title: HuES64_dMS_HIC2649_MboI

data_processing:
Raw Hi-C reads were mapped to the hg19 version of the human genome and preprocessed using the HiC-Pro pipeline (version 2.11.0-beta) to obtain uniquely mapped deduplicated interactions. These interactions were then processed by using Juicebox to generate .hic files.
Genome_build: hg19
Supplementary_files_format_and_content: hic

source_name: Human embryonic stem cell (hESC)

extract_protocol:
Hi-C libraries were prepared following the protocol described in Rao et. al. 20141. Briefly, one million cells were crosslinked with 1% formaldehyde for 10  minutes at room temperature and then quenched with 0.2M glycine solution. Cells were lysed and nuclei permeabilized with 0.5% sodium dodecyl sulphate for 10 minutes at 62°C. Chromatin was digested with 100 U of MboI restriction enzyme (New England Biolabs). Ends of the restriction fragments were blunted and labeled with a biotinylated nucleotide and then ligated. Nuclei were pelleted, proteins were digested with proteinase K and crosslinks were reversed by heating at 68°C overnight. DNA was sheared in a Covaris focused ultrasonicator to average fragment length of 400 bp. Size-selected DNA was enriched for biotinylated ligation products through binding to T1 streptavidin beads (Thermo Fisher).
Libraries were prepared for Illumina sequencing by performing the end-repair, A-tailing and adapter ligation steps with DNA attached to the beads. Hi-C libraries were amplified directly off the beads and purified for subsequent Illumina sequencing with 100 paired-ends.

value: mesendoderm

tag: restriction enzyme

value: MboI


title: Nanog bait 1_ESC_Rep1

status: Public on Jun 06 2021

type: SRA

city: London

first: Suzana

last: Hadjur

address: 72 Huntley street

department: Cancer biology

country: United Kingdom

institute: Ucl

library_source: genomic

data_processing:
Library strategy: UMI-4C
UMI-4C raw data were processed using the ‘umi4cPackage’ (v0.0.0.9000) pipeline from the Tanay Lab
To briefly summarize the pipeline
raw reads are parsed through the UMI-4C pipeline, those reads containing the bait and padding sequence are retained and demultiplexed if required
The retained reads are split based on a perfect match to the restriction enzyme sequence to create a segmented fastq file. The first 10 bases of read 2 are extracted and attached to the segments derived from each read pair. Segments are aligned to the mm10 genome using bowtie2.
UMI filtering is used to determine the number of molecules supporting each ligation event, this information is stored in an adj table
The resulting UMI-4C tracks are then imported into R where the molecule counts per ligated fragment can be visualized / interrogated
Genome_build: mm10
Supplementary_files_format_and_content: The final tracks after processing through the umi4cPackage pipeline, converted to a readable text file. Contains the number of molecules supporting each ligation event

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: Mouse embryonic stem cells (ESC) were cultured in naïve (2i) conditions and neural stem cells were cultured in EGF/FGF media.

extract_protocol:
cell were fixed and extracted nuclei were processed so to capture DNA fragments in close proximity.
Libraries were constructed according to the UMI-4C protocol. Please see methods section of manuscript for further information.
UMI-4C libraries were pooled and sequenced  on a HiSeq 2500 platform.

treatment_protocol: untreated

tag: cell type

value: Embryonic stem cells

tag: cell culture

value: 2i-LIF grown

tag: umi-4c bait

value: Nanog bait 1


title: HuES64_dMS_HIC1961_MseI

city: Beijing

first: Hua-Jun

last: Wu

state: Beijing

address: 8 science park road, zhongguancun life science park

department: School of Basic Medical Sciences

country: China

institute: Peking University Health Science Center

organism: Homo sapiens

value: MseI


title: F17 CA1_stressRep1

city: oxford

first: Haifei

last: Shi

state: OH

address: 700 E High Street

department: Biology

country: USA

institute: Miami University

library_source: transcriptomic

data_processing:
trimming of any low-quality reads with Phred quality score of Q30 was performed in CLC genomics workbench 10.0
After QC and adaptor read-through trimming, deconvoluting likely PCR based duplicates using UMIs, 98% of the reads mapped to the Rattus norvegicus (Ensembl, Rnor_6.0) genome
Assessment of sample variability was confirmed using Principal Component Analysis in CLC Genomics Workbench 10.0. Potential outliers were confirmed by notes obtained during my punches and discarded.
differential expression gene analysis was performed in CLC Genomics Workbench 10.0 using a bootstrapped receiver operating characteristic (bROC) approach with a Gini coefficient of CONF ≥ 0.95 cut-off for DE of identified genes between nonstress and stress groups
Genome_build: Ensembl, Rnor_6.0) genome.
Supplementary_files_format_and_content: Differential Expression analyses: Stress vs. Nonstress groups for each of the 9 brain regions from females and for each of the 9 brain regions from males

molecule: total RNA

organism: Rattus norvegicus

source_name: brain punches

extract_protocol:
Brain punches were vortexed for 10-20 seconds and total RNA was isolated following manufacturer’s instructions using Maxwell® 16 LEV simplyRNA Tissue kit (Promega, Madison, WI). 100 ng of total RNA was subjected to ribosomal RNA (rRNA) removal using Low Input Ribominus Eukaryote System v2 (Ambion # A15027). Concentration, purity, and integrity of all RNA samples were assessed using a Nanodrop and RNA 6000 pico chip on the Agilent 2100 Bioanalyzer.
An RNA-sequencing library was prepared from the rRNA-depleted RNA using Nextflex Rapid Directional qRNA-Seq Kit (Bioo Scientific, TX, USA).
final pooling and sequencing (Illumina 150bp Paired End HiSeq3000, Center for Genome Research and Biocomputing at Oregon State University, Corvallis, Oregon, USA)

tag: strain

value: Sprague Dawley

tag: postnatal day (pd)

tag: group

value: stress

tag: Sex

value: female

tag: brain region

value: Cornu Ammonis area 1 of the hippocampus


title: F7 OFC_nonstressRep2

value: nonstress

value: orbitofrontal cortex of the prefrontal lobe


title: F7 VMH_nonstressRep2

value: ventromedial hypothalamic nucleus


title: HuES64_dMS_HIC1960_MboI


title: ES FCS_Rep 1_SA1 SP KD_a

description:
ES_FCS_Rep1_SA1_SP_KD_Analysis.txt
ES_FCS_All_Reps_Analysis.txt

data_processing:
ES FCS RNA-seq data were processed using the RNA-seq Nextflow pipeline (v19.01.0), with the following parameters –aligner hisat2 –genome mm10, with –reverse_stranded specified for paired-end samples.
FeatureCounts output was parsed through edgeR (v3.16.5) and DESeq2 (v1.14.1) to generate normalized expression counts
The normalized counts for RNAseq Rep1 were calculated in edgeR. Very lowly expressed genes were removed (rowSum cpm <2 across SCR and SA1SP replicates), normalization factors were calculated using calcNormFactors and dispersions estimated using estimateDisp. The edgeR volcano plot statistics were calculated using the exactTest and topTags functions
To generate the normalized counts for all ES FCS RNAseq experiments for GSEA, the FeatureCounts output for all ES FCS experiments was combined into a single table and read it into DESeq2. A DESeq2 object was built using the function DESeqDataSetFromMatrix and estimation of size factors and dispersions were calculated using the DEseq function. Normalized counts were calculated using the ‘counts’ function. Very lowly expressed genes (rowSum normalized count <10 across all samples) were removed
The ES2i raw reads were parsed into VAST-TOOLS to calculate splicing statistics, therefore there is no processed data for them as the raw reads were used. VAST-TOOLS output reported in publication
Genome_build: mm10
Supplementary_files_format_and_content: ES_FCS_Rep1_SA1_SP_KD_Analysis.txt contains the EdgeR normalized counts  ES FCS Rep1
ES_FCS_All_Reps_Analysis.txt  contains the DESeq2 normalized counts for all ES_FCS experiments

growth_protocol: Mouse embryonic stem cells (ESC) were cultured in serum (FCS) or naïve (2i) conditions.

extract_protocol:
Total RNA was first depleted of rRNA (ES FCS) or enriched for PolyA (ES 2i). Two rounds of rRNA depletion were done.
RNA-seq libraries were prepared using NEBNext Ultra directional RNAseq kit with 8-10 cycles of PCR.

treatment_protocol: ESCs were treated for 24hrs with siRNA pools to Stag1 (SA1) including, SmartPool (SP), 5' or 3’ end of Stag1 (5p and 3p) and two sets of control siRNAs, scrambled (SCR) and Luciferase (Luc).

value: serum-grown

tag: treatment

value: SP siRNA

tag: rna prep

value: rRNA depletion


title: ES FCS_Rep 1_SA1 SP KD_b


title: ES FCS_Rep 1_SA1 SP KD_c


title: F3 VMH_nonstress_Rep1


title: ES FCS_Rep 1_SCR

value: scramble control siRNA


title: ES 2i_Rep 1

value: 2i_LIF grown

value: untreated

value: PolyA+


title: HuES64_dEN_HIC2647_MboI

value: endoderm

value: MboI


title: ES 2i_Rep 1_enriched

value: Embryonic stem cells

value: Probe capture RNAs


title: ES FCS_Rep 2_CTL


title: F3 CA1_nonstressRep1

value: Sprague Dawley


title: HuES64_dEN_HIC1969_MseI

value: MseI


title: F

city: Xi'an

first: Bai

last: Ruan

state: Shannxi

address: No.169, Changle Road

institute: Fourth Military Medical University

data_processing:
CellRanger v3.0.1 was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 16bp 10x barcode and the 10bp UMI. Index contains the sample barcode. Read 2 contains the cDNA information.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited xls files include UMI values of genes for each cell

source_name: liver non-parenchymal cells

extract_protocol:
Hepatic non-parenchymal cell suspensions were loaded on a Chromium Single Cell Instrument (10X Genomics) to generate single-cell GEMs according to the manufacturer's instructions.
Single-cell RNA-seq libraries were prepared using version 3 Chromium Single-cell 3' Library, Gel Bead & Mutiplex Kit (10X Genomics).

tag: tissue

value: liver

tag: status

value: CCl4-mediated liver fibrosis


title: ATAC_WNT_ACT_rep2

city: New York

first: Anna

last: Yoney

state: NY

address: 701 W 168th Street

department: Genetics and Development

institute: Columbia University

description:
replicate 2
ATAC_Peak_Location_combined.txt

data_processing:
RNAseq data were aligned to hg38 using Rsubread and the read counts associated with each gene were analyzed by featureCounts.
Fold changes relative to E7 were obtained using DESeq2.
ATAC-seq data were aligned to hg19 using bowtie2 and visualized using deepTools bamCoverage function.
Peaks were identified using MACS2 narrow peak calling. The area underneath each peak was calculated using the MultiCovBed function.
Genome_build: hg38 (GRCh38) or hg19 (GRCh37)
Supplementary_files_format_and_content: RNA-seq: Feature counts text files for both replicates.
Supplementary_files_format_and_content: ATAC-seq: Individual peak files (.bw) and combined peaks text file (all peaks in both replicates).

source_name: RUES2 human embryonic stem cells

growth_protocol: RUES2 human embryonic stem cells grown (hESCs) in TeSR E7 media + rock inhibitor.

extract_protocol:
For ATAC-seq samples, cells were collected and lysis of the outer membrane was carried out on ice. Nuclei were treated with Tn5 transposase for 30 minutes at 37 C.
For ATAC-seq samples, libraries were prepared from 10 µL of transposed DNA per sample with 10-11 cycles of PCR amplification.

treatment_protocol: hESCs were treated with or without Wnt3a (100 ng/mL) +/- CPI-203 (1 µM) on day 1 and with or without Activin A (10 ng/mL) on day 2. Samples were collected after day 1 or day 2.

tag: cell line

value: human embryonic stem cells

tag: treatment with cpi

tag: time point


title: ATAC_WNT_CPI_rep2


title: ATAC_WNT_E7_rep2


title: ATAC_E7_ACT_rep2


title: HuES64_dEC_HIC2697_MboI

value: ectoderm


title: F7 CA1_nonstressRep2

value: nonstress

value: female

value: Cornu Ammonis area 1 of the hippocampus


title: ATAC_WNT_rep2


title: Q

value: quiescent state


title: F18 DG_stressRep3

value: stress

value: Dentate Gyrus of the hippocampus


title: HuES64_dEC_HIC2694_MboI


title: HuES64_dEC_HIC2036_MboI


title: F7 DG_nonstressRep2


title: ATAC_WNT_CPI_ACT_rep2


title: HuES64_dMS_HIC1959_MboI

value: mesendoderm


title: sig5-3 4C ZT45 rep 3

city: Bristol

first: Antony

middle: N

last: Dodd

address: 24 Tyndall Avenue

department: Life Sciences Building

institute: University of Bristol

data_processing:
Base calling by RTA 2.4.6 and FASTQ creator by BaseSpace.
Sequence data were trimmed for adaptor sequence and imported into Partek Genomics Suite version 6.6
Sequenced reads were mapped to TAIR11 using STAR - 2.5.3a
Quantification to annotated model was performed using  Quantify to annotation model (Partek E/M) for strict paired-end settings.
Counts were normalized using the TMM with defaulst settings. Means  <= 1.0 were excluded.
Genome_build: TAIR 11
Supplementary_files_format_and_content: tab-delimited text file with locus ID and counts per sample (columns)

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: 11 days 12 h photoperiod 19°C

extract_protocol:
Total RNA was extracted from three samples of 10 seedlings each, using Macherey-Nagel Nucleospin II RNA extraction kits.
RNA sequencing libraries were prepared from total RNA using the Illumina TruSeq Stranded mRNA kit, according to manufacturer’s instructions.

treatment_protocol: 24 hours under constant light and then exposed to 19 °C or 4 °C starting at two different times of day (ZT 27  and ZT 45).

tag: temperature

tag: time in ll (zt)

tag: genotype


title: sig5-3 4C ZT45 rep 1


title: sig5-3 4C ZT45 rep 2


title: F22 DG_stressRep2


title: ATAC_E7_rep2

tag: cell type

value: untreated


title: HuES64_dEC_HIC2036_MboI_Rep

tag: restriction enzyme

value: MboI


title: Col-0 4C ZT45 rep 3

value: wild type


title: ATAC_WNT_ACT_rep1

description:
replicate 1
ATAC_Peak_Location_combined.txt


title: ATAC_WNT_E7_rep1


title: HuES64_dEC_HIC1968_MseI


title: F3 OFC_nonstressRep1

tag: strain

value: orbitofrontal cortex of the prefrontal lobe


title: ATAC_E7_ACT_rep1


title: F7 CA3_nonstressRep2

value: Sprague Dawley

tag: postnatal day (pd)

value: Cornu Ammonis area 3 of the hippocampus


title: Col-0 4C ZT45 rep 2


title: ATAC_WNT_CPI_ACT_rep1


title: F18 CEA_stressRep3

tag: group

value: central nucleus of the amygdala


title: HuES64_dEC_HIC1964_MseI_Rep

value: MseI


title: HuES64_HIC2699_MboI_Rep

value: embryonic stem cell


title: HuES64_dEC_HIC1964_MseI

value: ectoderm


title: F17 DG_stressRep1

tag: Sex


title: sig5-3 19C ZT45 rep 3


title: ATAC_E7_rep1

value: human embryonic stem cells


title: ATAC_WNT_rep1


title: HuES64_HIC2147_MseI


title: HuES64_HIC2035_MboI


title: F17 CEA_stressRep1

value: female

tag: brain region


title: F22 CEA_stressRep2


title: KO_undiff_ND23658528_onDMR_Rep3

description: SOX17 upstream TIR boundary CTCF knockout

data_processing:
Library strategy: 4C-Seq
The raw sequencing reads were trimmed by using cutadapt (--discard-untrimmed -e 0.05 -m 25) to remove primer sequences and restriction enzyme sequences. The reads without matching those sequences were removed from further analysis. The remaining reads were then mapped to the reference sequences GRCh37/hg19 by bowtie2 (default parameters). An iterative mapping procedure was performed. Specifically, the full-length reads were first mapped to genome. The unmapped reads were then cut by 5-nt from 3-prime each time until they were successfully mapped to genome. The final mapped reads were assigned to valid fragments. The fragment counts were then normalized by RPM (Reads Per Million) and smoothed by averaging the counts of the closest 5 fragments.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

source_name: Human induced pluripotent stem cell (hiPSC)

growth_protocol: ZIP13K2 cultures were treated with Accutase (Sigma-Aldrich, A6964) supplemented by 10 µM Y-27632 (Tocris, 1254) to obtain single cells. To quench and wash the cells, equal volumes of mTeSR1 (Stemcell Technologies) were added and cells spun down for 5 min. at 300 x g, 21°C. After resuspension in mTeSR1 supplemented by 10 µM Y-27632, cells were counted and seeded according to the manufacturer’s instructions on Matrigel (Corning) pre-coated culture plates / dishes. Media change using the STEMdiff Trilineage Endoderm Differentiation media (Stemcell Technologies) was performed on a daily base after washing the cultures with equal volumes of DPBS (Thermo Fischer Scientific, 14190250) according to the manufacturer’s instructions.

extract_protocol: Circularized Chromosome Conformation Capture (4C) library preparation of undifferentiated, or differentiated CXCR4 enriched cell populations was performed according to the Weintraub A.S. et al. protocol. Therefor NlaIII (NEB R0125) was used as the primary and DpnII (R0543) as a secondary cutter. Touchdown PCR on 4C libraries was performed accordingly using below listed primer-pairs for respective view-points. Illumina adapter ligated sequencing libraries were sequenced for 10 million 150 bp long read pairs per sample on the HiSeq4000 (Illumina).

tag: viewpoint


title: Col-0 19C ZT45 rep 3


title: F22 CA3_stressRep2


title: Col-0 4C ZT45 rep 1


title: F22 BLA_stressRep2

value: basolateral amygdala


title: Col-0 19C ZT45 rep 2


title: ATAC_WNT_CPI_rep1


title: KO_undiff_ND23658528_onDMR_Rep2


title: HuES64_HIC2699_MboI


title: F2 DG_nonstressRep1

value: nonstress


title: sig5-3 19C ZT45 rep 2


title: sig5-3 19C ZT45 rep 1


title: F2 CA3_nonstressRep1


title: RNA_WNT_E7_rep2

description:
replicate 2
RsubreadFeatureCounts_rep2.txt

extract_protocol:
For RNA-seq samples, cells were collected in Trizol and total RNA was extracted.
For RNA-seq samples, libraries were prepared for sequencing using standard Illumina protocols.


title: sig5-3 4C ZT27 rep 3


title: RNA_WNT_CPI_ACT_rep2


title: ESC_2i_PacBio_subreads

data_processing:
Library strategy: Iso-Seq
PacBio reads were processed using the SMRTLINK v8.0.0 IsoSeq3 pipeline.
Circular consensus sequences (CCS) were generated using default parameters (--minPasses = 1, --min-rq = 0.8, CCS Polish = No).  ).
FLNC were determined through further refining using lima (removal of adapters and correct orientation of sequences), poly-A trimming and concatemer removal
FLNC reads were then aligned to the mm10 genome using Minimap2 with the following parameters (-ax splice, -uf, -k14).
Results were visualized in Integrated Genome Viewer (v2.4.19).
Genome_build: mm10
Supplementary_files_format_and_content: Isoseq_flnc-vs-genome.sort.bam file contains the processed flnc reads representing the  Pacbio isoforms after processing through Isoseq3 pipeline
Isoseq_flnc-vs-genome.sort.bam.bai is the index for the above file, for visualisation in a genome browser

molecule: polyA RNA

source_name: embryonic stem cells

growth_protocol: mouse Embryonic stem cells were cultured on gelatin in 2i conditions

extract_protocol:
polyA+ extracted RNA
mRNAs were amplified using the Clontech SMARTer PCR cDNA Synthesis Kit with 9 cycles and used in the SMRTbell library prep.
Pacbio library sequenced on the SMRTseq 2000 platform

treatment_protocol: no treatment

value: embryonic stem cells

tag: cell culture

value: 2i grown

tag: treatment


title: F17 CA3_stressRep1

value: stress


title: KO_undiff_ND23660834_ongene_Rep2


title: RNA_WNT_ACT_rep2

value: untreated


title: RNA_E7_ACT_rep2


title: sig5-3 4C ZT27 rep 2


title: F17 BLA_stressRep1


title: Col-0 19C ZT45 rep 1


title: KO_undiff_ND23658528_onDMR_Rep1


title: RNA_WNT_CPI_rep2


title: Col-0 4C ZT27 rep 3


title: E14 TERATOMA

city: Gyeonggi-do

first: Hyonchol

last: Jang

address: 323, Ilsan-ro, Ilsandong-gu, Goyang-si

country: South Korea

institute: National Cancer Center

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to hg19 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Embryonic stem cell WT

extract_protocol:
RNAs were extracted from mouse embryonic stem cell line according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: teratoma

value: WT


title: sig5-3 4C ZT27 rep 1


title: RNA_E7_rep2

tag: cell line


title: KO_undiff_ND23660834_ongene_Rep1


title: Sox2 T258A ESC

source_name: Embryonic stem cell with Sox2 T258A mutant

value: Embryonic stem cell

value: Sox2 T258A mutant


title: KO_undiff_ND23660834_ongene_Rep3


title: Sox2 T258A TERATOMA


title: E14 ESC


title: RNA_WNT_rep2

tag: treatment with cpi


title: RNA_WNT_E7_rep1

description:
replicate 1
RsubreadFeatureCounts_rep1.txt

tag: time point


title: RNA_WNT_CPI_ACT_rep1


title: Col-0 4C ZT27 rep 1

tag: temperature

value: wild type


title: Col-0 4C ZT27 rep 2

tag: time in ll (zt)


title: WT_undiff_ND23658528_onDMR_Rep2

tag: genotype

value: Wildtype


title: WT_undiff_ND23658528_onDMR_Rep1


title: sig5-3 19C ZT27 rep 3


title: WT_undiff_ND23660834_ongene_Rep3


title: RNA_E7_ACT_rep1

tag: cell type


title: RNA_WNT_ACT_rep1


title: RNA_E7_CPI_rep2


title: sig5-3 19C ZT27 rep 2


title: NILER-COMBO-DAY5-T-CELLS

city: LOS ANGELES

first: Sixue

last: Liu

state: California

address: 10833 Le Conte Avenue

department: Medicine

institute: UCLA

description: 10x Genomics single cell barcoded mRNA from T cells, Sample #2

data_processing:
The reads are first mapped to Grch38 using cellranger software from 10x Genomics
Single-cell, gene-level raw read counts are read from cellranger output and analyzed using Seurat
The normalized count from the Seurat object after IntegrateData and ScaleData step are provided as processed data file
Subsequent clustering analyses are descibed in the full manuscript
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene level expression matrix

source_name: Nras mutated syngeneic mouse model

extract_protocol: Chromium Single Cell 3’ Reagent Kits v3

value: Nras mutated murine melanoma cell line

value: T cells

value: 3' sequencing

tag: cell number


title: sig5-3 19C ZT27 rep 1


title: WT_undiff_ND23660834_ongene_Rep2


title: WT_undiff_ND23660834_ongene_Rep1


title: WT_undiff_ND23658528_onDMR_Rep3


title: NILER-CTRL-DAY5-T-CELLS

description: 10x Genomics single cell barcoded mRNA from T cells, Sample #1

value: no


title: RNA_WNT_rep1

value: human embryonic stem cells


title: Col-0 19C ZT27 rep3


title: RNA-seq_D5_CTCF_p44_CXCR4_pos_Rep3

data_processing:
Gene counts are quantified by using RSEM default parameters with REFSEQ annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Gene quantification files (*.genes.results.txt) are generated using RSEM

growth_protocol: ZIP13K2 cultures were treated with Accutase (Sigma-Aldrich, A6964) supplemented by 10 µM Y-27632 (Tocris, 1254) to obtain single cells. To quench and wash the cells, equal volumes of mTeSR1 (Stemcell Technologies) were added and cells spun down for 5 min. at 300 x g, 21°C. After resuspension in mTeSR1 supplemented by 10 µM Y-27632, cells were counted and seeded according to the manufacturer’s instructions on Matrigel (Corning) pre-coated culture plates / dishes. Media change using the STEMdiff Trilineage Endoderm Differentiation media (Stemcell Technologies) was performed on a daily base after washing the cultures with equal volumes of DPBS (Thermo Fischer Scientific, 14190250) according to the manufacturer’s instructions. Triplicates of either undifferentiated or differentiated ZIP13K226 cultures were treated with Accutase® (Sigma-Aldrich, A6964) and differentiated cultures were further quenched with FACS-buffer containing 5 mM EDTA (ThermoFischer Scientific, 15575020) 10% Fetal bovine serum (FBS) (ThermoFischer Scientific, 26140079) in DPBS (Thermo Fischer Scientific, 14190250). In order to enrich for CXCR4- or CXCR4+ cell fractions of differentiated cultures, cells were stained for anti-Human CRCX4 (CD184) PE (as described under 21. FACS) and compared to Isotype and unstained control sorted for either CXCR4- or CXCR4+ on the Aria II (Beckton Dickinson).

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
RNA isolation including on-column DNase digest of enriched cell populations was performed using the RNeasy Mini Kit (Qiagen, 74104) according to the manufacturer’s instructions.

tag: differentiation days

value: Day 5

tag: cxcr4 status


title: RNA_E7_CPI_rep1


title: Col-0 19C ZT27 rep2


title: RNA-seq_D5_CTCF_p44_CXCR4_pos_Rep1


title: M296-P

data_processing:
The reads are first mapped to Grch38 using HISAT2
Gene level raw read counts are quantified using htseq-count
Ensemble ID to HUGO gene mapping using biomaRt R package
Using log2 counts per million (CPM) as normalized gene expression values
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene level normalized expression matrix

source_name: Human melanoma cell line

extract_protocol:
QIAGEN All Prep DNA/RNA Mini Kit and Ambion mirVana miRNA Isolation Kit
KAPA RNA-Seq Library Preparation Kits

value: Human melanoma cell line

tag: phenotype

value: MEKi sensitive


title: RNA-seq_D5_CTCF_p44_CXCR4_pos_Rep2


title: M245-R5

value: MEKi resistant


title: Col-0 19C ZT27 rep1


title: M245-R4


title: hiPSC-CM_DSG2Mut_r020

city: Baltimore

first: Suraj

last: Kannan

state: MD

address: 720 Rutland Avenue Ross 954

department: Cardiology

institute: Johns Hopkins University

data_processing:
Libraries were mapped to the human genome (GRCh38) using STAR (2.3.1a) with two-pass mode, and then counted using featureCounts (2.0.0) through the Subread package
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: We provide a counts table (output from featureCounts) as well as a phenotype table. Additionally, we include an R workspace with most of the requisite objects loaded. Please see https://github.com/skannan4/dsg2-mut for code and additional files of interest. Please note that the counts table has fractional values due to the multimapping settings from featureCounts. However these are counts, not normalized data.

growth_protocol: All procedures pertaining to human iPSC were conducted under the auspices of a Johns Hopkins IRB approval. Blood samples were collected from the donor (JHU013) and peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll-Paque PLUS density gradient media (GE Healthcare, Waukesha, WI, USA). PBMCs were plated at high density in PBMC growth media (PBMC-M) and expanded for 10 days before being harvested and reprogrammed using the Cytotune 2.0 Sendai virus kit containing Yamanaka factors (Thermo Fisher Scientific, Waltham, MA, USA), per manufacturer’s protocol. After 24 hours, the cells are resuspended in PBMC-M media and seeded into Synthemax-treated tissue plates (Corning, Corning NY, USA) and cultured for 6 days with media changes every other day. On Day 7 after viral reprogramming, the media is replaced with 50:50 PBMC-M:E8.  The cells are harvested with TrypLE Select Enzyme (Thermo Fisher Scientific, Waltham, MA, USA) and plated in E8 with 10µm Y-27632 dihydrochloride (Tocris Bioscience, Bristol, United Kingdom) on plates coated with Geltrex matrix (Thermo Fisher Scientific, Waltham, MA, USA). Colonies were then picked by pipette under a microscope, replated into separate wells of a tissue culture plate, and expanded until passage 10. DNA was then isolated to verify the loss of the Sendai virus and clones were screened via sanger sequencing and karyotyping.

extract_protocol:
hiPSC-CMs cultured to differentiation day 35 were gently dislodged with a cell scraper, suspended in TRIzol reagent and flash frozen for storage. Isolated RNA across the samples had a mean RIN of 9.2.
RNAseq libraries were prepared by an outside vendor (GENEWIZ, South Plainfield, NJ, USA) using a standard poly-A selection protocol for isolating mRNAs. Final libraries were sequenced as 2x150bp paired-end sequencing on an Illumina HiSeq. Samples were sequenced to a depth of ~30-40 million paired reads/cell.

treatment_protocol: hiPSCs were maintained in E8 culture media until the initiation of cardiogenic differentiation via previously described methods based on small molecule modulation of Wnt signaling. Spontaneous beating was observed in all hiPSC-CMs around day 7-10. On differentiation day 28, hiPSC-CMs were replated in RPMI1640 + B27 supplement (B27+ media; Thermo Fisher Scientific, Waltham, MA, USA) onto Geltrex-coated Thermanox coverslips (Thermo Fisher Scientific, Waltham, MA, USA) at a density of 250,000 cells/cm2. hiPSC-CM monolayers were then cultured for 7-10 days, with media changes every other day, until evaluation.

tag: strain/background

value: JHU013 (DSG2 c.2358delA)

tag: genotype/variation


title: RNA-seq_D5_CTCF_p44_CXCR4_neg_Rep3


title: NRAS-PDX9-V2

source_name: Human melanoma PDX

value: Human melanoma PDX


title: NRAS-PDX9-V1


title: RNA_WNT_CPI_rep1


title: RNA-seq_D5_CTCF_p44_CXCR4_neg_Rep2


title: NRAS-PDX9-R1


title: M245-R3


title: hiPSC-CM_DSG2Mut_r019


title: NRAS-PDX8-V1


title: RNA-seq_D5_CTCF_p44_CXCR4_neg_Rep1


title: hiPSC-CM_DSG2Mut_r018


title: hiPSC-CM_DSG2Mut_r017


title: RNA-seq_D5_WT_p40_CXCR4_pos_Rep3


title: hiPSC-CM_DSG2Mut_r016


title: RNA-seq_D5_WT_p40_CXCR4_pos_Rep2


title: NRAS-PDX8-R4


title: M207-R1


title: M296-R3


title: RNA_E7_rep1

value: untreated


title: M207-P


title: hiPSC-CM_WT_r005

value: JHU001 (age- and sex-matched donor)


title: RNA-seq_D5_WT_p40_CXCR4_neg_Rep3


title: NRAS-PDX8-R3


title: RNA-seq_D5_WT_p40_CXCR4_pos_Rep1


title: NRAS-PDX1-V2


title: hiPSC-CM_WT_r004


title: NRAS-PDX8-R2


title: NRAS-PDX8-R1


title: NRAS-PDX1-R4


title: hiPSC-CM_WT_r001


title: NRAS-PDX1-R3


title: hiPSC-CM_WT_r002


title: hiPSC-CM_WT_r003


title: RNA-seq_D5_WT_p40_CXCR4_neg_Rep2


title: M245-P


title: NRAS-PDX3-V2


title: NRAS-PDX1-R5


title: RNA-seq_D5_WT_p40_CXCR4_neg_Rep1


title: NRAS-PDX3-V1


title: NRAS-PDX1-R1


title: NRAS-PDX2-V2


title: NRAS-PDX3-R1


title: NRAS-PDX1-V1


title: RNA-seq_D5_WT_p36_Rep1


title: RNA-seq_D5_WT_p36_Rep3


title: RNA-seq_D0_CTCF_p42_Rep3

value: Day 0


title: NRAS-PDX2-R4


title: NRAS-PDX2-R3


title: RNA-seq_D5_WT_p36_Rep2


title: AM Patient 6 RTR 3

type: RNA

first: Qing

last: Zhang

address: Tiantan Xili 6, Dongcheng Distract

institute: Beijing Tian Tan Hospital, Capital Medical University

hyb_protocol: HOA v2.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on MOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: HOA v2.1 The arrays were scanned by Agilent Microarray Scanner (G2505C)  0.1 XDR protocol and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

source_name: atypical meningioma

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: All samples were formalin-fixed and paraffin-embedded

extract_protocol: RNA extraction by Trizol Reagent (RQ1, promega). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: All samples were obtained from the surgery right before any forms of radiotherapy

value: atypical meningioma (AM)

tag: age

value: 21 years

tag: gender

value: Female

tag: grade

value: WHO grade II

value: Gross total resection+EBRT

tag: recurrence

value: Yes

tag: status

value: Alive


title: NRAS-PDX1-R2

tag: tissue


title: RNA-seq_D0_CTCF_p42_Rep2

tag: cell line


title: NRAS-PDX2-V1


title: RNA-seq_D0_WT_p36_Rep1

value: Wildtype


title: AM Patient 5 RTR 2

value: 27 years

value: Male

tag: treatment


title: NRAS-PDX3-R2


title: AM Patient 1 RTS 1

value: 49 years

value: No


title: AM Patient 2 RTS 2

value: 53 years


title: WTTH1-2: Wild-type Th1, biological rep.2

city: Chongqing

first: Yifei

last: Wang

address: Gaotanya Street

department: Institute of Immunology

institute: Third Military Medical University

description: Gene expression data from Th1 cells in spleen of wild-type mice at day 60-post LCMV Armstrong infection

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 with constant rotation at the speed of 60 rpm.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method.

label: biotin

source_name: Wild-type, LCMV Armstrong D60

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

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

value: lymphocyte

tag: developmental stage

value: memory stage of CD4 T cells in LCMV acute infection


title: RNA-seq_D0_CTCF_p42_Rep1

tag: genotype


title: WTTFH-2: Wild-type Tfh, biological rep.2

description: Gene expression data from Tfh cells in spleen of wild-type mice at day 60-post LCMV Armstrong infection


title: RNA-seq_D0_WT_p36_Rep3


title: WTTFH-1: Wild-type Tfh, biological rep.1


title: WTTH1-1: Wild-type Th1, biological rep.1


title: KOTH1-2: Rictor-null Th1, biological rep.2

description: Gene expression data from Th1 cells in spleen of Rictor-null mice at day 60-post LCMV Armstrong infection

source_name: Rictor-null, LCMV Armstrong D60


title: S47988_Dreznica goat 96

status: Public on Jun 05 2021

type: genomic

city: Domžale

first: Neža

last: Pogorevc

address: Groblje 3

department: Department of Animal Science

country: Slovenia

institute: University of Ljubljana, Biotechnical Faculty

description: Animals were genotyped with Illumina Goat SNP50 BeadChip.

hyb_protocol: standard protocol by commercial lab

scan_protocol: standard protocol by commercial lab

data_processing:
standard protocol by commercial lab
value definition: Genotype: AA,AB,BB,or NC (no call).

label: Cy3, Cy5

organism: Capra hircus

source_name: Dreznica goat

label_protocol: standard protocol by commercial lab

growth_protocol: We sampled the goats on the farms, where they were reared.

extract_protocol: Extraction of genomic DNA from ear tissue was performed using proteinase K and repeated phenol-chloroform extraction.

treatment_protocol: Not treated.

tag: genetic background

value: Dreznica goat

value: Ear tissue


title: S47983_Dreznica goat 91


title: S47982_Dreznica goat 90


title: AM Patient 4 RTR 1

value: atypical meningioma (AM)

value: 64 years


title: S47979_Dreznica goat 87

value: Female


title: NRAS-PDX2-R2

value: Human melanoma PDX

value: MEKi resistant


title: AM Patient 3 RTS 3

value: 20 years

value: WHO grade II

value: Gross total resection+EBRT


title: RNA-seq_D0_WT_p36_Rep2

value: Day 0

value: Wildtype


title: NRAS-PDX2-R1


title: S47987_Dreznica goat 95


title: KOTFH-2: Rictor-null Tfh, biological rep.2

description: Gene expression data from Tfh cells in spleen of Rictor-null mice at day 60-post LCMV Armstrong infection


title: S47972_Dreznica goat 80


title: S47969_Dreznica goat 77


title: S47968_Dreznica goat 76


title: S47965_Dreznica goat 73


title: S47966_Dreznica goat 74


title: S47963_Dreznica goat 71


title: KOTFH-1: Rictor-null Tfh, biological rep.1


title: KOTH1-1: Rictor-null Th1, biological rep.1


title: S47986_Dreznica goat 94


title: S47984_Dreznica goat 92


title: S47980_Dreznica goat 88


title: S47958_Dreznica goat 66


title: S47961_Dreznica goat 69


title: S47985_Dreznica goat 93


title: S47957_Dreznica goat 65


title: S47978_Dreznica goat 86


title: S47977_Dreznica goat 85


title: S47952_Dreznica goat 60


title: S47951_Dreznica goat 59


title: S47975_Dreznica goat 83


title: S47954_Dreznica goat 62


title: S47976_Dreznica goat 84


title: S47974_Dreznica goat 82


title: S47981_Dreznica goat 89


title: S47949_Dreznica goat 57


title: S47946_Dreznica goat 54


title: S47945_Dreznica goat 53


title: S47973_Dreznica goat 81


title: S47970_Dreznica goat 78


title: S47967_Dreznica goat 75


title: S47964_Dreznica goat 72


title: S47944_Dreznica goat 52


title: S47960_Dreznica goat 68


title: S47943_Dreznica goat 51


title: S47959_Dreznica goat 67


title: S47962_Dreznica goat 70


title: S47942_Dreznica goat 50


title: S47971_Dreznica goat 79


title: S47956_Dreznica goat 64


title: S47937_Dreznica goat 45


title: S47940_Dreznica goat 48


title: S47934_Dreznica goat 42


title: S47939_Dreznica goat 47


title: S47935_Dreznica goat 43


title: S47955_Dreznica goat 63


title: S47933_Dreznica goat 41


title: S47948_Dreznica goat 56


title: S47953_Dreznica goat 61


title: S47936_Dreznica goat 44


title: S47930_Dreznica goat 38


title: S47932_Dreznica goat 40


title: S47947_Dreznica goat 55


title: S47931_Dreznica goat 39


title: S47929_Dreznica goat 37


title: S47938_Dreznica goat 46


title: S47950_Dreznica goat 58


title: S47924_Dreznica goat 32


title: S47925_Dreznica goat 33


title: S47922_Dreznica goat 30


title: S47928_Dreznica goat 36


title: S47923_Dreznica goat 31


title: S47920_Dreznica goat 28


title: S47941_Dreznica goat 49


title: S47926_Dreznica goat 34


title: S47921_Dreznica goat 29


title: S47918_Dreznica goat 26


title: S47915_Dreznica goat 23


title: S47914_Dreznica goat 22


title: S47917_Dreznica goat 25


title: S47916_Dreznica goat 24


title: S47919_Dreznica goat 27


title: S47910_Dreznica goat 18


title: S47913_Dreznica goat 21


title: S47912_Dreznica goat 20


title: S47907_Dreznica goat 15


title: S47908_Dreznica goat 16


title: S47927_Dreznica goat 35


title: S47909_Dreznica goat 17


title: S47900_Dreznica goat 8


title: S47904_Dreznica goat 12


title: S47903_Dreznica goat 11


title: S47902_Dreznica goat 10


title: S47905_Dreznica goat 13


title: S47899_Dreznica goat 7


title: S47898_Dreznica goat 6


title: S47897_Dreznica goat 5


title: S47896_Dreznica goat 4


title: S47911_Dreznica goat 19


title: S47895_Dreznica goat 3


title: S47893_Dreznica goat 1


title: S47894_Dreznica goat 2


title: S47906_Dreznica goat 14


title: S47901_Dreznica goat 9


title: 5198

city: Barcelona

first: Carlota

last: Dobaño

address: Rosselló 153

country: Spain

institute: ISGlobal, Hospital Clínic - Universitat de Barcelona

data_processing:
reads were aligned using BWA Aln version 0.7.10 using UCSC RefSeq (Human 19) with mitochondrial genes added
Quantified samples were then quality controlled using mapping summary statistics to remove low quality samples based on predetermined minimum values for the total number of mapped reads, percent of mapped reads mapped to the human genome, etc.
Downstream analysis was applied only to reads that mapped uniquely to a UMI and only mapped to isoforms of the same gene (UMI.unq).
The TMM normalization method was applied to account for differing number of read counts and to address unwanted technical variation. The voom transformation from the limma R package  was applied to transform the data into a form appropriate for linear models.
Genome_build: hg19
Supplementary_files_format_and_content: concatenated_unique_refseq_umi_counts.tsv contains the count matrix for all samples/cells

source_name: PBMC

extract_protocol:
RNA was extracted at the Center for Infectious Disease Research (CIDR, Seattle) using the Promega SV 96 RNA Isolation kit following the manufacturer’s protocol. Samples kept in RNAprotect were centrifuged at 4,000g for 7 minutes at 4°C, cell pellets were resuspended in 150 μL RLT Buffer, and 150 μL of 70% ethanol was added prior to processing with Promega SV 96 RNA Isolation kit. RNAs were eluted with 100 μL nuclease free water. Each 96-well extraction batch was spot checked by Bioanalyzer using Agilent RNA 6000 Pico chip and had an average RIN score of 7.4. RNA samples were distributed in 384 well plates for library preparation. Samples from the same individuals were in the same plate and key study variables (vaccine, site and cases-controls) were checked for balance across plates to avoid batch effects.
An optimized version of Digital Gene Expression (DGE) was used, further reducing the reverse transcriptase reaction volume. In brief, poly(A)+ mRNA from antigen-stimulated PBMCs was linked to unique molecular identifiers (UMIs) using a template-switching reverse transcriptase. Then, cDNA from multiple cells were pooled, amplified, and prepped for multiplexed sequencing using a transposon-based fragmentation method, enriching for 3′ ends and preserving strand information. Nextera XT library preparation and sequence paired-ends were employed on an Illumina NextSeq instrument at the Broad Institute.
SCRB-Seq

tag: cell type

value: PBMC

tag: plate

tag: pid

tag: stimulation

value: dmso

tag: visit

tag: site

value: BAGAMOYO

value: old

tag: vaccine

value: rtss

tag: case

value: control

tag: match

tag: sid

tag: waz

tag: haz

tag: hb

tag: Sex

value: M

value: High


title: 5195

value: hbs

value: MANHICA

tag: age

value: young

value: comparator

value: neither


title: 5193


title: 5200


title: 5196


title: 5197

value: csp


title: 5189


title: 5190


title: 5188


title: 5186


title: 5185


title: 5183


title: 5184


title: WT (wild type) _Day 1,biological rep2

first: Noton

middle: K

last: Dutta

address: 1550 Orleans Street, Room 110

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Raw CEL file data were extracted, RMA normalized and transformed to log2 notation with the Partek Genome Suite v6.6 platform.

organism: Mycobacterium tuberculosis H37Rv

source_name: WT (wild type) _Day 1,biological rep2

label_protocol: Biotinylated cRNAs were prepared with the Affymetrix FlashTag Biotin HSR 3' IVT Express Kit per manufacturer's instructions.

growth_protocol: Early stationary phase cultures of the WT and Δrel strains were resuspended in PBS.

treatment_protocol: Cultures were incubated for 7 days with /without the addition of GSK-X9.

tag: genotype

value: WT

tag: treatment


title: 5181

tag: cell type

value: F


title: WT (wild type) _Day 7,biological rep1

source_name: WT (wild type) _Day 7,biological rep1


title: WT+I (inhibitor) _Day 1,biological rep1

source_name: WT+I (inhibitor) _Day 1,biological rep1

value: Inhibitor


title: WT (wild type) _Day 7,biological rep2

source_name: WT (wild type) _Day 7,biological rep2


title: WT (wild type) _Day 0,biological rep1

source_name: WT (wild type) _Day 0,biological rep1


title: WT+I (inhibitor) _Day 7,biological rep2

source_name: WT+I (inhibitor) _Day 7,biological rep2


title: WT+I (inhibitor) _Day 7,biological rep1

source_name: WT+I (inhibitor) _Day 7,biological rep1


title: WT+I (inhibitor) _Day 1,biological rep2

source_name: WT+I (inhibitor) _Day 1,biological rep2


title: Mut (Mutant) _Day 7,biological rep1

source_name: Mut (Mutant) _Day 7,biological rep1

value: Mutant


title: Mut (Mutant) _Day 1,biological rep1

source_name: Mut (Mutant) _Day 1,biological rep1


title: WT (wild type) _Day 1,biological rep1

source_name: WT (wild type) _Day 1,biological rep1


title: 5192

value: PBMC

tag: plate


title: Mut (Mutant) _Day 0,biological rep1

source_name: Mut (Mutant) _Day 0,biological rep1


title: Mut (Mutant) _Day 7,biological rep2

source_name: Mut (Mutant) _Day 7,biological rep2


title: 5191

tag: pid


title: 5180

tag: stimulation


title: 5178

tag: visit


title: 5176

tag: site


title: 5175

tag: vaccine


title: 5179

value: dmso

tag: case


title: 5169

tag: match


title: 5165

tag: sid


title: 5166

tag: waz


title: Mut (Mutant) _Day 1,biological rep2

source_name: Mut (Mutant) _Day 1,biological rep2


title: 5125

tag: haz


title: 5127

tag: hb


title: 5124

tag: Sex


title: 5128

tag: age


title: 5118


title: 5114


title: 5115


title: 5087


title: 5078


title: 5112


title: 5117


title: 5085


title: 5113


title: 5084


title: 5168


title: 5109


title: 5077


title: 5110


title: 5088


title: 5075

value: case


title: 5073


title: 5076


title: 5072


title: 5045

value: BAGAMOYO

value: old

value: rtss

value: Low


title: 5064

value: hbs

value: control

value: M

value: High


title: 5062

value: MANHICA

value: young


title: 5065


title: 5029

value: comparator

value: neither


title: 5030

value: F


title: 5027


title: 5042


title: 5026

value: csp


title: 5014

value: PBMC


title: 5015


title: 5041


title: 5011


title: 5061


title: 5009


title: 5010


title: 5007

value: dmso


title: 5044


title: 5004

value: case


title: 5005

value: BAGAMOYO


title: 4996

value: old


title: 4995

value: rtss


title: 5002

value: Low


title: 5000


title: 4992

value: hbs


title: 4999

value: control


title: 4990

value: M


title: 4989

value: High


title: 4997


title: 4994


title: 5012


title: 4986

value: MANHICA


title: 4991

value: young


title: 4980


title: 4978


title: 5006

value: comparator


title: 4963


title: 4979

value: neither


title: 4977


title: 4966


title: 4965


title: 4962


title: 4956


title: 4953


title: 5001


title: 4952


title: 4955


title: 4938


title: 4941


title: 4936


title: 4937


title: 4933


title: 4940


title: 4987

value: F


title: 4930


title: 4932


title: 4935


title: 4928

value: csp


title: 4927

value: PBMC


title: 4931


title: 4918


title: 4920

value: dmso


title: 4917


title: 4921


title: 4906


title: 4903


title: 4902


title: 4905


title: 4893


title: 4892


title: 4888


title: 4890


title: 4891


title: 4887


title: 4881


title: 4878


title: 4880


title: 4875


title: 4877


title: 4872


title: 4873


title: 4876


title: 4856


title: 4854


title: 4855


title: 4857


title: 4859


title: 4895


title: 4851


title: 4836


title: 4839


title: 4896


title: 4840


title: 4837


title: 4832


title: 4834


title: 4831


title: 4827


title: 4830


title: 4826


title: 4860


title: 4824


title: 4822


title: 4821


title: 4819

value: case


title: 4829

value: BAGAMOYO


title: 4852

value: old


title: 4816

value: rtss


title: 4810


title: 4825

value: Low


title: 4807


title: 4835

value: hbs


title: 4817


title: 4802


title: 4805


title: 4804


title: 4800


title: 4801


title: 4772

value: control


title: 4806


title: 4775


title: 4774

value: M


title: 4820

value: High


title: 4769


title: 4770


title: 4771


title: 4767


title: 4755


title: 4757


title: 4754


title: 4766


title: 4748


title: 4747


title: 4809


title: 4745


title: 4728


title: 4727


title: 4725


title: 4797


title: 4719


title: 4796


title: 4722


title: 4724


title: 4709


title: 4713


title: 4720


title: 4712


title: 4703


title: 4700


title: 4688


title: 4699


title: 4702


title: 4687


title: 4685


title: 4799


title: 4744


title: 4684


title: 4683


title: 4682


title: 4680


title: 4679


title: 4678


title: 4675


title: 4663


title: 4723


title: 4659

value: MANHICA


title: 4658

value: young


title: 4662


title: 4660


title: 4657


title: 4655


title: 4654


title: 4649


title: 4650


title: 4643


title: 4652


title: 4642


title: 4653


title: 4639


title: 4640


title: 4677

value: comparator


title: 4674


title: 4632


title: 4633


title: 4635


title: 4637


title: 4638


title: 4617


title: 4629


title: 4618


title: 4614


title: 4615


title: 4613


title: 4609


title: 4610


title: 4612


title: 4593


title: 4592


title: 4590


title: 4589


title: 4587

value: neither


title: 4584

value: F


title: 4634


title: 4580


title: 4588

value: csp


title: 4585

value: PBMC


title: 4583


title: 4578


title: 4582

value: dmso


title: 4577


title: 4575


title: 4630


title: 4579


title: 4555


title: 4558


title: 4553


title: 4554


title: 4550


title: 4574


title: 4547


title: 4549


title: 4548


title: 4537


title: 4535


title: 4532


title: 4533


title: 4525


title: 4524


title: 4527


title: 4489


title: 4530


title: 4529


title: 4557


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title: 4185


title: 4184


title: 4186


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value: BAGAMOYO


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value: M


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title: 3621


title: 3620


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title: 38A

city: Charlotte

first: Peter

middle: E

last: Clark

state: North Carolina

address: 1021 Morehead Medical Dr Suite 5201

department: Urology

institute: Atrium Health Levine Cancer Institute

data_processing:
Sequenced reads were quality checked and reads were aligned to the human genome hg38 reference set using STAR aligner.
For gene expression analysis, counts of mapped reads for the genes were calculated by featureCounts in the R package SubRead.
These read counts were used as input for DESeq2 to identify significant differentially expressed genes between durable responders and BCG non-durable responder samples.
For RNA-seq variant calling, aligned reads were merged per sample and duplicates marked with Picard tools.
Sequence recalibration from GATK tools were used as input to Mutect2 for variant calling, following GATK recommended best practices.
Variant calling was performed with Mutect, using a panel of normal references created with MuTect2 to filter out potential germline variants.
Genome_build: hg38

source_name: stage 1 bladder cancer tumor

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: bcg response

value: No

tag: gender

value: Male


title: 45A


title: 42A

value: Female


title: 43A


title: 37A


title: 46A


title: 32A

value: Yes


title: 29A


title: 47A


title: 30A


title: 34A


title: 39A


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title: 26A


title: 3625

tag: cell type


title: 3619

tag: plate

value: comparator

value: neither


title: 25A


title: 23A


title: 22A


title: 19A


title: 20A


title: 35A


title: 24A


title: 36A


title: 21A


title: 18A


title: 16A


title: 15A


title: 9A


title: 12A


title: 7A


title: 6A


title: 14A


title: 13A


title: 5A


title: SSF-1784_unknown

value: unknown

tag: pid


title: SSF-1784_P23_CTRL+

value: PBMC

tag: stimulation


title: 1A


title: 4A


title: SSF-1784_A1_CTRL+

tag: visit


title: SSF-1783_unknown

tag: site


title: SSF-1783_P23_CTRL+

tag: vaccine


title: SSF-1783_H12_CTRL+

tag: case


title: SSF-1783_A1_CTRL+

tag: match


title: SSF-1782_unknown

tag: sid


title: SSF-1782_P23_CTRL+

tag: waz


title: SSF-1782_A1_CTRL+

tag: haz


title: SSF-1782_H12_CTRL+

tag: hb


title: SSF-1781_H12_CTRL+

tag: Sex


title: SSF-1781_P23_CTRL+

tag: age


title: 3A

tag: bcg response


title: SSF-1781_unknown


title: 2A

tag: gender


title: SSF-1780_unknown

tag: cell type


title: SSF-1780_P23_CTRL+

tag: plate


title: 17A


title: SSF-1784_H12_CTRL+

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tag: stimulation

value: csp

value: F

value: High


title: SSF-1780_H12_CTRL+

tag: visit


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value: dmso

tag: site

value: MANHICA

value: old


title: SSF-1780_A1_CTRL+

tag: vaccine


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value: rtss

tag: case


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tag: match


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tag: sid


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value: hbs

tag: waz


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title: 6128

tag: hb

value: M


title: 5937

value: control

tag: Sex


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tag: age


title: 5935


title: 8A

tag: bcg response

value: No

value: Male


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title: 5929


title: 5932


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value: MANHICA

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title: 5870


title: SSF-1781_A1_CTRL+


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title: 1292


title: 1293


title: 1287


title: 1284


title: 1289


title: 1279


title: 1282


title: 1280


title: 1283


title: 1275


title: 1277


title: 1278


title: 1274


title: 1270


title: 1272


title: 1269


title: 1273


title: 1267


title: 1265


title: 1263

value: MANHICA


title: 1264


title: 1252


title: 1260


title: 1259


title: 1262


title: 1250


title: 1248


title: 1285

value: High


title: 1247


title: 1249


title: 1245


title: 1242


title: 1239


title: 1232


title: 1230


title: 1229


title: 1228


title: 1224


title: 1233


title: 1240


title: 1222


title: 1253


title: 1223


title: 1227


title: 1225


title: 1218


title: 1217


title: 1215


title: 1214


title: 1219


title: 1213

value: old


title: 1244

value: rtss


title: 1199


title: 1209

value: M


title: 1202


title: 1203


title: 1200


title: 1197


title: 1198


title: 1192


title: 1220

value: young


title: 1193


title: 1194


title: 1189


title: 1190


title: 1195


title: 1185


title: 1184


title: 1183


title: 1182


title: 1188


title: 1187


title: 1210


title: 1177

value: control


title: 1175

value: hbs


title: 1180

value: BAGAMOYO


title: 1212


title: 1172

value: comparator


title: 1173


title: 1170


title: 1169


title: 1162


title: 1161

value: neither


title: 1160


title: 1156


title: 1157


title: 1155


title: 1154


title: 1152


title: 1149


title: 1147


title: 1174


title: 1179


title: 1151


title: 1137


title: 1140


title: 1127


title: 1139


title: 1121


title: 1125


title: 1122


title: 1129


title: 1126


title: 1124


title: 1119


title: 1159


title: 1117


title: 1116


title: 1114


title: 1115


title: 1146


title: 1111


title: 1106


title: 1110


title: 1136


title: 1105


title: 1100


title: 1102


title: 1101


title: 1104


title: 1097


title: 1096


title: 1099


title: 1092


title: 1091


title: 1095


title: 1109


title: 1090


title: 1087


title: 1079


title: 1086


title: 1080


title: 1094


title: 1112


title: 1107


title: 1077


title: 1076


title: 1074


title: 1072


title: 1071


title: 1065


title: 1067


title: 1089


title: 1059


title: 1052


title: 1062

value: case


title: 1053


title: 1060


title: 1054


title: 1058


title: 1064


title: 1057


title: 1049


title: 1045


title: 1055


title: 1050


title: 1043

value: Low


title: 1040

value: PBMC


title: 1042


title: 1075


title: 1047


title: 1044


title: 1039


title: 1028


title: 1026


title: 1025

value: csp


title: 1024


title: 1021


title: 1023


title: 1063

value: F


title: 1020


title: 1018


title: 1016


title: 1014


title: 1011


title: 1015

value: dmso


title: 1013

value: MANHICA


title: 1003

value: High


title: 1008

value: old


title: 1006

value: rtss


title: 994

value: M


title: 1004


title: 1009


title: 1000


title: 993

value: young


title: 1001


title: 991

value: control


title: 990


title: 983


title: 984


title: 981

value: hbs


title: 978


title: 980


title: 974


title: 976


title: 973


title: 971


title: 975


title: 969


title: 970


title: 1010


title: 1005


title: 968


title: 966


title: 964


title: 963


title: 965


title: 954


title: 956


title: 962


title: 961


title: 958


title: 949


title: 959


title: 957


title: 952


title: 953


title: 951


title: 939


title: 936


title: 943


title: 941


title: 948


title: 918

value: BAGAMOYO


title: 935


title: 923

value: comparator


title: 938


title: 915

value: neither


title: 919


title: 921


title: 940


title: 920


title: 916


title: 913


title: 914


title: 905


title: 904


title: 909


title: 906


title: 910


title: 908


title: 899


title: 944


title: 896


title: 924


title: 901


title: 898


title: 900


title: 895


title: 893


title: 891


title: 911


title: 889


title: 888


title: 890


title: 903


title: 866

value: case


title: 886

value: Low


title: 881

value: PBMC


title: 885

value: csp


title: 864

value: F


title: 861


title: 863


title: 854


title: 860

value: dmso


title: 855


title: 894


title: 844


title: 846


title: 847


title: 841


title: 845


title: 842


title: 849


title: 839


title: 837


title: 838


title: 836


title: 882


title: 851


title: 829


title: 832


title: 828


title: 823


title: 852


title: 831


title: 833


title: 822


title: 834


title: 827


title: 850


title: 821


title: 812


title: 826


title: 819


title: 818


title: 808


title: 809


title: 807


title: 806


title: 802


title: 801


title: 799


title: 824


title: 798


title: 796


title: 793


title: 791


title: 789


title: 794


title: 792


title: 788


title: 797


title: 776


title: 777


title: 779


title: 782


title: 803


title: 778


title: 811


title: 773


title: 774


title: 781


title: 772


title: 771


title: 804


title: 768


title: 766


title: 767


title: 764


title: 763


title: 769


title: 753


title: 750


title: 749


title: 744


title: 747


title: 752


title: 748


title: 743


title: 740


title: 742


title: 737


title: 734


title: 738


title: 739


title: 735


title: 729

value: MANHICA


title: 732

value: High


title: 733

value: old


title: 730

value: rtss


title: 727

value: M


title: 745


title: 728

value: young


title: 724

value: control


title: 725


title: 719

value: hbs


title: 718


title: 717


title: 723


title: 722


title: 715


title: 714


title: 707


title: 708


title: 703


title: 705


title: 704


title: 702


title: 700


title: 699


title: 697


title: 720


title: 695


title: 692


title: 682


title: 689


title: 683


title: 680


title: 678

value: BAGAMOYO


title: 677


title: 675

value: comparator


title: 672

value: neither


title: 674


title: 669


title: 667

value: case


title: 665


title: 664

value: Low


title: 661

value: PBMC


title: 690

value: csp


title: 673


title: 698

value: F


title: 668


title: 659

value: dmso


title: 670


title: 694

value: MANHICA


title: 693

value: High


title: 657

value: old


title: 656

value: rtss


title: 655


title: 679


title: 654

value: M


title: 652

value: young


title: 645

value: control


title: 644


title: 651


title: 642


title: 641

value: hbs


title: 663

value: BAGAMOYO


title: 638


title: 639


title: 660


title: 628


title: 631

value: comparator


title: 623


title: 624

value: neither


title: 621


title: 627


title: 619


title: 617


title: 622


title: 618


title: 613


title: 626


title: 614


title: 616

value: case


title: 609

value: Low


title: 611

value: PBMC


title: 608


title: 612


title: 607


title: 606


title: 604


title: 603


title: 599


title: 632


title: 598

value: csp


title: 600

value: F


title: 629

value: dmso


title: 589


title: 587


title: 584


title: 585


title: 562


title: 560


title: 581


title: 582


title: 559


title: 557


title: 555


title: 558


title: 553


title: 556


title: 596


title: 552


title: 545

value: MANHICA


title: 551


title: 542


title: 586


title: 550


title: 548


title: 595


title: 540


title: 563


title: 538


title: Input_BAF155_cKO_TSA

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

data_processing:
Base calling and fastq.gz conversion were performed using Illumina pipeline scripts.
Reads were mapped to mouse genome mm10.
In ChIP-Seq duplicate reads were filtered out by "rmdup" command of samtools.
In RNA-Seq reads were counted using FeaturesCount. In ChIP-Seq peaks were called using MACS2 with q-value < 0.1.
Genome_build: mm10
Supplementary_files_format_and_content: Peak files and count files.

source_name: Embryonic cortex bulk tissue

extract_protocol:
RNA was isolated using TRIZOL from whole tissue. Chromatin immunoprecipitation was performed as described in the study.
Libraries for ChIP-Seq were prepared using NEBNext Ultra DNA Library Preparation Kit for Illumina. Libraries for RNA-Seq were prepared using Illumina TruSeq RNA Sample Preparation v2 Kit.

tag: tissue

value: cortex

tag: genotype

value: BAF155 cKO

tag: treatment

value: TSA

tag: chip antibody

value: none (input)


title: 537

source_name: PBMC

tag: cell type

tag: plate

tag: pid

tag: stimulation

value: young


title: H3K9ac_BAF155_cKO_TSA_4

value: H3K9ac (Millipore 07-352)


title: H3K9ac_BAF155_cKO_TSA_3


title: Input_BAF155_cKO_Vehicle

value: Vehicle


title: 535

value: hbs

tag: visit

tag: site

tag: vaccine

value: rtss

tag: case


title: 543

value: comparator

value: neither

tag: match

tag: sid

tag: waz

tag: haz


title: 536

tag: age

value: control

tag: hb

tag: Sex

value: Low


title: 532

value: PBMC


title: H3K9ac_BAF155_cKO_TSA_2

tag: tissue

tag: genotype

tag: treatment


title: 533

tag: cell type

tag: plate

value: M


title: H3K9ac_BAF155_cKO_TSA_1

tag: chip antibody


title: 531

tag: pid

tag: stimulation

value: dmso

tag: visit

value: F


title: H3K9ac_BAF155_cKO_Vehicle_2

value: cortex


title: 547

value: csp

tag: site

value: BAGAMOYO

value: old

tag: vaccine

tag: case

value: case


title: 528

value: MANHICA

value: young

tag: match

tag: sid

tag: waz


title: 530

tag: age

tag: haz

tag: hb


title: H3K9ac_BAF155_cKO_Vehicle_1

tag: tissue

tag: genotype

value: BAF155 cKO

value: Vehicle

value: H3K9ac (Millipore 07-352)


title: H3K9ac_BAF155_cKO_Vehicle_3

tag: treatment


title: RNA_BAF155_cKO_TSA_4

value: TSA


title: 527

tag: cell type

tag: plate

value: comparator

value: neither

tag: Sex


title: 526

value: PBMC

tag: pid

tag: stimulation

value: rtss

value: control

value: Low


title: 524

tag: visit

tag: site

value: F


title: RNA_BAF155_cKO_TSA_3

value: cortex

tag: chip antibody


title: 523

value: BAGAMOYO

tag: vaccine

tag: case

tag: match


title: RNA_BAF155_cKO_TSA_2

tag: age


title: RNA_BAF155_cKO_TSA_1


title: 521

value: old

tag: sid

tag: waz

tag: haz

value: M


title: 522

value: case

tag: hb


title: RNA_BAF155_cKO_Vehicle_4

tag: tissue

tag: genotype

tag: treatment


title: H3K9ac_BAF155_cKO_Vehicle_4


title: RNA_BAF155_cKO_Vehicle_3


title: 518

tag: cell type

tag: plate

value: hbs

tag: Sex


title: RNA_BAF155_cKO_Vehicle_1

value: BAF155 cKO


title: 517

tag: pid

tag: stimulation

tag: visit


title: RNA_BAF155_cKO_Vehicle_2

value: Vehicle

tag: chip antibody


title: DG9GabLTM

city: Göttingen

state: NDS

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

institute: DZNE Göttingen

data_processing:
Illumina’s bcl2fastq (v2.20.2) was used for adapter trimming and converting the base calls
TotalRNASeq reads were aligned using the STAR aligner (v2.5.2b)
TotalRNASeq read counts were generated using featureCounts (v1.5.1)
Differential expression analysis with DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: count files, matrices with results from DE analysis

growth_protocol: 9-week-old male C57BL/6N mice were obtained from a commercial supplier (Envigo), individually housed on a 12-h light/dark cycle (lights on at 7 AM) and allowed ad libitum access to food and water. All procedures were approved by Northwestern University's Animal Care and Use Committee in compliance with US National Institutes of Health standards.

extract_protocol:
Total RNA was extracted using miRCURY RNA Isolation Kit-Tissue (Qiagen).
Illumina TruSeq RNA Library Prep Kit

treatment_protocol: Gaboxadol (0.5 μg, dissolved in artificial cerebrospinal fluid (ACSF); Millipore-Sigma) or vehicle (ACSF) infused 20 min prior to contextual fear conditioning at a volume of 0.5 μl per side, at a rate of 0.15 μl/min.

tag: strain

value: male

tag: drug treatment

value: gaboxadol

value: dorsal hippocampus

tag: time after conditioning (days)


title: 514

tag: site

tag: age

tag: vaccine

value: comparator

tag: case

tag: match

tag: sid


title: DG8GabSTM

tag: tissue


title: 513

tag: cell type

value: PBMC

value: neither

tag: waz

tag: haz

tag: hb


title: DG6GabLTM

tag: Sex


title: DG7GabSTM


title: 511

tag: plate

tag: pid

tag: stimulation

value: dmso

tag: visit


title: 512

value: rtss

value: control

value: Low


title: 516

value: BAGAMOYO


title: DG4GabSTM

tag: strain

tag: drug treatment

tag: time after conditioning (days)


title: DG5GabLTM


title: 509

tag: site

tag: age

value: old

tag: vaccine

value: F


title: DG3GabLTM


title: DG28VehLTM

value: vehicle


title: DG25VehSTM


title: DG2GabSTM


title: 507

tag: case

value: case

tag: match

tag: sid


title: 506

tag: cell type

tag: waz

value: M


title: 504

tag: haz

tag: hb


title: DG24VehSTM

tag: Sex

tag: tissue


title: 519

tag: plate

tag: pid

tag: stimulation


title: DG27VehLTM

tag: strain

tag: drug treatment


title: 503

value: csp

tag: visit

tag: site


title: 502

tag: age

tag: vaccine


title: DG23VehLTM

value: male

tag: time after conditioning (days)


title: 501

tag: case

tag: match

tag: sid


title: DG22VehSTM


title: DG20VehSTM


title: 498

tag: cell type

tag: waz

tag: haz


title: 499

tag: hb

tag: Sex


title: 494

tag: plate

tag: pid


title: DG1GabSTM

tag: strain

value: gaboxadol

tag: tissue


title: 496

tag: stimulation

tag: visit


title: DG19VehLTM

tag: drug treatment

value: dorsal hippocampus


title: 508

tag: site

tag: age

tag: vaccine

value: comparator


title: DG18VehSTM

tag: time after conditioning (days)


title: DG17VehSTM


title: 497

value: PBMC

tag: case

tag: match

tag: sid


title: DG16VehLTM


title: 492

tag: cell type

value: neither

tag: waz

tag: haz


title: 493

tag: plate

tag: hb

tag: Sex


title: 489

tag: pid

value: hbs


title: 491

tag: stimulation

value: rtss


title: 488

tag: visit

value: control


title: DG13GabSTM

tag: strain

tag: drug treatment

tag: tissue


title: DG15VehSTM


title: DG14GabLTM


title: 486

tag: site

tag: age

tag: vaccine

value: Low


title: 487

value: BAGAMOYO

tag: case

tag: match


title: 484

tag: cell type

value: old

tag: sid


title: DG10GabSTM

tag: time after conditioning (days)


title: Mother

city: Taizhou

first: Chunyan

last: Jin

state: Jiangsu

address: 399 Hailin South Road

institute: Taizhou People's Hospital

description: Chromosome microarray data of the peripheral blood from a pregnant woman.

hyb_protocol: Following fragmentation, more than 13.5 ug of DNA were hybridized for 16 to 18 hrs at 50 °C and 60 rpm in the GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned on the GeneChip Scanner 3000 as described in the CytoScan Assay User Manual.

data_processing: The data were analyzed with Chromosome Analysis Suite version 4.0 using Affymetrix default analysis settings and global scaling as normalization method. Data analysis was referenced by CytoScan750K_Array.na33.r3.REF_MODEL.

label: Biotin

source_name: Mother's peripheral blood

label_protocol: Biotinylated genomic DNA were prepared according to the standard Affymetrix protocol from 250 ng of total DNA.

growth_protocol: Amniotic fluid and peripheral blood were collected without growth.

extract_protocol: Genomic DNA extraction of amniotic fluid was conducted according to the manufacturer’s standard procedure of TIANamp Micro DNA Kit. Genomic DNA extraction of peripheral blood was conducted according to the manufacturer’s standard procedure of QIAamp DNA Blood Mini Kit.

treatment_protocol: Genomic DNA were extracted from amniotic fluid and peripheral blood without treatment.

value: Peripheral blood


title: Fetus

description: Chromosome microarray data of the amniotic fluid from a pregnant woman at 27+3 weeks of gestation by ultrasound-guided amniocentesis.

source_name: Amniotic fluid (fetus)

value: Amniotic fluid


title: 483

tag: plate

value: dmso

tag: waz

tag: haz


title: 481

tag: pid

tag: hb

tag: Sex

value: M


title: 478

tag: stimulation

tag: visit


title: 470

value: csp


title: Single cell miRNA-seq of THP-1 cell_THP-1_SC3

city: Saarbrücken

first: Tobias

last: Fehlmann

address: Campus E2 1

institute: Saarland University

description:
THP-1_SC3
cell_lines_mirna_expr_dedup_counts.txt

data_processing:
Basecalls performed with bcl2fastq (2.20.0.422)
Adapter trimming and quality trimming was performed with cutadapt 2.10. Reads were trimmed at the 3’ end with a quality cutoff of 20. In addition to the 3’ adapter, polyA tails, polyG tails, and PCR primers were removed. Trimming was performed up to 3 times per read while allowing an error rate of 10%, at most 2 N bases and requiring a minimum length of 18 bases to keep the read.
The remaining reads were mapped against the primary assembly of the human genome GRCh38 using STAR (2.7.5b) with parameters: “--outFilterMultimapNmax 50 --outFilterScoreMinOverLread 0 --outFilterMultimapScoreRange 0 --outFilterMatchNmin 18 --outFilterMatchNminOverLread 0 --outFilterMismatchNoverLmax 0.04 --alignIntronMax 1 --outSAMstrandField intronMotif”.
For the samples containing miRExplore an additional mapping was performed with RazerS 3 (3.5.3) with parameters: “--forward -so 1 -dr 0 -rr 100 --percent-identity 80”
Reads were quantified with featureCounts (1.5.2) with parameters -F SAF -O -M -f –fracOverlap 0 -s 0
MiRNAs were quantified with miRMaster 1.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: mirxplore_counts.txt: tab-delimited text file containing the raw counts of all miRExplore sequences for each sample.
Supplementary_files_format_and_content: sce_counts.txt: tab-delimited text file containing the raw counts of all RNAs of all single cell equivalent samples.
Supplementary_files_format_and_content: sce_mirna_expr_rpmmm_norm.txt: tab-delimited text file containing the RPMMM normalized miRNA counts for all single cell equivalent samples.
Supplementary_files_format_and_content: cell_lines_mirna_expr_dedup_counts.txt: tab-delimited text file containing the UMI deduplicated miRNA counts for all cell line samples.

source_name: monocyte from acute monocytic leukemia

extract_protocol: Single cell miRNA-Seq /w 19 protocols, miRExplore spike-in, single cell equivalents and 67 circulating tumor cells

tag: cell line

value: monocyte from acute monocytic leukemia

tag: culture collection

tag: disease

value: acute monocytic leukemia

tag: sample type

value: single cell

tag: replicate

tag: protocol

tag: genotype

value: not applicable


title: Single cell miRNA-seq of THP-1 cell_THP-1_SC2

description:
THP-1_SC2
cell_lines_mirna_expr_dedup_counts.txt

tag: cell type


title: Single cell miRNA-seq of THP-1 cell_THP-1_SC6

description:
THP-1_SC6
cell_lines_mirna_expr_dedup_counts.txt


title: Single cell miRNA-seq of THP-1 cell_THP-1_SC4

description:
THP-1_SC4
cell_lines_mirna_expr_dedup_counts.txt


title: Single cell miRNA-seq of THP-1 cell_THP-1_SC1

description:
THP-1_SC1
cell_lines_mirna_expr_dedup_counts.txt


title: Single cell miRNA-seq of THP-1 cell_THP-1_SC5

description:
THP-1_SC5
cell_lines_mirna_expr_dedup_counts.txt


title: 479

value: PBMC

tag: site

tag: age

tag: vaccine

value: comparator

tag: case

tag: match

tag: sid

value: F


title: 469

tag: plate

tag: pid

value: rtss

tag: waz

tag: haz

tag: hb

tag: Sex


title: 467

tag: stimulation

tag: visit

value: neither


title: Single cell miRNA-seq of REH cell_REH_SC5

description:
REH_SC5
cell_lines_mirna_expr_dedup_counts.txt

source_name: lymphoblast from acute lymphocytic leukemia

tag: cell line

value: REH

tag: culture collection

tag: disease

value: acute lymphocytic leukemia

tag: sample type

tag: replicate

tag: protocol


title: 464

tag: cell type

tag: site

value: BAGAMOYO

tag: age

value: old

tag: vaccine

tag: case

value: control

value: Low


title: Single cell miRNA-seq of REH cell_REH_SC4

description:
REH_SC4
cell_lines_mirna_expr_dedup_counts.txt

value: lymphoblast from acute lymphocytic leukemia

tag: genotype


title: 466

tag: plate

tag: pid

value: csp

tag: match

tag: sid

tag: waz

tag: haz


title: Single cell miRNA-seq of REH cell_REH_SC3

description:
REH_SC3
cell_lines_mirna_expr_dedup_counts.txt

tag: cell line

tag: culture collection


title: DG11GabLTM

tag: strain

tag: Sex

value: male

tag: drug treatment

value: gaboxadol

tag: tissue

value: dorsal hippocampus

tag: time after conditioning (days)


title: 463

tag: cell type

tag: stimulation

tag: visit

tag: site

value: MANHICA

tag: age

value: young

tag: hb

value: High


title: Single cell miRNA-seq of REH cell_REH_SC1

description:
REH_SC1
cell_lines_mirna_expr_dedup_counts.txt

tag: disease

tag: sample type

value: single cell

tag: replicate

tag: protocol

tag: genotype

value: not applicable


title: 459

value: PBMC

tag: plate

tag: pid

tag: vaccine

value: comparator

tag: case

value: neither

tag: match

tag: sid

tag: waz

tag: haz

value: F


title: 462

tag: cell type

tag: stimulation

value: hbs

tag: visit

tag: Sex


title: 482

value: dmso

tag: site

value: BAGAMOYO

tag: age

value: old

value: rtss

value: control

tag: hb

value: M


title: 458

value: Low


title: 461

value: MANHICA


title: Single cell miRNA-seq of KG1 cell_KG1_SC4

description:
KG1_SC4
cell_lines_mirna_expr_dedup_counts.txt

source_name: macrophage from acute myelogenous leukemia

tag: cell line

tag: culture collection

tag: disease

value: acute myelogenous leukemia

tag: sample type

tag: replicate

tag: protocol


title: Single cell miRNA-seq of REH cell_REH_SC6

description:
REH_SC6
cell_lines_mirna_expr_dedup_counts.txt

value: REH

value: lymphoblast from acute lymphocytic leukemia

value: acute lymphocytic leukemia

tag: genotype


title: Single cell miRNA-seq of KG1 cell_KG1_SC3

description:
KG1_SC3
cell_lines_mirna_expr_dedup_counts.txt

value: macrophage from acute myelogenous leukemia

value: single cell

value: not applicable


title: 456

value: PBMC

tag: plate

tag: pid

tag: vaccine

tag: case

value: neither

tag: match

tag: sid


title: 438

tag: cell type

tag: stimulation

value: hbs

tag: visit

tag: waz

tag: haz

tag: Sex


title: 441

tag: site

value: BAGAMOYO

tag: age

value: comparator

tag: hb

value: F


title: Single cell miRNA-seq of REH cell_REH_SC2

description:
REH_SC2
cell_lines_mirna_expr_dedup_counts.txt

tag: cell line

tag: culture collection

tag: disease

tag: sample type

tag: replicate

tag: protocol


title: 439

tag: plate

tag: pid

value: old

tag: vaccine

tag: case

value: control

tag: match


title: Single cell miRNA-seq of KG1 cell_KG1_SC1

description:
KG1_SC1
cell_lines_mirna_expr_dedup_counts.txt

tag: cell type

tag: genotype


title: Single cell miRNA-seq of Jurkat cell_Jurkat_SC4

description:
Jurkat_SC4
cell_lines_mirna_expr_dedup_counts.txt

source_name: T cell from acute T cell leukemia

value: Jurkat

value: T cell from acute T cell leukemia

value: acute T cell leukemia


title: 453

tag: stimulation

tag: visit

value: rtss

tag: sid

tag: waz

tag: haz

tag: Sex

value: M

value: High


title: 436

tag: site

tag: age

tag: hb

value: Low


title: 454


title: Single cell miRNA-seq of Jurkat cell_Jurkat_SC5

description:
Jurkat_SC5
cell_lines_mirna_expr_dedup_counts.txt

tag: cell line

tag: culture collection

tag: disease

tag: sample type

value: single cell

tag: replicate

tag: protocol


title: 457

tag: cell type

tag: plate

tag: pid

tag: vaccine

tag: case

tag: match


title: Single cell miRNA-seq of Jurkat cell_Jurkat_SC6

description:
Jurkat_SC6
cell_lines_mirna_expr_dedup_counts.txt

tag: genotype

value: not applicable


title: Single cell miRNA-seq of KG1 cell_KG1_SC6

description:
KG1_SC6
cell_lines_mirna_expr_dedup_counts.txt

value: macrophage from acute myelogenous leukemia

value: acute myelogenous leukemia


title: 431

value: PBMC

tag: stimulation

value: dmso

tag: visit

tag: sid

tag: waz

tag: haz

tag: Sex


title: 434

value: hbs

tag: site

value: BAGAMOYO

tag: age

value: comparator

tag: hb


title: Single cell miRNA-seq of KG1 cell_KG1_SC5

description:
KG1_SC5
cell_lines_mirna_expr_dedup_counts.txt

tag: cell line

tag: culture collection

tag: disease

tag: sample type

tag: replicate

tag: protocol


title: Single cell miRNA-seq of Jurkat cell_Jurkat_SC1

description:
Jurkat_SC1
cell_lines_mirna_expr_dedup_counts.txt

tag: cell type


title: 433

tag: plate

tag: pid

value: old

tag: vaccine

tag: case

value: neither

tag: match


title: Single cell miRNA-seq of HT29 cell_HT29_SC3

description:
HT29_SC3
cell_lines_mirna_expr_dedup_counts.txt

source_name: epithelial colon cell from colorectal adenocarcinoma

value: colorectal adenocarcinoma

tag: genotype


title: 429

tag: stimulation

tag: visit

tag: sid

tag: waz

tag: haz

tag: Sex


title: Single cell miRNA-seq of HT29 cell_HT29_SC4

description:
HT29_SC4
cell_lines_mirna_expr_dedup_counts.txt

tag: cell line

value: epithelial colon cell from colorectal adenocarcinoma

tag: culture collection

tag: disease


title: Single cell miRNA-seq of HT29 cell_HT29_SC5

description:
HT29_SC5
cell_lines_mirna_expr_dedup_counts.txt

tag: sample type

tag: replicate

tag: protocol


title: Single cell miRNA-seq of HT29 cell_HT29_SC6

description:
HT29_SC6
cell_lines_mirna_expr_dedup_counts.txt

tag: cell type


title: Single cell miRNA-seq of KG1 cell_KG1_SC2

description:
KG1_SC2
cell_lines_mirna_expr_dedup_counts.txt


title: 428

tag: plate

tag: pid

tag: site

tag: age

tag: vaccine

value: rtss

tag: hb


title: Single cell miRNA-seq of HT29 cell_HT29_SC2

description:
HT29_SC2
cell_lines_mirna_expr_dedup_counts.txt

tag: genotype


title: Single cell miRNA-seq of Jurkat cell_Jurkat_SC3

description:
Jurkat_SC3
cell_lines_mirna_expr_dedup_counts.txt

value: Jurkat

value: T cell from acute T cell leukemia

value: acute T cell leukemia


title: 426

tag: stimulation

tag: visit

tag: case

tag: match

tag: sid

tag: waz

value: M

value: High


title: Single cell miRNA-seq of HT29 cell_HT29_SC1

description:
HT29_SC1
cell_lines_mirna_expr_dedup_counts.txt

tag: cell line

tag: culture collection

tag: disease

tag: sample type

value: single cell

value: not applicable


title: 427

tag: cell type

value: PBMC

tag: plate

value: control

tag: haz

tag: Sex

value: F

value: Low


title: Single cell miRNA-seq of HepG2 cell_HepG2_SC6

description:
HepG2_SC6
cell_lines_mirna_expr_dedup_counts.txt

source_name: epithelial liver cell from hepatocellular carcinoma

value: hepatocellular carcinoma

tag: replicate

tag: protocol


title: Single cell miRNA-seq of HepG2 cell_HepG2_SC5

description:
HepG2_SC5
cell_lines_mirna_expr_dedup_counts.txt

value: epithelial liver cell from hepatocellular carcinoma

tag: genotype


title: Single cell miRNA-seq of Jurkat cell_Jurkat_SC2

description:
Jurkat_SC2
cell_lines_mirna_expr_dedup_counts.txt


title: 432

tag: pid

tag: stimulation

value: dmso

tag: site

value: BAGAMOYO

tag: age

value: old

tag: vaccine

value: comparator

tag: hb


title: 424

value: csp

tag: visit

tag: case

tag: match

tag: sid

tag: waz


title: Single cell miRNA-seq of HepG2 cell_HepG2_SC4

description:
HepG2_SC4
cell_lines_mirna_expr_dedup_counts.txt

tag: cell line

tag: cell type

tag: culture collection

tag: disease

tag: sample type


title: 423

tag: plate

tag: haz

tag: Sex


title: Single cell miRNA-seq of HepG2 cell_HepG2_SC3

description:
HepG2_SC3
cell_lines_mirna_expr_dedup_counts.txt

tag: replicate

tag: protocol

tag: genotype


title: 422

tag: pid

tag: stimulation

tag: site

tag: age

tag: vaccine

value: rtss

value: neither

tag: hb


title: 421

tag: visit

tag: case

tag: match

tag: sid

tag: waz

value: M


title: 419

tag: cell type

tag: plate


title: Single cell miRNA-seq of HepG2 cell_HepG2_SC1

description:
HepG2_SC1
cell_lines_mirna_expr_dedup_counts.txt

tag: cell line

tag: culture collection

tag: disease

tag: sample type


title: Single cell miRNA-seq of BJ cell_BJ_SC2

description:
BJ_SC2
cell_lines_mirna_expr_dedup_counts.txt

source_name: fibroblast from healthy foreskin

value: BJ

value: fibroblast from healthy foreskin

value: healthy

tag: replicate

tag: protocol

tag: genotype


title: 418

value: PBMC

tag: pid

tag: stimulation

tag: site

tag: age

tag: haz

tag: Sex

value: High


title: Single cell miRNA-seq of A549 cell_A549_SC6

description:
A549_SC6
cell_lines_mirna_expr_dedup_counts.txt

source_name: epithelial lung cell from carcinoma

value: epithelial lung cell from carcinoma

value: carcinoma

value: single cell

value: not applicable


title: 416

tag: visit

tag: vaccine

tag: case

value: control

tag: match

tag: sid

tag: hb

value: Low


title: 411

tag: cell type

tag: plate

value: hbs

value: BAGAMOYO

value: old

tag: waz


title: Single cell miRNA-seq of HepG2 cell_HepG2_SC2

description:
HepG2_SC2
cell_lines_mirna_expr_dedup_counts.txt

tag: cell line

value: epithelial liver cell from hepatocellular carcinoma

tag: culture collection

tag: disease

value: hepatocellular carcinoma

tag: sample type

tag: replicate

tag: protocol


title: Single cell miRNA-seq of BJ cell_BJ_SC5

description:
BJ_SC5
cell_lines_mirna_expr_dedup_counts.txt

tag: genotype


title: 406

tag: pid

tag: stimulation

tag: site

tag: age

value: rtss

tag: haz

tag: Sex

value: F


title: Single cell miRNA-seq of A549 cell_A549_SC4

description:
A549_SC4
cell_lines_mirna_expr_dedup_counts.txt


title: Single cell miRNA-seq of BJ cell_BJ_SC4

description:
BJ_SC4
cell_lines_mirna_expr_dedup_counts.txt

value: BJ

value: fibroblast from healthy foreskin


title: Single cell miRNA-seq of A549 cell_A549_SC2

description:
A549_SC2
cell_lines_mirna_expr_dedup_counts.txt


title: Single cell miRNA-seq of A549 cell_A549_SC1

description:
A549_SC1
cell_lines_mirna_expr_dedup_counts.txt


title: 402

value: PBMC

value: dmso

tag: visit

tag: vaccine

tag: case

value: case

tag: match

tag: sid

tag: hb


title: 412

tag: cell type

tag: plate

tag: waz

value: M