title: dmel head, young, ZT20, rep2

description:
20
adjCountsTable_youngRep2.txt
adjRPMMirReads_youngRep2.txt
adjCountsTable_piRNA_youngRep2.txt
adjRPMtable_piRNA_youngRep2.txt


title: IMR32_parental_rep2

status: Public on Aug 31 2022

type: SRA

city: Cambridge

first: Sarah

last: Gillen

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

country: United Kingdom

institute: Wellcome - MRC Cambridge Stem Cell Institute

description:
IMR32_ATAC_DiffBind.txt
IMR32_control_RPGC_mean.bw

library_source: genomic

data_processing:
TrimGalore 0.6.4 for adapter and quality trimming
Bowtie2 2.4.1 alignment to hg19 genome
Peaks called with MACS2 2.2.7.1 narrowPeak mode
Differential Peaks were determined using DiffBind v2.14.0 with default parameters and summits=200
bigWig files were generated by deeptools with RPGC normalisation and mean of the replicates generated with wiggletools
Assembly: hg19
Supplementary files format and content: narrowPeak files generated from MACS2
Supplementary files format and content: bigwig files are normalised RPGC per sample and the mean average of the 4 replicates
Supplementary files format and content: tables include differential binding outputs from DiffBind for ASCL1 knockout lines compared to parental

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: IMR32 and SHSY5Y were cultured in DMEM-F12 with GlutaMAX (Gibco) supplemented with 10% FBS (Sigma) and 1% Penicillin-Streptomycin (Sigma).

extract_protocol:
Cells were lysed using RLT buffer and RNA extracted following the RNeasy Protocol Part I (Qiagen)
libraries were prepared following the exact protocol in Corces et al, Nature Methods 2017, 50bp paired end sequencing

tag: cell type

value: neuroblastoma cell line

tag: cell line

tag: genotype

value: parental


title: IMR32_parental_rep1


title: eIF2A_0h_rep3

city: Vancouver

first: Howard

last: Cen

state: BC

address: 2350 Health Sciences Mall

country: Canada

institute: University of British Columbia

library_source: transcriptomic

data_processing:
Basecalls were made using RTA v2.1.
Demultiplexing was achieved using bcl2fastq2.
Alignment was performed using STAR.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes raw counts for each gene.

molecule: polyA RNA

organism: Mus musculus

source_name: MIN6 cells

growth_protocol: MIN6 cells were cultured in Dulbecco’s modified eagle’s medium (Thermo Fisher Scientific) containing 22.2 mM glucose, 100 units/ml penicillin, 100 mg/ml streptomycin and 10% (v/v) FBS.

extract_protocol:
RNA was isolated from cell or islet samples using RNeasy mini kit (Qiagen, #74106) according to manufacturer’s instructions.
tru seq stranded mRNA

treatment_protocol: MIN6 cells were treated with 1 μM thapsigargin for 1 (1h) or 3 (3h) hours or with DMSO vehicle control (0h) in cell culture media

value: MIN6 cells

tag: overexpression

tag: treatment

tag: time


title: eIF2A_0h_rep4


title: eIF2A_1h_rep1

value: thapsigargin


title: dmel head, young, ZT12, rep2

city: Corvallis

first: Rosalyn

middle: M.

last: Fey

state: OR

address: 1500 SW Jefferson Way

country: USA

institute: Oregon State University

description:
12
adjCountsTable_youngRep2.txt
adjRPMMirReads_youngRep2.txt
adjCountsTable_piRNA_youngRep2.txt
adjRPMtable_piRNA_youngRep2.txt

data_processing:
Reads were quality filtered and sequencing adapters were trimmed using skewer, with parameters set for a minimum quality score of 30 and a minimum read length of 18, using the adapter sequence “TGGAATTCTCGGGTGCCAAGG”.
Reads were aligned to the Drosophila melanogaster genome (BDGP release 6.21/dm6) with Bowtie using the parameters “-l 18 –n 1 -e 50 -a -m 50 -S --best --strata”.
The number of hits to the genome for each read was included by adding NH tags to the output SAM files.
We used a custom Python script to quantify reads by mapping to the miRBase version 22 genome annotation file (release 6). We adjusted reads to account for paralogous microRNAs (which map to multiple places in the genome) by dividing each count by the number of hits to the genome, stored in the NH tags in the SAM file for each sample. Final quantification is in adjusted Reads per Million Mapped MicroRNAs (aRPMMM). We used similar custom Python scripts to quantify reads mapping to piRNAs.
Assembly: dm6.21
Supplementary files format and content: adjCounts tables are replicate-specific tab-delimited text files containing raw counts for each microRNA for each ZT, which have been adjusted to account for paralogous microRNAs.
Supplementary files format and content: adjRPMMirReads tables are replicate-specific tab-delimited text files containing normalized counts for each microRNA in each ZT
Supplementary files format and content: adjCounts_piRNA tables are replicate-specific tab-delimited text files containing raw counts for each piRNA cluster for each ZT, which have been adjusted to account for paralogous clusters
Supplementary files format and content: adjRPM_piRNA tables are replicate-specific tab-delimited text files containing normalized counts for each piRNA cluster in each ZT

molecule: total RNA

organism: Drosophila melanogaster

source_name: whole heads

extract_protocol:
Each sample of 400 heads was homogenized in TRIzol (Thermo Fisher) with a Kontes handheld motorized pestle following the manufacturer’s instructions. Samples were treated with rDNAse I (Takara) followed by phenol/chloroform extraction. RNA was precipitated with ethanol and sodium acetate.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Library Prep Kit following manufacturer's protocols, with the addition of a DNA block oligo with sequence complimentarity to the Drosophila 30-nt 2S rRNA fragment.

tag: tissue

value: whole heads

tag: Sex

value: female

tag: condition

value: young (5 day)

value: ZT 12


title: E13.5 neocortex, Input, biol rep2

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Clean Data was mapped to the reference genome using STAR v2.7.9a.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by RSEM v1.3.3, and FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) was then calculated to estimate the expression level of genes in each sample.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: Forebrain

extract_protocol:
Mouse E13.5 cerebral cortices were dissected and enzymatically dissociated to a single-cell suspension. Cortical cells were washed in ice-cold DPBS and lysed in RIP lysis buffer A (10mM Tris pH7.4, 140mM NaCl, 1.5mM MgCl2, 0.5% NP-40, 1mM dithiothreitol, SUPERaseIn RNase inhibitor, proteinase inhibitor cocktail). Lysates were incubated on ice for 5 minutes, and then centrifuged 3 minutes at 4℃ and 1000g. The supernatant was collected as cytoplasmic fractions and used as input or for RIP with anti-eIF4E antibody or control immunoglobulin G (rabbit) incubating for 2 hours at 4℃ with gentle rotation. Then washing off unbound material from magnetic beads for 4 times. Isolate coprecipitated RNAs were extracted using TRIzol reagent (Invitrogen) and processed according to the manufacturer’s instruction.
cDNA libraries from pulled-down RNA and input RNA were prepared using standard Smart-seq2 protocols for Illumina novaseq 6000.

value: Forebrain

tag: rip antibody

value: Input

tag: age

value: Wild type


title: eIF2A_0h_rep2


title: N5

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
fastQ quality assessment
cutadapt adater trimming
bowtie1 genome alignment
miRDeep2 miRNA quantification
edgeR differential expression
Assembly: Homo sapiens (GRCh38.p12)
Supplementary files format and content: CSV with miRNA quantifications (raw and rpm)

source_name: Fibroblasts

growth_protocol: Joint tissue was collected peri-operatively from consenting OA patients following elective total joint replacement under ethical approval granted by UK National Research Ethics Committee (NRES 16/SS/0172). Isolated primary synovial fibroblasts were cultured in RMPI 1640 supplemented with 10% FSC, 5% non-essential amino acids, 5% L-glutamine, 5% sodium pyruvate and 1% penicillin/ streptomycin (Sigma Aldrich)(36-38). Once cells were 75% confluent, fibroblasts were seeded into T175 flasks at 2 x 10^6 cells per flask.

extract_protocol:
RNA extraction using Qiagen miRNAeasy kit
Trilink Cleantag Kit

treatment_protocol: Synovial fibroblasts were exposed  to 10gy of gamma irradiation to induce senescene. Irradiated and non-irradiated control cells were cultured for 18 days with media replenished every 3-4 days. After 18 days, media was changed to serum and phenol red free media for 72 hours upon which conditioned media was collected from which EVs were isolated by size exclusion chromatography.

tag: source

value: synovium

tag: group

value: control

value: non-irradiated


title: N7

value: senescence

value: irradiated


title: E13.5 neocortex, Input, biol rep1


title: dmel head, young, ZT8, rep2

description:
8
adjCountsTable_youngRep2.txt
adjRPMMirReads_youngRep2.txt
adjCountsTable_piRNA_youngRep2.txt
adjRPMtable_piRNA_youngRep2.txt

value: ZT 8


title: E13.5 neocortex, EIF4E, biol rep2

value: EIF4E (MBL, #RN001P)


title: N4


title: dmel head, young, ZT4, rep2

description:
4
adjCountsTable_youngRep2.txt
adjRPMMirReads_youngRep2.txt
adjCountsTable_piRNA_youngRep2.txt
adjRPMtable_piRNA_youngRep2.txt

value: ZT 4


title: eIF2A_1h_rep3

value: MIN6 cells


title: N6


title: E13.5 neocortex, EIF4E, biol rep1


title: eIF2A_0h_rep1


title: dmel head, young, ZT0, rep2

description:
0
adjCountsTable_youngRep2.txt
adjRPMMirReads_youngRep2.txt
adjCountsTable_piRNA_youngRep2.txt
adjRPMtable_piRNA_youngRep2.txt

value: ZT 0


title: N3


title: control_3h_rep3

value: GFP

value: thapsigargin


title: dmel head, young, ZT20, rep1

description:
20
adjCountsTable_youngRep1.txt
adjRPMMirReads_youngRep1.txt
adjCountsTable_piRNA_youngRep1.txt
adjRPMtable_piRNA_youngRep1.txt

value: whole heads

value: female

value: young (5 day)

value: ZT 20


title: dmel head, young, ZT16, rep2

description:
16
adjCountsTable_youngRep2.txt
adjRPMMirReads_youngRep2.txt
adjCountsTable_piRNA_youngRep2.txt
adjRPMtable_piRNA_youngRep2.txt

value: ZT 16


title: N2

value: synovium


title: eIF2A_1h_rep4


title: dmel head, young, ZT16, rep1

description:
16
adjCountsTable_youngRep1.txt
adjRPMMirReads_youngRep1.txt
adjCountsTable_piRNA_youngRep1.txt
adjRPMtable_piRNA_youngRep1.txt


title: control_3h_rep1


title: NPCs, polysome mRNA, Torin1, biol rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Clean Data was mapped to the reference genome using STAR v2.7.9a.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) was then calculated to estimate the expression level of genes in each sample.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: primary neural progenitor cells

extract_protocol:
Mouse cerebral cortices at E13.5 were dissected and enzymatically dissociated using Accutase (Thermo Fisher) with DNase I (Roche), and triturated using a Pasteur pipette to create a single-cell suspension. Cortical cells were cultured in medium containing DMEM/F12 (Gibico, Cat#11330-032), GlutaMax supplement (Gibico, Cat#35050061), Penicillin/Streptomycin (1x Thermo Fisher, Cat#15070063), B-27 supplement (1x, Thermo Fisher, Cat#12587010), bFGF (5ng/ml, Thermo Fisher, Cat#13256029), EGF (5ng/ml, Thermo Fisher, Cat# PHG0311). The cultures maintained in a humidified incubator at 37℃ with constant 5% CO2 supply. The next day, cells were treated with Torin 1 (250nM, Selleck, Cat#S2827) or DMSO (Sigma, Cat#D2650) for 2 hours, and subsequently with cycloheximide (100ug/ml) for 5 minutes. Cells were then washed in ice-cold DPBS plus cycloheximide (100ug/ml) for 2 times, and then lysed in polysome lysis buffer (20mM Tris 7.5,100mM NaCl,5mM MgCl2, 1% Triton X-100, 0.5% sodium deoxycholate, 1mM dithiothreitol, 100ug/ml cycloheximide, SUPERaseIn RNase inhibitor, proteinase inhibitor cocktail). Lysates were kept 10% as input, and the rest layered onto the 10.5 ml sucrose density gradients which prepared in advance and composed of 1.85 ml 50%, 3.65 ml 35%, 3.65 ml 20% and 1.35 ml 20% sucrose density gradients (20mM Tris-HCl ph7.5, 100mM NaCl, 5mM MgCl2, SUPERaseIn, proteinase inhibitor cocktail). To improve the quality of polysome preparations, after pouring each layer, keep the tubes in -80℃ freezer until complete freezing before adding the next sucrose layer, and then let the gradients thaw out in a fridge. Gradients were centrifuged at 36,000 rpm for 2 hours at 4℃ using SW41Ti rotor with “low” brake option. Fractions corresponding to mRNA associated with >3 ribosomes were collected. RNA was extracted with TRIzol reagent.
cDNA libraries were prepared for sequencing using standard Illumina protocols

value: primary neural progenitor cells

value: Wild type

tag: fraction

value: Polysome mRNA


title: dmel head, young, ZT12, rep1

description:
12
adjCountsTable_youngRep1.txt
adjRPMMirReads_youngRep1.txt
adjCountsTable_piRNA_youngRep1.txt
adjRPMtable_piRNA_youngRep1.txt

value: ZT 12


title: dmel head, young, ZT8, rep1

description:
8
adjCountsTable_youngRep1.txt
adjRPMMirReads_youngRep1.txt
adjCountsTable_piRNA_youngRep1.txt
adjRPMtable_piRNA_youngRep1.txt

value: ZT 8


title: control_3h_rep4


title: control_1h_rep3


title: control_1h_rep4


title: control_3h_rep2


title: NPCs, polysome mRNA, Torin1, biol rep1


title: dmel head, young, ZT0, rep1

description:
0
adjCountsTable_youngRep1.txt
adjRPMMirReads_youngRep1.txt
adjCountsTable_piRNA_youngRep1.txt
adjRPMtable_piRNA_youngRep1.txt


title: dmel head, young, ZT4, rep1

description:
4
adjCountsTable_youngRep1.txt
adjRPMMirReads_youngRep1.txt
adjCountsTable_piRNA_youngRep1.txt
adjRPMtable_piRNA_youngRep1.txt


title: control_1h_rep1


title: NPCs, polysome mRNA, DMSO, biol rep3

value: DMSO


title: NPCs, total mRNA, Torin1, biol rep3

value: Total mRNA


title: NPCs, polysome mRNA, DMSO, biol rep2


title: control_1h_rep2

value: MIN6 cells


title: control_0h_rep4


title: NPCs, polysome mRNA, Torin1, biol rep3


title: control_0h_rep2


title: NPCs, total mRNA, Torin1, biol rep2


title: control_0h_rep3


title: 6months Control_rep4

type: RNA

city: Dunedin

first: Paulomi

middle: M

last: Mehta

state: Otago

address: 56 Hanover street

department: Department of Pathology

country: New Zealand

institute: University of Otago

data_processing: Raw RCC file  generated by the Nanostring nCounter GEN2 Digital Analyzer and normalized using NanoStriDE

organism: Rattus norvegicus

source_name: Kidney cortex

extract_protocol: Kidney were removed, flash frozen with RNA later (cat#AM7021) and RNA was extracted using Trizol reagent and PureLink RNA mini kit (cat#12183018A) . Illumina TruSeq Stranded mRNA IDT for Illumina Unique Dual Indexing (cat#20020591) was used with 500ng/ul of total RNA for sequencing and Nanostring nCounter quantification ( only 6 months data).

treatment_protocol: Rats treated with lithium (60 mM Lithium carbonate in chow food), lithium+amiloirde (0.2 mM amiloirde in drinking water) or control (chow food) for 14 days, 28 days and 6 months.

value: Kidney cortex

value: Control


title: 6months Control_rep3


title: 6months Control_rep2


title: NPCs, polysome mRNA, DMSO, biol rep1


title: NPCs, total mRNA, DMSO, biol rep3


title: tls1 Rep3

first: Michaela

middle: Sylvia

last: Matthes

state: Bonn

address: Friedrich Ebert Allee 144

department: INRES-Crop Functional Genomics

country: Germany

institute: University of Bonn

data_processing:
software for base calling
Sequenced reads were trimmed for adaptor sequences using cutadapt. Genome and annotation files for maize genome v4, downloaded from Ensemble Plants (https://plants.ensembl.org/Zea_mays/Info/Index) were used to create a genome index using STAR (Dobin et al., 2013) with the option -runmode genomeGenerate. Trimmed sequence reads were mapped to the maize B73 genome (v4) also using STAR (Dobin et al., 2013). For gene counts STAR (Dobin et al., 2013) was used with the option quantMode genecounts.
Genome_build: maize B73 genome (v4)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Zea mays

source_name: tassel meristems_tls1

growth_protocol: Greenhouse experiments were done in the Sears Plant Growth Facility on the University of Missouri Campus, equipped with 1000 watt HPS lamps. Plants were grown under long day conditions (16 hours of light and 8 hours of dark) with an average day temperature of 87º F, an average night temperature of 77º F, and average humidity of 40% (day) and 60% (night). Plants were fertilized with Peters General Purpose 20-20-20 fertilizer (ICL specialty fertilizers, Tel-Aviv, Israel) with every watering, where the strength was adjusted to 238 ppm nitrogen, which corresponds to a boron content of 0.08 ppm (Matthes et al., 2018). Plants were grown to V6-V7 stage, when tassel meristems were 1mm.

extract_protocol:
1 mm tassel meristems of B73 and the boron deficient tassel-less1 (tls1) mutant of maize were dissected, flash frozen in liquid nitrogen, RNA isolated with the Macherey & Nagel Plant RNA extraction kit (). Librabries for RNA sequencing were constructed using a poly-A enrichment method and samples were sequenced on a NovaSeq 6000 (NovaSeq S1 PE100 flow cell) to an average read count of 50 million paired reads per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: tassel-less1 (tls1) mutant

tag: developmental stage

value: tassel meristem


title: NPCs, total mRNA, DMSO, biol rep2


title: HS-5, NOMO KO-2

city: Salamanca

first: Rogelio

last: González-Sarmiento

state: Salamanca

address: Alfonso X el Sabio, sn

department: Medicine

country: Spain

institute: University of Salamanca

data_processing:
trimming:  Adapter sequences and low-quality bases were trimmed using Trimmomatic (v.0.39)
alignment:  Reads were mapped to GRCh37 human reference genome from Ensembl with the STAR aligner (v.2.7.9a)
counting:  Gene level counts were calculated using the union mode from the HTSeq package (v.0.12.4)
normalization:  Gene expression count normalization through the median of ratios method using the DESeq2 R package (v.1.30.1)
Assembly: Ensembl GRCh37 human genome
Supplementary files format and content: Tab-delimited txt files with raw count values for each sample

source_name: stromal cell line HS-5

growth_protocol: The colon cancer cell line HCT-116 and the human stromal cell line HS-5 were acquired from ATCC (American Type Culture Collection). The cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich) supplemented with 10% of fetal bovine serum (FBS) (Sigma-Aldrich) and 1% penicillin/streptomycin (Gibco Life Technologies, Grand Island, NY). All cells were incubated at 37°C in a 5% CO2. The presence of mycoplasma was routinely checked with MycoAlert kit (Lonza, Basel, Switzerland) and only mycoplasma free cells were used in all subsequent experiments.

extract_protocol:
Total RNA was extracted from three NOMO-KO clones and three control clones for HCT-116 and HS-5 using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. DNA was removed from the samples using RNase-free DNase Set (Qiagen, Hilden, Germany). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).
0.5 µg of total RNA was used to construct cDNA libraries with TruSeq stranded total RNA with Ribo-Zero kit (Illumina, San Diego, CA, USA). cDNA libraries were sequenced with NovaSeq600 (paired-end 150bp x 2) with a range of 61.8-78.7M reads/sample according to the manufacturer instructions. Library construction and sequencing were performed by Macrogen Inc. (Macrogen, Seoul, Korea). Adapter sequences and low-quality bases were trimmed using Trimmomatic (v.0.39). Raw and trimmed reads quality was assessed with the FASTQC tool (v.0.11.9). The surviving paired reads after trimming were mapped to hg19 human genome with the STAR aligner (v.2.7.9a). The reference genome sequence (hg19, Genome Reference Consortium GRCh37) and annotation data (v.87) were downloaded from the Ensembl website (https://www.ensembl.org/). Gene level counts were calculated using the union mode from the HTSeq package (v.0.12.4). Gene expression count normalization through the median of ratios method(26) and differential gene expression analyses were performed with the DESeq2 R package (v.1.30.1). Batch-effects were adjusted through the ComBat_seq function from the sva R package (v.3.38.0).

treatment_protocol: CRISPR/cas9 technology was used to deleted endogenous NOMO1.

value: Bone marrow

value: Non tumoral

value: NOMO KO


title: WT Rep 3

source_name: tassel meristems_WT

value: WT

value: V6-V7 stage, when tassel meristems were 1mm


title: NPCs, total mRNA, DMSO, biol rep1

value: primary neural progenitor cells


title: 6months Lithium+Amiloride_rep4

value: Lithium+Amiloride


title: HS-5, PX458-3

value: NOMO WT


title: HS-5, NOMO KO-1


title: 6months Control_rep1


title: NPCs, total mRNA, Torin1, biol rep1

value: Wild type


title: HS-5, PX458-2


title: 6months Lithium+Amiloride_rep3


title: 6months Lithium+Amiloride_rep2


title: 6months Lithium+Amiloride_rep1


title: tls1 Rep 1


title: E13.5 neocortex, IgG

description: IgG

value: Forebrain

value: IgG (Bioss, #bs0295P)


title: HS-5, WT


title: control_0h_rep1

value: GFP


title: HS-5, NOMO KO-3


title: 6months Lithium_rep3

value: Lithium


title: WT Rep 1


title: 6months Lithium_rep4

value: Kidney cortex


title: HCT-116, NOMO KO-2

source_name: colorectal cancer cell line HCT-116

value: Colon

value: Tumoral


title: 6months Lithium_rep2


title: DH82Ondpi_S_d3_2

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

institute: University Münster

data_processing:
Reads were quality checked with package FastQC (version 0.11.4,), then trimmed using Trimgalore (version 0.4.4) with default settings.
Trimmed reads were mapped to Canis_lupus_familiaris genome using STAR aligner (Dobin and Gingeras, 2015) with default settings.
Mapped reads were counted using RsubRead (version 1.32.4, (Liao et al., 2019)). Raw counts were then normalized using DESeq2 (version 1.16.1, (Love et al., 2014)).
Genome_build: ENSEMBL release-100/Canis_lupus_familiaris.CanFam3.1.dna and CDV genome sequence (proprietry sequence, 99% identity to published GenBank Accession Number AF378705.1).
Supplementary_files_format_and_content: txt matrix with log2 normalized values per sample.

organism: Canis lupus familiaris

growth_protocol: DH82 cells were obtained from the European Collection of Authenticated Cell Cultures (ECACC).

extract_protocol:
Cells were harvested 1 d and 3 days after treatment and frozen at a density of 3*106 cells / aliquot. RNA isolation was performed directly out of cryopreserved cells. Cells were isolated using TRIzol® (Invitrogen / ThermoFisher, Langenselbold, Germany)  according to manufacturer’s instructions. After isolation RNA was cleaned up using RNeasy Mini-Kits (Qiagen, Hilden, Germany) with on column DNase treatment (RNase free DNase, Qiagen).
100ng total RNA was used for preparation of RNA Sequencing library with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (New England Biolabs).
The libraries were sequenced on Illumina NovaSeq 6000 using NovaSeq 6000 S1 Reagent Kit (300 cycles, paired end run 2x 150 bp) with an average of 6 x10E7 reads per RNA sample

treatment_protocol: DH82 cells persistently infected with canine distemper virus strain Onderstepoort (DH82Ondpi) were seeded at a density of 0.33*106 cells / T25 flask. Cells were cultured at normoxia, 5% CO2, 37°C, humidified atmosphere, in minimal essential medium (MEM) with Earle’s salts (PAA, Cölbe, Germany) supplemented with 10% fetal calf serum (PAA) , 1% penicillin/streptomycin (PAA) and 1% non-essential amino acids (Sigma-Aldrich, Taufkirchen, Germany).  3 days after seeding a medium change with the aforementioned medium was performed. 6 days after seeding the medium was changed according to the planned culture conditions. Control cultures received the aforementioned medium again and were cultured at 37°C, normoxia, 5% CO2, in a humidified atmosphere as described above. For hypoxic conditions, cells received the aforementioned medium again and were cultured at 37°C, 1% O2, 5% CO2, in a humidified atmosphere. For starvation conditions, cells received the aforementioned medium without fetal calf serum and were cultured at 37°C, normoxia, 5% CO2, in a humidified atmosphere.

tag: infection

tag: stress

value: starvation

value: day 3


title: DH82Ondpi_S_d3_3

tag: cell line

value: canine distemper virus strain Onderstepoort


title: eIF2A_3h_rep2

value: MIN6 cells

value: thapsigargin


title: WT Rep 2

tag: genotype

value: WT

value: V6-V7 stage, when tassel meristems were 1mm

value: tassel meristem


title: tls1 Rep2

value: tassel-less1 (tls1) mutant


title: 6months Lithium_rep1


title: CC_10_R

city: Livermore

first: Stephen

middle: Patrick

last: Wilson

state: CA

address: 7000 East Ave

department: BBTD

institute: LLNL

data_processing:
Sequence reads were aligned against rat reference genome (rn6) using STAR.  After read alignment, the number of read counts per gene locus was summarized with ‘featureCounts’ from Rsubread package. Read counts were subsequently normalized using TMM normalization from edgeR. RUVseq was then used to identify factors of unwanted variation. Differential expression analysis was performed using edgeR.
Assembly: rn6
Supplementary files format and content: CSV file with CPM values for each Sample .

organism: Rattus

source_name: Primary rat co-cultures containing cortical neurons, astrocytes, and oligodendrocyte-lineage cell

extract_protocol:
Primary cultures treated and untreated with fentanyl for 4 days were lysed with RLT buffer containing beta-mercaptoethanol, and the supernatant collected. Total RNA was extracted and purified from the collected supernatant using the RNAeasy mini spin columns (Qiagen).
Poly(A)+-enriched cDNA libraries were generated using the Illumina TruSeq RNA Library Prep kit v2 (Illumina Inc., Hayward, CA, USA).

treatment_protocol: Complex primary rat cultures containing cortical neurons (Lonza, Walkersville, MD), astrocytes (Lonza), and oligodendrocyte precursor cells (ScienCell, Carlsbad, CA) were treated without or with a high or low dose of fentanyl (Henry Schein, Melville, NY) for 4 days.

tag: strain

value: Sprague Dawley

tag: agent

value: 10 microM fentanyl


title: HCT-116, NOMO KO-3

tag: cell type

value: NOMO KO


title: DH82Ondpi_S_d3_1

tag: time


title: CC_10_I


title: CC_10_O


title: HCT-116, PX458-1

tag: tissue

value: NOMO WT


title: HCT-116, WT


title: DH82Ondpi_S_d1_3

value: day 1


title: CC_01_H

value: 0.01 microM fentanyl


title: Hulu_fluB_9

data_processing:
Reads were quality checked with package FastQC (version 0.11.4,), then trimmed using Trimgalore (version 0.4.4) with default settings.
Trimmed reads were mapped to human genome ENSEMBL hg38 release 91  and to Influenza B virus genome, using STAR aligner (Dobin and Gingeras, 2015) with default settings.
Mapped reads were counted using RsubRead (version 1.32.4, (Liao et al., 2019)).
Human and virus raw reads were combined before normalization.
Raw counts were then normalized using DESeq2 (version 1.16.1, (Love et al., 2014)) and batch corrected for donor using LIMMA (version 3.42.2).
Genome_build: ENSMBL human hg38 release 100
Supplementary_files_format_and_content: txt matrix with log2 normalized values per sample.

source_name: lung

extract_protocol:
Tissue blocks were transferred to Lysing Matrix A tubes (MP Biomedicals, Germany) in 600 µl RLT buffer supplemented with 1% β-Mercapthoethanol (Sigma, Germany). Tissue was lysed using FastPrep®-24 (MP Biomedicals, Germany) applying six rounds of tissue lysis at default settings (4 m/s, 20 s). Homogenates were centrifuged for 5 min full speed at 4°C and RNA was purified from the supernatant.
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). PolyA+RNA were purified  from 1µg total RNA using Dynabeads mRNA DIRECT Micro Kit (ThermoFisher). The RNA Sequencing library was prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs).
The libraries were sequenced on Illumina NovaSeq 6000 using NovaSeq 6000 S1 Reagent Kit (300 cycles, paired end run 2x 111 Nu) with an average of 6.4 x10E7 reads per RNA sample.

treatment_protocol: Methods: Tumor-free human lung explants were obtained from patients undergoing lung surgery at the University Hospital Muenster on the day of surgery. Tissue blocks were individually placed in a 12-well plate in RPMI medium. Tiussues were treated with infected with influenza B virus.

value: influenza B

value: Lung

tag: treatment


title: DH82Ondpi_S_d1_2

value: starvation


title: HCT-116, NOMO KO-1

value: Colon

value: Tumoral


title: CC_10_C


title: HCT-116, PX458-2


title: DH82Ondpi_K_d3_1

value: canine distemper virus strain Onderstepoort

value: controls

value: day 3


title: CC_01_Q


title: DH82Ondpi_K_d3_3


title: Hulu_fluB_7


title: CC_01_N


title: DH82Ondpi_K_d3_2


title: CC_01_B


title: DH82Ondpi_K_d1_3


title: Hulu_fluB_5

value: mock


title: Hulu_fluB_4


title: DH82Ondpi_S_d1_1


title: CC_0_P

value: Untreated


title: CC_0_M


title: Hulu_fluB_8


title: DH82Ondpi_K_d1_2


title: Hulu_fluB_3


title: Hulu_fluB_6


title: CC_0_G


title: CC_0_A


title: DH82Ondpi_H_d3_4

value: hypoxia


title: DH82Ondpi_K_d1_1


title: Patient_197 SAMPLE_197

city: roskilde

first: Soraya

last: Naimy

state: Sjaelland

address: sygehusvej 9

department: department of pathology

country: Denmark

institute: zealand universityhospital

description: raw data were quality checked in the nSolver software by using default parameters, imaging QC, bibdng density, positive control linearity and positive control limit detection (set to 0.5 fM) was evaluated

hyb_protocol: From each sample, 100-200 ng of RNA was used for hybridization using the nCounter PanCancer IO 360 Gene Expression Panel, according to the manufacturer’s nCounter XT protocol (NanoString Technologies, Seattle, Washington, US).

scan_protocol: digitl detection and counting of the hybridized probes wer done one an epifluorescence microscope in the digital analyzer mode, NanoString Technologies, Seattle, Washington, US

data_processing: Data analysis was performed in nSover software version 4.0

label: biotin

source_name: Primary Skin melanoma

label_protocol: biotinylated capture probe was used to pair withthe targit probe

extract_protocol: Total RNA was isolated from five 10-µm sections of whole FFPE tissue using Roche hi-pure FFPET kit (Roche Life Science, Mannheim, Germany) according to manufacturer`s protocol. NanoDrop™ Lite spectrophotometer (Thermo Fischer Scientific, Waltham, Massachusetts, US) was used to measure total RNA quality and quantity.

value: Primary Skin melanoma

tag: histology

value: Acral lentiginous melanoma

tag: status after 5 years

value: dead

tag: Sex

value: woman

tag: status

value: brisk

tag: braf v600e ihc status

value: negative

tag: Stage


title: Patient_198 SAMPLE_198

value: alive

tag: age

value: absent


title: Hulu_fluB_15

tag: infection

value: Lung


title: DH82Ondpi_H_d3_1

tag: stress


title: DH82Ondpi_H_d1_3

tag: cell line

value: day 1


title: DH82Ondpi_H_d3_2


title: Hulu_fluB_13

value: influenza B


title: Hulu_fluB_12


title: Patient_196 SAMPLE_196


title: Hulu_fluB_10


title: Hulu_fluB_1


title: Patient_195 SAMPLE_195


title: MDA-MB-231 siHMGN5 H3K27ac_CutTag

city: Haining

first: Chaochen

last: Wang

address: 718 East Haizhou Rd

department: ZJU-UoE Institute

institute: Zhejiang University

data_processing:
Library strategy: Cut&Tag
RNA-Seq reads were aligned to the GRCh38 human reference transcriptome using salmon (v1.4.0) for count matrix generation
Genome_build: hg38
Supplementary_files_format_and_content: raw counts
Basecalls performed using the CASAVA software  ChIP-seq reads were aligned to the hg38 genome assembly using the Bowtie2 program (Langmead et al., Nature method, 2012)
The HOMER ((http://homer.salk.  edu/homer/) software was used to convert alignment map files into bedGraph files with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: BedGraph files can be used to check ChIP-seq peaks through the UCSC genome browser.

growth_protocol: Cells are maintained in L15 medium (Invitrogen, USA) supplemented with 10% fetal bovine serum (Gibco) at 37 °C in air

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen).
For RNA-Seq, libraries were prepared for sequencing using standard Illumina protocols. For Cut&Tag, 50,000 cells were harvested and the CUT&Tag assay was performed using a commercial kit (Vazyme, China, TD901-TD902) according to the manufacturer’s protocol.

treatment_protocol: 30nM synthesized siRNAs were transfected with Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer’s instructions.

value: HMGN5 siRNA

tag: cut&tag antibody

value: H3K27ac antibody


title: DH82_S_d3_1

value: control

value: starvation

value: day 3


title: DH82Ondpi_H_d1_2

value: canine distemper virus strain Onderstepoort

value: hypoxia


title: Patient_193 SAMPLE_193

value: Primary Skin melanoma

value: Acral lentiginous melanoma

value: man

value: positive


title: Hulu_fluB_11


title: Hulu_fluB_2


title: Hulu_fluB_14


title: Patient_191 SAMPLE_191

value: woman


title: MDA-MB-231 Ctrl H3K27ac_CutTag

value: control siRNA


title: Patient_192 SAMPLE_192

value: alive

value: absent

value: negative


title: Patient_194 SAMPLE_194

value: brisk


title: DH82_S_d3_2


title: DH82_S_d3_3


title: DH82_S_d1_3

value: day 1


title: Patient_190 SAMPLE_190


title: DH82Ondpi_H_d1_1


city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

description:
RNA-seq of population CD33+CD19- of PDX sample SJMPAL046472
SJMPAL046472_X3-PAVRCX-063S5-1411_PT2

data_processing:
Sequencing reads were then mapped to the human genome reference by STAR. Mixture of Isoforms  (MISO) Bayesian Inference model was used for quantification and comparison of alternative splicing events.
Genome_build: hg19
Supplementary_files_format_and_content: read count and splicing pattern for ZNF384 exon 8

source_name: PDX sample SJMPAL046472

growth_protocol: PDX: NA; JIH-5: 80% Iscove's MDM + 20% h.i. FBS

extract_protocol:
RNA was extracted by ALLPrep Kit (Qiagen)
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020599). For the low input:  Starting with 1-2 ng of total RNA,  cDNA was created using the Tecan/NuGen Ovation RNA Seq System V2 kit (7102-32).  Then 500 ng of the cDNA was sheared  to 300 bp with the Covaris LE220 (settings:  450 peak incident power (W), 15% Duty factor, 1000 cycles per burst, and treatment time of 100 seconds).  Libraries of the sheared cDNA was prepared using the Kapa Hyper library prep kit according to the manufacturer’s instructions (KK8504).
Total stranded RNA sequencing was performed by the Hartwell Center at St. Jude Children’s Research Hospital. Libraries were prepared using the TruSeq Stranded Total RNA kit (Ilumina). 100 basepair, paired reads were generated by sequencing on the NovaSeq 6000 (Ilumina). For the low input:  Starting with 1-2 ng of total RNA,  cDNA was created using the Tecan/NuGen Ovation RNA Seq System V2 kit (7102-32).  Then 500 ng of the cDNA was sheared  to 300 bp with the Covaris LE220 (settings:  450 peak incident power (W), 15% Duty factor, 1000 cycles per burst, and treatment time of 100 seconds).  Libraries of the sheared cDNA was prepared using the Kapa Hyper library prep kit according to the manufacturer’s instructions (KK8504).

value: PDX

tag: molecule

value: Low input RNA-seq


title: DH82_K_d3_3

value: control

value: controls


title: DH82_K_d3_2

value: day 3


title: RNA-seq of population CD33-CD19+ of JIH-5 cells

description:
RNA-seq of population CD33-CD19+ of JIH5 cells
SJMPAL047180_C4-JIH5_PT3

source_name: JIH-5 cells

value: Cell line

value: MPAL


description:
RNA-seq of population CD33+CD19+ of PDX sample SJMPAL046472
SJMPAL046472_X2-PAVRCX-063S5-1411_PT1

value: Total RNA


title: DH82_S_d1_2

value: starvation


title: DH82_S_d1_1


title: RNA-seq of population CD33+CD19+ of JIH-5 cells

description:
RNA-seq of population CD33+CD19+ of JIH5 cells
SJMPAL047180_C2-JIH5_PT1


title: Patient_185 SAMPLE_185

value: Primary Skin melanoma

value: Acral lentiginous melanoma

value: man

value: nonbrisk


title: Patient_188 SAMPLE_188

value: alive


description:
RNA-seq of population CD33-CD19+ of PDX sample SJBALL004031
SJBALL004031_X18-4052_PT3

source_name: PDX sample SJBALL004031


title: Patient_184 SAMPLE_184

value: dead

value: positive


title: Patient_183 SAMPLE_183

value: Nodular melanoma

value: woman

value: brisk


title: DH82_K_d1_3

value: control

value: day 1


title: DH82_K_d1_2

value: controls


title: Patient_186 SAMPLE_186


title: Patient_189 SAMPLE_189

value: absent

value: negative


description:
RNA-seq of population CD33-CD19- of PDX sample SJBALL004031
SJBALL004031_X19-4052_PT4

value: PDX

value: Low input RNA-seq


title: DH82_H_d3_3

value: hypoxia

value: day 3


title: DH82_H_d3_2


title: DH82_K_d3_1


title: Patient_180 SAMPLE_180

value: Primary Skin melanoma

value: man


description:
RNA-seq of population CD33+CD19- of PDX sample SJBALL004031
SJBALL004031_X17-4052_PT2


title: DH82_H_d3_1


title: HuLu_251_1_Mock

data_processing:
Reads were quality checked with package FastQC (version 0.11.4), then trimmed using Trimgalore (version 0.4.4) with default settings.
Trimmed reads were mapped to human genome ENSEMBL hg38 release 91 using STAR aligner (Dobin and Gingeras, 2015) with default settings.
Mapped reads were counted using RsubRead (version 1.32.4, (Liao et al., 2019)). Raw counts were then normalized using DESeq2 (version 1.16.1, (Love et al., 2014)).
Data was batch corrected for donor effect using the function removeBatchEffect from the Limma package (version 3.42.2, (Ritchie et al., 2015; Smyth, 2004)).
Genome_build: ENSMBL human hg38 release 91 genome
Supplementary_files_format_and_content: btchCORR_norm_Brunotte_Hulu_IFN_2021_190621.txt: Tab-delimited matrix with log2 normalized values per sample.

source_name: lung slice

extract_protocol:
Tissue blocks were transferred to Lysing Matrix A tubes (MP Biomedicals, Germany) in 600 µl RLT buffer supplemented with 1% β-Mercapthoethanol (Sigma, Germany). Tissue was lysed using FastPrep®-24 (MP Biomedicals, Germany) applying six rounds of tissue lysis at default settings (4 m/s, 20 s). Homogenates were centrifuged for 5 min full speed at 4°C and RNA was purified from the supernatant.
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). PolyA+RNA were purified  from 1µg total RNA using Dynabeads mRNA DIRECT Micro Kit (ThermoFisher). The RNA Sequencing library was prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs).
The libraries were sequenced on Illumina NovaSeq 6000 using NovaSeq 6000 S1 Reagent Kit (300 cycles, paired end run 2x 150 bp) with an average of 8.4 x10^7 reads per RNA sample.

tag: donor

value: Lung

value: Mock


title: HuLu_251_1_hIFN_A6


description:
RNA-seq of population CD33+CD19+ of PDX sample SJBALL004031
SJBALL004031_X16-4052_PT1

tag: cell type


title: HuLu_251_1_hIFN_A5


title: DH82_H_d1_2

tag: time


title: DH82_K_d1_1


title: Patient_177 SAMPLE_177

tag: tissue

value: dead


title: Patient_182 SAMPLE_182

value: Nodular melanoma

value: alive

value: nonbrisk

value: positive


title: HuLu_251_1_hIFN_A4

tag: treatment


title: DH82_H_d1_1

value: control

value: day 1


title: Patient_187 SAMPLE_187

tag: histology

value: Acral lentiginous melanoma

value: woman

value: brisk


title: HuLu_251_1_hIFN_A2


title: Patient_181 SAMPLE_181

tag: status after 5 years


title: Patient_174 SAMPLE_174

tag: Sex

value: absent

value: negative


title: HuLu_251_1_hIFN_A8


title: Patient_179 SAMPLE_179

tag: status


title: HuLu_251_1_hIFN_A7


title: DH82_H_d1_3

value: hypoxia


title: Patient_178 SAMPLE_178

value: Primary Skin melanoma

tag: braf v600e ihc status


title: Patient_176 SAMPLE_176

value: man

tag: Stage


title: HuLu_251_1_hIFN_A16

value: Lung


title: Patient_175 SAMPLE_175

tag: age


title: Serum Evs, CM3

first: Mengling

address: No. 2 Yuanmingyuan West Road

institute: Institute of Animal Science, Chinese Academy of Agricultural Sciences

description: processed data file column: M3

data_processing:
Low-quality bases (Sanger base quality of < 20) of the 3’ end were trimmed using in-house perl scripts, and then the sequencing adapters were removed with the fastx toolkit software (http://hannonlab.cshl.edu/fastx_toolkit/).
All identical sequences of sizes ranging from 18 to 32 nt were counted and eliminated from the initial data set. Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) was used to annotate the chromosomal location against the reference genome data.
Through a BLAST search of the miRbase, version 22.0 (http://www.mirbase.org/), the perfectly matched sequences were used to count and analyze the known miRNA expression profile. Then the assembled unique sequences were used for a BLAST search of the Rfam database, version 12.3 (http://rfam.sanger.ac.uk/), to remove non-miRNA sequences (rRNA, tRNA, snoRNA, etc.).
The characteristics of hairpin structure of miRNA precursor can be used to predict novel miRNA. The available software miRDeep2 were integrated to predict novel miRNA. At the same time, in-house scripts were used to obtain the identified miRNA base bias on the first position with certain length and on each position of all identified miRNA.
The expression level of each miRNA was calculated according to the transcripts per million reads (TPM) method. Significant differently expressed (DE) miRNAs were extracted with |log2FC| >1 and P adjust < 0.05 by edgeR.
Assembly: ARS-UCD1.2
Supplementary files format and content: Excel file includes TPM values for each Sample

organism: Bos taurus

source_name: serum

extract_protocol:
Small RNA was extracted from serum EVs using the miRNeasy Mini kit (Qiagen)，3 ug of total RNA was used for the construction of sequencing libraries.
3μg of total RNA was ligated with sequencing adapters with TruseqTM Small RNA sample prep Kit (Illumina, San Diego, CA, USA).

value: serum

tag: condition

value: clinical mastitis


title: HuLu_251_1_hIFN_A17


title: Serum Evs, CM7

description: processed data file column: M10


title: Serum Evs, CM6

description: processed data file column: M6


title: Serum Evs, CM5

description: processed data file column: M5


title: Patient_170 SAMPLE_170

value: Nodular melanoma


title: HuLu_247_1_Mock

value: Mock


title: HuLu_251_1_hIFN_A1


title: Patient_173 SAMPLE_173

value: alive


title: Patient_172 SAMPLE_172


title: Serum Evs, CM4

description: processed data file column: M4


title: Serum Evs, CM1

description: processed data file column: M1


title: Serum Evs, SM7

description: processed data file column: SM8

value: subclinical mastitis


title: Patient_168 SAMPLE_168

value: nonbrisk


title: HuLu_251_1_hIFN_A14


title: Patient_171 SAMPLE_171


title: Serum Evs, CM2

description: processed data file column: M2


title: Patient_167 SAMPLE_167


title: HuLu_247_1_hIFN_A8


title: HuLu_251_1_hIFN_A10


title: Serum Evs, SM6

description: processed data file column: SM6


title: Patient_169 SAMPLE_169

value: positive


title: HuLu_247_1_hIFN_A7


title: HuLu_251_1_hIFN_A21


title: HuLu_247_1_hIFN_A6


title: Serum Evs, SM5

description: processed data file column: SM5


title: HuLu_247_1_hIFN_A5


title: Patient_165 SAMPLE_165

value: Superficial spreading melanoma

value: dead


title: Serum Evs, SM4

description: processed data file column: SM4


title: HuLu_247_1_hIFN_A4


title: Serum Evs, SM3

description: processed data file column: SM3


title: Patient_163 SAMPLE_163

value: woman


title: Patient_162 SAMPLE_162

value: brisk


title: Serum Evs, SM1

description: processed data file column: SM1


title: HuLu_247_1_hIFN_A21


title: Serum Evs, SM2

description: processed data file column: SM2


title: Serum Evs, H7

description: processed data file column: H9

value: healthy


title: Patient_164 SAMPLE_164


title: Patient_166 SAMPLE_166


title: Patient_160 SAMPLE_160

value: negative


title: RBM46 fl/+ rep2

city: Nanjin

first: Baomei

last: Qian

state: Jiangsu

address: Jiangning

institute: Nanjing Medical University

data_processing:
Clean data were obtained by trimming the adaptor sequence and removing sequences with low quality.
Clean reads were mapped to the mouse genome (mm10) with HISAT2 (v.2.1.0; Johns Hopkins University, Baltimore, MD, USA) with a GTF file download from the UCSC database (University of California,
The aligned reads of genes were counted using HTSeq followed by DESeq2 normalization to evaluate gene expression as normalized counts per million.
Genome_build: mm10
Supplementary_files_format_and_content: gene counts for every gene and every sample

source_name: mouse testes

extract_protocol:
Testes were collected from wild-type and Neurog-cre RBM46 KO mouse, and RNA was harvested using Trizol reagent.
Strand-specific libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina).

tag: strain

value: postnatal day 10

tag: genotype

value: wild type


title: Neurog-cre/Rbm46fl/- rep2

value: testis-specific RBM46 knockouts


title: Neurog-cre/Rbm46fl/- rep1


title: HuLu_247_1_hIFN_A17

value: Lung


title: Patient_161 SAMPLE_161

value: Primary Skin melanoma


title: Patient_158 SAMPLE_158


title: Serum Evs, H5

description: processed data file column: H5

value: serum


title: RBM46 fl/+ rep1


title: Patient_159 SAMPLE_159

value: man


title: input

description: input RNA

data_processing:
Library strategy: eCLIP-seq
eCLIP-seq reads were aligned to the mouse genome (mm10) using STAR software (STAR version 2.7.6A)
The aligned reads were further filtered to remove those with low mapping quality and duplicated arising as an artefact of sample amplification or sequencing.
Peak calling was carried out by using CLIPPER( with -s mm10 -o -bonferroni -superlocal-threshold-method binomial-save-pickle.) on eCLIP file against the input file.
Genome-wide normalized signal coverage tracks were created by bamCoverage in deepTools (version 3.5.1) and visualized in the Integrative Genomics Viewer (IGV version 2.3.88).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

extract_protocol:
Lysates were cross-linked by UV, sonicated, antibody-bound RNA complexes were immunoprecipitated, washed, and RNA was extracted.
RNA was amplified according to eCLIP Sequencing Sample Preparation Guide provided by Illumina using adaptors and primers.

value: postnatal day 12-14

value: wild-type

tag: eclip antibody


title: HuLu_247_1_hIFN_A14


title: Serum Evs, H4

description: processed data file column: H4


title: HuLu_247_1_hIFN_A10


title: Serum Evs, H6

description: processed data file column: H6


title: Patient_157 SAMPLE_157

value: nonbrisk


title: RBM46 eCLIP rep2

description: pulldown RNA

value: Abclonal, A16605


title: Serum Evs, H3

description: processed data file column: H3


title: HuLu_247_1_hIFN_A2


title: Patient_155 SAMPLE_155

value: Superficial spreading melanoma

value: alive


title: RBM46 eCLIP rep1

description: pulldown RNA


title: Patient_156 SAMPLE_156


title: Serum Evs, H1

description: processed data file column: H1


title: HuLu_214_3_Mock

value: Mock


title: HuLu_214_3_hIFN_A8


title: HuLu_247_1_hIFN_A16


title: TR_CD5CD19_EV_TCL1_Rep3

city: Luxembourg

first: Etienne

last: Moussay

address: 6 rue Nicolas-Ernest Barblé

department: Cancer Research

country: Luxembourg

institute: Luxembourg Institute of Health

description:
Eµ-TCL1-Rab27DKO
3'-RNA-Seq

data_processing:
After initial QCs using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/), fastq files were processed using a local Snakemake workflow including the following main steps.
First, raw reads were trimmed from their UMI index, poly A and adapter sequences using a combination of dedicated scripts and cutadapt (v2.10).
Next, filtered reads were submitted for mapping (STAR v2.5.3a) on the Mouse Reference genome (GRCm38).
Collapsing of reads originating from the same fragment was achieved with umi_tools (v 1.0.0) and counting was performed with featureCounts (subread v2.0.0).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: CD19TR+sEV_TRvsTCL1_counts.txt: Table with raw gene counts for every gene and every sample.

source_name: Spleen

extract_protocol:
RNA was harvested using NucleoZOL reagent and columns. QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina was used with 500 ng of total RNA for the construction of sequencing libraries. UMI were added to the protocol.
Libraries were prepared for sequencing using standard protocols.

treatment_protocol: Spleens from leukemic Eu-TCL1-Rab27DKO mice were removed, gently dissociated on ice, and cells were plated in complete RPMI-1640 medium. Cells were treated for 24h with 5 or 50ug/ml of splenic extracellular vesicles from Eu-TCL1-Rab27DKO or Eu-TCL1 mice, respectively.

value: leukemic B cells

tag: phenotype

value: splenic extracellular vesicles from mice


title: 9 day_rep3

city: Xianyang

first: Xinhao

last: Ma

state: Shaanxi

address: No. 3, Taicheng Road

institute: Northwest A&F University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Intramuscular adipocytes

growth_protocol: Intramuscular adipocytes were grown in complete medium, which consisted of DMEM-F12 (Gibco, USA) with 15% FBS and 1% penicillin/streptomycin, at 37°C and 5% CO2, The growth medium was replaced every two days.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When the adipocytes reached 90% confluence, the differentiation medium was used to induce differentiation, which was a complete medium containing 1 g/mL DEX(Sigma, USA) ,0.5 mM IBMX and 5 μg/ml insulin (Sigma, USA).After 48 hours, the medium was changed to a complete medium containing 5 μg/ml insulin. The  differentiation medium was replaced every two days.

value: Intramuscular fat


title: HuLu_214_3_hIFN_A7

tag: donor


title: 9 day_rep2


title: Patient_154 SAMPLE_154

value: woman

value: absent

value: positive


title: TR_CD5CD19_EV_TCL1_Rep1

description:
Eµ-TCL1-Rab27DKO
3'-RNA-Seq

tag: cell type


title: Patient_152 SAMPLE_152

value: brisk


title: Patient_153 SAMPLE_153

value: Primary Skin melanoma

value: negative


title: HuLu_214_3_hIFN_A5

value: Lung


title: HuLu_214_3_hIFN_A6


title: HuLu_247_1_hIFN_A1


title: Serum Evs, H2

description: processed data file column: H2

value: serum

value: healthy


title: TR_CD5CD19_EV_TR_Rep3

description:
Eµ-TCL1-Rab27DKO
3'-RNA-Seq


title: Patient_151 SAMPLE_151


title: TR_CD5CD19_EV_TR_Rep2

description:
Eµ-TCL1-Rab27DKO
3'-RNA-Seq


title: TR_CD5CD19_EV_TR_Rep1

description:
Eµ-TCL1-Rab27DKO
3'-RNA-Seq


title: Patient_150 SAMPLE_150


title: HuLu_214_3_hIFN_A4


title: 9 day_rep1


title: 6 day_rep2


title: 6 day_rep3


title: 6 day_rep1


title: HuLu_214_3_hIFN_A21


title: Patient_149 SAMPLE_149

value: dead

value: man


title: TCL1_Rep3

description: leukemic

data_processing:
After initial QCs using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/), fastq files were processed using a local Snakemake workflow including the following main steps.
First, raw reads were trimmed from their UMI index, poly A and adapter sequences using a combination of dedicated scripts and cutadapt (v2.10).
Next, filtered reads were submitted for mapping (STAR v2.5.3a) on the Mouse Reference genome (GRCm38).
Collapsing of reads originating from the same fragment was achieved with umi_tools (v 1.0.0) and counting was perfomed with featureCounts (subread v2.0.0).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Table with raw gene counts for every gene and every sample

extract_protocol:
Spleens were removed, gently dissociated on ice, and cells were antibody-stained and CD19+CD5+ cells were sorted by FACS (Aria III). RNA was harvested using NucleoZOL reagent and columns. QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina was used with 500 ng of total RNA for the construction of sequencing libraries. UMI were added to the protocol.
Libraries were prepared for sequencing using standard protocols

value: B cells


title: 3 day_rep3


title: TR_CD5CD19_EV_TCL1_Rep2

description:
Eµ-TCL1-Rab27DKO
3'-RNA-Seq


title: HuLu_214_3_hIFN_A2


title: TCL1_Rep2

description: leukemic


title: Patient_148 SAMPLE_148

value: Superficial spreading melanoma

value: alive


title: HuLu_214_3_hIFN_A17


title: HuLu_214_3_hIFN_A16


title: 3 day_rep1


title: TCL1_Rep1

description: leukemic


title: 3 day_rep2


title: Patient_146 SAMPLE_146


title: TCL1-RabDKO-Rep3

description: leukemic


title: HuLu_214_3_hIFN_A14


title: HuLu_214_3_hIFN_A10


title: 0 day_rep3


title: Patient_145 SAMPLE_145


title: TCL1-RabDKO-Rep2

description: leukemic


title: Patient_144 SAMPLE_144


title: Patient_143 SAMPLE_143


title: TCL1-RabDKO-Rep1

description: leukemic


title: CD8_EV_TCL1_Rep3

description: healthy

extract_protocol:
Spleens were removed, gently dissociated on ice, and cells were antibody-stained and sorted by FACS (Aria III). Cells were treated with sEV (100ug/ml) for 48h. RNA was harvested and isolated using NucleoZOL reagent and columns. QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina was used with 500 ng of total RNA for the construction of sequencing libraries. UMI were added to the protocol.
Libraries were prepared for sequencing using standard protocols

value: Foxp3 YFP/cre

value: T cells

value: leukemia EVs


title: 0 day_rep1

value: Intramuscular fat


title: HuLu_214_3_hIFN_A1


title: Patient_147 SAMPLE_147

value: absent


title: Patient_142 SAMPLE_142


title: Patient_141 SAMPLE_141

value: positive


title: 22Rv-1 cells, Experimental RNA, rep 1

city: Orlando

first: Ratna

last: Chakrabarti

address: 12722 Research Parkway

institute: University of Central Florida

data_processing:
Sequence quality was verified using FastQC
Cutadaptand perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Bowtie2 and HISAT2 software were used to map reads to the genome of Homo sapiens (Version: v101)
The mapped reads of each sample were assembled using StringTie
All transcriptomes from 6 samples were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare
Both gene level and transcript level were estimated by StringTie using FPKM
Genome_build: After the ﬁnal transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts.
Supplementary_files_format_and_content: Gene/transcript (isoform) expression levels in FPKM

source_name: Stably transfected 22Rv-1 Prostate cancer cells induced with doxycycline

growth_protocol: Stable sublines of 22Rv-1 prostate  cancer cells inducibly expressing miR-30e were maintained in RPMI1640 with 10% FBS.

extract_protocol:
Total RNA was extracted using Zymo RNA extraction kit and used for RNA-seq analysis.
Library was prepared following Illumina's TruSeq-stranded-total-RNA-sample preparation protocol.  RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Ribosomal RNA was removed, followed by fragmentation with divalent cation buffers in elevated temperature.   Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

treatment_protocol: Cells were induced with doxycycline for 48 hours or left ununduced. Overexprestion of miR-30e with a fold-change in expression 10.34±2.9 (Mean±SD) was determined by qRT-PCR in the extracted total RNA used for RNA -seq analysis

tag: cell line

value: prostate cancer cells

tag: vector

value: pLVX-TetOne +miR-30e precursor induced


title: 22Rv-1 cells, Experimental RNA, rep 2


title: CD8_EV_TCL1_Rep2

description: healthy

tag: treatment


title: CD8_EV_Ctrl_Rep4

description: healthy

value: control EVs


title: 0 day_rep2

tag: tissue


title: Patient_140 SAMPLE_140

value: Primary Skin melanoma

tag: histology

tag: status after 5 years

value: woman

value: nonbrisk

value: negative


title: CD8_EV_Ctrl_Rep3

description: healthy


title: Patient_139 SAMPLE_139

value: dead

tag: Sex

tag: status

value: brisk


title: 22Rv-1 cells, Control RNA rep 3

source_name: Stably transfected 22Rv-1 Prostate cancer cells uninduced

value: pLVX-TetOne +miR-30e precursor uninduced


title: HK2_4_TCMYY0486T_3

first: Lan

last: Xie

address: School of Medicine B410, Tsinghua University

institute: Tsinghua University

description: Paired-end was used for sequencing, and only R1 files were used for analysis

data_processing:
RNA-mediated oligonucleotide annealing, selection, and ligation with next-generation sequencing (RASL-Seq)
The sequencing data of HTS2 were mapped with Bowtie2(2.2.4.).
the differentially expressed genes were identified by DESeq2(1.22.1).
Assembly: Homo sapiens
Supplementary files format and content: read count files.

growth_protocol: HK-2 cells were maintained in DMEM containing 10% foetal bovine serum (FBS) and 100 U/mL penicillin–streptomycin in humidified atmosphere with 5% CO2 at 37°C. HK-2 cells (3,000 per well) were seeded in 384-well plates.

extract_protocol:
The samples were heated at 65°C for 8 min to denature RNA. Then, the samples were incubated at 45°C for 60 min so that probes were annealed to total RNA and were paired with target mRNA. Biotinylated oligo (dT) and streptavidin-coated magnetic beads were used to capture mRNA so that the aligned probes could resist washing. After washing, the aligned probes were ligated by T4 ligase at 37°C for 60 min.
Libraries were prepared by PCR amplification, products from a single sample were indexed by limited PCR amplification with a set of barcode primers.

treatment_protocol: HK-2 cells were treated with TCM crude extracts at 100 μg/mL or DMSO for 24 hours.

value: proximal tubular cells

value: 100 μg/mL_Yinyanghuo


title: 22Rv-1 cells, Control RNA rep 2


title: 22Rv-1 cells, Experimental RNA, rep 3


title: HK2_4_TCMYY0486T_2


title: Patient_138 SAMPLE_138

value: Superficial spreading melanoma

tag: braf v600e ihc status

tag: Stage


title: 22Rv-1 cells, Control RNA rep 1


title: HK2_4_TCMYY0486T_1


title: CD8_EV_Ctrl_Rep1

description: healthy

value: Foxp3 YFP/cre

value: T cells


title: Patient_137 SAMPLE_137

value: alive

tag: age


title: CD8_EV_TCL1_Rep1

description: healthy

tag: strain

value: leukemia EVs


title: HK2_4_DMSO_16


title: Patient_136 SAMPLE_136

value: man

value: positive


title: HK2_4_DMSO_15


title: GES-1 cells, Trx1 low-2

first: Xin

last: Guan

address: Peking University Third Hospital, 49 Huayuan North Road, Haidian District, Beijing

institute: Peking university Third Hospital

data_processing:
Differential expression analysis of three groups was performed using the DESeq2 R package (1.20.0) which provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution.
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Padj<0.05 and |log2(fold change)| > 1 were set as the threshold for significantly differential expression. We used cluster Profiler R package (3.8.1) to test the statistical enrichment of differential expression genes in KEGG pathways.
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: HISAT2 v2.0.5
Supplementary_files_format_and_content: gene_count_fpkm.txt (represents FPKM values for each Sample), matrix.txt  (represents raw gene counts for each Sample)

source_name: Gastric epithelial cells co-cultured with H.pylori with Trx1 low expression

growth_protocol: GES-1 cells co-cultured with H.pylori mentioned above were collected at 12h and three biological repeats were performed for each group.

extract_protocol: Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) and then prepared to structure library which was initially quantified by Qubit2.0 Fluorometer for Transcriptome sequencing and the insert size of the library is detected by Agilent 2100 bioanalyzer at the Novogene Bioinformatics Technology Co., Ltd.

value: Gastric epithelial cells


title: Patient_135 SAMPLE_135

value: Primary Skin melanoma

value: absent


title: HK2_4_DMSO_14


title: GES-1 cells, Trx1 low-1

value: co-cultured with H.pylori with Trx1 low expression


title: Patient_134 SAMPLE_134

value: negative


title: HK2_4_DMSO_13


title: TAF15-ZNF384 INPUT Replicate 2

description: SJMMNORM046373_C81-Arf-pre-B-TAF15-ZNF384-e6-e3-C-HA-6-INPUT

data_processing:
Data was analyzed using ENCODE pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2).
Reads were mapped to mouse genome mm10 with BWA (version 0.7.13-r1126).
Duplicated reads were marked with Picard and only uniquely mapped reads extracted by Samtools (version 1.2) were retained for analysis.
Peaks were called on all ChIP-seq data sets using MACS2 (version 2.1.1)
Supplementary_files_format_and_content: bigwig files were generated using deepTools v3.2.1 with RPKM used for normalization and a bin size of 50
Supplementary_files_format_and_content: significant peaks were called using MACS2 with FDR < 0.01 (bed format)

source_name: pre-B cells

growth_protocol: Cells were derived from C57BL/6 ARF-null BM cells as described (Randle et al, PNAS, 2001). Cells were transduced with lentiviral supernatants of ZNF384, TAF15-ZNF384, TCF3-ZNF384-no exon 8-HA or TCF3-ZNF384-yes exon 8-HA.

extract_protocol:
Chromatin was prepared as described (Zhang et.al, Nature Genetics, 2016). Breifly, 20 X 10^6 cells were crosslinked with 1% formaldehyde for 10 minutes. Cells were washed 3 times with PBS and lysed on ice for 10 minutes with lysis buffer. Chromatin was washed twice in wash buffer and once in shearing buffer before resuspending in 1ml of shearing buffer. Chromatin was sonicated with a Covaris E210 instrument and resuspended in dilution buffer. Finally, immunoprecipiation was performed with anti-HA antibody. Chipmentation was performed as described () on 1-2 x 10^6 cells.
To prepare ChIP–seq libraries, 10 ng of ChIP DNA was end repaired and adaptor ligation was performed using the NEBNext ChIP–Seq Library Prep Reagent Set for Illumina (New England BioLabs). Libraries were purified after 14 rounds of PCR amplification with Q5 DNA Hot-Start polymerase (New England BioLabs). Each ChIP–seq library underwent 50-cycle single-end sequencing using TruSeq SBS kit v3 on an Illumina HiSeq 2000. ChIPmentation libraries were prepared using Kapa HiFi HotStart ReadyMix and Nextera primers. The libraries were sequenced using the Illumina HiSeq3000/4000 platform and the 25 base pair, paired-end configuration.

treatment_protocol: No treatment

tag: genotype

value: ARF-null

value: pre-B cells

tag: transplant

tag: protocol

value: ChIPmentation

tag: antibody


title: TCF3-ZNF384 H3K27Ac Replicate 2

description: SJMMNORM046373_C82-Arf-pre-B-TCF3-ZNF384-e13-e5-C-HA-6-H3K27Ac-AB5

tag: cell type

value: H3K27Ac (Cell Signaling 8173S)


title: GES-1 cells, Trx1 high-3

source_name: Gastric epithelial cells co-cultured with H.pylori with Trx1 high expression

tag: cell line


title: TAF15-ZNF384 H3K27Ac Replicate 2

description: SJMMNORM046373_C81-Arf-pre-B-TAF15-ZNF384-e6-e3-C-HA-6-H3K27Ac-AB5


title: Patient_132 SAMPLE_132

value: woman

value: brisk


title: HK2_4_DMSO_11

value: proximal tubular cells


title: GES-1 cells, Trx1 high-1

value: co-cultured with H.pylori with Trx1 high expression


title: Patient_131 SAMPLE_131

value: Superficial spreading melanoma

value: dead


title: GES-1 cells, Trx1 high-2


title: HK2_4_DMSO_12


title: TCF3-ZNF384 INPUT Replicate 2

description: SJMMNORM046373_C82-Arf-pre-B-TCF3-ZNF384-e13-e5-C-HA-6-INPUT


title: TCF3-ZNF384 INPUT Replicate 1

description: SJMMNORM046373_C80-Arf-pre-B-TCF3-ZNF384-e13-e5-C-HA-5-INPUT


title: TAF15-ZNF384 INPUT Replicate 1

description: SJMMNORM046373_C79-Arf-pre-B-TAF15-ZNF384-e6-e3-C-HA-5-INPUT


title: ZNF384 INPUT Replicate 1

description: SJMMNORM046373_C78-Arf-pre-B-ZNF384-C-HA-5-INPUT


title: HK2_4_DMSO_9


title: GES-1 cells, NC-2

source_name: Gastric epithelial cells without H.pylori

value: without H.pylori


title: Patient_130 SAMPLE_130

description: raw data were quality checked in the nSolver software by using default parameters, imaging QC, bibdng density, positive control linearity and positive control limit detection (set to 0.5 fM) was evaluated

value: alive

value: positive


title: HK2_4_DMSO_8


title: GES-1 cells, NC-1

value: Gastric epithelial cells


title: GES-1 cells, NC-3


title: Patient_133 SAMPLE_133

value: Primary Skin melanoma


title: HK2_4_DMSO_7


title: TCF3-ZNF384 H3K27Ac Replicate 1

description: SJMMNORM046373_C80-Arf-pre-B-TCF3-ZNF384-e13-e5-C-HA-5-H3K27Ac-AB5


title: HK2_4_DMSO_10


title: Patient_128 SAMPLE_128

value: absent


title: HK2_4_DMSO_6


title: Patient_127 SAMPLE_127

value: man

value: negative


title: Patient_129 SAMPLE_129

value: nonbrisk


title: CD8_EV_Ctrl_Rep2

description: healthy

value: Foxp3 YFP/cre

value: T cells

tag: phenotype

value: control EVs


title: Isolate_5-TNF_60min

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

description: Total RNA-Seq of human retinal endothelial cells (HREC)

data_processing:
Quality control with Trimmomatic version 0.38
Gene count matrix was generated with FeatureCounts version 1.5.0-p2
Aligned to genome using HISAT2 version 2.1.0
Genome_build: grch38
Supplementary_files_format_and_content: FeatureCounts per gene counts

source_name: human retinal endothelial cells (HREC)

growth_protocol: Retinal endothelial cells were isolated from human cadaveric donor eyes using enzymatic digestion of tissue, followed by magnetic bead capture of endothelial cells based on expression of CD31. Cells were cultured in MCDB-131 medium with “EGM-2 SingleQuots” (Clonetics-Lonza) supplements (omitting FBS, hydrocortisone and gentamicin) and FBS (varying concentrations).

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

treatment_protocol: Cells were treated with recombinant human tumor necrosis factor-alpha or interleukin-1beta for 60 minutes or 24 hours.

value: human retinal endothelial cells (HREC)

tag: treatment

value: TNF

tag: timepoint


title: ZNF384 H3K27Ac Replicate 1

description: SJMMNORM046373_C78-Arf-pre-B-ZNF384-C-HA-5-H3K27Ac-AB5

value: ARF-null

value: pre-B cells

value: ChIPmentation

value: H3K27Ac (Cell Signaling 8173S)


title: HK2_4_DMSO_5

value: proximal tubular cells


title: Isolate_5-TNF_24hr


title: TCF3-ZNF384 +e8 HA Replicate 4

description: SJMMNORM046373_C93-Arf-pre-B-TCF3-ZNF384-e13-e5-C-HA-yes-e8-rep5-HA-AB

value: ChIP-seq

value: HA (Abcam, Ab9110)


title: Patient_126 SAMPLE_126

tag: tissue

value: Primary Skin melanoma

tag: histology

value: Superficial spreading melanoma

value: dead


title: Patient_125 SAMPLE_125

tag: status after 5 years

value: alive

tag: Sex

value: man

value: positive


title: Isolate_5-IL_1_24hr


title: HK2_4_DMSO_4


title: Patient_124 SAMPLE_124

value: woman

tag: status

value: absent

tag: braf v600e ihc status


title: TCF3-ZNF384 +e8 INPUT Replicate 4

description: SJMMNORM046373_C93-Arf-pre-B-TCF3-ZNF384-e13-e5-C-HA-yes-e8-rep5-INPUT


title: Isolate_5-CTRL_60min

value: human retinal endothelial cells (HREC)

value: CTRL


title: HK2_4_DMSO_3


title: TCF3-ZNF384 -e8 INPUT Replicate 4

description: SJMMNORM046373_C92-Arf-pre-B-TCF3-ZNF384-e13-e5-C-HA-no-e8-rep5-INPUT

value: ARF-null


title: TCF3-ZNF384 -e8 HA Replicate 4

description: SJMMNORM046373_C92-Arf-pre-B-TCF3-ZNF384-e13-e5-C-HA-no-e8-rep5-HA-AB

value: pre-B cells


title: Patient_123 SAMPLE_123

tag: age

value: brisk

value: negative

tag: Stage


title: TAF15-ZNF384 H3K27Ac Replicate 1

description: SJMMNORM046373_C79-Arf-pre-B-TAF15-ZNF384-e6-e3-C-HA-5-H3K27Ac-AB5

tag: strain

tag: genotype

value: ChIPmentation

value: H3K27Ac (Cell Signaling 8173S)


title: Isolate_5-CTRL_24hr


title: TCF3-ZNF384 +e8 INPUT Replicate 3

description: SJMMNORM046373_C91-Arf-pre-B-TCF3-ZNF384-e13-e5-C-HA-yes-e8-rep4-INPUT

tag: transplant

tag: protocol

value: ChIP-seq


title: HK2_4_DMSO_1

description: Paired-end was used for sequencing, and only R1 files were used for analysis

tag: cell type

value: proximal tubular cells


title: TCF3-ZNF384 +e8 HA Replicate 3

description: SJMMNORM046373_C91-Arf-pre-B-TCF3-ZNF384-e13-e5-C-HA-yes-e8-rep4-HA-AB

tag: antibody

value: HA (Abcam, Ab9110)


title: Patient_121 SAMPLE_121

value: Primary Skin melanoma

value: Superficial spreading melanoma


title: TCF3-ZNF384 -e8 HA Replicate 3

description: SJMMNORM046373_C90-Arf-pre-B-TCF3-ZNF384-e13-e5-C-HA-no-e8-rep4-HA-AB


title: Isolate_5-IL_1_60min


title: Isolate_4-TNF_24hr

value: TNF


title: Isolate_4-IL_1_60min


title: HK2_3_TCMYX0423T_2

tag: cell line

value: 100 μg/mL_Gusuibu


title: Isolate_4-TNF_60min

tag: treatment


title: Patient_119 SAMPLE_119

value: alive

value: man

value: nonbrisk

value: positive


title: Isolate_4-IL_1_24hr

value: human retinal endothelial cells (HREC)

tag: timepoint


title: HK2_3_TCMYX0423T_1


title: TCF3-ZNF384 -e8 INPUT Replicate 3

description: SJMMNORM046373_C90-Arf-pre-B-TCF3-ZNF384-e13-e5-C-HA-no-e8-rep4-INPUT

value: ARF-null

value: pre-B cells


title: Patient_118 SAMPLE_118

tag: tissue

value: dead

value: woman

value: negative


title: HK2_4_DMSO_2


title: HK2_3_DMSO_16


title: Patient_117 SAMPLE_117

tag: histology


title: Isolate_4-CTRL_60min

value: CTRL


title: Patient_122 SAMPLE_122

tag: status after 5 years

value: brisk


title: Isolate_4-CTRL_24hr


title: HK2_3_TCMYX0423T_3

value: proximal tubular cells


title: TCF3-ZNF384 +e8 INPUT Replicate 2

description: SJMMNORM046373_C89-Arf-pre-B-TCF3-ZNF384-e13-e5-C-HA-yes-e8-rep3-INPUT

value: ChIP-seq


title: HK2_3_DMSO_14


title: Patient_116 SAMPLE_116

value: Primary Skin melanoma

value: Superficial spreading melanoma

tag: Sex


title: Patient_120 SAMPLE_120

tag: status


title: HK2_3_DMSO_13


title: Isolate_3-TNF_60min

value: TNF


title: TCF3-ZNF384 -e8 HA Replicate 2

description: SJMMNORM046373_C88-Arf-pre-B-TCF3-ZNF384-e13-e5-C-HA-no-e8-rep3-HA-AB

value: HA (Abcam, Ab9110)


title: TCF3-ZNF384 -e8 INPUT Replicate 2

description: SJMMNORM046373_C88-Arf-pre-B-TCF3-ZNF384-e13-e5-C-HA-no-e8-rep3-INPUT


title: Patient_115 SAMPLE_115

description: raw data were quality checked in the nSolver software by using default parameters, imaging QC, bibdng density, positive control linearity and positive control limit detection (set to 0.5 fM) was evaluated

value: alive

tag: braf v600e ihc status


title: Isolate_3-TNF_24hr


title: TCF3-ZNF384 +e8 HA Replicate 2

description: SJMMNORM046373_C89-Arf-pre-B-TCF3-ZNF384-e13-e5-C-HA-yes-e8-rep3-HA-AB


title: Patient_114 SAMPLE_114

tag: age

value: absent


title: TCF3-ZNF384 +e8 HA Replicate 1

description: SJMMNORM046373_C87-Arf-pre-B-TCF3-ZNF384-e13-e5-C-HA-yes-e8-rep2-HA-AB


title: HK2_3_DMSO_11


title: HK2_3_DMSO_12


title: TCF3-ZNF384 +e8 INPUT Replicate 1

description: SJMMNORM046373_C87-Arf-pre-B-TCF3-ZNF384-e13-e5-C-HA-yes-e8-rep2-INPUT


title: Isolate_3-IL_1_60min

description: Total RNA-Seq of human retinal endothelial cells (HREC)


title: Patient_113 SAMPLE_113

value: man

value: positive

tag: Stage


title: HK2_3_DMSO_15


title: Patient_112 SAMPLE_112


title: HK2_3_DMSO_10


title: Isolate_3-IL_1_24hr

value: human retinal endothelial cells (HREC)


title: TCF3-ZNF384 -e8 HA Replicate 1

description: SJMMNORM046373_C86-Arf-pre-B-TCF3-ZNF384-e13-e5-C-HA-no-e8-rep2-HA-AB

tag: strain

value: ARF-null

value: pre-B cells


title: Patient_111 SAMPLE_111

value: nonbrisk


title: HK2_3_DMSO_9


title: HK2_3_DMSO_8


title: RNAseq of CTRL_BM_KD014

description: RNAseq of CTRL_BM_KD014

data_processing:
paired end reads mapped to hg38 for human samples and mm10 for mouse samples using STAR (v2.7)
gene quantification using RSEM v1.3.1
Genome_build: hg38 for human, mm10 for mouse
Supplementary_files_format_and_content: text file for gene counts, TPM and FPKM of each gene annotated in Gencode M22

source_name: BL6 lineage negative bone marrow

growth_protocol: Human CD34 cells were transplanted into NSG-SGM3 mice, harvested when the mice were sick, and GFP+ cells were sorted from the spleen. Wild type or ARF-null lineage negative cells were isolated from mouse bone marrow, transduced with lentivirus, transplanted into BL6 mice, harvested when mice were sick, and GFP+ cells were sorted from bone marrow or spleen.

extract_protocol:
RNA was harvested using the Qiagen AllPrep Kit (Qiagen AllPrep Micro Kit for Low input samples) and RNA was quantified using the Quant-iT RiboGreen RNA assay (ThermoFisher) and quality checked by the 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent) prior to library generation.
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020599). For the low input samples, cDNA was generated using Tecan/NuGen Ovation RNA-Seq System V2 (catalog 7102) with 1ng RNA, sheared to 300bp using Covaris, and libraries were prepped using the Kapa Hyper kit/protocol (catalog KK8504) and using Illumina True Seq IDT DNA UD Indexes (20020178). Low input library quality was evaluated on a D1000 tape using Agilent’s Tape Station 4200.

tag: growth conditions

value: lentiviral transduction, transplant into BL6 mice, harvest tissue and sort GFP+ cells

value: Bone Marrow

tag: genotype

value: Wild type

tag: input

value: Standard


title: Isolate_3-CTRL_24hr

tag: cell type

value: CTRL


title: Patient_110 SAMPLE_110

source_name: Primary Skin melanoma

extract_protocol: Total RNA was isolated from five 10-µm sections of whole FFPE tissue using Roche hi-pure FFPET kit (Roche Life Science, Mannheim, Germany) according to manufacturer`s protocol. NanoDrop™ Lite spectrophotometer (Thermo Fischer Scientific, Waltham, Massachusetts, US) was used to measure total RNA quality and quantity.

value: Primary Skin melanoma

value: brisk


title: Patient_109 SAMPLE_109

value: Superficial spreading melanoma

value: dead

value: negative


title: Isolate_2-TNF_60min

value: TNF


title: HK2_3_DMSO_7

value: proximal tubular cells


title: RNAseq of CTRL_BM_KD013

description: RNAseq of CTRL_BM_KD013


title: Isolate_2-TNF_24hr


title: Patient_108 SAMPLE_108

value: man

value: absent

value: positive


title: HK2_3_DMSO_5


title: Isolate_2-IL_1_60min

value: human retinal endothelial cells (HREC)


title: Patient_107 SAMPLE_107

value: alive

value: woman


title: RNAseq of SJMMAML066088_O1-UT_BM_KD029

description: RNAseq of SJMMAML066088_O1-UT_BM_KD029

value: lentiviral transduction, transplant into BL6 mice, harvest tissue and sort GFP+ cells

value: Bone Marrow


title: HK2_3_DMSO_4


title: Patient_106 SAMPLE_106


title: Isolate_3-CTRL_60min


title: TCF3-ZNF384 -e8 INPUT Replicate 1

description: SJMMNORM046373_C86-Arf-pre-B-TCF3-ZNF384-e13-e5-C-HA-no-e8-rep2-INPUT

value: ARF-null

value: pre-B cells

tag: transplant

tag: protocol

value: ChIP-seq

tag: antibody


title: Isolate_2-IL_1_24hr

tag: treatment

tag: timepoint


title: HK2_3_DMSO_3

tag: cell line


title: Patient_105 SAMPLE_105

tag: tissue

value: Primary Skin melanoma

tag: histology

tag: status after 5 years


title: Isolate_2-CTRL_24hr

value: CTRL


title: RNAseq of SJMMAML066085_O1-2714_SPL_KD025

value: Spleen

value: EP300-ZNF384, NRAS G12D

value: Standard


title: HK2_3_DMSO_2

value: proximal tubular cells


title: Isolate_2-CTRL_60min


title: Patient_104 SAMPLE_104

value: Superficial spreading melanoma

tag: Sex

value: man

tag: status

tag: braf v600e ihc status


title: RNAseq of 522_BM_KD025

description: RNAseq of 522_BM_KD025


title: HK2_3_DMSO_6


title: Isolate_1-TNF_60min

value: TNF


title: Patient_103 SAMPLE_103

value: dead

tag: age

value: brisk

value: positive

tag: Stage


title: Patient_102 SAMPLE_102

value: alive

value: woman

value: absent


title: RNAseq of SJMMAML066084_O1-523_SPL_KD025

tag: growth conditions

value: lentiviral transduction, transplant into BL6 mice, harvest tissue and sort GFP+ cells

tag: genotype


title: RNAseq of 67_SPL_KD029

description: RNAseq of 67_SPL_KD029

value: NRAS G12D

tag: input


title: HK2_2_TCMYR0216T_3

tag: cell type

value: 100 μg/mL_Roucongrong


title: Isolate_1-TNF_24hr

value: human retinal endothelial cells (HREC)


title: HK2_3_DMSO_1


title: Isolate_1-IL_1_60min


title: RNAseq of 515_SPL_KD025

description: RNAseq of 515_SPL_KD025

value: Spleen


title: Patient_101 SAMPLE_101

value: Primary Skin melanoma

value: nonbrisk

value: negative


title: HK2_2_TCMYR0216T_2

value: proximal tubular cells


title: HK2_2_TCMYR0216T_1


title: HK2_2_DMSO_16


title: RNAseq of SJMMAML066083_O1-2710_SPL_KD025

value: Standard


title: Patient_100 SAMPLE_100

value: Superficial spreading melanoma


title: RNAseq of 61_BM_KD022

description: RNAseq of 61_BM_KD022

value: Bone Marrow

value: TCF3-ZNF384 -e8, NRAS G12D


title: RNAseq of 82_BM_KD025

description: RNAseq of 82_BM_KD025


title: Isolate_1-CTRL_60min

value: CTRL


title: Isolate_1-CTRL_24hr


title: Patient_99 SAMPLE_99

value: alive

value: man

value: positive


title: Patient_98 SAMPLE_98

value: dead

value: absent


title: RNAseq of 65_BM_KD022

description: RNAseq of 65_BM_KD022

value: lentiviral transduction, transplant into BL6 mice, harvest tissue and sort GFP+ cells


title: Peripheral blood_DN_rep5

city: Ningbo

first: Jin

last: Xu

address: 818 Fenghua Road

institute: Ningbo University

data_processing:
Basecalls performed using CASAVA version 1.7
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to genome (GRCh38/hg19) using Hisat2 v2.0.5.
Reads counts aligned to each gene were expressed as FPKM using RSEM v.1.2.8. FPKM refers to the number of fragments per kilobase of transcript sequence per millions base pairs sequenced, considering the effect of sequencing depth and gene length for the reads count at the same time.
Genome_build: GRCh38/hg19
Supplementary_files_format_and_content: peak text files

source_name: Peripheral blood mononuclear cells

extract_protocol:
HP total RNA extraction kit was used to extract total RNA from 1mL PBMCs according to the manufacturer's instructions.
RNA-sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs).

value: Peripheral blood mononuclear cells


title: RNAseq of SJMMAML066074_O1-62_SPL_KD022

description: RNAseq of SJMMAML066074_O1-62_SPL_KD022

value: Spleen


title: Patient_97 SAMPLE_97

data_processing: Data analysis was performed in nSover software version 4.0

value: Primary Skin melanoma

value: woman


title: Peripheral blood_DN_rep4


title: HK2_2_DMSO_14


title: HK2_2_DMSO_13


title: Patient_96 SAMPLE_96

value: nonbrisk


title: RNAseq of SJMMAML066069_O1-75_SPL_KD022

description: RNAseq of SJMMAML066069_O1-75_SPL_KD022

value: TCF3-ZNF384 +e8, NRAS G12D


title: Peripheral blood_DN_rep3


title: Patient_95 SAMPLE_95

value: negative


title: RNAseq of SJMMAML066067_O1-66_SPL_KD022

description: RNAseq of SJMMAML066067_O1-66_SPL_KD022

value: Standard


title: Isolate_1-IL_1_24hr

value: human retinal endothelial cells (HREC)


title: RNAseq of SJMMAML066068_O1-68_SPL_KD022

description: RNAseq of SJMMAML066068_O1-68_SPL_KD022


title: HK2_2_DMSO_11

value: proximal tubular cells


title: Peripheral blood_DN_rep2


title: RNAseq of 984_SPL_KD019

description: RNAseq of 984_SPL_KD019

value: NRAS G12D


title: HK2_2_DMSO_15


title: Patient_94 SAMPLE_94

value: Superficial spreading melanoma

value: alive


title: Patient_93 SAMPLE_93

value: man

value: brisk


title: Peripheral blood_DN_rep1


title: Peripheral blood_DPN_rep5


title: HK2_2_DMSO_10


title: RNAseq of SJMMAML066086_O1-UT_BM_KD019

description: RNAseq of SJMMAML066086_O1-UT_BM_KD019

value: Bone Marrow

value: Wild type


title: Patient_92 SAMPLE_92

value: positive


title: HK2_2_DMSO_9


title: Peripheral blood_DPN_rep4

value: Peripheral blood mononuclear cells


title: RNAseq of SJMMAML066073_O1-996_SPL_KD021

value: lentiviral transduction, transplant into BL6 mice, harvest tissue and sort GFP+ cells

value: Spleen

value: TCF3-ZNF384 -e8, NRAS G12D


title: Patient_91 SAMPLE_91

value: Primary Skin melanoma

value: woman

value: absent


title: HK2_2_DMSO_12


title: HK2_2_DMSO_8


title: Patient_90 SAMPLE_90

value: nonbrisk


title: RNAseq of SJMMAML066072_O1-3871_SPL_KD020

value: Standard


title: HK2_2_DMSO_7

value: proximal tubular cells


title: RNAseq of SJMMAML066071_O1-1723_SPL_KD019


title: Peripheral blood_DPN_rep2


title: Patient_89 SAMPLE_89

value: Superficial spreading melanoma


title: RNAseq of SJMMAML066070_O1-1718_SPL_KD018


title: Peripheral blood_DPN_rep1


title: HK2_2_DMSO_5


title: HK2_2_DMSO_6


title: RNAseq of SJMMAML066087_O1-UT_BM_KD018

description: RNAseq of SJMMAML066087_O1-UT_BM_KD018

value: wild type


title: Patient_88 SAMPLE_88

value: alive

value: man

value: negative


title: Peripheral blood_DR_rep4


title: Peripheral blood_DR_rep5


title: RNAseq of SJMMAML066080_O1-1751_SPL_KD023

source_name: ARF-null lineage negative bone marrow

value: ARF-null TCF3-ZNF384 -e8, NRAS G12D


title: Patient_86 SAMPLE_86

value: dead

value: brisk


title: Patient_87 SAMPLE_87


title: HK2_2_DMSO_3


title: Patient_85 SAMPLE_85

value: positive


title: Peripheral blood_DPN_rep3

value: Peripheral blood mononuclear cells


title: RNAseq of SJMMAML066079_O1-172_SPL_KD023

value: lentiviral transduction, transplant into BL6 mice, harvest tissue and sort GFP+ cells

value: Spleen


title: RNAseq of SJMMAML066078_O1-171_SPL_KD023


title: HK2_2_DMSO_2


title: Patient_84 SAMPLE_84

value: Primary Skin melanoma


title: HK2_2_DMSO_1


title: Peripheral blood_DR_rep3


title: RNAseq of 173_BM_KD023

description: RNAseq of 173_BM_KD023

value: Bone Marrow


title: Peripheral blood_DR_rep2


title: Peripheral blood_T2DM_rep5


title: 18098D-02-43

city: Washington

first: Valerie

middle: Wailin

last: Hu

state: DC

department: Biochemistry and Molecular Medicine

institute: The George Washington University School of Medicine and Health Sciences

data_processing:
Filtered raw fastq files using Illumina quality flag
Followed CpG_Me workflow which included the steps below.
Trimmed to remove adapters and 5' and 3' methylation bias with Trim Galore!
Aligned to hg38 reference genome with Bismark
Removed PCR duplicates with Bismark
Extracted CpG methylation counts at all covered sites to generate genome-wide cytosine methylation reports with Bismark
Genome_build: hg38
Supplementary_files_format_and_content: Bismark genome-wide cytosine methylation report for each sample with columns for chromosome, CpG position, strand, methylated count, unmethylated count, dinucleotide context, and trinucleotide context

source_name: male from the Faroe Islands (Denmark)

extract_protocol:
Sperm was isolated from semen (which contains various cell types) using a published discontinuous gradient protocol (Wu, de Gannes, Luchetti, & Richard Pilsner, 2015). DNA was isolated from the purified sperm cells using a Qiagen AllPrep DNA/RNA mini kit following the manufacturer's protocol. Somatic cell contamination after sperm isolation never exceeded 1% of total cells.
The samples were sent to Admera Health (South Plainfield, NJ), a CLIA-certified laboratory, for WGBS analyses. The directional Illumina TruSeq DNA Methylation library kit was used for sample preparation following the manufacturer's protocol. WGBS was then performed on an Illumina HiSeq X sequencer resulting in 150 bp PE reads achieving roughly 4x coverage genome wide per sample. Raw FASTQ files were received from Admera Health for further analyses. All samples were processed blindly without the processors' knowledge of tertile level from sperm isolation through the WGBS analyses.

treatment_protocol: Genomic DNA was treated with bisulfite for downstream whole genome bisulfite sequencing analyses of DNA methylation as described below

tag: sample group

value: Validation

tag: tertile

value: Third

value: male

value: sperm

tag: bmi

tag: storage (days)

tag: batch

tag: sperm motility (%)

tag: smoking

value: No

tag: pp'-dde    (mg/mg lipid)


title: HK2_2_DMSO_4

tag: cell line

value: proximal tubular cells

tag: treatment


title: Patient_82 SAMPLE_82

tag: tissue

tag: histology

value: Superficial spreading melanoma

tag: status after 5 years

value: alive

tag: Sex

value: man

tag: status

value: absent

tag: braf v600e ihc status


title: RNAseq of 182_BM_KD023

description: RNAseq of 182_BM_KD023

tag: growth conditions

tag: genotype

value: ARF-null TCF3-ZNF384 +e8, NRAS G12D

tag: input

value: Standard


title: Peripheral blood_DR_rep1

value: Peripheral blood mononuclear cells

tag: age


title: Peripheral blood_T2DM_rep4


title: 18098D-02-38

tag: sample group

tag: tertile

tag: bmi

tag: storage (days)

value: Yes


title: RNAseq of SJMMAML066077_O1-181_SPL_KD023

value: lentiviral transduction, transplant into BL6 mice, harvest tissue and sort GFP+ cells

value: Spleen


title: RNAseq of 174_BM_KD023

description: RNAseq of 174_BM_KD023

value: Bone Marrow

value: ARF-null TCF3-ZNF384 -e8, NRAS G12D


title: Patient_81 SAMPLE_81

value: Primary Skin melanoma

value: woman

value: nonbrisk

value: positive

tag: Stage


title: Patient_80 SAMPLE_80

value: brisk

value: negative


title: 18098D-02-34

value: Validation

value: Third

value: male

value: sperm

tag: batch

tag: sperm motility (%)

tag: smoking

value: No

tag: pp'-dde    (mg/mg lipid)


title: RNAseq of SJMMAML066076_O1-179_SPL_KD023

tag: tissue

value: ARF-null TCF3-ZNF384 +e8, NRAS G12D

value: Standard


title: Peripheral blood_T2DM_rep3

value: Peripheral blood mononuclear cells


title: Peripheral blood_T2DM_rep2


title: 18098D-02-31

tag: Sex


title: Patient_79 SAMPLE_79

tag: histology

value: Superficial spreading melanoma

tag: status after 5 years

value: alive

value: man

tag: status


title: RNAseq of CTRL_BM_KD023

description: RNAseq of CTRL_BM_KD023

tag: growth conditions

value: lentiviral transduction, transplant into BL6 mice, harvest tissue and sort GFP+ cells

value: Bone Marrow

tag: genotype

value: ARF-null


title: Patient_83 SAMPLE_83

value: Primary Skin melanoma

value: dead

tag: age

value: absent

tag: braf v600e ihc status


title: Patient_78 SAMPLE_78

value: woman

value: positive


title: Peripheral blood_T2DM_rep1


title: 18098D-02-25

tag: sample group

value: Validation

tag: tertile

value: Third

value: male

value: Yes


title: 18098D-02-23

value: sperm

tag: bmi

tag: storage (days)


title: Peripheral blood_HC_rep5

value: Peripheral blood mononuclear cells


title: 18098D-02-19

tag: batch


title: TCF3-ZNF384 HiCHIP H3K27Ac Replicate 1

data_processing:
Library strategy: HiChIP
Paired-end reads of 100bp were trimmed for adapters cutadapt(version 1.9, paired-end mode, default parameter with “ -m 25 -O 6 ”).
Trimmed reads were then processed by HiC-Pro(version 2.11.4) on mouse genome mm10 (GRCm38 from GENCODE) and Arima fragment file(Ligation sites GATC,GANTC).
Bowtie2-2.2.4, samtools-1.2, R-3.4.0, Python-2.7.12 were configured for HiC-Pro.
allValidPairs files from HiC-Pro pipeline were then used to generate bigwig file(make_viewpoints.py from HiC-Pro) for IGV inspection.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
All H3K27ac HiChIP experiments were performed using the Arima-HiC+ kit (Arima Genomics A101020) according precisely to the manufacturer’s protocols (Arima-HiC+ document numbers A160430 v00 (HiChIP).
Libraries were constructed using the Arima-HiC+ kit (Arima Genomics A101020) according precisely to the manufacturer’s protocols (Arima-HiC+ document numbers A160169 v00 (library preparation))

tag: cell type

value: pre-B cells

tag: strain

tag: transduction

value: TCF3-ZNF384-e13-e5-C-HA (represents TCF3-ZNF384-no exon 8-HA)

tag: protocol

value: HiChIP H3K27Ac

tag: antibody

value: H3K27ac (Active Motif am91193 lot#22420004)


title: TAF15-ZNF384 HiCHIP H3K27Ac Replicate 2


title: Peripheral blood_HC_rep4

tag: tissue


title: Peripheral blood_HC_rep3


title: 18098D-02-13

tag: Sex

tag: sperm motility (%)

tag: smoking

value: No

tag: pp'-dde    (mg/mg lipid)


title: 18098D-02-08

tag: age


title: TAF15-ZNF384 HiCHIP H3K27Ac Replicate 1

tag: genotype

value: ARF-null


title: ZNF384 HiCHIP H3K27Ac Replicate 2


title: Peripheral blood_HC_rep2


title: 18098D-02-05

tag: sample group


title: Patient_74 SAMPLE_74

value: Primary Skin melanoma

tag: histology

value: Superficial spreading melanoma

tag: status after 5 years

value: alive

value: man

tag: status

tag: braf v600e ihc status

tag: Stage


title: Peripheral blood_HC_rep1


title: Patient_73 SAMPLE_73

value: brisk

value: positive


title: ZNF384 HiCHIP H3K27Ac Replicate 1

tag: cell type

tag: strain


title: 18098D-02-51

value: Validation

tag: tertile

value: First

tag: bmi

tag: storage (days)

tag: batch


title: TCF3-ZNF384 HiCHIP H3K27Ac Replicate 2

tag: transduction

tag: protocol

tag: antibody


title: 18098D-02-50

tag: Sex

value: male

tag: tissue

tag: age

tag: sperm motility (%)

tag: smoking

tag: pp'-dde    (mg/mg lipid)


title: scRNA-seq of HEB59

description: sc RNAseq of HEB59

data_processing:
bcl2fastq/2.20.0.422 software used for basecalling.
Sequenced reads were mapped using 10X Cellranger (v5.0.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: cell barcodes
Supplementary_files_format_and_content: gene list
Supplementary_files_format_and_content: gene expression  in each cell

source_name: bone marrow

extract_protocol:
Fresh bone marrow cells were harvested from mouse femur and tibia. They were treated with red cell lysis. Samples were divided into two samples (half for bulk bone marrow and half for lineage negative selection). Lineage negative cells were isolated with Miltenyi Biotec kit (130-090-858) and stained with anti-biotin. Live cells were sorted from bulk bone marrow samples or live, biotin-negative cells were sorted from lineage negative samples. 5000 bulk and 5000 lineage negative were pooled together for library preparation.
10X Genomics Single Cell RNA version 3.1

value: bone marrow

tag: genotype

value: 6 weeks


title: Donor 3 SARS-CoV-2 Replicate 5

city: St. Louis

first: Stacey

middle: Lynn

last: Rentschler

state: Missouri

address: 660 S Euclid Ave

institute: Washington University in St. Louis

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Genome_build: Ensembl GRCm38.76 and GRCh38.76
Supplementary_files_format_and_content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Isolated primary cardiac pericytes

growth_protocol: Cardiac pericytes were plated at 8 x 103 cells/cm2 in flat-bottomed 24-well plates 2-4 days before the start of an experiment and cultured in Pericyte Medium (Sciencell cat#1201)

extract_protocol:
RNA was extracted using the 5X MagMax Pathogen RNA/DNA isolation kit (Thermo Scientific cat# 4462359) on the Kingfisher Flex extraction robot (Thermo Scientific).
Takara-Clontech SMARTer Ultra Low RNA

treatment_protocol: Cardiac pericytes were replated for the experiments and allowed to settle for at least 2 days before the infection. The SARS-CoV-2 mNeonGreen viral stock was diluted by the Pericyte Growth Medium at a multiplicity of infection (MOI of 1) and added onto cells instead of the growth medium for 3 hours to allow viral entry. After incubation, cells were washed with 1 mL of warm PBS three times and replaced with fresh culture medium.

value: Primary cardiac pericytes

tag: treatment

value: SARS-CoV-2 mNeonGreen MOI=1

tag: tissue source

value: Non-failing Explanted Adult Left Ventricle


title: 18098D-02-42

tag: sample group

value: sperm

value: Yes


title: scRNA-seq of HEB57

description: sc RNAseq of HEB57

value: Wild type


title: Patient_77 SAMPLE_77

value: Primary Skin melanoma

tag: histology

tag: status after 5 years

value: woman

tag: status

tag: braf v600e ihc status

tag: Stage


title: Patient_72 SAMPLE_72

value: Superficial spreading melanoma

value: alive


title: Donor 3 SARS-CoV-2 Replicate 4

tag: cell type


title: Patient_71 SAMPLE_71

value: brisk


title: Patient_75 SAMPLE_75

value: man

value: negative


title: Patient_76 SAMPLE_76

value: positive


title: 18098D-02-39

value: Validation

tag: tertile

value: First

value: male

tag: bmi

tag: storage (days)

tag: batch


title: Donor 3 SARS-CoV-2 Replicate 3

value: Primary cardiac pericytes


title: scRNA-seq of HEB55

description: sc RNAseq of HEB55

tag: tissue

value: bone marrow

tag: Sex

tag: age

value: 6 weeks


title: Patient_70 SAMPLE_70

value: nonbrisk