title: SP28

status: Public on Jan 12 2022

city: London

first: Rachel

last: Lai

address: Du Cane Road

department: Infectious Disease

institute: Imperial College London

data_processing:
Trimmomatic v0.36
STAR v2.5.2a
SAMtools v1.2
BEDTools v2.26
DESeq2 v1.18.1
Genome_build: H37Rv Assembly ASM19595v2
Supplementary_files_format_and_content: Raw Counts

organism: Mycobacterium tuberculosis

source_name: Human sputum

growth_protocol: H37Rv was grown in 7H9 media and collected in Trizol at OD=0.6-0.8 for exponential phase samples and at 4 weeks after OD=1 for stationary phase samples. Human sputa were collected directly in Trizol.

extract_protocol:
Total RNA were extracted using standard Trizol extraction method with chloroform and isopropanol.
Libraries were constructed using NuGen FFPE RNA-Seq System with custom-made depletion oligos for rRNA of Mtb

tag: sample type

value: Sputum from TB patients


title: SP61

type: SRA

country: United Kingdom

library_source: transcriptomic

molecule: total RNA


title: SP43


title: SP23


title: F_to_M_Donor_6_6m

status: Public on Feb 17 2022

type: genomic

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2
Raw data was received as .iDAT files, which were pre-processed using the MissMethyl packages (available from Bioconductor) in R. Data was normalised for technical variation between and within arrays using the SWAN (Subset-quantile Within Array Normalization). Probes with poor average quality scores (p<0.01), cross-reactive probes and probes associated with single nucleotide polymorphisms (SNPs) were filtered from analysis. Differential analysis was carried out using a linear regression model with limma and the DMRCate tool was used to determine differentially methylated regions (DMRs).

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Adult Human Peripheral Blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from concentrated whole blood (buffy coat) using the QIAGEN AllPrep DNA/RNA micro-kit according to manufacturer’s instructions.

tag: individual

tag: tissue

value: Whole blood

tag: treatment

value: 6 months following masculinizing GAHT


title: SP29


title: SP24


title: F_to_M_Donor_11_6m


title: F_to_M_Donor_9_6m


title: F_to_M_Donor_10_6m


title: SP20


title: Rv_S1

source_name: M. tuberculosis H37Rv strain

tag: strain

value: laboratory culture

tag: growth protocol

value: Grown to stationary phase


title: Rv_E2

value: Grown to exponential phase


title: Rv_E1


title: Pnpla2_PKO_3

status: Public on Jan 01 2022

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

country: USA

institute: Purdue University

data_processing:
The original raw data from Illumina HiSeq are transformed to sequenced reads by base calling.
Raw reads are filtered to remove reads containing adapters or reads of low quality, then mapped to GRCm38/mm10 whole genome using TopHat2.
For the quantification of gene expression level, HTSeq V0.6.1 was used to analyze the read numbers mapped for each gene. The Fragments Per Kilobase of transcript per Million mapped reads (FPKM) of each gene was calculated based on the gene read counts mapped to genes or exons.
A differential expression analysis was performed using the DESeq2 R/EdgeR R package with the threshold of significance set as adjusted p < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: Muscle stem cell

extract_protocol:
mRNA from 1 ug of total RNA is enriched using oligo(dT) beads for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Hind limb muscles

tag: cell type

value: Muscle stem cell

tag: age

value: 2-month old


title: Rv_S2


title: Pnpla2_PKO_1


title: F_to_M_Donor_5_6m


title: Pnpla2_WT_3

value: WT


title: Pnpla2_WT_2


title: F_to_M_Donor_6_baseline

value: Baseline, before masculinizing GAHT


title: Pnpla2_WT_1


title: INPUT_2

status: Public on Dec 16 2021

city: oklahoma

first: roberto

middle: jose

last: pezza

state: OK

department: cell cycle and cancer biology

institute: oklahoma medical research foundation

description: Spermatocytes from mice synchronized with Fertilysin/retinoic acid treatment

library_source: genomic

data_processing:
Only for INO80_replicate_2: 10 bases were trimmed at the begining of the reads for both R1 and R2
Reads were adapter-trimmed and quality-pruned using fastp with default settings. Then, reads were aligned to GRCm38/mm10 using bwa mem (10) (Version 0.7.15) with default settings except for option ‘-M’ for Picard compatibility. Picard (version 2.21.2, http://broadinstitute.github.io/picard/) and SAMtools (version 1.11) (11) were used to obtain mapping quality metrics, remove duplicates and filter reads. Only primary alignment reads that were not duplicated, properly paired, with a MAPQ > 30, and not placed in mitochondrial chromosome were kept.
Peaks were called using MACS2 (version 2.2.7.1), broad mode, default parameters.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigWig files were generated using bamCoverage tool from deepTools (version 3.4.3, (17)) with a bin size of 1 bp, no smoothing and RPKM normalization.
Supplementary_files_format_and_content: Table_*.xlsx: Excel files include the mapping statistics of the ChIP-seq data, annotated peaks in the mouse genome, Genome ontology, functional study annotations, and genes ID peaks.

source_name: spermatocytes

growth_protocol: starting at 2 dpp mice were injected for seven consecutive days with fertilysin (MP Biomedicals, cat. # 158050) to arrest gametogenesis at the spermatogonia stage. The next day (9 dpp), mice were injected with retinoic acid (Sigma, cat. # R2625). Spermatocytes were collected at 8 days after retinoic acid injection

extract_protocol:
Testes were digested using proteases to get single cell suspension. Spermatocytes were separated from other cells by centrifugation on isotonic Percoll gradient (28%). Cells were sonicated, cleared by centrifugation and protein-DNA complexes were isolated using antibody and magnetic beads. Proteins were digested with proteinase K, RNA was degraded with RNAse A and crosslinking was reversed by incubation overnight at 65 °C
DNA was incubated with 30 µl of end-repair mix (0.66 mM dNTP mix (NEB, cat. # N0447S), 100 U/ml T4 DNA polymerase (NEB, cat. # M0203L), 33 U/ml Klenow fragment (NEB, cat. # M0210S), 333 U/ml T4 PNK (cat. # M0201L), and 1.67 x T4 PNK buffer) at 20 °C for 30 minutes. DNA was purified using Qiagen Minelute kit using 7 volumes of PB buffer and eluted in 12 µl of EB buffer. 10 µl of eluted DNA were mixed with 40 µl of A-tailing mix (0.25 mM dATP, 125 U/ml Klenow fragment (cat. # NEB M02105S), and Klenow buffer 1.25 X) and incubated at 37 °C for 30 minutes. DNA was purified again using Qiagen Minelute kit using 7 volumes of PB buffer and eluted in 12 µl of EB buffer. Truseq single index adaptors (Illumina, cat. # 20015960 or 20015961) were diluted according to the DNA concentra-tion (insert:adaptor molar ratio of 1:2, with maximal dilution of 1:50) and 1 µl of a specific diluted adaptor was added to each sample. 20 µl of ligation mix (30 U/µl T4 DNA ligase (cat. # NEB M0202L), and 1.58 X ligase buffer) was added to 10 µl of the insert:adaptor mix and incubated for 30 minutes at 20 °C. DNA was purified using Qiagen Minelute kit using 7 volumes of PB buffer and eluted in 12 µl of EB buff-er. Finally, DNA was amplified using the Kapa HiFi Hot Start library amplification kit (cat. # KK2621) ac-cording to manufacturer’s instructions.

value: DBA/2J x C57BL/6J F1

value: testis

value: first-wave early zygotene spermatocyte


title: M_to_F_Donor_2_baseline

value: Baseline, before feminizing GAHT


title: INO80_zyg_replicate_1

extract_protocol:
Library was prepared using adaptase technology. ACCEL-NGS® 1S PLUS DNA LIBRARY KIT (cat. # 10024) was used in conjunction with Swift unique dual indexing kit (cat. # X9096), following manufacturer’s instructions.
Testes were digested using proteases to get single cell suspension. Spermatocytes were separated from other cells by centrifugation on isotonic Percoll gradient (28%). Cells were sonicated, cleared by centrifugation and protein-DNA complexes were isolated using antibody and magnetic beads. Proteins were digested with proteinase K, RNA was degraded with RNAse A and crosslinking was reversed by incubation overnight at 65 °C
DNA was incubated with 30 µl of end-repair mix (0.66 mM dNTP mix (NEB, cat. # N0447S), 100 U/ml T4 DNA polymerase (NEB, cat. # M0203L), 33 U/ml Klenow fragment (NEB, cat. # M0210S), 333 U/ml T4 PNK (cat. # M0201L), and 1.67 x T4 PNK buffer) at 20 °C for 30 minutes. DNA was purified using Qiagen Minelute kit using 7 volumes of PB buffer and eluted in 12 µl of EB buffer. 10 µl of eluted DNA were mixed with 40 µl of A-tailing mix (0.25 mM dATP, 125 U/ml Klenow fragment (cat. # NEB M02105S), and Klenow buffer 1.25 X) and incubated at 37 °C for 30 minutes. DNA was purified again using Qiagen Minelute kit using 7 volumes of PB buffer and eluted in 12 µl of EB buffer. Truseq single index adaptors (Illumina, cat. # 20015960 or 20015961) were diluted according to the DNA concentra-tion (insert:adaptor molar ratio of 1:2, with maximal dilution of 1:50) and 1 µl of a specific diluted adaptor was added to each sample. 20 µl of ligation mix (30 U/µl T4 DNA ligase (cat. # NEB M0202L), and 1.58 X ligase buffer) was added to 10 µl of the insert:adaptor mix and incubated for 30 minutes at 20 °C. DNA was purified using Qiagen Minelute kit using 7 volumes of PB buffer and eluted in 12 µl of EB buff-er. Finally, DNA was amplified using the Kapa HiFi Hot Start library amplification kit (cat. # KK2621) ac-cording to manufacturer’s instructions.


title: F_to_M_Donor_5_12m

value: 12 months following masculinizing GAHT


title: F_to_M_Donor_5_baseline


title: F_to_M_Donor_3_6m


title: F_to_M_Donor_3_12m


title: F_to_M_Donor_4_6m


title: F_to_M_Donor_1_6m


title: Pnpla2_PKO_2


title: F_to_M_Donor_4_12m


title: F_to_M_Donor_10_12m


title: F_to_M_Donor_1_baseline


title: F_to_M_Donor_2_6m


title: F_to_M_Donor_2_12m


title: INO80_zyg_replicate_2


title: F_to_M_Donor_3_baseline


title: F_to_M_Donor_4_baseline


title: M_to_F_Donor_2_12m

value: 12 months following feminizing GAHT


title: INPUT_1


title: GDM_20

status: Public on Dec 14 2021

label: cy3, cy5

source_name: Umbilical Cord Blood

value: Endothelial Colony Forming Cells

tag: mother phenotype

value: Gestational Diabetes Mellitus


title: GDM_18


title: F_to_M_Donor_2_baseline

value: Whole blood


title: GDM_14


title: GDM_17


title: F_to_M_Donor_1_12m


title: GDM_12


title: GDM_16


title: GDM_6


title: GDM_9


title: GDM_7


title: GDM_10


title: Overweight_20

value: Overweight


title: GDM_5


title: Overweight_15


title: Overweight_16


title: Overweight_19


title: GDM_13


title: GDM_4


title: GDM_19


title: GDM_1


title: GDM_11


title: Overweight_14


title: Overweight_18


title: Overweight_17


title: GDM_8


title: GDM_3


title: Overweight_11


title: Overweight_8


title: Overweight_6


title: Overweight_5


title: Overweight_7


title: Overweight_12


title: Overweight_13


title: GDM_2


title: GDM_15


title: Overweight_9


title: Overweight_1


title: MOC1_scRNA_aCTLA4

status: Public on Dec 01 2021

city: Boston

first: Ravindra

last: Uppaluri

state: Massachusetts

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

description:
scRNA-seq of mus musculus: tumor infiltrating T cells
single cell RNA
MOC1_scRNA_counts.txt

data_processing:
The raw sequencing data were processed with Cell Ranger 3.0.2 software
Filtered gene-barcode matrix files were further parsed with Seurat 3.0.01 for fine-grain quality control and downstream analyses
Paired read data was adapted and quality trimmed using Trimmomatic v0.36
Trimmed reads were quantified by pseudoalignment against mm10 using Kallisto v0.46.0
Differential expression analysis was performed using DESeq2
Genome_build: GRCH38
Supplementary_files_format_and_content: txt, csv containg raw counts and scTCR
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx

source_name: MOC1 bearing mice received antiCTLA4 treatment

growth_protocol: Mouse oral squamous cell carcinoma models, MOC1, MOC1esc1, and MOC22 were maintained as previously described [35-37] in IMDM/Hams-F12 (2:1) supplemented with 5% heat inactivated FBS, 100 U/ml penicillin streptomycin, 5 ng/ml EGF (Millipore), 400 ng/ml hydrocortisone (Sigma Aldrich), and 5 mg/ml insulin (Sigma Aldrich). Cell lines were routinely tested for mycoplasma every 6 months.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini kit (QIAGEN) according to manufacturer’s protocol. Genomic DNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen)
WES Library construction was performed using the Agilent Sure Select Whole Exome Capture and captured using the Agilent SureSelect XT Mouse All Exon probe sets according to the manufacturer protocol.For bulk RNAseq, standard mRNA library preparation kit (RS-122-2101, Illumina) was used for library preparation. The single-cell RNA-seq libraries were processed using ChromiumTM single-cell 5’ library & gel bead kit and coupled TCR-seq libraries were obtained using ChromiumTM single-cell V(D)J enrichment kit (10x Genomics).
RNA-seq, genomic DNA-seq, scRNA-seq&TCRseq

treatment_protocol: isotype, antiPD1, and antiCTLA4 antibodies were ip injected on Day 3, 6, 9 post tumor inoculation

value: Tumor


title: MOC1_scRNA_aPD1

source_name: MOC1 bearing mice received antiPD1 treatment


title: MOC1_scRNA_ctrl

source_name: MOC1 bearing mice received isotype control treatment

value: isotype control


title: Control_18

value: Healthy control


title: TRα(-/-)_Intestine_ T3+_rep3

status: Public on Nov 29 2021

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

description:
WT_Tra_Reads_counts.txt
T3Homo3

data_processing:
Short reads mapping (STAR 2.5.3a)
Reads counting (featureCounts v1.4.6-p3)
Genome_build: Xenopus_tropicalis.JGI_4.2.90
Supplementary_files_format_and_content: Tab-delimited text file for reads counts of each gene.

organism: Xenopus tropicalis

source_name: Intestine

growth_protocol: Intestinal samples were collected from WT and TRα (-/-) tadpoles which born from same parents.

extract_protocol:
Intestinal RNA was harvested by using RNeasy. One ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When tadpoles reached to around stage 54, tadpoles were treated ot nontreated with 10nM T3 for 18 hours.

value: T3 treatment for 18 hours

tag: Stage

tag: genotype/variation

value: TR[alpha](-/-)


title: TRα(-/-)_Intestine_ T3+_rep1

description:
WT_Tra_Reads_counts.txt
T3Homo1


title: TRα(-/-)_Intestine_ T3-_rep3

description:
WT_Tra_Reads_counts.txt
T3WT3


title: Overweight_3


title: Overweight_10


title: TRα(-/-)_Intestine_ T3-_rep2

description:
WT_Tra_Reads_counts.txt
T3WT2


title: TRα(-/-)_Intestine_ T3-_rep1

description:
WT_Tra_Reads_counts.txt
T3WT1


title: TRα(-/-)_Intestine_ T3+_rep2

description:
WT_Tra_Reads_counts.txt
T3Homo2


title: Control_17


title: WT_Intestine_ T3+_rep3

description:
WT_Tra_Reads_counts.txt
contHomo3

value: wild type


title: WT_Intestine_ T3+_rep1

description:
WT_Tra_Reads_counts.txt
contHomo1


title: WT_Intestine_ T3-_rep3

description:
WT_Tra_Reads_counts.txt
contWT3


title: WT_Intestine_ T3-_rep2

description:
WT_Tra_Reads_counts.txt
contWT2


title: Control_10


title: hDRG3

status: Public on Nov 08 2021

first: Minh

middle: Q

last: Nguyen

state: MARYLAND

address: 9000, Rockville Pike

institute: NIDCR/NIH

data_processing:
bcl2fastq (v2.17) was used for basecalling
Sequence reads from 10x libraries were processed using Cell Ranger 2 and 3 from 10x Genomics (http://www.10xgenomics.com/)
Reads were aligned to a pre-mRNA GRCh38 genome.
Seurat (v3) was used for downstream analysis in R as described by the Satija lab (https://satijalab.org/)
Genome_build: GRCh38.v25.premRNA
Supplementary_files_format_and_content: csv files with cell barcodes and corresponding gene expression counts; only nuclei meeting minimum threshold of transcripts are included for analysis

molecule: polyA RNA

source_name: dorsal root ganglia

extract_protocol:
Dorsal root ganglia were harvested and incubated in RNAlater (ThermoFisher) at 4oC overnight.  Tissues were then transferred and stored at -80oC until use.  Tissues were homogenized using a glass dounce homogenizer on ice.  Neuronal nuclei were isolated using rabbit anti-NeuN antibody (Abcam) followed by anti-rabbit IgG microbeads (Miltenyi Biotec) and LS column (Miltenyi Biotec).
Libraries construction were performed using 10x Genomics according to the manufacturer's instructions using v2 chemistry kits.

tag: gender

value: female

value: 34 years

value: dorsal root ganglia

tag: molecule subtype

value: pre-mRNA


title: WT_Intestine_ T3+_rep2

description:
WT_Tra_Reads_counts.txt
contHomo2


title: hDRG2

value: male

value: 36 years


title: WT_Intestine_ T3-_rep1

description:
WT_Tra_Reads_counts.txt
contWT1


title: Control_19


title: HUVEC_Donor_2_48hr_4h_polyIC

status: Public on Nov 06 2021

data_processing:
Fastq files were assessed for quality using the FastQC package and no samples were excluded from analysis. Bowtie was used to map 100-bp paired end reads to the human transcriptome (Ensembl, GRCh37v70), and gene expression estimates were derived using the mmseq.txt pipeline. DESeq2  was used to normalise count data and determine gene expression differences between treatments.
Genome_build: hg19
Supplementary_files_format_and_content: .gene.mmseq.txt files contain counts per gene

source_name: Umbilical Cord Vein

extract_protocol:
Total RNA were extracted using the QIAGEN AllPrep DNA/RNA micro-kit according to manufacturer’s instructions.
Library preparation was performed using the Illumina TruSeq stranded mRNA kit with a starting input of 300ng and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 20 million reads per sample.

value: Human Umbilical Vein Endothelial Cell

value: Poly(I:C) exposed for 24 hours, followed by 24 hours media only, then exposed to LPS for 4 hours


title: hDRG1


title: Overweight_4

value: Endothelial Colony Forming Cells


title: HUVEC_Donor_2_48hr_4h_media

value: Media only for 48 hours, then exposed to LPS for 4 hours


title: Control_15


title: HUVEC_Donor_2_24hr_polyIC

value: Poly(I:C) exposed, collected at 24 hours post exposure.


title: HUVEC_Donor_2_24hr_media

value: Media only, collected at 24 hours post culture


title: HUVEC_Donor_2_4hr_PolyIC

value: Poly(I:C) exposed, collected at 4 hours post exposure.


title: HUVEC_Donor_2_4hr_media

value: Media only, collected at 4 hours post culture


title: Control_20

value: Healthy control


title: HUVEC_Donor_2_0h

value: Baseline


title: Overweight_2

value: Overweight


title: Control_9


title: HUVEC_Donor_1_T52h_Media


title: Control_7


title: HUVEC_Donor_1_T24h_PolyIC


title: HUVEC_Donor_1_T48h_Media

value: Media only, collected at 48 hours post culture


title: HUVEC_Donor_1_T24h_Media


title: HUVEC_Donor_1_T52h_PolyIC


title: Control_4


title: HUVEC_Donor_2_48hr_polyIC

value: Poly(I:C) exposed for 24 hours, then 24 hours media only.


title: Control_16


title: HUVEC_Donor_1_T0h_Media


title: ECFC_Donor_2_T52h_Media

value: fetal endothelial progenitor


title: ECFC_Donor_2_T48h_Media


title: ECFC_Donor_2_T24h_PolyIC


title: ECFC_Donor_2_T24h_Media


title: ECFC_Donor_2_T52h_PolyIC


title: ECFC_Donor_2_T4h_PolyIC


title: ECFC_Donor_2_T48h_PolyIC


title: Control_1


title: ECFC_Donor_2_T4h_Media


title: Control_5


title: ECFC_Donor_1_T48h_Media


title: Control_11


title: ECFC_Donor_1_T48h_PolyIC


title: ECFC_Donor_1_T52h_PolyIC


title: Control_13


title: ECFC_Donor_1_T24h_PolyIC


title: Control_3


title: ECFC_Donor_1_T24h_Media


title: Control_12


title: Control_2


title: ECFC_Donor_1_T4h_Media


title: ECFC_Donor_1_T0h_Media


title: Control_6


title: Control_14


title: Control_8


title: DC_d1_oxLDL

status: Public on Oct 03 2021

data_processing:
Illumina Casava software 1.8.2  used for basecalling of Hiseq2000 data.
MMSEQ package was used to infer gene expression levels. Reads were mapped to human gene annotation using Bowtie1 (Ensemble release 68).
Genome_build: hg19
Supplementary_files_format_and_content: RNA files are in a .gene.mmseq format, containing counts per gene.

growth_protocol: Monocytes were negatively selected from peripheral blood andplaced in Trizol for RNA.

extract_protocol:
RNA was extracted using the Trizol protocol.
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit

value: Monocyte

tag: treatment protocol

value: exposed to oxLDL for 24 hours

tag: donor


title: DC_d6_oxLDL_LPS

value: Trained Macrophage, exposed to oxLDL for 24 hours, RPMI media for 5 days then exposed to LPS for 4 hours


title: DC_d6_oxLDL

value: Trained Macrophage, exposed to oxLDL for 24 hours then RPMI media for 5 days


title: DC_d6_RPMI_LPS

value: Macrophage, exposed to RPMI media for 6 days then exposed to LPS for 4 hours


title: DC_d1_RPMI

value: exposed to RPMI media for 24 hours


title: DB_d6_RPMI_LPS


title: DC_d0

value: baseline monocyte


title: DB_d6_oxLDL


title: DB_d1_oxLDL


title: DB_d6_RPMI

value: Macrophage, exposed to RPMI media for 6 days


title: DB_d0


title: DA_d6_RPMI_LPS


title: DA_d6_oxLD_LLPS


title: DB_d1_RPMI


title: DA_d6_oxLDL


title: DA_d6_RPMI


title: DA_d0


title: DC_d6_RPMI


title: DA_d1_RPMI


title: DB_d6_oxLDL_LPS


title: HUVEC_Donor_2_48hr_media

value: Human Umbilical Vein Endothelial Cell


title: HUVEC_Donor_1_T48h_PolyIC


title: DA_d1_oxLDL


title: HUVEC_Donor_1_T4h_Media


title: HUVEC_Donor_1_T4h_PolyIC

value: Poly(I:C) exposed, collected at 4 hours post exposure.


title: ECFC_Donor_1_T52h_Media

value: Media only for 48 hours, then exposed to LPS for 4 hours


title: RNA-Seq Multi_Allergic_6

status: Public on Sep 01 2021

data_processing:
Fastq files were assessed for quality using the FastQC package and no samples were excluded from analysis. Bowtie was used to map 100-bp paired end reads to the human transcriptome (Ensembl, GRCh37v70), and gene expression estimates were derived using the mmseq pipeline. Genes with low expression (mean reads per kilobase of transcript, per million of mapped reads (RPKM) <1 across all samples) were removed from analysis, leaving expression data for 20,025 genes. DESeq  was used to normalise count data and determine gene expression differences between group comparisons.
Genome_build: hg19
Supplementary_files_format_and_content: .gene.mmseq files contain counts per gene

source_name: CD3-CD19+ B cell

growth_protocol: PBMCs were viably thawed and total B cell populations (CD3-CD19+) were isolated using fluorescence activated cell sorting (BD FACS-ARIA Fusion cell sorter).

extract_protocol:
Total B cell populations were sorted into 350ul RLT buffer. Genomic DNA and total RNA were extracted using the QIAGEN AllPrep DNA/RNA micro-kit according to manufacturer’s instructions.
Library preparation was performed using the Illumina TruSeq stranded mRNA kit with a starting input of 100ng and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 20 million reads per sample.

tag: individual id

value: B cells

tag: Sex

value: F

value: multi

value: MULTI FA (PN + TN + milk)

value: RNA-seq


title: ECFC_Donor_1_T4h_PolyIC

tag: individual

value: fetal endothelial progenitor


title: ECFC_Donor_2_T0h_Media

value: Baseline


title: RNA-Seq Multi_Allergic_7

value: M


title: RNA-Seq Multi_Allergic_5

value: MULTI FA (PN + TN + egg)


title: RNA-Seq Multi_Allergic_4

value: MULTI FA (PN + TN)


title: RNA-Seq Single_Allergic_10

value: single

value: PEANUT ONLY


title: Multi_Allergic_6

description: Sample 25

data_processing:
BeadStudio software v3.2
Raw data was received as .iDAT files, which were pre-processed using the minfi and MissMethyl packages (available from Bioconductor) in the R statistical environmen. Sample quality assessment showed that all samples had a mean detection p-value <0.01, allowing all samples to remain for analysis. Data was normalised for technical variation between and within arrays using the SWAN (Subset-quantile Within Array Normalization). Probes with poor average quality scores (p<0.01), cross-reactive probes and probes associated with single nucleotide polymorphisms (SNPs) were filtered from analysis, leaving 770,475 probes. Differential analysis was carried out on the 770,475 probes using a linear regression model with limma and the DMRCate tool was used to determine differentially methylated regions (DMRs).
Raw matrix: The Methylated and unmethylated signal intensities and detP

extract_protocol: Total B cell populations were sorted into 350ul RLT from purified PBMCs using flow cytometry. Genomic DNA and total RNA were extracted using the QIAGEN AllPrep DNA/RNA micro-kit according to manufacturer’s instructions.

value: DNAme


title: Single_Allergic_10

description: Sample 22


title: RNA-Seq Multi_Allergic_3

value: MULTI FA (PN + TN + sesame)


title: RNA-Seq Single_Allergic_9


title: RNA-Seq Multi_Allergic_2


title: Multi_Allergic_7

description: Sample 26


title: Multi_Allergic_2

description: Sample 20


title: Non_Allergic_7

description: Sample 13

value: control

value: NO FA


title: RNA-Seq Single_Allergic_8


title: Multi_Allergic_5

description: Sample 24


title: Single_Allergic_7

description: Sample 16


title: Multi_Allergic_4

description: Sample 23


title: Single_Allergic_9

description: Sample 19


title: Single_Allergic_8

description: Sample 18


title: RNA-Seq Single_Allergic_6


title: Non_Allergic_8

description: Sample 14


title: RNA-Seq Non_Allergic_8


title: RNA-Seq Non_Allergic_7


title: Multi_Allergic_1

description: Sample 8


title: RNA-Seq Non_Allergic_6


title: Multi_Allergic_3

description: Sample 21


title: Non_Allergic_2

description: Sample 2


title: RNA-Seq Single_Allergic_5


title: RNA-Seq Non_Allergic_5


title: RNA-Seq Single_Allergic_4


title: RNA-Seq Multi_Allergic_8


title: RNA-Seq Single_Allergic_7


title: RNA-Seq Multi_Allergic_1


title: RNA-Seq Non_Allergic_9


title: Single_Allergic_1

description: Sample 3


title: Single_Allergic_3

description: Sample 7


title: RNA-Seq Single_Allergic_3


title: RNA-Seq Non_Allergic_4


title: Single_Allergic_5

description: Sample 11


title: RNA-Seq Non_Allergic_3


title: Single_Allergic_6

description: Sample 15


title: RNA-Seq Single_Allergic_2


title: Single_Allergic_2

description: Sample 4


title: RNA-Seq Non_Allergic_2


title: RNA-Seq Non_Allergic_1


title: Single_Allergic_4

description: Sample 9


title: IL15_TUMOR_CD11_S6_L002_Nextseq

status: Public on Jul 30 2021

first: Katherine

last: Goldfarbmuren

address: 41 Center Dr

department: Advanced Biomedical Computational Science

institute: NCI, Frederick National Laboratory for Cancer Research

description: IL15 treated E0771 tumor

data_processing:
cellranger (v4.0.0)
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger HDF5

extract_protocol: none provided by the submitter


title: IL15_TUMOR_CD11_S6_L003_Nextseq

description: IL15 treated E0771 tumor


title: IL15_TUMOR_CD11_S6_L004_Nextseq

description: IL15 treated E0771 tumor


title: C_TUMOR_CD11_S5_L004_Nextseq

description: Control treated E0771 tumor


title: Non_Allergic_5

description: Sample 10


title: IL15_TUMOR_CD11_S6_L001_Nextseq

description: IL15 treated E0771 tumor


title: RNA-Seq Single_Allergic_1


title: C_TUMOR_CD11_S5_L002_Nextseq

description: Control treated E0771 tumor


title: C_TUMOR_CD11_S5_L001_Nextseq

description: Control treated E0771 tumor


title: Non_Allergic_3

description: Sample 5


title: IL15_TUMOR_CD11_S6_L002_Novaseq

description: IL15 treated E0771 tumor


title: IL15_TUMOR_CD11_S6_L001_Novaseq

description: IL15 treated E0771 tumor


title: C_TUMOR_CD11_S5_L002_Novaseq

description: Control treated E0771 tumor


title: C_TUMOR_CD11_S5_L001_Novaseq

description: Control treated E0771 tumor


title: R14d

status: Public on Jul 01 2021

city: Houston

first: Guangyu

last: Wang

address: 6670 Bertner Ave

institute: Houston methodist research institute

description: Week 14 of Recovery after heart failure

data_processing:
Sequenced reads were mapped to mm9 whole genome using tophat2
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cuffdiff.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: whole heart

treatment_protocol:
Heart Failure Protocol: 3 month old mice drink water with 1% NaCl and 0.3 mg/ml L-NAME for 5 weeks.  One week after water is started Osmotic pump implanted to deliver 0.7 mg/kg/day Angiotensin II.  Heart Failure is at the end of the 5th week.
Recovery Protocol : Mice undergo heart failure protocol for 5 weeks.  Water is returned to normal and osmotic pump runs out (28 day pump).
Controls: Control mice are age matched for each phase of the protocol to control for aging changes.

tag: tissue

value: Whole Ventricle


title: Non_Allergic_6

description: Sample 12

value: B cells


title: R14b

description: Week 14 of Recovery after heart failure


title: R14e

description: Week 14 of Recovery after heart failure


title: C14c

description: Control for Week 14 of Recovery


title: R14c

description: Week 14 of Recovery after heart failure


title: C14e

description: Control for Week 14 of Recovery


title: Non_Allergic_9

description: Sample 17


title: R14f

description: Week 14 of Recovery after heart failure


title: C14b

description: Control for Week 14 of Recovery


title: Non_Allergic_1

description: Sample 1

value: F


title: Non_Allergic_4

description: Sample 6


title: C14a

description: Control for Week 14 of Recovery


title: R8b

description: Week 8 of Recovery after heart failure


title: R8c

description: Week 8 of Recovery after heart failure


title: R4b

description: Week 4 of Recovery after heart failure


title: C14d

description: Control for Week 14 of Recovery


title: HF5e

description: Week 5 of heart failure protocol


title: R6a

description: Week 6 of Recovery after heart failure


title: R4a

description: Week 4 of Recovery after heart failure


title: HF5a

description: Week 5 of heart failure protocol


title: HF5d

description: Week 5 of heart failure protocol


title: R4c

description: Week 4 of Recovery after heart failure


title: C5d

description: Control for Week 5 of heart failure protocol


title: C5c


title: R2a

description: Week 2 of Recovery after heart failure


title: R2b

description: Week 2 of Recovery after heart failure


title: C5b


title: C5a


title: HF3b

description: Week 3 of heart failure protocol


title: HF3c

description: Week 3 of heart failure protocol


title: HBA37

status: Public on Jun 12 2021

city: Pittsburgh

first: Xiangning

last: Xue

address: 4200 Fifth Ave

department: Department of Biostatistics

institute: University of Pittsburgh

data_processing:
Quality control was performed by Fastqc
Perform trimming by trimmomatic, allign the sequence using Hisat2 with Ensembl reference and read count with Hiseq
Genes are filtered to retain those with count per millon (CPM) greather than 1 in more than 50% samples
The library size is normalized using count per million (CPM) and tthen the data is log2 transformed with prior count 1.
Genome_build: GRCh38
Supplementary_files_format_and_content: comma-separated file of log2CPM of the original count for filtered genes and all samples
Supplementary_files_format_and_content: comma-separated file of raw counts for all genes and samples

source_name: DLPFC

extract_protocol:
Tissue was homogenized in TRIzol (Invitrogen, Carlsbad, CA) and RNA extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: diagnosis

value: CONT

tag: timeofdeath

value: Female

tag: race

value: Black or African-American

tag: pmi

tag: avgph

tag: bloodtexicology

value: No substances detected

value: Arthritis

tag: medicationsatodc

value: O

tag: tobaccoatod

value: N

tag: mannerofdeath

value: Natural

tag: causeofdeath

value: Congestive Heart Failure

tag: correctedtod


title: HBA40

value: Male

tag: age

value: White

value: U

value: Accidental

value: Aspiration


title: HBA38

value: Asthma

value: Drowning


title: HBA36

value: Osteomyelitis

value: Pulmonary Embolism


title: HBA39

value: CONT

value: Female

value: Bronchitis; Degenerative Joint Disease

value: Blunt Force Trauma


title: HBA34

value: Ethanol

value: Y

value: Cardiomyopathy


title: HBA33

value: Black or African-American

value: No substances detected

value: O

value: N

value: Natural

value: Chronic Obstructive Pulmonary Disease


title: R6c

description: Week 6 of Recovery after heart failure

tag: strain

value: Whole Ventricle


title: R6b

description: Week 6 of Recovery after heart failure


title: HBA32

value: Male

value: White

value: Cardiac Tamponade


title: HBA31

value: CONT

value: Endocardial Fibroelastosis


title: HBA29

value: Cardiovascular Disease


title: HBA28

value: Female

value: Hepatitis C Without Hepatic Coma

value: Coronary Artery Dissection


title: HBA21

value: Undetermined


title: HBA25


title: HBA22

value: Black or African-American

value: U


title: HBA23

value: No substances detected

value: Arthritis

value: O

value: Y


title: HBA20

value: OUD

value: Morphine, Fentanyl

value: O, Z

value: Accidental

value: Combined Drug Overdose


title: HBA27

value: CONT

value: Male

value: White

value: Bronchitis

value: N

value: Natural


title: HBA19

value: Female

value: Methadone, Cyclobenzaprine, Norcyclobenzaprine,  Trazodone, Quetiapine

value: B, D, O, P, Z


title: HBA24

value: Black or African-American

value: No substances detected

value: Asthma

value: Pulmonary Embolism


title: HBA18

value: OUD

value: Oxycodone, Trazodone, Citalopram, Desmethylcitalopram, Diazepam, Nordiazepam, Mirtazapine, Ibuprofen

value: Degenerative Joint Disease

value: Y


title: HBA14

value: Fentanyl, Norfentanyl, Lidocaine, Butalbital, Cocaine Metabolites, Trazodone, Alprazolam, Citalopram,  Acetaminophen

value: B, D

value: Accidental

value: Combined Drug Overdose


title: HBA17

value: White

value: Fentanyl, Doxepin, Desmethyldoxepin, Salicylate

value: Degenerative Arthritis

value: B, D, Z


title: HBA35

value: CONT

value: Female

value: N

value: Natural

value: Subarachnoid Hemorrhage


title: HBA13

value: OUD

value: Methadone, Citalopram, Ethanol

value: Hepatitis A without Hepatic Coma; E. Coli Sepsis; Pancreatitis; Asthma; Pneumonia; Bronchitis

value: D, P


title: HBA11

value: Methadone, Methadone Metabolite, Trazodone

value: Osteoarthritis; Degenerative Changes of Cervical Spine

value: B, O, Z

value: Y


title: HBA8

value: Black or African-American

value: Fentanyl, Cocaine, Benzoylecgonine, Diazepam, Nordiazepam

value: B, O

value: Accidental

value: Combined Drug Overdose


title: HBA10

value: Female

value: White

value: Tramadol, Cyclobenzaprine, Norcyclobenzaprine, Zolpidem, Verapamil, Desmethylverapamil, Venlafaxine

value: Arthritis; Asthma; Recurrent Bronchitis

value: B, D, O, P, Z


title: HBA12

value: OUD

value: Male

value: Morphine, Oxycodone

value: Osteomyelitis with Non-healing Ulcer; Recurring Foot Infections

value: O, Z


title: HBA7

value: Morphine

value: Asthma; Allergic Rhinitis; Degenerative Joint Disease

value: B, C, D, O

value: Heroin Overdose


title: HBA6

value: Fentanyl, Meprobamate

value: B, C, D, L, O, P

value: Y

value: Fentanyl Overdose


title: HBA9

value: White

value: Fentanyl, Cocaine, Norcocaine, Ecgonine Methyl Ester,   Benzoylecgonine

value: Hepatitis A without Hepatic Coma; Hepatitis B without Hepatic Coma; Hepatitis C without Hepatic Coma

value: O

value: Accidental

value: Combined Drug Overdose


title: HBA5

value: OUD

value: Male

value: Fentanyl, Trazodone, Mirtazapine

value: C, D, O, P, Z


title: HBA4

value: Morphine, Phenobarbital, Cocaine Metabolites

value: Arthritis

value: O, Z


title: HBA30

value: CONT

value: Female

value: Black or African-American

value: Acetaminophen

value: C, O

value: N

value: Natural

value: Cardiovascular Disease


title: HBA3

value: White

value: Cyclobenzaprine, Norcyclobenzaprine, Fluoxetine, Norfluoxetine, Ethanol

value: Asthma; Recurrent Bronchitis; Degenerative Joint Disease

value: B, D, O, P, Z

value: Y

value: Accidental


title: HBA26

value: No substances detected

value: Degenerative Joint Disease

value: O


title: HBA2

value: OUD

value: Male

value: Morphine

value: Recurrent Bronchitis

value: D

value: U

value: Combined Drug Overdose


title: HBA1

value: Female

value: Methadone, Tramadol, Alprazolam, Diphenhydramine

value: Asthma; Recurrent Bronchitis

value: B, O, Z


title: HBA16

value: White

value: Oxycodone, Fentanyl, Citalopram, Acetaminophen

value: Recurrent Pneumonia

value: D, O


title: HN39

source_name: NAC

value: CONT

value: No substances detected

value: Bronchitis; Degenerative Joint Disease

value: N

value: Accidental

value: Blunt Force Trauma


title: HN38

value: Male

value: Asthma

value: O

value: Drowning


title: HN36

value: Osteomyelitis

value: Natural

value: Pulmonary Embolism


title: HN37

value: Female

value: Black or African-American

value: Arthritis

value: Congestive Heart Failure


title: HN35

value: CONT

value: White

value: Subarachnoid Hemorrhage


title: HBA15

value: OUD

value: Methadone, Methadone Metabolite, Diphenhydramine, Diazepam, Nordiazepam, Alprazolam, 7-Aminoclonazepam

value: B, O

value: Y

value: Combined Drug Overdose


title: HN33

value: No substances detected

value: O

value: N

value: Chronic Obstructive Pulmonary Disease


title: HN32

value: Male

value: Natural

value: Cardiac Tamponade


title: HN40

value: U

value: Accidental

value: Aspiration


title: HN30

value: CONT

value: Female

value: Black or African-American

value: Acetaminophen

value: C, O

value: Cardiovascular Disease


title: HN28

value: White

value: Hepatitis C Without Hepatic Coma

value: Coronary Artery Dissection


title: HN29

value: No substances detected

value: N


title: HN34

value: Male

value: Ethanol

value: Asthma

value: Y

value: Cardiomyopathy


title: HN27

value: Bronchitis

value: O

value: Natural


title: HN31

value: CONT

value: Female

value: Endocardial Fibroelastosis


title: HN26

value: Degenerative Joint Disease

value: Cardiovascular Disease


title: HN24

value: Black or African-American

value: Pulmonary Embolism


title: HN25

value: White

value: No substances detected


title: HN21

value: N

value: Undetermined


title: HN20

value: OUD

value: Male

value: Morphine, Fentanyl

value: O, Z

value: Accidental

value: Combined Drug Overdose


title: HN22

value: CONT

value: U

value: Natural

value: Cardiac Tamponade


title: HN19

value: Female

value: Methadone, Cyclobenzaprine, Norcyclobenzaprine,  Trazodone, Quetiapine

value: B, D, O, P, Z

value: Y


title: HN17

value: White

value: Fentanyl, Doxepin, Desmethyldoxepin, Salicylate

value: Degenerative Arthritis

value: B, D, Z


title: HN18

value: OUD

value: Male

value: Oxycodone, Trazodone, Citalopram, Desmethylcitalopram, Diazepam, Nordiazepam, Mirtazapine, Ibuprofen

value: Degenerative Joint Disease


title: HN16

value: Oxycodone, Fentanyl, Citalopram, Acetaminophen

value: Recurrent Pneumonia

value: D, O

value: Accidental

value: Combined Drug Overdose


title: HN13

value: Female

value: Methadone, Citalopram, Ethanol

value: Hepatitis A without Hepatic Coma; E. Coli Sepsis; Pancreatitis; Asthma; Pneumonia; Bronchitis

value: D, P


title: HN12

value: White

value: Morphine, Oxycodone

value: Osteomyelitis with Non-healing Ulcer; Recurring Foot Infections

value: O, Z

value: Y


title: HN15

value: OUD

value: Methadone, Methadone Metabolite, Diphenhydramine, Diazepam, Nordiazepam, Alprazolam, 7-Aminoclonazepam

value: B, O


title: HN14

value: Male

value: Fentanyl, Norfentanyl, Lidocaine, Butalbital, Cocaine Metabolites, Trazodone, Alprazolam, Citalopram,  Acetaminophen

value: B, D

value: N


title: HN9

value: Fentanyl, Cocaine, Norcocaine, Ecgonine Methyl Ester,   Benzoylecgonine

value: Hepatitis A without Hepatic Coma; Hepatitis B without Hepatic Coma; Hepatitis C without Hepatic Coma

value: O

value: Accidental

value: Combined Drug Overdose


title: HN10

value: Female

value: White

value: Tramadol, Cyclobenzaprine, Norcyclobenzaprine, Zolpidem, Verapamil, Desmethylverapamil, Venlafaxine

value: Arthritis; Asthma; Recurrent Bronchitis

value: B, D, O, P, Z


title: HN8

value: OUD

value: Black or African-American

value: Fentanyl, Cocaine, Benzoylecgonine, Diazepam, Nordiazepam

value: Y


title: HN5

value: Male

value: Fentanyl, Trazodone, Mirtazapine

value: C, D, O, P, Z


title: HN7

value: Morphine

value: Asthma; Allergic Rhinitis; Degenerative Joint Disease

value: B, C, D, O

value: Heroin Overdose


title: HN4

value: Morphine, Phenobarbital, Cocaine Metabolites

value: Arthritis

value: O, Z

value: Accidental

value: Combined Drug Overdose


title: HN23

value: CONT

value: Female

value: No substances detected

value: O

value: Natural

value: Cardiovascular Disease


title: HN2

value: OUD

value: Male

value: White

value: Recurrent Bronchitis

value: D

value: U


title: HN1

value: Methadone, Tramadol, Alprazolam, Diphenhydramine

value: Asthma; Recurrent Bronchitis

value: B, O, Z

value: Y


title: D100_Ctrl

status: Public on Jun 11 2021

city: Los Angeles

first: Bennett

last: Novitch

state: California

address: 650 Charles E Young Dr. S, CHS 66-200

department: Department of Neurobiology

institute: University of California, Los Angeles

description: Sample represents a pool of 3 cortex + ganglionic eminence fusion organoids created from Rett syndrome patient iPSC expressing a WT MECP2 allele.  The sample was collected at Day 100 in the differentiation scheme.

data_processing:
Sample reads were aligned with cellranger-4.0.0 (10X Genomics) to GRCh38 (cellranger version GRCh38-2020-A) and the filtered_feature_bc_matrices were loaded into R using the Read10X() function.
Sample count matrices were loaded in R using the Seurat package.
The samples were merged to one matrix using Seurat and filtered with these parameters: nFeatures_RNA > 500, nFeatures_RNA < mean+3*(standard deviation), and percent mitochondria genes < 10%
The data was normalized using Seurat defaults for NormalizeData() and FindVariableFeatures().
Data integration/batch correction was performed with the Seurat-wrapper functions for LIGER including RunOptimizeALS(datExpr, k = 20, lambda = 5, split.by = "orig.ident"), and RunQuantileNorm(datExpr, split.by = "orig.ident").
The data were then clustered using FindNeighbors(datExpr, reduction = "iNMF", dims = 1:20) and FindClusters(datExpr, resolution = 0.3).
Genome_build: GRCh38
Supplementary_files_format_and_content: Files ending in "Raw_counts.csv" are the filtered_feature_bc_matrix produced by cellranger read using the Read10X() function in R. Normalized_counts_all_samples.txt contains the processed count matrix after filtering, normalization, and batch correction with LIGER. Metadata_all_samples.csv contains sample info for each cell including cluster assignments.

source_name: hPSC-dervied brain organoids - Cortex-MGE fusions

growth_protocol: isogenic Rett syndrome patient iPSC (WT control and MECP2 mutant) were maintained under mouse embryonic fibroblast-supported conditions using DMEM/F12 (HyClone) with 20% knockout serum replacement (KSR, Invitrogen) and media supplements as described in Watanabe et al Cell Reprorts 2017 (https://doi.org/10.1016/j.celrep.2017.09.047)

extract_protocol:
At the times of collection, organoids were washed in PBS and chopped into small chunks using a single edge razor blade, passed through a 40 µm strainer, and then dissociated into a single cell suspensiosn using papain dissociation kit (Worthington #LK003150, with the papain reconstituted in Hibernate E media (Brainbits # HE).   into  At day 56, organoids were either dissociated and subjected to single cell sequence using the 10X Genomics Chromium Single Cell 3' v3 (10X Genomics)
Single Cell 3' v3 (10X Genomics)

treatment_protocol: iPS were diferentiated into brain orgaonids following the methods outlined in Watanabe et al Cell Reprorts 2017 (https://doi.org/10.1016/j.celrep.2017.09.047). At days 15-21, a subset of organoids were exposed to Smoothened Agonist (SAG) to direct formation of ganglionic eminence organoids.  untreated organoids were observed to differentate into cortical tissue.  Organoids were collected for single cell analysis at day 56 (before fusion), or fused togetether at day 56 to form Cortex+Ganglionic Eminence organoids and then collected at either day 70 or 100.

tag: timepoint

tag: genotype

value: MECP2 +/705delG (WT MECP2 expression)

value: Fused cortex and ganglionic eminance organoids created from Rett syndrome iPSC expressing a WT MECP2 allele.


title: D70_Mut

description: Sample represents a pool of 3 cortex + ganglionic eminence fusion organoids created from Rett syndrome patient iPSC expressing a 705delG mutant MECP2 allele.  The mutation results in a frameshift truncation (E235fs). The sample was collected at Day 70 in the differentiation scheme.

value: MECP2 705delG/+ (Mutant MECP2 expression)

value: Fused cortex and ganglionic eminance organoids created from Rett syndrome iPSC expressing a MECP2 707delG allele (functional null)


title: D70_iCtrl

description: Sample represents a pool of 3 cortex + ganglionic eminence fusion organoids created from Rett syndrome patient iPSC expressing a WT MECP2 allele.  The sample was collected at Day 70 in the differentiation scheme.


title: 192567_PBMC

status: Public on Jun 07 2021

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

institute: Yale University

data_processing:
Bulk repertoire data processing and analysis was carried out using tools from the Immcantation framework (http://immcantation.org).
Preprocessing was carried out using pRESTO v0.5.11 and the IMGT human germline IGHV reference database (IMGT/GENE-DB v3.1.19; retrieved May 30, 2019)
BCR isotypes were assigned by local alignment of the 3’ end of each sequence to a set of constant region sequences.
Genome_build: IMGT/GENE-DB v3.1.19
Supplementary_files_format_and_content: One annotation file in AIRR-C Rearrangement format was generated for each sample. The files are in tab-delimited format and gzip compressed.

source_name: PBMC

extract_protocol:
PBMCs were isolated by Ficoll-Paque PLUS (GE Healthcare) gradient centrifugation. Red blood cells (RBCs) were lysed using ACK buffer (ThermoFisher A1049201).
RNA was prepared from frozen PBMCs using the RNAEasy Mini kit (Qiagen) per the manufacturer’s instructions. BCR and TCR RNA libraries were prepared using reagents from New England Biolabs as part of the NEBNext® Immune Sequencing Kit (a kind gift of Drs. Eileen Dimalanta and Chen Song, Ipswich, MA). These steps were performed as described previously with the inclusion of an additional set of TCRB-specific primers on the 3’ end. Libraries were sequenced by 325 cycles for read 1 and 275 cycles for read 2 base-pair paired-end sequencing with a 20% PhiX spike on the Illumina MiSeq platform according to manufacturer’s recommendations.

tag: Sex

value: Female

tag: ethnicity

value: Not Hispanic or Latino

tag: disease stage

value: Acute/Recent onset

tag: isolate

value: Subject 192567

tag: assay

value: bulk BCR


title: HN11

tag: diagnosis

value: OUD

tag: timeofdeath

tag: race

value: White

tag: pmi

value: Methadone, Methadone Metabolite, Trazodone

value: Osteoarthritis; Degenerative Changes of Cervical Spine

value: Accidental

value: Combined Drug Overdose


title: HN6

tag: avgph

tag: bloodtexicology

value: Fentanyl, Meprobamate

tag: medicationsatodc

value: B, C, D, L, O, P

tag: tobaccoatod

value: Fentanyl Overdose


title: 192565_PBMC

tag: age

value: Subject 192565


title: 192566_PBMC

value: Male

value: Subject 192566


title: D100_Mut

description: Sample represents a pool of 3 cortex + ganglionic eminence fusion organoids created from Rett syndrome patient iPSC expressing a 705delG mutant MECP2 allele.  The mutation results in a frameshift truncation (E235fs). The sample was collected at Day 100 in the differentiation scheme.

value: MECP2 705delG/+ (Mutant MECP2 expression)

tag: tissue

value: Fused cortex and ganglionic eminance organoids created from Rett syndrome iPSC expressing a MECP2 707delG allele (functional null)


title: D56_iCtrl

description: Sample represents a pool of 3 cortex and 3 ganglionic eminence organoids created from Rett syndrome patient iPSC expressing a WT MECP2 allele.  The sample was collected at Day 56 in the differentiation scheme.

source_name: hPSC-dervied brain organoids - Cortex and MGE

tag: timepoint

value: MECP2 +/705delG (WT MECP2 expression)

value: Unfused cortex and ganglionic eminance organoids created from Rett syndrome iPSC expressing a WT MECP2 allele.


title: 192564_PBMC

value: Female

value: Not Hispanic or Latino

value: Acute/Recent onset

value: Subject 192564

value: bulk BCR


title: 192561_PBMC

value: Subject 192561


title: HepG2_dsRNA_ALKBH7-mutant_rep2

status: Public on Jun 02 2021

city: Chicago

first: Li-Sheng

last: Zhang

state: IL

address: 929 E 57th St Rm E313

department: Department of Chemistry

institute: The University of Chicago

data_processing:
The sequencing data was all trimmed with cutadapt tool to remove adapters and low-quality reads (length shorter than 18). Reads were processed with BBMap tool (https://sourceforge.net/projects/bbmap/) to remove PCR duplicates, and then further trimmed the random barcode using cutadapt tool and remove low-quality reads again. Reads were then aligned to the relevant genome (human-hg19) using Tophat2 (version 2.1.1) and bowtie2 (version 2.3.5.1) with at most three mismatches. The generated .bam files were split into positive strand and negative strand using Samtools, and then sorted. Identification of sequence variants was conducted by measuring the base composition at each position using fine-tuned bam-readcount (https://github.com/genome/bam-readcount). The generated bam-readcount results were parsed and analyzed by in-house scripts. Misincorporation ratio at each methylated site (m1A, and m22G) in dsRNA were calculated by data output from bam-readcount pipeline, and also confirmed by direct visualization through IGV software.
Library strategy: DAMM-seq
Genome_build: hg19

source_name: cell culture

growth_protocol: Human HepG2 cell line used in this study were all purchased from ATCC (the American Type Culture Collection). HepG2 cell line was maintained in DMEM (GIBCO, 11995), supplemented with 10% FBS and 1% 100X Pen/Strep (GIBCO). All cells were cultured at 37°C under 5.0% CO2, at Heracell™ VIOS 160i incubator (Thermo Scientific).

extract_protocol:
Basically, as the first step of harvesting cells, the cells were washed once with DPBS buffer for each plate after aspirating the media. ALKBH7 knockdown HepG2 cells were prepared as described (two replicates each, five 15-cm plates per replicate). For each sample, 250 µL of Protein G Dynabeads (Invitrogen™, 10004D) was washed twice and resuspended in 1 mL of IP wash buffer (50 mM HEPES, pH 7.5, 150 mM NaCl, 1 mM MgCl2, 0.5% NP-40). 25 µg of anti-dsRNA mAb (J2)28,30 was added to the beads and incubated for 1 hour at room temperature, followed by another 1-2 hours at 4 °C. Cultured cells were washed once with cold DPBS. Each plate of cells was soaked in 5 mL cold DPBS and collected by cell lifters, combining 5 plates for each sample. The cell suspension was spun at 300 g at 4 °C for 2 mins. Cells were resuspended in 1 mL NP-40 lysis buffer (10mL solution: 50 mM HEPES pH 7.5, 150 mM NaCl, 2 mM EDTA, 10 mM MgCl2, 0.5% NP-40, plus 50 µL TURBO™ DNase (2 U/µL, AM2238, Invitrogen), 500 µL SUPERase•In™ RNase Inhibitor (20 U/µL, AM2694, Invitrogen), Pierce™ EDTA-free Protease Inhibitor Tablet) and incubated at 4 °C for 30 mins. The lysate was spun at 16,000 g at 4 °C for 5 mins. The supernatant was transferred to a new Eppendorf tube and 10 µL of that was kept as the “input”. The lysate was diluted to 4.75 mL with IP wash buffer. 250 µL of J2-Dynabeads was added to the lysate and incubated at 4 °C for 2 hours. The magnetic beads were washed once with 1 mL IP wash buffer and transferred to a new Eppendorf tube. The beads were further washed twice by 1 mL of IP wash buffer. Then the enriched dsRNA was eluted from beads and purified by TRIzol reagent.
Around 50 ng human cellular double-stranded RNA by J2-IP (dsNRA) was fragmented into 40-70 nt using RNA Fragmentation Reagent (AM8740, Invitrogen) following the manufacturer’s protocol and Oligo Clean & Concentrator (Zymo Research). These RNAs can be from diverse cellular treatments such as siALKBH7+empty-vector vs. siALKBH7+wild-type ALKBH7 vs. siALKBH7+mutant ALKBH7. Then the library construction procedures will be conducted with T4 PNK end repair, RNA 3’-adapter ligation, HIV RT reverse transcription, cDNA 3’-adapter ligation and PCR amplification respectively, according to standard steps in section “DAMM-seq for methylated site detection”. All libraries were sequenced on Illumina NovaSeq 6000 with paired-end 50 bp read length.

treatment_protocol: siRNA knockdown and plasmid transfection. Typical 15-cm plates of human HepG2 cells were prepared for 48-hour ALKBH7 knockdown and plasmid rescue. AllStars negative control siRNA from Qiagen (1027281) was used as control siRNA (siControl). Human ALKBH7 siRNA was ordered from Qiagen with catalog number as Hs_SPATA11_3 FlexiTube siRNA (SI00730793). Transfection was achieved by using Lipofectamine RNAiMAX (Invitrogen) for siRNA. The plasmid for human ALKBH7 overexpression was purchased from VectorBuilder with Vector ID: VB180629-1142wpx, where the inactive mutant was generated by deleting the mitochondria targeting sequnence. Typical 15-cm plates of human HepG2 cells were used for siALKBH7 knockdown, and then transfected with ALKBH7 wild-type or mutant plasmids after 16-hour konckdown, where Lipofectamine LTX Plus (Invitrogen) was used for plasmid transfection following the manufacturer’s protocols. Cells were harvested after 48 hours.

tag: cell type

tag: treatment group


title: HepG2_dsRNA_ALKBH7-WT_rep2


title: HepG2_dsRNA_ALKBH7-mutant_rep1


title: HepG2_dsRNA_ALKBH7-WT_rep1


title: HepG2_dsRNA_empty-vector_rep2

value: siALKBH7+empty vector


title: HepG2_dsRNA_empty-vector_rep1


title: KCR3

status: Public on May 05 2021

city: Hangzhou

first: Huizeng

last: Sun

state: Zhejiang

address: 866 Yuhangtang Road

department: College of Animal Sciences

country: China

institute: Zhejiang University

data_processing:
Low-quality bases and adapter sequence was trimmed and quality of reads was filtered using fastq-mcf with parameters quality score ³ 20 and length ³ 75
The cleaned reads were then aligned to the reference bovine genome UMD3.1 (http://bovinegenome.org/?q=umd_downloads) and assembled with TopHat2 (v2.0.9) software package
Samtools (v1.1) was then applied to generate BAM alignment files and convert them into SAM format
HTSeq-count (v0.6.1) was used to quantify the number of mapped reads per each bovine gene
the number of mapped reads was normalized into counts per million (CPM) according to the formula: CPM = (number of reads mapped to a gene) ÷ (total number of reads mapped to all annotated genes) × 106.
Genome_build: bovine genome UMD3.1 (http://bovinegenome.org/?q=umd_downloads)
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample

organism: Bos taurus

source_name: rumen epithelium

extract_protocol:
Approximately 100 mg of frozen tissue samples were ground to fine powder in a sterilized mortar and then rumen epithelium, liver, and muscle tissue samples were applied to isolate the total RNA using a mirVana total RNA Isolation Kit (Ambion, Carlsbad, CA, USA) while backfat tissue was applied to isolate total RNA using RNeasy Lipid Tissue Mini Kit (Qiagen, Germany) following the manufacturer’s instructions. The RNA was quantified using the Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA) and checked for purity and integrity using the Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA, USA). RNA with the ration of 28S/18S ranging from 1.7 to 2.4 and the RNA integrity number greater than 7.0 was used for RNA-Seq library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: rumen epithelium

tag: feed efficiency

value: Low

tag: breed

value: Kinsella


title: Colon-2 [TMG126_32_S39]

status: Public on Apr 30 2021

city: Suita

first: Hiroyuki

last: Mizuguchi

state: Osaka

address: 1-6, Yamadaoka

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Osaka University

data_processing:
Illumina Real-Time Analysis (RTA) v2.7.7 software used for basecalling.
Sequenced reads were mapped to GRCh38 whole genome using STAR aligner.
After filtering out duplicate reads, RNA quantification and normarization with Trimmed mean of M-values (TMM ) or Transcripts per million (TPM )  were done by using Strand NGS 3.4 (Strand Life Sciences).
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with TMM or TPM-normalized gene counts for every gene and every sample

source_name: Colon

growth_protocol: Caco-2 cells were obtained from the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany. Caco-2 cells were maintained at 37℃, 8% CO2 and 95% relative humidity in a cell culture dish supplemented with DMEM + 3.7 g/L NaHCO3 (Biochrom AG), MEM-NEAA (Thermo Fisher Scientific), L-Glutamine (Biochrom AG), penicillin-streptomycin (Thermo Fisher Scientific) and 10% FBS (Gibco, Themo Fisher Scientific). The passage number of the Caco-2 cells was between 60 and 90. Total RNA was extracted and purified by using an RNeasy Mini kit (QIAGEN) according to manufacturer’s standard protocol. RNA quality was evaluated in the same way as the biopsy samples using the BioAnalyzer (Agilent Technologies).  The human iPS cell line, YOW-iPS cell, was maintained on a feeder layer of mitomycin C-treated MEF (mouse embryonic fibroblasts, Millipore) with ReproStem medium (ReproCELL) supplemented with 10 ng/ml fibroblast growth factor 2 (FGF2, KATAYAMA CHEMICAL INDUSTRIES).Intestinal differentiation of human iPS cells was performed according to our previous report. Before the initiation of intestinal differentiation, human iPS cells were dissociated into clumps by using dispase (Roche) and plated onto the BD Matrigel Matrix Growth Factor Reduced (BD Biosciences)-coated apical chamber of BD Falcon cell culture inserts (6-well plate, 1.0 μm pore size, 1.6×106 pores/cm, PET Membrane). These cells were cultured in the MEF-conditioned medium for 2-3 days. For the definitive endoderm differentiation, human iPS cells were cultured for 4 days in RPMI1640 medium (Sigma-Aldrich) containing 100 ng/ml Activin A (R&D Systems), 1×GlutaMAX (Thermo Fisher Scientific), penicillin-streptomycin, and 1×B27 Supplement Minus Vitamin A (Thermo Fisher Scientific). During the definitive endoderm differentiation, the mesendoderm cells (day 2) were transduced with 3,000 vector particles (VP)/cell of FOXA2-expressing adenovirus (Ad) vector (Ad-FOXA2) for 1.5 hr to promote definitive endoderm differentiation.  For the induction of intestinal progenitor cells, the definitive endoderm cells were cultured for 4 days in the intestinal differentiation medium [DMEM, high glucose (FUJIFILM Wako) containing 5 μM 6-bromoindirubin-3'-oxime (BIO; Calbiochem), 1×MEM Non-Essential Amino Acids Solution (Thermo Fisher Scientific), penicillin-streptomycin, 1×GlutaMAX, and 100 μM β-mercaptoethanol] supplemented with 10 μM N-[(3,5-difluorophenyl) acetyl]-L-alanyl-2-phenyl-1, 1-dimethylethyl ester-glycine (DAPT; Peptide Institute), and 10% Knockout Serum Replacement (Thermo Fisher Scientific).  For the induction of intestinal epithelial cell monolayers, the intestinal progenitor cells were cultured for 11 days in intestinal differentiation medium supplemented with 1 μM BIO and 2.5 μM DAPT, and then cultured for 15 days in the Wnt-3A-conditioned intestinal differentiation medium supplemented with 0.1 μM BIO, 1 μM DAPT, 250 ng/ml EGF, and 10 μM SB431542. During the intestinal differentiation, the intestinal progenitor cells (day 8) were transduced with 3,000 VP/cell of Ad-CDX2 (caudal-related homeobox transcription factor 2) for 1.5 hr to promote intestinal differentiation.

extract_protocol:
RNA was harvested using QIAzol reagent.Illumina TruSeq stranded totalRNA (#20020596) was used with 300 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Crohn’s Disease (CD) or Ulcerative colitis (UC)

tag: sampling region

value: non-inflammatory area

tag: age (year)

tag: Sex

value: male

value: Japanese


title: Rectum-1 [TMG126_39_S44]

source_name: Rectum

tag: race


title: Colon-6 [TMG126_41_S32]


title: Ileum-5 [TMG126_45_S29]

source_name: Ileum


title: Ileum-7 [TMG126_49_S35]

value: female


title: HN3

tag: diagnosis

value: OUD

tag: timeofdeath

value: White

tag: pmi

value: Cyclobenzaprine, Norcyclobenzaprine, Fluoxetine, Norfluoxetine, Ethanol

value: Asthma; Recurrent Bronchitis; Degenerative Joint Disease

value: B, D, O, P, Z

value: Y

tag: mannerofdeath

value: Accidental

tag: causeofdeath

value: Combined Drug Overdose

tag: correctedtod


title: D56_Mut

description: Sample represents a pool of 3 cortex and 3 ganglionic eminence organoids created from Rett syndrome patient iPSC expressing a 705delG mutant MECP2 allele.  The mutation results in a frameshift truncation (E235fs). The sample was collected at Day 56 in the differentiation scheme.

tag: genotype

value: MECP2 705delG/+ (Mutant MECP2 expression)

tag: tissue

value: Unfused cortex and ganglionic eminance organoids created from Rett syndrome iPSC expressing a MECP2 707delG allele (functional null)


title: Colon-9 [TMG126_48_S34]


title: Ileum-4 [TMG126_40_S31]


title: KCL3

source_name: Liver tissue

value: liver

value: Low


title: Colon-5 [TMG126_38_S28]

value: Crohn’s Disease (CD) or Ulcerative colitis (UC)


title: Colon-10 [TMG126_50_S36]

value: non-inflammatory area


title: KCR1

value: rumen epithelium

value: Kinsella


title: Rectum-2 [TMG126_42_S45]

value: male

value: Japanese


title: Colon-1 [TMG126_29_S26]


title: 192563_PBMC

value: Female

tag: age

tag: ethnicity

value: Not Hispanic or Latino

tag: disease stage

value: Acute/Recent onset

tag: isolate

value: Subject 192563

tag: assay

value: bulk BCR


title: Colon-8 [TMG126_46_S30]

tag: disease state

tag: sampling region


title: Colon-3 [TMG126_33_S43]

tag: age (year)

tag: Sex


title: KCL2

tag: feed efficiency

tag: breed


title: Ileum-2 [TMG126_31_S38]

tag: race


title: Duodenum-4 [TMG126_43_S46]

source_name: Duodenum


title: Ileum-1 [TMG126_28_S25]


title: Colon-7 [TMG126_44_S47]


title: Colon-4 [TMG126_34_S40]


title: KCR2


title: Ileum-6 [TMG126_47_S33]


title: Ileum-3 [TMG126_37_S27]


title: Duodenum-3 [TMG126_36_S42]


title: Duodenum-1 [TMG126_30_S37]


title: STINGseq-v1_HTO

status: Public on Apr 08 2021

city: New York

first: John

middle: A

last: Morris

state: New York

address: 101 Avenue of the Americas, 4th Floor

institute: New York Genome Center

library_source: other

data_processing:
cDNA reads were mapped to the human genome (hg38, ensembl v96). cDNA, HTO, ADT, and GDO reads were quantified using 10x Cell Ranger v.6.0.0 to generate UMI count matrices.
Cells were demultiplexed based on their HTO counts into their singlets after normalization (centered log ratio transformation) using the HTOdemux function in Seurat v.4.0.1.
For STINGseq-v1 and STINGseq-v2, gRNAs per cell were identitied with the 10x Cell Ranger v.6.0.0 determined threshold (with a minimum UMI = 3 threshold applied). For BeeSTINGseq, we tested each gRNA at UMI thresholds from 1-5.
Assembly: hg38
Supplementary files format and content: Processed data provided in standard UMI count matrix format for cDNA, GDO, HTO, and ADT modalities. Each sample has three files separated into features, barcodes and a sparse matrix file. STINGseq-v1 and STINGseq-v2 GDO files have the UMI threshold files included.

molecule: other

source_name: Human erythroleukemic cell line, K562, expressing KRAB-dCas9-MeCP2

growth_protocol: K562 cells were acquired from ATCC (CCL-243) and were maintained at 37C with 5% CO2 in R10 media: RPMI with stabilized L-glutamine (Thermo Fisher 11875119) supplemented with 10% fetal bovine serum (Thermo Fisher 16000044).

extract_protocol:
For STINGseq-v1, we ran one lane of a 10x Genomics 5’ kit (Chromium Single Cell Immune Profiling Solution v1.0, 1000014, 1000020, 1000151) with cell hashing performed using four hashtag-derived oligonucleotides (HTOs). For STINGseq-v2, we ran four lanes of a 10x Genomics 5' kit (Chromium Next GEM Single Cell 5' Kit v2 1000265) with cell hashing performed using eight HTOs. For BeeSTINGseq, we ran three lanes of a 10x Genomics 5’ v2 kit (Chromium Next GEM Single Cell 5' Kit v2 1000265) with cell hashing performed using nine HTOs.
Gene expression (cDNA), hashtags (HTOs), guide RNA (Guide-derived oligos, GDOs) libraries, and oligo-tagged antibodies (ADTs) were constructed by following 10x Genomics and ECCITE-seq protocols. We sequenced all cDNA, HTO, GDO, and ADT libraries with  a NextSeq 500 or NovaSeq 6000 (Illumina).
ECCITE-seq sequencing strategy, with the following read recipe: R1 = 26; i7 = 8; R2 = 57

treatment_protocol: Transductions were performed with concentrated lentivirus and, after 48 hours, selected with puromycin for 10 days.

tag: cell line

tag: genotype/variation

value: expressing KRAB-dCas9-MeCP2


title: St61-TRDKO2_S11

status: Public on Mar 31 2021

data_processing:
Short reads mapping (STAR 2.6.1c)
Reads counting (featureCounts v1.6.3)
Genome_build: X. tropicalis v9.1
Supplementary_files_format_and_content: Tab-delimited text file for reads counts of each gene.

source_name: Intestinge of stage61, TR knockout

growth_protocol: All animal care were performed as approved by Animal Use and Care Committee of NICHD. The Intestine samples were collected from WT and TRDKO tadpoles at stage 54 and stage 61.

extract_protocol:
Intestine RNA was extracted by using RNeasy kit. One ug of total RNA was used for the constuction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

value: intestine

value: TR knockout


title: St61-TRDKO3_S12

tag: genotype


title: St61-WT3_S9

source_name: Intestine of stage61, wild type

tag: tissue

value: wild type


title: St61-WT2_S8


title: STINGseq-v1_GDO

value: Human erythroleukemic cell line, K562, expressing KRAB-dCas9-MeCP2


title: St61-TRDKO1_S10

source_name: Intestinge of stage61 , TR knockout


title: Duodenum-2 [TMG126_35_S41]


title: RosaWT_MCMV_scRNA-seq

status: Public on Apr 17 2021

city: SAINT LOUIS

first: Megan

last: Cooper

state: MISSOURI

address: MPRB, 6th floor, 4905 Childrens Place

department: Pediatrics

institute: Washington University in St Louis

data_processing:
Raw FASTQ files were aligned to the mm10 reference using CellRanger (v3.1.0) count algorithm
Barcode and UMI count files were aggregated and normalized using CellRanger (v.3.1.0) aggr default options
Quality control and analysis of the matrix file was performed using Seurat V3 software for R. Filtering criteria excluded cells with mt RNA % > 10 and cells with < 200 features
Clustering was done using pca (20 PCS) and Umap on the integrated data
Genome_build: mm10
Supplementary_files_format_and_content: matrix file (h5)containing gene expression information for each feature (gene) and its respective barcode (individual cell). A processed and filtered Seurat R object containing the project metadata, normalization and clustering.

source_name: spleen - sorted NK cells

extract_protocol: Illumina 10X genomics 3’ V3

treatment_protocol: Murine NK cells were enriched from spleens using negative selection beads. Sorting was accomplished on a FACSAria Fusion sorter (BD) using FACSDiva software (BD)

value: spleen - sorted NK cells

value: Wild type

tag: infection

value: MCMV


title: RosaWT_Control_scRNA-seq

value: Control


title: St54-TRDKO3_S6

source_name: Intestinge of stage54, TR knockout


title: St54-WT2_S2

source_name: Intestine of stage54, wild type


title: St54-TRDKO2_S5


title: St61-WT1_S7


title: St54-WT3_S3


title: St54-WT1_S1


title: R076 Month 0

status: Public on Feb 17 2021

first: Rachel

last: Lai

institute: Imperial College London

data_processing:
basecalling with bcl2fastq v2.20.0
alignment and quantification with BABS-RNASeq (https://github.com/crickbabs/BABS-RNASeq) and default parameters
Genome_build: GRCh38 Ensembl release-89
Supplementary_files_format_and_content: tab-delimited expression matrix for estimated raw counts in each replicate from RSEM

source_name: Whole blood

extract_protocol:
Total RNA was extracted from whole blood collected in PAXgene Blood RNA Tubes (QIAGEN/BD Biosciences) using the PAXgene Blood RNA Kit (QIAGEN, Venlo, Netherlands). The quantity and quality of the extracted RNA were measured by the Qubit fluorometer and the Caliper LabChip system, respectively.
RNA libraries for whole blood RNA were constructed using the Ovation Human Blood RNA-Seq Library Systems (Tecan, Mannedorf, Switzerland) where ribosomal and globin RNA were removed according to the manufacturer’s protocol. The final libraries were assessed using TapeStation 2200 System (Agilent, Santa Clara, CA). All libraries were sequenced on Illumina Hi-Seq 4000 instrument with paired-end 100 cycle reactions and 40 million reads per sample.

value: HIV-TB co-infected

tag: treatment

value: control

tag: time

value: month 0

value: Whole blood


title: R075 Month 0


title: R089 Month 0


title: R047 Month 6

value: Antiretroviral treatment (ART)

value: month 6


title: R041 Month 0


title: R037 Month 6


title: Cox10KO_Control_scRNA-seq


title: R028 Month 6


title: Cox10KO_MCMV_scRNA-seq


title: STINGseq-v1_cDNA


title: St54-TRDKO1_S4

source_name: Intestinge of stage54 , TR knockout


title: R006 Month 6


title: R009 Month 6


title: R013 Month 0


title: R006 Month 0


title: Leukapheresis_Donor_1

status: Public on Jan 22 2021

city: Shanghai

first: Xiaonan

address: 227 Chongqing South Road

department: School of Public Health

institute: Shanghai Jiao Tong University School of Medicine

library_source: transcriptomic single cell

data_processing:
Reads aligned to hg19 and processed using Cell Ranger v2.0.0. The expected number of cells was set to 10,000.
The downstream analysis was done using Scanpy (version 0.2.3).
Genome_build: hg19
Supplementary_files_format_and_content: h5 files from Cell Ranger output with UMI count matrix, gene names and cell barcodes

source_name: PBMC

growth_protocol: MM.1S cells were obtained from ATCC (CRL-2974) and cultured in RPMI (Lonza) supplemented with 10% FBS (Gibco) and 1% Glutamax (Gibco). Leukapheresis samples were thawed, washed and seeded at a concentration of 2x10e6 cells/ml in TexMacs (Miltenyi) supplemented with human AB serum (Seralab) and IL-7 and IL-15 (Miltenyi) in 24 well plates.   Similarly, product samples were thawed, washed and resuspended at a concentration of 1x 10e5 CAR+ cells/ml in 0.5 ml of culture media and cultured for 24 hours in 48 well plates. For the antigen-exposure experiments, product samples were co-cultured in the presence of MM1.s cells in a 1:1 effector (CAR+ cells)/target (MM1.s) ratio.

extract_protocol:
PBMCs were derived from healthy donors leukapheresis. Peripheral blood leukapaheresis were obtained from the NHS as part of a research study (IRAS ID 185945) or purchased as Leuko Paks from AllCells.
Samples were processed following manufacturer’s recommendations for Chromium Single Cell 3′ Library & Gel Bead Kit v2 (10X Genomics).

treatment_protocol: Genetically modified T cells were generated using the CliniMacs Prodigy (Milteny) following manufacturer’s instructions. Transduction was performed using an APRIL-CAR retroviral vector as previously described (PMID 29284597).

tag: individual

tag: condition

value: WT

tag: cell type

value: PBMC


title: Product_Donor_1

source_name: CAR T cells

value: Unstimulated

value: CAR T cells


title: Product_Donor_2


title: Stimulated_product_Donor_1

value: Stimulated


title: Stimulated_product_Donor_3


title: RNA-seq siRRP40 rep 2

status: Public on Jan 03 2021

city: Aarhus C

first: Søren

last: Lykke-Andersen

address: C.F.Møllers Allé 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

description:
total RNA
batch 2

data_processing:
Illumina software used for basecalling (Casava) and demultiplexing
TT-seq/RNA-seq: the fastq files were mapped to the reference genome (GRCh38 + RNA spike-ins) using STAR aligner to generate the BAM alignment files
TT-seq/RNA-seq: the BAM files were filtered to contain only uniquely mapped reads with Samtools
TT-seq/RNA-seq: Size-factors for sequencing depth normalization were obtained using the DESeq2 algorithm from counts on reduced GenCode v21 annotation generated with HTSeq. The reads mapping to spike-ins were used to estimate antisense and contamination bias (contaminating unlabeled RNA in 4sU-labeledRNA).  TT- and RNA-seq data were corrected accordingly. The experiments were done in duplicates in two batches and the data were batch corrected using the limma package.
TT-seq/RNA-seq: TT-seq/RNA-seq: Size-factors for sequencing depth normalization were obtained using the DESeq2 algorithm from counts on reduced GenCode v21 annotation generated with HTSeq. The reads mapping to spike-ins were used to estimate antisense and contamination bias (contaminating unlabeled RNA in 4sU-labeledRNA).  TT- and RNA-seq data were corrected accordingly. The experiments were done in duplicates in two batches and the data were batch corrected using the limma package.
3'-seq: reads were trimmed using the bbduk.sh script from BBMAP and homopolymeric A-stretches removed from reads.
3'-seq: the data was mapped using STAR against a compound index composed of hg38 merged with ERCC spike-ins.
3'-seq: 5' ends of uniquely mapped reads were used for downstream analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig; normalized and bias corrected coverage generated with…

source_name: tissue culture cells

growth_protocol: HeLa cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol:
TT-seq/RNA-seq: Six in vitro transcribed spike-in RNAs were added to the lysates (TRIzol, Thermo) followed by extraction of RNA according to the manufacturer’s protocol. The RNA was then sonicated and used as input for RNA-seq or for further purification of 4sU-labeled RNA. 4sU-labeled RNA was first biotinylated with EZ-Link HPDP-Biotin (Pierce) and isolated with µMACS Streptavidin Kit (Miltenyi). 4sU-labeld RNA was eluted by cleaving off the biotin with DTT. Both total RNA and 4sU-labeled RNA purified prior to libary preparation using the miRNeasy Micro Kit (Qiagen) including DNse I treatment to remove genomic DNA.
3'-seq:
TT-seq/RNA-seq RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded Total RNA Sample Prep kit).
3'-seq libraries were generated with standard and modified Lexogen 3'-seq protocols. The modified preapration included 3'end polydenylation in vitro using E.coli poly(A) polymerase ('xPAP') preceeding the NGS library preparation with the QuantSeq REV kit according to manufacturer's protocol (Lexogen).
RNA-Seq, paired-end; RNA 3'end seq, single-end

treatment_protocol: Two rounds of transfections were performed. The first transfections were performed using SilentFect (final dilution 1:1000) in RPMI 1640 medium. Two days after the first transfection, the media was changed, and the transfection was repeated using Lipofectamine 2000 (final dilution 1:1000) in RPMI 1640 medium. siRNAs were used at a final concentration of 15 nM of each siRNA. 24 hours after the second round of transfections, cells were labelled for 5 min or 10 min for TT-seq or 3'-seq, respectively, with 500 µM 4-thiouridine minutes and harvested.

value: HeLa Kyoto

value: cervix

value: epithelial

tag: sirna


title: Stimulated_product_Donor_2


title: Leukapheresis_Donor_3


title: Product_Donor_3


title: RNA-seq siRRP40 rep 1

description:
total RNA
batch 2


title: TT-seq siRRP40 rep 2

description:
4sU-labeled RNA
batch 2


title: TT-seq siRRP40 rep 1

description:
4sU-labeled RNA
batch 2


title: TT-seq siINTS11 rep 2

description:
4sU-labeled RNA
batch 2


title: TT-seq siCPSF3 rep 1

description:
4sU-labeled RNA
batch 1


title: TT-seq siCPSF3 rep 2

description:
4sU-labeled RNA
batch 2


title: TT-seq siINTS11 rep 1

description:
4sU-labeled RNA
batch 1


title: TT-seq siEGFP rep 2

description:
4sU-labeled RNA
batch 2

value: EGFP


title: R025 Month 6

city: London

address: Du Cane Road

tag: disease state


title: TT-seq siEGFP rep 1

description:
4sU-labeled RNA
batch 1


title: HT29 DMSO #2

status: Public on Dec 14 2020

city: Ottawa

first: Yannick

middle: D.

last: Benoit

state: Ontario

address: 451 Smyth road

country: Canada

institute: University of Ottawa

description: processed data file: HT29_vs_HIEC.DMSO_all_salmon.txt

data_processing:
Quantified transcripts from GENCODE v27 with salmon v0.9.1 using --gcBias flag.
Performed fold change analysis using DESeq2 as follows
Read transcript quantification data with tximport library and summarized to gene level quantification.
Filtered to retain genes with at least 5 reads assigned in at least two samples.
Constructed DESeqDataSet object with fourteen samples (two replicates of seven conditions), using the model ~condition (cell type/treatment).
Calculated fold changes using the lfcShrink() function with the apeglm method.
Genome_build: GRCh38
Supplementary_files_format_and_content: *_quant.sf.txt: Salmon transcript quantification: Quantification of GENCODE v27 transcripts using salmon v0.9.1.
Supplementary_files_format_and_content: *_all.txt: DESeq2 fold change results: Results from the DESeq2 lfcShrink() function comparing two conditions, including results for all genes retained after filtering.

source_name: Colorectal cancer cell line

extract_protocol:
RNA was extracted using the total RNA purification kit by Norgen Biotech Corp, following the manufacturer's guidelines. Quantification of total RNA samples was performed with a Qubit HS RNA assay (ThermoFisher Scientific) and fragment size was evaluated with a Fragment Analyzer HS NGS assay (AATI). A RNA Quality Number (RQN) of 8.0 or higher was considered satisfactory for library construction. Library construction was performed with a TruSeq RNA v2 (Illumina) with unique barcodes compatible with the Illumina NextSeq 500 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Colorectal cancer cell line

tag: origin

value: Colorectal adenocarcinoma

value: 48 hours DMSO


title: HT29 YB-1471 10uM #1

value: 48 hours 10uM YB-1471


title: t-hESC YB-1471 10uM #2

source_name: Transformed pluripotent stem cells

value: t-hESC

value: Transformed pluripotent stem cells

value: Spontaneous transformation of H9 ES line


title: t-hESC YB-1471 10uM #1


title: t-hESC DMSO #2

description: processed data file: t_hESC_BIX_all_salmon.txt


title: t-hESC BIX 1uM #1

value: 48 hours 1uM BIX


title: t-hESC BIX 1uM #2


title: t-hESC DMSO #1


title: Leukapheresis_Donor_2

value: WT


title: C_TUMOR_CD11_S5_L003_Nextseq

description: Control treated E0771 tumor

tag: strain


title: HT29 DMSO #1


title: whole blood-CF-18

status: Public on Dec 01 2020

type: RNA

city: Dallas

first: Nicole

last: Baldwin

address: 3434 Live Oak St

institute: Baylor Research Institute

hyb_protocol: Amplified labeled RNA were hybridized overnight to Illumina Beadchips (Illumina) following manufacturer's protocols. Following hybridization each chip was washed, blocked and stained following the manufacturer’s protocols.

scan_protocol: Data was scanned on Illumina Beadstation 500

label: biotin

source_name: whole blood-CF

label_protocol: Following extraction, a LabChip GX instrument (Caliper Life Sciences Inc.) was used to measure the RNA Quality Score (RQS) for each sample. RNA concentration was measured using a Nanodrop 8000 (Nanodrop Technologies). Following RNA extraction and quality control analysis, Globin mRNA was depleted from a portion of each total RNA sample using the GLOBINclear™ 96-well format kit (Ambion). This was followed by another round of RQS and concentration determinations for quality control purposes. 250ng of globin reduced RNA from all samples passing quality control were then amplified and labeled using the Illumina® TotalPrep™-96 RNA Amplification Kit (Ambion).

extract_protocol: Blood was collected in Tempus tubes (Applied Biosystems, Foster City, CA), immediately placed on ice and stored within 2-4 hours at -20°C until further analyses in batches. RNA was extracted, amplified, quantified and globin reduced according to manufacturer’s instructions [ref]. Subsequently RNA was converted to cDNA and hybridized into Illumina Human HT-12 v4 microarray chips (47,323 probes; Illumina, San Diego, CA) as described (ref). After hybridization data was scanned on Illumina Beadstation 500 and Illumina BeadStudio/GenomeStudio software were used for background subtraction and to scale average signal intensities (average normalization)

tag: identifier

tag: age

tag: Sex

value: M

value: White

value: Toddler

tag: state

value: CF

tag: nicotine

value: Nicotine


title: whole blood-CF-16

data_processing: Illumina BeadStudio/GenomeStudio software were used for background subtraction and to scale average signal intensities (average normalization)

tag: race


title: whole blood-CF-20

value: F


title: whole blood-CF-13


title: whole blood-CF-25


title: whole blood-CF-8

value: No nicotine


title: whole blood-CF-15


title: whole blood-CF-23


title: whole blood-CF-6


title: whole blood-CF-28


title: whole blood-CF-5


title: whole blood-CF-2


title: whole blood-CF-24


title: whole blood-CF-22


title: whole blood-CF-3


title: whole blood-CF-7


title: whole blood-CF-1


title: whole blood-CF-12


title: whole blood-CF-14


title: whole blood-CF-27


title: whole blood-CF-11


title: whole blood-CF-26


title: whole blood-Healthy-12

source_name: whole blood-Healthy

value: Healthy

value: Healthy (no nicotine)


title: whole blood-CF-10


title: whole blood-CF-4


title: whole blood-CF-9


title: whole blood-CF-17


title: whole blood-CF-19


title: whole blood-Healthy-11


title: 48h_WT [EB5]

status: Public on Nov 16 2020

data_processing:
Trimmomatic v0.36
STAR v2.5.2a
RSEM v1.2.29
DESeq2 v1.18.1
Genome_build: GRCh38 release 88
Supplementary_files_format_and_content: counts

source_name: Human stem cell-derived macrophage

growth_protocol: Not applicable

extract_protocol:
Total RNA was extracted from human stem cell derived macrophages collected in trizol
RNA-Seq libraries were constructed using Illumina TruSeq Stranded Total RNA library kit

treatment_protocol: Not applicable

tag: agent

value: Infected with WT Mtb

tag: time point


title: 48h_Uninfected [EB4]

value: Uninfected


title: 48h_RD [EB12]

value: Infected with RD1 mutant Mtb


title: 2h_RD [EB9]


title: 48h_RD [EB18]


title: 48h_WT [EB11]


title: 2h_Uninfected [EB7]


title: 2h_Uninfected [EB13]


title: 2h_RD [EB3]


title: 2h_RD [EB15]


title: 48h_RD [EB6]


title: 48h_WT [EB17]


title: 48h_Uninfected [EB16]


title: 48h_Uninfected [EB10]


title: 2h_WT [EB2]


title: 2h_Uninfected [EB1]


title: 2h_WT [EB14]


title: 2h_WT [EB8]


title: whole blood-Healthy-9


title: whole blood-Healthy-4

value: Black


title: whole blood-Healthy-6


title: C2C12 on 100Kpa-hard

status: Public on Oct 27 2020

first: Louis

last: Faure

state: NY

address: 321 E 61st Street

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Count matrices were generated from the fastq files via CellRanger 3.1.0 using mm10-1.2.0 genome annotation
Ambient and background RNA from the count matrices were first removed using CellBender remove-background tool v0.2
Corrected count matrices were cleaned from low quality cells by removing cells having less than 1000 genes or cells that don't fit the expected detected gene vs molecule count relationship.
BAM files from Cellranger pipeline were processed using python command-line velocity tool, using run-10X command with GENCODE M21 genome and repeat masker annotation files
Batch correction, dimensionality reduction, knn graph (cosine distance, knn=100) and clustering (leiden community detection, resolution 1) of the sequencing data from hard and soft conditions was performed using pagoda2 R package
Genome_build: mm10
Supplementary_files_format_and_content: Files ending by _raw_feature_bc_matrix.h5 contain the unfilterted count matrix generated by Cellranger pipeline. Files ending by _cellbender_filtered.h5 contains the filtered and background removed count matrix generated by CellBender remove-backgroudn function. Files ending by _velo.loom contains the spliced/unspliced(ambiguous count matrices generated by velocyto pipeline. p2w_batch_corrected.RData is a RData object that contain the combined and batch corrected datasets, as a web pagoda2 oject. p2w_batch_corrected.bin contain the combined and batch corrected datasets as a pagoda2 web app, which can be opened on http://pklab.med.harvard.edu/nikolas/pagoda2/frontend/current/pagodaLocal/index.html.

growth_protocol: Cells are maintained in 10% fetal bovine serum (FBS) (A3160401, Thermo Fisher Scientific) and 1% Penicillin-Streptomycin (15140-122, Thermo Fisher Scientific) in Dulbeco’s Modified Eagle’s Medium-high glucose (DMEM) (D5796, Sigma).

extract_protocol:
Cells were harvested using 0.05% Trypsin/EDTA, fixed in ice-cold methanol, and stored at -80 C prior to single-cell library preparation
RNA libraries were prepared according to 10X protocol.

treatment_protocol: C2C12 cells were seeded on soft (0.5 kPa) and 933 hard (100 kPa) laminin-coated PDMS gel, and collected every day until 5 days after seeding

tag: cell line

tag: culture condition

value: hard (100 kPa) laminin-coated PDMS gel


title: whole blood-Healthy-8

value: Biracial


title: whole blood-Healthy-7


title: whole blood-Healthy-5


title: whole blood-Healthy-1


title: whole blood-Healthy-2


title: whole blood-Healthy-3


title: Diaphragm, mdx_2

status: Public on Oct 06 2020

city: West Lafayette

first: Shihuan

last: Kuang

address: 901 W State St

institute: Purdue University

data_processing:
The original raw data from Illumina HiSeq are transformed to sequenced reads by base calling.
Raw reads are filtered to remove reads containing adapters or reads of low quality, then mapped to GRCm38/mm10 whole genome using TopHat2.
For the quantification of gene expression level, HTSeq V0.6.1 was used to analyze the read numbers mapped for each gene. The Fragments Per Kilobase of transcript per Million mapped reads (FPKM) of each gene was calculated based on the gene read counts mapped to genes or exons.
A differential expression analysis was performed using the DESeq2 R/EdgeR R package with the threshold of significance set as adjusted p < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Diaphragm

extract_protocol:
mRNA from 1 ug of total RNA is enriched using oligo(dT) beads for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Diaphragm

value: 10-week old

tag: genotype

value: mdx


title: Diaphragm, mdx_3


title: Diaphragm, mdx_1


title: Diaphragm, mdx_PtencKO_2


title: ChIP-Seq Donor_9_visit_1

status: Public on Sep 30 2020

city: Parkville

first: Boris

last: Novakovic

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

institute: Murdoch Children's Research Institute

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using bwa. For peak calling the BAM files were first filtered to remove the reads with mapping quality less than 15, followed by fragment size modeling (http://code.google.com/p/phantompeakqual-tools/). The peak calling algorithm MACS2 http://github.com/taoliu/MACS/) was used to detect the binding sites for the three studied histone marks at p-value of 10-5. H3K4me3 peaks were called using the default (narrow) setting in MACS2.
Genome_build: hg38
Supplementary_files_format_and_content: ChIP-seq files are in bigWig format.

source_name: Adult Human Peripheral Blood

growth_protocol: Neutrophils were isolated from peripheral blood and fixed.

extract_protocol:
ChIP was performed using BLUEPRINT protocols.
Libraries were prepared using the KAPA hyperprep kit.

treatment_protocol: Purified cells were fixed with 1% formaldehyde (Sigma) at a concentration of approximately 10 million cells/ml. Fixed cell preparations were sonicated using a Diagenode Bioruptor UCD-300 for 3x 10 minutes (30 seconds on; 30 seconds off). 33 µl of chromatin was used for immunoprecipitation.

tag: cell type

value: neutrophil

tag: treatment protocol

value: Before vaccination

tag: library strategy

value: ChIP-seq

tag: donor

tag: chip antibody

value: Rabbit polyclonal anti-H3K4me3 (Diagenode, cat. # pAb-003-050)


title: RNA-Seq Donor_22_visit_3

data_processing:
MMSEQ package was used to infer gene expression levels. Reads were mapped to the genome using Bowtie
Genome_build: hg19
Supplementary_files_format_and_content: RNA files are in a .gene.mmseq format, containing counts per gene and log RPKM.

extract_protocol:
RNA was extracted using the RNEasy mini kit.
Libraries were prepared by Novogene

treatment_protocol: Cells were collected in Trizol.

value: 3 months after BCG vaccination

value: RNA-seq


title: ChIP-Seq Donor_23_visit_3


title: ChIP-Seq Donor_15_visit_1


title: ChIP-Seq Donor_22_visit_1


title: ChIP-Seq Donor_9_visit_3


title: Diaphragm, mdx_PtencKO_3

tag: strain


title: whole blood-Healthy-10

tag: identifier

tag: age

value: M

value: White

tag: condition

value: Healthy


title: whole blood-CF-21

tag: Sex

value: F

value: Toddler

tag: state

value: CF

tag: nicotine

value: Nicotine


title: RNA-Seq Donor_23_visit_3


title: Diaphragm, mdx_PtencKO_1


title: ChIP-Seq Donor_21_visit_1


title: ChIP-Seq Donor_23_visit_1


title: RNA-Seq Donor_23_visit_1


title: RNA-Seq Donor_22_visit_1


title: RNA-Seq Donor_9_visit_1


title: ChIP-Seq Donor_21_visit_3


title: ChIP-Seq Donor_22_visit_3


title: ChIP-Seq Donor_15_visit_3


title: RNA-Seq Donor_9_visit_3


title: whole_blood;virus+;S68

status: Public on Aug 18 2020

hyb_protocol: Amplified labeled RNA were hybridized overnight to Illumina HumanHT-12 v4 Beadchips (Illumina) following manufacturer's protocols. Following hybridization each chip was washed, blocked and stained following the manufacturer’s protocols.

scan_protocol: Scanned on an Illumina Beadstation 500

data_processing: Data was normalized using GenomeStudio's Global Average Normalization

source_name: whole blood

label_protocol: total RNA was globin reduced using the GlobinClear Human- SOP.GLOB4.v2; results were amplified using Illumina TotalPrep SOP. AMP1.v2

growth_protocol: Blood samples (1–3 ml) were collected in Tempus tubes (Applied Biosystems) and stored at −20°C.

extract_protocol: Tempus Spin RNA Isolation SOP.EXT8.1

tag: subject

tag: age in days

tag: gender

value: Male

tag: race

tag: respiratory virus detected

value: Yes

value: major


title: whole_blood;virus-;S70

value: No


title: whole_blood;virus-;S67

value: Female


title: whole_blood;virus-;S63


title: whole_blood;virus-;S58

value: other


title: whole_blood;virus-;S57


title: whole_blood;virus+;S51


title: whole_blood;virus-;S69


title: whole_blood;virus+;S71


title: whole_blood;virus-;S49


title: whole_blood;virus-;S62


title: whole_blood;virus-;S66


title: whole_blood;virus-;S56


title: whole_blood;virus+;S46


title: whole_blood;virus+;S53


title: whole_blood;virus-;S52


title: whole_blood;virus-;S64


title: whole_blood;virus-;S59


title: whole_blood;virus-;S45


title: whole_blood;virus+;S47


title: whole_blood;virus-;S60


title: whole_blood;virus-;S55


title: whole_blood;virus+;S54


title: whole_blood;virus-;S50


title: whole_blood;virus-;S65


title: whole_blood;virus+;S43


title: whole_blood;virus+;S61


title: whole_blood;virus+;S48


title: whole_blood;virus+;S44


title: whole_blood;virus+;S42


title: whole_blood;virus-;S41


title: whole_blood;virus+;S38


title: whole_blood;virus-;S34


title: whole_blood;virus-;S29


title: whole_blood;virus-;S40


title: whole_blood;virus-;S39


title: whole_blood;virus+;S33


title: whole_blood;virus-;S26


title: whole_blood;virus+;S20


title: whole_blood;virus-;S31


title: whole_blood;virus-;S36


title: whole_blood;virus-;S25


title: whole_blood;virus-;S28


title: whole_blood;virus+;S21


title: whole_blood;virus+;S30


title: whole_blood;virus-;S18


title: whole_blood;virus-;S35


title: whole_blood;virus-;S15


title: whole_blood;virus-;S32


title: whole_blood;virus+;S37


title: whole_blood;virus-;S17


title: whole_blood;virus+;S23


title: whole_blood;virus-;S27


title: whole_blood;virus-;S22


title: whole_blood;virus-;S19


title: whole_blood;virus-;S24


title: whole_blood;virus-;S13


title: whole_blood;virus+;S14


title: whole_blood;virus-;S16


title: whole_blood;virus+;S11


title: whole_blood;virus-;S9


title: whole_blood;virus+;S6


title: whole_blood;virus-;S10


title: whole_blood;virus-;S8


title: whole_blood;virus-;S7


title: whole_blood;virus-;S12


title: whole_blood;virus-;S4


title: whole_blood;virus+;S1


title: whole_blood;virus+;S5


title: whole_blood;virus-;S3


title: 4447846337_E: whole blood-SoJIA-SoJIA

status: Public on Jun 16 2020

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: tandard Illumina scanning protocol with BeadArray Reader 500X

data_processing: The data were normalised using average normalization with Genome Studio

source_name: whole blood-SoJIA-SoJIA

label_protocol: biotin Biotinylated cRNA were prepared with the Illumina® TotalPrep-96 RNA Amplification Kit

extract_protocol: RNA was extracted with MagMAX™ RNA Isolation Kit

tag: tissue

value: whole blood

tag: dataset

value: SoJIA

tag: sample class


title: 4447846119_K: whole blood-SoJIA-SoJIA


title: C2C12 on 0.5Kpa-soft

tag: cell line

tag: culture condition

value: soft (0.5 kPa) laminin-coated PDMS gel


title: 4447846291_C: whole blood-SoJIA-SoJIA


title: whole_blood;virus+;S2


title: 4447846119_B: whole blood-SoJIA-SoJIA


title: 4447846174_J: whole blood-SoJIA-SoJIA


title: 4447846287_A: whole blood-SoJIA-SoJIA


title: 4447846338_H: whole blood-SoJIA-SoJIA


title: 4447846337_A: whole blood-SoJIA-SoJIA


title: 4447846175_B: whole blood-SoJIA-SoJIA


title: 4447846308_G: whole blood-SoJIA-SoJIA


title: 4447846175_G: whole blood-SoJIA-SoJIA


title: 4447846174_A: whole blood-SoJIA-SoJIA


title: 4447846287_K: whole blood-SoJIA-SoJIA


title: 4447846173_I: whole blood-SoJIA-SoJIA


title: 4447846119_C: whole blood-SoJIA-SoJIA


title: 4447846173_D: whole blood-SoJIA-SoJIA


title: 4447846287_E: whole blood-SoJIA-SoJIA


title: 4447846287_G: whole blood-SoJIA-SoJIA


title: 4447846337_F: whole blood-SoJIA-SoJIA


title: 4447846291_D: whole blood-SoJIA-SoJIA


title: 4447846119_G: whole blood-SoJIA-SoJIA


title: 4447846174_B: whole blood-SoJIA-SoJIA


title: 4447846287_C: whole blood-SoJIA-SoJIA


title: 4447846174_K: whole blood-SoJIA-SoJIA


title: 4447846119_I: whole blood-SoJIA-SoJIA


title: 4447846174_C: whole blood-SoJIA-SoJIA


title: 4447846173_B: whole blood-SoJIA-SoJIA


title: 4447846408_B: whole blood-SoJIA-SoJIA


title: 4447846173_J: whole blood-SoJIA-SoJIA


title: 4447846173_A: whole blood-SoJIA-SoJIA


title: 4447846338_I: whole blood-SoJIA-SoJIA


title: 4447846291_E: whole blood-SoJIA-SoJIA


title: 4447846173_E: whole blood-SoJIA-SoJIA


title: 4447846337_B: whole blood-SoJIA-SoJIA


title: 4447846338_E: whole blood-SoJIA-SoJIA


title: 4447846174_G: whole blood-SoJIA-SoJIA


title: 4447846175_I: whole blood-SoJIA-SoJIA


title: 4447846287_H: whole blood-SoJIA-SoJIA


title: 4447846119_E: whole blood-SoJIA-SoJIA


title: 4447846287_L: whole blood-SoJIA-SoJIA


title: 4447846175_E: whole blood-SoJIA-SoJIA


title: 4447846175_C: whole blood-SoJIA-SoJIA


title: 4856050051_L: whole blood-SLE-SLE

source_name: whole blood-SLE-SLE

value: SLE


title: 4447846119_A: whole blood-SoJIA-SoJIA


title: 4856076024_D: whole blood-SLE-SLE


title: 4447846287_D: whole blood-SoJIA-SoJIA


title: 4447846337_D: whole blood-SoJIA-SoJIA


title: 4447846175_A: whole blood-SoJIA-SoJIA


title: 4856050053_G: whole blood-SLE-SLE


title: 4856050051_C: whole blood-SLE-SLE


title: 4856050053_J: whole blood-SLE-SLE


title: 4856076024_J: whole blood-SLE-SLE


title: 4856050053_A: whole blood-SLE-SLE


title: 4856076024_F: whole blood-SLE-SLE


title: 4856076053_H: whole blood-SLE-SLE


title: 4856050051_E: whole blood-SLE-SLE


title: 4447846173_K: whole blood-SoJIA-SoJIA


title: 4856050051_J: whole blood-SLE-SLE


title: 4856050050_E: whole blood-SLE-SLE


title: 4856050050_A: whole blood-SLE-SLE


title: 4856050053_C: whole blood-SLE-SLE


title: 4856076053_I: whole blood-SLE-SLE


title: 4856050053_L: whole blood-SLE-SLE


title: 4856076053_G: whole blood-SLE-SLE


title: 4856076044_K: whole blood-SLE-SLE


title: 4856050050_D: whole blood-SLE-SLE


title: 4856050051_A: whole blood-SLE-SLE


title: 4856076053_F: whole blood-SLE-SLE


title: 4856050053_K: whole blood-SLE-SLE


title: 4856076053_B: whole blood-SLE-SLE


title: 4856050053_I: whole blood-SLE-SLE