize inbred line Q6-56DAP-Grain-rep3


title: Maize inbred line Q7-21DAP-Grain-rep2


title: Maize inbred line Q7-28DAP-Grain-rep1


title: Maize inbred line Q6-49DAP-Grain-rep1


title: Maize inbred line Q6-49DAP-Grain-rep3


title: Maize inbred line Q6-49DAP-Grain-rep2


title: Maize inbred line Q7-28DAP-Grain-rep2


title: Maize inbred line Q7-35DAP-Grain-rep1


title: Maize inbred line Q6-56DAP-Grain-rep2


title: Maize inbred line Q7-42DAP-Grain-rep3


title: Maize inbred line Q7-21DAP-Grain-rep1


title: Maize inbred line Q7-35DAP-Grain-rep2


title: Maize inbred line Q6-42DAP-Grain-rep3


title: Maize inbred line Q6-28DAP-Grain-rep1


title: Maize inbred line Q6-28DAP-Grain-rep2


title: Maize inbred line Q6-21DAP-Grain-rep3


title: Maize inbred line Q7-35DAP-Grain-rep3


title: Maize inbred line Q7-28DAP-Grain-rep3