title: K562 DHX34-3


title: K562 UPF1-1

status: Public on Aug 24 2022

type: SRA

city: Edinburgh

first: Javier

last: Caceres

address: Crewe Road

department: MRC HGU

country: United Kingdom

institute: University of Edinburgh

library_source: transcriptomic

data_processing:
pseudoalignment using Salmon
differential expression calling using Sleuth
splicing event calling using SUPPA2
Assembly: GRCh38.93
Supplementary files format and content: DHX34_sleuth.csv
Supplementary files format and content: DHX34_suppa2.csv
Supplementary files format and content: UPF1_sleuth.csv
Supplementary files format and content: UPF1_suppa2.csv

molecule: total RNA

organism: Homo sapiens

growth_protocol: standard culture conditions , RPMI, 10% FCS, 1% Pen/Strep

extract_protocol: mRNA library preparation (poly A enrichment) Library construction and sequencing was done by  Novogene

treatment_protocol: siRNA transfection, harvest 4 days post transfection

tag: cell line

tag: cell type

value: immortalised myelogenous leukemia cell line

tag: treatment


title: K562 UPF1-3


title: Microbiota of stool from patient PST19 [FS54]

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description: 16s rRNA v3-v4 sequencing of human stool

library_source: genomic

data_processing:
demultiplexing: from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
primer check and trimming: qiime cutadapt trim-paired  --i-demultiplexed-sequences demux-paired-end.qza --p-adapter-f  CCTACGGGNGGCWGCAG   --p-adapter-r  GACTACNVGGGTWTCTAATCC  –o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --verbose
quality check: qiime demux summarize  --i-data trimmed-seqs.qza --o-visualization demux.qzv --p-n 500000
quality trimming, pair merging and ASV table creation: qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 244 --p-trunc-len-r 198 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 8
taxonomic assignment (RDP): qiime feature-classifier classify-consensus-vsearch --i-query rep-seqs.qza --i-reference-reads silva-138-99-seqs.qza --i-reference-taxonomy silva-138-99-tax.qza --p-perc-identity 0.99 --p-threads 8 --o-classification taxonomy_vsearch.qza –verbose
further analyses: R phyloseq package (see https://github.com/matteoramazzotti/papers)
Supplementary files format and content: feature_table.csv: CSV text file containing the abundance table
Supplementary files format and content: taxonomy.tsv: TSV text file containing the complete taxonomic classification of the reference sequence
Supplementary files format and content: dna-sequences.fasta: fasta file containing the reference sequences used for taxonomy classification
Library strategy: paired-end (2x300) amplicon sequencing

molecule: genomic DNA

organism: human feces metagenome

source_name: Stool

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

tag: tissue

value: Stool

tag: patient id

tag: timepoint

value: Pre-ANG

tag: diet

value: ANG


title: K562 DHX34-1


title: K562 SCR-2

value: WT


title: K562 SCR-3


title: K562 SCR-1


title: Microbiota of stool from patient PST17 [FS52]


title: HMLE_final_rep2

city: Istanbul

first: Ayse Derya

last: Cavga

address: Rumelifeneri Yolu, Sariyer

country: Turkey

institute: Koc University

description: Last collection. EPIKOL-transduced HMLE cells were collected after 16 doublings.

data_processing:
Library strategy: CRISPR Amplicon Sequencing
Base calling was performed with Illumina HiSeq platforms (Genewiz, USA)
sgRNA counting, gene summarization and comparative analyses between samples were performed using MAGeCK version 0.5.8 (Li, W., et al., 2014) using median normalization and the RRA method. R1 fastq files were used in counting.
Genome_build: sgRNA counted by matching to custom CRISPR Screen library; Epigenetic Knock-out Library (EPIKOL)
Supplementary_files_format_and_content: txt files containing MAGeCK outputs; normalized counts, gene summary and sgRNA summary

source_name: mammary epithelium cells

growth_protocol: MDA-MB-231 cells were cultured in DMEM supplemented with 10% fetal bovine serum and %1 Penicillin/Streptomycin. SUM159 and SUM149 cell lines were cultured with Ham’s F12 nutrient mix supplemented with 5% FBS, 5 µg/ml insulin, 1 µg/ml hydrocortisone and 10 mM HEPES. Immortalized human breast epithelial cells (HMLE) were cultured in MEGM medium. Briefly, MEGM Bullet Kit (Lonza,Swiss) (by excluding gentamicin/amphotericin-B) was used and supplemented with the same volume of DMEM:F12 (1:1), 10 µg/ml insulin, 0.5 µg/ml hydrocortisone, 20 ng/ml EGF, and %1 Penicillin/Streptomycin. All prostate cell lines except RWPE-1 were cultured in RPMI 1640 supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. RWPE-1 cells were cultured in Keratinocyte SFM media supplemented with 0.05 mg/mL bovine pituitary extract and 5 ng/mL human recombinant epidermal growth factor.

extract_protocol:
Genomic DNA (gDNA) was isolated by NucleoSpin Tissue kit (Macherey-Nagel, Germany) for TNBC cell lines and by PureLink Genomic DNA mini kit (ThermoFischer K-1820) for PCa cell lines according to manufacturer’s instructions
Library was constructed with Illumina-compatible adapters. sgRNA cassettes were amplified from genomic DNA using pLentiGuide specific forward and reverse primers in the first PCR. For second PCR, %1-2.5 of the first PCR product was amplified with forward stagger and reverse index primers (specific to sample). Final library fragments of ~350 bp were agarose gel purified. Fragments were quality checked with fragment analyzer and sequenced with Illumina Hiseq (Genewiz, USA)

treatment_protocol: Cells were transduced with EPIKOL at low MOI (0.3-0.4) with 1000x coverage for TNBC and 500x coverage for PCa in the presence of 8 μg/ml protamine sulphate. Following three days of puromycin selection, initial reference point pellets were collected as 8 million cells for TNBC and 4 million cells for PCa. Later, cells were maintained with the indicated coverage for each line. After 15-16 population doublings, screens were ended and cell pellets were collected.

value: HMLE

value: mammary epithelium cells


title: Microbiota of stool from patient PST18 [FS53]

value: Pre-EVO

value: EVO


title: K562 UPF1-2


title: Microbiota of stool from patient PST5 [FS5]


title: Microbiota of stool from patient PST13 [FS50]


title: g30_2

city: Urbana

first: Thomas

last: Gaj

state: IL

address: 1406 W. Green St.

department: Bioengineering

country: USA

institute: University of Illinois Urbana-Champaign

data_processing:
FastQ read files were generated and demultiplexed using the bcl2fastq v2.20 Conversion Software (Illumina) and adapters were trimmed using Trimmomatic v0.39.
Salmon  version 1.5.2 was used to quasi-map reads to the transcriptome and to quantify the abundance of each transcript, using the decoy-aware method with the entire genome file as a decoy.
Gene-level counts were estimated on the basis of transcript-level counts using the “lengthScaled TPM” method from the tximport package.
Trimmed mean of M values (TMM) normalization was performed using the edgeR package.
Genes were filtered that did not have at least 0.5 counts-per-million (CPM) in at least three samples, and TMM normalization was peformed again on the filtered dataset.
Assembly: NCBI human genome assembly GRCh38.p13, annotation 109.20201120
Supplementary files format and content: For each library, a tarball is provided containing transcript quantification results output by Salmon 1.5.2.
Supplementary files format and content: Tab-delimited text files are provided containing gene-level quantification across all samples.  Raw counts output by Salmon and aggregated across transcripts are provided, as well as log-counts-per-million after filtering and TMM normalization.

molecule: polyA RNA

source_name: HEK293T cells, single, rep s

growth_protocol: HEK293T cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Corning) supplemented with 10% (v/v) fetal bovine serum (FBS; Gibco) and 1% (v/v) antibiotic-antimycotic (Gibco) in a humidified 5% CO2 incubator at 37°C.

extract_protocol:
RNA from was extracted using the PureLink RNA Mini Kit (Invitrogen).
Library construction was performed by the Roy J. Carver Biotechnology Center (University of Illinois, Urbana, IL, USA). Briefly, DNase-treated RNA was converted into barcoded polyadenylated mRNA libraries using the Kapa Hyper Stranded mRNA Sample Prep Kit (Roche). Libraries were barcoded with unique dual indexes to prevent index switching and adaptor-ligated double-stranded cDNAs were PCR-amplified for eight cycles with KAPA HiFi DNA Polymerase (Roche). Final libraries were quantitated by Qubit (Thermo Fisher Scientific), and the average cDNA fragment sizes were determined on a fragment analyzer. Libraries were then diluted to 10 nM and quantitated by qPCR on a CFX Connect Real-Time qPCR system (Bio-Rad) to confirm accurate pooling of barcoded libraries and to maximize the number of clusters in the flowcell. Barcoded RNA-seq libraries were sequenced using a NovaSeq 6000 on one SP lane with single-reads 100 nt in length (Illumina).

treatment_protocol: For transfections, HEK293T cells were seeded onto a 24-well plate at a density of 2 x 10^5 cells per well. All transfections were conducted 16 hr after seeding. Cells were transfected with 750 ng of plasmid encoding a third generation cytidine base editor (pCMV-BE3) and 500 ng of plasmid encoding the sgRNA (pSP-gRNA) using polyethylenimine (1 mg/mL; PEI) at a 1 mg to 3 ng ratio of plasmid to PEI.

value: transfection with HTT promoter-targeting guide RNA + CRISPR base editor


title: NTG_1

value: transfection with non-targeting guide RNA + CRISPR base editor


title: g30_3


title: g30_1


title: NTG_2


title: Microbiota of stool from patient PST12 [FS49]


title: Microbiota of stool from patient PST16 [FS51]


title: Microbiota of stool from patient PST11 [FS48]


title: Microbiota of stool from patient PST10 [FS47]


title: NTG_3


title: Polysome fractions – Control – Rep3

city: Madrid

first: Encarnacion

last: Martinez-Salas

state: Madrid

address: Nicolás Cabrera 1

country: Spain

institute: Centro de Biologia Molecular Severo Ochoa, CSIC-UAM

description: Total RNA from polysomes of untreated HEK-293 cells – Rep3

data_processing:
Sequences were aligned against the human reference genome GRCh38 downloaded from Ensembl release 91 using STAR aligner (version 2.5.3a)
Reads in the appropriate sense (fr-firststrand) for each gene were quantified with QoRTs (version 1.3.0)
Assembly: GRCh38
Supplementary files format and content: Tab delimited file with raw gene counts for every gene and every sample
Library strategy: Polysome fraction RNA

source_name: Cell culture

growth_protocol: HEK293 cells and siRNA Gemin5-silenced cells grown in DMEM medium

extract_protocol:
RNA from cytoplasmic lysates and polysomes was extracted using phenol-chloroform, isopropanol precipitated, and resuspended in RNase-free H2O. RNA samples were cleaned with the RNeasy kit (Qiagen). RNA quality and concentration was determined using Agilent 2100 Bioanalyzer (Agilent Technologies). The cDNA libraries were prepared with 1 µg of RNA using the Illumina TruSeq Stranded mRNA (Macrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
siRNAs targeting Gemin5 (CCUUAAUCAAGAAGAGAAAUU) and a control siRNA (AUGUAUUGGC CUGUAUUAGUU) were purchased from Dharmacon. HEK293 cells grown to 70% confluent were treated with 100 nM siRNA using Lipofectamine 2000 (Thermo-Fisher Scientific).
Polysomal fractionation: ~2x10^7 cells per gradient were incubated with 0.1   mg/mL cycloheximide for 10   min on ice to block ribosomes in the elongation step. Then, cells were washed twice with 0.1   mg/mL cycloheximide in cold PBS, lysed in buffer A (15 mM Tris-HCl pH 7.4, 80 mM KCl, 5 mM MgCl2, 0.1 mg/ml cycloheximide), 1% (v/v) Triton X-100, 40 U/ml RNase OUT, Protease inhibitors), and centrifuged 10 min at 14000 g, 4  C. The clear supernatants were loaded into a linear 10-50% (w/v) sucrose gradient in buffer A, centrifuged at 39000 rpm SW40 Ti rotor 2 h 15 min at 4  C. Sucrose gradients were fractionated using a gradient fractionation system measuring the absorbance at A260 to record the polysome profile.

value: Untreated

tag: rna fraction

value: RNA isolated from polysome fractions


title: Microbiota of stool from patient PST9 [FS46]


title: Polysome fractions – Control – Rep4

description: Total RNA from polysomes of untreated HEK-293 cells – Rep4


title: Polysome fractions – siRNAG5 treatment – Rep3

description: Total RNA from polysomes of HEK-293 cells treated with si-RNA targeting Gemin5 – Rep3

value: GEMIN5 Knockdown (siRNA)


title: Polysome fractions – siRNAG5 treatment – Rep1

description: Total RNA from polysomes of HEK-293 cells treated with si-RNA targeting Gemin5 - Rep1


title: Polysome fractions – siRNAG5 treatment – Rep2

description: Total RNA from polysomes of HEK-293 cells treated with si-RNA targeting Gemin5 – Rep2


title: Microbiota of stool from patient PST8 [FS45]


title: Polysome fractions – Control – Rep1

description: Total RNA from polysomes of untreated HEK-293 cells – Rep1


title: Input RNA – siRNAG5 treatment – Rep3

description: Total RNA from cytoplasmic lysates of HEK-293 cells treated with si-RNA targeting Gemin5 – Rep3

data_processing:
Sequences were aligned against the human reference genome GRCh38 downloaded from Ensembl release 91 using STAR aligner (version 2.5.3a)
Reads in the appropriate sense (fr-firststrand) for each gene were quantified with QoRTs (version 1.3.0)
Assembly: GRCh38
Supplementary files format and content: Tab delimited file with raw gene counts for every gene and every sample

treatment_protocol: siRNAs targeting Gemin5 (CCUUAAUCAAGAAGAGAAAUU) and a control siRNA (AUGUAUUGGC CUGUAUUAGUU) were purchased from Dharmacon. HEK293 cells grown to 70% confluent were treated with 100 nM siRNA using Lipofectamine 2000 (Thermo-Fisher Scientific).

value: Total RNA


title: Input RNA – siRNAG5 treatment – Rep2

description: Total RNA from cytoplasmic lysates of HEK-293 cells treated with si-RNA targeting Gemin5 – Rep2


title: Polysome fractions – siRNAG5 treatment – Rep4

description: Total RNA from polysomes of HEK-293 cells treated with si-RNA targeting Gemin5 – Rep4


title: Polysome fractions – Control – Rep2

description: Total RNA from polysomes of untreated HEK-293 cells – Rep2


title: Microbiota of stool from patient PST7 [FS44]


title: Input RNA – siRNAG5 treatment – Rep1

description: Total RNA from cytoplasmic lysates of HEK-293 cells treated with si-RNA targeting Gemin5 - Rep1


title: Input RNA – Control – Rep4

description: Total RNA from cytoplasmic lysates of untreated HEK-293 cells – Rep4


title: Input RNA – siRNAG5 treatment – Rep4

description: Total RNA from cytoplasmic lysates of HEK-293 cells treated with si-RNA targeting Gemin5 – Rep4


title: Input RNA – Control – Rep3

description: Total RNA from cytoplasmic lysates of untreated HEK-293 cells – Rep3


title: Microbiota of stool from patient PST6 [FS43]


title: Input RNA – Control – Rep1

description: Total RNA from cytoplasmic lysates of untreated HEK-293 cells - Rep1


title: Input RNA – Control – Rep2

description: Total RNA from cytoplasmic lysates of untreated HEK-293 cells – Rep2


title: Microbiota of stool from patient PST4 [FS41]

description: 16s rRNA v3-v4 sequencing of human stool


title: Microbiota of stool from patient PST3 [FS40]


title: Liver_CC_Female_Mice_ID_95

type: RNA

city: Davis

first: Brian

middle: J

last: Bennett

state: CA

address: 430 West Health Sciences Drive

institute: USDA ARS-WHNRC

description: Gene expression in liver tissue obtained from female CC mouse

scan_protocol: Done according to Affymetrix MoGene 2.1 ST 96-Array Plate Protocol using the Affymetrix GeneTitan instrument

data_processing: Probes containing known SNPs from the founder strains were masked. We used the robust multiarray average method (RMA) implemented in the Affymetrix gene expression console with default settings (median polish and sketch-quantile normalization) to estimate the normalized expression levels of transcripts.

label: biotin

organism: Mus musculus

source_name: Liver from CC female mice

growth_protocol: Collaborative Cross (CC) mice between 6-9 weeks of age were obtained from were obtained from University of North Carolina’s CC Mouse Core and maintained on a synthetic chow diet (AIN-76A) for 2 weeks prior to administration of experimental diets

extract_protocol: Total RNA was extracted from about 25 mg of liver tissue using Norgen Total RNA Purification Kit, Norgen

treatment_protocol: Mice were fed either a high protein (HP) or high fat high sucrose (HS) experimental diet for 8 weeks

tag: gender

value: Female

tag: mouse type

tag: experimental diet

value: HP

value: Liver


title: Liver_CC_Female_Mice_ID_93

hyb_protocol: Done according to Affymetrix MoGene 2.1 ST 96-Array Plate Protocol


title: Microbiota of stool from patient PST4 [FS4]

value: Stool


title: Microbiota of stool from patient PST5 [FS42]


title: Liver_CC_Female_Mice_ID_96

label_protocol: Done according to Affymetrix MoGene 2.1 ST 96-Array Plate Protocol


title: Liver_CC_Female_Mice_ID_8

value: HS


title: WRN_2_L1_ASO

city: Barcelona

first: Alfonso

last: Saera-Vila

address: Dr. Trueta 179

institute: Sequientia Biotech

data_processing:
RNA-seq read quality control (QC) analyses and filtering of high-quality reads were executed using FastQC and BBDuk (Bushnell et al. 2017) by setting a minimum read length of 35 bp and a minimum Phred-quality score of 25. After trimming quality control, high quality reads were aligned to the mouse genome reference (GrCm38p6/mm10) with STAR 2.7.3a (Dobin et al. 2012), while FeatureCounts 1.6.3 package (Liao et al. 2014) was used to assign reads to genes.
Genes with low, constant levels of raw counts across one or more experimental conditions were filtered to eliminate the “uninformative” genes using HTSFilter 1.30.1 (Rau et al. 2013). Filtered gene data was further processed with the EdgeR package (Robinson et al. 2009) to normalize (Trimmed Mean of M-values, TMM, method) the raw counts.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with fpkm normalized gene counts for every gene and every sample
Supplementary files format and content: Matrix table with tmm normalized gene counts for every gene and every sample

source_name: Werner Syndrome donor derived primary dermal fibroblasts treated with L1 Antisense oligonucleotide

growth_protocol: DMEM high glucos + glutamax+ 10%FBS+non essential amminoacids

extract_protocol: Monarch Total RNA Miniprep Kit (NEB #T2010)

treatment_protocol: transfection of scramble or LINE-1 antisense oligonucleotides

tag: disease state

value: Werner Syndrome

tag: age

value: 27 years old

value: skin dermal fibroblast

value: LINE-1 Antisense oligonucleotide


title: Liver_CC_Female_Mice_ID_97


title: Liver_CC_Female_Mice_ID_89


title: Liver_CC_Female_Mice_ID_92


title: Liver_CC_Female_Mice_ID_9


title: Liver_CC_Female_Mice_ID_91


title: WRN_3_L1_ASO


title: WRN_3_NT

source_name: Werner Syndrome donor derived primary dermal fibroblasts

value: 25 years old

value: no treatment


title: WRN_1_SCR

source_name: Werner Syndrome donor derived primary dermal fibroblasts treated with scramble Antisense oligonucleotide

value: 26 years old

value: scramble Antisense oligonucleotide


title: WRN_2_SCR


title: WRN_2_NT


title: WRN_1_L1_ASO


title: Liver_CC_Female_Mice_ID_88


title: WRN_3_SCR


title: HGPS_917_L1_ASO

source_name: Hutchinson Gilford Progeria Syndrome donor derived primary dermal fibroblasts treated with LINE-1 Antisense oligonucleotide

value: Hutchinson Gilford Progeria Syndrome

value: 8 years old


title: Liver_CC_Female_Mice_ID_87


title: Liver_CC_Female_Mice_ID_94


title: Liver_CC_Female_Mice_ID_90


title: Liver_CC_Female_Mice_ID_84


title: Liver_CC_Female_Mice_ID_86


title: Liver_CC_Female_Mice_ID_85


title: Liver_CC_Female_Mice_ID_83


title: Microbiota of stool from patient PST20 [FS38]

value: Post-EVO

value: EVO


title: WRN_1_NT


title: Microbiota of stool from patient PST2 [FS39]

value: Pre-ANG

value: ANG


title: HGPS_478_L1_ASO


title: HGPS_297_L1_ASO


title: HGPS_478_SCR

source_name: Hutchinson Gilford Progeria Syndrome donor derived primary dermal fibroblasts treated with scramble Antisense oligonucleotide


title: Microbiota of stool from patient PST19 [FS37]


title: HGPS_917_SCR


title: HGPS_297_SCR


title: Microbiota of stool from patient PST18 [FS36]

value: Post-ANG


title: Liver_CC_Female_Mice_ID_80

value: Female

value: Liver


title: HGPS_917_NT

source_name: Hutchinson Gilford Progeria Syndrome donor derived primary dermal fibroblasts


title: Microbiota of stool from patient PST17 [FS35]

value: Stool


title: HGPS_478_NT


title: Liver_CC_Female_Mice_ID_81

value: HS


title: Microbiota of stool from patient PST16 [FS34]


title: Microbiota of stool from patient PST15 [FS33]


title: HGPS_297_NT

value: skin dermal fibroblast


title: WT_3

source_name: healthy donor primary dermal fibroblasts

value: healthy donor

value: 17 years old


title: 001_FLU_1_ROI_012_well_B01

city: Seattle

first: Wei

last: Yang

state: WA

address: 530 Fairview Ave N

institute: Nanostring

description: Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

data_processing:
Library strategy: GeoMx Seq
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4
Genome_build: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Hs_R_NGS_WTA_COVID19_v1.0.pkc)
Supplementary_files_format_and_content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary_files_format_and_content: Values  represented in the collapsed target counts tab are the geometric mean of the probes for a given target--in the case that multiple probes were used-- and excludes any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments and features.

source_name: Trachea/bronchi

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

value: Trachea/bronchi

tag: slide id

tag: roi number

tag: segment type

value: Full

value: IAPA patient 2

tag: sample name

value: IAPA ROI Epith 2

tag: maintissue

value: Epithelium

tag: disease

value: IAPA

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: WT_2

tag: disease state

tag: cell type

tag: treatment

value: no treatment


title: 001_FLU_1_ROI_011_well_A12

tag: tissue

tag: slide id

tag: roi number

tag: patient id

value: IAPA ROI Infl 5

value: Subepithelial


title: Liver_CC_Female_Mice_ID_79

tag: gender

tag: mouse type

tag: experimental diet


title: WT_1

tag: age


title: Microbiota of stool from patient PST12 [FS31]

tag: timepoint

value: Post-EVO

tag: diet

value: EVO


title: Microbiota of stool from patient PST13 [FS32]


title: 001_FLU_1_ROI_010_well_A11

tag: segment type

value: IAPA patient 1

tag: sample name

value: IAPA ROI Epith 6

tag: maintissue

tag: disease

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: Liver_CC_Female_Mice_ID_76

value: Female

value: HS

tag: tissue

value: Liver


title: 001_FLU_1_ROI_009_well_A10

tag: slide id

tag: roi number

tag: patient id

value: IAPA ROI Epith 4

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: Liver_CC_Female_Mice_ID_77

tag: gender

tag: mouse type

tag: experimental diet


title: Microbiota of stool from patient PST11 [FS30]

value: Stool

tag: timepoint

tag: diet


title: 001_FLU_1_ROI_008_well_A09

value: Trachea/bronchi

tag: segment type

value: Full

tag: sample name

value: IAPA ROI Infl 4

tag: maintissue

tag: disease

tag: area

tag: roi x coordinate


title: Microbiota of stool from patient PST3 [FS3]

tag: tissue

value: Pre-ANG

value: ANG


title: 001_FLU_1_ROI_004_well_A05

tag: slide id

tag: roi number

value: IAPA ROI Infl 3

value: IAPA

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: 001_FLU_1_ROI_007_well_A08

tag: patient id

value: IAPA patient 2

value: IAPA ROI Epith 5

value: Epithelium

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: Liver_CC_Female_Mice_ID_78

tag: gender

tag: mouse type

tag: experimental diet


title: 001_FLU_1_ROI_002_well_A03

tag: segment type

value: IAPA patient 1

tag: sample name

value: IAPA ROI Infl 1

tag: maintissue

value: Subepithelial

tag: disease


title: 001_FLU_1_ROI_003_well_A04

tag: tissue

tag: slide id

value: IAPA ROI Epith 1

tag: area

tag: roi x coordinate


title: Liver_CC_Female_Mice_ID_74

value: Female

value: HS

value: Liver


title: 001_FLU_1_ROI_001_well_A02

value: Trachea/bronchi

tag: roi number

value: IAPA ROI Epith 3

tag: roi y coordinate

tag: rawreads

tag: alignedreads


title: Microbiota of stool from patient PST9 [FS28]

value: Stool

tag: patient id

tag: timepoint

value: Post-ANG

tag: diet


title: Microbiota of stool from patient PST8 [FS27]

value: ANG


title: Microbiota of stool from patient PST10 [FS29]


title: Liver_CC_Female_Mice_ID_73

tag: gender

tag: mouse type


title: NPNF2_3h

city: Taoyuan

first: Po-Ju

middle: Gordon

last: Lee

address: No. 300, Zhongda Rd, Zhongli District

department: Biomedical Sciences and Engineering

country: Taiwan

institute: National Central University

data_processing:
Base calling perfomed using NovaSeq RTA (Real Time Analysis) version 3.4.4
Sequenced read quality was checked using the FastQC.
Trimmomatic was used to generate clean reads by removing adaptors.
Clean reads are imported into HISAT2 alignnment program and mapped to GRCh37 genome into BAM files.
Trancript abundance was measured by processing BAM files using the featureCounts package in R software to calculate raw read counts, and FPKM was calculated for gene expression quantification.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for every gene for every sample.
Supplementary_files_format_and_content: Tab delimited text file contains raw gene read counts for every sample .

source_name: Nasopharynx

growth_protocol: Primary fibroblasts were cultured in DMEM supplemented with 10% FBS and 1% penicillin/ strepromycin and incubated at 37 °C, 5% CO2.

extract_protocol:
Cells were lysed by RLT buffer containing 2-mercaptoethanol.  Total RNA was extracted using the RNeasy Mini kit (Qiagen) and 2 mg of RNA was used for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were grown in a T25 flask to 60~70% confluence. Culture medium were replaced with 3% FBS medium for 16 hours before exosome stimulation. Fibroblasts were treated then with 10 mg/ml of HK1EBV exosomes for 3 hours or 6 hours.

tag: cell type

value: Pimary fibroblasts

tag: treatment

value: Treated with HK1EBV exosomes for 3 hours


title: Microbiota of stool from patient PST7 [FS26]


title: NPNF2_C

value: untreated


title: RB029 - Primary Retinoblastoma - scRNA-Seq

city: Miami

first: Matthew

last: Field

state: FL

address: 900 NW 17th St

institute: University of Miami

data_processing:
CellRanger (3.0.2) “mkfastq” command was used to generate fastq files from Illumina bcl files
CellRanger (3.0.2) “count” command was used to generate bam files and raw gene-barcode matrices aligned to the GRCh38 Ensembl build 93 genome.
The data from all five samples were combined using the Seurat package (3.0.0) and an aggregate Seurat object was generated. To ensure our analysis was on high-quality cells, filtering was conducted by retaining cells that had unique molecular identifiers (UMIs) greater than 400, expressed 100 to 6000 genes inclusive, and had mitochondrial content less than 10 percent. This resulted in 6,371 cells for RB025, 12,808 cells for RB026, 10,675 cells for RB027, 1,354 cells for RB028, and 1,445 cells for RB029. Doublets were assessed using the DoubletFinder (2.0.3) algorithm using the multiplet rates in the 10X Genomics Chromium Single Cell 3′ Reagent Kits User Guide (v3 Chemistry).
Doublets were assessed by individual samples based on the number of captured cells. Data for all 5 samples were combined using the Standard Integration Workflow (https://satijalab.org/seurat/v3.0/integration.html). Data from each sample were normalized using the NormalizeData() function and variable features were identified using FindVariableFeatures() with 5000 genes and the selection method set to "vst", a variance stabilizing transformation. To identify integration anchor genes among the five samples the FindIntegrationAnchors() function was used with 30 principal components and 5000 genes. Using Seurat’s IntegrateData() the samples were combined into one object. The data were scaled using the ScaleData() function to reduce dimensionality of this dataset. Principal component analysis (PCA) was performed, and the first 30 principal components were summarized using uniform manifold approximation and projection (UMAP) dimensionality reduction. 30 principal components (PCs) were chosen based on results from analysis using JackStraw() and elbow plots. The DimPlot() function was used to generate the UMAP plots. Clustering was conducted using the FindNeighbors() and FindClusters() functions using 30 PCA components and a resolution parameter set to 1.8. The original Louvain algorithm was used for modularity optimization. The resulting 36 louvain clusters were visualized in a two-dimensional UMAP representation. Differentially expressed genes were identified for each cluster using FindAllMarkers() and filtered for |log fold-change| greater than 0.5 and adjusted p-value less than 0.05. Dot plots were generated using the DotPlot() function, Violin plots were generated with the vlnplot() function, and scatter plots were generated with FeatureScatter() in Seurat with “assay” set to “RNA”.
assembly: GRCh38 Ensembl build 93
Barcode, feature and matrix files for each sample

source_name: Primary Retinoblastoma

extract_protocol:
Single-cell suspensions were counted using the Cellometer K2 Fluorescent Viability Cell Counter (Nexcelom), verified manually using a hemocytometer, and adjusted to 1,000 cells/ul.
Samples were prepared using the Chromium Single Cell 5’ Library & Gel Bead Kit v2 (10X Genomics) according to the manufacturer’s protocol with a capture target of 10,000 cells. Each sample was processed on an independent Chromium Single Cell A Chip (10X Genomics) and run on a thermocycler (Eppendorf). 5’ gene expression libraries were sequenced using NextSeq 500 150-cycle high-output flow cells or NovaSeq 6000 200 cycle S4 flow cells.

value: primary retinoblastoma

tag: iirc tumor class

value: Class E

tag: familial

value: No


title: RB028 - Primary Retinoblastoma - scRNA-Seq

tag: tissue

value: Class D


title: Pacritnib_R3

city: Badalona

first: IFEANYI

middle: JUDE

last: EZEONWUMELU

state: Barcelona

address: C. Canyet s/n

department: Virus Host interactions team

institute: AIDS Research Institute - IrsiCaixa  Hospital Germans Trias i Pujol

description:
In title file R3 refers to replicate 3
Rs3P

data_processing:
Mapping was performed with HISAT2 against GRCh37
Transcript was assembled with StringTie
Genome_build: GRCh37_NCBI_105.20190906
Supplementary_files_format_and_content: Counts.txt (raw counts)

source_name: HL60 cell line

extract_protocol:
Maxwell® HT simplyRNA Kit
TruSeq Stranded mRNA LT Sample Prep Kit

tag: latent hiv-1 infection

value: Yes

tag: treatment condition


title: Liver_CC_Female_Mice_ID_75

tag: experimental diet


title: Liver_CC_Female_Mice_ID_72


title: Microbiota of stool from patient PST6 [FS25]


title: Liver_CC_Female_Mice_ID_71


title: Ruxolitinib_R3

description:
In title file R3 refers to replicate 3
Rs3R


title: Fedratinib_R3

description:
In title file R3 refers to replicate 3
Rs3F


title: Microbiota of stool from patient PST5 [FS24]


title: Liver_CC_Female_Mice_ID_6


title: PMA_R3

description:
In title file R3 refers to replicate 3
Rs3Pi

value: Positive HIV reactivation control


title: Microbiota of stool from patient PST4 [FS23]


title: NPNF2_6h

value: Treated with HK1EBV exosomes for 6 hours


title: Untreated control_R3

description:
In title file R3 refers to replicate 3
Rs3N

value: Untreated condition


title: Pacritnib_R2

description:
In title file R2 refers to replicate 2
Rs2P


title: Ruxolitinib_R2

description:
In title file R2 refers to replicate 2
Rs2R


title: Fedratinib_R2

description:
In title file R2 refers to replicate 2
Rs2F


title: PMA_R2

description:
In title file R2 refers to replicate 2
Rs2Pi


title: Pacritnib_R1

description:
In title file R1 refers to replicate 1
Rs1P


title: Microbiota of stool from patient PST1 [FS20]


title: Microbiota of stool from patient PST2 [FS21]

value: Post-EVO

value: EVO


title: Untreated control_R2

description:
In title file R2 refers to replicate 2
Rs2N


title: Microbiota of stool from patient PST2 [FS2]

value: Pre-EVO


title: Ruxolitinib_R1

description:
In title file R1 refers to replicate 1
Rs1R


title: Untreated control_R1

description:
In title file R1 refers to replicate 1
Rs1N


title: Fedratinib_R1

description:
In title file R1 refers to replicate 1
Rs1F


title: Liver_CC_Female_Mice_ID_66

value: Female

value: HP

value: Liver


title: Microbiota of stool from patient PST3 [FS22]

description: 16s rRNA v3-v4 sequencing of human stool

value: Stool

value: Post-ANG

value: ANG


title: Liver_CC_Female_Mice_ID_5

description: Gene expression in liver tissue obtained from female CC mouse

value: HS


title: Microbiota of stool from patient PST20 [FS19]


title: TPC2-4 TNFα

city: Tianjin

first: xudong

last: Wu

address: Qixiangtai Road

country: China

institute: Tianjin medical university

data_processing:
Clean reads were aligned to human reference genome (hg19)  using Bowtie 2 version 2.2.9.
SAMtools was used to remove PCR duplicate and unmapped reads. Peak calling and annotation were performed using MACS version 1.4.2 and ChIPseeker  package
Bigwig files, heatmaps, and average profiles were generated by deepTools V2.4.0
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file for each Sample

source_name: Brain tumor

growth_protocol: The glioblastoma cell line TPC 2-4  were cultured in DMEM/Ham’s F12 (12,400,024, Gibco) supplemented with 2% B27 Supplement (17,504,044, Gibco), 1% P/S, 1% L-Glutamine 200 mM (100×, 25030081, Gibco), 20 ng/ml human fibroblast growth factor-basic (bFGF, 10,014-HNAE, Sino Biological) and 20 ng/ml epidermal growth factor-basic (EGF, 10,605-HNAE, Sino Biological). Cells were maintained at 37 °C in a humid incubator with 5% CO2.

extract_protocol:
For ATAC-seq, 50,000 TPC2-4 cells were precipitated and subsequently re-suspended with 50 μl cold lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) igepal CA-630) and incubated on ice for 10 minutes (min). After centrifuge at 500 g for 10 min at 4℃, the nuclei were re-suspended with 100 μl wash buffer (10 mM Tris-HCl pH7.5, 10 mM NaCl, 3 mM MgCl2). Followed by washing twice, the transposable reaction and DNA library preparation was performed accordingly with TruePrep DNA Library Prep Kit V2 (TD501-01, Vazyme). The successfully prepared libraries were sequenced on the Illumina PE150 platform (Novogene).
Library preparation was performed accordingly with TruePrep DNA Library Prep Kit V2 (TD501-01, Vazyme). The successfully prepared libraries were sequenced on the Illumina PE150 platform (Novogene).

treatment_protocol: TNFα (10 ng/mL, 10602-HNAE), and JNK-IN-8  (1 μM, HY-13319) dissolved in dimethyl sulfoxide (DMSO, D8418, Sigma) was used

tag: cell line

value: Brain tumor

value: TNFα


title: TPC2-4 con

value: control


title: Liver_CC_Female_Mice_ID_61


title: RNA-Seq: TPC2-4 TNFα+JNKi

data_processing:
Reads were aligned to human reference genome (hg19)  using HISAT2.
FPKM were generated by StringTie V2.1.1.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM for all samples
Supplementary_files_format_and_content: Bigwig files for all samples

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using NEBNext Ultra RNA library Prep Kit for Illumina.

value: TNFα+JNKi


title: Liver_CC_Female_Mice_ID_51


title: Microbiota of stool from patient PST19 [FS18]

source_name: Stool


title: Microbiota of stool from patient PST18 [FS17]

value: Pre-ANG


title: TPC2-4 TNFα+JNKi


title: Liver_CC_Female_Mice_ID_4


title: Microbiota of stool from patient PST17 [FS16]


title: RNA-Seq: TPC2-4 TNFα


title: PMA_R1

description:
In title file R1 refers to replicate 1
Rs1Pi

value: Yes

value: Positive HIV reactivation control


title: RNA-Seq: TPC2-4 con


title: Liver_CC_Female_Mice_ID_38


title: Liver_CC_Female_Mice_ID_40


title: Liver_CC_Female_Mice_ID_56


title: Liver_CC_Female_Mice_ID_3


title: Microbiota of stool from patient PST16 [FS15]


title: Liver_CC_Female_Mice_ID_39


title: Liver_CC_Female_Mice_ID_37


title: Liver_CC_Female_Mice_ID_35


title: Liver_CC_Female_Mice_ID_36


title: TX1242_8_GEX

city: Durham

first: Elliott

middle: Daniel

last: SoRelle

state: NC

address: 130 Research Drive (CARL Building)

department: Molecular Genetics & Microbiology

institute: Duke University

description:
Sample 8G
Single-cell gene expression (split across 2 flow cell lanes -- L001 / L002)

data_processing:
Base-calling (cellranger-arc mkfastq; wrapper of Illumina bcl2fastq function for multiome samples)
Alignment (cellranger-arc count; tabulates cell-matched transcript counts and Tn5 insertion sites)
Filtering (cellranger-arc count -- default QC parameters for read filtering)
Peak-calling (ATAC) -- MACS2 / MACS3
Normalized abundance measurement (GEX) -- Seurat / Signac
Genome_build: hg38 ; hg38 + type 1 EBV (NC_007605)
Supplementary_files_format_and_content: count matrices (gene expression) and ATAC fragments (chromatin accessibility)

source_name: peripheral B lymphocytes

growth_protocol: Culture in R15 media (RPMI1640 + 15% Heat-inactivated FBS + Pen/Strep/Glutamine + Cyclosporine A) @ 37°C, 5% CO2

extract_protocol:
10x Genomics scATAC + Gene Expression kit (single-cell mRNA and Tn5-accessible chromatin fragment capture)
10x Genomics scATAC + Gene Expression kit
Single-end gene expression libraries @ target of 50k reads per cell ; paired-end ATAC fragment libraries @ target of 50k total reads per cell (25k + / 25k - )

treatment_protocol: Infection with B95-8 strain of EBV for 1 hr @ MOI of 5 (37°C, 5% CO2) [except for uninfected samples at Day 0]

value: PBMC-derived B cells

tag: donor

value: TX1242 (donor 2)

tag: infection

value: 8 days post EBV infection


title: Microbiota of stool from patient PST15 [FS14]

value: Pre-EVO

value: EVO


title: TX1242_2_GEX

description:
Sample 6G
Single-cell gene expression (split across 2 flow cell lanes -- L001 / L002)

value: 2 days post EBV infection


title: TX1242_5_ATAC

description:
Sample 7A
Single-cell chromatin accessibility (split across 2 flow cell lanes -- L001 / L002)

value: 5 days post EBV infection


title: TX1242_5_GEX

description:
Sample 7G
Single-cell gene expression (split across 2 flow cell lanes -- L001 / L002)


title: TX1242_8_ATAC

description:
Sample 8A
Single-cell chromatin accessibility (split across 2 flow cell lanes -- L001 / L002)


title: Microbiota of stool from patient PST13 [FS13]

value: Stool


title: Liver_CC_Female_Mice_ID_33

value: Female

value: HP

value: Liver


title: TX1242_2_ATAC

description:
Sample 6A
Single-cell chromatin accessibility (split across 2 flow cell lanes -- L001 / L002)


title: Microbiota of stool from patient PST12 [FS12]


title: TX1242_0_GEX

description:
Sample 5G
Single-cell gene expression (split across 2 flow cell lanes -- L001 / L002)

value: Uninfected (day 0)


title: Microbiota of stool from patient PST11 [FS11]


title: TX1242_0_ATAC

description:
Sample 5A
Single-cell chromatin accessibility (split across 2 flow cell lanes -- L001 / L002)


title: Liver_CC_Female_Mice_ID_31


title: TX1241_5_GEX

description:
Sample 3G
Single-cell gene expression (split across 2 flow cell lanes -- L001 / L002)

value: TX1241 (donor 1)


title: TX1241_8_GEX

description:
Sample 4G
Single-cell gene expression (split across 2 flow cell lanes -- L001 / L002)


title: TX1241_8_ATAC

description:
Sample 4A
Single-cell chromatin accessibility (split across 2 flow cell lanes -- L001 / L002)


title: Liver_CC_Female_Mice_ID_32


title: TX1241_5_ATAC

description:
Sample 3A
Single-cell chromatin accessibility (split across 2 flow cell lanes -- L001 / L002)


title: Microbiota of stool from patient PST10 [FS10]

value: ANG


title: TX1241_2_GEX

description:
Sample 2G
Single-cell gene expression (split across 2 flow cell lanes -- L001 / L002)


title: TX1241_2_ATAC

description:
Sample 2A
Single-cell chromatin accessibility (split across 2 flow cell lanes -- L001 / L002)


title: 002_COV_2_ROI_010_well_B11

description: Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

value: Trachea/bronchi

tag: slide id

tag: roi number

tag: segment type

value: Full

value: CAPA patient 1

tag: sample name

value: CAPA ROI Infl 2

tag: maintissue

value: Subepithelial

tag: disease

value: CAPA

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: TX1241_0_GEX

description:
Sample 1G
Single-cell gene expression (split across 2 flow cell lanes -- L001 / L002)

tag: cell type

value: PBMC-derived B cells

tag: donor


title: TX1241_0_ATAC

description:
Sample 1A
Single-cell chromatin accessibility (split across 2 flow cell lanes -- L001 / L002)

tag: infection


title: Liver_CC_Female_Mice_ID_30

description: Gene expression in liver tissue obtained from female CC mouse

tag: gender

tag: mouse type

tag: experimental diet

tag: tissue


title: Subject_50_PolyIC_5yo

city: Perth

first: James

last: Read

address: 15 Hospital Ave.

country: Australia

institute: Telethon Kids Institute

data_processing:
Data was generated with the Illumia NovaSeq 6000 platform and the bcl2fastq pipeline was used to convert base calls (BCL) to fastq files.
Read libraries were mapped to the human genome (hg38) using HISAT2. Gene-level quantitation (counts) of HISAT2 alignments was performed using SummarizeOverlaps, and Pre- and post-alignment QC was assessed with FastQC and SAMStat, respectively.
(For corrected gene counts) Raw transcripts were removed if they had no counts in any sample, lacked annotation, or had 0.5 counts per million in ≤ 25 samples. Size factors were estimated using the median ratio method with the 'estimateSizeFactors' function (DESeq2 R package) and variance stabilizing transformation (VST) was applied to the count data (DESeq2). Unwanted variation was identified with the 'RUVg' function from the RUVSeq R package. RUVg trends which related to technical variation and culture batch were removed as covariates with a linear model ('removeBatchEffect' function from the limma R package).
Genome_build: hg38
Supplementary_files_format_and_content: genecounts.txt file contain a matrix of raw gene counts (unfiltered and un-normalised data). Corrected_genecounts.csv contains a matrix of VST transformed and batch/RUV corrected gene counts

source_name: PBMC

extract_protocol:
Total RNA was extracted with TRIzol (Ambion) followed by RNAeasy (QIAGEN). Total RNA libraries were prepared using NEBNext Ultra II Kits (New England BioLabs). Sequencing was performed by the Australian Genome Research Facility (Illumina NovaSeq 6000, 100bp paired-end reads).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cord and 5 year mononuclear cells were stimulated with LPS, Imiquimod or Poly(I:C), of left untreated, and cultures at 37oC (5% CO2) for 18 hrs.

tag: stimuli

value: PolyIC

tag: Sex

value: Male

value: No


title: Liver_CC_Female_Mice_ID_2

value: HS


title: Subject_50_IMIQ_5yo

value: IMIQ


title: Subject_50_LPS_5yo

value: LPS


title: 002_COV_2_ROI_009_well_B10

tag: slide id

tag: roi number

tag: segment type

tag: patient id

tag: sample name

value: CAPA ROI Infl 1

tag: maintissue

tag: disease

tag: area

tag: roi x coordinate


title: Liver_CC_Female_Mice_ID_29

value: Female

value: HP

value: Liver


title: Liver_CC_Female_Mice_ID_27


title: 002_COV_2_ROI_007_well_B08

value: Trachea/bronchi

value: CAPA ROI Epith 3

value: Epithelium

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: Subject_50_CTRL_5yo

tag: stimuli

value: CTRL

tag: Sex


title: Subject_48_PolyIC_5yo


title: Subject_48_LPS_5yo


title: 002_COV_2_ROI_004_well_B05

tag: tissue

tag: slide id

tag: roi number

value: Full

value: CAPA patient 2

value: CAPA ROI Epith 2


title: Subject_48_IMIQ_5yo


title: Microbiota of stool from patient PST1 [FS1]

description: 16s rRNA v3-v4 sequencing of human stool

value: Stool

tag: patient id

tag: timepoint

value: Pre-ANG

tag: diet

value: ANG


title: Liver_CC_Female_Mice_ID_261

tag: gender

tag: mouse type

tag: experimental diet


title: Liver_CC_Female_Mice_ID_26


title: Subject_45_PolyIC_5yo

value: PolyIC

value: Male

value: No


title: Subject_48_CTRL_5yo


title: Subject_45_LPS_5yo

value: LPS


title: BT549_tetWDR5_DOXplus_3

city: Boston

first: Atrayee

last: Bhattacharya

state: Massachusetts

address: 450 Brookline Avenue, Boston 02215

institute: Dana Farber Cancer Institute, Harvard Medical School

description: puromycin resistance

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).
Supplementary files format and content: baseMean,log2FoldChange,lfcSE,stat,pvalue,padj

source_name: TNBC

growth_protocol: BT549  cells were cultured in RPMI 1640 medium (Corning, Corning, NY, USA) supplemented with 10% FBS and 10 ug/ml insulin.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNeasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

treatment_protocol: Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline.

tag: agent

value: DOXplus

tag: cell line


title: BT549_tetWDR5_DOXplus_2

description: puromycin resistance


title: 002_COV_2_ROI_002_well_B03

tag: segment type

tag: sample name

value: CAPA ROI Epith 1

tag: maintissue

tag: disease

value: CAPA

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: Subject_42_LPS_5yo

tag: stimuli

tag: Sex

value: Female

value: Yes


title: Subject_42_PolyIC_5yo


title: Subject_45_CTRL_5yo


title: Subject_42_IMIQ_5yo

value: IMIQ


title: Subject_40_PolyIC_5yo


title: Subject_40_IMIQ_5yo


title: Subject_45_IMIQ_5yo


title: Liver_CC_Female_Mice_ID_28

source_name: Liver from CC female mice

tag: gender

value: HP

tag: tissue

value: Liver


title: BT549_tetWDR5_DOXplus_1

description: puromycin resistance


title: Liver_CC_Female_Mice_ID_260

tag: mouse type

tag: experimental diet


title: BT549_tetWDR5_DOX-_3

description: puromycin resistance

tag: agent

value: DMSO

tag: cell line


title: Liver_CC_Female_Mice_ID_255

value: HS


title: Liver_CC_Female_Mice_ID_24


title: Liver_CC_Female_Mice_ID_25


title: Liver_CC_Female_Mice_ID_257


title: Liver_CC_Female_Mice_ID_259


title: Subject_40_CTRL_5yo

value: CTRL


title: 002_COV_2_ROI_001_well_B02

value: Trachea/bronchi

tag: slide id

tag: roi number

tag: segment type

value: Full

tag: patient id

value: CAPA patient 2

tag: sample name

value: CAPA ROI Infl 3

value: Subepithelial

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: Subject_39_PolyIC_5yo

value: PolyIC

value: No


title: Liver_CC_Female_Mice_ID_23


title: BT549_tetWDR5_DOX-_1

description: puromycin resistance


title: Case 2 - relapsed

first: Kirsi

middle: J.

last: Rautajoki

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

data_processing:
Base-calling Illumina HiSeq 2000
Aligment STAR 2.7.0 against human genome assembly GRCh38 using GENCODE v.30 annotations
Gene counts using featureCounts Rsubread package v. 1.34.6
Differential expression and normalization using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: normalized expresison matrix txt file

source_name: oligodendroglioma grade III

extract_protocol:
mirVana™ miRNA Isolation Kit (Life Technologies), large RNA (>200 nucleotides) molecules were divided into a separate fraction
Illumina, strand-specific 140-160 bp short insert library protocol

value: brain

tag: tumor stage

value: grade III

value: female

tag: age


title: Subject_39_CTRL_5yo

tag: stimuli

tag: Sex

value: Female


title: 001_FLU_1_ROI_005_well_A06

tag: tissue

value: IAPA patient 2

value: IAPA ROI Infl 2

tag: maintissue

tag: disease

value: IAPA

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: Subject_42_CTRL_5yo

value: Yes


title: Subject_39_LPS_5yo

value: LPS


title: Subject_38_IMIQ_5yo

value: IMIQ


title: Case 1 - relapsed

tag: gender


title: Case 2 - primary

source_name: oligodendroglioma grade II

value: grade II


title: Subject_38_CTRL_5yo

value: CTRL


title: Subject_40_LPS_5yo

value: Male


title: Subject_38_LPS_5yo


title: Case 1 - primary


title: Subject_37_PolyIC_5yo


title: Liver_CC_Female_Mice_ID_22

tag: mouse type

tag: experimental diet

value: HP

value: Liver


title: Subject_37_IMIQ_5yo


title: Subject_37_LPS_5yo


title: Subject_37_CTRL_5yo


title: Subject_39_IMIQ_5yo


title: Liver_CC_Female_Mice_ID_21


title: MM27_USP7_rep3

city: Milano

first: Marine

last: Melixetian

address: via Adamello 16

institute: European Institute of Oncology

data_processing:
Data were filtered using the Illumina quality control flag
Reads were aligned to the homo sapiens genome build hg19 using tophat (v2.0.8), which uses Bowtie (2.1.0) and Samtools (v0.1.18) using default parameters and --transcriptome H. sapiens index, UCSC hg19 gtf.
Raw read counts were summarised using HTSeq (v0.5.3p9), then normalized for library size differences using estimateSizeFactors function from DESeq package (v1.10.1).
Differential expression of genes was calculated with the same R package, using three biological replicas for each interference condition (shLuc and shKMT2D) for each MM patient.
hg19
Genome_build: A tab delimited file with normalized read counts for  all samples
Supplementary_files_format_and_content: raw HT counts  tab delimited file

source_name: metastasis of cutaneous melanoma

extract_protocol:
total RNA was extracted with Quick-RNA MiniPrep (cat #R1055, Zymo Research) according to manufacturer protocol
libraries were constructed using Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) starting from 1µg of total RNA

treatment_protocol: Cells isolated from  PDXs were infected with lentiviral vector silencing  USP7  or shscr control vector. After 48h of infection, cells were harvested for further analysis

tag: cell type

value: patient derived xenograft cells

tag: passage

tag: melanoma mutation

tag: infected shrna

value: shUSP7 hairpin


title: Subject_36_PolyIC_5yo

tag: stimuli

value: PolyIC

tag: Sex

value: No


title: Liver_CC_Female_Mice_ID_20

value: HS

tag: tissue


title: MM27_USP7_rep2


title: Liver_CC_Female_Mice_ID_196

value: Female


title: Liver_CC_Female_Mice_ID_198


title: Subject_36_LPS_5yo


title: Subject_36_CTRL_5yo


title: Subject_34_PolyIC_5yo


title: Liver_CC_Female_Mice_ID_195


title: Subject_34_IMIQ_5yo


title: MM27_shSCR1_rep3

value: Scrambled control hairpin


title: Subject_34_LPS_5yo


title: MM27_shSCR1_rep2


title: Liver_CC_Female_Mice_ID_1


title: Subject_34_CTRL_5yo


title: Subject_31_LPS_5yo


title: Subject_31_IMIQ_5yo


title: Subject_38_PolyIC_5yo


title: Subject_36_IMIQ_5yo


title: Subject_31_CTRL_5yo


title: MM27_USP7_rep1


title: Subject_30_PolyIC_5yo


title: Liver_CC_Female_Mice_ID_188


title: MM16_USP7_rep3


title: Liver_CC_Female_Mice_ID_180


title: Liver_CC_Female_Mice_ID_193


title: Liver_CC_Female_Mice_ID_18


title: Subject_30_IMIQ_5yo


title: MM16_USP7_rep2


title: Liver_CC_Female_Mice_ID_176


title: MM16_USP7_rep1


title: Subject_30_LPS_5yo


title: MM27_shSCR1_rep1


title: Subject_28_IMIQ_5yo


title: Subject_28_LPS_5yo


title: Liver_CC_Female_Mice_ID_175


title: Subject_28_PolyIC_5yo


title: Liver_CC_Female_Mice_ID_17


title: Subject_28_CTRL_5yo


title: Subject_26_PolyIC_5yo


title: Subject_26_IMIQ_5yo


title: MM16_shSCR1_rep2


title: Liver_CC_Female_Mice_ID_173


title: MM16_shSCR1_rep1


title: Subject_26_LPS_5yo


title: Liver_CC_Female_Mice_ID_174


title: Subject_30_CTRL_5yo


title: Subject_25_PolyIC_5yo


title: Subject_26_CTRL_5yo


title: Liver_CC_Female_Mice_ID_171


title: MM16_shSCR1_rep3


title: Liver_CC_Female_Mice_ID_172


title: KO

city: Stanford

first: Kamir

last: Hiam-Galvez

address: 240 Pasteur Drive

institute: Stanford University

data_processing:
Reads were processed with Cell Ranger v3.1.0
R1 contains barcode at 1-16bp and UMI at bp 17-26
R2 contains the biological sequence
Assembly: mm10
Supplementary files format and content: "barcodes.tsv.gz" contains filtered cellular barcodes, "features.tsv.gz" contains genes, "matrix.mtx.gz" contains the barcoded gene expression matrix

source_name: lung

extract_protocol: 10x Chromium Next Gem 3' reagent kit (v3.1)

tag: challenge

value: House Dust Mite

tag: sorted population

value: Cell Trace Violet low donor CD4 T cells

tag: host strain


title: GFP_IP 5

city: Edinburgh

first: Javier

last: Caceres

address: Crewe Road

institute: University of Edinburgh

data_processing:
Adaptor removal using cutadapt, umi exraction using umi_tools, mapping using bowtie and peak calling using macs2
see methods for full details
Assembly: GRCh38.93
Supplementary files format and content: seCLIP_mapping,xlsx
Supplementary files format and content: DHX34_peaks.bed
Supplementary files format and content: mapping information
Supplementary files format and content: bed file of peaks

growth_protocol: standard culture conditions , DMEM, 10% FCS, 1% Pen/Strep

extract_protocol:
Briefly 150-300 nt fragment library was constructed and dual indices with i7 (D701-D704) and i5 (D501-D504) used as described by Van Nostrand et al..: Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP). Methods Mol Biol. 2017;1648:177-200. doi: 10.1007/978-1-4939-7204-3_14
SE 75 bp) on NextSeq done at WTCRF

treatment_protocol: UV crosslinking

tag: cell line

value: embryonic kidney cell line

tag: treatment

value: anti-GFP

tag: tag


title: WT


title: Subject_22_IMIQ_5yo

value: IMIQ

value: Yes


title: Subject_22_PolyIC_5yo


title: Subject_22_LPS_5yo

value: LPS


title: Subject_22_CTRL_5yo

value: CTRL


title: Subject_25_IMIQ_5yo

value: Male


title: GFP_IP 3


title: Subject_21_PolyIC_5yo


title: Liver_CC_Female_Mice_ID_16

value: Liver


title: Liver_CC_Female_Mice_ID_170

value: HP


title: Subject_25_CTRL_5yo


title: Subject_21_IMIQ_5yo


title: Subject_21_LPS_5yo


title: Subject_20_PolyIC_5yo


title: Liver_CC_Female_Mice_ID_168


title: Liver_CC_Female_Mice_ID_167


title: Subject_25_LPS_5yo


title: NEG GFP INPUT 4

value: no tag


title: Liver_CC_Female_Mice_ID_169


title: GFP_IP 2


title: Liver_CC_Female_Mice_ID_166


title: Subject_21_CTRL_5yo


title: Subject_19_IMIQ_5yo


title: Subject_19_PolyIC_5yo

value: PolyIC


title: GFP_IP 4


title: NEG GFP INPUT 3


title: NEG GFP INPUT 2


title: Subject_20_CTRL_5yo

value: No


title: Subject_20_LPS_5yo


title: GFP_IP 1


title: BT549_tetWDR5_DOX-_2

description: puromycin resistance

tag: agent

value: DMSO


title: Liver_CC_Female_Mice_ID_164

tag: gender

value: Female


title: Subject_18_PolyIC_5yo


title: Liver_CC_Female_Mice_ID_165

tag: mouse type


title: Subject_31_PolyIC_5yo


title: Subject_19_CTRL_5yo


title: Subject_20_IMIQ_5yo


title: NEG GFP INPUT 1


title: Subject_15_LPS_5yo


title: Liver_CC_Female_Mice_ID_160

tag: experimental diet


title: Subject_19_LPS_5yo


title: Subject_18_IMIQ_5yo


title: Subject_10_IMIQ_5yo


title: Subject_10_PolyIC_5yo


title: Subject_15_PolyIC_5yo


title: Subject_18_LPS_5yo


title: Subject_15_IMIQ_5yo


title: Subject_18_CTRL_5yo


title: Subject_15_CTRL_5yo


title: Liver_CC_Female_Mice_ID_157

value: HS


title: Subject_08_IMIQ_5yo


title: 000008512269_H12

city: Nantes

first: Richard

last: Danger

address: 30 Boulevard Jean Monnet

country: France

institute: CHU Nantes - INSERM- Nantes Universite

data_processing:
Data was separated by barcode and aligned using Tophat version 2.0.10 (Kim et al. 2013) with default settings.
Transcripts were quantified by the Broad Technology Labs computational pipeline using Cuffquant version 2.2.1 (Trapnell et al. 2012).
Data were processed through CuffNorm if 50% of the reads aligned and if at least 100,000 pairs were aligned per sample. Normalization used the default settings, including “geometric” normalization, and expression level information as FPKM (Fragments per kilobase of transcript per million mapped fragments) are provided.
Assembly: hg19
Supplementary files format and content: tab-delimited text file including FPKM for each sample

source_name: TEM

extract_protocol:
Naïve (CD45RA+CD28+), EM (CD45RA-CD28-) and TEMRA (CD45RA+CD28-) CD3+CD8+ T cells were FACS sorted (FACSAria, BD Biosciences; purity greater than 95%) from freshly isolated human PBMCs obtained from 6 KT. Cell pellets were resuspended in RLT buffer (Qiagen) containing 1% β-mercaptoethanol before subsequent RNA extraction using a RNeasy Micro Kit according to the manufacturer’s instructions (Qiagen). Quality and quantity of the RNA were assessed by spectrometry (Nanodrop) and electrophoresis (Agilent RNA 6000 Pico Kit).
Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform according to the SmartSeq2 protocol (Picelli et al, 2013, 2014) with some modifications (Trombetta et al, 2014). Briefly, total RNA was purified using RNA-SPRI beads, polyA mRNA was converted to cDNA and amplified cDNA was subject to transposon-based fragmentation that used dual-indexing to barcode each fragment of each converted transcript with a combination of barcodes specific to each sample. Sequencing was carried out as paired-end 2x25bp with an additional 8 cycles for each index.

tag: patient

tag: rin


title: Liver_CC_Female_Mice_ID_15


title: Liver_CC_Female_Mice_ID_161


title: Liver_CC_Female_Mice_ID_158


title: Liver_CC_Female_Mice_ID_163


title: Subject_10_LPS_5yo


title: Subject_10_CTRL_5yo


title: Subject_08_PolyIC_5yo


title: Liver_CC_Female_Mice_ID_156


title: 000008512269_H06

tag: cell type

value: TEMRA (CD45RA+CD28-) CD8+ T


title: Subject_07_IMIQ_5yo


title: Subject_07_CTRL_5yo


title: Liver_CC_Female_Mice_ID_152


title: Liver_CC_Female_Mice_ID_155


title: Subject_06_IMIQ_5yo


title: Liver_CC_Female_Mice_ID_153


title: Liver_CC_Female_Mice_ID_154


title: Subject_06_LPS_5yo


title: Subject_08_LPS_5yo


title: 000008512269_H09


title: Subject_08_CTRL_5yo


title: Subject_07_PolyIC_5yo


title: 000008512269_H10

source_name: Naive

value: Naive (CD45RA+CD28+)


title: Subject_05_PolyIC_5yo


title: Subject_07_LPS_5yo


title: Subject_06_CTRL_5yo


title: 000008512269_H03


title: Subject_05_LPS_5yo


title: 000008512269_H07


title: Subject_06_PolyIC_5yo


title: 000008512269_H04


title: 000008512269_G12


title: Liver_CC_Female_Mice_ID_147


title: Liver_CC_Female_Mice_ID_151


title: Liver_CC_Female_Mice_ID_148


title: Subject_05_IMIQ_5yo


title: Subject_05_CTRL_5yo


title: Liver_CC_Female_Mice_ID_149


title: Subject_04_PolyIC_5yo


title: Subject_04_IMIQ_5yo


title: Liver_CC_Female_Mice_ID_150


title: 000008512269_H01


title: Subject_50_PolyIC_Cord

data_processing:
Data was generated with the Illumia NovaSeq 6000 platform and the bcl2fastq pipeline was used to convert base calls (BCL) to fastq files.
Read libraries were mapped to the human genome (hg38) using HISAT2. Gene-level quantitation (counts) of HISAT2 alignments was performed using SummarizeOverlaps, and Pre- and post-alignment QC was assessed with FastQC and SAMStat, respectively.
(For corrected gene counts) Raw transcripts were removed if they had no counts in any sample, lacked annotation, or had 0.5 counts per million in ≤ 25 samples. Size factors were estimated using the median ratio method with the 'estimateSizeFactors' function (DESeq2 R package) and variance stabilizing transformation (VST) was applied to the count data (DESeq2). Unwanted variation was identified with the 'RUVg' function from the RUVSeq R package. RUVg trends which related to technical variation and culture batch were removed as covariates with a linear model ('removeBatchEffect' function from the limma R package).
Genome_build: hg38
Supplementary_files_format_and_content: CBMC_genecounts.txt file contain a matrix of raw gene counts (unfiltered and un-normalised data), with transcripts as rows and samples as columns. Transcript information (e.g. EnsembleID, gene symbol) are supplied in the final columns. CBMC_corrected_counts.txt contains a matrix of VST transformed and batch/RUV corrected gene counts, formatted as the raw gene count file.

source_name: CBMC

treatment_protocol: Cryopreserved cord blood mononuclear cells were thawed and stimulated with LPS, Imiquimod or Poly(I:C), of left untreated, and cultured at 37oC (5% CO2) for 18 hrs.

value: Cord


title: Subject_04_LPS_5yo


title: Liver_CC_Female_Mice_ID_146

data_processing: Probes containing known SNPs from the founder strains were masked. We used the robust multiarray average method (RMA) implemented in the Affymetrix gene expression console with default settings (median polish and sketch-quantile normalization) to estimate the normalized expression levels of transcripts.


title: 000008512269_G09


title: Liver_CC_Female_Mice_ID_142


title: Liver_CC_Female_Mice_ID_144


title: Subject_49_PolyIC_Cord


title: 000008512269_H11

source_name: EM

value: EM (CD45RA-CD28-)


title: Subject_50_LPS_Cord


title: Subject_50_IMIQ_Cord

value: IMIQ


title: MZT7_E2_2

city: Changchun

first: Peng

last: Hao

address: Xincheng Street

institute: Jilin Agricultural University School of Veterinary Medicine

description: Bacteria

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). We used KOBAS software to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: NCBI accession number of CP082781.1.
Supplementary files format and content: gene-fpkm-expression.txt: Tab-separated text file includes counts and FPKM values.

organism: Microbacterium resistens

extract_protocol:
RNA quantification and qualification: [1] RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA); [2] RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: strain

value: 20 mg/L E2


title: Subject_50_CTRL_Cord

tag: stimuli


title: 000008512269_H08


title: Liver_CC_Female_Mice_ID_139

extract_protocol: Total RNA was extracted from about 25 mg of liver tissue using Norgen Total RNA Purification Kit, Norgen


title: Subject_49_IMIQ_Cord

tag: Sex

value: Yes


title: 000008512269_G11


title: Liver_CC_Female_Mice_ID_141

tag: tissue


title: Subject_48_PolyIC_Cord


title: MZT7_3

description: Bacteria

value: Control


title: MZT7_E2_3

description: Bacteria


title: 000008512269_H05


title: Liver_CC_Female_Mice_ID_131


title: Subject_04_CTRL_5yo

value: CTRL

value: Male


title: pBCC3

city: Tsukuba

first: Yun Hsuan

last: Chang

state: Ibaraki

address: Tennodai 1-1-1

country: Japan

institute: University of Tsukuba

data_processing:
FASTQ files were imported to CLC Genomics Workbench (Ver.10.1.1, Qiagen).
Reads were grouped by sequence then matched to miR-base annotated microRNAs (miRbase v21)
Total counts were normalized by adjusting total counts to 1x10^6.
Genome_build: miRbase v21
Supplementary_files_format_and_content: Microsoft Excel file format, containing gene name, raw read counts and normalized read counts.

source_name: breast cancer

growth_protocol: All the cells were cultured under a hypoxic condition (1%O2) for 48 hours.

extract_protocol:
The cell samples were collected, and RNA was purified using Trizol reagent according to the standard protocol.
500 ng of total RNA was applied for sequencing. The NEBNext Small RNA Library Prep Kit was used to build a sequencing small RNA library, which was selected according to size using AMPure beads and verified using a Bioanalyzer DNA High-sensitivity Kit.
NEBNext Small RNA Library Prep Kit, small RNA library

treatment_protocol: The BCC treated with 150ng of WJ-EV at 0 and 24 hours, called pBCC.

tag: genotype

value: wild type

value: WJ-EV


title: Liver_CC_Female_Mice_ID_13

first: Brian

last: Bennett

address: 430 West Health Sciences Drive

institute: USDA ARS-WHNRC

value: Liver


title: 000008512269_H02


title: Subject_49_LPS_Cord

value: LPS

value: No


title: Liver_CC_Female_Mice_ID_130

value: Female

value: HP


title: Subject_49_CTRL_Cord


title: MZT7_E2_1

description: Bacteria


title: 000008512269_G10


title: MZT7_2

description: Bacteria


title: MZT7_1

description: Bacteria


title: Subject_48_IMIQ_Cord


title: pBCC2


title: AD3924: Ejaculated sperm rep pool 4

city: Bellaterra (Barcelona)

first: Joan

last: Cerdà

state: Spain

address: Parc de Recerca UAB, Mòdul B

institute: IRTA

data_processing:
RNA-seq reads were mapped with STAR 2.5.3a against the Sparus saurata reference genome (http://biocluster.her.hcmr.gr/myGenomeBrowser?portalname = Saurata_v1; PMID: 30271999)
Genes were quantified with RSEM 1.3.0 based on the improved annotation performed in the study
Supplementary_files_format_and_content: raw counts matrix

organism: Sparus aurata

source_name: Ejaculated sperm

extract_protocol:
Haploid germ cells were isolated from the testis by fluorescence-activated cell sorting. Ejaculated spermatozoa was collected from after a soft pressure to the abdominal area of the fish.
RNA libraries were prepared with the SMARTseq2 (Illumina) unstranded protocol for low-input RNA

value: Spermatozoa

value: Ejaculated sperm


title: BCC3

value: untreated


title: Liver_CC_Female_Mice_ID_134

city: Davis


title: Liver_CC_Female_Mice_ID_121


title: Subject_48_LPS_Cord

value: Cord


title: Subject_47_IMIQ_Cord

value: IMIQ


title: AD3921: Ejaculated sperm rep pool 2


title: Liver_CC_Female_Mice_ID_120


title: Liver_CC_Female_Mice_ID_129


title: Subject_47_LPS_Cord


title: Liver_CC_Female_Mice_ID_12

value: HS


title: Subject_48_CTRL_Cord


title: Subject_47_CTRL_Cord

value: Yes


title: pBCC1


title: AD3920: Ejaculated sperm rep pool 3


title: BCC1


title: BCC2


title: Liver_CC_Female_Mice_ID_11


title: Subject_46_IMIQ_Cord


title: Subject_47_PolyIC_Cord

value: PolyIC


title: AD3908: Haploid germ cells rep pool 4

source_name: Testis

value: Spermatocytes II and Spermatids

value: Testis


title: Subject_46_PolyIC_Cord


title: RB026 - Primary Retinoblastoma - scRNA-Seq

data_processing:
CellRanger (3.0.2) “mkfastq” command was used to generate fastq files from Illumina bcl files
CellRanger (3.0.2) “count” command was used to generate bam files and raw gene-barcode matrices aligned to the GRCh38 Ensembl build 93 genome.
The data from all five samples were combined using the Seurat package (3.0.0) and an aggregate Seurat object was generated. To ensure our analysis was on high-quality cells, filtering was conducted by retaining cells that had unique molecular identifiers (UMIs) greater than 400, expressed 100 to 6000 genes inclusive, and had mitochondrial content less than 10 percent. This resulted in 6,371 cells for RB025, 12,808 cells for RB026, 10,675 cells for RB027, 1,354 cells for RB028, and 1,445 cells for RB029. Doublets were assessed using the DoubletFinder (2.0.3) algorithm using the multiplet rates in the 10X Genomics Chromium Single Cell 3′ Reagent Kits User Guide (v3 Chemistry).
Doublets were assessed by individual samples based on the number of captured cells. Data for all 5 samples were combined using the Standard Integration Workflow (https://satijalab.org/seurat/v3.0/integration.html). Data from each sample were normalized using the NormalizeData() function and variable features were identified using FindVariableFeatures() with 5000 genes and the selection method set to "vst", a variance stabilizing transformation. To identify integration anchor genes among the five samples the FindIntegrationAnchors() function was used with 30 principal components and 5000 genes. Using Seurat’s IntegrateData() the samples were combined into one object. The data were scaled using the ScaleData() function to reduce dimensionality of this dataset. Principal component analysis (PCA) was performed, and the first 30 principal components were summarized using uniform manifold approximation and projection (UMAP) dimensionality reduction. 30 principal components (PCs) were chosen based on results from analysis using JackStraw() and elbow plots. The DimPlot() function was used to generate the UMAP plots. Clustering was conducted using the FindNeighbors() and FindClusters() functions using 30 PCA components and a resolution parameter set to 1.8. The original Louvain algorithm was used for modularity optimization. The resulting 36 louvain clusters were visualized in a two-dimensional UMAP representation. Differentially expressed genes were identified for each cluster using FindAllMarkers() and filtered for |log fold-change| greater than 0.5 and adjusted p-value less than 0.05. Dot plots were generated using the DotPlot() function, Violin plots were generated with the vlnplot() function, and scatter plots were generated with FeatureScatter() in Seurat with “assay” set to “RNA”.
assembly: GRCh38 Ensembl build 93
Barcode, feature and matrix files for each sample

source_name: Primary Retinoblastoma

value: primary retinoblastoma

tag: iirc tumor class

value: Class E

tag: familial


title: RB027 - Primary Retinoblastoma - scRNA-Seq


title: AD3906: Haploid germ cells rep pool 3


title: AD3915: Ejaculated sperm rep pool 1


title: RB018 Input DNA - ChIP-Seq

data_processing:
Adapter trimming and alignment was done using Novoalign (V3.06.04) with the following parameters -k -H 20 -t 15,3 --softclip 20 --hlimit 7 -p 5,20 -c 8
Alignment files from RB006 and RB018 were merged using MergeSamFiles from Picard (1.128) to create a pooled sample
Normalization of sequencing of ESRRG pulldown to followed by initial peak calling was done on RB006, RB018 and pooled samples by MACS2 (2.1.3.3) using callpeak with the following parameters -B --nomodel --extsize 147 --SPMR -g hs
Output of callpeak was turned into a bigwig using MACS2 bdgcmp with the parameter -m FE
Each called peak file was re-analyzed with MACS2 to generate a peaks file with peaks caleld at p < 0.001 and the resulting files were analyzed with HOMER (v.4.8) using mergePeaks to come up with a list of all overlapping peaks that were shared across samples.  The merged file with overlapping peaks was then analyzed for significantly enriched motifs using Homer annotatepeaks.
assembly: hg19
Bigwig files of shESRRG pulldown of Rb006 and Rb018 normalized by input DNA
ChiP-Seq called overlapping peaks (p<0.001) across all samples (RB006, RB018 and the pooled sample) with enriched motifs

source_name: Low-passaged primary retinoblastoma cell line

extract_protocol:
Cell pellets were fixed in 1% formaldehyde for 10 minutes to crosslink protein-DNA interactions. Cell nuclei were extracted and subjected to sonication in a Biorupter Pico (Diagenode). Shearing was optimized to yield chromatin fragments of 200-500bp. Chromatin was incubated in ChIP-qualified antibody against ESRRG. Antibodies were captured using protein-G coupled magnetic beads and protein-DNA was eluted. DNA was purified for downstream analysis. Successful ChIP was validated with RT-PCR for known binding genes and known negative controls. Technical controls included non-specific IgG incubation of cell lysates as well as no-antibody (input) controls for non-specific DNA binding to protein-G coupled beads.
Libraries were prepared using the NEBNext Ultra kit and sequenced on the Illumina NextSeq 500 according to the manufacturer’s protocol.


title: Liver_CC_Female_Mice_ID_118

value: Liver


title: RB025 - Primary Retinoblastoma - scRNA-Seq

extract_protocol:
Single-cell suspensions were counted using the Cellometer K2 Fluorescent Viability Cell Counter (Nexcelom), verified manually using a hemocytometer, and adjusted to 1,000 cells/ul.
Samples were prepared using the Chromium Single Cell 5’ Library & Gel Bead Kit v2 (10X Genomics) according to the manufacturer’s protocol with a capture target of 10,000 cells. Each sample was processed on an independent Chromium Single Cell A Chip (10X Genomics) and run on a thermocycler (Eppendorf). 5’ gene expression libraries were sequenced using NextSeq 500 150-cycle high-output flow cells or NovaSeq 6000 200 cycle S4 flow cells.


title: Subject_46_LPS_Cord

value: LPS


title: Liver_CC_Female_Mice_ID_111


title: AD3904: Haploid germ cells rep pool 1


title: RB006 Input DNA - ChIP-Seq

value: Low-passaged primary retinoblastoma cell line

value: No


title: AD3905: Haploid germ cells rep pool 2


title: RB018 ESRRG-pulldown - ChIP-Seq


title: Subject_46_CTRL_Cord

value: CTRL

value: Female


title: Subject_45_PolyIC_Cord

value: Male


title: ID#18

city: Madrid

first: CRISTINA

last: Montero-Conde

address: C/Melchor Fdez Almagro, 3

institute: CNIO

data_processing:
RNA-seq processing:
Fifty one bp single-reads were analyzed with the Nextpresso pipeline (http://http://bioinfo.cnio.es/nextpresso/) as follows: sequencing quality was checked with FastQC v0.11.0 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), reads were aligned to the human genome (GRCh37/hg19) with TopHat-2.0.10 and Bowtie 1.0.0, allowing 2 mismatches and 20 multihits. Expression count normalization was performed using DESeq2 .
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tabulated text with DESeq2 normalized gene counts.

source_name: Short telomere tumor

extract_protocol:
Fresh frozen in OCT. RNA was harvested using Trizol reagent.
One ug of total RNA from each sample was used. Average sample RNA Integrity Number was 9.8 (range 9.6-10) when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB, Cat. No. E7760) as recommended by the manufacturer. This kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced. Adapter-ligated library was completed by PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument HiSeq2500 by following manufacturer's protocols.

value: Thyroid tumor


title: Old, replicate 3, scRNAseq

city: Beijing

first: XIN

last: FU

address: 33 Ba-Da-Chu Road

department: Research Center

institute: Plastic Surgery Hospital (Institute), Peking Union Medical College & Chinese Academy of Medical Sciences

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: inguinal subcutaneous adipose tissue

extract_protocol:
Inguinal subcutaneous adipose was carefully dissociated from female C57BL/6N mice. Excised inguinal subcutaneous adipose was rinsed twice thoroughly with Dulbecco's Phosphate-Buffered Saline (DPBS, supplemented with 1% Penicillin-Streptomycin Solution), and then the hair stuck to the adipose tissue was removed carefully. The minced adipose tissues were digested with collagenase D (2mg/ml; Roche) and collagenase type I (2mg/ml; Gibco) in DMEM (Hyclone, USA) for 45 min at 37°C incubator shaker. DNase-I (Sigma, USA) was added at 15min and 30min during digestion. The digestive mixture was quenched with DMEM supplemented with 10% FBS and filtered via 100μm nylon filter, then centrifuged at 400×g for 5 min. Supernatant were discarded and the cell pellet was resuspended with red blood cell lysis buffer (Solarbio, China) for 3min on the ice. The cell lysate was quenched with DMEM supplemented with 10% FBS and centrifuged at 400×g for 5 min. DPBS supplemented with 0.4% bovine serum albumin (Gibco,USA) was used to resuspend the cell pellet. Finally, the cell suspension was filtered through a 40μm filter for 10×Genomics single-cell RNA sequencing.
Library was performed according to the manufacturer’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, Stromal vascular fractions (SVFs) were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina TruSeq R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: inguinal subcutaneous adipose tissue

value: Stromal vascular fraction

tag: age

value: 18 months


title: Liver_CC_Female_Mice_ID_101

value: HS


title: Liver_CC_Female_Mice_ID_114


title: Liver_CC_Female_Mice_ID_110


title: PAR1-KO PC3

city: London

first: Rithwik

last: Ramachandran

state: ON

address: 1151 Richmond Street

country: Canada

institute: University of Western Ontario

hyb_protocol: Hybridized to GeneChip Mouse Gene 2.0 ST Arrays (Affymetrix) at 45 °C for 16 h (SACRI Microarray and Genomics Facility, University of Calgary). Arrays were stained and washed with GeneChip Fluidics Station 450.

scan_protocol: Scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Probe cell intensity data CEL files were generated on GeneChip Command Console (Affymetrix) software. The PrimeView array gene expression analyses were performed on Transcriptome Analysis Console (TAC 4.0, Affymetrix) software. Robust Multi-Array Average (RMA) summarization method was used to log 2 transform and normalize the data. Differentially expressed genes with <-2 and >2 fold-change were filtered and associated signalling pathways were identified by WikiPathways as well as manual extraction.

source_name: PAR1 knockout PC3 cells

label_protocol: 250 ng of total RNAs with a RIN of ≥8 were labelled using the GeneChip Whole Transcript Express Labeling Assay.

growth_protocol: Cells were cultured in F-12K complete media.

extract_protocol: Total RNA from WT, PAR1-KO and PAR2-KO PC3 cells were extracted using a RNeasy Mini Kit (Qiagen).

tag: cell line

value: a cell line initiated from a bone metastasis of a grade IV prostatic adenocarcinoma from a 62-year-old, White, male.

tag: genotype/variation

value: PAR1 knockout


title: PAR2-KO PC3

source_name: PAR2 knockout PC3 cells

value: PAR2 knockout


title: Liver_CC_Female_Mice_ID_109

source_name: Liver from CC female mice


title: Old, replicate 2, scRNAseq

description: 10x Genomics


title: WRB6 w/ shESRRG - RNA-Seq

city: Miami

first: Matthew

last: Field

address: 900 NW 17th St

institute: University of Miami

data_processing:
Reads were aligned and gene counts were made using STAR (2.5.2a) with parameters --runThreadN 16 --genomeSAindexNbases 12 --genomeSAsparseD 2 --twopassMode Basic --twopass1readsN -1 --outReadsUnmapped None --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignMatesGapMax 200000 --alignIntronMax 200000 --alignSJDBoverhangMin 10 --quantMode GeneCounts
Gene expression was normalized and batch corrected using EdgeR (3.32.1) according to tutorial recommendations
For knockdown experiments, batch correction was utilized for cell line and adjusted using estimateDisp()
assembly: hg19
tab-delimited text files for RNA-Seq data with STAR gene counts for all RNA-Seq samples
normalized abundance measurements using EdgeR for RNA-Seq data with p-values calculated for knockdown experiments (shESRRG compared to shGFP)

extract_protocol:
RNA was extracted using TriZol and the RNeasy Mini RNA isolation kit
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA prep kit with Ribo-Zero Gold to remove cytoplasmic and mitochondrial rRNA according to the manufacturer's recommendation (Illumina, San Diego, CA). Total RNA-seq libraries were run on an Illumina NextSeq 500 sequencing instrument according to the manufacturer’s protocol.

value: Class D


title: Subject_45_LPS_Cord

extract_protocol:
Total RNA was extracted with TRIzol (Ambion) followed by RNAeasy (QIAGEN). Total RNA libraries were prepared using NEBNext Ultra II Kits (New England BioLabs). Sequencing was performed by the Australian Genome Research Facility (Illumina NovaSeq 6000, 100bp paired-end reads).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cord


title: RB006 ESRRG-pulldown - ChIP-Seq

value: Class E


title: Liver_CC_Female_Mice_ID_10

value: Liver


title: RB018 w/ shGFP - RNA-Seq

value: Low-passaged primary retinoblastoma cell line


title: Subject_44_IMIQ_Cord

value: IMIQ

value: Yes

value: No


title: WRB6 w/ shGFP - RNA-Seq


title: RB018 w/ shESRRG - RNA-Seq


title: ID#22


title: WT PC3

source_name: wild-type PC3 cells

value: Wild-type


title: Liver_CC_Female_Mice_ID_100

value: Female


title: Subject_45_CTRL_Cord

value: CTRL

value: Male


title: Young, replicate 4, scRNAseq

description: 10x Genomics

value: inguinal subcutaneous adipose tissue

value: Stromal vascular fraction

value: 11-12 weeks


title: ID#14

value: Thyroid tumor


title: RB016 w/ shGFP - RNA-Seq


title: ID#37


title: Subject_45_IMIQ_Cord


title: Young, replicate 2, scRNAseq

description: 10x Genomics


title: Subject_44_PolyIC_Cord

value: PolyIC


title: ID#39


title: Subject_44_LPS_Cord

value: LPS


title: Old, replicate 1, scRNAseq

description: 10x Genomics

value: 18 months


title: Young, replicate 1, scRNAseq

description: 10x Genomics


title: ID#19


title: Young, replicate 3, scRNAseq

description: 10x Genomics


title: Subject_44_CTRL_Cord

value: Cord


title: ID#26


title: RB006 w/ shESRRG - RNA-Seq

value: Class E


title: RB016 w/ shESRRG - RNA-Seq

value: Low-passaged primary retinoblastoma cell line

value: Class D


title: RB006 w/ shGFP - RNA-Seq


title: Subject_43_PolyIC_Cord


title: ID#103


title: ID#104

source_name: Normal telomere tumor


title: wRb3 - Primary Retinoblastoma - RNA-Seq

value: primary retinoblastoma


title: wRb6 - Primary Retinoblastoma - RNA-Seq

value: No


title: OPA1-WT-Muscle stem cells-T=0hrs_a-Int7/VCAM_rep 3

city: Ottawa

first: Mireille

last: Khacho

state: Ontario

address: 451 Smyth Rd

department: BMI

institute: University of Ottawa

data_processing:
Adapters trimmed using Trim Galore v 0.5.0 running Cutadapt v2.5 and parameters -q 25 (trim 3' bases with quality < 25), --clip_R1 6 --clip_R2 6 (clip 6nt from the 5' end of both reads), -stringency 5 (trim Illumina adapters with at least 5bp match), --length 20 (discard trimmed reads <20nt).
Trimmed paired-end reads mapped to GRCm38/GENCODE vM25 using STAR v2.6.0c with default parameters
Reads assigned to genes using HTSeq-count v0.6.1p2 in 'intersection_nonempty' mode.
Fold changes between Wt and KO treatments calculated with EdgeR and DESeq2.
Assembly: GRCm38
Supplementary files format and content: Text files from HTSeq-count containing counts of reads assigned to each gene (Ensembl GeneID)

source_name: hindlimb muscle

growth_protocol: Muscle stem cells were FACS-purified from hindlimb muscle of uninjured OPA1-WT and OPA1-KO mice at 8-10 weeks (3 days following 5 consecutives Tamoxifen gavage administration)

extract_protocol: Total RNA was extracted from freshly isolated muscle stem cells using the PicoPure RNA isolation kit (ThermoFisher, KIT0214)

value: hindlimb muscle

value: FACS sorted satellite cells, a-integrin-7+ / VCAM+ / Sca1- / CD45- / CD31-

value: 8-10 weeks

value: OPA1-Pax7-CreERT2; Cre negative

tag: treatment

value: 5 days TAM gavage; uninjured


title: OPA1-KO-Muscle stem cells-T=0hrs_a-Int7/VCAM_rep 1

value: OPA1-Pax7-CreERT2; Cre positive


title: Subject_43_IMIQ_Cord

value: IMIQ

value: Male


title: Subject_43_CTRL_Cord

value: CTRL


title: OPA1-KO-Muscle stem cells-T=0hrs_a-Int7/VCAM_rep 2


title: Subject_43_LPS_Cord

value: LPS


title: OPA1-WT-Muscle stem cells-T=0hrs_a-Int7/VCAM_rep 2


title: wRb4 - Primary Retinoblastoma - RNA-Seq


title: OPA1-KO-Muscle stem cells-T=0hrs_a-Int7/VCAM_rep 3


title: Subject_42_IMIQ_Cord

value: Female

value: Yes


title: ID#24

value: Thyroid tumor


title: ID#63


title: Rb016 - Primary Retinoblastoma - RNA-Seq


title: Subject_42_LPS_Cord

value: Cord


title: ID#105


title: ID#99


title: Subject_42_CTRL_Cord


title: Rb015 - Primary Retinoblastoma - RNA-Seq

value: Class E


title: Rb013 - Primary Retinoblastoma - RNA-Seq

value: primary retinoblastoma


title: Sertoli26_MSUS

city: Zurich

first: Kristina

middle: Maria

last: Thumfart

address: Winterthurerstrasse 190

country: Switzerland

institute: ETH

data_processing:
Fastq files were trimmed with Trimgalore (v 0.6.5)
pseudo-mapped with Salmon (v 1.1.0)
Assembly: GENCODE annotation of transcripts (vM23)
Supplementary files format and content: csv-file includes raw counts for each sample obtained from Salmon

source_name: testis

extract_protocol:
RNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen)
Libraries for RNA sequencing were prepared from 5 ng RNA per sample using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara)

treatment_protocol: pups in the MSUS group were separated from their mother for 3 h per day at unpredictable times from postnatal day (PND) 1 to 14. During separation, the mothers underwent an acute swim in cold water (18°C for 5 min) or 20-min restraint in a tube.

value: testis

value: Sertoli cell

value: Bl6 wt

value: MSUS


title: Subject_41_PolyIC_Cord

first: James

last: Read

address: 15 Hospital Ave.

institute: Telethon Kids Institute

value: PolyIC

value: No


title: Subject_42_PolyIC_Cord


title: ID#102


title: Rb008 - Primary Retinoblastoma - RNA-Seq


title: Sertoli24_CTRL

value: Control


title: OPA1-WT-Muscle stem cells-T=0hrs_a-Int7/VCAM_rep 1

value: hindlimb muscle

value: FACS sorted satellite cells, a-integrin-7+ / VCAM+ / Sca1- / CD45- / CD31-

value: 8-10 weeks

value: OPA1-Pax7-CreERT2; Cre negative

value: 5 days TAM gavage; uninjured


title: Subject_41_IMIQ_Cord

value: IMIQ

value: Male

value: Yes


title: 6483-5-A549-SASP-medium

city: Amsterdam

first: Liqin

last: Wang

address: Plesmanlaan 121

country: Netherlands

institute: NKI-AVL

data_processing:
The reads were sequenced using a stranded protocol and aligned against the human genome, build 38, using Tophat 2.1 with bowtie 1.1
The parameters used are --bowtie1 --prefilter-multihits --no-coverage-search --transcriptome-index --library-type firststrand
Readcounts were generated using a custom script based on the same strategy as HTSeq-count.
normalized based on 10M read
Genome_build: Homo sapiens (hg38)
Supplementary_files_format_and_content: Excel read counts file: tab-separated gene counts and gene annotation for all samples

growth_protocol: A549 and PC9 were cultured in a RPMI-based medium supplemented with 10% FBS, 1% penicillin/streptomycin and 2 mM L-glutamine.  SK-HEP1 was cultured in a RPMI-based medium supplemented with 10% FBS, 1% penicillin/streptomycin and 2 mM L-glutamine

extract_protocol:
RNA samples were isolated with qiagen rneasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
1 week of treatment, NEO2734 0.5uM, CFI-400945 50nM
A549 or SK-Hep1 cells were seeded in 4-5 million cells in the 15cm dishes and treated with different senescence inducers for one week, such as 0.5 µM alisertib, 1 µM barasertib, 50 nM CFI-400945, 0.5 µM PF-06873600, 2 µM etoposide or 100 nM doxorubicin. The drugs were refreshed twice within a week. Afterwards, the drugs were suspended, the senescent cells were cultured and refreshed twice with a standard medium for one week. After the second time fresh, the SASP medium was collected after three days and diluted with fresh standard medium either one time or two times to generate ½ SASP or ¼ SASP media
SASP medium generation: A549 cells were seeded in 4-5 million cells in the 15cm dishes and treated with 0.5 µM alisertib. alisertib were refreshed twice within a week. Afterwards, the drugs were suspended, the senescent cells were cultured and refreshed twice with a standard medium for one week. After the second time fresh, the SASP medium was collected after three days and diluted with fresh standard medium one time to generate SASP medium. The control medium in the experiments was generated as described below. 2-3 million proliferating cells were cultured with a standard medium for three days. The cultured medium was collected and diluted with a freshly standard medium one time.

value: lung cancer cells

value: 1 week senescence conditional medium treated


title: Rb003 - Primary Retinoblastoma - RNA-Seq

value: primary retinoblastoma

value: Class E


title: Subject_41_LPS_Cord

city: Perth

value: LPS

value: Cord


title: Sertoli22_CTRL

value: testis

value: Sertoli cell

value: Bl6 wt


title: Sertoli23_MSUS

value: MSUS


title: 6483-4-A549-ctrl-medium

value: ctrl medium treated


title: 6483-1-A549-Ctrl

value: untreated


title: Subject_41_CTRL_Cord

value: CTRL

value: No


title: Rb54 - Primary Retinoblastoma - RNA-Seq


title: 6483-2-A549-PLK4i

value: 1 week 50nM CFI-400945 treated


title: Sertoli14_CTRL

value: Control


title: Rb33 - Primary Retinoblastoma - RNA-Seq


title: Subject_40_PolyIC_Cord

value: PolyIC

value: Male


title: Sertoli13_MSUS


title: 6258-9-Hep1-NEO

value: liver cancer cells

value: 1 week 0.5uM NEO2734 treated


title: Rb47 - Primary Retinoblastoma - RNA-Seq

value: primary retinoblastoma

value: Class E


title: Subject_40_LPS_Cord

value: LPS

value: Cord


title: Subject_40_IMIQ_Cord

value: IMIQ


title: Sertoli12_CTRL

value: testis

value: Sertoli cell

value: Bl6 wt


title: ID#12

value: Thyroid tumor


title: Rb26 - Primary Retinoblastoma - RNA-Seq


title: 6258-2-PC9-NEO

value: lung cancer cells


title: 6258-8-Hep1-ctrl

value: untreated


title: Sertoli11_MSUS

value: MSUS


title: Subject_40_CTRL_Cord

value: CTRL

value: No


title: Rb24 - Primary Retinoblastoma - RNA-Seq


title: Rb001 - Primary Retinoblastoma - RNA-Seq


title: Sertoli10_CTRL

value: Control


title: Subject_39_PolyIC_Cord

value: PolyIC

value: Female


title: Subject_39_IMIQ_Cord


title: Sertoli9_CTRL


title: 6258-1-PC9-ctrl


title: Rb23 - Primary Retinoblastoma - RNA-Seq

value: primary retinoblastoma


title: Sertoli6_MSUS


title: Sertoli5_MSUS


title: Treatment 2

city: Scottsdale

first: Alfred

last: Doyle

state: Arizona

address: 13400 E Shea Blvd

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using FastQC
The RNA paired end reads were aligned using the STAR aligner 2.6.1c
Gene counts were generated using subread featuerCounts
Assembly: mm10
Supplementary files format and content: tab-delimited files with RNA-Seq gene expression

source_name: esophagus

extract_protocol:
Total RNA was extracted from fresh frozen cell pellet samples using Qiagen RNeasy Plus Universal mini kit (Qiagen).
Library Preparation with PolyA selection and Illumina Sequencing. RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep for Illumina using  manufacturer’s instructions.

treatment_protocol: To investigate the effects of the common household detergent Sodium Dodecyl Sulfate (SDS) on the esophagus we provided mice with 0.5% SDS in their drinking water for 14 days and assessed the effects by various methods including RNA-Seq of whole esophagus homogenates.

value: esophagus

value: WT

value: 0.5% SDS in drinking water

tag: time

value: Day 14


title: Treatment 3


title: Treatment 1


title: Subject_39_CTRL_Cord

source_name: CBMC

value: Cord