title: Ngn2 iNeurons isogenic 7Dup isoDup (242K) 3

city: Milano

first: Alessandro

last: Vitriolo

state: MI

address: Via Rita Levi Montalcini 1

department: Neurogenomics

country: Italy

institute: Fondazione Human Technopole

description: RNA.SE.rds

data_processing:
Quantification was done using Salmon 0.9.1 (Patro et al., 2017) on the ensembl 92 transcriptome.
Only protein-coding transcripts were retained, and counts were aggregated at the level of gene symbols.
Only genes with at least 20 reads in at least a number of samples corresponding to 75% of the smallest experimental group were included in the analysis.
Differential expression analysis was done using DESeq2 (Love et al., 2014), and for pairwise comparisons between groups foldchanges were shrunken using the apeglm method (Zhu et al., 2019). In addition, a regression on 7q11.23 copy-numbers was performed.
Assembly: GRCh38
Supplementary files format and content: RNA.SE.rds.zip are RNA.restExperiment.SE.rds.zip are R SummarizedExperiment objects containing the quantification and annotation for the different samples.

source_name: isoDup (242K)

growth_protocol: In order to obtain cortical glutamatergic neurons (iNeurons), iPSCs were dissociated with Accutase (GIBCO, Thermo Fisher Scientific) and plated on Matrigel-coated plates (final 2% v/v, Corning) in mTeSR™ or TeSR-E8 (Stemcell Technologies) supplemented with 5 μM Y-27632 (Sigma). iPSCs were then cultured in MEM1 (DMEM/F12 1:1 (Euroclone/Gibco) supplemented with NEAA 1%, N2 1%, BDNF 10 ng/ml, NT-3 10 ng/ml, Laminin 0,2 μg/ml and 2 μg/ml doxycycline hydrochloride, penicillin 100 U/ml and streptomycin 100 μg/ml) for 2 days. On the second day of MEM1, cells were selected with 1 μg/ml puromycin, to reassure that only the cells with Ngn2-inducible cassette will survive. For patient-derived iNeurons, after two days of MEM1, media was change to Neurobasal medium (NB, Thermo Fisher Scientific) supplemented with BDNF 10 ng/ml, NT-3 10 ng/ml, B27 (1:50), GlutaMax (Gibco, 1:100), penicillin 100 U/ml, streptomycin (100 μg/ml), which was previously conditioned on mouse astrocytes for 24 h. Half of media was changed every other day. Instead, for isogenic iNeurons after two days of MEM1, media was change to Neurobasal Plus medium (NB-Plus) composed of B-27™ Plus Neuronal Culture System (Thermo Fisher Scientific) supplemented with Glutamax 0.25% (Thermo Fisher Scientific), 2 μg/ml, doxycycline hydrochloride and penicillin 100 U/ml, streptomycin (100 μg/ml). The media was changed twice a week. On day 7-8, cells that already acquired neuron-like shape were dissociated with Accutase, counted and seeded into plates coated with 15 μg/ml of poly-D-lysine at a density of 1 x 10^6 cells/well of multiwell 6, 2 x10^6 in 6 cm dishes or 4 x10^6 in 10 cm dishes (Nunc Edge plates, Thermo Fisher Scientific) in conditioned NB or NB-Plus. Half of media was changed twice a week until day 30-35.

extract_protocol:
RNA was isolated using the RNeasy mini Kit (QIAGEN) and genomic DNA was removed using the RNase-Free DNase Set (QIAGEN). Retrotranscribed cDNA was obtained from 1 μg of total RNA using the SuperScript VILO Retrotranscription kit from Life Technologies according to the manufacturer’s instructions.
Library preparation for RNA-seq was done with the Ribo-Zero Total RNA sample preparation kit (Illumina), starting from 250 ng to 1 g of total RNA. The quality of cDNA libraries was assessed by Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit.

tag: cell line

value: isoDup (242K)

value: Ngn2 iNeurons

tag: model

value: Isogenic

value: isogenic


title: Ngn2 iNeurons isogenic 7Dup isoDup (242K) 2

status: Public on Mar 20 2024

type: SRA

description: RNA.SE.rds

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell type

tag: genotype

tag: group


title: ob_ob_ETS_2

city: Seoul

first: Seung Min

last: Jeong

address: 222, Banpo-daero, Seocho-gu

department: Department of Biochemistry

country: South Korea

institute: College of Medicine, The Catholic University of Korea

description: allograft tumor from C57BL/6J-ob/ob, post chemotherapy

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to mm10 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: cell from allograft tumor (B16F10 cell)

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

value: post chemotherapy


title: gcWS, iMac, oxLDL, neg, 3

city: Chiba

first: Naoya

last: Takayama

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Graduate School of Medicine

country: Japan

institute: Chiba University

description: iPS_macrophage_limma_lcpm_padj0.01_lfc1.txt

data_processing:
Genomic coordinates of RTEs, along with their names, classes, and families, were downloaded from the UCSC Genome Browser using the Table Browser with “group” set to “Repeats” and “track” set to “RepeatMasker”
Each RTE was assigned reads obtained from the mapped RNA-seq samples within its genomic coordinates.
Read counts were normalized using limma.
Differentially expressed RTEs between sample groups were calculated using limma-voom.
Assembly: hg19

source_name: iPSC-derived macrophages

extract_protocol:
Total RNA from untreated or oxLDL-treated healthy-, WS-, and gcWS-iMφs was isolated using an RNeasy Micro Kit (QIAGEN)
~10 ng total RNA was used as input for cDNA conversion using a SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (cat. #634890, Clontech, Takara). cDNA was fragmented using an S220 Focused-ultrasonicator (Covaris). The cDNA library was then amplified using a NEBNext® Ultra™ DNA Library Prep Kit for Illumina (cat. #E7370L, New England Biolabs).

value: iPSC-derived macrophages

tag: treatment


title: ob_ob_ETS_1


title: gcWS, iMac, oxLDL, neg, 2


title: M_2_T

city: Melbourne

first: Jeremy

last: Anderson

state: Victoria

address: 50 Flemington Rd, Parkville

department: Infection and Immunity

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
Fastq files were assessed for quality using the FastQC package and no samples were excluded from analysis. Bowtie was used to map 100-bp paired end reads to the human transcriptome (Ensembl, GRCh37v70), and gene expression estimates were derived using the limma-voom pipeline. Genes with low expression (CPM <1) were removed from analysis, leaving expression data for 14,574 genes. limma-voom was used to normalise count data and determine gene expression differences between group comparisons.
Genome_build: hg19
Supplementary_files_format_and_content: .counts.txt files contain counts per gene

source_name: Cord blood

extract_protocol:
mRNA were extracted using the QIAGEN Rneasy mini-kit according to manufacturer’s instructions.
Library preparation was performed using the Illumina TruSeq stranded mRNA kit with a starting input of 100ng and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 20 million reads per sample.

treatment_protocol: Samples were left unstimulated or stimulated with RSVA or RSVB for 24h

tag: individual

value: Cord blood mononuclear cells

tag: stimulation

value: Unstimulated

tag: preterm/term

value: Term

tag: gender

value: F


title: gcWS, iMac, oxLDL, neg,1


title: M_6_T


title: Ngn2 iNeurons isogenic 7Dup isoDup (242K) 1

description: RNA.SE.rds


title: M_1_T


title: ob_ob_ctrl_3

description: allograft tumor from C57BL/6J-ob/ob

value: pre-therapy


title: ob_ob_ctrl_4

description: allograft tumor from C57BL/6J-ob/ob


title: B_53_P

value: RSVB

value: Preterm

value: M


title: Ngn2 iNeurons isogenic WBS isoWBS 3

description: RNA.SE.rds

source_name: isoWBS

value: isoWBS

value: WBS


title: WS, iMac, oxLDL, neg, 4


title: ob_ob_ctrl_2

description: allograft tumor from C57BL/6J-ob/ob


title: WS, iMac, oxLDL, neg, 2


title: WS, iMac, oxLDL, neg, 3


title: B_52_P


title: B_51_P


title: B6_ETS_4

description: allograft tumor from C57BL/6J, post chemotherapy


title: B_50_P


title: Ngn2 iNeurons isogenic CTL isoCTL 2

description: RNA.SE.rds

source_name: isoCTL

value: isoCTL

value: CTL


title: B6_ETS_3


title: Ngn2 iNeurons isogenic WBS isoWBS 1

description: RNA.SE.rds

value: Ngn2 iNeurons


title: Ngn2 iNeurons isogenic CTL isoCTL 3

description: RNA.SE.rds

value: Isogenic


title: WS, iMac, oxLDL, neg,1


title: Healthy, iMac, oxLDL, neg, 2


title: B_49_P


title: Ngn2 iNeurons isogenic CTL isoCTL 1

description: RNA.SE.rds

value: isogenic


title: B6_ETS_2

value: post chemotherapy


title: B_48_P


title: Ngn2 iNeurons isogenic WBS isoWBS 2

description: RNA.SE.rds


title: B6_ETS_1


title: Healthy, iMac, oxLDL, neg, 1

value: iPSC-derived macrophages


title: Ngn2 iNeurons patientDerived CTL MIFF3

description: RNA.SE.rds

value: Patient-derived

value: patientDerived


title: WS, iPS-VSMC, oxLDL, pos, 3

data_processing:
TopHat (version 2.1.1; with default parameters) was used to map to the reference genome (UCSC/hg19) with annotation data from iGenomes (Illumina).
Levels of gene expression were quantified using Cuffdiff (Cufflinks version 2.2.1; with default parameters).
Assembly: hg19

source_name: iPSC-derived vascular smooth muscle cells

extract_protocol:
Total RNA from untreated or oxLDL-treated healthy- and WS-iPS-EC was isolated using an RNeasy Micro Kit (QIAGEN)
~10 ng total RNA was used as input for cDNA conversion using a SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (cat. #634890, ClontVECh, Takara). cDNA was fragmented using an S220 Focused-ultrasonicator (Covaris). The cDNA library was then amplified using a NEBNext® Ultra™ DNA Library Prep Kit for Illumina (cat. #E7370L, New England Biolabs).

value: oxLDL


title: Healthy, iMac, oxLDL, pos, 1


title: B6_ctrl_4

description: allograft tumor from C57BL/6J


title: B_47_P

value: Cord blood mononuclear cells

value: F


title: ob_ob_ctrl_1

description: allograft tumor from C57BL/6J-ob/ob

value: pre-therapy


title: B_46_P

value: RSVB

value: Preterm


title: Ngn2 iNeurons patientDerived CTL 809-9

description: RNA.SE.rds


title: WS, iPS-VSMC, oxLDL, pos, 2

value: iPSC-derived vascular smooth muscle cells


title: Ngn2 iNeurons patientDerived CTL 809-1

description: RNA.SE.rds


title: B_43_P


title: B_44_P


title: Healthy, iMac, oxLDL, neg, 3


title: Ngn2 iNeurons patientDerived WBS 339C7

description: RNA.SE.rds

value: WBS


title: Ngn2 iNeurons patientDerived CTL 3391S

description: RNA.SE.rds


title: Healthy, iPS-VSMC, oxLDL, pos, 2


title: B6_ctrl_1

description: allograft tumor from C57BL/6J


title: Ngn2 iNeurons patientDerived 7Dup CFG

description: RNA.SE.rds

source_name: CFG

value: CFG


title: NP3

city: Atlanta

first: Liwei

last: Lang

state: GA

address: 1701 Uppergate Drive

country: USA

institute: Emory University

data_processing:
CASAVA  was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, reads containing N > 10% (N represents base that could not be determined) and  low-quality reads, then mapped to hg19 whole genome using STAR (v2.5).
The counts coincide with those produced by htseq-count with default parameters. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
The read counts were adjusted by edgeR program package through one scaling normalized factor for each sequenced library. Differential expression analysis of two conditions was performed using the edgeR R package (v3.16.5).
Differential expression analysis between WT and KO was performed using the DESeq2 R package (v2_1.6.3). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR).
Assembly: mm10
Supplementary files format and content: readcount.txt (Matrix table with raw gene counts for every gene of each sample)
Supplementary files format and content: ProcessedDataMatrix.txt (Tab-delimited text files including FPKM values for each Sample)

source_name: Mice BMDC

growth_protocol: Mouse bone marrow derived dendritic cells were grown in DMEM medium containing 10% FBS, 100 units/mL penicillin and 100 µg/mL streptomycin.

extract_protocol:
Total RNA of cells was extracted with NucleoSpin miRNA Kit. NEBNext Ultra™ II RNA Library Prep Kit (Cat#NEB-E7765) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells treated with Ca(OH)2 nanoparticles or vehicle for 12 hours

value: BMDC

value: Ca(OH)2 nanoparticles


title: B_45_P

value: M


title: B6_ctrl_2

description: allograft tumor from C57BL/6J


title: NP2


title: Healthy, iPS-VSMC, oxLDL, pos, 3


title: B_42_P


title: Ngn2 iNeurons patientDerived WBS 316M

description: RNA.SE.rds

value: Ngn2 iNeurons


title: B6_ctrl_3

description: allograft tumor from C57BL/6J


title: Healthy, iPS-VSMC, oxLDL, pos, 1


title: B_40_P


title: WS, iPS-VSMC, oxLDL, neg, 3


title: Ngn2 iNeurons patientDerived 7Dup 242K

description: RNA.SE.rds


title: B_41_P


title: NP1


title: Ngn2 iNeurons patientDerived WBS 306O

description: RNA.SE.rds


title: WS, iPS-VSMC, oxLDL, neg, 2


title: WS, iPS-VSMC, oxLDL, pos, 1


title: CTRL3

value: vehicle


title: CTRL2


title: Ngn2 iNeurons ribosomeFootprinting 7Dup isoDup (242K) rep3

description: ribosomeFootprinting

data_processing:
Trimmed reads were mapped with STAR v2.5.2b (Dobin et al., 2013) using the ensembl 92 transcriptome as splice junction guide. One sample (7Dup) was excluded due to poor mapping rate and codon periodicity.
Reads mapping to coding sequences were quantified at the gene level using featureCounts v1.5.1 (Liao et al., 2014). Differential expression was performed as described for RNAseq.
In addition, differential translation efficiency was assessed by fitting a ∼Replicate+Genotype+SeqType+SeqType:Genotype model using DESeq2, and testing for the interaction terms.
Assembly: GRCh38
Supplementary files format and content: riboFoot.SE.rds.zip is a R SummarizedExperiment object containing the quantification (RNA/RPF/TE) and annotation for all samples.
Library strategy: Ribosome footprinting (Ribo-seq)

extract_protocol:
iNeurons were treated with cycloheximide at 0.1mg/mL for 5 min and lysed according to the manufacturer’s instructions, then cell lysates were digested with TruSeq Ribo Profile Nuclease.
The Ribosome Protected fragments were first purified using MicroSpin S-400 columns (GE) and then size-selected (28-30 nt) from 15% polyacrylamide/7-8 M urea/TBE gel. rRNA was removed using the Ribo-Zero Gold Kit (Illumina). After 3’ adaptor ligation and reverse transcription of the library, cDNA (70-80 nt) was purified from 10% polyacrylamide/7-8 M urea/TBE gel. After cDNA circularization and limited amplification (9 cycles), the RPF libraries were purified using an 8% native polyacrylamide gel.

value: isoDup (242K)

value: Isogenic


title: B_38_P


title: B_37_P


title: WS, iPS-VSMC, oxLDL, neg, 1


title: Ngn2 iNeurons ribosomeFootprinting WBS isoWBS rep3

description: ribosomeFootprinting

value: isoWBS


title: KO-3

city: New Haven

first: Wenwen

last: Tang

state: CT

address: Rm 320, 10 Amistad St

institute: Yale Univeristy

data_processing:
Illumina’s Pipeline software package used for image analysis and basecalling.
Gerald performs sequence analysis. Gerald filters low quality base calls; aligns sequences to mmp9 genome; visualizes the results; and generates statistics, diagnostic quality control plots, and summary tables.
Transcripts Per Million (TPM) were calculated using the DESeq2 package.
Genome_build: MM9
Supplementary_files_format_and_content: tab-delimited text files include TPM values for every gene in each Sample

source_name: primary neutrophils

extract_protocol:
Bone marrow cells were flushed out from mice tibia and femur and neutrophils were isolated using discontinuous percoll gradient. RNA was extracted using Direct-zol RNA MiniPrep kit (Cat#: R2050)
RNA libraries were prepared for sequencing using mRNA Seq Kit supplied by Illumina (Cat # 1004814).

tag: strain

tag: tissue

value: Bone marrow

value: primary neutrophils

tag: age

value: 10 weeks old


title: CTRL1


title: Healthy, iPS-VSMC, oxLDL, neg, 2


title: Healthy, iPS-VSMC, oxLDL, neg, 3


title: B_36_P

value: Cord blood mononuclear cells

value: F


title: B_35_P

value: RSVB

value: Preterm


title: KO-2


title: gcWS, iMac, oxLDL, pos, 3

value: iPSC-derived macrophages

value: oxLDL


title: KO-1


title: B_34_P


title: WT-2

value: WT


title: Healthy, iPS-VSMC, oxLDL, neg, 1

value: iPSC-derived vascular smooth muscle cells


title: Ngn2 iNeurons ribosomeFootprinting CTL isoCTL rep1

description: ribosomeFootprinting

value: isoCTL

value: CTL


title: WT-3


title: Ngn2 iNeurons ribosomeFootprinting CTL isoCTL rep3

description: ribosomeFootprinting

value: Ngn2 iNeurons


title: B_32_P

value: M


title: gcWS, iMac, oxLDL, pos,1


title: B_31_P


title: B_33_P


title: B_30_P


title: WT-1


title: Ngn2 iNeurons ribosomeFootprinting 7Dup isoDup (242K) rep2

description: ribosomeFootprinting

value: isoDup (242K)

value: Isogenic


title: WS, iMac, oxLDL, pos, 3


title: Ngn2 iNeurons ribosomeFootprinting WBS isoWBS rep1

description: ribosomeFootprinting

value: isoWBS

value: WBS


title: B_29_T

value: Term


title: Embryo, otk1 RNAi and otk2 RNAi [O1O2_KO_1]

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

data_processing:
The raw fastq files were aligned to the dm6 genome (Ensembl v97) using STAR v2.7.1a
The reads were then quantified using RSEM v1.3.1
Assembly: dm6
Supplementary files format and content: raw counts of sequencing reads; genes.results were generated using RSEM v1.3.1 and includes the quantified reads for each sample

organism: Drosophila melanogaster

source_name: Embryo

growth_protocol: For each cross, flies were housed in cages with a grape juice agar plate containing yeast paste. Females were allowed to lay eggs at 25°C for 24h, after which the agar plates were changed to harvest the mixed stage embryos.

extract_protocol:
The embryos were dechorionated in bleach, washed in water and 100% ethanol prior to RNA extraction using the ISOLATE II RNA Mini Kit’s protocol (Bioline, UK). The extracted RNA was quantified using Nanodrop (Thermo Fisher Scientific).
Library preparation was performed using 1µg of total RNA and sequencing was performed using Illumina HiSeq 4000 System (2 × 151 bp read length, 40 million reads per sample).

value: Embryo

value: otk1 RNAi, otk2 RNAi


title: Ngn2 iNeurons ribosomeFootprinting 7Dup isoDup (242K) rep1

description: ribosomeFootprinting


title: Ngn2 iNeurons ribosomeFootprinting CTL isoCTL rep2

description: ribosomeFootprinting


title: Embryo, otk2 RNAi and wnt4 RNAi [O2W4_KO_2]

value: otk2 RNAi, wnt4 RNAi


title: VCaP_LLC0150_2uM_24h_rep2

city: Ann Arbor

first: Arul

last: Chinnaiyan

address: 1500 East Medical Center Dr

department: MCTP

institute: University of Michigan

data_processing:
Libraries passing quality control were trimmed of sequencing adaptors and aligned to the human reference genome, GRCh38. Samples were demultiplexed into paired-end reads using Illumina’s bcl2fastq conversion software v2.20. The reference genome was indexed using bowtie2-build, and reads were aligned onto the GRCh38/hg38 human reference genome using TopHat2 with strand-specificity and allowing only for the best match for each read. The aligned file was used to calculate strand-specific read count for each gene using HTSeq-count (version 0.13.5). EdgeR (version 3.34.1) was used to compute differential gene expression using raw read-counts as input. Heatmaps were generated using the ComplexHeatmap package in R.
Assembly: hg38

source_name: Prostate

growth_protocol: Standard growth culture media

extract_protocol:
Qiagen mRNeasy RNA extraction kit
RNA-seq libraries were prepared using 200–1,000 ng of total RNA. RiboErase to enrich for mRNA, cDNA synthesis, end-repair, A-base addition, and ligation of the Illumina indexed adapters were performed according to the TruSeq RNA protocol (Illumina). Libraries were size selected for 250–300 bp cDNA fragments on a 3% Nusieve 3:1 (Lonza) gel, recovered using QIAEX II reagents (QIAGEN), and PCR amplified using Phusion DNA polymerase (New England Biolabs). Library quality was measured on an Agilent 2100 Bioanalyzer for product size and concentration. Paired-end libraries were sequenced with the Illumina HiSeq 2500, (2 × 100 nucleotide read length) with sequence coverage to 15–20M paired reads.

treatment_protocol: LNCaP or VCaP cells were treated with EPZ6438 (2uM for 72h), LLC0150 (2uM for 24h), or DMSO (control). For siRNA knockdowns, cell were treated twice with siRNAs (25nM each) against the target gene or control non-targeting siRNAs for 72h. For stable CRISPR deletion, cells were treated with the gene targeting sgRNAs via transfection and selected with puromycin for 48h. The surviving stable knock-out polyclonal cells were cultured for at least 2 weeks (4-5 cell divisions) prior to sequencing.

value: Prostate

value: VCaP

value: metatatic castration resistant prostate cancer; AR-positive

tag: Sex

value: Male

value: LLC0150 2uM for 24h


title: VCaP_LLC0150_2uM_24h_rep1


title: gcWS, iMac, oxLDL, pos, 2

value: iPSC-derived macrophages

value: oxLDL


title: WS, iMac, oxLDL, pos, 2


title: WS, iMac, oxLDL, pos,1


title: VCaP_DMSO_rep2

value: DMSO


title: Ngn2 iNeurons ribosomeFootprinting WBS isoWBS rep2

description: ribosomeFootprinting

value: Ngn2 iNeurons


title: B_27_T

value: Cord blood mononuclear cells

value: RSVB

value: M


title: Healthy, iMac, oxLDL, pos, 3


title: VCaP_DMSO_rep1


title: WS, iMac, oxLDL, pos, 4


title: B_26_T


title: Embryo, otk2 RNAi and wnt4 RNAi [O2W4_KO_1]


title: B_28_T


title: B_25_T


title: Healthy, iMac, oxLDL, pos, 2


title: Embryo, otk1 RNAi and wnt4 RNAi [O1W4_KO_1]

value: otk1 RNAi, wnt4 RNAi


title: LNCaP_NSD2_WT_R2

value: LNCaP

value: Transiently with non-targeting sgRNA pool


title: Healthy, iMac, oxLDL, pos, 1


title: Embryo, otk1 RNAi and otk2 RNAi [O1O2_KO_2]

value: Embryo

value: otk1 RNAi, otk2 RNAi


title: Embryo, otk1 RNAi and wnt4 RNAi [O1W4_KO_2]


title: LNCaP_NSD2_WT_R1

value: Prostate


title: B_24_T

value: Term

value: F


title: B_23_P

value: Preterm


title: Embryo, otk1 RNAi [O1_KO_1]

value: otk1 RNAi


title: Embryo, otk1 RNAi [O1_KO_2]


title: gcWS, iMac, oxLDL, neg, 3

value: iPSC-derived macrophages


title: LNCaP_NSD2_WT_DHT_12hr_R1

value: metatatic castration resistant prostate cancer; AR-positive

value: Male

value: Transiently with non-targeting sgRNA pool + DHT (10nM for 12h)


title: Embryo, wnt4 RNAi [W4_KO_2]

value: wnt4 RNAi


title: gcWS, iMac, oxLDL, neg, 2


title: gcWS, iMac, oxLDL, neg,1


title: LNCaP_NSD2_WT_DHT_12hr_R2


title: LNCaP_NSD2_KO_R2

value: Transiently with NSD2-targeting sgRNA pool


title: Embryo, wnt4 RNAi [W4_KO_1]


title: B_21_T

value: Cord blood mononuclear cells

value: RSVB

value: M


title: WS, iMac, oxLDL, neg, 4


title: Embryo, otk2 RNAi [O2_KO_2]

value: otk2 RNAi


title: LNCaP_NSD2_KO_R1

value: LNCaP


title: B_20_T


title: WS, iMac, oxLDL, neg, 3


title: B_19_T


title: LNCaP_NSD2_KO_DHT_12h_R2

value: Transiently with NSD2-targeting sgRNA pool + DHT (10nM for 12h)


title: B_17_T


title: LNCaP_NSD2_KO_DHT_12h_R1

value: Prostate


title: B_18_T

value: Term


title: WS, iMac, oxLDL, neg,1


title: Embryo, Wnt4 and Otk1 overexpression [O1W4_OE_1]

value: Embryo

value: UAS-otk1, UAS-wnt4


title: B_22_T


title: LNCaP_LLC0150_24hr_rep2

value: LLC0150 2uM for 24h


title: LNCaP_LLC0150_24hr_rep1


title: B_16_T


title: Healthy, iMac, oxLDL, neg, 2

value: iPSC-derived macrophages


title: Embryo, otk2 RNAi [O2_KO_1]


title: Healthy, iMac, oxLDL, neg, 3


title: Embryo, Wnt4 and Otk1 overexpression [O1W4_OE_2]


title: Healthy, iMac, oxLDL, neg, 1


title: Embryo, Otk1 overexpression [O1_OE_1]


title: B_15_T

value: F


title: LNCaP_DMSO_rep1

value: metatatic castration resistant prostate cancer; AR-positive

value: Male

value: DMSO


title: Embryo, Wnt4 overexpression [W4_OE_2]


title: B_13_T


title: gcWS, iPS-macrophage, oxLDL, pos, 3

library_source: genomic

data_processing:
Sequences were aligned to human genome sequences (hg19) with Bowtie2(default setting) . Mapped reads are subsampled with samtools to make numbers of reads same in all samples.
Macs2(ver2.2.6) was used to call peaks with nomodel, narrow peak option. With a q-value cutoff of 0.01
The catalogue of all peaks called in any samples was produced by merging all called peaks that overlapped by, at least, one base pair using the Bedtools merge function.
The Bedtools map function was used to count the reads at each region in the catalog using bed files of each sample.
The read count matrix of each sample was used for the detection of differentially accessible regions (DARs) by using DESeq2.
Assembly: hg19

molecule: genomic DNA

extract_protocol:
On day 21 of differentiation, healthy-, WS- and gcWS-iMφs were stained with anti-CD14 and anti-CD11b antibodies, incubated for 30 min on ice, and washed and sorted into 5,000 CD14+ CD11b+ cells in PBS containing 2% FBS.
Library preparation for ATAC-seq was performed on 10,000 cells with a Nextera DNA Sample Preparation kit (cat. #FC-121-1030, Illumina)

value: oxLDL


title: Embryo, Wnt4 overexpression [W4_OE_1]


title: WS, iMac, oxLDL, neg, 2


title: gcWS, iPS-macrophage, oxLDL, pos, 2


title: VCaP_siNSD2_DMSO_Rep1

value: VCaP

value: NSD1 and NSD2 -targeting siRNA pool for 32days + DMSO


title: gcWS, iPS-macrophage, oxLDL, pos,1


title: B_11_T

value: Cord blood mononuclear cells

value: RSVB

value: M


title: VCaP_siNSD1and2_DMSO_Rep2

value: NSD1-targeting siRNA pool for 32days + DMSO


title: B_12_T


title: Embryo, Otk1 overexpression [O1_OE_2]


title: B_10_T


title: Embryo, WT [Ctrl_1]

value: Control


title: LNCaP_DMSO_rep2

value: Prostate

value: LNCaP


title: VCaP_siNSD1and2_DMSO_Rep1


title: WT3

city: Bern

first: Mayuresh

last: Sarangdhar

address: Murtenstrasse 40

department: DBMR

country: Switzerland

institute: University Bern

data_processing:
RNA-seq data was assessed using fastqc v.0.11.9
mapped to the reference genome using HiSat2 v.2.2.1
FeatureCounts v.2.0.1
DEG with DESeq2 v1.36.0
Assembly: GRCh38
Supplementary files format and content: excel (.xlsx)

source_name: bone marrow

growth_protocol: cells grown in RPMI 1640 GlutaMAX™-I medium (Invitrogen)

extract_protocol:
Polysomal RNA was isolated from polysome fractions by Trizol (Invitrogen) according to the manufacturer’s protocol.
TruSeq

treatment_protocol: About 5-8 million cells were washed with PBS containing cycloheximide (CHX) (100 ug/ml) and resuspended in 200 μl of hypotonic buffer (1.5 mM KCl, 2.5 mM MgCl2, and 5.0 mM Tris-Cl, pH 7.4) and 200 μl hypotonic lysis buffer (same with 2% sodium deoxycholate, 2% Triton X-100, and 2.5 mM DTT) plus CHX and gently disrupted using a Dounce homogenizer. The lysates were centrifuged at 8,000 g for 10 minutes at 4°C. Linear 10% to 50% sucrose gradients (80 mM NaCl, 5 mM MgCl2, 20 mM Tris-Cl, pH 7.4, and 1 mM DTT) were formed manually.  Supernatants with equal OD were loaded onto the pre-prepared sucrose gradients. Gradients were placed onto a pre-cooled SW41 Ti rotor (Beckman Coulter) and were centrifuged at 39,000 rpm for 2.45 hours at 4°C using Optima XPN-80 Ultracentrifuge (Beckman Coulter). Following centrifugation, gradients were replaced onto a gradient density fractionation system (Brandel) and separated through a live OD 254 nm using UA-6 UV/Vis detector (Teledyne Isco). Polysome fractions were collect using Foxy R1 fraction collector (Teledyne Isco).

value: bone marrow

value: lymphoblast

value: RNH1 WT

value: Polysome Isolation


title: WS, iPS-macrophage, oxLDL, pos, 3

value: iPSC-derived macrophages


title: VCaP_siNSD1_DMSO_Rep2

value: metatatic castration resistant prostate cancer; AR-positive

value: Male


title: B_14_T

value: Term


title: B_9_T


title: B_6_T

value: F


title: WT1


title: WS, iPS-macrophage, oxLDL, pos, 2

value: oxLDL


title: WS, iPS-macrophage, oxLDL, pos,1


title: VCaP_siNSD1_DMSO_Rep1

value: VCaP


title: VCaP_siNSD2_DMSO_Rep2

value: NSD1 and NSD2 -targeting siRNA pool for 32days + DMSO


title: Embryo, WT [Ctrl_2]

value: Embryo


title: B_4_T

value: Cord blood mononuclear cells

value: RSVB


title: B_5_P

value: Preterm

value: M


title: VCaP_siNC_EPZ6438_72h_Rep2

value: Prostate

value: non-targeting siRNA (32days) + EPZ6438 2uM for 72h


title: VCaP_siNC_EPZ6438_72h_Rep1


title: KO1

value: bone marrow

value: lymphoblast

value: RNH1 KO


title: B_3_T


title: KO2

value: Polysome Isolation


title: Healthy, iPS-macrophage, oxLDL, pos, 2

value: iPSC-derived macrophages


title: VCaP_siNC_DMSO_Rep2

value: metatatic castration resistant prostate cancer; AR-positive

value: Male

value: non-targeting siRNA (32days) + DMSO


title: WT2

value: RNH1 WT


title: Healthy, iPS-macrophage, oxLDL, pos, 1

value: oxLDL


title: VCaP_siNC_DMSO_Rep1

value: VCaP


title: gcWS, iPS-macrophage, oxLDL, neg, 3


title: Healthy, iPS-macrophage, oxLDL, pos, 3


title: 20210331_Hide 033121_emCD8-D21-2_12

type: RNA

city: cleveland

first: Hidetoshi

last: Tsuda

state: ohio

address: 9500 euclid ave

institute: cleveland clinic

description: Pancancer panel includes 784 probes including 6 positive control and 8 negative control.

hyb_protocol: Hybridization was followed NanoString nCounter XT gene expression assay protocol. Briefly,  for pereparation of master mix,  hybridization buffer was mixed with the Reporter CodeSet, the master mix, samples and Rnase-fee water were added to each tube and then Panel Capture codeset was added.All samples were incubated for 16 hours at 65 degree.

scan_protocol: Targeted mRNA hybridized with the capture probe was counted using the NanoString nCounter instrument (Nanostring)

data_processing: Row Data  was normalized and analyzed in the nCounter Advanced Analysis 2.0 software (Nanostring)

source_name: Cell lysate

extract_protocol: Freshly sorted graft-infiltrating CD45.2+CD44+CD8+ T cells from the digested allografts were resuspended in a lysis solution of 1 part RLT buffer from the QIAGEN RNeasy Mini Kit to 2 parts nuclease-free water, and 4.5 μL of the lysate was added directly to the Nano String hybridization according to the instructions.

value: Sorted memory CD8 T cells from the grafts

tag: status

value: Alive

tag: cartridgeid


title: KO3


title: LNCaP_sgNSD3_rep1

value: LNCaP

value: Transiently with NSD3-targeting sgRNA pool


title: B_1_T

value: Cord blood mononuclear cells

value: RSVB

value: Term

value: F


title: B_2_T


title: LNCaP_sgNSD1_rep2

value: Prostate

value: Transiently with NSD1-targeting sgRNA pool


title: A_52_P

value: RSVA

value: Preterm


title: 20210331_Hide 033121_emCD8-D21-1_11

value: Male


title: gcWS, iPS-macrophage, oxLDL, neg,1

value: iPSC-derived macrophages


title: 20210331_Hide 033121_emCD8-D2-2_10


title: WS, iPS-macrophage, oxLDL, neg, 4


title: A_51_P

value: M


title: gcWS, iPS-macrophage, oxLDL, neg, 2


title: WS, iPS-macrophage, oxLDL, neg, 3


title: 20210331_Hide 033121_emCD8-D2-1_09


title: LNCaP_sgNCx3_rep2

value: metatatic castration resistant prostate cancer; AR-positive

value: Transiently with non-targeting sgRNA pool


title: WS, iPS-macrophage, oxLDL, neg, 2


title: A_49_P


title: A_50_P


title: LNCaP_sgNSD3_rep2


title: WS, iPS-macrophage, oxLDL, neg,1


title: LNCaP_sgNCx3_rep1


title: A_53_P


title: 20210331_Hide 033121_dmCD8-D7-2_04

value: Sorted memory CD8 T cells from the grafts


title: A_48_P


title: LNCaP_H3K27Ac_LLC0150

data_processing:
ChIP-Seq analysis was carried out by first assessing reads and performing trimming using Trimmomatic version 0.39 (settings TruSeq3-PE-2.fa:2:30:10, minlen 50). Paired end reads were aligned to hg38 (GRCh38) human genome reference using bwa (“bwa mem” command with options -5SP -T0, version 0.7.17-r1198-dirty). Alignments were then filtered using both samtools (quality score cutoff of 20) and picard MarkDuplicates (removed duplicates). Peak calling was performed using MACS2 using narrowpeak setting  for narrow peaks and a second set for broad peaks (eg H3K27Ac, --broad -B --cutoff-analysis --broad-cutoff 0.05 --max-gap 500). Finally, bedtools was used to remove blacklisted regions of the genome from the peaks list (Encode’s exclusion list ENCFF356LFX.bed). UCSC’s tool wigtoBigwig was used for conversion to bigwig formats.
Assembly: Hg38
Supplementary files format and content: Bigwig and BED files

source_name: prostate

extract_protocol:
Diagenode iDeal ChIP-seq kit for Transcription Factors / Histones
Chromatin immunoprecipitation experiments were carried out using the Ideal ChIP-seq Kit for Transcription Factors or Histones (Diagenode) as per the manufacturer’s protocol. Chromatin from 2 × 106 cells (for transcription factors) and 1x106 cells (for histones) was used for each ChIP reaction with 4 or 2  μg of the target protein antibody respectively. In brief, cells were trypsinized and washed twice with 1× PBS, followed by cross-linking for 8 min in 1% formaldehyde solution. Crosslinking was terminated by the addition of 1/10 volume 1.25 M glycine for 5 min at room temperature followed by cell lysis and sonication (Bioruptor, Diagenode), resulting in an average chromatin fragment size of 200 bp. Fragmented chromatin was then used for immunoprecipitation using various antibodies, with overnight incubation at 4 °C. ChIP DNA was de-crosslinked and purified using the iPure Kit V2 (Diagenode) using the standard protocol. Purified DNA was then prepared for sequencing as per the manufacturer’s instructions (Illumina). ChIP samples (1–10 ng) were converted to blunt-ended fragments using T4 DNA polymerase, Escherichia coli DNA polymerase I large fragment (Klenow polymerase), and T4 polynucleotide kinase (New England BioLabs (NEB)). A single adenine base was added to fragment ends by Klenow fragment (3′ to 5′ exo minus; NEB), followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-ligated DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size-selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (Qiagen). Libraries were quantified and quality checked using the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).

treatment_protocol: LNCaP cells were treated with DMSO (control) or LLC0150 (2uM for 24h). For stable CRISPR deletion, cells were treated with the gene targeting sgRNAs via transfection and selected with puromycin for 48h. The surviving stable knock-out polyclonal cells were cultured for at least 2 weeks (4-5 cell divisions) prior to ChIPseq and sequencing.

value: prostate

tag: chip antibody

value: H3K27Ac (Active Motif:39336)

value: LLC0150 2uM for 24h


title: A_47_P

value: Cord blood mononuclear cells


title: Healthy, iPS-macrophage, oxLDL, neg, 3


title: LNCaP_H3K27Ac_DMSO

tag: cell line

value: LNCaP

value: DMSO


title: 20210331_Hide 033121_dmCD8-D2-2_02

value: Alive


title: A_46_P


title: Healthy, iPS-macrophage, oxLDL, neg, 2


title: LNCaP_FOXA1_LLC0150

value: FOXA1 (Thermo:PA5-27157)


title: LNCaP_sgNSD1_rep1

value: Prostate

value: Transiently with NSD1-targeting sgRNA pool


title: 20210331_Hide 033121_dmCD8-D2-1_01


title: 20210331_Hide 033121_AJB6-D7-2_08


title: A_45_P

value: RSVA

value: Preterm


title: LNCaP_FOXA1_DMSO

value: Male


title: 20210331_Hide 033121_AJB6-D7-1_07


title: 20210331_Hide 033121_dmCD8-D7-1_03


title: LNCaP_AR_LLC0150

value: AR (Abcam:ab133273)


title: A_43_P

value: F


title: WS, iPS-VEC, oxLDL, pos, 2

source_name: iPSC-derived vascular endothelial cells

value: iPSC-derived vascular endothelial cells

value: oxLDL


title: LNCaP_AR_DMSO

value: prostate

value: metatatic castration resistant prostate cancer; AR-positive


title: A_44_P


title: 20210331_Hide 033121_AJB6-D2-2_06

value: Sorted memory CD8 T cells from the grafts


title: WS, iPS-VEC, oxLDL, pos,1


title: A_42_P

value: Cord blood mononuclear cells

value: M


title: 20210331_Hide 033121_AJB6-D2-1_05


title: LNCaP_H3k27Ac_NSD2WT

value: LNCaP

value: H3K27Ac (Active Motif:39336)

value: Transiently with non-targeting sgRNA pool


title: Healthy, iPS-macrophage, oxLDL, neg, 1

value: iPSC-derived macrophages


title: Healthy, iPS-VEC, oxLDL, pos, 2


title: A_41_P


title: Healthy, iPS-VEC, oxLDL, pos, 3


title: LNCaP_H3k27Ac_NSD2KO

value: Transiently with NSD2-targeting sgRNA pool


title: A_40_P

value: RSVA


title: Healthy, iPS-VEC, oxLDL, pos, 1


title: LNCaP_FOXA1_NSD2WT

value: FOXA1 (Thermo:PA5-27157)


title: A_38_P

value: Preterm


title: WS, iPS-VEC, oxLDL, pos, 3


title: LNCaP_FOXA1_NSD2KO

value: Male


title: WS, iPS-VEC, oxLDL, neg, 3


title: A_37_P


title: LNCaP_AR_NSD2WT

value: AR (Abcam:ab133273)


title: WS, iPS-VEC, oxLDL, neg, 2

value: iPSC-derived vascular endothelial cells


title: A_36_P

value: F


title: Muscle_baseline_untrained_SED8

city: Tübingen

first: Thomas

last: Beiter

address: Hoppe-Seyler-Str. 6

department: Sports Medicine

country: Germany

institute: Eberhard-Karls-University Tübingen

description:
Gene expression data from vastus lateralis muscle at baseline.
All study participants absolved an acute exercise protocol that consisted of 60 min of high intensity cycling exercise on a cycle ergometer at a power requiring 80% of the individual VO2max (including 10 min of initial warm-up cycling at 60% VO2max). All exercise sessions were conducted in the morning (9:00 AM) after an overnight fast and after receiving a standardized breakfast (8:00 AM).

hyb_protocol: GeneAtlas Hybridization, Wash, and Stain Kit for 3' IVT Arrays, Affymetrix

scan_protocol: Scanned images (DAT files) were transformed into intensities (CEL files) by GCOS (Affymetrix).

data_processing: Raw intensity values were background corrected, Log2 transformed, quartile normalized and summarized using the RMA algorithm in Genomics Suite 6.6 (Partek).

label: biotin

source_name: vastus lateralis muscle, baseline

label_protocol: Affymetrix's SensationPlusTM FFPE Amplification and 3'IVT Labeling kit.

extract_protocol: All muscle biopsies were taken under sterile conditions from the lateral portion of the m. vastus lateralis of the right leg using a fine-needle punch biopsy technique under local anesthesia (1% Meaverin). Snap-frozen muscle biopsy samples were homogenized with a TissueRuptor homogenizer (Qiagen, Hilden, Germany), and total RNA was extracted and purified using RNeasy Fibrous Tissue Mini kit and RNeasy Micro Kit (Qiagen).

tag: training status

value: untrained

tag: time point

value: baseline


title: WS, iPS-VEC, oxLDL, neg,1

tag: cell type


title: Muscle_+30min_untrained_SED8

description:
Gene expression data from vastus lateralis muscle 30 min after acute exercise.
All study participants absolved an acute exercise protocol that consisted of 60 min of high intensity cycling exercise on a cycle ergometer at a power requiring 80% of the individual VO2max (including 10 min of initial warm-up cycling at 60% VO2max). All exercise sessions were conducted in the morning (9:00 AM) after an overnight fast and after receiving a standardized breakfast (8:00 AM).

source_name: vastus lateralis muscle, exercised, 60 min


title: LNCaP_AR_NSD2KO

value: prostate

value: metatatic castration resistant prostate cancer; AR-positive


title: Muscle_+30min_untrained_SED7


title: Muscle_+3h_untrained_SED7

description:
Gene expression data from vastus lateralis muscle 3 hours min after acute exercise.
All study participants absolved an acute exercise protocol that consisted of 60 min of high intensity cycling exercise on a cycle ergometer at a power requiring 80% of the individual VO2max (including 10 min of initial warm-up cycling at 60% VO2max). All exercise sessions were conducted in the morning (9:00 AM) after an overnight fast and after receiving a standardized breakfast (8:00 AM).


title: Muscle_+3h_untrained_SED8


title: Healthy, iPS-VEC, oxLDL, neg, 3


title: A_35_P

value: Cord blood mononuclear cells


title: A_34_P

value: M


title: HUVEC_AP13_2

city: Sherbrooke

first: C Florian

last: Bentzinger

state: Quebec

address: Campus de la santé, 3001 12e Avenue N

department: Pharmacologie-Physiologie

country: Canada

institute: Université de Sherbrooke

data_processing:
Reads were trimmed with Trim Galore version 0.6.9
Reads were aligned and mRNA expresion quantify with Kallisto version 0.48.0
Assembly: Homo sapiens GRCh38 cDNA version p13
Supplementary files format and content: tab separated value (tsv) file included target_id (Ensembl cDNA id), est_count and tpm

source_name: HUVEC

growth_protocol: HUVECs (ATCC, CRL-1730) were cultured in endothelial cell growth medium MV2 (PromoCell, C-22022), MV2 supplement mix (PromoCell, C-39226), and 1% Penicillin-Streptomycin solution (Wisent, 450-201-EL).

extract_protocol:
After three washes in PBS the cells were collected and the pellet was stored in liquid nitrogen. Cells stored at -80°C were lysed and RNA was isolated using the Agencourt RNAdvance Tissue Kit (Beckman Coulter).
Libraries were generated using cDNA prepared and amplified from 50 ng of RNA based on the user guide (3‘mRNA-Seq Library Prep Kit FWD HT) without modifications. Subsequently Quant it Picogreen (Invitrogen, #10545213) for quantification of the libraries. Library size was determined using the High Sensitivity NGS Fragment Analysis kit with a Fragment Analyzer (Agilent)

treatment_protocol: For MM54 or AP-13 treatment, growth medium was replaced with endothelial cell basal medium (Sigma, C-22216) supplemented with 10% FBS (Wisent, 2300040033) and 1% Penicillin-Streptomycin solution (Wisent, 450-201-EL). The cells were then treated with AP-13 or MM54 (Tocris, 5992) at a final concentration of 1uM for 3 days.

value: HUVEC

value: Endothelial cell

tag: genotype


title: HUVEC_AP13_3

tag: treatment


title: Healthy, iPS-VEC, oxLDL, neg, 2


title: Healthy, iPS-VEC, oxLDL, neg, 1


title: HUVEC_AP13_1


title: HUVEC_MM54_3


title: A_32_P

tag: individual


title: Muscle_baseline_untrained_SED7


title: A_33_P

tag: stimulation


title: gcWS, iPS-macrophage, 3

data_processing:
Sequences were aligned to human  genome sequences (hg19) with Bowtie2(default setting) .
The Bedtools map function was used to count the reads at selected RTE regions using bed files of each sample.
The read count matrix of each sample was used for the normalization by using DESeq2.
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: iPSC-derived macrophages

extract_protocol:
On day 21 of differentiation, healthy-, WS- and gcWS-iMφs were stained with anti-CD14 and anti-CD11b antibodies, incubated for 30 min on ice, and washed and sorted into 20,000 CD14+ CD11b+ cells in PBS containing 2% FBS. Next we used CUT&Tag-IT™ Assay Kit (Active motif).  Histone H3K9me3 antibody (mAb)  (#61013, Active motif) antibody were used.
Libraries were prepared using CUT&Tag-IT™ Assay Kit (Active motif) according to manufacturer’s protocol.

value: iPSC-derived macrophages

value: H3K9me3 (#61013, Active motif)


title: Muscle_+3h_trained_ET8

value: trained


title: Muscle_baseline_trained_ET8


title: Muscle_+30min_trained_ET8


title: Muscle_+3h_untrained_SED6


title: A_31_P

source_name: Cord blood

value: RSVA

tag: preterm/term


title: HUVEC_MM54_2


title: A_30_P

value: Preterm

tag: gender


title: HUVEC_MM54_1


title: gcWS, iPS-macrophage, 1


title: A_29_T

value: Term


title: Muscle_+30min_untrained_SED6


title: WS, iPS-macrophage, 3


title: Muscle_baseline_untrained_SED6


title: A_27_T


title: WS, iPS-macrophage, 2


title: TNF-α+Glutamine group2

city: Guangzhou

first: Yang

middle: yang

last: Zhang

state: Guangdong

address: 107 Yanjiang West Road

country: China

institute: Sun Yat Sen Memorial Hospital

data_processing:
MGISEQ-T7
Raw data (or Raw reads) of fastq format were firstly processed through in house perl scripts. Inthis step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads.
Differential expression analysis was performed using the DESeq2 (http://bioconductor.org/packages/release/bioc/html/DESeq2.html)
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: primary nucleus pulposus cells

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

extract_protocol:
A total of 1×106cells were collected from each group, washed twice with PBS, collected in trizol and frozen in liquid nitrogen.RNA extraction and RNA quality determination was performed
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Primary nucleus pulposus cells were devided to three group and treated with no stimualtion, TNF-α，TNF-α&glutamine individually

value: primary nucleus pulposus cells

value: TNF-alpha+glutamine

tag: time

value: Day 2


title: A_28_T


title: Muscle_+3h_trained_ET7


title: WS, iPS-macrophage, 1


title: TNF-α-group3

value: TNF-alpha


title: A_26_T


title: Healthy, iPS-macrophage, 3


title: Muscle_+30min_trained_ET7


title: TNF-α+Glutamine group1


title: Muscle_baseline_trained_ET7

value: baseline


title: A_25_T


title: Healthy, iPS-macrophage, 2


title: A_24_T

value: F


title: TNF-α-group1


title: TNF-α-group2


title: Healthy, iPS-macrophage, 1


title: NC-group3

value: no


title: TNF-α+Glutamine group3


title: Muscle_+3h_trained_ET6


title: gcWS, iPS-macrophage, 2


title: Muscle_+30min_trained_ET6


title: Muscle_baseline_trained_ET6


title: A_23_P

value: Cord blood mononuclear cells


title: A_22_T

value: M


title: RNA_SMC_D8_3

city: Dallas

first: Benjamin

last: Sabari

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

data_processing:
For ChIP-seq, reads were aligned to the hg19 genome assembly using bowtie (v1.0.0) with parameters –k 1 –m 1 –best and –strata. Subsequent analyses were performed using a combination of samtools (v1.6) and BEDtools (v 2.29.2). Counts Per Million normalized bigwig files were displayed on the UCSC genome browser for the visualization of ChIP-seq tracks. Peak calling was done with MACS (v1.4.2).
For RNA-seq, eight mRNA sequencing data samples were analyzed, comprising two biological replicates of Day 0 hiPSC cells and three biological replicates each of CM (Day 5) and SMC (Day 8) samples. To ensure quality, FastQC (version 0.11.8.1) was used to confirm the quality of the Fastq files from the RNA sequencing samples, and only reads with a minimum length of more than 1 base were selected for further analysis. The demultiplexed mRNA sequencing reads were mapped to the human reference genome version hg19 using STAR (v2.7.3a), and subsequent analyses were performed with samtools (v1.6)43 and BEDtools (v2.29.2). Bigwig files were generated using deeptools (v.3.5.0) and normalized with the following parameters: -bs 50 -normalize using CPM. These files were displayed in the UCSC genome browser. For each transcript, expression was quantified as FPKMs using featureCounts from the subread (v.1.6.3) package and annotated to the genes.gtf file of the human reference genome version hg19.
Assembly: hg19
Supplementary files format and content: Bigwig files

extract_protocol:
For RNA-seq, RNA from iPSCs, SMC-meso (Day 8) and CM-meso (Day 5) cells were extracted using Trizol reagents (300 μL per well of 6-well plate) according to manufacturer’s protocol .For ChIP-seq, cells (Wildtype and MYOCD-mEGFP knock-in hiPSCs) were crosslinked with 4% PFA in PBS for 15 minutes and quenched with 0.125 M glycine for 10 minutes at room temperature. For mesodermal CMs, we use hiPSCs at cardiac lineage differentiation Day 5. For mesodermal SMCs, we use hiPSCs at smooth muscle lineage differentiation Day 8. Crosslinked samples were then washed with cold PBS. Samples were collected by a brief spin and treated with 10 mM Tris-HCl (pH 8.0), 10mM NaCl and 0.2% NP-40 for 30 minutes to collect nuclei. After nuclear extraction, chromatin was sheared on a Bioruptor Pico (Diagenode) for 16 cycles (30 sec on/ 30 sec off for each cycle) at 4°C in sonication buffer (0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl, 1 mM EDTA, 0.1% sodium deoxycholate, 0.25% sarkosyl, 1 mM DTT, 1x cOmplete Protease Inhibitor Cocktail (Sigma, 11836170001) and 200 μM PMSF, pH 8.0). After sonication, 1% of the sonicated chromatin from each sample was taken out as ‘Input’ samples. Take 20 μL of sonicated sample from each group for electrophoresis on the 1% agarose gel for sonication efficiency and quality control. The remaining sonicated chromatin was evenly split for MYOCD-GFP or H3k27ac ChIP. NaCl was then added to a final concentration of 300 mM for histone ChIP and 150 mM for MYOCD-GFP ChIP. 1 μg/mL H3k27ac antibody (Diagenode, C15410196) or 10 μg/mL GFP antibody (Thermo Fisher Scientific, A-11122) was added to each sample and incubated at 4°C overnight with gentle rotation. The next day, 30 μL/mL of pre-washed Dynabeads Protein G (Invitrogen, 10004D) was added to each sample for a two-hour incubation. After that, the beads were washed twice with 1 mL RIPA 0 buffer (0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl, 1 mM EDTA, 0.1% sodium deoxycholate, pH 8.0), twice with 1 mL RIPA 0.3 buffer (0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl, 1 mM EDTA, 0.1% sodium deoxycholate, 300 mM NaCl, pH 8.0), twice with 1 mL LiCl wash buffer (250 mM LiCl, 0.5% IGEPAL CA-630, 0.5% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.0), and finally twice with 1 mL TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0). For each ChIP sample or input sample, 100 μL of SDS elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0) was added and incubation was done at 65°C overnight on a ThermoMixer (Eppendorf) at 1,000 RPM. The next day, supernatant was collected and further treated with 0.5 μg RNaseA (Sigma, 11119915001) for 30 minutes at 37°C, followed by 20 μg Proteinase K (NEB, P8107S) treatment at 37°C for 2 hours. DNA was recovered using MinElute PCR Purification Kit (QIAGEN, 28004) according to manufacturer’s protocol.
For RNA-seq, stranded mRNA-Seq libraries were generated using KAPA mRNA HyperPrep Kit (Roche, KK8581) following manufacturer’s protocol. Sequencing was performed on an Illumina Nextseq 500 system for 1x75bp single-end sequencing. For ChIP-seq, libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit complemented with NEBNext Multiplex Oligos for Illumina from NEB (NEB, E6177S). 10 ng of DNA was used as starting material for Input samples and 1 ng for IP samples. Libraries were amplified using 12 cycles for Input samples and 15 cycles for IP samples on the thermocycler. Post amplification libraries were size selected at 250-450 bp in length using SPRISelect beads from Beckman Coulter. Libraries were validated using the Agilent D1000 ScreenTape.

treatment_protocol:
For CM differentiation, cells were cultured in mTeSRTM1 medium until they reached 80 to 90% confluency, and then cultured in CDM3-C medium, consisting of RPMI 1640 (Life Technologies, 11875), 500 µg/mL Oryza sativa-derived recombinant human albumin (Sigma-Aldrich, A0237), and 213 µg/mL L-ascorbic acid 2-phosphate supplemented with 6 µM CHIR-99021 (Selleckchem, S2924) for 2 days. Cells were then cultured in CDM3-C medium, supplemented with 2 µM WNT-C59 (Selleckchem, S7037) for 2 days. Cells were cultured in BASAL medium (RPMI-1640 with B27 Supplement (Thermo Fisher Scientific, 17504044)) for 6 days, and medium was changed every 2 days. CMs were selected by culturing in SELECTIVE medium (RPMI-1640, no glucose (Gibco, 11879-020) with B27 Supplement (Thermo Fisher Scientific, 17504044)) for 6 days. Then, purified CMs were dissociated using TrypLE Express Enzyme (Gibco, 12604021) and replated.
For SMC differentiation, hiPSCs were cultured in mTeSRTM1 medium on Matrigel-coated plates, with daily medium changes to reach 90% confluency. The differentiation into mesodermal-lineage cells was initiated on Day 0 by culturing the cells with CHIR99021 (5 μM) and BMP-4 (10 ng/mL, PeproTech, 120-05ET) in RPMI1640 medium and 2% B27. Replenish the culture medium with CHIR99021 and BMP-4 on Day 1.5. The expression of MYOCD is high in contractile SMCs. Contractile SMCs were produced by culturing the cells with 25 ng/mL VEGF-A and FGFβ in RPMI1640 and 2% B27 minus insulin from Day 3 to Day 7 and replenishing the culture medium with VEGF-A (PeproTech, 100-20) and FGFβ (PeproTech, AF-100-18B) on Day 4. Treat cells with 5 ng/mL PDGFβ (PeproTech, AF-100-14B) and 2.5 ng/mL TGFβ (PeproTech, 100-21) in RPMI1640 and 2% B27 from Day 7 to Day 14 and replenish the culture medium with PDGFβ and TGFβ on Day 9, Day 11. The differentiated cells were enriched for SMCs by maintaining them in 4 mM lactate RPMI1640 metabolic medium for 4 to 6 days. Then, purified SMCs were dissociated using TrypLE Express Enzyme and replated.

value: induced pluripotent stem cell

value: GFP knockin

value: Day 8 of SMC differentiation

value: Day 8


title: A_21_T


title: NC-group2


title: NC-group1


title: Muscle_+3h_trained_ET5

value: trained


title: Muscle_+30min_trained_ET5


title: RNA_SMC_D8_2


title: A_20_T

value: RSVA


title: Muscle_baseline_trained_ET5


title: A_19_T


title: RNA_CM_D5_3

value: Day 5 of CM differentiation

value: Day 5


title: RNA_CM_D5_2


title: RNA_CM_D5_1


title: Muscle_+3h_untrained_SED5

value: untrained


title: A_18_T

value: Term


title: A_17_T


title: Muscle_+30min_untrained_SED5


title: RNA_D0_1

value: untreated

value: Day 0


title: A_16_T


title: A_15_T


title: RNA_SMC_D8_1


title: ChIP_Input_D8_SMC


title: A_14_T


title: RNA_D0_2


title: ChIP_MYOCD_D8_SMC


title: A_13_T


title: Muscle_baseline_untrained_SED5

value: baseline


title: Muscle_+30min_untrained_SED4


title: B.gargarizans_PG, ScRNAseq

city: Chengdu

first: Lingyu

last: zhang

address: No.1166, Liutai Avenue, Wenjiang District, Chengdu, Sichuan, China

institute: Chengdu University of TCM

description: 10x genomices

library_source: transcriptomic single cell

data_processing:
the demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software(7.1.0)
Assembly: ASM1485885v1
Supplementary files format and content: matrix files

organism: Bufo gargarizans

source_name: postauricular glands

extract_protocol:
Adult toad postauricular glandular tissue was used, cut into approximately 1 mm pieces with sterilized scissors at room temperature, transferred into 15 ml centrifuge tubes, washed with PBS, and suspended in 3-4 ml of solution (TrypLE (1 mg /ml) containing collagenase I) and digested for 60 min until no tissue fragments were visible. To collect free cells, the tubes were centrifuged at 600 × g for 5 min at 4°C, the supernatant was removed and resuspended in 2 ml PBS. The dissociated cells were then passed through a 70 µm filter (Cat. No. 10) and then through a 40 µm filter (Cat. No. 10). After washing 2 times (centrifugation at 600 × g for 5 min at 4°C), they were resuspended in DPBS at a density of 1 × 105 cells/ml. Generation of single-cell RNA sequencing libraries and signature barcode matrices.
library was performed according to the manufacter's instructing (Single Cell 3' V3.1, 10x genomices)

tag: tissue

value: postauricular glands

value: composite


title: Muscle_+3h_untrained_SED4


title: A_12_T

data_processing:
Fastq files were assessed for quality using the FastQC package and no samples were excluded from analysis. Bowtie was used to map 100-bp paired end reads to the human transcriptome (Ensembl, GRCh37v70), and gene expression estimates were derived using the limma-voom pipeline. Genes with low expression (CPM <1) were removed from analysis, leaving expression data for 14,574 genes. limma-voom was used to normalise count data and determine gene expression differences between group comparisons.
Genome_build: hg19
Supplementary_files_format_and_content: .counts.txt files contain counts per gene

extract_protocol:
mRNA were extracted using the QIAGEN Rneasy mini-kit according to manufacturer’s instructions.
Library preparation was performed using the Illumina TruSeq stranded mRNA kit with a starting input of 100ng and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 20 million reads per sample.

value: Cord blood mononuclear cells


title: ChIP_Input_D5_CM


title: HepG2 treated with GSH+HP_rep3

city: Inashiki

first: Yoshiaki

last: Uchida

state: Ibaraki

description: Gene expression data from HepG2  pretreated with 1 mM GSH  for 24 h and then, treated with2 mM HP for 4 h

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S array, Human; ThermoFisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (ThermoFisher Scientific).

data_processing:
The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. Further, gene-level analysis was performed using the Limma Bioconductor package. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above background (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7.
Signal intensity of all the samples derived from Transcriptome analysis console software (sheet 2 ). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CEL files). filter criteria was set as p value < 0.05 (one-way between-subjects ANOVA) and fold change > 1.1 (in linear space)
signal space transformation robust multi-chip analysis (SST-RMA) algorithm (Transcriptome Analysis Console, version 4)

source_name: HepG2 cells were pretreated with GSH and then, treated with HP

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol (ThermoFisher Scientific) from 100 ng/ uL total RNA

growth_protocol: HepG2 cells were purchased from the Riken BRC Cell Bank (Tsukuba, Japan). Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich, Japan), supplemented with 10% foetal bovine serum (Gibco, USA) and 1% penicillin/streptomycin (Lonza, Japan) at 37 degrees in 5% CO2 humidified incubator.

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: Cells were treated with 1 mM of GSH for 24 h and then, treated with 2 mM of HP. Control samples were maintained in the medium.

value: HepG2 cells

tag: agent


title: HepG2 treated with GSH+HP_rep2

value: pretreated with 1 mM GSH  for 24 h and then, treated with2 mM HP for 4 h


title: HepG2 treated with HP_rep3

description: Gene expression data from HepG2  treated with 2 mM HP for 4 h

source_name: HepG2 cells were treated with HP

value: treated with 2 mM HP for 4 h


title: Muscle_+3h_trained_ET4


title: Muscle_+30min_trained_ET4


title: HepG2 treated with HP_rep1


title: Muscle_baseline_untrained_SED4


title: HepG2 treated with GSH+HP_rep1


title: HepG2 treated with HP_rep2


title: ChIP_MYOCD_D5_CM

value: induced pluripotent stem cell

value: GFP knockin


title: A_10_T

value: M


title: HepG2 treated with GSH_rep3

description: Gene expression data from HepG2  treated with 1 mM GSH for 24 h

source_name: HepG2 cells were treated with GSH

value: treated with 1 mM GSH for 24 h


title: HepG2 treated with GSH_rep2


title: ChIP_Input_D0


title: A_11_T

value: RSVA


title: ChIP_MYOCD_D0


title: A_9_T


title: AD_5_Near1

city: Groningen

first: Anna

middle: Pilar

last: Ainslie

address: Antonius Deusinglaan, 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

data_processing:
Sequencing read alignement Lexogen Quantseq 2.3.1 FWD UMI pipeline on the BlueBee Genomics Platform
Sequence reads were trimmed for adaptor sequence/low-quality sequence using the Lexogen BlueBee Genomics Platform
Trimmed sequence reads were mapped to GRCh38 using the Lexogen BlueBee Genomics Platform
Read count extraction and CPM normalization were performed using RStudio, DEG analysis was performed using the function "edgeR"
Assembly: hg38
Supplementary files format and content: tab-delimited text files of raw read counts

source_name: brain

extract_protocol:
RNA was harvested from human brain tissue using the Qiagen RNA Lipid Tissue kit.
RNA libraries for bulk RNA-sequencing were prepared using Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit (FWD) following manufacturer's protocols.

tag: disease state

value: Alzheimer's disease

value: brain

tag: brodmann area

tag: age

tag: Sex

value: Male

tag: biomaterial provider

value: NIH NeuroBioBank Maryland


title: A_6_T

value: Term

value: F


title: A_5_P

value: Preterm


title: p21218-s004_ZIKV-Vero-cells-4

first: Gregory

middle: K

last: Tharp

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description: *features.tsv.gz files are available on the series record.

data_processing:
Composite host/virus references were created by concatenating sequence and annotation files for the host and virus and running cellranger mkref
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline
Further processing was done with Seurat v4.1 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: KU501215.1 Zika virus strain PRVABC59
Assembly: ChlSab1.1.104
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

organism: Chlorocebus aethiops

source_name: kidney

growth_protocol: CD14+ monocytes were isolated from PMBCs of healthy human blood using the MojosortTM Human CD14 Selection Kit (BioLegend, Cat# 480026) To generate monocyte derived dendritic cells (moDCs), CD14+ monocytes were stimulated in non-tissue culture treated plates with 100ng/mL GM-CSF (R&D Systems, Cat# 7954-GM-020/CF) and IL-4 (R&D Systems, Cat# 6507-IL-025/CF) in complete RPMI. Complete RPMI was prepared as follows: RPMI 1640 (Corning, Cat# 10-040-CI) supplemented with 10% FBS, 2mM L-glutamine (Corning, Cat# 25-005-CI), 1mM HEPES (Corning, Cat# 25-060-CI), 1mM Sodium Pyruvate (Corning, Cat# 25-000-CI), 1x NEAA (Corning, Cat# 25-025-CI), and 1x Penicillin-Streptomycin. The next day, the media was replaced with fresh cytokines, removing un-adherent cells. After 4 more days in culture, differentiated moDCs consistently expressing CD14− CD11c+ HLA-DR+ DC-SIGN+ were harvested in the supernatant. For experiments, moDCs were cultured in complete RPMI in U-bottom 96-well plates at 1e5 cells per well.

extract_protocol:
Cells were washed with 0.04% w/v bovine serum albumin (BSA) in PBS and counted.
Feature Barcoding was performed on moDCs prior to single cell RNAseq to label mock and ZIKV treated cells. Cells were blocked with Human TruStain FcX on ice for 10 minutes and then surface stained with BioLegend antibodies (TotalSeq™-C0253 anti-human Hashtag 3 Antibody and TotalSeq™-C0252 anti-human Hashtag 2 Antibody) on ice for 20 minutes.
The 10X Genomics Chromium Next GEM Single Cell 5’ v2 assay protocol (PN-1000264) was modified to be ZIKV-inclusive by adding a ZIKV-specific primer to the reverse transcription reaction mixture (Fig 1). All other steps were followed according to the manufacturer’s protocol. The ZIKV-specific primer (5’-AAGCAGTGGTATCAACGCAGAGTACCCTTCCACAAAGTCCCTATTGC-3’) was previously published by Lanciotti et al. (49) and modified to contain the non-poly-dT tag (underlined sequence) for cDNA amplification. After bead cleanup, cDNA was amplified 13 cycles, and gene expression (5’ GEX) and feature barcoded libraries were generated using the 5’ v2 Library Construction Kit (PN-1000190). 5’ GEX libraries were constructed using cDNA that was first fragmented at 32ºC for 5 min. Each sample was indexed with the Dual Index Kit TT Set A plate (PN-1000215) for 14 cycles of 98ºC for 20s, 54ºC for 30s, 72ºC for 20s, with a final extension of 72ºC for 1 min. Amplified feature barcoded libraries were constructed using DNA from supernatant cleanup. Each sample was indexed with the Dual Index Kit TN Set A plates (PN-1000250) for cycles of 98ºC for 20s, 54ºC for 30s, and 72ºC for 20s, with a final extension of 72ºC for 1 min. For QC, final libraries un on a HS DNA chip on an Agilent Bioanalyzer 2100. The 5’GEX and feature barcoded libraries were pooled separately and then combined at an appropriate ratio in order to obtain the targeted read depth of 50,000/cell and 5,000/cell for the 5’ GEX and feature barcoded libraries, respectively.

treatment_protocol: soluble human IFN-β treatment for 23 hrs

value: kidney

tag: cell line

value: VeroE6 (ATCC)

value: epithelial

tag: library type

value: mRNA

tag: antibodies/tags

tag: infection

value: ZIKV

tag: primer concentration


title: AD_4_Near1


title: Muscle_baseline_trained_ET3

tag: training status

value: trained

tag: time point

value: baseline


title: Muscle_+3h_trained_ET3


title: A_4_T

tag: individual

tag: cell type

value: Cord blood mononuclear cells

tag: stimulation

tag: preterm/term


title: AD_3_Near1

tag: tissue

value: Female


title: A_3_T

value: RSVA

tag: gender

value: M


title: AD_2_Near1

tag: disease state

value: Alzheimer's disease

value: brain

tag: brodmann area


title: AD_1_Near1

tag: age

tag: Sex

value: Male

value: NIH NeuroBioBank Sepulveda


title: p21218-s003_ZIKV-Vero-cells-3

tag: cell line

tag: treatment


title: HepG2_rep2

description: Gene expression data from HepG2

source_name: HepG2 cells

value: HepG2 cells

tag: agent


title: Muscle_baseline_trained_ET4


title: HepG2 treated with GSH_rep1

value: treated with 1 mM GSH for 24 h


title: A_2_T

value: Term

value: F


title: Muscle_+30min_trained_ET3


title: HepG2_rep3

description: Gene expression data from HepG2


title: NA_GBM_5_Near1

value: Glioblastoma multiforme

tag: biomaterial provider

value: NIH NeuroBioBank Maryland


title: HepG2_rep1

description: Gene expression data from HepG2


title: Muscle_+3h_untrained_SED3

value: untrained


title: Muscle_baseline_untrained_SED3


title: Muscle_+30min_untrained_SED3


title: A_1_T


title: HEK293T cells, Inputnuc

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

description: Sample 3

data_processing:
For the samples 1 to 3, the raw sequenced reads were subjected to proprietary quality trimming (minimum Q20) for the IonTorrent platform. Quality-filtered reads with minimum length of 100 bases were used for further analysis. For the rest of the samples, the sequenced reads on the ONT platform were basecalled in real-time (minimum Qscore = 8) using guppy basecaller. The failed reads were subjected to basecalling in a locally installed guppy basecaller. The qualified reads were combined and subjected removal of sequencing adapters using Porechop with default options.
The reads were aligned using minimap2 against the unmasked hg38 (annotated chromosomes except chromosomes Y and M). The uniquely aligned reads were further analyzed for coverage on 0.2 kb genomic bins. Bins with coverage <3 and > 100 were eliminated for downstream analyzes.
Broadpeaks were called using MACS2 callpeak on the datasets against the inputs. A broadpeak q-value cutoff of 0.01 was used to call the peaks with a fixed background local lambda.
Assembly: hg38 (unmasked)
Supplementary files format and content: BED, broadpeaks discovered using MACS2 callpeak

source_name: HEK293T (pooled from CTnuc and KDnuc)

growth_protocol: HEK293T cells, transduced with non-targeting lentiviral (CT) or CGGBP1-targeting (KD) shRNA, as described elsewhere (PMID 31547883), were cultured in DMEM supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic solution at 5% CO2 and 80% RH.

extract_protocol:
For all the G4-quadruplex immunoprecipitations, the cells were processed from two 10 cm dishes for each sample. The inputs were derived either from respective samples or by pooling from CT and KD samples. The immunoprecipitated DNA was purified using ethanol precipitation follwed by dissolution nuclease-free water.
Libraries were synthesized as follows:
(i) End-repair and pre-processing: As per the manufacturer’s instruction for Ion Express Plus Fragment Library kit (Cat. No. 4471269) from ThermoFisher Scientific for samples 1 to 3.
(ii) Sequencing library preparation: As per the manufacturer’s instruction for PCR sequencing kit (SQK-PSK004) from Oxford Nanopore Technologies for samples 4 to 16.
For samples 4 to 16, 4 – 8 ng of DNA were subjected to end-repair, ligation of PCR-adapters followed by fragment size selection using 0.4x AMPure XP beads. The adapter-ligated fragments were subjected to PCR amplification followed by size selection using 0.6x AMPure XP beads. The library was then subjected to sequencing adapter ligation followed by sequencing on MinION device using flow cells (R9.4.1). The mean length of the sequenced reads was in the range of 0.8 – 1 kb.
G4-quadruplex immunoprecipitation
Ion Torrent S5, ONT MinION Mk1B

treatment_protocol: Samples 1 and 2 were processed for G4-quadruplex immunoprecipitation using the AbC G4-ChIP protocol. The corresponding pooled input was also processed (Sample 3). Sample 4 was processed using the conventional G4-quadruplex immunoprecipitation (PMID: 29470465) alongside the corresponding input (Sample 5). For samples 6 and 7, the genomic DNA were extracted from untransduced HEK293T cells. The sonicated genomic DNA were  processed for in vitro G4-quadruplex immunoprecipitation directly (Sample 6) or after heat-denaturation and snap-chilling (Sample 7). The input (Sample 8) corresponding to the Samples 6 and 7 was the genomic DNA without any immunoprecipitation. Samples 9 and 11 were processed using AbC G4-ChIP without any transfection of control DNA (pGEMT Easy vector carrying an insert with G4-quadruplex-forming signature sequence). For samples 9 and 11, 500ng of each of the control DNA and a carrier DNA (vector carrying an insert devoid of G4-quadruplex-forming sequence signature) were first mixed, treated with 150 mM KCl, incubated with 1H6 antibody, crosslinked and added to the respective cell lysates for sonication and subsequent steps. Samples 10 and 12 were the inputs for samples 9 and 11 respectively. Samples 13 and 15 were transfected with 1.25 ug of each of control and carrier DNA mix per 10 cm dish using calcium-phosphate transfection method. Following 12 hours of transfection, the cells were processed for G4-quadruplex immunoprecipitation using AbC G4-ChIP. Samples 14 and 16 were the inputs for samples 13 and 15 respectively. From the step of reverse-crosslinking till elution, the inputs were treated the same way as the immunoprecipitated samples.

value: pooled from CTnuc and KDnuc

tag: antibody

tag: fraction

value: Chromatin


title: NA_GBM_4_Near1


title: Muscle_baseline_untrained_SED2

tag: training status

tag: time point

value: baseline


title: HUVEC cells - shHGDILnc1_rep4 [RNA-seq]

city: Shanghai

first: Qing-Wei

address: Pujian Road 160

institute: Renji Hospital

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100)
And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome(Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam)
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam)
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64)
StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs
Genome_build: ftp://ftp.ensembl.org/pub/release-101/fasta/homo_sapiens/dna/
Supplementary_files_format_and_content: gene_count_matrix.txt

source_name: HUVEC cells

growth_protocol: HUVECs were cultured in the Endothelial Cell Medium (ECM) (ScienCell, USA) medium. Both cell lines were grown in an incubator at 37°C and in a 5% CO2 humidified environment.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp

treatment_protocol: shHGDILnc1 vs shNC

value: HUVEC

tag: genotype/variation


title: HEK293T cells, KDnuc

description: Sample 2

source_name: HEK293T (stable cell line; CGGBP1-targeting shRNA)

value: CGGBP1-targeting shRNA

value: Anti-G4 1H6 antibody (Sigma; MABE1126)


title: p21218-s002_ZIKV-Vero-cells-2

value: kidney

value: VeroE6 (ATCC)

tag: cell type

value: epithelial

tag: library type

value: mRNA

tag: antibodies/tags

tag: infection

value: ZIKV

tag: primer concentration


title: NA_GBM_3_Near1

tag: disease state

tag: tissue

value: brain

tag: brodmann area

value: Female


title: HUVEC cells - shHGDILnc1_rep3 [RNA-seq]

tag: cell line


title: p21218-s001_ZIKV-Vero-cells-1

tag: treatment


title: HEK293T cells, CTnuc

description: Sample 1

source_name: HEK293T (stable cell line; non-targeting shRNA)

value: non-targeting shRNA


title: Muscle_+3h_untrained_SED2


title: NA_GBM_2_Near1

value: Glioblastoma multiforme

tag: age

tag: Sex


title: Muscle_+30min_untrained_SED2


title: HUVEC cells - shHGDILnc1_rep1 [RNA-seq]


title: MU1350 - Replicate 3

city: Murcia

first: Carlos

last: Lax

address: Facultad de Biología

department: Genetics and Microbiology

country: Spain

institute: University of Murcia

data_processing:
Raw paired-end (PE) reads from M. lusitanicus RNA-seq datasets were quality-checked using FastQC v0.11.9
Adapters were removed with Trim Galore! V0.6.7
Reads with a Phred quality score (q) ≤ 33 and/or a total length < 20 nt were removed from the analysis
Assembly: Mucor lusitanicus (CBS 277.49) v3 (https://mycocosm.jgi.doe.gov/Mucci3/Mucci3.home.html)
Supplementary files format and content: Spreadsheet including counts, log2FC, differential expression statistics and functional annotation for every gene
Supplementary files format and content: Spreadsheet including raw counts for each gene

organism: Mucor lusitanicus

source_name: Mycelium

growth_protocol: MU636 and MU1350 strains were grown on solid YPG media  at 26 ºC for 24 hours

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen) and treated with DNase (Sigma, On-Column DNaseI treatment set)
NEBNext® Ultra™ Directional RNA Library Prep Kit

value: Mycelium

tag: strain

tag: genotype

value: set1 KO


title: NA_GBM_1_Near1

tag: biomaterial provider

value: NIH NeuroBioBank Maryland


title: Control_5_Near1

value: Unaffected control

value: Male


title: HUVEC cells - shNC_rep4 [RNA-seq]

value: HUVEC

value: shNC


title: MU1350 - Replicate 2


title: Muscle_+30min_trained_ET2

source_name: vastus lateralis muscle, exercised, 60 min

tag: training status

value: trained

tag: time point


title: MU1350 - Replicate 1


title: HUVEC cells - shNC_rep3 [RNA-seq]

tag: genotype/variation


title: Control_3_Near1


title: Muscle_+3h_trained_ET1


title: Control_4_Near1


title: MU636 - Replicate 3

value: control


title: HUVEC cells - shNC_rep2 [RNA-seq]


title: Muscle_baseline_trained_ET2

source_name: vastus lateralis muscle, baseline

value: baseline


title: Muscle_+3h_trained_ET2


title: MU636 - Replicate 2


title: Muscle_+30min_trained_ET1


title: Control_2_Near1


title: HUVEC cells - shNC_rep1 [RNA-seq]


title: MU636 - Replicate 1


title: HUVEC cells - shHGDILnc1_rep2 [RNA-seq]


title: Muscle_+3h_untrained_SED1

value: untrained


title: Control_1_Near1


title: Aged-WT#2

status: Public on Mar 19 2024

city: Chicago

first: Yan

last: Liu

state: IL

address: 303 E. Superior Street, Lurie 5-107, Northwestern University

department: Department of Medicine

institute: Northwestern University

data_processing:
The sequencing reads were first quality checked using FastQC (v.0.11.5, Babraham Bioinformatics, Cambridge, UK). The sequence data were then mapped to the mouse reference genome mm10 using the RNA-seq aligner STAR (v.2.7.10a).
To evaluate quality of the RNA-seq data, the number of reads that fell into different annotated regions of the reference genome (exonic, intronic, splicing junction, intergenic, UTR, etc.) were assessed using bam-stats (from ngsutilsj v.0.4.17). Uniquely mapped reads were used to quantify gene expression levels employing featureCounts (subread v.2.0.3)
The data were normalized using the TMM (trimmed mean of M values) method. Differential expression analysis was performed using edgeR (v.3.40.2) , and false discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure.
Assembly: mm10
Supplementary files format and content: txt file

source_name: Bone marrow

extract_protocol:
LSKs were sorted from bone marrow. RNAs were isolated using RNAeasy Plus Micro or mini Kit
Standard mRNASeq Library Preparation

value: Bone marrow

value: primary mouse cells

tag: cell type

value: hematopoietic stem cells _LSKs

value: WT


title: Muscle_+30min_untrained_SED1


title: Aged-R248W#1


title: Aged-R248W#2


title: Aged-WT#1


title: buccal DNA 359

type: genomic

city: Beaverton

first: Lyndsey

middle: Elizabeth

last: Shorey-Kendrick

state: Oregon

address: 505 NW 185th Ave

institute: Oregon Health and Science University

hyb_protocol: none provided

scan_protocol: Buccal DNAm was assessed on the MethylationEPIC BeadChips, measuring over 850,000 CpGs at a nucleotide resolution, at the Fred Hutchinson Cancer Research Center Genomics Resource. In brief, 500ng of DNA was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research) following the Illumina-specified instructions.  Converted DNAs were applied to Illumina Infinium Methylation EPIC 8-Sample Beadchips following the Infinium HD Methylation 15019521v01 protocol.  Processed BeadChips were scanned using the Illumina iScan+ with ICS v3.3.28 and intensity data was extracted with Illumina GenomeStudio software (GenomeStudio v2011.1 with Methylation Analysis Module v1.9.0).

data_processing:
Data normalization and QC were performed using ChAMP: non-CpG probes, probes with a beadcount <3 in at least 5% of samples, probes annotated to SNPs, probes with a detection p-value > 0.01 in one or more samples, cross-hybridizing probes, and probes on X/Y chromosomes were removed and remaining probes (n=746,421) were normalized using via functional normalization.
functional normalized beta
Unmethylated and methylated signal intensities

label: Cy3 and Cy5

source_name: buccal swab

label_protocol: none provided

extract_protocol: Buccal DNA was extracted using the Maxwell® 16 Instrument (Promega AS3000) and   Maxwell® 16 Blood DNA Extraction Kit (Promega AS1010). Proteinase K (Promega   20mg/ml) was added to 15ml conicals containing 4 swabs and ~1.6ml SLB. Tubes were   vortexed to collect SLB at bottom. Tubes were incubated in s 56°C water bath for 1 hr  and then vortexed. Lysate (800ul) was added to well #7 of the Maxwell® 16 Blood DNA  cartridge. The remaining lysate was stored for a second DNA extraction. Alcohol Wash  Buffer (2 parts Milli-Q water, 1 part 100% EtOH, 1 part 100% isopropanol) was added to  wells #4, #5 and #6. Cartridges were processed using the Buffy Coat Protocol on the  Maxwell® 16 Instrument and eluted in 400ul elution buffer. Purity was measured by  spectrophotometer and concentration measured with the Quant-iT PicoGreen dsDNA  Assay (Invitrogen® P7589).

treatment_protocol: Patients were instructed not to eat or drink at least 30 minutes before buccal sample   collection. Buccal DNA was collected using 4 Sterile HydraFlock® Large Tip Flocked  Swabs (Puritan 253406H). Each swab was applied to the inside of the child’s cheek and  rolled up and down for 30-60 seconds, making certain to roll the swab over the entire  inner cheek and upper gum. Swabs were placed together in a 15 ml conical tube  containing 1600ul of 1X Saliva Lysis Buffer (SLB) before capping tube and vortexing for  10 seconds. The swabs were frozen upright in SLB at -20°C within 1 week from sampling  and stored until DNA extraction.  2X Saliva Lysis Buffer: 0.3 M TRIS-HCl; 0.67 M urea;   0.67 M NaOAc;  0.6% sodium dodecyl sulfate;  3.3 mM EDTA;  30% ethanol)

value: F

tag: age days

tag: dataset

tag: smoking


title: buccal DNA 356

value: M


title: buccal DNA 357


title: neural crest, Cut and Run, Pax7_3

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

institute: MRC Weatherall Institute of Molecular Medicine

description: Pax7 CuT_and_Run

data_processing:
Reads were mapped using  Bowtie -m 2 (v.1.0.0) to galGal6. Read counts were obtained using subread (v.1.4.5) FeatureCounts
Peak calling was performed using MACS2, de novo motif search was performed using Homer (v.4.7)
Assembly: galGal6
Supplementary files format and content: Bigwig files (bw)
Supplementary files format and content: Peaks (bed)

organism: Gallus gallus

source_name: cranial microdissection

growth_protocol: Fertilised wild-type chicken eggs were obtained from Henry Stewart & Co (Norfolk), staged according to Hamburger and Hamilton (1951) (24). All experiments were performed on chicken embryos younger. than 12 days of development, and as such were not regulated by the Animals (Scientific Procedures) Act 1986.

extract_protocol:
Snap-frozen embryos were quenched with 125 mM of glycine for 5min. Cross-linker was washed-out by 3x pellet washes with 1x PBS (with 1X PI, 1 mM DTT and 0.2 mM PMSF) centrifuging at 2000 x g for 4min at 4C. Pellets were re-suspended in NEB. Cell nuclei were expulsed with 20 strokes using pestle B in a glass homogeniser, pelleted and washed with 1 xPBS (with 1X PI, 1 mM DTT and 0.2 mM PMSF). Nuclei were lysed in SDS lysis buffer (0.7% SDS, 10mM EDTA, 50 mM Tris-HCl (pH 7.5), 1x PI). Cross-linked chromatin was sonicated at 12A 10x (10s ON 30s OFF) followed by 8A 4x (30s ON 30s OFF). Sheared chromatin samples were pre-cleared in pre-blocked Protein G beads (Dynabeads Protein G, Life Technologies) for 1 hour at 4C. 1/20 of biotinChIP was collected as an input fraction and stored at -80C. Pre-cleared chromatin samples were incubated on pre-blocked streptavidin beads (Dynabeads M-280 streptavidin beads, Life Technologies) o/n at 4C. Beads were washed with SDS Wash Buffer (2% SDS, 10mM Tris-HCl (pH 7.5), 1 mM EDTA) at room temperature, followed by 4x RIPA washes (50 mM Hepes-KOH (pH 8.0), 500 mM LiCl, 1mM EDTA, 1% NP40, 0.7% Na-Deoxycholate, 1x PI) and 1x Na-Cl TE wash (1x TE, 50mM NaCl) at 4C. Chromatin was eluted from the beads with SDS ChIP elution buffer (50 mM Tris-HCl (pH 7.5), 10 mM EDTA, 1% SDS). Cross-linking was reversed o/n at 70C in the thermomixer at 1300 rpm. Cellular RNA was digested with RNAse A (0.2 g/ml) at 37C for 1 hour, and cellular protein with Proteinase K (0.4 mg/ml) at 55C for 2 hours. Chromatin samples were separated from the streptavidin beads. Input and ChIP DNA was extracted using a standard phenol-chloroform extraction method.
Libraries were prepared using MicropPlex Library Preparation kit (Diagenode) and sequenced using NextSeq 500/550 High Output Kit v2 (75 cycles) on NextSeq 500 sequencing system.

treatment_protocol: Electroporated embryos were manually dissected, cells were dissociated with 20 strokes using pestle A in isotonic nuclei extraction buffer (NEB: 0.5% NP40, 0.25% Triton X, 10 mM Tris-HCl (pH 7.5), 3 mM CaCl2, 0.25 M sucrose, 1mM DTT, 0.2 mM PMSF, 1X Proteinase inhibitor (PI) ) in a glass homogeniser and cross-linked using 1% formaldehyde at room temperature for 10 min and snap-frozen.

value: cranial microdissection

value: neural crest

value: wt


title: neural crest, Sox10_ChIP_1


title: neural crest, Cut and Run, Pax7_1

description: Pax7 CuT_and_Run


title: neural crest, Cut and Run, Pax7_2

description: Pax7 CuT_and_Run


title: buccal DNA 358


title: buccal DNA 353


title: buccal DNA 354


title: buccal DNA 355


title: buccal DNA 352


title: Muscle_baseline_untrained_SED1


title: buccal DNA 351


title: buccal DNA 349


title: Muscle_baseline_trained_ET1


title: buccal DNA 350


title: buccal DNA 347


title: neural crest, Sox10_ChIP_2


title: buccal DNA 346


title: buccal DNA 345


title: neural crest, ChIP-seq_Input


title: buccal DNA 341


title: buccal DNA 340


title: buccal DNA 343


title: buccal DNA 339


title: buccal DNA 344


title: buccal DNA 342


title: buccal DNA 338


title: buccal DNA 335


title: buccal DNA 332


title: buccal DNA 334


title: buccal DNA 331


title: buccal DNA 330


title: buccal DNA 325


title: buccal DNA 326


title: buccal DNA 333


title: buccal DNA 327


title: buccal DNA 323


title: buccal DNA 329


title: buccal DNA 324


title: buccal DNA 348


title: buccal DNA 321


title: buccal DNA 319


title: buccal DNA 318


title: buccal DNA 320


title: buccal DNA 317


title: buccal DNA 316


title: buccal DNA 315


title: buccal DNA 314


title: buccal DNA 311


title: buccal DNA 313


title: buccal DNA 337


title: buccal DNA 312


title: buccal DNA 336


title: buccal DNA 310


title: buccal DNA 308


title: buccal DNA 328


title: buccal DNA 307


title: buccal DNA 322


title: buccal DNA 302


title: buccal DNA 300


title: buccal DNA 301


title: buccal DNA 303


title: buccal DNA 298


title: buccal DNA 297


title: buccal DNA 296


title: buccal DNA 295


title: buccal DNA 293


title: buccal DNA 292


title: buccal DNA 291


title: buccal DNA 289


title: buccal DNA 309


title: buccal DNA 286


title: buccal DNA 283


title: buccal DNA 285


title: buccal DNA 288


title: buccal DNA 305


title: buccal DNA 284


title: buccal DNA 306


title: buccal DNA 287


title: buccal DNA 282


title: buccal DNA 304


title: buccal DNA 299


title: buccal DNA 280


title: buccal DNA 279


title: buccal DNA 281


title: buccal DNA 277


title: buccal DNA 278


title: buccal DNA 276


title: buccal DNA 275


title: buccal DNA 290


title: buccal DNA 294


title: buccal DNA 270


title: buccal DNA 269


title: buccal DNA 272


title: buccal DNA 273


title: buccal DNA 271


title: buccal DNA 268


title: buccal DNA 266


title: buccal DNA 267


title: buccal DNA 263


title: buccal DNA 262


title: buccal DNA 264


title: buccal DNA 260


title: buccal DNA 261


title: buccal DNA 274


title: buccal DNA 257


title: buccal DNA 258


title: buccal DNA 259


title: buccal DNA 265


title: buccal DNA 256


title: buccal DNA 255


title: WT_18 DAP3

city: Beijing

first: Jinfang

last: Wang

address: No.50 Zhanghua Road, Haidian District

institute: Beijing Academy of Agricultural and Forestry Sciences

data_processing:
NovaSeq 6000
fastx_toolkit_0.0.14/SeqPrep/Sickle were used for estimating sequencing quality to gain clean reads.
TopHat2 / HISAT2 were used to analysis the mapped data quality.
The mapped reads were spliced using StringTie or Cufflinks software
TPM （Fragments Per Kilobases per Millionreads）values were used to show gene expression level.
Genome_build: http://cucurbitgenomics.org/organism/21;
Supplementary_files_format_and_content: text files include TPM values for each Sample

organism: Citrullus lanatus

source_name: WT 18 DAP3

extract_protocol: none provided by the submitter

value: 18 days after pollination

value: wild type

value: flesh


title: OE2_18 DAP1

source_name: OE2 18 DAP1

value: ClSnRK2.3 OE2


title: OE2_18 DAP3

source_name: OE2 18 DAP3


title: OE1_18 DAP3

source_name: OE1 18 DAP3

value: ClSnRK2.3 OE1


title: OE1_18 DAP1

source_name: OE1 18 DAP1


title: WT_18 DAP2

source_name: WT 18 DAP2


title: OE1_18 DAP2

source_name: OE1 18 DAP2


title: buccal DNA 254


title: buccal DNA 253


title: WT_10 DAP2

source_name: WT 10 DAP2

value: 10 days after  pollination


title: buccal DNA 252


title: WT_10 DAP3

source_name: WT 10 DAP3


title: WT_18 DAP1

source_name: WT 18 DAP1


title: WT_10 DAP1

source_name: WT 10 DAP1


title: buccal DNA 251


title: buccal DNA 250


title: buccal DNA 249


title: OE2_18 DAP2

source_name: OE2 18 DAP2


title: OE2_10 DAP1

source_name: OE2 10 DAP1


title: OE2_10 DAP2

source_name: OE2 10 DAP2


title: OE2_10 DAP3

source_name: OE2 10 DAP3


title: buccal DNA 248

source_name: buccal swab


title: OE1_10 DAP3

source_name: OE1 10 DAP3


title: buccal DNA 246


title: OE1_10 DAP2

source_name: OE1 10 DAP2


title: buccal DNA 247


title: OE1_10 DAP1

source_name: OE1 10 DAP1

value: 10 days after pollination


title: R248W#4-IL1Beta

data_processing:
The sequencing reads were quality checked using FastQC (v.0.11.5, Babraham Bioinformatics, Cambridge, UK). The sequence data were then mapped to the human reference genome hg38 using the RNA-seq aligner STAR (v.2.7.10a).
To evaluate quality of the RNA-seq data, the number of reads that fell into different annotated regions of the reference genome (exonic, intronic, splicing junction, intergenic, UTR, etc.) were assessed using bam-stats (from ngsutilsj v.0.4.17). Uniquely mapped reads were used to quantify gene expression levels employing featureCounts (subread v.2.0.3)
The data were normalized using the TMM (trimmed mean of M values) method. Differential expression analysis was performed using edgeR (v.3.40.2) , and false discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure.
Assembly: hg38
Supplementary files format and content: The excel table including fold change, log2 fold change, p-values, FDR, log2CPM, and raw counts

source_name: Bone marrow

growth_protocol: Bone marrow cells were culture in IMDM with 10% of serum and cytokines (TPO, Flt3, IL6, M-IL3, M-SCF)

extract_protocol:
LSKs were sorted from bone marrow. RNAs were isolated using RNAeasy Plus Micro or mini Kit
Srandard RNA-Seq Library Preparation

treatment_protocol: LSKs were treated with 10 ng/ml of IL-1β or PBS for 90 minutes

value: IL-1β (10ng/ml)


title: buccal DNA 244


title: buccal DNA 245


title: R248W#3-IL1Beta

value: Bone marrow


title: buccal DNA 242


title: buccal DNA 243


title: R248W#2-IL1Beta

value: primary mouse cells


title: buccal DNA 240


title: R248W#1-IL1Beta

value: hematopoietic stem cells _LSKs


title: WT#4-IL1Beta

value: WT


title: WT#3-IL1Beta


title: buccal DNA 239


title: WT#2-IL1Beta


title: buccal DNA 238

value: F


title: buccal DNA 237

value: M


title: WT#1-IL1Beta


title: buccal DNA 236


title: R248W#-3-PBS

value: PBS


title: R248W#-2-PBS


title: buccal DNA 235


title: buccal DNA 234


title: R248W#-4-PBS


title: buccal DNA 233


title: R248W#-1-PBS


title: buccal DNA 232


title: buccal DNA 241


title: WT#2-PBS


title: buccal DNA 231


title: buccal DNA 230


title: buccal DNA 228


title: WT#1-PBS


title: WT#3-PBS


title: buccal DNA 226


title: WT#4-PBS


title: buccal DNA 225


title: Cultured astrocytes KO2

city: Atlanta

first: Fu Hung

last: Shiu

email: fshiu@emory.edu, fshiu@mgh.harvard.edu

address: 615 Michael Street Suite 361

institute: Emory

data_processing:
Reads were trimmed aligned to the mouse genome GRCM38(mm9) using TopHat2
Quality checks were conducted on the raw reads and the trimmed reads
The number of sequence reads for each gene was quantified using "featureCounts" function
Assembly: mm9
Supplementary files format and content: Raw counts are included in each sample

source_name: Brain

extract_protocol:
Cultured astrocytes were homogenized in TRIzol (200 μL). Chloroform (800 μL) was added followed by centrifugation. The top aqueous layer was transferred to a new tube and sodium acetate solution (3M, 20 μL), glycogen (5 mg/ml, 4 μL), and isopropanol (200 μL) were added. The samples were stored overnight at − 80°C, followed by centrifugation. The pellet was washed in 75% ethanol and centrifuged again. The RNA pellet was then dissolved in nuclease-freewater (30 μL).
Bulk RNA-seq libraries were created with the NEB Next Ultra II kit using poly-A selection and sequenced to a depth of 40 million paired-end reads per sample (20 million in each direction)

value: Brain

value: Astrocytes

value: KO


title: buccal DNA 224


title: buccal DNA 227


title: Cultured astrocytes KO3


title: buccal DNA 223


title: buccal DNA 229


title: Cultured astrocytes KO1


title: buccal DNA 222