title: ctrl1 BAT

tag: source organ


title: F9_2

status: Public on Mar 04 2021

type: SRA

city: Freising

first: Tobias

last: Fromme

address: Gregor-Mendel-Str. 2

department: Molecular Nutritional Medicine

country: Germany

institute: Technical University of Munich

library_source: transcriptomic

data_processing:
Sequencing software: HiSeq Control Software 2.2.58 Image analysis and base calling: Real-Time Analysis (RTA) 1.18.64 fastq-file generation: CASAVA BCL2FASTQ Conversion Software 1.8.3
Sequenced reads with masked adaptor sequence were mapped to the murine genome, NCBI build 38, by the Genomatix Mapper 3.7.6 (Genomatix Mining Station, settings: 'deep', min. quality 92%).
Unique hits were subjected to expression analysis for RNA-seq (Genomatix Genome Analyzer, ElDorado version 12-2013) and provided as reads per kilobase of exon per megabase of library size (RPKM).
Genome_build: murine NCBI genome build 38
Supplementary_files_format_and_content: tab-delimited text file providing RPKM values for each sample.

molecule: total RNA

organism: Mus musculus

source_name: immortalized preadipocytes

extract_protocol:
Preadipocytes were washed with ice-cold PBS, placed on ice and scraped into Trisure (Bioline). Total RNA was prepared from Trisure (Bioline) and column-purified (SV Total RNA Isolation System, Promega).
Libraries were constructed from total RNA (TruSeq RNA Sample Prep kit v2 (Illumina)).

value: interscapular BAT

tag: strain

tag: agent

value: FGF9 + heparin


title: F9_3


title: H3K27ac ChIP_TAZ4SA_Rep2

city: Iowa City

first: Michael

middle: S

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

country: USA

institute: University of Iowa

library_source: genomic

data_processing:
BCL basecalls were converted to FASTQ with Illumina 'bcl2fastq"
fastq data were processed using the 'bcbio-nextgen.py' pipeline in "chip-seq" mode.   Genome build was "GRCh37".
reads were trimmed with "atropos", aligned with 'bwa', and peaks called with 'macs2' running in "narrowPeak" mode.  Peaks with FDR p-value < 0.05 were accepted.

molecule: genomic DNA

organism: Homo sapiens

source_name: SW872 liposarcoma cells ATCC

growth_protocol: SW872 cells were stably transduced and grown to 90% confluence 48 hrs before collection (except CAMTA1 collected at sub-confluence)

extract_protocol:
Cells were cross-linked and prepared using the SimpleChIP Enzymatic Chromatin IP KIt according to manufacturer's instructions. Flag tagged proteins were immunoprecipated with the anti-DYKDDDDK rabbit monoclonal antibody (Cell Signaling)
The SimpleChIP ChIP-seq DNA Library Prep Kit for Illumina was used to prepare the DNA library according to manufacturer's instructions

tag: cell line

tag: antibody

tag: transduction


title: F4324-Meth-4

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

description:
raw_counts.csv
normalized_counts.csv

data_processing:
Reads were trimmed to remove adapter sequence and low-quality base calls using Trimmomatic v0.38
Reads were aligned to the rat genome rn06 using HISAT2 v2.1.0
Aligned reads were mapped to known transcripts from Ensembl genes version 94 using GenomicAlignments v1.16.0
Differentially epxressed genes were identified using DESeq2 v1.20.0 with a Benjamini-Hochberg estimated false discovery rate of 0.1 used as a threshold for statistical significance.
Sample F4329-Sal-3 failed to cluster with other samples and was omitted from further processing.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Counts per gene per sample in CSV format.

organism: Rattus norvegicus

source_name: Left ventricular tissue

growth_protocol: Male and female Sprague Dawley rats (Charles River Laboratories, strain code 001) were pair housed in standard cages with free access to food and water and were maintained on a 12 hour / 12 hour light / dark schedule (lights on at 07:00).

extract_protocol:
Hearts were either isolated on day 11 (24 hours after the last saline /methamphetamine injection) or isolated 30 days after the last saline / methamphetamine injection to investigate the effects of a 30 day period of abstinence on myocardial gene expression. Total RNA was isolated using Trizol (Thermo Fisher, Waltham, MA) according to the manufacturer’s instructions.
RNA libraries were prepared from each heart using the Truseq RNA mRNA library prep kit from Illumina (San Diego, CA).  RNA sequencing (2 x 50 paired end reads; 20 million reads / sample) was performed on an Illumina HiSeq1500 sequencer.

treatment_protocol: Adult male and female rats (8 weeks of age) received daily (10:00) subcutaneous injections with methamphetamine (5 mg/ kg/day) or saline for 10 consecutive days.

tag: Sex

value: F

tag: treatment

value: Methamphetamine

tag: abstinence

value: No


title: 3yr_Muscle_OLD_rep4

city: Tokyo

first: Shigeharu

last: Kinoshita

state: Bunkyo

address: 1-1-1,Yayoi, Bunkyo, Tokyo, 113-8657 Japan room 251

department: Aquatic Bioscience

country: Japan

institute: The University of Tokyo

data_processing:
Illumina Casava1.7 software used for basecalling.
HISAT2 software was used according to the instructions from the program designers to map the raw reads of acromegaly and WT samples to zebrafish genome reference (GRCz10) retrieved from Ensembl database together with the annotation file.
The Cufflinks pipeline was used to assign reads to known transcripts and test for differential expression between acromegaly model and the WT samples. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads (FPKM).
Genome_build: GRCz10
Supplementary_files_format_and_content: One tab-delimited text file containing all RPKM values for all Sample.

organism: Danio rerio

source_name: Muscle

extract_protocol:
tissues were removed, and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep Kit(Cat# RS-122-2101) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.

tag: genotype/variation

value: AGED zebrafish

tag: tissue

value: Muscle

tag: age

value: 3-years old


title: F4323-Meth-3

description:
raw_counts.csv
normalized_counts.csv


title: 3yr_Muscle_OLD_rep5


title: 3yr_Muscle_OLD_rep3


title: F9_1


title: H3K27ac ChIP_TAZ4SA_Rep1


title: F8_3


title: H3K27ac ChIP_Input_TAZ4SA_Rep2


title: F4322-Meth-2

description:
raw_counts.csv
normalized_counts.csv


title: 3yr_Muscle_OLD_rep2


title: H3K27ac ChIP_Input_TAZ4SA_Rep1


title: F3996-Meth-abs-2

description:
raw_counts.csv
normalized_counts.csv

value: Yes


title: Kidney Control 60 min

city: Irvine

first: Jered

last: Haun

state: CA

address: Nat Sci II 3107

department: Biomedical Engineering

institute: University of California, Irvine

data_processing:
Alignmnet of libraries was completed using 10x Genomics Cell Ranger 3.1.0
Each library was aligned to an indexed mm10 reference genome
Libraires from each set were normalized with Cell Rnager Aggr, to normalize mean reads per cells across each libraries
Genome_build: mm10
Supplementary_files_format_and_content: mtx, features, barcodes

molecule: polyA RNA

source_name: Kidney

extract_protocol:
Kidneys and mammary tumor were dissected, minced into ~ 1 mm3  pieces, and processed using either the microfluidic platform (15 and 60 min digestion device intervals, single pass through integrated dissociation/filter device) or control (60 min digest) using 0.25% type I collagenase. Recovered cells were centrifuged (400xg, 5 min), treated with 100 Units of DNase I for 5 min at 37°C, and washed by centrifugation into PBS+. Samples were then incubated with RBC lysis buffer for 5 min on ice, centrifuged, and resuspended in PBS+. Cells were stained with SytoxBlue (Life Technologies, Carlsbad, CA, USA) prior to FACS (FACSAria Fusion, BD Biosciences, Franklin Lakes, NJ) to remove dead cells and ambient RNA. Sorted live single cells (SytoxBlue-neg) were centrifuged and resuspended at a concentration of 1000 cells/µL in PBS with 0.04% BSA. The 10x Chromium system (10x Genomics, Pleasanton, CA) was then used for droplet-enabled scRNA-seq. Oil, cells, reagents, and beads were loaded onto an eight-channel microfluidic chip. Lanes were loaded with ~17,000 cells from each of the samples, determined using an automated cell counter (Countess II, Invitrogen, Carlsbad, CA).
Library generation for 10x Genomics Single Cell Expression v3 chemistry was performed according to manufacturer’s instructions.

value: Kidney

value: 12 weeks

tag: protocol

value: Control

tag: time point

value: 60 min


title: F4321-Meth-1

description:
raw_counts.csv
normalized_counts.csv


title: F8_2


title: 3yr_Muscle_OLD_rep1


title: H3K27ac ChIP_Input_Empty Vector_Rep2

value: empty vector


title: F4333-Meth-5

description:
raw_counts.csv
normalized_counts.csv


title: H3K27ac ChIP_Empty Vector_Rep2


title: 1yr_Muscle_WT_rep3

value: wild type

value: 1-years old


title: F8_1


title: F1_3


title: F1_2


title: 1yr_Muscle_WT_rep2


title: 1yr_Muscle_WT_rep1


title: H3K27ac ChIP_Input_Empty Vector_Rep1


title: GH_Muscle_ACRO_rep3

value: Acromegaly zebrafish model


title: NS14Unt2

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

data_processing:
Cellranger v3.1.0 (10X Genomics) cellranger mkfastq was used to demultiplex fastq files from raw base call (BCL) files.
Fastq files were aligned to Homo sapiens (human) genome assembly GRCh38-3.0.0 (hg38), filtered, and barcodes/UMIs counted using the cellranger count function.
scRNA-seq data was visualized using Loupe Cell Browser (10X Genomics).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: MTX, TSV; Cellranger raw counts output: matrix with the number of UMIs associated with each feature (row) and each barcode (column)

source_name: primary human bronchial epithelial cells (HBECs)

growth_protocol: Primary human bronchial epithelial cells (HBECs) from nonsmokers cultured on air-liquid interface (ALI) for 9 days. Briefly, 1 x 105 cells in 100 µl of BronchiaLifeTM epithelial airway medium (BLEAM) (Cat# LL-0023, Lifeline® Cell Technology, Oceanside, CA, USA) were seeded in the apical chamber of a 0.4 µm pore-sized Transwell® insert (Cat# 3470, Corning®, Corning, NY, USA) pre-coated with human type IV collagen (Cat# C7521, Sigma Aldrich, St. Louis, MO, USA) with 1 ml of BLEAM in the basolateral chamber (ALI day -2). The following day, fresh BLEAM media was replaced in the apical and basolateral chambers (100 µl and 1 ml, respectively). Following two days of submerged culture, media from the apical chamber was removed to expose the cells to air (ALI day 0), and 1 ml of HBTEC ALI differentiation medium (Cat# LM-0050, Lifeline® Cell Technology) supplemented with Penicillin (100 I.U./ml) - Streptomycin (100 µg/ml) was added to the basolateral chamber. The media was replaced every other day and the cells allowed to differentiate for 9 days.

extract_protocol:
To generate single cell suspensions, the cells were trypsinized for 3 mins and following neutralization passed through a FlowmiTM tip strainer (40 µm porosity, catalog number H13680-0040, SP Bel-Art, Wayne, NJ, USA). Cells were counted on a hemocytometer prior to diluting cells to 800 cells/µL in 0.1% BSA/PBS buffer for scRNA-seq library preparation with Chromium Single Cell 3ʹ Reagent Kits v3 (catalog number PN-1000075, 10X Genomics, Pleasanton, CA, USA).
scRNA-seq libraries were generated according to 10X Genomics User Guide CG000183 Rev C. Briefly, a reaction mix containing 12,800 cells was loaded into a Chromium Chip B, targeting cell recovery of 8000 cells. After generating Gel Beads-in-emulsion (GEMS) on the Chromium controller, GEMS were transferred to PCR tubes (catalog number 951010022, Eppendorf, Hamburg, Germany) for GEM-Reverse Transcription (GEM-RT). After cleanup with Dynabeads MyOne Silane (catalog number PN-2000048, 10X Genomics), cDNA was amplified with 11 cycles. Amplified cDNA was cleaned with 0.6X SPRISelect reagent (catalog number B23318, Beckman Coulter, Pasadena, CA, USA). Cleaned cDNA was then quality checked on an Agilent Tapestation 4150 (catalog number G2992AA, Agilent, Santa Clara, CA, USA) using a High Sensitivity D5000 ScreenTape (catalog number 5067-5592, Agilent) and quantified using Qubit dsDNA High Sensitivity Assay Kit (catalog number Q32851, Thermo Fisher Scientific) read on a Qubit 4 Fluorometer (catalog number Q33238, Thermo Fisher Scientific). An aliquot of 25% of the cleaned cDNA was used for library construction (fragmentation, end repair, A-tailing, adaptor ligation), according to the manufacturer’s instructions. Libraries were indexed (catalog number PN-220103, 10X Genomics) using 10 cycles of PCR. Amplified libraries were cleaned with SPRISelect reagent using a double-sided size selection protocol. Cleaned libraries were quality checked on an Agilent Tapestation 4150 using a High Sensitivity D1000 ScreenTape (catalog number 5067-5584, Agilent) and quantified using Qubit dsDNA High Sensitivity Assay Kit.
Libraries were diluted to 4nM prior to sequencing on a NovaSeq 6000 S1 PE50 flow cell.

treatment_protocol: No treatments to report.

tag: patient

value: nonsmoker donor 8

value: air-liquid interface (ALI)

tag: cell

value: HBEC (Primary human bronchial epithelial cells )


title: BF8_3

value: interscapular BAT

value: Ffg8b + Bay-876


title: GH_Muscle_ACRO_rep2


title: HEK293_snoRNA

city: Los Angeles

first: Minjie

last: Zhang

address: 1985 Zonal Avenue

department: Department of Pharmacology and Pharmaceutical Sciences

institute: University of Southern California

description: crosslinked snoRNA

data_processing:
Sequencing data were preprocessed to remove adapters form the 5'end and 3’end using Trimmomatic software; PCR duplicates are removed using splitFastqLibrary (in the icSHAPE pipeline)
Reads were mapped to hg38 or mm10 genome using STAR program.
The primary mapping alignments were filtered to remove low-confidence segments, rearranged and classified into six different types using gaptypes.py (https://github.com/zhipenglu/CRSSANT).
Filtering alignments were assembled to DGs and NGs using the crssant.py script (https://github.com/zhipenglu/CRSSANT).
Bedtools v2.25.0 was used to annotate gapped and chimeric alignments.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: bam files contain grouped snRNA structures and interactions; BEDPE file contains disjoint RNA structures and interaction.

source_name: HEK293T cells

growth_protocol: HEK293T and HeLa cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) + 10% fetal bovine serum (FBS, Gibco) + Pen/Strep antibiotic, in 37°C incubator with 5% CO2.

extract_protocol:
TNA method was used to extract crosslinked RNA.
Library was prepared using optimized PARIS protocol (Lu. et al. Cell, 2016).

treatment_protocol: 0.5 mg/ml AMT or Amotosalen in vivo crosslinking; mRNAs were enriched using Poly(A)Purist™ MAG Kit (Invitrogen); EVD68 viral RNA is enriched using seven antisense oligos.

tag: cell type

value: embryonic kidney cells

tag: passages


title: SHSY5Y_US47_AG

description: crosslinked total RNA

source_name: SH-SY5Y cells

value: neuroblastoma cells

tag: infection

value: US/MO/14-18947 strain of EV-D68 (with rupintrivir inhibitor)


title: GH_Muscle_ACRO_rep1

value: Muscle


title: BF8_2

tag: source organ

tag: strain

tag: agent


title: H3K27ac ChIP_Empty Vector_Rep1

tag: cell line

tag: antibody

tag: transduction


title: H3K27ac ChIP_Input_TAZ_CAMTA1_Rep2


title: BF8_1


title: 3yr_Liver_OLD_rep5

source_name: Liver

value: AGED zebrafish

value: Liver

value: 3-years old


title: SHSY5Y_US47_GA

description: crosslinked total RNA

value: US/MO/14-18947 strain of EV-D68 (with geldanamycin inhibitor)


title: SHSY5Y_US47

description: crosslinked total RNA

value: US/MO/14-18947 strain of EV-D68


title: 3yr_Liver_OLD_rep4


title: F1_1


title: STARR_1.8_Input

city: Berlin

first: Till

last: Schwämmle

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

institute: Max Planck Institute for Molecular Genetics

description: Mouse embryonic stem cells

data_processing:
Library strategy: STARR-seq
FASTQ files were mapped to the mm10 genome using bowtie (1.1.2) with options [-S -t -v 3 -m 1 -I 250 -X 2000] (Langmead et al. 2009).
SAM files were translated into BAM files, filtered for mapped and paired reads and sorted using samtools (1.10) with options [view -b -h -f 2 -q 10] and [sort] (Li et al. 2009)
Duplicates were marked and removed using Picard (2.18.25) with options [MarkDuplicates VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=TRUE] (http://broadinstitute.github.io/picard)
BigWig tracks were created using deepTools2 (3.4.1) with options [bamCoverage -e -bs 10 --normalizeUsing CPM] (Ramírez et al. 2016) and visualized using the UCSC Genome Browser (Kent et al. 2002).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig: Coverage tracks

source_name: Mouse embryonic stem cells

growth_protocol: 1.8 XX and 1.8 XO Cells were grown on gelatin-coated flasks in serum-containing ES cell medium (DMEM (Sigma), 15% ESC-grade FBS (Gibco), 0.1mM β-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF, Millipore)), supplemented with 2i (3 μM Gsk3 inhibitor CT-99021, 1 μM MEK inhibitor PD0325901, Axon) at a density a density of 40.000 cells/cm2 (XO) or 70.000 cells/cm2 (XX).

extract_protocol:
Cells were lysed in 300 µl Trizol (Invitrogen). RNA was isolated using the Direct-Zol RNA Miniprep Kit (Zymo Research) following the manufacturer’s instructions. The mRNA fraction was recovered from the total RNA using Dynabeads Oligo-dT25 (Invitrogen) with 1 mg beads per 50 μg of total RNA. For the input library, Plasmid DNA from 1.8 XX cells was isolated 48 hours after transfection using the QIAprep Spin Miniprep kit (Qiagen) according to manufacturer’s instructions.
RNA was reverse transcribed using Superscript III Reverse Transcriptase (Invitrogen) with a gene specific primer. Three RT reactions were performed for each sample. After first strand synthesis, the reactions were then treated with RNaseI (Thermo) for 60 minutes at 37 °C and cleaned up using the MinElute PCR Purification Kit (Qiagen). Subsequently, a junction PCR was performed using an intron-spanning primer pair  and 8 μl cDNA with the KAPA Hot Start HiFi Ready Mix (KAPA Biosystems) for 15 cycles. Three reactions each were pooled using the QIAquick PCR Purification Kit (Qiagen). Following, sequencing adapters were added in a second PCR using three reactions with 10 μl of the purified junction PCR product with the KAPA Hot Start HiFi Ready Mix (KAPA Biosystems) for 12 cycles. Lastly, the samples were isolated via agarose gel extraction and the QIAquick Gel Extraction Kit (Qiagen) and purified once more using the QIAquick PCR Purification and MinElute PCR Purification Kits (Qiagen). The input library was prepared for Illumina sequencing via three PCR reactions using 100 ng plasmid DNA and index primers using KAPA Hot Start HiFi Ready Mix (KAPA Biosystems) for 10 cycles. The amplified DNA was purified as the sequencing library of the samples. Input and sample libraries were pooled in equimolar ratios and sequenced paired-end 50 bp on the HiSeq 2500 platform yielding approximately 10.000.000 fragments per sample.

treatment_protocol: The preparation of the STARR-seq plasmid followed the description given in Arnold et al. 2013 with modification. For the generation of the input library, 5 Bacterial Artificial Chromosomes (BACs) were used as the source of DNA. The BAC clones of the RPCI-23 Female (C57BL/6J) Mouse BAC Library (RP23-106C4, RP23-11P22, RP23-423B1, RP23-273N4, RP23-71K8) were purchased from the BAC PAC Resource Center of the Children’s Hospital Oakland Research Institute. E.coli BAC clones were grown in 200 ml Lysogeny broth (LB) medium (10 g/l NaCl, 10 g/l Bacto Tryptone, 5 g/l Yeast extract, 1 mM NaOH) supplemented with 12.5 μg/ml Chloramphenicol (Sigma) in a shaking incubator at 30 °C for 20 hours. The BAC DNA was isolated using the NucleoBond BAC 100 kit (Machery-Nagel). For preparation of the screening library, the BAC DNA was pooled (2.5 μg each) and split into four tubes, which were filled with TE buffer to a total volume of 100 μl. The DNA was sheared by sonication (Bioruptor Plus, low intensity, 3 cycles with 32s ‘on’/ 28 s ‘off’), size-selected on a 1% agarose gel and extracted with the QIAquick Gel Extraction Kit (Qiagen). The eluates were pooled and purified using the QIAquick PCR Purification Kit (Qiagen). The purified fragments were end-repaired, dA-tailed and ligated to adaptors compatible with Illumina sequecing according to the NEBnext DNA library prep master mix set for Illumina (NEB, oligonucleotide sequences shown in Supplemental Table S5). The ligated fragments were purified using Agencourt AMPure XP beads (Beckman Coulter) and eluted in 25 μl elution buffer. Four PCR reaction were then carried out with 1μl of the purified DNA using the KAPA Hot Start HiFi Ready Mix (KAPA Biosystems) for 10 cycles inserting a 15 nt homology sequence for the subsequent cloning step (Primers shown in Supplemental Table S5). The PCR product were size-selected on a 1% agarose gel and purified using the MinElute PCR Purification Kit (Qiagen). The pSTARR-seq_human vector (kindly provided by Alexander Stark) was digested with AgeI-HF and SalI-HF for 3.5 hours at 37 °C and purified as described above. The DNA library was then cloned into the vector using four In-Fusion cloning reactions according to the manufacturer’s instructions (Clonetech In-Fusion HD). The reactions were pooled, ethanol precipitated and transformed into MegaX DH10BTM T1R ElectrocompTM Cells (Invitrogen) according to the manufacturer’s instructions in a total of eight separate reactions. Plasmid DNA was amplified overnight and isolated using the NucleoBon Xtra Midi Plus Kit (Macherey-Nagel). Good library complexity was verified via a dilution series of the pooled transformations. The STARR-seq library was transfected into 1.8 XX and 1.8 XO cells under Serum/LIF/2i or differentiating conditions in three biological replicates. The cells were transfected with 2.5 μg of the STARR-seq library vector via lipofection (Lipofectamine LTX, Thermo) according to manufacturer’s instructions. Differentiation was induced for 2 days by 2i/LIF withdrawal in DMEM supplemented with 10% FBS and 0.1mM β-mercaptoethanol in fibronectin-coated (10 μg/ml) tissue culture plates (In the d2 samples).

tag: condition

value: Input

tag: replicate

tag: assay

value: STARR-seq


title: 3yr_Liver_OLD_rep3

tag: genotype/variation

tag: tissue

tag: age


title: HeLa_US47_AG

description: crosslinked total RNA

source_name: HeLa cells

value: HeLa

value: epithelial cells


title: 3yr_Liver_OLD_rep2


title: STARR_1.8_XO_d2_r2

description: Mouse embryonic stem cells

value: Day 2


title: In vitro differentiated Langerhans cells_3

type: RNA

city: Strasbourg

first: Henri

last: de la Salle

address: 10 rue Spielmann

country: France

institute: EFS Grand-Est

hyb_protocol: Following fragmentation 12.5ug of cRNA were hybridized on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following Affymetrix recommendations.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip® Scanner 3000 at 570nm driven by GCOS software v1.4 according to manufactuer's protocol

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA) using the R/Bioconductor package affy.

label: biotin

source_name: Cord blood CD34+ cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2ug total RNA (Expression Analysis Technical Manual 701021 Rev. 5.)

growth_protocol: CD1a+ Langerhans cells were isolated using Myltenyi beads from human cord blood CD34+ cells purified using Myltenyi beads in the presence of recombinant TGFb, SCF, GM-CSF, FLT3.

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

treatment_protocol: Human skin epidermal sheets were digested with dispase. CD1a+ cells were isolated using Myltenyi beads. CD1a-depleted cells were used to control keratinocyte contamination.


title: 3yr_Liver_OLD_rep1


title: Skin Langerhans cells_2

source_name: Skin epidermis

value: Skin Langerhans cells


title: Skin keratinocytes_1

value: Skin keratinocytes


title: Skin keratinocytes_2


title: Skin Langerhans cells_3


title: Skin Langerhans cells_1


title: Refractory cells P001-02S-ZNF589-SZF1

city: Gainesville

first: Sumita

middle: A

last: Bhaduri-McIntosh

state: FL

address: ARB  R1-118G, 1600 SW Archer Road

department: Depts. of Pediatrics & of Molecular Genetics and Microbiology

institute: University of Florida

data_processing:
Sequencing reads were trimmed and filtered to remove barcodes and low quality reads
Clean reads from untreated, refractory and lytic samples were aligned to human (Hg38) and EBV (NC_007605) reference genome, respectively, with Bowtie 2.
Peaks were called using default parameters of GeneTrack and GEM algorithms
Genome_build: Hg38 and NC_007605
Supplementary_files_format_and_content: Peak text files

source_name: HH514-16 cells

growth_protocol: Cells were routinely seeded in 10% FBS and RPMI after 72hrs

extract_protocol:
Untreated and flow cytometry sorted cell pellets stained with EBV-seropositive and EBV-seronegative serum were recovered, washed twice with 1x PBS. Pelleted cells from 3 independent experiments were sent for ChIP-exo processing
Genomic DNA libraries immunoprecipitated by anti-SZF1 antibody and treated with a 5’-to-3’ exonuclease (Exo) were prepared for sequencing using standard Illumina protocols

treatment_protocol: HH514-16 cells per each of 3 replicates were treated for 24hrs with 3mM sodium butyrate (NaB) or left untreated

tag: disease state

value: Epstein-Barr virus

value: Burkitt Lymphoma cells

tag: treatment

value: NaB treated


title: Untreated cells P001-03S-ZNF589-SZF1

tag: cell type

value: NaB untreated


title: In vitro differentiated Langerhans cells_1


title: In vitro differentiated Langerhans cells_2


title: ATAC H7 rep3

city: NEW YORK

first: Alex

last: Penev

state: NY

address: 540 First Ave

institute: NYU Langone Medical Center

data_processing:
Sequencing of libraries was performed by NYU Genome Technology on Illumina HiSeq 2500 sequencer.
Alignment was performed as in (Buenrostro et al. 2013) to the hg19 human reference genome.
Peak calling was done using macs2 using parameters described in (Corces et al. 2017).
IGV was used to visualize sequencing data tracks and bedtools was used for find regions of overlap between ATAC-seq and 4C data.
4C sequencing data was analyzed using the 4Cker software package described in (Raviram et al. 2016) using the recommended parameters.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak ATAC-seq files, .bed 4C files

source_name: Embryonic stem cell line

growth_protocol: ARPE-19 cells were growth in culture-coated 10cm plates in Dulbecco’s Modified Eagle Medium (DMEM, Corning) supplemented with 10% fetal bovine serum (FBS, Gibco), 2 mM L-glutamine (Gibco), 100 U/ml Penicillin-Streptomycin (Gibco), and 0.1 mM MEM non-essential amino acids (Gibco). H7 cells were cultured in mTeSR Plus (STEMCELL) media supplemented with 100 U/ml Penicillin-Streptomycin (Gibco) and passaged with EDTA every 2-3 days.

extract_protocol:
Library preparation for Circular Chromosome Conformation Capture (4C) was performed as described in (van de Werken et al. 2012) with the exception of initial fixation and lysis procedure, which was adapted from (Miele et al. 2009). 1x107 ARPE or H7 ESCs were dissociated and resuspended in 5ml PBS containing 10% BCS. Cells were crosslinked by adding 5ml of 4% formaldehyde in PBS and incubating at room temperature (RT) for 10 minutes with gentle rocking. Reaction was quenched by adding 2.5ml 2.5M glycine, mixing well and incubating at RT for 5 minutes, then on ice for 15 minutes. Cells were pelleted at 800xg for 10 minutes, resuspended in 1ml of cold Lysis Buffer 1 (10mM Tris pH 8.0, 10mM NaCl, 0.2% IGE-PAL, Protease inhibitor (Roche)) and incubated on ice for 15 minutes. Cells were then dounce-homogenized on ice with a B-type pestle twice for 15 minutes with a minute rest on ice in between. Sample was pelleted at 2500xg for 5 minutes and the pellet was washed with 1x Cutsmart buffer (NEB) and pelleted again. Samples were further processed as described in (van de Werken 2012) using DpnII primary digestion and Csp6I secondary digestion.  ATAC-seq was performed on 5x10^5 ARPE and H7 cells in triplicate as described in (Buenrostro et al. 2015).
Sequencing library was prepared as described using Expand Long Template polymerase (Roche) and Illumina adaptor sequence-containing primers unique to the hTERT fragend. ATAC-seq was performed on 5x10^5 ARPE and H7 cells in triplicate as described in (Buenrostro et al. 2015).

value: embryonic stem cell


title: STARR_1.8_XO_d2_r1

description: Mouse embryonic stem cells


title: HeLa_US47

description: crosslinked total RNA

tag: passages


title: HeLa_VR1197_AG

description: crosslinked total RNA

tag: infection

value: VR-1197 strain of EV-D68 (with rupintrivir inhibitor)


title: 1yr_Liver_WT_rep3

value: wild type

value: Liver

value: 1-years old


title: STARR_1.8_XO_d0_r3

description: Mouse embryonic stem cells

value: Day 0


title: HeLa_VR1197_GA

description: crosslinked total RNA

value: VR-1197 strain of EV-D68 (with geldanamycin inhibitor)


title: ATAC H7 rep1


title: STARR_1.8_XO_d2_r3

description: Mouse embryonic stem cells

value: STARR-seq


title: HeLa_US47_GA

description: crosslinked total RNA

value: HeLa

value: US/MO/14-18947 strain of EV-D68 (with geldanamycin inhibitor)


title: 1yr_Liver_WT_rep1


title: HeLa_VR1197

description: crosslinked total RNA

value: epithelial cells

value: VR-1197 strain of EV-D68


title: ATAC H7 rep2


title: Lytic cells P001-ZNF589-SZF1


title: STARR_1.8_XO_d0_r1

description: Mouse embryonic stem cells


title: ATAC ARPE19 rep3

source_name: Retinal pigment epithelial cell line

value: retinal pigment epithelial cell


title: GH_Liver_ACRO_rep3

value: Acromegaly zebrafish model


title: GH_Liver_ACRO_rep2


title: 1yr_Liver_WT_rep2


title: STARR_1.8_XX_d2_r3

description: Mouse embryonic stem cells

value: Day 2


title: ATAC ARPE19 rep1


title: STARR_1.8_XX_d2_r2

description: Mouse embryonic stem cells


title: STARR_1.8_XO_d0_r2

description: Mouse embryonic stem cells


title: ATAC ARPE19 rep2


title: TC5

city: Botucatu

first: Bruno

middle: Evaristo de Almeida

last: Fantinatti

state: São Paulo

address: Prof Antonio Celso Wagner Zanin

department: Morphology

country: Brazil

institute: Unesp

data_processing:
Removing adaptors and quality filtering
Alignment against D. rerio precursors
Quantification using featureCounts
Differential expression using DESeq2
Genome_build: MirBase 22
Supplementary_files_format_and_content: Plain text. Raw and Normalized Counts

organism: Piaractus mesopotamicus x Colossoma macropomum

growth_protocol: Controlled water conditions. Photoperiod 12/12h. Food twice a day.

extract_protocol:
TRIZOL
Truseq-small-rna-sample-prep

treatment_protocol: No treatment.

value: muscle

tag: development stage

value: Juvenile


title: TC8


title: TC6


title: GH_Liver_ACRO_rep1


title: STARR_1.8_XX_d2_r1

description: Mouse embryonic stem cells


title: 3yr_Brain_OLD_rep5

source_name: Brain

value: AGED zebrafish

value: Brain

value: 3-years old


title: STARR_1.8_XX_d0_r3

description: Mouse embryonic stem cells


title: 3yr_Brain_OLD_rep4


title: STARR_1.8_XX_d0_r2

description: Mouse embryonic stem cells


title: STARR_1.8_XX_d0_r1

description: Mouse embryonic stem cells


title: TC3


title: 3yr_Brain_OLD_rep3


title: 3yr_Brain_OLD_rep2


title: Infected_treated

city: Doylestown

first: Jinhong

last: Chang

state: PA

address: 3805 Old Easton Road

institute: Baruch S. Blumberg Institute

data_processing:
Raw sequence reads were aligned to the mouse genome (mm10) using the Tophat algorithm
 Cufflinks  was implemneted to assemble transcripts and estimate their abundance.
Cuffdiff was used to statistically assess expression changes in quantified genes in different conditions
Genome_build: mm10
Supplementary_files_format_and_content: tab-limited text files include FPKM values for each sample…

source_name: embryonic kidney cells

extract_protocol:
A total amount of 1.5μ g 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.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HEK293 cells were either uninfected or infected with YFV at MOI of 10 for 1 h. At 18 hours post infection (hpi), the cells were either mock treated with DMSO or treated with 3µM of BDAA for 2 h.

tag: infection status

value: Infected

value: Treated with BDAA


title: HEK293_mRNA

description: crosslinked mRNA

value: HEK293T cells

value: embryonic kidney cells


title: SBC5, parental

city: Chiyoda-ku

first: Shogo

last: Okazaki

state: Tokyo

address: 1-8-13 Kanda-Surugadai

department: School of Dentistry

institute: Nihon University

data_processing:
Sequenced reads were mapped to hg38 genome using TopHat2
Gene expression data were calculated FPKM (Fragments Per Kilobase of exon per Million mapped reads) and compared between samples by using NGS data analysis system MASER 5
Genome_build: hg38
Supplementary_files_format_and_content: GEO_submission_FPKM.txt

source_name: small cell lung cancer cell line

growth_protocol: Both cell lines were maintained under 5% CO2 at 37°C in RPMI 1640 medium (Nacalai) supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted and purified with the use of RNeasy Mini Kit (Qiagen).
500 ng of the purified RNA were used to prepare RNA-seq libraries with TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: SBC5 Cpr cells were generated by exposing the parental cell lines to stepwise increases in the concentration of cisplatin (1, 2, 4, and 20 μg/ml).

tag: phenotype

value: Parental


title: Infected

tag: cell line

value: Untreated


title: Dux KO Replicate 4 [delta58_S8]

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description: mRNA-Seq Dux KO Replicate 4

data_processing:
Reads were trimmed with Trimmomatic Version 0.32 parameters: ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:25
Trimmed reads were mapped to the GRCm38 (mm10) genome with STAR (version 2.6.1a) using the optional argument --outFilterMultimapNmax 100.
Mapped reads were indexed and sorted with samtools (version 1.7).
Expression level estimates were generated using Rsubread( version 1.28.1).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: NA

source_name: Dux KO_2 cell stage embryos

extract_protocol:
2-cell embryos harvested from timed matings.  12-18 embryos were pooled per sample.
NEBNext® Single Cell/Low Input cDNA Synthesis & Amplification kit (New England Biolabs) was used to make the cDNA from the pooled embryos. Nextera XT DNA Library Preparation Kit (Illumina) was used to make the sequencing library.

tag: strain background

tag: developmental stage

value: 2 cell stage embryos

value: Dux KO


title: SBC5, CPr

value: Cisplatin-resistant


title: 3yr_Brain_OLD_rep1


title: WT Replicate 4 [b657_S7]

description: mRNA-Seq WT Replicate 4

source_name: WT_2 cell stage embryos

value: wild type


title: Non-infected

value: Non-infected


title: 1yr_Brain_WT_rep3

value: 1-years old


title: PC8

organism: Piaractus mesopotamicus

source_name: Muscle

value: muscle


title: 1yr_Brain_WT_rep2


title: PC5

value: Juvenile


title: TC4


title: WT Replicate 1 [b654_S4]

description: mRNA-Seq WT Replicate 1


title: PC4


title: Dux KO Replicate 3 [delta53_S3]

description: mRNA-Seq Dux KO Replicate 3


title: PC3


title: Non-infected_treated


title: 1yr_Brain_WT_rep1


title: GH_Brain_ACRO_rep3

value: Acromegaly zebrafish model


title: Dux KO Replicate 2 [delta52_S2]

description: mRNA-Seq Dux KO Replicate 2


title: GH_Brain_ACRO_rep2

value: Brain


title: PC10


title: Dux KO Replicate 1 [delta51_S1]

description: mRNA-Seq Dux KO Replicate 1


title: WT Replicate 3 [b656_S6]

description: mRNA-Seq WT Replicate 3


title: WT Replicate 2 [b655_S5]

description: mRNA-Seq WT Replicate 2


title: GH_Brain_ACRO_rep1


title: Microglia WT 12m, biological rep4

status: Public on Mar 03 2021

city: Seville

first: Carmen

last: Romero-Molina

state: Seville

address: Profesor Garcia Gonzalez, 2

department: Faculty of Pharmacy. Biochemistry and Molecular Biology

country: Spain

institute: University of Seville. Institute of Biomedicine of Seville

description: Gene expression data from Microglia (Cortex and Hippocampus) from aged WT mouse

hyb_protocol: 6.6ug of ds-cDNA were hybridized for 16 hours at 45°C at 60rpm on Clariom S Mouse array. GeneChips were washed and stained in the GeneChip Fluidics Station 450 (Applied Biosystems)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Applied Biosystems)

data_processing: Data were normalized using Signal Space Transformation Robust Multi-Chip Analysis (sst-RMA) method and differential expression analysis was done using Transcriptome Analysis Console (TAC 4.0, Applied Biosystems).

source_name: Microglia from 12 month old C57BL6 mouse

label_protocol: Samples were enzymatically fragmented and biotinylated using the 3'IVT Pico Kit (Applied Biosystem) from 5ng total RNA.

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

value: cortex and hippocampus

value: Microglia

tag: strain

tag: condition

value: Aged WT mice

value: 12 months


title: Microglia TAU12m, biological rep4

description: Gene expression data from Microglia (Cortex and Hippocampus) from aged P301S mouse

source_name: Active Microglia from 9 month old P301S mouse

value: Active Microglia

value: Pathologic TAU mice

value: 9 months


title: Microglia WT 12m, biological rep3


title: Microglia APP 12m, biological rep1

description: Gene expression data from Microglia (Cortex and Hippocampus) from aged APPswlnd mouse

source_name: Active Microglia from 12 month old APPswlnd mouse

value: APPswlnd

value: Pathologic APP mice


title: Microglia APP 12m, biological rep3


title: Microglia TAU 3m, biological rep1

description: Gene expression data from Microglia (Cortex and Hippocampus) from young P301S mouse

source_name: Microglia from 3 month old P301S mouse

value: Pre-pathology TAU mice

value: 3 months


title: Microglia WT 12m, biological rep1


title: Microglia TAU 3m, biological rep2


title: Microglia APP 3m, biological rep3

description: Gene expression data from Microglia (Cortex and Hippocampus) from young APPswlnd mouse

source_name: Microglia from 3 month old APPswlnd mouse

value: Pre-pathology APP mice


title: Microglia APP 12m, biological rep4


title: Microglia TAU 3m, biological rep4


title: Microglia WT 3m, biological rep3

description: Gene expression data from Microglia (Cortex and Hippocampus) from young WT mouse

source_name: Microglia from 3 month old C57BL6 mouse

value: Young WT mice


title: Microglia APP 12m, biological rep2


title: Microglia TAU12m, biological rep1


title: Microglia TAU12m, biological rep3


title: Microglia TAU12m, biological rep2


title: Microglia WT 3m, biological rep4


title: Microglia APP 3m, biological rep1


title: Microglia TAU 3m, biological rep3


title: Microglia WT 12m, biological rep2


title: Prdm16_wt_Chip-seq_Rep2_tech1

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

data_processing:
ATAC-Seq: The replicated Prdm16 KO (x3) and control (x3) ATAC-seq samples, after the adaptor trimming by Trimmomatic, were mapped to the UCSC Mus musculus (mm10) genome assembly using Bowtie2 with the default parameters. The high quality and uniquely mapped reads (with mapping quality >= 20) were used for further analysis. ATAC-seq differential expression analysis between Prdm16 mutants and wild types on the Prdm16 bound ChIP-seq peaks were performed by Limma R package. The ATAC-seq peak calling was performed by HOMER using the “broad peak” option with parameters “-region -size 1000 -minDist 2500”, separately for the mutant and wild type. To compare active enhancers between E13.5 and E15.5, we further re-analyzed the publicly available histone mark H3K27ac and PRDM16 ChIP-seq data at E15.5. We called the peaks against Input using “narrow peak” option by HOMER with the default parameters.
RNA-Seq: After trimming the adaptor sequences using Trimmomatic, we mapped RNA-seq reads from the replicated Prdm16 wild type (x3) and mutant samples (x3) to the UCSC Mus musculus (mm10) genome assembly using HISAT2. We normalized RNA-seq by the “Relative Log Expression” method implemented in the DESeq2 Bioconductor library (Love et al., 2014). Gene annotation was obtained from the iGenomes UCSC Mus musculus gene annotation. Differentially expressed mRNAs between Prdm16 mutants versus wild type were identified, and FDR (Benjamini-Hochberg) was estimated, using DESeq2.
ChIP-Seq: The replicated Prdm16 KO (x3) and control (x3) ChIP-seq samples, after the adaptor trimming by Trimmomatic, were mapped to the UCSC Mus musculus (mm10) genome assembly using Bowtie2 with the default parameters. The uniquely mapped reads (with mapping quality >= 20) were used for further analysis. The PRDM16 peaks were called by HOMER (v4.10) (Heinz et al., 2010). The peak replicate reproducibility was estimated by Irreproducibility Discovery Rate (IDR), using the HOMER IDR pipeline (https://github.com/karmel/homer-idr). As suggested by the Encode IDR guideline that IDR requires to initially call peaks permissively for the replicates, we used a relatively relaxed parameter “-F 2 -fdr 0.3 -P .1 -L 3 -LP .1” for the true/pseudo/pooled replicates by the HOMER peak calling. The final confident peaks were determined by an IDR < 5%. The peaks that were overlapped with mm10 blacklist were also removed.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig for coverage; xlsx file for RNA-seq count table

source_name: whole head

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
DNA libraries were made using the NEBNext Ultra™ II DNA Library Prep Kit and sequenced on the Illumina Hiseq2500 platform.

value: whole head

tag: genotype

value: heterozygous or willd-type control little

tag: target


title: Prdm16_wt_Chip-seq_Rep2_tech2

tag: tissue


title: Prdm16_wt_Chip-seq_Rep3


title: AD-MSCs_cloupe 2

city: Niigata

first: Atsunori

last: Tsuchiya

state: %null%

address: 1-757, Asahimachi-dori, Chuo-ku, Niigata

institute: Niigata University

data_processing:
The Cell Ranger Single-Cell Software Suite (https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger) was used to perform sample demultiplexing, barcode processing, and single-cell 3' gene counting.
Genome_build: mm10
Supplementary_files_format_and_content: .cloupe contains tSNE plot of each samples. The files were generated using the Cell Ranger pipeline provided from 10X Genomics and open with Loupe Cell Browser also provided from 10X Genomics.

source_name: Liver

growth_protocol: we analyzed the effects of MSCs and sEVs on the behavior of hematopoietic cells (mainly macrophages) in the liver, using single-cell RNA-sequencing. Cirrhosis was induced by injecting mice with CCl4 for 8 weeks, followed by injection of PBS (vehicle)(cloupe 1), AD-MSCs (cloupe 2), γ-AD-MSCs (cloupe 3), AD-MSC-sEVs (5 μg cloupe 4), and AD-MSC-γ-sEVs (5 μg cloupe 5). Livers were harvested 48 h after the injection. We analyzed 663 cells in the vehicle group, 1,215 cells in the AD-MSC group, 1,505 cells in the γ-AD-MSC group, 1,588 cells in the AD-MSC-sEVs group, and 1,591 cells in the AD-MSC-γ-sEV group.

extract_protocol:
Forty-eight hours after MSC or sEVs injection, mice were euthanized, cirrhotic livers were perfused with PBS, and then harvested and dissociated into single cells using the liver dissociation kit (Miltenyi Biotec, Bergisch Gladbach, Germany) according to the manufacturer’s protocol. The dissociated cells were sorted using Mofl XDP (Beckman Coulter Inc.) after propidium iodide (PI) staining (1 µg/ml) to exclude dead cells.
Cells were prepared as scRNA-seq library using Chromium Single Cell 3’ Reagent Kits v3 (10x Genomics, Pleasanton, CA, USA).

value: Liver

value: mainly hematopoietic cells


title: AD-MSC-γ-sEVs cloupe 5

treatment_protocol: we analyzed the effects of MSCs and sEVs on the behavior of hematopoietic cells (mainly macrophages) in the liver, using single-cell RNA-sequencing. Cirrhosis was induced by injecting mice with CCl4 for 8 weeks, followed by injection of PBS (vehicle)(cloupe 1), AD-MSCs (cloupe 2), γ-AD-MSCs (cloupe 3), AD-MSC-sEVs (5 μg cloupe 4), and AD-MSC-γ-sEVs (5 μg cloupe 5). Livers were harvested 48 h after the injection. We analyzed 663 cells in the vehicle group, 1,215 cells in the AD-MSC group, 1,505 cells in the γ-AD-MSC group, 1,588 cells in the AD-MSC-sEVs group, and 1,591 cells in the AD-MSC-γ-sEV group.


title: AD-MSC-sEVs_cloupe 4


title: γ-AD-MSCs_cloupe 3


title: ChIP_p300_Th1723_WT_100505L8

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

data_processing:
BCL conversion and demultiplexing (Casava 1.8.2 for ChIP, miRNA and mRNA)( Bcl2fastq and CellRanger for scRNA).  scRNA-seq raw files: read1_26/i7index_8/read2_98.
Mapping (Tophat 2.0.8 and Bowtie 2-2.1.0  for mRNA) (Bowtie v0.12.8 for ChIP and miRNA) (CellRanger for scRNA)
peak calling (MACS v1.4.2: default p-value threshold of 1E-5 for ChIP-seq)
BigWig tracks (BEDTOOLS v2.24, UCSC tool bedGraphToBigWig)
Genome_build: mm9 (ChIP, miRNA, mRNA); mm10 (scRNA)
Supplementary_files_format_and_content: BigWig files (ChIP, miRNA, mRNA); Robj, CellRanger output files (scRNA)

source_name: in vitro cultured CD4+ T cells

growth_protocol: CD4+ T cells were enriched by negative selection (Miltenyi), then purified to naïve population by sorting (CD4+CD62L+CD44-CD25-), then cultured with plate-bound anti-CD3 and anti-CD28 for 3 days with cytokines/antibodies indicated in treatment section.

extract_protocol:
Whole cell lysates were clarified and TF-DNA complexes were isolated with antibody
Purified DNA fragments (10ng) were blunt-end ligated to illumina adaptors, amplified and made into a library

value: spleen and lymph node

value: Wild type

tag: growth condition

value: 3 day in vitro culture

value: IL-6, IL-23, anti-IFNg, anti-IL4

tag: chip antibody

value: anti-p300 (Santa Cruz, sc-585)


title: ChIP_STAT3_Th1723_WT_100122L6

tag: treatment

value: anti-STAT3 (Thermo Fisher, 14-6727-81)


title: PBS (vehicle)_cloupe 1

tag: cell type


title: ChIP_STAT3_Th17b_WT_100122L4

value: Th17 (TGFb)

value: IL-6, TGFb, anti-IFNg, anti-IL4


title: ChIP_K27m3_Th1723_WT_100910L6

extract_protocol:
Whole cell lysates were clarified and histone-DNA complexes were isolated with antibody
Purified DNA fragments (10ng) were blunt-end ligated to illumina adaptors, amplified and made into a library

value: anti-K27m3 (Millipore, 07-449)


title: Microglia WT 3m, biological rep2

value: cortex and hippocampus

value: Microglia

tag: age


title: 3021_1_C: shCHD7, line 3021, replica 2

type: genomic

city: London

first: Silvia

last: Marino

address: 4, Newark St

country: United Kingdom

institute: Queen Mary University of London

hyb_protocol: DNA methylation data were amplified, fragmented and hybridised to Illumina Infinium HumanMethylation850 microarray after bisulfite conversion following standard Illumina protocol

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

data_processing: Raw data were pre-processed using the Bioconductor ChAMP package in R to remove failed detections and probes with design flaws (Feber et al., 2014). Normalisation was performed using the SWAN algorithm (Maksimovic et al., 2012).

label: Cy3, Cy5

source_name: Tumour Sample

label_protocol: Standard Illumina Protocol

growth_protocol: ICb1299 were cultured in DMEM (high glucose, GlutaMAX™, ThermoFisher) supplemented with 10% foetal bovine serum (FBS, Gibco) and 1% Penicillin-Streptomycin (Gibco). CHLA-01-Med G4 MB cells were purchased from ATCC (CRL3021) and cultured as described previously (Badodi et al., 2019). Briefly, cells were grown in DMEM-F12 (Gibco) supplemented with B27 (Gibco), 20 ng/mL human epidermal growth factor (EGF, Peprotech) and 10 ng/mL human basic fibroblast growth factor (FGF, Peprotech). MB subtype identity for the two cell lines has been previously shown (Badodi et al., 2017; Shu et al., 2008).

extract_protocol: Total genomic DNA was extracted with RNA/DNA/Protein Purification Plus kit (Norgen)

treatment_protocol: GIPZ lentiviral shRNA vectors containing a hairpin sequence targeting CHD7 and the coding sequences for GFP and puromycin resistance gene were purchased from Dharmacon, UK. Packaging, virus production and determination of titre were carried out as previously reported (Badodi et al., 2017). Cells were infected overnight at a multiplicity of infection (MOI) of 1. After 96h from the infection, puromycin selection at a concentration of 2.5 µg/ml was applied to enrich for the transduced population. The efficacy of gene silencing was assessed by qRT-PCR or Western blot analysis.

value: medulloblastoma


title: 1299_1_S: Scramble, line 1299, replica 2


title: Microglia APP 3m, biological rep2

value: APPswlnd

value: Pre-pathology APP mice

value: 3 months


title: ChIP_K27m3_Th17b_WT_101020L7


title: Microglia WT 3m, biological rep1

value: Young WT mice


title: Prdm16_wt_Chip-seq_Rep1_tech1

value: whole head

value: heterozygous or willd-type control little


title: Prdm16_wt_Chip-seq_Rep1_tech2


title: Prdm16_mutant_Chip-seq_Rep2_tech2

value: homozygous mutant


title: Prdm16_mutant_Chip-seq_Rep2_tech1


title: Prdm16_mutant_Chip-seq_Rep1_tech2


title: Prdm16_mutant_Chip-seq_Rep3


title: 3021_C: shCHD7, line 3021, replica 1


title: 1299_S: Scramble, line 1299, replica 1


title: 3021_1_S: Scramble, line 3021, replica 2


title: Prdm16_mutant_Chip-seq_Rep1_tech1


title: ChIP_K4m1_Th1723_WT_100910L8

value: spleen and lymph node

value: Wild type

value: 3 day in vitro culture

value: anti-H3K4m1(Abcam, ab8895)


title: Prdm16_mutant_FB_RNA-seq_Rep3

source_name: forebrain

growth_protocol: Standard mouse growth condition

extract_protocol:
Forebrain from E13.5 wt and mut embryos were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) ).

treatment_protocol: No

value: forebrain


title: Prdm16_wt_FB_RNA-seq_Rep2


title: Prdm16_mutant_FB_RNA-seq_Rep2


title: ChIP_K4m1_Th17b_WT_100910L3

value: Th17 (TGFb)

value: IL-6, TGFb, anti-IFNg, anti-IL4


title: ChIP_K4m3_Th17b_WT_100910L1

value: anti-H3K4m3 (Abcam, ab8580)


title: ChIP_K4m3_Th1723_WT_100910L4

value: IL-6, IL-23, anti-IFNg, anti-IL4


title: Prdm16_wt_FB_RNA-seq_Rep3


title: miRNA_iTreg_KO_OS1782

extract_protocol:
Total RNA was isolated using TRIzol or mirVana miRNA Isolation kit (Thermo Fisher Scientific)
TruSeq Small RNA sample Prep Kit (RS-200-0012, Illumina) using 1000 ng of total RNA

value: iTreg

value: IL-2, TGFb, anti-IFNg, anti-IL4


title: Prdm16_mutant_FB_RNA-seq_Rep1


title: miRNA_Th17_b_KO_OS1780


title: miRNA_naive_KO_OS1777

value: naive CD4+ T


title: miRNA_Th17_23_KO_OS1781


title: miRNA_Th1_KO_OS1779

value: IL-12, anti-IL4


title: Prdm16_wt_FB_RNA-seq_Rep1


title: 1299_C: shCHD7, line 1299, replica 1

value: medulloblastoma


title: miRNA_iTreg_WT_OS1776


title: 1299_1_C: shCHD7, line 1299, replica 2


title: 3021_S: Scramble, line 3021, replica 1


title: miRNA_Th17_23_WT_OS1775


title: miRNA_Th17_b_WT_OS1774


title: miRNA_naive_WT_OS1771

source_name: ex vivo CD4+ T cells


title: sample.e145_18_ff.i3c

city: Chapel Hill

first: Misty

last: Good

state: NC

address: 101 Manning Drive 4th Floor CB 7596

department: Pediatrics

institute: University of North Carolina at Chapel Hill

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.
Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
All gene counts were then imported into the R/Bioconductor package EdgeR5 and TMM normalization size factors were calculated to adjust for samples for differences in library size.
Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.
The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma.
Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights.
The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals.
Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Genome_build: MM10
Supplementary_files_format_and_content: geo_submission_7.7.20_Ahr_JI_Nolan excel.xls- spreadsheet normalized gene counts for individual samples.

source_name: mouse small intestine

growth_protocol: All animal experiments were performed in an American Association for the Accreditation of Laboratory Animal Care-accredited and specific pathogen-free animal facility at the Washington University School of Medicine in St. Louis. C57BL/6 mice were bred, maintained and housed in accordance with the procedures outlined in the Guide for the Care and Use of Laboratory Animals under an animal study proposal approved by the Institutional Animal Care and Use Committee (IACUC) (protocol #20190190) of the Washington University School of Medicine in St. Louis.

extract_protocol:
Total RNA was extracted using Trizol with Ambion's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: NEC was induced in neonatal mice using a model of hypoxic stress and infant formula supplemented with lipopolysaccharide and enteric bacteria. Four-day-old mice were randomly assigned to experimental groups and pups either remained with the mother or were separated from the dams and placed in a new cage maintained in an infant incubator at 37oC. Experimental NEC was induced in pups by gavage feeding a formula mixture containing Similac® Advance® OptigroTM with Iron infant formula (Abbott Nutrition) and Esbilac canine milk replacer (ratio 2:1). The formula was prepared daily and inoculated with enteric bacteria cultured from a human infant with NEC totalis, the most severe form of NEC. The aliquot of enteric bacteria was obtained from a frozen bacterial glycerol stock and prepared daily in an overnight culture with autoclaved Luria-Bertani (LB) broth culture medium (Lambda Biotech). Lipopolysaccharide (LPS) (Sigma-Aldrich) at a concentration of 2.5 g/gram average body weight was added to the formula. The I3C formulation was prepared each morning at a concentration of 50 mg/gram body weight using the daily average weight of the pups. The I3C was then homogenized in corn oil (Sigma Life Sciences) using a sonicator (Fisher Scientific) and 30 mL of the I3C solution was administered to pups twice daily by oral gavage. Breast fed and formula fed pups that did not receive I3C instead received the vehicle corn oil (30 mL) twice daily via oral gavage.


title: sample.e145_20_ff.i3c


title: sample.e145_19_ff.i3c


title: sample.e145_21_ff.i3c


title: S2_Atx2_RNAi_rep_3

city: Mandi

first: Baskar

last: Bakthavachalu

state: Himachal Pradesh

address: Kamand

department: School of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology

data_processing:
Sequencing Data obtained was processed similar to McMahon et al, 2016
Briefly the transcriptome data was mapped to dm6 genome using Tophat2
Uniquely mapped SAM file was converted to a matrix file.
A threshold of 20 reads and 15 percent editing was employed to identify editing events. Code for RNA editing analysis is available at (https://github.com/rosbashlab/TRIBE)
Genome_build: dm6
Supplementary_files_format_and_content: tab delimeted text file
Atx2-RNAi transcriptome data was mapped to dm6 genome using STAR
Read counts were obtained using HTseq with “-s reverse” parameter
DESeq2 was used to perform differential expression analysis
Genome_build: dm6
Supplementary_files_format_and_content: tab delimeted text file

organism: Drosophila melanogaster

growth_protocol: S2 cells were cultured in Schneider’s medium with 10% FBS, penicillin and streptomycin at 25°C

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) as per the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Plasmid transfections and dsRNA transfections were done using Mirus TransIT-X2 Dynamic Delivery System (MIR6000) and effectene reagents respectively as per manufacturer’s instructions.

value: Ataxin-2 RNAi


title: sample.e144_9_bf.i3c


title: sample.e144_19_ff

value: FF+corn oil


title: sample.e144_17_ff


title: sample.e145_5_bf.i3c


title: sample.e145_6_bf.i3c


title: S2_Atx2_RNAi_rep_1


title: S2_Mock_RNAi_rep_3

value: GFP RNAi


title: sample.e145_15_ff


title: S2_Mock_RNAi_rep_2


title: miRNA_Th1_WT_OS1773

value: spleen and lymph node


title: sample.e145_7_bf.i3c


title: S2_Mock_RNAi_rep_1


title: SAMPLE.X09O20_O20

city: Houston

first: Maria da Graca

last: Cabreira

state: TX

address: 6770 Bertner Ave

department: Regenerative Medicine Research

institute: Texas Heart Institute

description: Gene expression for MSC from donor2 cultured at 20% condition

hyb_protocol: Hybridization cocktails containing Affymetrix spike-in controls and 15.0ug of each fragmented, labeled cRNA were loaded onto Affymetrix GeneChip® Human U133 Plus 2.0 arrays. The arrays were hybridized for 16 hours at 45°C with rotation at 60 rpm in the Affymetrix GeneChip® Hybridization Oven 640. The arrays were washed and stained with a streptavidin, R-phycoerythrin conjugate stain using the Affymetrix GeneChip® Fluidics Station 450. Signal amplification was done using biotinylated antistreptavidin

scan_protocol: The stained arrays were scanned on the Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control metrics recorded using Affymetrix Command Console software version 3.0.0.

label: Biotin

label_protocol: Samples were labeled using the standard Affymetrix linear amplification protocol using the 3’ IVT Express Kit (protocol GeneChip® 3’ IVT Express Kit, p/n 702646, Rev. 7, 2008-2009). 250 ng of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for the vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was tested for integrity on the Agilent Bioanalyzer and quantified using the NanoDrop® ND-1000 spectrophotometer. 15.0 µg of the labeled cRNA was fragmented and re-checked for concentration and size.

growth_protocol: MSC expanded in Alpha Medium supplemented with Hyclone Fetal Bovine Serum (10%), no antibiotics, using 37C incubator and conventional tissue culture conditions (5% CO2 in air:19.95% O2 ) and InVivo2 cell culture workstation (5% CO2, 5% O2, 90% N2)

extract_protocol: Qiagen RNeasy KIT

value: heathy adult bone marrow samples purchase from LONZA


title: sample.e145_2_bf

value: BF+corn oil


title: S2_WT_mRNA_rep_2

value: No Transfection


title: SAMPLE.X05O05_O05

description: Gene expression for MSC from donor1 cultured at 5% condition


title: SAMPLE.X09O05_O05

description: Gene expression for MSC from donor2 cultured at 5% condition


title: S2_WT_mRNA_rep_1


title: sample.e145_4_bf


title: SAMPLE.X10O20_O20

description: Gene expression for MSC from donor3 cultured at 20% condition


title: sample.e145_3_bf


title: SAMPLE.X10O05_O05

description: Gene expression for MSC from donor3 cultured at 5% condition


title: S2_Atx2_WT_rep_1

description: TRIBE experimental samples

value: Ataxin-2 WT TRIBE


title: S2_Atx2_RNAi_rep_2


title: sample.e144_14_ff


title: S2_Atx2_WT_rep_3

description: TRIBE experimental samples


title: S2_Atx2_WT_rep_2

description: TRIBE experimental samples


title: Atx2_RNAi_rep_1

data_processing:
TRIBE: Sequencing Data obtained was processed similar to McMahon et al, 2016
TRIBE: Briefly the transcriptome data was mapped to dm6 genome using Tophat2
TRIBE: Uniquely mapped SAM file was converted to a matrix file.
TRIBE: A threshold of 20 reads and 15 percent editing was employed to identify editing events. Code for RNA editing analysis is available at (https://github.com/rosbashlab/TRIBE)
Atx2-RNAi transcriptome data was mapped to dm6 genome using STAR
Read counts were obtained using HTseq with “-s reverse” parameter
DESeq2 was used to perform differential expression analysis
Genome_build: dm6
Supplementary_files_format_and_content: tab delimeted text file

source_name: Brain

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

value: Brain


title: sample.e144_1_bf


title: Control_GAL4_rep_3

value: Elav Gal4


title: Control_GAL4_rep_2


title: Atx2_RNAi_rep_2


title: Control_GAL4_rep_1


title: UAS_Atx2_WT_rep_2

description: TRIBE control: Used to analyse TRIBE experimental samples. No processed data available

value: UAS-Ataxin-2 TRIBE


title: UAS_Atx2_WT_rep_1


title: Atx2_Lsm LsmAD_rep_2

description: TRIBE experimental samples

value: Ataxin-2 Only Lsm_LsmAD Domain TRIBE


title: Elav_GAL4_rep_1


title: Elav_GAL4_rep_2


title: Atx2_Lsm_LsmAD_rep_1

description: TRIBE experimental samples


title: Atx2_delta_cIDR_rep_2

description: TRIBE experimental samples

value: Ataxin-2 cIDR Domain Deletion TRIBE


title: SAMPLE.X05O20_O20

description: Gene expression for MSC from donor1 cultured at 20% condition


title: Atx2_delta_cIDR_rep_1

description: TRIBE experimental samples


title: Atx2_delta_mIDR_rep_2

description: TRIBE experimental samples

value: Ataxin-2 mIDR Domain Deletion TRIBE


title: Atx2_delta_LsmAD_rep_1

description: TRIBE experimental samples

value: Ataxin-2 LsmAD Domain Deletion TRIBE


title: Atx2_delta_Lsm_rep_2

description: TRIBE experimental samples

value: Ataxin-2 Lsm Domain Deletion TRIBE


title: Atx2_WT_rep_2

description: TRIBE experimental samples


title: Atx2_delta_Lsm_rep_1

description: TRIBE experimental samples


title: Atx2_delta_LsmAD_rep_2

description: TRIBE experimental samples


title: Atx2_WT_rep_1

description: TRIBE experimental samples


title: Atx2_RNAi_rep_3


title: WM983b-MX2-3

city: Solna

first: Gert-Jan

last: Hendriks

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

data_processing:
Raw data was mapped to Hg38 using STAR aligner 2.7
Count tables were produced using the feature counts function from the Rsubread package
Genome_build: Hg38
Supplementary_files_format_and_content: Juraleviciute2021_countTable.csv

growth_protocol: WM983b melanoma cells were routinly grown in 5% FCS RPMI medium before lentiviral trasnfections

extract_protocol:
Total RNA was extracted from cell samples and tissues using a NucleoSpin RNA extraction kit (Macherey-Nagel) according to manufacturer’s instruction.
Libraries were prepared using 10 µg extracted RNA and the TruSeq library preparation kit (Illumina)
Sequencing was performed using a NextSeq500 instrument (Illumina) using a 75-cycle high output kit

treatment_protocol: Stably transfected with lentivirus constructs (pLenti-CMV-Puro-MX2 or pLenti-CMV-Puro-GFP) and selected with 2 µg /ml pouromycine for 3 days

value: Plenti-CMV-Puro-MX2 transduced

value: MX2 overexpression


title: WM983b-MX2-1


title: C.elegans L4_BaP 20_rep3

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

institute: King's College London

description:
Raised on NGM for 48 hours (L1 to L4 stage) in the presence of 20 μM benzo[a]pyrene
20-C_S1

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality (error rate < 0.05) at the end. After trimming, sequence reads shorter than 30 nucleotides were discarded.
The  sequence reads were mapped  to the C.elegans reference genome using CLC Genomics Server program
The  hit counts and RPKM values for genes were calculated. After quantile normalization and log2-transformation on RKPM values, unsupervised hierarchical clustering and Principal Component Analysis (PCA) were performed.
Comparisons of gene between various groups of samples were performed. Student t test was conducted for each comparison after quantile normalization and log2-transformation. A list of genes were selected if the p value < 0.05 and fold-change of normalized RPKMs > 2.
To analyze the variation of gene expression across the duplicates, the mean normalized RPKMs, standard deviation, coefficient of variation (CV) were calculated within each group.
Genome_build: WBcel235
Supplementary_files_format_and_content: MS Excel files containing gene expression for each comparison.
Supplementary_files_format_and_content: MS Excel files containing variation analysis results within each group.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Caenorhabditis elegans

source_name: C.elegans L4_BaP 20_3

growth_protocol: Parent population (P0) maintained at 20 ºC on standard nematode growth media (NGM) plates using Escherichia coli OP50 as food source. A synchronous L1 culture was generated by standard bleach preparation and grown to L4 stage in the presence or absence of benzo[a]pyrene.

extract_protocol:
The RNA isolation followed the standard procedures using Trizol reagent (Invitrogen), however modified to include a homogenization step with 0.5 mm glass beads (Sigma) to maximize cell breakage.
Libraries were prepared according to Illumina's instructions. Briefly, mRNAs were purified using Poly(A) selection from total RNA and then fragmented. First strand of cDNA was synthesized using random priming, followed by the synthesis of the second strand of cDNA. The resulting double-strand cDNA was end repaired, phosphorylated and A-tailed. Adapter ligation and PCR amplification were performed, rendering the library ready for Illumina flow cell clustering and sequencing on an Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: L1 stage animals were exposed 48 hours at 20 ºC to benzo[a]pyrene supplemented to both the agar medium and the food source (E. coli OP50).

value: staged L4 hermaphrodite

tag: agent

value: Benzo[a]pyrene exposed (20 microM)


title: WM983b-GFP-3

value: Plenti-CMV-Puro-GFP transduced

value: GFP overexpression


title: Atx2_delta_mIDR_rep_1

description: TRIBE experimental samples


title: C.elegans L4_BaP 20_rep2

description:
Raised on NGM for 48 hours (L1 to L4 stage) in the presence of 20 μM benzo[a]pyrene
20-B_S8

source_name: C.elegans L4_BaP 20_2


title: WM983b-MX2-2


title: C.elegans L4_BaP 20_rep1

description:
Raised on NGM for 48 hours (L1 to L4 stage) in the presence of 20 μM benzo[a]pyrene
20-A_S7

source_name: C.elegans L4_BaP 20_1


title: WM983b-GFP-2


title: WM983b-CTR-3

value: not transduced

value: control


title: WM983b-GFP-1


title: C.elegans L4_BaP 5_rep2

description:
Raised on NGM for 48 hours (L1 to L4 stage) in the presence of 5 μM benzo[a]pyrene
5-B_S5

source_name: C.elegans L4_BaP 5_2

value: Benzo[a]pyrene exposed (5 microM)


title: C.elegans L4_BaP 5_rep1

description:
Raised on NGM for 48 hours (L1 to L4 stage) in the presence of 5 μM benzo[a]pyrene
5-A_S4

source_name: C.elegans L4_BaP 5_1


title: WM983b-CTR-2


title: WM983b-CTR-1


title: C.elegans L4_BaP 0_rep3

description:
Raised on NGM for 48 hours (L1 to L4 stage)
0-C_S3

source_name: C.elegans L4_BaP 0_3

value: Control (unexposed)


title: C.elegans L4_BaP 0_rep1

description:
Raised on NGM for 48 hours (L1 to L4 stage)
0-A_S1

source_name: C.elegans L4_BaP 0_1


title: C.elegans L4_BaP 0_rep2

description:
Raised on NGM for 48 hours (L1 to L4 stage)
0-B_S2

source_name: C.elegans L4_BaP 0_2


title: S40N_miRNA-seq

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

data_processing:
Base calling was performed by Illumina Genome Studio(V2010.1).
After TruSeq small RNA adapters were eliminated among the sequenced reads by Trimommatic software (v.0.38), the remained sequence data were mapped to the human genome (GRCh38) using bowtie2 (v.2.3.4).
The quantification of each miRNA was estimated using HTSeq software package.
Then, the counts
per
million

mapped reads (CPM) of each sample was estimated.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text format with CPM values of miRNA

source_name: Normal thyroid tissue

extract_protocol:
Total RNA was isolated using the mirVana miRNA isolation kit (Ambion).
Small RNAs (20 - 30 nt) were purified from 15% Novex TBE-Urea gel (Invitrogen) and ligated first with the 5’ RNA adaptor and then with the 3’ RNA adaptor provided by Illumina TruSeq small RNA sample preparation protocol. In each step, the ligated product was PAGE-gel purified. After first-strand synthesis and 11 cycles of PCR amplification, the product was PAGE-gel purified.

tag: pathological type

value: non-tumor


title: S39N_miRNA-seq


title: S34N_miRNA-seq


title: S23N_miRNA-seq


title: U1 + LL34 I24A

city: San Diego

first: Richard

middle: L

last: Gallo

address: 9452 Medical Center Drive

department: Dermatology

institute: UCSD

data_processing:
All the steps including trim bases, alignment with bowtie 2, quantification to annotation model (Partek E.M), Normalization (CPM/Add 1.0 E-4), Gene Set Enrichment (GSA), Differential Gene Analysis and hierarchial clustering, and Gene Ontology analysis was performed with the Partek Flow Genomics Suite.
Genome_build: hg19

source_name: Normal human keratinocytes

growth_protocol: Normal human keratinocytes were cultures in Epilife medium supplemented with HKGS and Antibiotics-Antimycotics

extract_protocol:
total RNA was isolated with RNA mini kit from Ambion/ Life Technologies
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Keratinocytes were treated with U1 dsRNA (2.5 ug/ml) and/or LL34 peptides Parent, I24A or L31A at 2.5 uM concentration for 18 h.

value: skin

value: U1 dsRNA (2.5 ug/ml) and LL34 I24A


title: S27N_miRNA-seq


title: U1 + LL34 L31A

value: U1 dsRNA (2.5 ug/ml) and LL34 L31A


title: S09N_miRNA-seq


title: LL34 L31A

value: LL34 L31A


title: U1 + LL34 Parent

value: U1 dsRNA (2.5 ug/ml) and LL34 peptides Parent


title: LL34 I24A

value: LL34 I24A


title: C.elegans L4_BaP 5_rep3

description:
Raised on NGM for 48 hours (L1 to L4 stage) in the presence of 5 μM benzo[a]pyrene
5-C_S6

source_name: C.elegans L4_BaP 5_3


title: S02N_miRNA-seq


title: S41T_miRNA-seq

source_name: Thyroid tumor tissue

value: Classic

tag: gender

value: F


title: LL34 Parent

value: LL34 peptides Parent


title: U1 dsRNA

value: U1 dsRNA (2.5 ug/ml)


title: Control


title: S38T_miRNA-seq

value: Tall cell

value: M


title: S35T_miRNA-seq


title: S39T_miRNA-seq

value: NIFTP


title: S37T_miRNA-seq


title: S34T_miRNA-seq


title: S32T_miRNA-seq


title: S28T_miRNA-seq

value: EFV, invasive


title: Phase II melanoma NS16 ROI7 [NS16-07]

city: Seattle

first: Michelle

last: Kriner

state: WA

address: 500 Fairview Ave North

institute: NanoString Technologies

data_processing:
Library strategy: GeoMX-Seq
Adapter trimming with trim galore,  trimGaloreOpts = " --hardtrim5 26 --dont_gzip"
Merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27"
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1"
Genome_build: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini file
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: Summarized count files generated by parsing DCC files and merging with sample annotations. Count values are the geometric mean of the probes for a given target, after removing any probes flagged as outliers.
Supplementary_files_format_and_content: For Phase II (MK008), genes not detected in any AOIs were removed from the dataset, and the counts for each AOI were normalized to the upper quartile, yielding finalData file

source_name: FFPE skin biopsy

extract_protocol:
Following standard ISH protocols, samples were incubated with 1) DNA oligo-barcoded ISH probes containing a UV-photocleavable linker and 2) flourescently labeled antibodies for visualization of morphological structures. Areas of interest (AOI) 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 AOI 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. Concentration and purity of the resulting libraries was measured using a Bioanalyzer high-sensitivity DNA assay and Qubit high-sensitivity dsDNA kit.

tag: patient

tag: case class

value: melanoma

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

value: Immune

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other

tag: % tme

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase II melanoma NS16 ROI11 [NS16-11]

tag: patient

tag: case class

value: Keratinocyte/melanocyte


title: Phase II melanoma NS16 ROI6 [NS16-06]

tag: dsp replicate

tag: roi number


title: Phase II melanoma NS16 ROI10 [NS16-10]

tag: sequencing replicate

tag: roi diameter (um)


title: Phase II melanoma NS16 ROI12 [NS16-12]

tag: roi type

tag: % keratinocyte


title: S27T_miRNA-seq

tag: pathological type

tag: age

tag: gender


title: Phase II melanoma NS16 ROI8 [NS16-08]

tag: % melanocyte

tag: % immune cells

tag: % other

tag: % tme

tag: rawreads


title: Phase II melanoma NS16 ROI5 [NS16-05]

value: Immune/melanocyte

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: S25T_miRNA-seq


title: S23T_miRNA-seq


title: Phase II melanoma NS16 ROI3 [NS16-03]

tag: patient

tag: case class

tag: dsp replicate

tag: roi number

tag: sequencing replicate


title: Phase II melanoma NS16 ROI4 [NS16-04]

tag: roi diameter (um)

tag: roi type

tag: % keratinocyte


title: Phase II melanoma NS16 ROI2 [NS16-02]

value: Melanocyte

tag: % melanocyte

tag: % immune cells


title: S22T_miRNA-seq

tag: pathological type

tag: age

tag: gender


title: S40T_miRNA-seq


title: S20T_miRNA-seq


title: Phase II melanoma NS16 ROI9 [NS16-09]

tag: % other

tag: % tme

tag: rawreads

tag: trimmedreads

tag: stitchedreads


title: Phase II melanoma NS16 ROI1 [NS16-01]

tag: patient

tag: case class

value: Keratinocyte

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase II melanoma NS15 ROI12 [NS15-12]

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type


title: S15T_miRNA-seq

tag: pathological type

tag: age


title: Phase II melanoma NS15 ROI11 [NS15-11]

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other


title: S19T_miRNA-seq

tag: gender


title: S12T_miRNA-seq


title: S13T_miRNA-seq


title: S11T_miRNA-seq


title: S14T_miRNA-seq


title: Phase II melanoma NS15 ROI7 [NS15-07]

tag: patient

tag: % tme

tag: rawreads

tag: trimmedreads

tag: stitchedreads


title: Phase II melanoma NS15 ROI10 [NS15-10]

tag: case class

tag: dsp replicate

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase II melanoma NS15 ROI8 [NS15-08]

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type


title: S06T_miRNA-seq

tag: pathological type

tag: age


title: S10T_miRNA-seq

tag: gender


title: S07T_miRNA-seq


title: S09T_miRNA-seq


title: Phase II melanoma NS15 ROI6 [NS15-06]

tag: patient

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other


title: Phase II melanoma NS15 ROI5 [NS15-05]

tag: case class

tag: % tme

tag: rawreads

tag: trimmedreads

tag: stitchedreads


title: Phase II melanoma NS15 ROI4 [NS15-04]

tag: dsp replicate

tag: roi number

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: S03T_miRNA-seq

tag: pathological type

tag: age


title: Phase II melanoma NS15 ROI3 [NS15-03]

tag: patient

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type


title: Phase II melanoma NS15 ROI1 [NS15-01]

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other


title: Phase II melanoma NS14 ROI13 [NS14-13]

tag: case class

tag: % tme

tag: rawreads

tag: trimmedreads


title: Phase II melanoma NS14 ROI12 [NS14-12]

tag: dsp replicate

tag: roi number

tag: stitchedreads

tag: alignedreads


title: RNA-Seq PASMC Nutlin Replicate 2

city: Stanford

first: Jan

middle: K

last: Hennigs

state: California

address: 269 Campus Dr

department: Wall Center for Pulmonary Vascular Diseases, Cardiovascular Institute and Pediatrics - Cardiology

institute: Stanford University

data_processing:
Raw reads trimmed using FASTQ groomer.
Aligned to the human genome using BWA-aln
Quality control and read quantification using SeqMonk 1.46.0
Differentially expressed merged transcripts were quantified using DESeq2 (FDR < 0.05, Benjamini-Hochberg).
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes raw transcript counts from SeqMonk quantification

source_name: Lung

growth_protocol: PASMC were cultured in complete SMC media (SM basal medium supplemented with Insulin, hEGF, hFGF-B, 5% FBS and Gentamicin/Amphotericin (GA-1000), Lonza, Cologne, Germany).

extract_protocol:
After trypsinization, cells were collected by centrifugation and snap-frozen in liquid N2.  Total RNA was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany).
Opposing strand-specific RNA library preparation was performed with the NEBNext Ultra II RNA directional Kit (New England Biolabs, Hoechst, Germany) following standard Illumina protocols

treatment_protocol: PASMC  were kept in complete SmGM-2 media and treated  for 24 h with either Doxorubicin (0.5 µg/ml), Nutlin-3 (10 µM) or vehicle control before total RNA extraction.

tag: cell type

value: PASMC, healthy donor 2

tag: passages

tag: pharmacological treatment

value: Nutlin-3 (10 µM) for 24 h


title: RNA-Seq PASMC Nutlin Replicate 1

value: PASMC, healthy donor 1


title: Phase II melanoma NS14 ROI11 [NS14-11]

tag: patient

tag: sequencing replicate

tag: roi diameter (um)

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase II melanoma NS15 ROI9 [NS15-09]

tag: roi type

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other


title: RNA-Seq PASMC Vehicle Replicate 2

value: PBS (20 µL)/DMSO (10µL) for 24 h


title: Phase II melanoma NS14 ROI10 [NS14-10]

tag: case class

tag: dsp replicate

tag: % tme

tag: rawreads

tag: trimmedreads


title: RNA-Seq PASMC Vehicle Replicate 1

tag: cell type

tag: passages


title: RNA-Seq PASMC Dox Replicate 2

tag: pharmacological treatment

value: Doxorubicin (0.5 µg/ml) for 24 h


title: Phase II melanoma NS14 ROI8 [NS14-08]

tag: patient

tag: roi number

tag: sequencing replicate

tag: stitchedreads

tag: alignedreads


title: Phase II melanoma NS14 ROI7 [NS14-07]

tag: roi diameter (um)

tag: roi type

tag: % keratinocyte

tag: deduplicatedreads

tag: sequencingsaturation


title: RNA-Seq PAAF Nutlin Replicate 2

growth_protocol: PAAF were cultured in complete AF media (FM basal medium, 1%FGS , 2% FBS and 1x Penicillin/Streptomycin, ScienCell, Carlsbad, CA).

treatment_protocol: PAAF were kept in complete AF media and treated  for 24 h with either Doxorubicin (0.5 µg/ml), Nutlin-3 (10 µM) or vehicle control before total RNA extraction.

value: PAAF

tag: disease

value: healthy donor 2

value: Nutlin-3 (10 microM)

tag: time point


title: Phase II melanoma NS14 ROI6 [NS14-06]

tag: case class

tag: dsp replicate

tag: % melanocyte

tag: % immune cells

tag: % other

tag: % tme

tag: rawreads


title: Phase II melanoma NS14 ROI9 [NS14-09]

tag: patient

tag: roi number

tag: sequencing replicate

value: Mixed

tag: trimmedreads


title: RNA-Seq PAAF Nutlin Replicate 1

tag: cell type

value: healthy donor 1

tag: passages

tag: pharmacological treatment


title: RNA-Seq PAAF Vehicle Replicate 2

value: PBS (20 microL)/DMSO (10microL)


title: S04T_miRNA-seq

tag: pathological type

value: Classic

tag: age

tag: gender

value: F


title: RNA-Seq PAAF Vehicle Replicate 1

tag: disease

tag: time point


title: Phase II melanoma NS15 ROI2 [NS15-02]

tag: case class

value: melanoma

tag: dsp replicate

tag: roi diameter (um)

tag: roi type

tag: % keratinocyte

tag: % melanocyte

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase II melanoma NS14 ROI3 [NS14-03]

tag: patient

tag: roi number

tag: sequencing replicate

value: Immune

tag: % immune cells

tag: % other

tag: % tme

tag: rawreads

tag: trimmedreads


title: Phase II melanoma NS14 ROI4 [NS14-04]

tag: case class

tag: dsp replicate


title: Phase II melanoma NS14 ROI5 [NS14-05]

tag: roi diameter (um)

tag: roi type


title: S02T_miRNA-seq

tag: pathological type

value: EFV, invasive

tag: age

tag: gender

value: M


title: RNA-Seq PAAF Dox Replicate 2

tag: cell type

tag: disease

tag: passages

tag: pharmacological treatment

value: Doxorubicin (0.5 microg/ml)

tag: time point


title: RNA-Seq PAAF Dox Replicate 1


title: Phase II melanoma NS14 ROI2 [NS14-02]

tag: patient

tag: roi number

tag: sequencing replicate

value: Keratinocyte/melanocyte

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: SW_HD_CD8_EM

city: Birmingham

first: Paul

last: Moss

state: West Midlands

address: Vincent Drive

department: Immunology and Immunotherapy

institute: University of Birmingham

data_processing:
Sequenced reads were mapped to hg19 whole genome using STAR with default parameters and raw feature counts were generated using HTSeq with paramters HTSeq.scripts.count -f bam -r name -m union -s reverse
Genome_build: hg19
Supplementary_files_format_and_content: Counts matrix with raw counts for each feature in each sample

source_name: Peripheral Blood

extract_protocol:
Fresh peripheral blood T cells were cell sorted by flow cytometry into CD8 and CD4 Effector Memory populations and  RNA libraries were prepared using a TruSeq Stranded Total RNA Library preparation kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD8 Effector Memory T cell

tag: disease state

value: Healthy Donor


title: SM_HD_CD8_EM


title: Phase II melanoma in situ NS13 ROI13 [NS13-13]

tag: case class

value: melanoma in situ

tag: dsp replicate

tag: roi diameter (um)

tag: roi type

tag: % other

tag: % tme

tag: rawreads

tag: trimmedreads


title: Phase II melanoma in situ NS13 ROI11 [NS13-11]

tag: patient

tag: roi number

tag: sequencing replicate


title: KK_HD_CD8_EM

tag: cell type


title: VN_HD_CD8_EM


title: Phase II melanoma in situ NS13 ROI12 [NS13-12]

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: stitchedreads


title: RNA-Seq PASMC Dox Replicate 1

value: PASMC, healthy donor 1

tag: passages

tag: pharmacological treatment

value: Doxorubicin (0.5 µg/ml) for 24 h


title: SW_HD_CD4_EM

value: CD4 Effector Memory T cell

tag: disease state


title: SM_HD_CD4_EM


title: KK_HD_CD4_EM


title: Phase II melanoma in situ NS13 ROI9 [NS13-09]

tag: case class

tag: dsp replicate

tag: roi diameter (um)

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase II melanoma in situ NS13 ROI7 [NS13-07]

tag: patient

tag: roi type

tag: % other

tag: % tme

tag: rawreads

tag: trimmedreads


title: SJ_AUTO_CD8_EM

tag: cell type

value: Day 12 post autograft


title: Phase II melanoma in situ NS13 ROI8 [NS13-08]

tag: roi number

tag: sequencing replicate

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: stitchedreads


title: Phase II melanoma NS14 ROI1 [NS14-01]

tag: case class

tag: dsp replicate

tag: roi diameter (um)

value: Keratinocyte


title: Phase II melanoma in situ NS13 ROI4 [NS13-04]

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase II melanoma in situ NS13 ROI5 [NS13-05]

tag: patient

tag: roi type

tag: % other


title: JW_AUTO_CD8_EM

tag: disease state


title: SJ_AUTO_CD4_EM

tag: cell type


title: Phase II melanoma in situ NS13 ROI3 [NS13-03]

tag: roi number

tag: % tme

tag: rawreads

tag: trimmedreads


title: SH_AUTO_CD4_EM


title: SH_AUTO_CD8_EM


title: GB_AUTO_CD8_EM


title: Phase II melanoma in situ NS12 ROI14 [NS12-14]

tag: sequencing replicate

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells


title: Phase II melanoma in situ NS13 ROI14 [NS13-14]

tag: case class

tag: dsp replicate

tag: roi diameter (um)

tag: stitchedreads


title: Phase II melanoma in situ NS13 ROI2 [NS13-02]

tag: patient

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase II melanoma in situ NS13 ROI10 [NS13-10]

tag: roi type

tag: % other


title: JW_AUTO_CD4_EM

tag: cell type

tag: disease state


title: Phase II melanoma in situ NS12 ROI13 [NS12-13]

tag: roi number

value: Mixed

tag: % tme

tag: rawreads

tag: trimmedreads


title: Phase II melanoma in situ NS12 ROI12 [NS12-12]

tag: sequencing replicate

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells


title: Phase II melanoma in situ NS12 ROI11 [NS12-11]

tag: case class

tag: dsp replicate

tag: roi diameter (um)

tag: stitchedreads


title: VN_HD_CD4_EM


title: BJ BRAF-OIS YBX1-KD rep2

city: Copenhagen

first: Anders

middle: H.

last: Lund

address: Ole Maaløes Vej 5

department: Biotech Research & Innovation Centre (BRIC)

country: Denmark

institute: University of Copenhagen

data_processing:
Illumina Basespace GenerateFASTQ: 1.1.0.64
Raw reads were trimmed using Cutadapt to remove adapters and minimum read length after trimming was set to 18
Trimmed reads were mapped to hg38 using STAR aligner (version 2.5.1a)
Uniquely mapped reads were counted towards genes using featureCounts (version 1.5.1)
Differential expression analysis and read normalization were performed with DESeq2 using FDR < 0.01. Normalized reads are represented as normalized read output from DESeq2 and normalized by library depth as RPM
Genome_build: hg38
Supplementary_files_format_and_content: Excel file with RPM of all libraries

source_name: BJ hTERT fibroblast

extract_protocol:
QIAzol-chloroform-isopropanol extraction
RNA-seq libraries were prepared from 2 µg total RNA with CATS mRNA-seq Kit (with polyA selection) v2 x24 (Diagenode) according to the manufacturer’s protocol
The libraries were sequenced on Illumina NextSeq500 with 75 bp single-end

value: BJ hTERT fibroblast

tag: type

value: Oncogene-induced senescent

tag: genotype


title: BJ BRAF-OIS YBX1-KD rep3


title: Phase II melanoma in situ NS12 ROI10 [NS12-10]

tag: patient

tag: roi type

tag: % other

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: BJ BRAF-OIS MIR31HG-KD rep3

tag: cell type


title: Phase II melanoma in situ NS12 ROI9 [NS12-09]

tag: roi number

tag: sequencing replicate

tag: % tme

tag: rawreads

tag: trimmedreads


title: GB_AUTO_CD4_EM

tag: disease state


title: BJ BRAF-OIS MIR31HG-KD rep2


title: Phase II melanoma in situ NS12 ROI8 [NS12-08]

tag: case class

tag: dsp replicate

tag: roi diameter (um)

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells


title: Phase II melanoma in situ NS13 ROI6 [NS13-06]

tag: patient

tag: roi type

tag: % other

tag: stitchedreads


title: Phase II melanoma in situ NS13 ROI1 [NS13-01]

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: scRNA_IL17GFP_CD4_T_gut_KO_JJO218E1

source_name: ex vivo IL-17GFP+ CD4+ T cells

extract_protocol:
Target cells (CD4+ IL17GFP+) were isolated via FACS
Chromium Single Cell 3' Reagent Kits v2 (10x Genomics)

tag: strain

tag: tissue

value: intestine

tag: cell type

value: IL17GFP+CD4+ T cells

tag: genotype

tag: growth condition

tag: treatment


title: BJ BRAF-OIS rep2

tag: type

value: wild type


title: scRNA_IL17GFP_CD4_T_gut_WT_JJO218C1

value: Wild type


title: Phase II melanoma in situ NS12 ROI7 [NS12-07]

tag: case class

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: % keratinocyte

tag: % tme

tag: rawreads

tag: trimmedreads


title: Phase II melanoma in situ NS12 ROI6 [NS12-06]

tag: patient

tag: roi type

tag: % melanocyte

tag: % immune cells

tag: % other

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: BJ BRAF-OIS rep1

tag: cell type

tag: type

tag: genotype


title: Phase II melanoma in situ NS12 ROI5 [NS12-05]

tag: case class

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)


title: BJ BRAF-OIS YBX1-KD rep1


title: BJ control cells rep3

value: control


title: Phase II melanoma in situ NS12 ROI3 [NS12-03]

tag: patient

value: Immune

tag: % keratinocyte

tag: % tme

tag: rawreads

tag: trimmedreads


title: BJ control cells rep2


title: BJ control cells rep1


title: Phase II melanoma in situ NS12 ROI2 [NS12-02]

tag: roi type

value: Keratinocyte/melanocyte

tag: % melanocyte

tag: % immune cells

tag: % other

tag: stitchedreads


title: BJ BRAF-OIS MIR31HG-KD rep1

tag: cell type

tag: type


title: Phase II melanoma in situ NS12 ROI1 [NS12-01]

tag: case class

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase I melanoma ROI8 rep2.2 [NS4-B-8-2]

value: melanoma

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

value: keratinocyte/melanocyte

value: ND


title: Phase I melanoma ROI8 rep2.1 [NS4-B-8-1]

tag: patient

tag: % keratinocyte

tag: % tme

tag: rawreads


title: Phase I melanoma ROI5 rep2.2 [NS4-B-5-2]

tag: roi type

value: immune

tag: % melanocyte

tag: % immune cells

tag: trimmedreads


title: Phase I melanoma ROI7 rep2.1 [NS4-B-7-1]

tag: % other

tag: stitchedreads


title: Phase I melanoma ROI6 rep2.1 [NS4-B-6-1]

tag: case class

tag: alignedreads


title: Phase I melanoma ROI6 rep2.2 [NS4-B-6-2]

tag: deduplicatedreads

tag: sequencingsaturation


title: BJ BRAF-OIS rep3

tag: cell type

tag: type

tag: genotype


title: 40_ZIKV

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

institute: SAHMRI

description: isolation_time is the time from death to cell isolation.

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome with hisat v2.1.0 with default parameters.
Alignments to genes were counted with FeatureCounts and Ensembl 93 annotation.
Differential expression analysis and normalization were conducted with EdgeR.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.featureCounts.txt: Tab-delimited text files include raw read counts from FeatureCounts.

source_name: Human iris pigment epithelial cell

growth_protocol: Iris pigment epithelial cells were isolated from human cadaveric donor eyes using enzymatic digestion of tissue, followed by culture in Epithelial Cell Medium (ScienCell Research Laboratories) supplemented with 2% FBS and 100 U/ml penicillin-100 μg/ml streptomycin.

extract_protocol:
Total RNA was extracted using Thermo Fisher Scientific TRIzol Reagent, following the manufacturer’s instructions.
The library was constructed using the Illumina TruSeq Stranded Total RNA Sample Preparation kit, following the manufacturer’s instructions.

treatment_protocol: Cells were infected with Zika virus (PRVABC59 strain, MOI 5) or mock-infected for 90 minutes and held for a total of 24 hours before RNA extraction.

tag: age

value: 62 yr

value: Iris pigment epithelial cell

tag: treatment

value: Zika virus infection

tag: donor

tag: batch


title: Phase I melanoma ROI7 rep2.2 [NS4-B-7-2]

tag: patient

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

tag: % keratinocyte

tag: % tme

tag: rawreads


title: Phase I melanoma ROI9 rep2.1 [NS4-B-9-1]

tag: case class

tag: % melanocyte

tag: % immune cells

tag: % other

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase II melanoma in situ NS11 ROI10 [NS11-10]

tag: patient

value: melanoma in situ

tag: dsp replicate


title: Phase II melanoma in situ NS11 ROI9 [NS11-09]

tag: roi number

tag: sequencing replicate


title: 38_ZIKV

tag: age

value: 52 yr

tag: cell type

tag: treatment

tag: donor

tag: batch


title: Phase I melanoma ROI4 rep2.1 [NS4-B-4-1]

tag: case class

tag: roi diameter (um)

tag: roi type

value: control (keratinocyte)

tag: % keratinocyte

tag: % melanocyte

tag: % tme

tag: rawreads


title: 39_UI

value: Mock infection


title: Phase II melanoma in situ NS11 ROI8 [NS11-08]

tag: % immune cells

tag: % other

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase I melanoma ROI2 rep2.2 [NS4-B-2-2]

tag: patient

tag: dsp replicate

tag: roi number

tag: sequencing replicate


title: Phase I melanoma ROI9 rep2.2 [NS4-B-9-2]

tag: case class

tag: roi diameter (um)


title: Phase I melanoma ROI4 rep2.2 [NS4-B-4-2]

tag: roi type

tag: % keratinocyte


title: Phase II melanoma in situ NS12 ROI4 [NS12-04]

tag: % melanocyte

tag: % tme


title: Phase I melanoma ROI3 rep2.2 [NS4-B-3-2]

tag: % immune cells

tag: rawreads


title: Phase I melanoma ROI3 rep2.1 [NS4-B-3-1]

tag: % other

tag: trimmedreads


title: 37_UI

tag: age

tag: cell type

tag: treatment

tag: donor

tag: batch


title: 36_ZIKV

value: 61 yr


title: Phase I melanoma ROI17 rep2.2 [NS4-B-17-2]

tag: patient

tag: dsp replicate

tag: roi number

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase I melanoma ROI17 rep2.1 [NS4-B-17-1]

tag: case class

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

tag: % keratinocyte

tag: % melanocyte

tag: % tme


title: Phase II melanoma in situ NS11 ROI7 [NS11-07]

tag: % immune cells

tag: % other

tag: rawreads

tag: trimmedreads


title: Phase I melanoma ROI16 rep2.2 [NS4-B-16-2]

tag: patient

tag: dsp replicate

value: melanocyte


title: Phase I melanoma ROI16 rep2.1 [NS4-B-16-1]

tag: roi number

tag: stitchedreads


title: Phase II melanoma in situ NS11 ROI6 [NS11-06]

tag: alignedreads

tag: deduplicatedreads


title: Phase I melanoma ROI5 rep2.1 [NS4-B-5-1]

tag: case class

tag: sequencingsaturation


title: 34_ZIKV

tag: age

value: 53 yr

tag: cell type

tag: treatment

tag: donor

tag: batch


title: Phase I melanoma ROI15 rep2.1 [NS4-B-15-1]

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % tme


title: Phase II melanoma in situ NS11 ROI4 [NS11-04]

tag: patient

tag: dsp replicate

tag: roi number

value: Mixed

tag: % other

tag: rawreads

tag: trimmedreads

tag: stitchedreads


title: Phase I melanoma ROI15 rep2.2 [NS4-B-15-2]

tag: case class

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase I melanoma ROI14 rep2.2 [NS4-B-14-2]

tag: sequencing replicate

tag: roi diameter (um)


title: 33_UI

tag: age

tag: cell type

tag: treatment

tag: donor

tag: batch