title: Nplus_1


title: BDBV 3dpi [RNA-474]

status: Public on Dec 25 2018

type: SRA

city: Atlanta

first: César

last: Albariño

state: GA

address: 1600 Clifton Rd, MS G14

country: USA

institute: Centers for Disease Control and Prevention

library_source: transcriptomic

data_processing:
RNA-Seq Analysis performed using default parameters on CLC Genomics Workbench 11.0
reference sequences were used for EBOV, SUDV, BDBV, and RESTV
Genome_build: EBOZ-2014-IC (KT589389); SUDV Gulu-2000 (NC_006432); BDBV 2007 (NC_014373); RESTV_ITA_1992_(KY798007)
Supplementary_files_format_and_content: each table file (.xlxs format) contains measurments of mRNA abundance for each virus from 1-3 dpi (3 sheets per table)

molecule: total RNA

organism: Bundibugyo virus

source_name: Huh7 cells_BDBV

growth_protocol: cell monolayers were infected with low moi, and harvested at 1-3 dpi

extract_protocol:
total RNA was harvested, and mRNA was purified
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: cell type

value: human liver cells

tag: infected with

value: BDBV

tag: time point

value: 3 dpi


title: E11_WT_3

city: Jeddah

first: Qingtian

last: Guan

address: Thuwal

country: Saudi Arabia

institute: King Abdallah University of Science and Technology

description: processed data file: Mmar_Mmar_ESX1.txt

data_processing:
bcl2fastq2 Conversion Software
Trimming of Illumina adaptor sequences and low quality reads were done using Trimmomatic (v 0.33)
For the wild type and ESX1 mutants comparision, the Illumina reads were mapped with SMALT (default parameters) against the M. tuberculosis H37Rv or M. marinum M reference. From the read count, which was obtained with bedtools, parameter multicov, with -D to include duplicates and -q 5 to exclude repetitive mapping reads, we performed a differential expression analysis with DESeq using default parameters. For the whib6 knockout and complementary comparision, we mapped the trimmed reads back to the same reference genome with bowtie2 and the differently expressed genes were called by cuffdiff2.
Normalization of raw read counts and differential expression analysis was performed using DeSeq or CuffDiff2
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Mycobacterium marinum E11

source_name: M. marinum wild type E11

extract_protocol:
M. marinum and M. tuberculosis cultures were pelleted and bead beated in 1 ml of TRIzol (Invitrogen) with 0.1-mm zirconia/silica beads (BioSpec Products). After centrifugation, supernatants were extracted with chloroform, and RNA was precipitated with isopropanol. RNA pellets were washed with 80% ethanol and dissolved in RNAse-free water. Contaminant DNA was removed by incubation with DNAse I (Fermentas).
Total RNA was extracted with TRIzol (Invitrogen) and then purified on RNeasy spin columns (Qiagen) according to the manufacturer’s instructions. RNA integrity (RNA integrity score ≥ 6.8) and quantity were determined on an Agilent 2100 Bioanalyzer (Agilent; Palo Alto, CA, USA). As ribosomal RNA constitutes a vast majority of the extracted RNA population, depletion of these molecules via RiboMinus-based rRNA depletion was conducted. For mRNA enrichment, Invitrogen’s RiboMinus Transcriptome Isolation Kit, bacteria was used according to manufacturer’s instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA-sequence-specific 5′-biotin-labelled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinus concentrate module according to the manufacturer’s protocol. The final RiboMinus RNA sample was subjected to thermal mRNA fragmentation using the Elute, Prime, Fragment Mix from the Illumina TruSeq RNA Sample Preparation Kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeq RNA Sample Preparation Kit (low-throughput protocol) according to the manufacturer’s protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III reverse transcriptase (Invitrogen) and the SRA RT primer (Illumina). The cDNA was further converted into double-stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer’s instructions. A small aliquot (1 µl) was analysed on an Invitrogen Qubit and an Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled at equal concentrations before sequencing on an Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with Illumina Pipeline software v1.82.

tag: tissue

value: M. marinum wild type E11

tag: genotype/variation

value: wild type


title: Col_0_1h_rep2

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

country: China

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

data_processing:
Raw RNA-seq reads were trimmed by quality using Trimmomatic and paired reads mapped to the Arabidopsis thaliana genome (TAIR10) using STAR 2.5.4b with default settings.
The returned alignments were stringently filtered so as to remove ambiguously mapped reads and read pairs with conflicting alignments.
RSEM v1.2.31 is used to quantitate gene abundance and the expression of individual gene is shown as the average of transcripts per million (TPM) in two biological replicates, all genes were filtered by the average of TPM > 1 at eight timepoints to remove genes with low transcript levels.
Differentially expressed genes were detected by EBSeq based on the combined criteria: |log2(fold change)| > 1 and false discovery rates < 0.05.
Genome_build: TAIR10
Supplementary_files_format_and_content: expression for genes(TAIR10) was provided. The format is tab delimited file format. Each row contains seven columns: gene_id, transcript_id, length, effective_length, expected_count,TPM and FPKM.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Col-0 detached first-pair rosette leaves 1h after culture from 12-day-old seedlings

growth_protocol: Arabidopsis seeds were germinated on ½ MS medium at 22°C under a 16-h light/8-h dark photoperiod. Detached leaf explants from 12-day-old seedlings were cultured on B5 medium without sucrose at 22°C under 24-h light conditions.

extract_protocol:
RNA extraction using Trizol protocols.
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 3000 following the manufacturer’s instructions (Illumina)

treatment_protocol: cultured 1h on B5 medium without sucrose.

tag: ecotype

value: Columbia

tag: developmental stage

value: leaves of 12-day-old seedlings

tag: growth conditions

value: 16-h light/8-h dark


title: EBOV 1dpi [RNA-476]

organism: Ebola virus

source_name: Huh7 cells_EBOV

value: EBOV

value: 1 dpi


title: E11_ESX1_1

description: processed data file: Mmar_Mmar_ESX1.txt

source_name: M. marinum E11 ESX1 mutant

value: M. marinum E11 ESX1 mutant

value: ESX1 mutant


title: MUSA_EmptyVector_2

description: processed data file: USA_EmptyVector_Complementary.txt

organism: Mycobacterium marinum M

source_name: M. marinum MUSA with empty vector

value: M. marinum MUSA with empty vector

value: empty vector


title: Nminus_3

city: Frederick

first: Jack

last: Chen

state: MD

address: SAIC-Frederick Miller Dr

institute: NIH

data_processing:
Illumina HiSeq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to E.coli K-12 genome using bowtie2 with default parameters.
Reads were counted by featurecount and then Reads per Megabase of library size (CPM) were generated and normalized by the limmaVoom pipeline.
Genome_build: E. coli K-12
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

organism: Escherichia coli str. K-12 substr. MG1655

source_name: ATCC

growth_protocol: MG1655 E. coli were grown in Gutnick minimal media to induce nitrogen starvation.

extract_protocol:
RNA was stabilized after 80 minutes after treatment using the RNAprotect Bacteria Reagent (Qiagen), and purified using the RNeasy Mini Kit and RNase-free DNase (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At OD600 0.5, cells were treated with 10 µM stapled peptide.

tag: strain

tag: treatment

value: no treatment

tag: nitrogen condition

value: nitrogen-starved


title: TT 24h_10nM_1

city: Columbus

first: Matthew

last: Ringel

state: Oh

address: 565 McCampbell Hal

department: Division of Endocrinology, Diabetes, and Metabolism

institute: The Ohio State University Wexner Medical Center and Arthur G. James Comprehensive Cancer Center

description: FeatureCounts.txt

data_processing:
Illumina BaseCalling pipeline
RNA sequencing reads were first mapped to the human genome GRCh38 build using TopHat (Version 2.0.13). Raw read counts for each gene were quantified by using featureCounts (Version 1.4.6). Then NCBI RefSeq was used for gene annotation.
Genes with raw read counts below 5 for more than 50% of samples within each condition were first filtered out.
Count data were normalized using Trimmed Mean of M-values (TMM) method within controls or drug treatments due to global drug inhibition effect. To improve the estimate of gene variability and to identify genes differentially expressed between samples, R package limma with Voom transformation. was used for testing differential expression between conditions. The p-value cut-offs were determined by controlling the mean number of false positives.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes raw read counts

organism: Homo sapiens

source_name: TT medullary thyroid cancer cells

growth_protocol: TT and MZ-CRC-1 cells were seeded in 10cm plates and incubated for 24h, then washed with PBS and incubated in 2% FBS-RPMI medium for another 24h. After this time, the untreated cells were incubated with vehicle control at 37deg celcius for 12 or 24h.

extract_protocol:
At the desired exposure time, the supernatant and scraped cells were collected into 50mL tubes, centrifuged at 300xg for 5min, the supernatant aspirated, and the pellet washed with 1mL of PBS and transferred into 1.5mL tubes. After a centrifugation step at 500xg for 5min, the supernatant was aspirated and the pellet resuspended in 1mL of TRIzol reagent (Invitrogen) to isolate the total RNA present in the cells. The RNA isolation was performed following the protocol provided by Invitrogen for TRIzol reagent use.
TruSeq Stranded Total RNA Ribo-Zero H/M/R Gold (RS-122-2301)

treatment_protocol: TT and MZ-CRC-1 cells were seeded in 10cm plates and incubated for 24h, then washed with PBS and incubated in 2% FBS-RPMI medium for another 24h. After this time, the cells were treated with Dinaciclib and incubated at 37deg celsius for 12 or 24 hours.

value: TT medullary thyroid cancer cells

tag: agent

value: Dinaciclib

tag: dose

tag: time


title: RESTV 2dpi [RNA-481]

organism: Reston ebolavirus

source_name: Huh7 cells_RESTV

value: human liver cells

value: RESTV

value: 2 dpi


title: BDBV 2dpi [RNA-473]

value: BDBV


title: E11_ESX1_3

description: processed data file: Mmar_Mmar_ESX1.txt


title: E11_WT_2

description: processed data file: Mmar_Mmar_ESX1.txt

value: M. marinum wild type E11

value: wild type


title: MUSA_EmptyVector_1


title: Nminus_2


title: E11_WT_1

description: processed data file: Mmar_Mmar_ESX1.txt


title: Nminus_1


title: SUDV 3dpi [RNA-470]

organism: Sudan ebolavirus

source_name: Huh7 cells_SUDV

value: SUDV

value: 3 dpi


title: ZPT 20 uM

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using Trimmomatic 0.35 as default parameter, then mapped to Salmonella enterica serivar Typhimurium 14028s whole genome using bowtie v. 2.2.4 with parameters -t --very-sensitive
The mapped reads were counted by featureCounts (http://bioinf.wehi.edu.au/featureCounts/) and normalized as TMM value by using edgeR.
Genome_build: Malassezia restricta KCTC 27527
Supplementary_files_format_and_content: Excel file including TMM values and locus_tags for genes of M. restricta.

organism: Malassezia restricta

source_name: Clinical isolate

growth_protocol: M. restricta cells were cultured on LNA medium at 34C for 3 days

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiqagen, Cat#74104).
Illumina Stranded TruSeq Total RNA Sample Prep Kit (Cat#FC-122-2201) 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: LNA medium containing ZPT 0, 5, 10 or 20 µM for 6h at 34C.

value: ZPT 20 uM


title: DMSO_3_3

value: vehicle treatment (DMSO)


title: ZPT 10 uM

value: ZPT 10 uM


title: SUDV 2dpi [RNA-469]


title: sp_local_w2_3

city: Taipei

first: Ming-Jung

last: Liu

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Academia sinica

description: Processed_data_RNA-expression_MJL_new_sample.xlsx

data_processing:
Adaptor sequences were trimmed from the sequence reads. Adaptor sequences is for TrueSeq-3.
The RNA-seq reads to the genome through TopHat with the options (-I 500 -g 1; otherwise with default). Transcript levels of annotated genes were determined and shown as FPKM (Fragments Per Kilobase per Million fragments mapped) calculated with Cufflinks
Genome_build: The reference genome sequences and gene annotation of  Solanum pennellii (Spenn_v2.0) were retrieved from Sol Genomics Network
Supplementary_files_format_and_content: The "Processed data_RNA-expression" contains the RNA expression (FPKM value) of annotated genes in the samples listed above.

organism: Solanum pennellii

source_name: leaves

growth_protocol: Tomato was grown on Jiffy-7 peat pot (Hummert International, Earth City, MO) in a growth chamber under 16 h light (6:00 to 22:00, 200 μmol m-2 s-1)/ 8 h dark cycle at 28ºC.

extract_protocol:
Total RNA from the leaf tissues were extracted with RNeasy Plant Mini Kit (Qiagen, Germantown, MD, USA).
The purified total RNA was used to construct a library for 100-bp paired-end sequencing following the Illumina protocol.
TruSeq Stranded Total RNA Library Prep Kit was used for library preparation.

treatment_protocol: Three to four weeks old plants with 3-4 true leaves were used for wound treatment. For the wound-elicitation, the lower 1st and 2nd true leaves were crushed with a hemostat to cross the midrib of all leaflets.

tag: cultivar

tag: replicate

value: 2 hour wounded leaves


title: DMSO_2_2


title: ZPT 5 uM

value: ZPT 5 uM


title: sp_local_w2_2


title: sp_local_w2_1


title: ZPT no treatment

value: ZPT no treatment


title: SUDV 1dpi [RNA-468]

tag: cell line

value: 1 dpi


title: DMSO_1_1

value: nitrogen-starved


title: BDBV 1dpi [RNA-472]

tag: cell type


title: AVB_122_CV_PBMC

status: Public on Dec 24 2018

city: Nedlands

first: Anya

last: Jones

state: Western Australia

address: Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue

country: Australia

institute: Telethon Kids Institute, The University of Western Australia

data_processing:
The Illumina bcl2fastq 2.17.1.14  pipeline was used to generate the sequence data.
FASTQC (Andrews Trop Med Int Health. 2011) was employed for pre-alignment quality control (QC) of raw sequence data. Raw sequencing reads were aligned to the human reference genome (hg19; Pertea Nat Protocol. 2016) using HISAT2 (Kim Nat Methods. 2015), and summarised as gene-level counts employing summariseOverlaps (Anders Nat Protoc. 2013), followed by post-alignment QC with SAMStat (Lassmann Bioninformatics. 2011). Genes with an official HUGO Gene Nomenclature Committee (HGCN) symbol were retained.
Prior to network analysis (WGCNA), gene counts were log-transformed and normalised employing DESeq2 VST transformation (Love Genome Biol. 2014). Latent variation was removed with the removeBatchEffect function from the limma package (Ritchie Nucleic Acids Res. 2015).
Genome_build: hg19
Supplementary_files_format_and_content: AVB_PBMC_raw_counts.txt file includes raw-gene level counts.
Supplementary_files_format_and_content: AVB_PBMC_VST_transformed_counts includes DESeq2 vst transformed counts.

source_name: PBMC

extract_protocol:
Total RNA was extracted from viable PBMC employing TRizol (Ambion, Life Technologies) followed by RNeasy MinElute (Qiagen, Hilden, Germany). The integrity of the RNA was 9.0±0.5  (mean ± SD), as assessed on the Bioanalyzer (Agilent Technologies, California, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: subjectid

tag: visit

value: CV

tag: group

value: child

tag: age at visit (years)

tag: sex(0=female, 1=male)

tag: pbmc batch


title: AVB_122_AV_PBMC

value: AV

tag: steroids_av (1=yes, 0=no)

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)

tag: rsv positive at av (1=yes, 0=no, 9=not measured)

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)

tag: influenza positive at av (1=yes, 0=no, 9=not measured)

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)

tag: human polyomavirus at av (1=yes, 0=no, 9=not measured)

tag: parainfluenza virus at av (1=yes, 0=no, 9=not measured)

tag: bocavirus at av (1=yes, 0=no, 9=not measured)

tag: enterovirus at av (1=yes, 0=no, 9=not measured)

tag: metapneumovirus at av (1=yes, 0=no, 9=not measured)


title: AVB_118_CV_PBMC

tag: subjectid

tag: visit


title: AVB_120_AV_PBMC

tag: group

value: infant

tag: age at visit (years)

tag: virus positive at av (1=yes, 0=no, 9=not measured)


title: AVB_118_AV_PBMC

tag: sex(0=female, 1=male)

tag: steroids_av (1=yes, 0=no)

tag: pbmc batch


title: SAonly5

city: Seattle

first: Ying

last: Zheng

state: WA

address: 850 Republican

department: Bioengineering

institute: University of Washington

data_processing:
Base calling was performed using Illumina's Real-Time Analysis software v1.18.66.3 (https://support.illumina.com/sequencing/sequencing_software/real-time_analysis_rta.html), using the default settings.
Reads that didn't pass Illumina's base call quality filter were discarded, followed by using Cutadapt v1.11 to trim adapter sequence, discarding paired reads where either read in the pair has a length < 25
Generated counts for each gene using htseq-count v0.6.1p1 (using the "intersection-strict" overlapping mode)
Alignments were performed using TopHat v2.1.0, using the default parameters, with the exceptions of:  --mate-inner-dist = 80  --library-type = fr-firststrand  --no-coverage-search
Normalized data and performed significance testing using the GLM method in edgeR v3.18.1
Genome_build: Reads were aligned using UCSC assembly hg38
Supplementary_files_format_and_content: edgeR results files are in tab-delimited text format and contain columns for logFC(log2 ratio), logCPM(average log2 counts per million), sig (a value of 1 if |logFC| >= 0.585 & FDR 5% , otherwise 0), normalized gene counts, raw gene counts, as well annotation. Ratio formulation can be determined by the file naming convention, where the sample in the numerator comes first (e.g., x-y.txt would contain data where ratios were calculated as log2(x/y)

source_name: Endothelial cell

growth_protocol: hESC-derived endothelial cells were generated by differentiation of hESCs through cardiac mesoderm using high Activin A and low BMP4. Briefly, single cell suspensions of hESCs were plated on Matrigel (105K cells per cm^2)in mTeSR-1 and 1 μM CHIR-99021. After 24 hours, they were fed with 100 ng/mL Activin A  in RPMI + B27 supplement (without insulin) and 1X Matrigel. 18 hours later, the cells were fed with 5 ng/mL BMP4  and 1 μM CHIR-99021 in RPMI + B27 (without insulin). 24 hours later, the media was changed to endothelial induction media: Stempro34 containing 200 ng/mL VEGF, 5 ng/mL bFGF, 10 ng/mL BMP4, 4x10-4 M monothioglycerol, 50 μg/mL Ascorbic Acid, 2 nM L-Glutamine and pen-strep. 72 hours later, endothelial progenitor cells were fed with fresh Stempro (with L-glutamine and pen-strep) 1-2 hours later, cells were re-plated in 0.2% gelatin coated tissue culture flasks with endothelial growth media (EGM) containing 20 ng/mL VEGF, 20 ng/mL bFGF, and 1 μM CHIR-99021. Media was replenished every other day. hESC-ECs were harvested at differentiation day 10 and used to generate engineered constructs.

extract_protocol:
Total RNA from three types of constructs was purified using the RNAeasy Mini Kit (Qiagen) and residual DNA was removed by on-column DNase digestion. RNA quality was assessed with the Agilent RNA 6000 Nano Kit using the Agilent 2100 Bioanalyzer (Agilent Technologies). Only samples with RNA integrity number higher than 8 were kept for further analysis. RNA sequencing was performed on poly-A-enriched samples using Illumina TruSeq
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 15 mg/mL stock collagen (dissolved in 0.1% acetic acid) was neutralized and diluted to 6 mg/mL on ice with 1M NaOH (20 mM final), 10X M199, and EGM. hESC-derived endothelial cells were added after the collagen was neutralized at a density of 3 x 10^6 per mL. Liquid 6 mg/mL collagenin was molded an 8 mm diameter x 1 mm height PDMS well. Constructs were then cultured for 3 days with EGM + factors media.

tag: cell type

value: ESC-derived endothelial cell

tag: cell line


title: MVonly2

treatment_protocol: Engineered microvessels were generated using injection molding and soft lithography techniques. Briefly, 15 mg/mL stock collagen (dissolved in 0.1% acetic acid) was neutralized and diluted to 6 mg/mL on ice with 1M NaOH (20 mM final), 10X M199, and EGM. Specially designed devices that contain holes for collagen injection, inlet, and outlet were used during injection molding, assembly, and microvessel culture. The microchannels were created by molding liquid 6 mg/mL collagen around a microfabricated polydimethylsiloxane (PDMS) stamp that contains vessel network geometry. After gelation, the channel was enclosed with a separately generated flat layer of collagen to create embedded microfluidic channels surrounded by native collagen matrix on all sides. hESC-derived endothelial cells were seeded in the channel by perfusing at a density of 10 x 10^6 per mL. The cells were allowed to circumferentially attach overnight in static conditions, followed by flow through the lumen to remove the non-attached cells in the lumen and reservoir. Constructs were then cultured under gravity driven flow for 3 days with EGM + factors media by replacing the media at the device inlet every 12 hours for the duration of the culture period.


title: SAonly6


title: MVonly1


title: AVB_120_CV_PBMC


title: MV_SA4

treatment_protocol: Engineered microvessels were generated using injection molding and soft lithography techniques. Briefly, 15 mg/mL stock collagen (dissolved in 0.1% acetic acid) was neutralized and diluted to 6 mg/mL on ice with 1M NaOH (20 mM final), 10X M199, and EGM. hESC-derived endothelial cells were added after the collagen was neutralized at a density of 3 x 10^6 per mL. Specially designed devices that contain holes for collagen injection, inlet, and outlet were used during injection molding, assembly, and microvessel culture. The microchannels were created by molding liquid 6 mg/mL collagen around a microfabricated polydimethylsiloxane (PDMS) stamp that contains vessel network geometry. After gelation, the channel was enclosed with a separately generated flat layer of collagen to create embedded microfluidic channels surrounded by native collagen matrix on all sides. hESC-derived endothelial cells were seeded in the channel by perfusing at a density of 10 x 10^6 per mL. The cells were allowed to circumferentially attach overnight in static conditions, followed by flow through the lumen to remove the non-attached cells in the lumen and reservoir. Constructs were then cultured under gravity driven flow for 3 days with EGM + factors media by replacing the media at the device inlet every 12 hours for the duration of the culture period.


title: AVB_115_AV_PBMC

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)

tag: rsv positive at av (1=yes, 0=no, 9=not measured)

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)

tag: influenza positive at av (1=yes, 0=no, 9=not measured)


title: AVB_113_CV_PBMC


title: AVB_112_CV_PBMC


title: AVB_113_AV_PBMC

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)

tag: human polyomavirus at av (1=yes, 0=no, 9=not measured)

tag: parainfluenza virus at av (1=yes, 0=no, 9=not measured)

tag: bocavirus at av (1=yes, 0=no, 9=not measured)

tag: enterovirus at av (1=yes, 0=no, 9=not measured)


title: AVB_111_AV_PBMC

tag: subjectid

tag: visit

tag: group

tag: age at visit (years)

tag: metapneumovirus at av (1=yes, 0=no, 9=not measured)


title: AVB_112_AV_PBMC

tag: sex(0=female, 1=male)

tag: steroids_av (1=yes, 0=no)

tag: virus positive at av (1=yes, 0=no, 9=not measured)

tag: pbmc batch


title: AVB_110_CV_PBMC


title: AVB_110_AV_PBMC

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)

tag: rsv positive at av (1=yes, 0=no, 9=not measured)

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)


title: AVB_109_CV_PBMC


title: AVB_109_AV_PBMC

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)

tag: influenza positive at av (1=yes, 0=no, 9=not measured)

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)


title: MV_SA3

tag: cell type

tag: cell line


title: AVB_115_CV_PBMC

tag: subjectid


title: AVB_108_CV_PBMC

tag: visit


title: AVB_108_AV_PBMC

tag: group

tag: human polyomavirus at av (1=yes, 0=no, 9=not measured)

tag: parainfluenza virus at av (1=yes, 0=no, 9=not measured)

tag: bocavirus at av (1=yes, 0=no, 9=not measured)

tag: enterovirus at av (1=yes, 0=no, 9=not measured)


title: AVB_106_CV_PBMC

tag: age at visit (years)

tag: sex(0=female, 1=male)


title: AVB_106_AV_PBMC

tag: steroids_av (1=yes, 0=no)

tag: virus positive at av (1=yes, 0=no, 9=not measured)

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)

tag: metapneumovirus at av (1=yes, 0=no, 9=not measured)

tag: pbmc batch


title: AVB_101_AV_PBMC

tag: rsv positive at av (1=yes, 0=no, 9=not measured)

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)

tag: influenza positive at av (1=yes, 0=no, 9=not measured)

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)


title: AVB_101_CV_PBMC

tag: subjectid

tag: visit

tag: group


title: AVB_099_CV_PBMC


title: AVB_095_CV_PBMC


title: AVB_111_CV_PBMC


title: AVB_099_AV_PBMC

tag: human polyomavirus at av (1=yes, 0=no, 9=not measured)

tag: parainfluenza virus at av (1=yes, 0=no, 9=not measured)

tag: bocavirus at av (1=yes, 0=no, 9=not measured)


title: Coi1_2_time0_rep1

source_name: coi1-2 detached first-pair rosette leaves before culture from 12-day-old seedlings

treatment_protocol: No treatment applied.

tag: ecotype

value: Columbia

tag: genotype/variation

tag: developmental stage

tag: tissue

value: leaves of 12-day-old seedlings

tag: growth conditions

value: 16-h light/8-h dark


title: AVB_095_AV_PBMC

tag: age at visit (years)

tag: sex(0=female, 1=male)

tag: steroids_av (1=yes, 0=no)

tag: virus positive at av (1=yes, 0=no, 9=not measured)

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)

tag: enterovirus at av (1=yes, 0=no, 9=not measured)

tag: metapneumovirus at av (1=yes, 0=no, 9=not measured)

tag: pbmc batch


title: AVB_094_AV_PBMC

tag: subjectid

tag: visit

tag: group

tag: rsv positive at av (1=yes, 0=no, 9=not measured)

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)

tag: influenza positive at av (1=yes, 0=no, 9=not measured)

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)


title: AVB_094_CV_PBMC


title: AVB_092_CV_PBMC


title: AVB_089_AV_PBMC

tag: human polyomavirus at av (1=yes, 0=no, 9=not measured)

tag: parainfluenza virus at av (1=yes, 0=no, 9=not measured)

tag: bocavirus at av (1=yes, 0=no, 9=not measured)


title: AVB_093_CV_PBMC

tag: age at visit (years)

tag: sex(0=female, 1=male)


title: AVB_088_AV_PBMC

tag: steroids_av (1=yes, 0=no)

tag: virus positive at av (1=yes, 0=no, 9=not measured)

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)


title: AVB_092_AV_PBMC

tag: enterovirus at av (1=yes, 0=no, 9=not measured)

tag: metapneumovirus at av (1=yes, 0=no, 9=not measured)

tag: pbmc batch


title: AVB_088_CV_PBMC

tag: subjectid

tag: visit

tag: group


title: AVB_087_CV_PBMC


title: AVB_086_CV_PBMC


title: AVB_087_AV_PBMC

tag: rsv positive at av (1=yes, 0=no, 9=not measured)

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)


title: AVB_084_AV_PBMC

tag: influenza positive at av (1=yes, 0=no, 9=not measured)

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)

tag: human polyomavirus at av (1=yes, 0=no, 9=not measured)


title: AVB_086_AV_PBMC

tag: age at visit (years)

tag: parainfluenza virus at av (1=yes, 0=no, 9=not measured)

tag: bocavirus at av (1=yes, 0=no, 9=not measured)


title: AVB_089_CV_PBMC

tag: sex(0=female, 1=male)


title: AVB_083_AV_PBMC

tag: steroids_av (1=yes, 0=no)

tag: virus positive at av (1=yes, 0=no, 9=not measured)

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)


title: AVB_083_CV_PBMC

tag: pbmc batch


title: AVB_067_CV_PBMC

tag: subjectid


title: AVB_067_AV_PBMC

tag: visit

tag: enterovirus at av (1=yes, 0=no, 9=not measured)

tag: metapneumovirus at av (1=yes, 0=no, 9=not measured)


title: AVB_082_CV_PBMC

tag: group


title: AVB_082_AV_PBMC

tag: rsv positive at av (1=yes, 0=no, 9=not measured)

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)


title: AVB_034_CV_PBMC


title: AVB_084_CV_PBMC


title: AVB_093_AV_PBMC

tag: influenza positive at av (1=yes, 0=no, 9=not measured)

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)

tag: human polyomavirus at av (1=yes, 0=no, 9=not measured)


title: AVB_020_CV_PBMC

tag: age at visit (years)


title: AVB_021_CV_PBMC

tag: sex(0=female, 1=male)


title: AVB_021_AV_PBMC

tag: steroids_av (1=yes, 0=no)

tag: parainfluenza virus at av (1=yes, 0=no, 9=not measured)

tag: bocavirus at av (1=yes, 0=no, 9=not measured)


title: AVB_012_CV_PBMC

tag: pbmc batch


title: AVB_012_AV_PBMC

tag: subjectid

tag: virus positive at av (1=yes, 0=no, 9=not measured)

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)


title: AVB_034_AV_PBMC

tag: visit

tag: enterovirus at av (1=yes, 0=no, 9=not measured)

tag: metapneumovirus at av (1=yes, 0=no, 9=not measured)


title: AVB_007_AV_PBMC

tag: group

tag: rsv positive at av (1=yes, 0=no, 9=not measured)

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)


title: AVB_020_AV_PBMC

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)

tag: influenza positive at av (1=yes, 0=no, 9=not measured)

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)


title: AVB_007_CV_PBMC

tag: age at visit (years)

tag: sex(0=female, 1=male)


title: AVB_006_CV_PBMC


title: AVB_006_AV_PBMC

tag: steroids_av (1=yes, 0=no)

tag: human polyomavirus at av (1=yes, 0=no, 9=not measured)

tag: parainfluenza virus at av (1=yes, 0=no, 9=not measured)


title: AVB_122_CV_NMS

data_processing:
The Illumina bcl2fastq 2.17.1.14  pipeline was used to generate the sequence data.
FASTQC (Andrews Trop Med Int Health. 2011) was employed for pre-alignment quality control (QC) of raw sequence data. Raw sequencing reads were aligned to the human reference genome (hg19; Pertea Nat Protocol. 2016) using HISAT2 (Kim Nat Methods. 2015), and summarised as gene-level counts employing summariseOverlaps (Anders Nat Protoc. 2013), followed by post-alignment QC with SAMStat (Lassmann Bioninformatics. 2011). Genes with an official HUGO Gene Nomenclature Committee (HGCN) symbol were retained.
Genome_build: hg19
Supplementary_files_format_and_content: AVB_NMS_raw_counts.txt file includes raw-gene level counts.

source_name: NMS

extract_protocol:
Total RNA was extracted from nasal mucosal scrapings (NMS) employing TRizol (Ambion, Life Technologies) followed by RNeasy MinElute (Qiagen, Hilden, Germany). The integrity of the RNA was 9.0±0.5  (mean ± SD), as assessed on the Bioanalyzer (Agilent Technologies, California, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: subjectid

value: Child

tag: sex (f=female, m=male)


title: Mix 367 sgRNA pool: HL7702 CATE-seq

city: Nanjing

first: Xu

last: Xinhui

address: Sipailou 2#

institute: SEU

description: Mix 367 sgRNA pool CATE-seq

library_source: genomic

data_processing:
Library strategy: CATE-seq
The raw reads data were separated according to the barcode using a homemade Python scripts.
All reads were cut 25 bp at 5' by a homemade Python scripts.
The trimmed reads were aligned to the human genome (hg19) using Bowtie program (version 1.1.2)
The sorted bam files were convert to bedgraph files using genomeCoverageBed.
The bedgraph files were convert to bigwig using the program wigToBigWig.
Genome_build: hg19

molecule: genomic DNA

growth_protocol: 293T, HepG2, HeLa, SiHa, and C-33A cells were cultivated with the DMEM medium (HyClone) supplemented with 10% fetal bovine serum (HyClone), 100 U/mL penicillin, and 100 μg/mL streptomycin (Biosharp). The HL7702 cell was cultivated with the RPMI-1640 medium (HyClone) supplemented with 10% fetal bovine serum (HyClone), 100 U/mL penicillin, and 100 μg/mL streptomycin (Biosharp). Cells were incubated at 37°C in a 5% CO2 incubator.

extract_protocol:
Cells were inoculated into a 25 cm2 culture flask and cultured in complete medium for 24 h (degree of fusion greater than 80%). Cells were then washed twice with pre-chilled PBS and collected by trypsinization. The genomic DNA (gDNA) was extracted from cells by using the TIANamp Genomic DNA Kit (Tiangen).
The extracted gDNAs of 293T, HepG2, HL7702, C-33a, SiHa, and HeLa cells were tagmented by the Tn5 transposomes T-B-1 to T-B-6, respectively. Additionally, the 293T gDNA was also tagmented by the Tn5 transposome T-B-7, which was called as 293Tm. The tagmentation reaction (30 μL) contained 200 ng gDNA, 5 μL transposome, 6 μL 5× LM buffer, and certain volume of ddH2O that supplemented the total reaction to 30 μL. The reaction was incubated at 55°C for 15 min. The reaction contained no transposome was used as control. The tagmentation products were run with agarose gel and the fragments of 200–1000 bp were recovered, which were used as the input DNA for enriching target sequences.The dCas9 protein was diluted to 0.3 μM with stock solution and stored at -20° C. The csgRNAs were mixed into four groups according to their numbering. In each mixing, about 7.5 ng of each csgRNA was used. Five μL of magnetic beads with streptavidin was added to 50 μL of PBS containing 0.5% BSA and placed on a magnetic stand for 15 s. The supernatant was aspirated. After washing three times with 50 μL of PBS-BSA solution, the beads were added with 50 μL of 1×dCas9 buffer and 2 μL of capture oligonucleotide (10 μM). The sequence of capture oligonucleotide was 5′-Biotin-TTTTTTTGCA TCTGGTATTC GTAAGGTTCC G-3′. The beads were mixing by rotation for 1 hour. The beads were washed three times with 50 μL of 1×dCas9 buffer.

tag: cell type

tag: fragment method

value: Tagmentation

tag: barcode

value: Barcode 3:TGACCA


title: Mix 367 primer pool: 293T CATE-seq

description: Mix 367 primer pool CATE-seq

value: Barcode 8:ACAGTG


title: Mix 367 sgRNA pool: C-33A CATE-seq

description: Mix 367 sgRNA pool CATE-seq

value: Barcode 4:CAGATC


title: AVB_121_AV_NMS

tag: visit

value: Infant

tag: virus positive at av (1=yes, 0=no, 9=not measured)

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)

tag: bocavirus at av (1=yes, 0=no, 9=not measured)

tag: enterovirus at av (1=yes, 0=no, 9=not measured)

tag: metapneumovirus at av (1=yes, 0=no, 9=not measured)


title: Mix 367 sgRNA pool: HeLa CATE-seq

description: Mix 367 sgRNA pool CATE-seq

source_name: HeLa

value: HeLa

value: Barcode 6:CTTGTA


title: Mix 367 sgRNA pool: HepG2 CATE-seq

description: Mix 367 sgRNA pool CATE-seq

value: Barcode 2:CGATGT


title: AVB_120_AV_NMS

tag: group

tag: rsv positive at av (1=yes, 0=no, 9=not measured)

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)

tag: influenza positive at av (1=yes, 0=no, 9=not measured)

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)


title: AVB_119_AV_NMS

tag: subjectid

tag: age at visit (years)

tag: steroids_av (1=yes, 0=no)


title: Mix 367 sgRNA pool: 293T CATE-seq

description: Mix 367 sgRNA pool CATE-seq

tag: cell type

tag: fragment method


title: AVB_118_AV_NMS

tag: visit

tag: sex (f=female, m=male)

tag: human polyomavirus at av (1=yes, 0=no, 9=not measured)

tag: parainfluenza virus at av (1=yes, 0=no, 9=not measured)


title: AVB_118_CV_NMS

value: CV


title: AVB_117_AV_NMS


title: Mix 367 primer pool: HL7702 CATE-seq

description: Mix 367 primer pool CATE-seq

tag: barcode

value: Barcode 9:GCCAAT


title: AVB_116_AV_NMS

value: AV

tag: virus positive at av (1=yes, 0=no, 9=not measured)

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)

tag: bocavirus at av (1=yes, 0=no, 9=not measured)

tag: enterovirus at av (1=yes, 0=no, 9=not measured)

tag: metapneumovirus at av (1=yes, 0=no, 9=not measured)


title: AVB_113_CV_NMS

tag: group


title: AVB_110_AV_NMS

tag: rsv positive at av (1=yes, 0=no, 9=not measured)

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)

tag: influenza positive at av (1=yes, 0=no, 9=not measured)

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)


title: Mix 367 sgRNA pool: SiHa CATE-seq

description: Mix 367 sgRNA pool CATE-seq

source_name: SiHa

tag: cell type

value: SiHa

tag: fragment method

value: Barcode 5:GATCAG


title: ABBL (AGA, balding area, bulb) [miRNA-seq]

city: GuangZhou

first: Qian

last: Qu

address: 1838 North Guangzhou AV

institute: Nanfang Hospital of Southern Medical University

description: bulb portion of hair follicle

data_processing:
Basecalls performed using CASAVA for all libraries.
Sequenced reads were stripped of adaptor sequence and sequences between 18-30nt were selected and mapped Silva?GtRNAdb?Rfam and Repbase using Bowtie to get unannotated reads.unannotated reads were mapped human genome version GRCh38 using miRDeep2.
The read abundance of predicted miRNAs was normalized and expressed as transcripts per million (TPM) to measure the expression levels of these miRNAs in different samples.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Hair follicle

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following manufacturers recommendations. RNA quality and quantity of all samples were evaluated by using Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RI
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hair follicles obtained by FUE technique(0.8mm, 0.9mm, 1mm wide) were immediately placed in a sterile petri dish containing normal saline at 4?.With an operating microscope and microsurgical instruments, fat and redundant tissues were removed from the hai

tag: tissue

value: hair follicle

tag: tissue section

value: bulb

tag: age

value: range27-45, median 31.9

tag: diagnosis

value: HamiltonNorwood baldness scale score 3-5


title: CNBG (control, non-balding area,bugle) [miRNA-seq]

description: bugle portion of hair follicle

value: bugle

value: range21-34, median 29.1

value: normal


title: ABBG (AGA, balding area, bugle) [miRNA-seq]

description: bugle portion of hair follicle


title: CNBL (control, non-balding area, bulb) [miRNA-seq]

description: bulb portion of hair follicle


title: ANBG (AGA, non-balding area, bugle) [miRNA-seq]

description: bugle portion of hair follicle


title: AVB_109_AV_NMS

tag: subjectid

tag: visit

value: Child

tag: age at visit (years)

tag: sex (f=female, m=male)

tag: steroids_av (1=yes, 0=no)

tag: virus positive at av (1=yes, 0=no, 9=not measured)

tag: human polyomavirus at av (1=yes, 0=no, 9=not measured)

tag: parainfluenza virus at av (1=yes, 0=no, 9=not measured)


title: AVB_109_CV_NMS

tag: group


title: Mix 50 sgRNA: 293T CATE-seq

description: Mix 50 sgRNA pool CATE-seq

value: Tagmentation

tag: barcode

value: Barcode 7:GGCTAC


title: AVB_107_AV_NMS

value: Infant

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)

tag: rsv positive at av (1=yes, 0=no, 9=not measured)

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)

tag: influenza positive at av (1=yes, 0=no, 9=not measured)

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)

tag: bocavirus at av (1=yes, 0=no, 9=not measured)

tag: enterovirus at av (1=yes, 0=no, 9=not measured)

tag: metapneumovirus at av (1=yes, 0=no, 9=not measured)


title: Cont 574_135

city: Miami

first: Derek

middle: Michael

last: Dykxhoorn

state: FL

address: 1501 NW 10th Ave, BRB 406

department: Human Genetics

institute: University of Miami

description:
day 135 post differentiation
day135_raw.tsv
sample name:
201503086-01

data_processing:
Adapter Trimming: TrimGalore
Read Alignment: STAR v2.5.0a
Read Counting: HTSeq-count
Genome_build: GRCh37
Supplementary_files_format_and_content: day35_raw.tsv and day135_raw.tsv are a raw count matrices with given Ensembl IDs corresponding to the sample read counts.

source_name: induced pluripotent stem cell-derived cortical neurons

growth_protocol: All of the neurons, both ASD and control, were differentiated from iPSC lines using the following protocol. Prior to inducing neural differentiation, iPSCs were isolated from MEF feeder layer cells through magnetic column separation using MEF-specific antibodies (anti-mEF-SK4) coupled to paramagnetic beads (Miltenyi Biotec). Magnetic separation of the cells was carried out according to the manufacturer’s instructions with few exceptions. Briefly, iPSC colonies were dissociated into a single cell suspension through a 10-minute treatment with Accutase. In lieu of MACS buffer, mTeSR1 containing 2 µM thiazovivin and 20 µM Y27632 was used for both incubation of the cells in MEF-specific antibodies and for column washes during magnetic separation.  Cortical neuron differentiation of the iPSCs was performed by providing recombinant growth factors and small molecule compounds in the growth media in a specific schedule.  Cortical neurogenesis was initiated through the formation of neural EBs using AggreWell™800 plates (STEMCELLTechnologies) according to the manufacturer’s protocol. Briefly, a single cell suspension of 3–4.5 × 106iPSCs (10,000 to 15,000 cells per neural aggregate) was dispensed into each well of an Aggrewell™800 plate in neural induction media (NIM; STEMCELL technologies) supplemented with 10 μM Y27632, 10 μM SB431542 (Stemgent), 1 μM dorsomorphin (Stemgent), and 1 μM thiazovivin.  After five days, neural aggregates were collected from the AggreWell™800 plate and transferred to 6-well plates coated with 15 μg/mL Poly-L-Ornithine (Sigma) and 10 μg/mL laminin (Trevigen) and cultured for another five days in NIM. On day 12, the differentiation medium was transitioned from NIM to an N2/B27 enriched neurobasal medium (ENB) consisting of a 1:1 mixture of DMEM/F12 (with L-Glutamine) and Neurobasal™ medium (minus phenol red; GIBCO), 0.5% N2® Supplement (GIBCO), 1% B-27® Supplement (GIBCO), 0.5% non-essential amino acids, 0.5% GlutaMAX (GIBCO), 1% Insulin-Transferrin-Selenium-A (GIBCO), 1% Antibiotic-Antimycotic, 30 ng/mL tri-iodothyronine (Sigma), 40 ng/mL thyroxine (Sigma), 100 µg/ml bovine-serum albumen (Sigma), 60 ng/ml progesterone (Sigma), 16 µg/mL putrescine(Sigma)78, 5 μg/mL N-acetyl-L-cysteine (Sigma), and 5 μM foreskolin (Sigma). Between days 12–35, cortical progenitor cells were expanded by enzymatically passaging the cells with Accutase or Accumax (Sigma) every 4–7 days and replated at a density of 4–8 × 104cells/cm2. On day 35, the cells were plated for terminal differentiation on culture plates coated with 100 μg/mL Poly-D-Lysine (Trevigen), 20 μg/mL laminin, and 10 μg/mL fibronectin (Trevigen) at a density of 2–4 × 104 cells/cm2. Of note, the seeding densities listed are based on single cell counts and do not reflect cells contained within neural aggregates, which were numerous in culture.

extract_protocol:
Total RNA was extracted from the cells using a PureLink RNA Mini kit (Ambion). Cell lysates were homogenized using QIAshredder spin columns (Qiagen). Two distinct methods were used to remove genomic DNA during the RNA purification: (1) homogenized lysates were filtered through a gDNA eliminator spin columns (Qiagen) and (2) on-column DNase treatment (Qiagen). The chemistry behind silica-membrane spin column-based RNA purification necessitates ethanol concentrations ≥50% (final concentration) during precipitation and wash steps in order to obtain RNA from approximately 18 nucleotides (nt) upwards. Thus, to extract all species of RNA, including those <200 nt such as miRNA, after homogenized lysates were passed through gDNA eliminator spin columns, 100% ethanol (Sigma) was used to precipitate RNA out of solution (final ethanol concentration of 50%). To this end, we additionally used Buffer RWT (Qiagen) in place of PureLink RNA Mini Kit Wash Buffer I. Finally, RNA was eluted in the Ambion® RNA Storage Solution. The concentration and quality of RNA samples was assessed using a Bioanalyzer RNA kit (Agilent Technologies) to determine the RNA integrity number (RIN).
For each sample, ≥750 ng of total RNA (RIN between 7.9 to 10) was processed for RNA-Seq. Ribosomal RNA was depleted using the Ribo-Zero rRNA Removal Kit (Epicentre) and cDNA libraries were generated with ScriptSeq mRNA-Seq Library Preparation Kit (Epicentre), which enables directional sequencing through stand-specific tagging. Paired-end sequencing was performed on indexed samples and run on the HiSeq. 2500, yielding a minimum of 50 million reads/sample. Alignment of RNA-Seq reads against the human genome (GRCh38) was performed using STAR Aligner and Htseq-count was used to count the number of overlapping reads with genes. Differential expression analysis was conducted using EdgeR.

tag: disease state

value: healthy control

tag: tissue

tag: iPSc source

value: peripheral blood mononuclear cells

tag: reprogramming method

value: Sendai virus

tag: gender

value: male

tag: ethnicity

value: non-hispanic white


title: AVB_106_CV_NMS

tag: subjectid

tag: visit

value: CV

tag: group

tag: age at visit (years)

tag: sex (f=female, m=male)


title: AVB_111_AV_NMS

value: AV

tag: steroids_av (1=yes, 0=no)

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)

tag: rsv positive at av (1=yes, 0=no, 9=not measured)

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)

tag: human polyomavirus at av (1=yes, 0=no, 9=not measured)

tag: parainfluenza virus at av (1=yes, 0=no, 9=not measured)


title: AVB_105_AV_NMS

tag: virus positive at av (1=yes, 0=no, 9=not measured)

tag: influenza positive at av (1=yes, 0=no, 9=not measured)

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)

tag: bocavirus at av (1=yes, 0=no, 9=not measured)

tag: enterovirus at av (1=yes, 0=no, 9=not measured)

tag: metapneumovirus at av (1=yes, 0=no, 9=not measured)


title: Cont 102_135

description:
day 135 post differentiation
day135_raw.tsv
sample name:
201503083-01

tag: disease state

tag: tissue

value: induced pluripotent stem cell-derived cortical neurons

tag: iPSc source

value: fibroblast

tag: reprogramming method

value: Retrovirus

tag: gender

tag: ethnicity


title: Cont 1021_135

description:
day 135 post differentiation
day135_raw.tsv
sample name:
201503085-01


title: ASD 110_135

description:
day 135 post differentiation
day135_raw.tsv
sample name:
201503081-01

value: ASD


title: ASD 725_135

description:
day 135 post differentiation
day135_raw.tsv
sample name:
201503080-01


title: Cont 114_135

description:
day 135 post differentiation
day135_raw.tsv
sample name:
201503084-01


title: AVB_106_AV_NMS

tag: subjectid

tag: visit

tag: group

tag: age at visit (years)

tag: sex (f=female, m=male)

tag: steroids_av (1=yes, 0=no)

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)

tag: rsv positive at av (1=yes, 0=no, 9=not measured)


title: Cont 101_135

description:
day 135 post differentiation
day135_raw.tsv
sample name:
201503082-01


title: ANBL (AGA, non-balding area, bulb) [miRNA-seq]

description: bulb portion of hair follicle

value: hair follicle

tag: tissue section

value: bulb

tag: age

value: range27-45, median 31.9

tag: diagnosis

value: HamiltonNorwood baldness scale score 3-5


title: AVB_103_AV_NMS

value: Child

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)

tag: influenza positive at av (1=yes, 0=no, 9=not measured)

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)

tag: human polyomavirus at av (1=yes, 0=no, 9=not measured)

tag: parainfluenza virus at av (1=yes, 0=no, 9=not measured)

tag: bocavirus at av (1=yes, 0=no, 9=not measured)

tag: enterovirus at av (1=yes, 0=no, 9=not measured)

tag: metapneumovirus at av (1=yes, 0=no, 9=not measured)


title: AVB_108_CV_NMS

tag: subjectid

tag: visit

tag: group

value: Infant

tag: age at visit (years)


title: AVB_102_CV_NMS

tag: sex (f=female, m=male)


title: ASD 134_135

description:
day 135 post differentiation
day135_raw.tsv
sample name:
201503078-01

tag: disease state

tag: tissue

tag: iPSc source

tag: reprogramming method

tag: gender

tag: ethnicity


title: AVB_102_AV_NMS

tag: steroids_av (1=yes, 0=no)

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)

tag: rsv positive at av (1=yes, 0=no, 9=not measured)

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)

tag: influenza positive at av (1=yes, 0=no, 9=not measured)

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)


title: AVB_100_AV_NMS

tag: subjectid

tag: visit

tag: virus positive at av (1=yes, 0=no, 9=not measured)

tag: human polyomavirus at av (1=yes, 0=no, 9=not measured)

tag: parainfluenza virus at av (1=yes, 0=no, 9=not measured)

tag: bocavirus at av (1=yes, 0=no, 9=not measured)

tag: enterovirus at av (1=yes, 0=no, 9=not measured)

tag: metapneumovirus at av (1=yes, 0=no, 9=not measured)


title: ASD 709_135

description:
day 135 post differentiation
day135_raw.tsv
sample name:
201503077-01

tag: disease state

tag: tissue

tag: iPSc source

tag: reprogramming method

tag: gender


title: Cont 114_35

description:
day 35 post differentiation
day35_raw.tsv
sample name:
201415815-01

value: healthy control

tag: ethnicity


title: ASD 110_35

description:
day 35 post differentiation
day35_raw.tsv
sample name:
201415811-01

value: peripheral blood mononuclear cells


title: Cont 574_35

description:
day 35 post differentiation
day35_raw.tsv
sample name:
201415814-01

value: Sendai virus


title: AVB_098_CV_NMS

tag: group

tag: age at visit (years)

tag: sex (f=female, m=male)


title: ASD 725_35

description:
day 35 post differentiation
day35_raw.tsv
sample name:
201415810-01

value: male


title: AVB_095_AV_NMS

tag: subjectid

tag: steroids_av (1=yes, 0=no)

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)

tag: rsv positive at av (1=yes, 0=no, 9=not measured)

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)

tag: influenza positive at av (1=yes, 0=no, 9=not measured)

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)


title: AVB_094_CV_NMS

tag: visit


title: ASD 691_135

description:
day 135 post differentiation
day135_raw.tsv
sample name:
201503079-01

tag: disease state

tag: tissue

value: non-hispanic white


title: ASD 691_35

description:
day 35 post differentiation
day35_raw.tsv
sample name:
201415809-01

tag: iPSc source

tag: reprogramming method


title: AVB_092_AV_NMS

tag: virus positive at av (1=yes, 0=no, 9=not measured)

tag: human polyomavirus at av (1=yes, 0=no, 9=not measured)

tag: parainfluenza virus at av (1=yes, 0=no, 9=not measured)

tag: bocavirus at av (1=yes, 0=no, 9=not measured)

tag: enterovirus at av (1=yes, 0=no, 9=not measured)

tag: metapneumovirus at av (1=yes, 0=no, 9=not measured)


title: AVB_093_CV_NMS

tag: subjectid

value: CV

tag: group

tag: age at visit (years)

tag: sex (f=female, m=male)


title: AVB_093_AV_NMS

value: AV

tag: steroids_av (1=yes, 0=no)

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)

tag: rsv positive at av (1=yes, 0=no, 9=not measured)

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)

tag: influenza positive at av (1=yes, 0=no, 9=not measured)


title: Cont 102_35

description:
day 35 post differentiation
day35_raw.tsv
sample name:
201408367-01

tag: disease state

tag: tissue

value: induced pluripotent stem cell-derived cortical neurons

tag: iPSc source

tag: reprogramming method

tag: gender

tag: ethnicity


title: ASD 709_35

description:
day 35 post differentiation
day35_raw.tsv
sample name:
201402471-03


title: ASD 732_35

description:
day 35 post differentiation
day35_raw.tsv
sample name:
201408343-01


title: AVB_092_CV_NMS

tag: visit


title: AVB_089_AV_NMS

tag: subjectid

tag: virus positive at av (1=yes, 0=no, 9=not measured)

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)

tag: human polyomavirus at av (1=yes, 0=no, 9=not measured)

tag: parainfluenza virus at av (1=yes, 0=no, 9=not measured)

tag: bocavirus at av (1=yes, 0=no, 9=not measured)

tag: enterovirus at av (1=yes, 0=no, 9=not measured)

tag: metapneumovirus at av (1=yes, 0=no, 9=not measured)


title: Cont 101_35

description:
day 35 post differentiation
day35_raw.tsv
sample name:
201408366-01

value: fibroblast


title: AVB_094_AV_NMS

tag: group

tag: age at visit (years)

tag: sex (f=female, m=male)

tag: steroids_av (1=yes, 0=no)

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)

tag: rsv positive at av (1=yes, 0=no, 9=not measured)

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)


title: ASD 732_135

description:
day 135 post differentiation
day135_raw.tsv
sample name:
201503076-01

tag: disease state

tag: tissue

tag: iPSc source

tag: reprogramming method

tag: gender

tag: ethnicity


title: Capture-C of Hoxa1 in Mus musculus: WT rep3

city: Tianjin

first: Dianhao

last: Guo

address: 94 Weijin Road

institute: Nankai University

description: E14_RA-ed_hoxa1_capture-c_combined_interaction.wig

data_processing:
Library strategy: Capture-C
RNA-seq analysis: Clean reads were mapped to Ensemble mm10 using Hisat2 with default parameters. Gene reads were counted by Htseq. Fold changes were computed as the log2 ratio of normalized reads per gene using DEseq2 R package.
Capture-C analysis: The analysis of Capture-C processing step referred to previously reported procedures (Davies, J.O., Telenius, J.M.2016 Nature methods).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include genes count for each Sample and wig

organism: Mus musculus

source_name: embryo, blastocyst embryo, blastocyst

growth_protocol: Mouse ESCs were grown in culture dishes coated with 0.1% gelatin in Glasgow Minimum Essential Medium (GMEM) supplemented with 15% fetal bovine serum (FBS), 100nM nonessential amino acids, 1% sodium pyruvate, 200mM glutamate, 1% penicillin- streptomycin, 50uM β-mercaptoethanol, 10ng/mL LIF, 1uM PD0325901 (a MEK inhibitor) and 3uM CHIR99021 (a GSK inhibitor). The medium was replaced every 2-3 days (32,33)

extract_protocol:
1. For RNA -seq: cells were lysed with Trizol reagent (Life Technologies) and RNA was extracted according to the manufacturer's instructions. 2. For Capture-C：Briefly, cells were fixed with 1% (vol/vol) formaldehyde for 10 min at room temperature, quenched with 125 mM glycine in PBS, and then lysed in cold lysis buffer (10 mM Tris–HCl, pH7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.2% NP-40, 1× complete protease inhibitor cocktail (Roche)). Chromatin was digested with DpnII (New England Biolabs) at 37°C overnight. Fragments were then diluted and ligated with T4 DNA ligase (Takara) at 16°C overnight. Cross-linking was reversed by overnight incubation at 60°C with proteinase K (Bioline). Then 3C libraries were purified by phenol-chloroform followed by chloroform extraction and ethanol-precipitated at −80°C overnight. Sequencing libraries were prepared from 10μg of the 3C library by sonication to an average size of 200 ~300 bp and indexed using NEBnext reagents (New England Biolabs), according to the manufacturer's protocol. Enrichment of 2μg of an indexed library incubated with 3uM of a pool of biotinylated oligonucleotides (probe sequences are listed in Supplementary Table 7) was performed using the SeqCap EZ Hybridization reagent kit (#05634261001, Roche/NimbleGen), following the manufacturer's instructions. Two rounds of capture employing 48~72 and 24 hr hybridizations, respectively, were used. Correct library size was confirmed by agarose gel electrophoresis, and DNA concentrations were determined using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). All sequencing was performed on Hi-Seq 2500 platforms using paired 150 bp protocols (Illumina).
The Capture-C library was constructed with NEBNext DNA Library Prep Master Mix Set for Illumina (NEB).

treatment_protocol: For RA treatment, ESCs were induced to differentiate by LIF/2i withdrawal and addition of 2uM RA (Sigma). Culture medium was replaced every day.

tag: genotype/variation

value: WT

tag: cell type

value: Embryonic stem cell

tag: strain

tag: treatment

value: RA induced differentiation

tag: cell line


title: AVB_088_CV_NMS

tag: subjectid

tag: visit

tag: group

tag: age at visit (years)

tag: sex (f=female, m=male)


title: AVB_089_CV_NMS


title: AVB_095_CV_NMS


title: AVB_097_AV_NMS

tag: steroids_av (1=yes, 0=no)

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)

tag: rsv positive at av (1=yes, 0=no, 9=not measured)

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)

tag: influenza positive at av (1=yes, 0=no, 9=not measured)

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)

tag: human polyomavirus at av (1=yes, 0=no, 9=not measured)

tag: parainfluenza virus at av (1=yes, 0=no, 9=not measured)

tag: bocavirus at av (1=yes, 0=no, 9=not measured)

tag: enterovirus at av (1=yes, 0=no, 9=not measured)

tag: metapneumovirus at av (1=yes, 0=no, 9=not measured)


title: AVB_088_AV_NMS

tag: subjectid

tag: virus positive at av (1=yes, 0=no, 9=not measured)


title: AVB_087_AV_NMS

tag: visit

tag: group


title: AVB_086_CV_NMS

tag: age at visit (years)

tag: sex (f=female, m=male)


title: AVB_086_AV_NMS

tag: steroids_av (1=yes, 0=no)

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)


title: Capture-C of Hoxa1 in Mus musculus: WT rep1

tag: genotype/variation

tag: cell type

tag: strain

tag: treatment

tag: cell line


title: Cont 1021_35

description:
day 35 post differentiation
day35_raw.tsv
sample name:
201415808-01

tag: disease state

tag: tissue

tag: iPSc source

tag: reprogramming method

tag: gender

tag: ethnicity


title: AVB_085_AV_NMS

tag: subjectid

tag: visit

tag: rsv positive at av (1=yes, 0=no, 9=not measured)

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)

tag: influenza positive at av (1=yes, 0=no, 9=not measured)

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)

tag: human polyomavirus at av (1=yes, 0=no, 9=not measured)

tag: parainfluenza virus at av (1=yes, 0=no, 9=not measured)

tag: bocavirus at av (1=yes, 0=no, 9=not measured)

tag: enterovirus at av (1=yes, 0=no, 9=not measured)

tag: metapneumovirus at av (1=yes, 0=no, 9=not measured)


title: AVB_084_CV_NMS

tag: group

tag: age at visit (years)

tag: sex (f=female, m=male)


title: AVB_084_AV_NMS

tag: steroids_av (1=yes, 0=no)


title: ASD 134_35

description:
day 35 post differentiation
day35_raw.tsv
sample name:
201408342-01

tag: disease state

value: ASD

tag: tissue

tag: iPSc source

tag: reprogramming method

tag: gender

tag: ethnicity


title: AVB_082_CV_NMS

tag: subjectid

tag: visit


title: AVB_083_CV_NMS


title: AVB_083_AV_NMS

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)

tag: rsv positive at av (1=yes, 0=no, 9=not measured)

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)

tag: influenza positive at av (1=yes, 0=no, 9=not measured)

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)

tag: human polyomavirus at av (1=yes, 0=no, 9=not measured)


title: AVB_073_AV_NMS

tag: group

tag: age at visit (years)

tag: sex (f=female, m=male)

tag: virus positive at av (1=yes, 0=no, 9=not measured)

tag: parainfluenza virus at av (1=yes, 0=no, 9=not measured)

tag: bocavirus at av (1=yes, 0=no, 9=not measured)

tag: enterovirus at av (1=yes, 0=no, 9=not measured)

tag: metapneumovirus at av (1=yes, 0=no, 9=not measured)


title: AVB_071_AV_NMS

tag: subjectid

tag: steroids_av (1=yes, 0=no)


title: AVB_073_CV_NMS

tag: visit


title: AVB_069_AV_NMS

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)

tag: rsv positive at av (1=yes, 0=no, 9=not measured)


title: Capture-C of Hoxa1 in Mus musculus: WT rep2

tag: genotype/variation

tag: cell type

tag: strain

tag: treatment

tag: cell line


title: AVB_059_AV_NMS

tag: group

tag: age at visit (years)

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)

tag: influenza positive at av (1=yes, 0=no, 9=not measured)

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)

tag: human polyomavirus at av (1=yes, 0=no, 9=not measured)


title: AVB_058_AV_NMS

tag: subjectid

tag: sex (f=female, m=male)

tag: virus positive at av (1=yes, 0=no, 9=not measured)

tag: parainfluenza virus at av (1=yes, 0=no, 9=not measured)

tag: bocavirus at av (1=yes, 0=no, 9=not measured)

tag: enterovirus at av (1=yes, 0=no, 9=not measured)

tag: metapneumovirus at av (1=yes, 0=no, 9=not measured)


title: AVB_058_CV_NMS

tag: visit


title: AVB_040_AV_NMS

tag: steroids_av (1=yes, 0=no)

tag: co-infection (1=1 infection, 2= 2 infections, 3= 3 infections, 4= 4 infections)

tag: rsv positive at av (1=yes, 0=no, 9=not measured)


title: AVB_049_AV_NMS

tag: group

tag: age at visit (years)


title: AVB_054_AV_NMS

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: adenovirus positive at av (1=yes, 0=no, 9=not measured)


title: AVB_043_AV_NMS

tag: influenza positive at av (1=yes, 0=no, 9=not measured)

tag: human coronavirus at av (1=yes, 0=no, 9=not measured)


title: JZ8

city: New York

first: Robert

last: Roeder

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
RNAseq raw sequencing reads were mapped using BWA software with default settings.
Uniquely mapped reads were retained for further analysis.
Gene expression were calculated by counting reads on exonic regions of genes using in house python program.
EdgeR software was then used to compare differential gene expressions between samples.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using in house python code to count reads in 10bps window size. Reads were then normalized by the total library size to obtain normalized read counts.

source_name: obstructive azoospermia patients haploid cells

growth_protocol: PSC lines were maintained in chemically defined Essential 8 medium (StemCell Technology). Cells were passaged every 5-7 days and dissociated by 1 mg/mL Collagenase IV (Millipore). PSCs differentiation into germ cells in differentiation medium when they reached 80-90% confluence (components of differentiation medium below all come from Invitrogen/Gibco, unless otherwise noted): α-MEM, 2 mM L-glutamine, 1X Insulin-Transferrin-Selenium-X, 0.2% BSA or substituted by 0.2-3% KnockOut™ SR XenoFree CTS™ (Gibco), 1 ng/mL recombinant human -FGF, 20 ng/mL recombinant human GDNF (Sino Biological Inc.), 0.2% chemically defined lipid concentrate and 200 μg/mL vitamin C (Sigma).

extract_protocol:
Cells were collected in Trizol and total RNA were extracted
NuGen Ultralow Library System V2
Hiseq-2500 Paired-end sequencing

treatment_protocol: The cells were cultured at 37 °C in a humidified 5% CO2 atmosphere.

tag: cell type

value: Haploid isolated from two obstructive azoospermia patients (in vivo haploid)


title: JZ7

source_name: PSC-derived haploid cells

value: Haploid from day 12 of PSC differentiation (in vitro haploid)


title: JZ9

source_name: obstructive azoospermia patients CD90+ spermatogonia cells

value: CD90 positive cells isolated from biopsied human testes of two obstructive azoospermia patients (CD90-1)


title: JZ6

source_name: PSC-derived SLCs

value: SLCs from day 12 of PSC differentiation with PLZF overexpression (OE-2)


title: JZ5

value: SLCs from day 12 of PSC differentiation with PLZF overexpression (OE-1)


title: JZ10

source_name: obstructive azoospermia patients CD91+ spermatogonia cells

value: CD90 positive cells isolated from biopsied human testes of two obstructive azoospermia patients (CD90-2)


title: E14 mESC WGBS

city: Oxford

first: Gergana

last: Velikova

address: Roosevelt Drive

country: United Kingdom

institute: University of Oxford

description: whole-genome bisulfite sequencing

data_processing:
WGBS and TAPS data were paired-end trimmed with Trim Galore! (v0.4.4) employing cutadapt (v1.5) removing reads with Phred score ≤ 20, and shorter length after adapter trimming than 35 bp.
The WGBS quality trimmed reads are mapped to the bisulfite-converted combined mm9 and lambda genomes with added phiX (sequence from iGENOMES Illumina) using Bismark (v0.19) wrapper around Bowtie2 (v2.2.3). The trimmed TAPS reads were mapped to an artificial genome combining spike-ins and mm9 with BWA mem (v.0.7.15) default end-to-end mapping paired-end settings.
WGBS data was filtered using Bismark filter_non_conversion tool. TAPS reads were split into coming from the original top (OT) and original bottom (OB) strands with a python3 script (MF-filter.py)
Both datasets were deduplicated with Picard (v1.119) MarkDuplicates.
Methylation calling on WGBS data with Bismark after sorting the reads by read name. Any overlaps between shorter than twice the read length (160bp) paired-end reads were removed with BamUtil tool clipOverlap on the deduplicated OT and OB .bam files. The overlap removed files were then indexed with Samtools (v1.31) and the separate runs were merged at this stage. The OT and OB reads were split by chromosome using a python3 script (MF-chrom_splitter.py), followed by the application of mpileup on each chromosome bam. The modified bases were counted and output using MF-caller_MOD.py on the newly generated vcf files.
Genome_build: mm9
Supplementary_files_format_and_content: CpG modification values bedGraph

source_name: E14 mESC

growth_protocol: E14 mESC cells were cultured on gelatin-coated 100 mm plates in Dulbecco’s Modified Eagle Medium (DMEM) (Invitrogen) supplemented with 15 % FBS (GIBCO), 2 mM L-glutamine (Gibco), 1% non-essential amino acids (Gibco), 1 % penicillin/streptavidin (Gibco), 0.1 mM β-mercaptoethanol (Sigma), 1000 units/mL LIF (Millipore), 1 μM PD0325901 (Stemgent), and 3 μM CHIR99021 (Stemgent). Cultures were maintained at 37°C and 5% CO2 and passaged every 2 days.

extract_protocol:
Confluent E14 mESC were dissociated from the plates and collected by centrifugation for 5 min at 1000 xg. Genomic DNA was extracted from 40 mln cells with Quick-DNA Plus kit (Zymo Research) according to manufacturer’s protocol
For Whole Genome TAPS, 1 μg of mESC gDNA was spiked-in with control oligos, fragmented with Covaris M220 instrument and size-selected to 200-400 bp on Ampure XP beads. Subsequently, DNA underwent oxidation with NgTet1. End-repaired and A-tailing reaction and adapter ligation were prepared with KAPA HyperPlus kit according to manufacturer’s protocol and sample was reduced with pic-borane. Final sequencing library was amplified with KAPA Hifi Uracil Plus Polymerase for 6 cycles and cleaned-up on 1X Ampure beads. Whole-genome TAPS sequencing library was pair-end 75 bp sequenced on NextSeq Illumina instrument. For Whole Genome Bisulfite Sequencing (WGBS), 200 ng of mESC gDNA spiked-in with 0.5% of unmethylated lambda DNA were fragmented to 200-400 bp. End-repaired and A-tailing reaction and ligation of methylated adapter (NextFlex) were prepared with KAPA HyperPlus kit (Kapa Biosystems) according to manufacturer’s protocol. Subsequently, DNA underwent bisulfite conversion with EpiTect Bisulfite Kit (Qiagen) according to manufacturer’s protocol. Final library was amplified with KAPA Hifi Uracil Plus Polymerase (Kapa Biosystems) for 6 cycles and cleaned-up on 1X Ampure beads. WGBS sequencing library was pair-end 75 bp sequenced on NextSeq Illumina instrument.

value: E14 mouse embryonic stem cells

tag: passages


title: RNA-Seq of Mus musculus: EN-KO+Hoxa1 rep2

description:
E14_RNA_seq_htseq_gene_count_martix.xls
A1-E32

data_processing:
RNA-seq analysis: Clean reads were mapped to Ensemble mm10 using Hisat2 with default parameters. Gene reads were counted by Htseq. Fold changes were computed as the log2 ratio of normalized reads per gene using DEseq2 R package.
Capture-C analysis: The analysis of Capture-C processing step referred to previously reported procedures (Davies, J.O., Telenius, J.M.2016 Nature methods).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include genes count for each Sample and wig

tag: genotype/variation

value: HoxA1 enhancer-KO + Hoxa1

tag: strain

tag: treatment

tag: cell line


title: TAPS

description: whole-genome TAPS sequencing


title: JZ4

value: SLCs from day 12 of PSC differentiation (12d-2)


title: JZ3

value: SLCs from day 12 of PSC differentiation (12d-1)


title: RNA-Seq of Mus musculus: EN-KO+Hoxa1 rep1

description:
E14_RNA_seq_htseq_gene_count_martix.xls
A1-E31


title: RNA-Seq of Mus musculus: EN-KO rep2

description:
E14_RNA_seq_htseq_gene_count_martix.xls
E3-402

value: HoxA1 enhancer-KO


title: RNA-Seq of Mus musculus: EN-KO rep1

description:
E14_RNA_seq_htseq_gene_count_martix.xls
E3-401


title: RNA-Seq of Mus musculus: WT rep-2

description:
E14_RNA_seq_htseq_gene_count_martix.xls
WT-E32


title: JZ1

source_name: PSC

value: pluripotent stem cells (PSC-1)


title: RNA-Seq of Mus musculus: WT rep-1

description:
E14_RNA_seq_htseq_gene_count_martix.xls
WT-E31


title: JZ2

value: pluripotent stem cells (PSC-2)


title: S9_CEBPaKO

city: Berlin

first: Achim

last: Leutz

address: Robert-Rössle-Str. 10

department: Cancer Research

country: Germany

institute: MDC Berlin

data_processing:
Read Alignment with Bowtie 2 (v. 2.2.9)
RSEM (v. 1.2.31)-based quantification
Differential expression analysis with DESeq2 (v.1.14.1) package in R with LRT method
Genome_build: mm9
Supplementary_files_format_and_content: The NormalizedCounts were generated with DESeq.

growth_protocol: Small intestinal crypts were isolated and cultured as 3D organoids as described by Sato et al. (Nature. 2009 May 14;459(7244):262-5). Recombination was induced by 400nM 4-Hydroxytamoxifen for two consecutive days.

extract_protocol:
RNA was purified with Purification Kit (Roboklon), according to the manufacturer’s instructions.
Sequencing libraries were prepared using TruSeq Stranded mRNA kit (Illumina)

tag: tissue

value: Small intestinal crypts

value: CEBPaKO


title: S7_CEBPaKO


title: S1_Control

value: wildtype


title: S3_Control


title: S8_CEBPaKO


title: S2_Control


title: Treated replica 2

type: RNA

city: Porto

first: Rune

last: Matthiesen

address: Rua Dr. Roberto Frias s/n

country: Portugal

institute: IPATIMUP

description: cells were plated (1 × 105 cells/well in 6-well plates), incubated for 24 h to allow adhesion and then treated with of TXA1.HCl

scan_protocol: For expression analysis, quality of the RNA isolated from NCI-H460 cells was carried out in RNA 6000 Nano LabChip using BioAnalyzer 2100 (Agilent).  For microarray cDNA analysis, 100 ng of total RNA for each sample was used in GeneChip Human Genome Arrays (Affymetrix), as an outsorced service to the Gene Expression Unit at Instituto Gulbenkian de Ciência.

data_processing: The data were collectively analyzed by using the R package “AFFYLMGUI” (http://www.bioconductor.org). Background adjustment was done by using robust multichip average (RMA)

label: biotin

source_name: Treated replica 2

growth_protocol: The non-small lung cancer (NSCLC) cell line NCI-H460 (a kind gift from NCI, Bethesda, USA) used in this study was genotyped and routinely cultured

extract_protocol: Total RNA was extracted from NCI-H460 frozen xenografted cells using TRI Reagent® (Ambion), according to manufacturer´s instructions. For this, tissue samples were mechanically disrupted and homogenized in TRI Reagent® using a tissue homogenizer (IKA-Werke).  Total RNA (500 ng) was treated with TurboDNase I (Ambion) for genomic DNA removal. For total RNA extraction from NCI-H460 cells, the Pure Link RNA Mini kit (Thermo Fisher Scientific) was used according the manufacturer's instructions. RNA concentration and quality were analyzed using the NanoDrop ND-1000 Spectrophotometer (Thermo Scientific).

treatment_protocol: For each experiment, cells were plated (1 × 105 cells/well in 6-well plates), incubated for 24 h to allow adhesion and then treated with 6.9 µM of TXA1.Hcl  for 24 h. Control treatments consisting of untreated cells (Blank) or cells treated with equivalent volumes of H20 (Control).

tag: protocol


title: Treated replica 1

source_name: Treated replica 1

label_protocol: For expression analysis, quality of the RNA isolated from NCI-H460 cells was carried out in RNA 6000 Nano LabChip using BioAnalyzer 2100 (Agilent).  For microarray cDNA analysis, 100 ng of total RNA for each sample was used in GeneChip Human Genome Arrays (Affymetrix)

value: cells were plated (1 × 105 cells/well in 6-well plates), incubated for 24 h to allow adhesion and then treated with of TXA1.HCl


title: Sulfisoxazole (SFX) treated MDA-MB231 exsomes (24 h treatment)_rep1

city: Daegu

first: Moon-Chang

last: Baek

address: Gukchebosang-ro 680

institute: Kyungpook National University

description: miRNA gene expression data of exosomes derived from SFX-treated MDA-MB231

hyb_protocol: Labeled targets were hybridized to the Affymetrix miRNA 4.0 chip, GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC).

data_processing: The CEL files import, miRNA level RMA+DABG-All analysis and result export using Affymetrix® Power Tools (APT) Software.

label: Biotin

source_name: Exosomes from Sulfisoxazole (SFX) treated MDA-MB231 (24 h treatment)_rep1

label_protocol: RNA was labeled using Affymetrix® FlashTag™ Biotin HSR RNA Labeling Kit

growth_protocol: MDA-MB231 cells were grown under following condition: Dulbecco Modified Eagle Medium (DMEM) with 10 % fetal bovine serum (FBS) and 1% antibiotic and antimycotic agent.

extract_protocol: Exosomes were isolated by Exoquick reagent (SBI). Total RNA was extracted using Total exosome RNA and protein isolation kit. Experiment was performed according to the manufacturer's instruction

treatment_protocol: Cells were treated 100μM of SFX for 24 hours under serum-free condition.

value: mammary gland/breast

value: epithelial

tag: disease state

value: adenocarcinoma/derived from metastatic site

value: SFX


title: SMMC-7721 Negative Control, biological rep3

city: Xi'an

first: Xiang

last: Zhang

address: Changle west road #169

institute: the Fourth Military Medical University

description: Gene expression data from SMMC-7721 transfected by Negative control mimics.

hyb_protocol: Following fragmentation, aRNAs were hybridized for 16 hr at 45C on Affymetrix PrimeView™ Human Gene Expression Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: The data were analyzed with Affymetrix GeneChip Command Console and Genespring using Affymetrix default analysis settings and global scaling as normalization method.

source_name: SMMC-7721 Negative Control

label_protocol: Transfer 30µL of IVT Master Mix to each (30µL) double-stranded cDNA sample.

growth_protocol: SMMC-7721 cell lines were maintained in RPMI-1640 medium (GIBCO) supplemented with 10% fetal bovine serum (FBS).  Cells were routinely grown to 80% confluence at 37°C in 5% CO2.

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

treatment_protocol: SMMC-7721 cells at 70–80% confluence in 6-well plates were transfected using Lipofectamine 2000 (Invitrogen). Negative control mimics or miR-26a mimics (100nM) were transfected in each well. Cell extracts were prepared 48 h after transfection.


title: Control replica 1

description: Control treatments consisting of untreated cells (Blank) or cells treated with equivalent volumes of H20 (Control)

hyb_protocol: For microarray cDNA analysis, 100 ng of total RNA for each sample was used in GeneChip Human Genome Arrays (Affymetrix)

source_name: Control replica 1


title: SMMC-7721 Negative Control, biological rep1


title: Treated replica 3

source_name: Treated replica 3


title: Control replica 2

source_name: Control replica 2

value: Control treatments consisting of untreated cells (Blank) or cells treated with equivalent volumes of H20 (Control)


title: SMMC-7721 miR-26a over-expression, biological rep3

description: Gene expression data from SMMC-7721 transfected by miR-26a mimics.

source_name: SMMC-7721 miR-26a over-expression


title: SMMC-7721 Negative Control, biological rep2


title: DMSO treated MDA-MB231 exosomes (24 h treatment)_rep1

description: miRNA gene expression data of exosomes derived from DMSO (vehicle)-treated MDA-MB231

source_name: Exosomes from DMSO treated MDA-MB231 (24 h treatment)_rep1

value: control


title: Control replica 3

source_name: Control replica 3


title: SMMC-7721 miR-26a over-expression, biological rep1


title: SMMC-7721 miR-26a over-expression, biological rep2


title: PHBI_085

status: Public on Dec 23 2018

city: Indianapolis

last: Stearman

state: IN

address: 950 W Walnut St

department: Medicine/Pulmonary

institute: Indiana Univeristy School of Medicine

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: GC-RMA and batch-remove algorthims as implemented in Partek Genomics Suite v 6.6

source_name: Lung_all PAH

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250ng total RNA  250 ng of total RNA was processed using the Whole Transcript Expression kit (Ambion) and Whole Transcript Terminal Labeling kit (Affymetrix).  250 ng of total RNA was processed using the Whole Transcript Expression kit (Ambion) and Whole Transcript Terminal Labeling kit (Affymetrix).

growth_protocol: Human lung tissue preserved in RNALater (Ambion) in histology cassettes at time of explant. Stored at 4C up to 6 months and then cassettes were spun at low speed centrifugation, wrapped in foil, and stored at -20C

extract_protocol: Approximately 30-50mg of tissue was homogenized in Trizol with a Polytron homogenizer, and purified as recommended by supplier. Total RNA >200 nucleotides in length was purified using Qiagen RNEasy columns using their standard protocol.

treatment_protocol: Human lung tissue obtained at time of transplant for end-stage PAH disease (all PAH) or from donors which did not have suitable match (Failed Donor)

value: Lung

value: all PAH

value: FPAH

tag: Sex

value: Female


title: PHBI_078

value: IPAH

value: Male


title: PHBI_080


title: PHBI_084


title: PHBI_079

value: Other


title: PHBI_082

value: FD

value: Failed Donor


title: PHBI_077


title: PHBI_076


title: PHBI_083


title: PHBI_068


title: PHBI_069


title: PHBI_067


title: PHBI_063


title: PHBI_064


title: PHBI_073


title: PHBI_062


title: PHBI_065

value: APAH


title: PHBI_061


title: PHBI_075


title: PHBI_071


title: PHBI_074


title: PHBI_072


title: PHBI_059


title: PHBI_060


title: PHBI_070


title: PHBI_057


title: PHBI_058


title: PHBI_055


title: RL-/-  low rep1

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

institute: Institute of Molecular Biology (IMB)

description:
replicate 1
212

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol using an Illumina BeadArray Reader.

data_processing: The data was normalised using quantile normalisation with Illumina GenomeStudio.

source_name: bone marrow

label_protocol: Biotin-aRNA was made using the TargetAmp-Nano Labeling kit for Illumina Expression BeadChip from Epicentre.

growth_protocol: For the isolation of monocytes, femurs and tibiae were taken, bone marrow was flushed out with RPMI 1640 +1% FCS, red blood cell lysis was performed and cells were filtered through a 70 µm mesh to obtain a single cell suspension.

extract_protocol: RNA was isolated using RNeasy mini kit from Qiagen, RNA concentration was increased by evaporation for 18 min in a SpeedVac system. RNA integrity was analyzed using the Agilent RNA 6000 Nano total RNA kit and an Agilent 2000 Bioanalyzer system. RNA was transcribed into cDNA with SuperScript III Reverse Transcriptase (ThermoFisher Scientific).

treatment_protocol: After Fc receptor block (CD16/32), cells were labelled with CD3e-PE, CD11b-Alexa488, CD19-PE, CD49b-PE, CD117-PE, Ly6C-PerCP-Cy5.5, Ly6G-PE  and NK1.1-PE for 30 min on ice in the dark. DAPI was added shortly before measurements. Monocyte subsets were sorted by a MoFlo Legacy cell sorter from Beckman Coulter.

tag: age

value: 8-10 weeks

value: monocytes

tag: genotype

value: low


title: PHBI_050


title: PHBI_053


title: RL-/-  low rep2

description:
replicate 2
222


title: PHBI_054


title: PHBI_056


title: PHBI_066


title: PHBI_052


title: RL-/-  low rep6

description:
replicate 6
292


title: PHBI_051


title: RL-/-  low rep3

description:
replicate 3
242


title: PHBI_043


title: PHBI_049


title: PHBI_048


title: PHBI_041


title: RL-/-  high rep3

description:
replicate 3
241

value: high


title: PHBI_044


title: RL-/-  low rep4

description:
replicate 4
252


title: PHBI_047


title: PHBI_045


title: RL-/-  high rep2

description:
replicate 2
221


title: PHBI_037


title: RL-/-  high rep6

description:
replicate 6
291


title: PHBI_036


title: RL-/-  high rep1

description:
replicate 1
211


title: PHBI_035


title: PHBI_040


title: PHBI_042


title: PHBI_046


title: RL-/-  high rep4

description:
replicate 4
251


title: PHBI_038


title: PHBI_034


title: PHBI_032


title: PHBI_033


title: SRL-/- low rep4

description:
replicate 4
152

value: SRL-/-


title: SRL-/- low rep3

description:
replicate 3
142


title: PHBI_031


title: SRL-/- low rep1

description:
replicate 1
122


title: RL-/-  high rep5

description:
replicate 5
261


title: PHBI_029


title: PHBI_030


title: PHBI_023


title: PHBI_028


title: PHBI_026


title: PHBI_027


title: PHBI_024


title: Root RNA seq Lib 3

city: Ramat Gan

first: Ofir

last: Hakim

address: Bar-Ilan University

country: Israel

institute: Bar-Ilan University

data_processing:
Sequenced reads were aligned to the TAIR10 Arabidopsis genome using STAR.
Htseq was used to count reads on genes and rpkm values were calculated using EdgeR
Genome_build: TAIR10
Supplementary_files_format_and_content: text file with RPKM

source_name: roots

growth_protocol: Arabidopsis plant (Col-0) was grown under long day conditions at 22C on vertical agar plates. Roots were harvested from 14-day old plants, and RNA-seq was performed.

extract_protocol:
RNA was extracted using TRIZOL (Life Technologies) reagent and cleaned with RNA Clean & Concentrator™-5 (Zymo).
Libraries were prepared for NGS sequencing with NEBNext RNA library prep kit (module E7530-E7490).

value: roots

tag: background ecotype

value: expressing INTACT

value: 14 days


title: SRL-/- high rep6

description:
replicate 6
171


title: SRL-/- high rep5

description:
replicate 5
161


title: SRL-/- low rep2

description:
replicate 2
132


title: SRL-/- high rep3

description:
replicate 3
141


title: PHBI_020

value: Lung


title: PHBI_021

value: all PAH


title: SRL-/- high rep2

description:
replicate 2
131


title: PHBI_018

value: Female


title: PHBI_019


title: PHBI_016

value: IPAH


title: PHBI_017

value: Male


title: PHBI_025


title: PHBI_015


title: PHBI_022


title: SRL-/- high rep4

description:
replicate 4
151


title: PHBI_012


title: PHBI_011


title: PHBI_014


title: SRL-/- high rep1

description:
replicate 1
121


title: PHBI_013


title: PHBI_010

value: WHO 4


title: L-/- low rep6

description:
replicate 6
372


title: L-/- low rep5

description:
replicate 5
362


title: PHBI_009


title: HCT-8_C.parvum uninfection_12h_rep3

city: Zhengzhou

first: Chenrong

last: Wang

state: Henan

address: 95 Wenhua Road

department: College of Animal Science and Veterinary Medicine

institute: Henan Agricultural University

description: HCT-8 infected by heat-inactivated (100℃, 5 min) C.parvum oocysts was as a control group at 12h

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) . On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 　L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.  After RNA hybridization, tag-conjugating Cy3 dye were circulated through the microfluidic chip for dye staining.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression)

source_name: HCT-8 cell

label_protocol: Labeling of total RNA was performed according to the protocol from LC Sciense for a single-color experiment with modification.

growth_protocol: Human ileocecal adenocarcinoma cells (HCT-8; ATCC, Manassas, VA) were cultured and maintained in Dulbecco’s modiﬁed Eagle’s medium (DMEM) medium supplemented with 10% fetal bovine serum, 4 mmol/L L-glutamine, 100 U/ml penicillin, and 100 U/ml streptomycin, and then held at 37℃ in a humidiﬁed 5% CO2 incubator.

extract_protocol: At 4 and 12 h post-infection, cells were washed three times with PBS, and 1 ml TRIZOL reagent (Invitrogen, Carlsbad, CA, USA) was added to each well. Total RNA was isolated according to the manufacturer’s protocols.

treatment_protocol: Monolayers in six well cell cultrue cluster were inoculated with purified oocysts (1×107/well) in DMEM. Heat-inactivated (100℃, 5 min) oocysts were used as controls.

value: Human ileocecal adenocarcinoma


title: PHBI_007


title: PHBI_006


title: WT iWAT, biological rep3

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

hyb_protocol: Following fragmentation, 12.5 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were quantified with the Factor Analysis for Robust Microarray Summarization (FARMS) method, using the statistical language R (R-2.14.0) and Bioconductor 2.9.

source_name: inguinal white adipose tissue excised from WT mouse

label_protocol: biotinylated aRNA was obtained from 100 ng of purified total RNA using a GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated from the tissues and cells with RNeasy Lipid Tissue Mini Kit (Qiagen K.K., Tokyo, Japan), in accordance with the manufacturer’s instructions.

treatment_protocol: Excised inguinal white adipose tissue sample wassnap frozen in liquid nitrogen.

tag: strain background

value: wild type

tag: gender

value: 12 weeks

value: inguinal white adipose tissue


title: WT iWAT, biological rep2


title: L-/- low rep3

description:
replicate 3
342

value: 8-10 weeks

value: monocytes


title: PHBI_004


title: HCT-8_C.parvum uninfection_12h_rep1

description: HCT-8 infected by heat-inactivated (100℃, 5 min)C.parvum oocysts was as a control groupat 12h


title: HCT-8_C.parvum uninfection_12h_rep2

description: HCT-8 infected by heat-inactivated (100℃, 5 min) C.parvum oocysts was as a control groupl at 12h


title: L-/- low rep1

description:
replicate 1
312

value: low


title: HCT-8_C.parvum infection_12h_rep3

description: HCT-8 infected by activated C.parvum oocysts was as a experimental group at 12h


title: L-/- low rep2

description:
replicate 2
332


title: PHBI_005

value: APAH


title: L-/- low rep4

description:
replicate 4
352


title: LPA4-KO iWAT, biological rep4

source_name: inguinal white adipose tissue excised from LPA4-KO mouse

value: lysophosphatidic acid receptor 4-deficient (Lpar4 -/Y)


title: WT iWAT, biological rep4


title: PHBI_002


title: HCT-8_C.parvum infection_12h_rep2


title: L-/- high rep4

description:
replicate 4
351

value: high


title: LPA4-KO iWAT, biological rep3


title: L-/- high rep5

description:
replicate 5
361


title: WT iWAT, biological rep1


title: PHBI_003


title: L-/- high rep6

description:
replicate 6
371


title: PHBI_001


title: HCT-8_C.parvum infection_12h_rep1


title: PHBI_008


title: LPA4-KO iWAT, biological rep2


title: HCT-8_C.parvum uninfection_4h_rep3

description: HCT-8 infected by heat-inactivated (100℃, 5 min)C.parvum oocysts was as a control group at 4h


title: Fubp1 shRNA 2

city: Frankfurt

first: Daniela

last: Krause

address: Paul-Ehrlich-Straße 42-44

institute: Georg-Speyer-Haus

description:
ReadCounts_DeSeqRes.csv
p329sCML14

data_processing:
CASAVA 1.8
Data were analyzed for differential expression using DESeq2 (version 1.18.1)
Supplementary_files_format_and_content: comma separated file contains raw read counts for each gene and sample as well as results from differential analysis using DESeq2.

source_name: Bone marrow Lineage- BCR-ABL1+ shRNA+

extract_protocol:
Lineage- BCR-ABL1-RFP+ shRNA-Venus+ DAPI- cells from bone marrow of CML mice were sorted directly into TRIzol.
500 ng were used as start Material for library construction. The TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (Cat. No. RS-122-2201) and TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Cat. No. RS-122-2301) were used according to manuf. Recommendations
TruSeq total stranded RNA Seq approach

value: Fubp1 knockdown

value: Bone marrow


title: Fubp1 shRNA 4

description:
ReadCounts_DeSeqRes.csv
p329sCML16


title: Fubp1 shRNA 1

description:
ReadCounts_DeSeqRes.csv
p329sCML13


title: Fubp1 shRNA 3

description:
ReadCounts_DeSeqRes.csv
p329sCML15


title: LPA4-KO iWAT, biological rep1


title: Scrambled shRNA 4

description:
ReadCounts_DeSeqRes.csv
p329sCML12

value: scrambled control


title: HCT-8_C.parvum uninfection_4h_rep1

description: HCT-8 infected by heat-inactivated (100℃, 5 min) C.parvum oocysts was as a control group at 4h


title: L-/- high rep3

description:
replicate 3
341


title: HCT-8_C.parvum infection_4h_rep3

description: HCT-8 infected by activated C.parvum oocysts was as a experimental group at 4h


title: WT eWAT, biological rep4

source_name: epididymal white adipose tissue excised from WT mouse

treatment_protocol: Excised epididymal white adipose tissue sample wassnap frozen in liquid nitrogen.

value: male

value: epididymal white adipose tissue


title: L-/- high rep2

description:
replicate 2
331


title: WT eWAT, biological rep3


title: Scrambled shRNA 2

description:
ReadCounts_DeSeqRes.csv
p329sCML10


title: HCT-8_C.parvum infection_4h_rep2


title: Scrambled shRNA 3

description:
ReadCounts_DeSeqRes.csv
p329sCML11


title: L-/- high rep1

description:
replicate 1
311


title: WT eWAT, biological rep1


title: LPA4-KO eWAT, biological rep4

source_name: epididymal white adipose tissue excised from LPA4-KO mouse


title: HCT-8_C.parvum uninfection_4h_rep2


title: LPA4-KO eWAT, biological rep2


title: LPA4-KO eWAT, biological rep3


title: LPA4-KO eWAT, biological rep1


title: WT eWAT, biological rep2


title: HCT-8_C.parvum infection_4h_rep1


title: Mid-trimester placenta_rep1 (RNA-seq)

status: Public on Dec 22 2018

city: New Brunswick

first: Bingbing

state: New Jersey

address: 125 Paterson St Room 2143

institute: Rutgers RWJMS

data_processing:
Torrent suite software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Output of the Cuffnorm software
Genome_build: hg18
Supplementary_files_format_and_content: Normalized counts in FPKM values.

source_name: Placenta

growth_protocol: Placental cytotrophoblast (CTB) were purified and maintained at 37C and 5% CO2 at least for 48 hr for spontaneous syncytialization prior to further analysis.

extract_protocol:
Total RNAs were extracted from 4 individual placentas at either mid-trimester or term pregnancy with use of Trizol method.
RNA libraries were prepared for sequencing using standard IonTorrent.

treatment_protocol: Not applicable.

value: placenta

value: Cytotrophoblast

tag: Stage

value: Mid-trimester


title: Mid-trimester placenta_rep4 (RNA-seq)


title: Term placenta_rep4 (RNA-seq)

value: Term


title: Term placenta_rep3 (RNA-seq)


title: Mid-trimester placenta_rep2 (RNA-seq)


title: Term placenta_rep2 (RNA-seq)


title: Term placenta_rep1 (RNA-seq)


title: AC non-stretched hiPS-derived cardiomyocytes, repl. 2

city: Bologna

first: Camilla

last: Luni

address: Via Terracini 28

department: DICAM

country: Italy

institute: University of Bologna

data_processing:
Filtering: removal of reads with adaptors; removal of reads in which unknown bases are more than 10%; removal of low quality reads (if the percentage of low quality bases is over 50% in a read).
Alignment: expression levels for all the genes from ENSEMBL 89 were quantified using RSEM 1.3.05 with STAR 2.5.3a (human genome GRCh38.89); we built the genome index for STAR alignment using "rsem-prepare-reference" with options '--star-sjdboverhang' set to 48, according to STAR guidelines. Alignment and quantification were performed with default parameters.
Normalization and filtering: all RNA-seq statistical analyses were performed in R environment (version 3.4.2) with Bioconductor 3.6. We excluded genes not annotated in Ensembl database and genes not having a count per million (CPM) of at least 0.5 in at least one sample. Data were normalized using edgeR Bioconductor package.
Genome_build: human genome GRCh38.89
Supplementary_files_format_and_content: tab-delimited text file including CPM (count per million) for each sample in each column.

source_name: Cardiomyocytes

growth_protocol: The cells were let attach and spread on Matrigel Reduced Growth Factor (MRGF)-coated polydimethylsiloxane (PDMS) membranes with patterned microgroves for 5 days before stretching experiments. During the stretching experiments cardiac basal medium was pre-warmed and supplemented with 25 mM HEPES to buffer the solution, given the absence of CO2 within the stretching device environment.

extract_protocol:
RNA was isolated with TRIzol Reagent followed by purification with RNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: hiPS cell-derived cardiomyocytes

tag: patient status

value: arrhythmogenic cardiomyopathy (homozygous C-terminal frame-shift mutation in PKP2 gene c.2484C>T)

tag: stimulus

value: unstimulated


title: Healthy stretched hiPS-derived cardiomyocytes, repl. 1

tag: cell type

value: healthy

value: 10% uniaxial tensile strain at 1 Hz for 60 minutes