title: Bamse217

description: Total RNA from whole blood from Bamse217


title: Bamse216

status: Public on Dec 03 2021

type: RNA

city: La Tronche

first: Nathanaël

last: Lemonnier

address: Allée des Alpes

department: Institute for Advanced Biosciences

country: France

institute: University Grenoble Alpes

description: Total RNA from whole blood from Bamse216

hyb_protocol: Hybridization, Wash and Stain Kit (Affymetrix): Affymetrix protocol was followed with Fluidics washing is FS450_0001

scan_protocol: 7000G scanner (Affymetrix)

data_processing:
CEL files were processed in R with RMA/limma
probe group file: HTA-2_0.na36.hg19.probeset.csv
meta-probeset file: HTA-2_0.na36.hg19.transcript.csv

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

label_protocol: WT PLUS (Affymetrix): Affymetrix protocol was followed

growth_protocol: whole blood drawn from BAMSE subjects

extract_protocol: PAXgene Blood RNA Kit (QIAGEN) eluted in 80 µl of elution buffer, 7 µl were aliquoted for quality control

treatment_protocol: not applicable

tag: gender

tag: age (months)

tag: allergy

tag: asthma

tag: dermatitis

tag: rhinitis

tag: tissue

value: whole blood


title: Bamse214

description: Total RNA from whole blood from Bamse214


title: Bamse219

description: Total RNA from whole blood from Bamse219


title: Bamse212

description: Total RNA from whole blood from Bamse212


title: Bamse210

description: Total RNA from whole blood from Bamse210


title: Bamse21

description: Total RNA from whole blood from Bamse21


title: Bamse211

description: Total RNA from whole blood from Bamse211


title: Bamse209

description: Total RNA from whole blood from Bamse209


title: Bamse225

description: Total RNA from whole blood from Bamse225


title: Bamse207

description: Total RNA from whole blood from Bamse207


title: Bamse208

description: Total RNA from whole blood from Bamse208


title: Bamse203

description: Total RNA from whole blood from Bamse203


title: Bamse213

description: Total RNA from whole blood from Bamse213


title: Bamse206

description: Total RNA from whole blood from Bamse206


title: Bamse204

description: Total RNA from whole blood from Bamse204


title: Bamse205

description: Total RNA from whole blood from Bamse205


title: Bamse2

description: Total RNA from whole blood from Bamse2


title: Bamse198

description: Total RNA from whole blood from Bamse198


title: Bamse201

description: Total RNA from whole blood from Bamse201


title: Bamse202

description: Total RNA from whole blood from Bamse202


title: Bamse200

description: Total RNA from whole blood from Bamse200


title: Bamse197

description: Total RNA from whole blood from Bamse197


title: Bamse190

description: Total RNA from whole blood from Bamse190


title: Bamse199

description: Total RNA from whole blood from Bamse199


title: Bamse20

description: Total RNA from whole blood from Bamse20


title: Bamse22

description: Total RNA from whole blood from Bamse22


title: Bamse224

description: Total RNA from whole blood from Bamse224


title: Bamse196

description: Total RNA from whole blood from Bamse196


title: Bamse195

description: Total RNA from whole blood from Bamse195


title: Bamse222

description: Total RNA from whole blood from Bamse222


title: Bamse187

description: Total RNA from whole blood from Bamse187


title: Bamse215

description: Total RNA from whole blood from Bamse215


title: Bamse189

description: Total RNA from whole blood from Bamse189


title: Bamse193

description: Total RNA from whole blood from Bamse193


title: Bamse19

description: Total RNA from whole blood from Bamse19


title: Bamse188

description: Total RNA from whole blood from Bamse188


title: Bamse184

description: Total RNA from whole blood from Bamse184


title: Bamse186

description: Total RNA from whole blood from Bamse186


title: Bamse18

description: Total RNA from whole blood from Bamse18


title: Bamse185

description: Total RNA from whole blood from Bamse185


title: Bamse194

description: Total RNA from whole blood from Bamse194


title: Bamse176

description: Total RNA from whole blood from Bamse176


title: Bamse183

description: Total RNA from whole blood from Bamse183


title: Bamse175

description: Total RNA from whole blood from Bamse175


title: Bamse180

description: Total RNA from whole blood from Bamse180


title: Bamse179

description: Total RNA from whole blood from Bamse179


title: Bamse181

description: Total RNA from whole blood from Bamse181


title: Bamse177

description: Total RNA from whole blood from Bamse177


title: Bamse178

description: Total RNA from whole blood from Bamse178


title: Bamse182

description: Total RNA from whole blood from Bamse182


title: Bamse192

description: Total RNA from whole blood from Bamse192


title: Bamse191

description: Total RNA from whole blood from Bamse191


title: Bamse173

description: Total RNA from whole blood from Bamse173


title: Bamse171

description: Total RNA from whole blood from Bamse171


title: Bamse170

description: Total RNA from whole blood from Bamse170


title: Bamse174

description: Total RNA from whole blood from Bamse174


title: Doug12_root_MG132_8hr

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

description: Root, MG132 8hr

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
Raw CEL files were normalized using the RMA background correction with quantile normalization, log base 2 transformation and mean probe-set summarization with adjustment for GC content.
The file normalized_data_matrix.txt includes  the RMA signal intensity values.

molecule: polyA RNA

organism: Brassica napus

source_name: Root, MG132 8hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Brassica napus plant were grown hydroponically in a growth chamber (26 C) with a 14/10 light/dark cycle

extract_protocol: cDNA was created using Invitrogen's SuperScript III synthesis kit

treatment_protocol: Brassica napus roots were treated with either 0.1% DMSO or 50 micromolar MG132 dissolved in DMSO

value: root


title: Doug8_root_MG132_8hr

description: Root, MG132 8hr


title: Doug11_root_control_8hr

description: root, control 8hr

source_name: root, control 8hr


title: Bamse172

description: Total RNA from whole blood from Bamse172


title: Doug7_root_control_8hr

description: root, control 8hr


title: Bamse154

description: Total RNA from whole blood from Bamse154


title: Bamse16

description: Total RNA from whole blood from Bamse16


title: Bamse156

description: Total RNA from whole blood from Bamse156


title: Doug4_root_MG132_8hr

description: Root, MG132 8hr


title: Bamse167

description: Total RNA from whole blood from Bamse167


title: Bamse164

description: Total RNA from whole blood from Bamse164


title: Bamse168

description: Total RNA from whole blood from Bamse168


title: Bamse159

description: Total RNA from whole blood from Bamse159


title: Bamse17

description: Total RNA from whole blood from Bamse17


title: Bamse169

description: Total RNA from whole blood from Bamse169


title: CW-2

type: SRA

city: Daqing

first: jili

last: zhang

address: 5 Xinfeng Road

country: China

institute: heilongjiang bayi agricultural university

library_source: transcriptomic

data_processing:
Data quality control application software FastQC version 0.10.1; RNAseq quality control application software RSeQC version 2.6.4; Genome comparison application software Hisat version 2.0; Transcript splicing and merging application software StringTie version 1.3.4; Transcript quantification and difference comparison And the visualization application software edgeR;
Application database information: Genome: ftp://ftp.ensemblgenomes.org/pub/release-45/plants/fasta/zea_mays/dna/  GO: http://geneontology.org  KEGG: http://www.kegg.jp/kegg
The expression level of genes mainly adopts FPKM (Fragments Per Kilobase of exon model per Million mapped reads)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Zea mays

source_name: CW-leaf2 represent drip irrigation repeat 3 sample,named CW-2

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

value: leaf

tag: treatment

value: soil moist treatment


title: CW-3

source_name: CW-leaf3 represent drip irrigation repeat 3 sample,named CW-3


title: Bamse155

description: Total RNA from whole blood from Bamse155


title: Bamse165

description: Total RNA from whole blood from Bamse165


title: Bamse161

description: Total RNA from whole blood from Bamse161


title: Bamse160

description: Total RNA from whole blood from Bamse160


title: Bamse151

description: Total RNA from whole blood from Bamse151


title: Bamse166

description: Total RNA from whole blood from Bamse166


title: Bamse162

description: Total RNA from whole blood from Bamse162


title: Doug3_root_control_8hr

description: root, control 8hr


title: Bamse15

description: Total RNA from whole blood from Bamse15


title: Bamse157

description: Total RNA from whole blood from Bamse157


title: Bamse163

description: Total RNA from whole blood from Bamse163


title: Bamse152

description: Total RNA from whole blood from Bamse152


title: Bamse153

description: Total RNA from whole blood from Bamse153


title: CW-1

source_name: CW-leaf1 represent drip irrigation repeat 1 sample,named CW-1


title: Bamse150

description: Total RNA from whole blood from Bamse150


title: Bamse158

description: Total RNA from whole blood from Bamse158


title: LW-3

source_name: LW-leaf3 represent negative pressure irrigation repeat 3 sample,named LW-3

value: drought conditions with negative pressure continuous water supply


title: LW-2

source_name: LW-leaf2 represent negative pressure irrigation repeat 2 sample,named LW-2


title: LW-1

source_name: LW-leaf1 represent negative pressure irrigation repeat 1 sample,named LW-1


title: R_6545_ST

city: JOUY-en-JOSAS

first: gilles

last: charpigny

state: ILe de France

address: domaine de Vilvert

department: Physiologie Animale Systeme Elevage

institute: INRAE

data_processing:
The cDNA sequence database for Bos taurus was obtained from Ensembl genome browser (release-98; Bos_taurus.ARS-UCD1.2.cdna.all.fa) and used to build a reference index for the bovine transcriptome.
RNA-Seq reads were pseudo-aligned to the reference index with Salmon (Release 1.1.0).
Gene-level counts were prepared for differential expression analysis with tximport (release 1.14.2) as part of the Bioconductor package.
Differential expression was measured using DESeq2 (release 1.26.0) with default parameters as part of the Bioconductor package.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: GSCN*.quant.sf is the quantification file output of Salmon (quasi-mapping and transcript quantification tool for RNA-seq data). This is a plain text, tab-separated file. The columns have the following interpretation:
Name: the name of the target transcript.
Length: the length of the target transcript in nucleotides.
EffectiveLength: the computed effective length of the target transcript.
TPM: salmon's estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM). TPM is the recommended relative abundance measure to use for downstream analysis.
NumReads: Salmon's estimate of the number of reads mapping to each transcript that was quantified. It is an estimate insofar as it is the expected number of reads that have originated from each transcript given the structure of the uniquely mapping and multi-mapping reads and the relative abundance estimates for each transcript.

organism: Bos taurus

source_name: endometrium

extract_protocol:
Total RNA was extracted using the Arcturus PicoPure RNA isolation kit (Applied Biosystems, Life Technologies), according to the manufacturer’s instructions.
Full length cDNA were generated from 2.5 ng of total RNA using Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 10 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, CA) followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoresis.

treatment_protocol: The three endometrial cell types (luminal epithelium, glandular epithelium and stroma cells) were collected by laser microdissection from endometrial biopsies performed at 45 days postpartum.

tag: breed

value: Holstein

tag: cell type

value: stromal cells

tag: p4 level


title: 20211006_R941_pxr1d_YPD

city: Santa Cruz

first: Manuel

last: Ares

state: CA

address: 1156 High St

country: USA

institute: University of California, Santa Cruz

data_processing:
Basecalling with Guppy 3.1.5+781ed57
split fast5's with multi_to_single_fast5
index with nanopolish
align to yeast 18S and 25S rRNA reference
signalAlign produced posterior probabilities of events aligned to reference kmers
embed_fast5 aggregated posterior probabilites to produce probability of modification
Genome_build: Saccharomyces cerevisiae S288c ribosomal RNA sequences
Supplementary_files_format_and_content: embed_fast5 outputs contain modification calls (read_id,contig,reference_index,strand,variants,prob1,prob2,prob3,prob4) for each modification site for each read. Prob1 is probability of being unmodified and prob2 is modified. Prob3 and prob4 are not used.

organism: Saccharomyces cerevisiae

growth_protocol: Yeast strains GAL-NOP58 and GAL-CBF5 are described in (Lafontaine and Tollervey 1999)(Lafontaine et al. 1998). Cells were grown at 30 °C in YEPgal liquid medium (2% galactose, 2% peptone, 1% yeast extract) or shifted to liquid YEPD (2% dextrose, 2% peptone, 1% yeast extract) to mid-log phase (OD600 = 0.25-0.5) for 16 hours to repress expression of Nop58 or Cbf5.  Cells were harvested by centrifugation and RNA was isolated. The spp382-1 strain is described in (Pandit et al. 2006). The strains deleted for the SNR80 (YWD448a), SNR83 (YWD451a) or SNR87 (YWD452a) genes are described in (Schattner et al. 2004). Yeast strains deleted for the SNR4 and SNR45 genes are described in (Parker et al. 2018).

extract_protocol:
RNA was extracted from approximately five total OD600 of cells (usually 10 ml culture at OD600 = 0.5 for mid log cells, 0.5 ml of stationary cells at OD600 = 10) using a hot phenol protocol 1 described in (Ares 2012).
Direct RNA sequencing libraries were constructed using the SQK-RNA002 (Oxford Nanopore Technologies) kit following the manufacturer’s protocol with the following modifications.  Briefly, 750 ng of total yeast RNA was used as input material.  To facilitate ligation of sequencing adapters to endogenous yeast 18S and 25S rRNA, 1 ul of 10 pmol/ul custom oligonucleotide duplexes complementary to the 3’ ends of 18S and 25S rRNA and the 5’ end of the ONT RMX sequencing adapter were used instead of the kit provided RTA adapter (Supplemental Table S5).  To create duplexes, 100 pmol of either 18S or 25S splint oligo was incubated with 100 pmol of sequencing adapter and nuclease free H20 in a total volume of 10 ul.  Reactions were heated to 95 °C for 2 minutes and gradually cooled at 65 °C for 10 minutes, 48 °C for 10 minutes, room temperature for 10 minutes and then placed on ice. Annealed oligonucleotide duplexes targeting 18S and 25S rRNAs were then pooled in equimolar ratio and 1 ul of the pool was used for sequencing library preparation. In the case of T7 rRNA sequencing libraries, T7-18S splint and T7-25S splint oligos were used to capture the 3’ end generated by HindIII digestion and run-off transcription.  To enhance ligation efficiency during library preparation, the first and second ligation steps were increased from 10 minutes to 15 minutes and performed at room temperature. Reverse transcription was omitted. Sequencing-adapted libraries were eluted in 21 ul of elution buffer.

treatment_protocol: Unless indicated, all other strains were grown in YEPD at 30 °C to mid-log phase.  Cells exposed to various environmental conditions were treated as follows: 1% KOAc (1 hr, 30 °C), cycloheximide (1 ug/ml for 1 hour), rapamycin (200 ng/ml for 1 or 5 hours), and pladienolide B (5 uM for 1 hour). Stationary phase cells were grown to an OD600 = 10. Strains carrying prp16-302 (Madhani and Guthrie 1994) and prp43 Q423N (Leeds et al. 2006) mutations, and wild type (Schattner et al. 2004) were grown to mid log phase at 30 °C and shifted to 18 °C for 1 hour by addition of an equal volume of 6 °C YEPD.

tag: strain

value: BY4742 pxr1<delta>::KanMX4

tag: strain information

value: MATalpha; his3<delta>1; leu2<delta>0; lys2<delta>0; ura3<delta>0 pxr1<delta>::KanMX4; pYCplac111 (LEU2 CEN)

tag: genotype/treatment

value: pxr1 KO

tag: stress

tag: molecule subtype

value: ribosomal RNA


title: 20211021_R941_pxr1d_YPD_repeat2


title: 20211008_R941_prp43_18deg_YPD_repeat2

value: YJPS575 prp43 Q423N

value: MATa; his3<delta>; leu2<delta>; LYS2; met15<delta>0; ura3<delta>; prp43<delta>::KanMX4; (pJPS261 prp43 Q423N URA3 CEN)

value: prp43 mutant shifted to cold for 1hr to inhibit prp43 function

value: shifted to 18 °C for 1


title: 20211011_R941_dbp3d_YPD_repeat2

value: BY4741 dbp3<delta>::KanMX4

value: MATa; his3<delta>1; leu2<delta>0; met15<delta>0; ura3<delta>0; dbr1<delta>::KanMX4

value: dbp3 KO


title: R_6545_LE

value: luminal cells


title: Bamse146

description: Total RNA from whole blood from Bamse146

value: whole blood


title: Bamse148

description: Total RNA from whole blood from Bamse148


title: Bamse145

description: Total RNA from whole blood from Bamse145


title: Bamse143

description: Total RNA from whole blood from Bamse143


title: R_6545_GE

value: glandular cells


title: Bamse142

description: Total RNA from whole blood from Bamse142


title: Bamse147

description: Total RNA from whole blood from Bamse147


title: Bamse140

description: Total RNA from whole blood from Bamse140


title: 20211001_R941_YS602_WT_repeat3

value: Wild type


title: Bamse14

description: Total RNA from whole blood from Bamse14


title: 20210930_R941_YS602_WT_repeat2


title: Bamse144

description: Total RNA from whole blood from Bamse144


title: Bamse141

description: Total RNA from whole blood from Bamse141


title: R_6494_LE

value: Holstein


title: Bamse138

description: Total RNA from whole blood from Bamse138


title: 20210902_R941_snR4d_alpha_YPD

value: BY4742 snr4<delta>::KanMX4 (18S ac4c1280)

value: MATalpha; his3<delta>1; leu2<delta>0; lys2<delta>0; ura3<delta>0 snr4<delta>::KanMX4

value: snR4 KO


title: R_6494_ST

value: stromal cells


title: 20211007_R941_YS602_18_YPD3

value: wild type yeast shifted to cold for 1 hour

value: ribosomal RNA


title: 20210825_R941_mutant448

value: snR80 KO


title: R_6494_GE


title: Bamse137

description: Total RNA from whole blood from Bamse137


title: Bamse139

description: Total RNA from whole blood from Bamse139


title: Bamse135

description: Total RNA from whole blood from Bamse135


title: R_6492_LE


title: R_6492_ST


title: 20210722_R941_YS602_18_YPD2


title: R_6492_GE


title: 20210729_R941_dbr1d_YPD

value: BY4741 dbr1<delta>::KanMX4

value: Dbr1 KO


title: Bamse133

description: Total RNA from whole blood from Bamse133


title: 20210730_R941_sqs1d_YPD

value: BY4741 sqs1<delta>::kanMX4

value: MATa; his3<delta>1; leu2<delta>0; met15<delta>0; ura3<delta>0 sqs1<delta>::KanMX4

value: sqs1 KO


title: Bamse136

description: Total RNA from whole blood from Bamse136


title: 20210824_R941_snR45d_YPD

value: MATalpha; his3<delta>1; leu2<delta>0; lys2<delta>0; ura3<delta>0 snr45<delta>::KanMX4

value: snR45 KO


title: Bamse131

description: Total RNA from whole blood from Bamse131

value: whole blood


title: 20210720_R941_spp382_YPD

value: MATa; ura3<delta>0; trp1-289; leu2<delta>0; his3<delta>1; spp382∷KAN; pYCplac111-spp382-1

value: Spp382 KO


title: Bamse130

description: Total RNA from whole blood from Bamse130


title: Bamse132

description: Total RNA from whole blood from Bamse132


title: Bamse134

description: Total RNA from whole blood from Bamse134


title: R_5780_ST

value: Holstein


title: R_5780_LE

value: luminal cells


title: R_5780_GE

value: glandular cells


title: R_5771_ST

value: stromal cells


title: 20210719_R941_prp16_18deg_YPD

value: MATa; ade2; his3; leu2; lys2; prp16-302; trp1; ura3; snr6<delta>::LEU2; pSX6U (SNR6 URA3 CEN)

value: prp16 mutant shifted to cold for 1hr to inhibit prp16 function

value: shifted to 18 °C for 1


title: 20210716_R941_MIX

value: ribosomal RNA


title: Bamse125

description: Total RNA from whole blood from Bamse125


title: Bamse129

description: Total RNA from whole blood from Bamse129


title: Bamse13

description: Total RNA from whole blood from Bamse13


title: GRWT_NI-6

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

description: run 2

data_processing:
Obtained reads were checked for quality and adapter contamination with fastqc
Reads were mapped to the mm10 reference genome using the ensembl structural annotation (release 100) using the hisat2 aligner (v 2.1.0) with additional options, next to index, splice sites and reads: --avoid-pseudogene and -p 8
A count matrix was made with featurecounts (v 2.0.0) wih extra options --primary and -T 8
The count matrix was processed using DESeq2 to obtain differentially expressed genes (v 1.26.0) according to a multifactorial model incorporating the condition and run (formula ~ run + condition)
Genome_build: mm10
Supplementary_files_format_and_content: count matrix

organism: Mus musculus

source_name: mouse embryonic fibroblast

growth_protocol: cells were cultured in DMEM (Dulbecco’s modified Eagle’s medium, Gibco®, Life TechnologiesTM) supplemented with 10% FCS, 1mM sodium pyruvate, 0.1mM non-essential amino acids, 2mM L-glutamate, 0.2% β-mercapto-ethanol, 0.1mM pen/strep and 0.2% prophylactic PlasmocinTM at 37°C and 5% CO2

extract_protocol:
Total RNA was isolated from solvent- or Dex-stimulated MEF cells with Aurum total RNA mini kit (732‐6820; Bio‐Rad) according to the manufacturer's instructions. RNA concentration was measured and RNA quality was checked with the Agilent RNA 6000 Pico Kit (Agilent Technologies)
Library preparation and sequencing was performed according to the manufacturer’s instruction with the illumina Truseq library prep kit

treatment_protocol: MEF cells were seeded in 6-well plates in supplemented DMEM. Cells were treated for 5 hours with 1 µM Dex or solvent.

value: FVB/NJ

tag: genotype

value: GRwt/wt

value: vehicle 5h


title: R_5771_GE


title: Bamse128

description: Total RNA from whole blood from Bamse128

tag: gender


title: Bamse126

description: Total RNA from whole blood from Bamse126

tag: age (months)


title: Bamse127

description: Total RNA from whole blood from Bamse127

tag: allergy


title: Bamse124

description: Total RNA from whole blood from Bamse124

tag: asthma


title: Bamse121

description: Total RNA from whole blood from Bamse121

tag: dermatitis


title: Bamse120

description: Total RNA from whole blood from Bamse120

tag: rhinitis


title: Bamse123

description: Total RNA from whole blood from Bamse123

tag: tissue


title: Bamse119

description: Total RNA from whole blood from Bamse119


title: 20210619_R941_prp43

value: YJPS575 prp43 Q423N

value: MATa; his3<delta>; leu2<delta>; LYS2; met15<delta>0; ura3<delta>; prp43<delta>::KanMX4; (pJPS261 prp43 Q423N URA3 CEN)

value: prp43 mutant shifted to cold for 1hr to inhibit prp43 function


title: Bamse12

description: Total RNA from whole blood from Bamse12

value: whole blood


title: 20210618_R941_Mix


title: GRWT_NI-4

description: run 2

tag: treatment


title: R_5626_ST

tag: breed


title: GRWT_NI-5

description: run 2


title: 20210717_R941_YS602_18_YPD

value: wild type yeast shifted to cold for 1 hour


title: R_5626_GE

tag: cell type


title: Bamse122

description: Total RNA from whole blood from Bamse122


title: GRWT_DEX-6

description: run 2

value: 1 µM Dexamethasone 5h


title: 20210531_R941_WT_rapa5

value: rapamycin treated wild type

value: rapamycin (200 ng/ml for 1 or 5 hours)


title: 20210527_R941_Dbp3d_YPD

value: BY4741 dbp3<delta>::KanMX4

value: MATa; his3<delta>1; leu2<delta>0; met15<delta>0; ura3<delta>0; dbp3<delta>::KanMX4

value: dbp3 KO


title: R_5614_ST

value: Holstein

value: stromal cells

tag: p4 level


title: GRWT_DEX-5

description: run 2

tag: strain


title: G_6480_ST


title: G_6480_LE

value: luminal cells


title: R_5771_LE


title: GRDIM2-NI-2

description: run 2

value: FVB/NJ

value: GRL/L


title: Bamse117

description: Total RNA from whole blood from Bamse117


title: GRDIM2-NI-3

description: run 2

value: vehicle 5h


title: 20210413_R941_mutant452

value: YWD452a snR87<delta>::TRP1 (18S Am436)

tag: strain information

value: snR87 KO

value: ribosomal RNA


title: 20210414_R941_WT_CY

tag: genotype/treatment

value: Cycloheximide treated wild type

value: cycloheximide (1 ug/ml for 1 hour),


title: 20210521_R941_WT_stationary

value: stationary phase

tag: stress

value: grown to an OD600 = 10


title: G_6460_ST


title: GRDIM2-NI-1

description: run 2


title: G_6480_GE

value: glandular cells


title: 20210412_R941_WT_KOAC

value: KOAc treated wild type

value: 1% KOAc (1 hr, 30 °C)

tag: molecule subtype


title: G_6450_ST


title: Bamse118

description: Total RNA from whole blood from Bamse118

value: whole blood


title: GRDIM2-DEX-3

description: run 2

tag: genotype

value: 1 µM Dexamethasone 5h


title: Bamse114

description: Total RNA from whole blood from Bamse114

tag: gender


title: Bamse116

description: Total RNA from whole blood from Bamse116

tag: age (months)


title: GRWT_DEX-4

description: run 2

value: GRwt/wt


title: Bamse115

description: Total RNA from whole blood from Bamse115

tag: allergy


title: 20210415_R941_mutant451

value: snR83 KO


title: G_6450_GE

value: Holstein


title: Bamse149

description: Total RNA from whole blood from Bamse149

tag: asthma


title: Bamse111

description: Total RNA from whole blood from Bamse111

tag: dermatitis


title: Bamse110

description: Total RNA from whole blood from Bamse110

tag: rhinitis


title: GRDIM2-DEX-2

description: run 2

value: FVB/NJ

value: GRL/L


title: GRWT_NI-3

description: run 1

value: vehicle 5h


title: G_5645_LE

value: luminal cells


title: GRDIM2-DEX-1

description: run 2


title: G_5645_ST

value: stromal cells


title: 20210405_R941_mutant448

value: snR80 KO

value: ribosomal RNA


title: G_4463_GE


title: 20190619_R941_NOP58GLU

value: MAT:a; ura3-52; trp-; leu2-<delta>1; nop58::GAL-NOP58 HIS3; gal2; gal<delta>108

value: repressed expression of Nop58

value: shift to YEPD(extrose)


title: 20191014_R941_IVT

value: Invitro transcribed 18S and 25S yeast rRNA


title: Bamse112

description: Total RNA from whole blood from Bamse112

tag: tissue


title: Bamse113

description: Total RNA from whole blood from Bamse113


title: GRWT_NI-1

description: run 1

tag: treatment


title: 20190611_R941_CBF5GLU

value: MAT:a; ura3-52; trp-; leu2-<delta>1; cbf5::GAL-CBF5 HIS3; gal2; gal<delta>108

value: repressed expression of Cbf5


title: 20210410_R941_WT_YPD

value: Wild type


title: 20190610_R941_CBF5GAL

value: Cbf5 expressed

value: YEPGal(actose)


title: GRWT_NI-2

description: run 1

value: GRwt/wt


title: 20190617_R941_NOP58GAL

value: Nop58 exresssed


title: Bamse109

description: Total RNA from whole blood from Bamse109

value: whole blood


title: GRWT_DEX-3

description: run 1

value: FVB/NJ

value: 1 µM Dexamethasone 5h


title: G_5645_GE

tag: breed

value: Holstein

value: glandular cells


title: Bamse11

description: Total RNA from whole blood from Bamse11


title: GRWT_DEX-1

description: run 1


title: Para6: Paradoxical feedback, Replicate6

city: Pasadena

first: Yitong

last: Ma

address: 1200 E California Blvd

department: Division of Biology and Biological Engineering

institute: Caltech

data_processing:
trimmed and filtered by Trim Galore! (Babraham Institute)
counted with kallisto (Bray et al. 2016)
Genome_build: RefSeq GCF_000223135.1
Supplementary_files_format_and_content: Abundance count by kallisto

organism: Cricetulus griseus

source_name: CHO-K1 cell line

extract_protocol:
Cells were cultured for 2 days at under 80% confluence before harvested for bulk RNA extrusion (Qiagen #74104)
RNA-seq libraries were constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770) following manufacturer’s instructions

tag: cell line

tag: culture condition

value: Paradoxical feedback

tag: replicate


title: Bamse108

description: Total RNA from whole blood from Bamse108


title: Bamse107

description: Total RNA from whole blood from Bamse107


title: Bamse106

description: Total RNA from whole blood from Bamse106


title: Para7: Paradoxical feedback, Replicate7


title: Para5: Paradoxical feedback, Replicate5


title: GRMON_NI-2

description: run 1

tag: strain

value: GRD+L/D+L

value: vehicle 5h


title: G_3030_ST

tag: cell type

value: stromal cells

tag: p4 level


title: GRWT_DEX-2

description: run 1


title: GRMON_NI-3

description: run 1


title: Para3: Paradoxical feedback, Replicate3


title: Para4: Paradoxical feedback, Replicate4


title: Bamse105

description: Total RNA from whole blood from Bamse105


title: Bamse104

description: Total RNA from whole blood from Bamse104


title: Para2: Paradoxical feedback, Replicate2


title: Bamse103

description: Total RNA from whole blood from Bamse103


title: Bamse101

description: Total RNA from whole blood from Bamse101


title: GRMON_DEX-2

description: run 1


title: Homc-D4-BAP1-KO-2

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

country: Japan

institute: Kinjo Gakuin University

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression v3 8x60K Microarray (G) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37Â°C GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MeT-5A  cells were cultivated in RPMI1640 and HOMC-D4cells were cultivated in Iscove’s modified Dulbecco’s medium (IMDM; Gibco, Grand Island, NY), supplemented with 10% fetal bovine serum, penicillin (100U/ml) and streptomycin (100U/ml). The cells were typically passaged at a split.

extract_protocol: RNA was prepared using  NucleoSpin RNA kit (TaKaRa Bio Inc., Shiga, Japan) following the manufacturer's recommendations.  RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: MeT-5A  and HOMC-D4  cells were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: human mesothelial cell line

tag: source gender

value: male

tag: genotype/variation

value: BAP-KO


title: GRMON_DEX-3

description: run 1

tag: genotype


title: GRMON_NI-1

description: run 1


title: GRMON_DEX-1

description: run 1


title: Homc-D4-BAP1-KO-1


title: Homc-D4-WT1

value: WT


title: Neg6: Negative feedback, Replicate6

value: Negative feedback


title: GRKO_NI-3

description: run 1

value: GRko/ko


title: Bamse102

description: Total RNA from whole blood from Bamse102

tag: gender

tag: age (months)


title: Bamse100

description: Total RNA from whole blood from Bamse100

tag: allergy

tag: asthma


title: Homc-D4-parent

value: parent


title: Bamse1

description: Total RNA from whole blood from Bamse1

tag: dermatitis

tag: rhinitis


title: Para1: Paradoxical feedback, Replicate1


title: MeT-5A-WT1


title: MeT-5A-BAP-KO2


title: GRKO_NI-2

description: run 1

tag: treatment


title: Neg5: Negative feedback, Replicate5


title: Neg7: Negative feedback, Replicate7


title: MeT-5A-BAP-KO1


title: Bamse10

description: Total RNA from whole blood from Bamse10

tag: tissue


title: scRNAseq_T1L_Ileum_D4PI_reovirus_xGen

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: Weill Hall, 237 Tower Road

department: Meinig School of Biomedical Engineering

institute: Cornell University

description: Single-cell reoviral RNA sequencing of ileum tissue from T1L-infected neonatal mice at 4 dpi

data_processing:
Sequencing data were aligned to a combined mouse and reovirus reference genome using the Cell Ranger 6.0.0 pipeline (10x Genomics) to obtain a feature cell-barcode matrix.
Mus musculus genome and gene annotations (assembly: GRCm38) were downloaded from the Ensembl genome browser, and Reovirus strain Type 1 lang genome and gene annotations were downloaded from the NCBI browser. Genomes were processed using the Cell Ranger (10x Genomics) pipeline’s mkref command.
Genome_build: GRCm38
Supplementary_files_format_and_content: HDF5 file containing filtered feature barcode expression matrix (UMI counts)

source_name: Neonatal murine ileum

growth_protocol: Confirmed pregnant female C57BL/6J mice were ordered from Jackson Laboratories to be delivered at embryonic stage E14.5. The mice pups were weighed every day until the time points used in the study.

extract_protocol:
Intestinal ileum from respective stages were isolated aseptically, washed with ice-cold Hank’s Balanced Salt Solution, HBSS (without Calcium and Magnesium Chloride) to remove contamination. The ileum tissue was then opened longitudinally, washed again with HBSS, and minced into 1-2mm pieces. To isolate the epithelial layer of cells, ileum tissue pieces were incubated in HBSS with 10mM Ethylenediaminetetraacetic acid (EDTA) and 1mM Dithiothreitol, DTT for two cycles of 10 minutes under mild agitation at 37°C. After every 10 minute cycle, cell suspension containing the intestinal epithelial cells was collected, added to ice-cold phosphate buffered saline, PBS with 0.04% bovine serum albumin, BSA. The undigested pieces of lamina propria were then washed thoroughly with PBS (with calcium and magnesium chloride) to get rid of all EDTA. These pieces were then transferred  to fresh tubes and incubated in 200U/ml Collagenase type I (Gibco 17100-017) and 3mM calcium chloride in PBS for three cycles of 10 minutes under mild agitation at 37°C in 1.5 ml eppendorf tubes. After every 10 minute cycle, cell suspension containing the lamina propria cells was collected, added to ice-cold phosphate buffered saline, PBS with 0.04% BSA in separate tubes. At the end of the digestion, the cells were passed through a 40µm filter and washed twice in PBS with 0.04% BSA and then resuspended at 1 × 106 cells per ml. Cells from intestinal epithelium and lamina propria for each sample were stained with Trypan Blue and cell viability was calculated on automated cell counters. Cell counts adjusted with viability were then pooled as 40% epithelial cells and 60% lamina propria for each sample before loading on 10x Chromium.
10x Genomics Chromium Next GEM Single Cell 3’ RNA-seq Library Construction V3 Kit followed by IDT xGen Hybridization Capture Kit

treatment_protocol: Neonatal mice pups weighing 3 gram/ pup were gavaged using intramedic tubing (Becton Dickinson 427401) per os with 50 μl with 107 PFU reovirus type 1 lang (T1L): wildtype or K287T mutant in phosphate buffered saline (PBS) containing green food color (McCormick) via a 1ml tuburculin slip tip syringe (BD 309659) and 30G x 1/2 needle (BD 305106). Litters treated with PBS alone on the same day were used as mock controls for the respective infection groups.

value: Ileum

tag: infection state

tag: days post infection (dpi)

value: 4 dpi


title: scRNAseq_T1L_Ileum_D1PI_reovirus_xGen

description: Single-cell reoviral RNA sequencing of ileum tissue from T1L-infected neonatal mice at 1 dpi

value: 1 dpi


title: Neg4: Negative feedback, Replicate4

tag: cell line

tag: culture condition

tag: replicate


title: GRKO_DEX-3

description: run 1

tag: strain

value: FVB/NJ

value: 1 µM Dexamethasone 5h


title: AD6732

city: Bellaterra

first: Jesus

last: Amo-Aparicio

state: Barcelona

address: Av Can Domenech s/n, Facultad de Medicina M4-129

country: Spain

institute: Universitat Autonoma de Barcelona

description: IL-4  at 48h after SCI - Microglia

data_processing:
Aligment using STAR v2.5.3a with parameters --outFilterType BySJout     --outFilterMultimapNmax 20 --alignSJoverhangMin 8     --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20     --alignIntronMax 1000000 --alignMatesGapMax 1000000
Quantification using RSEM v1.3.0 with params --paired-end --bam --no-bam-output
Genome_build: GRCm38 / gencode M16
Supplementary_files_format_and_content: Table with RSEM counts for all samples (txt)

source_name: Mouse 10 IL-4 Microglia

growth_protocol: Macrophages and microglia were obtained from injured spinal cord at 24 hours after treatment

extract_protocol:
Macrophages and microglia were separated thorugh cell sorter. RNA extraction was performed using the RNeasy Micro Kit (Qiagen)
RNA sequencing libraries were prepared following the SMARTseq2 protocol with some modifications. Briefly, RNA was quantified using the Qubit RNA HS Assay Kit (ThermoFisher Scientific) and the input material used for the initial cDNA synthesis varied in function of the available sample concentration (0.12ng-10ng). Reverse transcription was performed using SuperScrpit II (Invitrogen) in the presence of oligo-dT30VN, template-switching oligonucleotides (1µM) and betaine (1M). The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Kappa Biosystems), 100 nM ISPCR primer, and 15 cycles of amplification. The amplified cDNA (200 ng) was fragmented using Nextera® XT (Illumina) and amplified for 10-12 cycles with indexed Nextera® PCR primers. The Nextera® library was purified twice with Agencourt Ampure XP beads (0.8:1 ratio). The libraries were sequenced on HiSeq2500 (Illumina, Inc) in paired-end mode with a read length of 2x76bp using TruSeq SBS Kit v4 and Nextera XT Index Kit of 8bp+8bp.

treatment_protocol: Mice were treated with IL-13, IL-4 or PBS at 48 hours after spinal cord injury

tag: mouse id

value: Mouse 10

tag: cell type

value: Microglia

value: Injured spinal cord


title: Neg2: Negative feedback, Replicate2


title: GRKO_NI-1

description: run 1

tag: genotype

value: vehicle 5h


title: AD6730

description: IL-4  at 48h after SCI - Microglia

source_name: Mouse 9 IL-4 Microglia

value: Mouse 9


title: AD6731

description: IL-4  at 48h after SCI - Macrophages

source_name: Mouse 10 IL-4 Macrophage

value: Macrophage


title: GRKO_DEX-2

description: run 1


title: AD6729

description: IL-4  at 48h after SCI - Macrophages

source_name: Mouse 9 IL-4 Macrophage


title: Neg1: Negative feedback, Replicate1


title: GRKO_DEX-1

description: run 1


title: Father with mild ID

type: genomic

city: Mumbai

first: Jitendra

middle: Vasudeo

last: Suralkar

state: Maharashtra

address: 13th floor, NMS Building, KEM Hospital Campus, Parel

department: Cytogenetics

country: India

institute: ICMR - National Institute of Immunohaematology

description: Male with mild intellecutal disability and no Albinism

hyb_protocol: Agilent Technologies SurePrint Technology G4450A SurePrint G3 Human Array Kit 8*60K glass slides each formatted with eight SurePrint G3 60K arrays was used for this purpose.

scan_protocol: Agilent G4900DA SureScan Microarray Scanner System was used.

data_processing: CytoGenomics software was used for data analysis. Analysis includes comparision with hg19 genome build. Default Analysis method - CGH V2 was used with GC correction window size =2kb, centralisation was OFF and diploid peak centralisation was kept ON. Algorhythm threshold was kept 6. LOH filter was kept OFF. Genomic filters were kept OFF with Default abberation filters ON (Minimum number of probes for amplification >=3 AND minimum size(kb) of Region for Amplification >=0.0 and Minimum Avg. Absolute Log ration for amplification>=0.25 AND Minimum number of probes for deletion >=3AND minimum size (Kb) of region for deletion >= 0.0 AND minimum average absolute log ratio for deletion >= 0.25 AND Nesting level <= 100 and minimum number of probes for gain >=3 and minimum number of probes for loss >=3 and minimum average absolute log ratio for gain >=0.25 and minimum average absolute log ratio for loss >=0.25 and minimum size (kb) of region for gain >=0.0 and minimum size(kb) of region for loss >= 0.0).

molecule: genomic DNA

label_protocol: High quality genomic DNA was extracted and labeled enzymatically with Cy3(Ref. DNA) or Cy5(Sample) dyes.

growth_protocol: peripheral blood was collected in EDTA vaccutainers

extract_protocol: Qiagen DNA isolation kit (Cat.51106) was used to isolate genomic DNA from stored samples

tag: Sex

value: Male

value: Blood

tag: disease state

value: mild ID

source_name: Reference gDNA

tag: sample type

value: Reference gDNA


title: GRDIM_NI-3

description: run 1

value: GRD/D


title: MeT-5A-parent

value: human mesothelial cell line

tag: source gender

value: male

tag: genotype/variation

value: parent


title: AD6728

description: IL-4  at 48h after SCI - Microglia

source_name: Mouse 8 IL-4 Microglia

value: Mouse 8


title: Proband

description: Male with Severe Intellectual disability with OCA1

value: ID (proband)


title: Neg3: Negative feedback, Replicate3

value: Negative feedback


title: Experimental group 2

city: Luzhou

first: tongjie

last: xu

state: sichuan

address: No. 25, Taiping street, Luzhou city

department: Department of Vascular Surgery

institute: The Affiliated Hospital of Southwest Medical University

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal ('All Targets Value') were chosen for further data analysis.

source_name: Human aortic vascular smooth muscle cells

label_protocol: standard protocol

extract_protocol: TRIzol® Reagent (Invitrogen life technologies)

value: human aortic smooth muscle cells (HASMCs)

value: induced by DPP4 for 4 days


title: Experimental group 3


title: unCt3: uncontrolled growth, Replicate3

value: uncontrolled growth


title: Experimental group 1


title: AD6727

description: IL-4  at 48h after SCI - Macrophages

source_name: Mouse 8 IL-4 Macrophage

value: Injured spinal cord


title: AD6726

description: IL-13  at 48h after SCI - Microglia

source_name: Mouse 7 IL-13  Microglia

value: Mouse 7

value: Microglia


title: unCt2: uncontrolled growth, Replicate2


title: GRDIM_NI-2

description: run 1

value: FVB/NJ

value: vehicle 5h


title: Parental

value: Parental


title: Sibling 2 with ID

description: Male with Intellectual disability and ADHD and OCA1

value: Male

value: Blood

value: ID

value: Reference gDNA


title: wk12-2 [snATAC-seq]

city: Seattle

first: David

last: Beier

state: WA

address: 1900 9th Avenue

department: CDBRM

institute: Seattle Children's Research Institute

description: single nucleus ATAC-Seq

library_source: genomic

data_processing:
Library strategy: single-nucleus (sn)ATAC-Seq
Cell Ranger (for snRNA-seq experiments) or Cell Ranger ATAC (for snATAC-seq experiments) was used to demultiplex input files and generate feature-barcode matrices, which were then further analyzed via Seurat (RNA) or ArchR (ATAC). Specific details including software versions and parameters are described in Thomas, et al bioRxiv 2021.07.31.454254.
Genome_build: hg38
Supplementary_files_format_and_content: .tsv; fragment/feature/barcode matrices for each sample

source_name: Human induced pluripotent stem cell derived organoid

growth_protocol: Human induced pluripotent stem cells (hiPSCs) and Retinal Organoids were generated according to Olemacher et al., (2015) doi:10.1002/9780470151808.sc01h08s32 ; Gantner et al., (2020) doi:10.1056/NEJMoa1815111

extract_protocol:
Nuclear isolation from flash frozen tissue described in Thomas et al. bioRxiv 2021.07.31.454254; doi: https://doi.org/10.1101/2021.07.31.454254
10X Genomics scATAC-Seq and scRNA-Seq protocols. Detail described in Thomas et al. bioRxiv 2021.07.31.454254; doi: https://doi.org/10.1101/2021.07.31.454254

treatment_protocol: Enhancer knockout iPSCs generated as described in Thomas et al. bioRxiv 2021.07.31.454254; doi: https://doi.org/10.1101/2021.07.31.454254

tag: donor apparent sex

value: Female

tag: donor age

value: 58 years

tag: donor apparent race

value: caucasian

tag: postmortem interval


title: Control group 1

tag: treatment

value: Normal culture for 4 days


title: unCt1: uncontrolled growth, Replicate1

tag: cell line


title: unCt4: uncontrolled growth, Replicate4

tag: culture condition


title: AD6725

description: IL-13  at 48h after SCI - Macrophages

source_name: Mouse 7 IL-13  Macrophage

value: Macrophage

tag: tissue


title: AD6724

description: IL-13  at 48h after SCI - Microglia

source_name: Mouse 6 IL-13  Microglia

value: Mouse 6

tag: strain


title: GRDIM_DEX-2

description: run 1

value: GRD/D

value: 1 µM Dexamethasone 5h


title: GRDIM_DEX-1

description: run 1


title: AD6723

description: IL-13  at 48h after SCI - Macrophages

source_name: Mouse 6 IL-13  Macrophage

tag: mouse id

value: Injured spinal cord


title: pd9 PBMC

city: Shanghai

first: Jiadai

last: Xu

state: Shanghai

address: Fenglin Road 180, Shanghai, China

department: Hematology

institute: Zhongshan Hospital, Fudan University

description: one PBMC sample from a relapsed and refractory multiple myeloma patient

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was   used to demultiplex cellular barcodes, map reads to the genome and transcriptome   using the STAR aligner, and down-sample reads as required to generate normalized   aggregate data across samples, producing a matrix of gene counts versus cells. We   processed the unique molecular identifier (UMI) count matrix using the R package   Seurat (version 3.1.1).
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: PBMC

extract_protocol:
the blood specimen was centrifuged at 3,000 rpm for 10 min,  and the supernatant was collected as plasma. An equal volume of  PBS was added to the sedimentation and mixed well to generate  solution A. Second, in a new centrifuge tube, solution A was  added to the human lymphocyte separation solution (Hao Yang  Biological, Tianjin, China, LTS1077), ensuring a clear interface  between the two layers. After centrifugation at 3,000 rpm for  15 min, the middle white suspension layer and mononuclear cell  layer were carefully pipetted into a new centrifuge tube and  washed three times with PBS.
RNA libraries were prepared with Chromlum Single cell 3'regent v3 kits according to the manufacture's protocol.

tag: cell type

value: PBMC

tag: age

value: 63 years old

value: female

value: relapsed and refractory multiple myeloma (RRMM)


title: wk12-3 [snATAC-seq]

description: single nucleus ATAC-Seq


title: Control group 3

value: human aortic smooth muscle cells (HASMCs)


title: AD6721

description: IL-13  at 48h after SCI - Macrophages

source_name: Mouse 5 IL-13 Macrophage

value: Mouse 5


title: AD6722

description: IL-13  at 48h after SCI - Microglia

source_name: Mouse 5 IL-13  Microglia

value: Microglia


title: Sample11_cDUXCinter_rep2_CnM

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

description:
processed data file:
CALTinC.ens.dds.rda, rmsk.dds.rda
HinC-CinC-CALTinC-ENSEMBL-canFam3-genecounts.xlsx, HinC-CinC-CALTinC-rmsk-canFam3-counts.xlsx

data_processing:
Illumina CASAVA software was used for basecalling and sample de-multiplexing.
Removed reads with at least one "N" in the sequence from the raw FASTQ files.
Aligned FASTQ files against canFam3 using tophat-2.1.0 and bowtie2-2.2.6.
Counted gene (ENSEMBL 88) hits using Bioconductor's GenomicAlignments::summerizeOverlaps() function with "Intersection-Strict" mode.
Counted gene hits on canFam3 RMSK annotation; adjusted hits by the number of reported alignments.
Genome_build: canFam3
Supplementary_files_format_and_content: DESeq2's DESeqDataSet instances (*.dds.rda) and excel sheets (*.xlsx) containing gene counts on canFam3 ENSEMBL and RMSK annotations

organism: Canis lupus familiaris

source_name: cultured canine skeletal muscle

growth_protocol: Immortalized canine myoblastes were transduced  with the pCW57.1 vector containing a doxycycline inducible DUXC, DUXC-ALT, human DUX4, or Luciferase.

extract_protocol:
Total RNA was extracted from whole cells using NucleoSpin RNA kit (Macherey-Nagel) following the manufacturer's instructions.
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep v2 Kit (Illumina, Inc., San Diego, CA, USA) and a Sciclone  NGSx Workstation (PerkinElmer, Waltham, MA, USA).
RNA-seq libraries were pooled (14-plex) and clustered onto two flow cell lanes.

treatment_protocol: 1 ug/ml doxycycline for 24 hours and then RNA harvested for RNA-seq

value: Immortalized canine myoblaste

value: pCW57.1 vector containing a doxycycline inducible DUXC-ALT

value: DOXYCYCLINE


title: GRDIM_DEX-3

description: run 1

source_name: mouse embryonic fibroblast

value: FVB/NJ

tag: genotype


title: DDX5KO Tumor rep2

city: San Diego

first: Wendy

last: Huang

address: 9500 Gilman Drive #0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

description:
Epithelial knockout of APC and DDX5
tumor_colon.txt

data_processing:
Sequenced reads were mapped to mm10 using STAR v2.6.1a with parameters "--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000".
Uniquely mapped reads overlapping with the exons were counted using featureCounts for each gene in GENCODE.vM19 annotation.
Differential expression analysis were performed by DESeq2(v1.18.1) package
Genome_build: MM10
Supplementary_files_format_and_content: tab-delimited text files include raw counts, normalized counts values log2FoldChange and pvalue for each gene

source_name: Tumor Colon

growth_protocol: Healthy epithelial cells were harvested from small intestine of 8wk adult mice using 5 mM EDTA in PBS containing 1 mM of DTT for 20 min at 37°C. Tumor tissues were excised from large intestine-colon from each mice and processed for total RNA.

extract_protocol:
RNA was harvested using Qiagen Rneasy kit
Ribodepleted RNA Stranded

treatment_protocol: N/A for healthy epithelial cells. To obtain large intestine-colon tumors, mice were injected with Tamoxifen 3 times on day 1, 2, 3 by i.p with 100 ul of tamoxifen at 20 mg/ml in 5% EtOH and 95% corn oil. Tumor tissues were harvested on Day 30, 33, 37 post tamoxifen injection

value: Large intestine-colon

value: Tumor excision_day 33 post TAM


title: AD6718

description: PBS  at 48h after SCI - Microglia

source_name: Mouse 3 PBS Microglia

value: Mouse 3

value: PBS


title: MUT-2 (Sample 29)

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
The reads are trimmed for adapters and filtered by sequencing Phred quality (>= Q15) using fastp.
Adapter-trimmed reads are aligned to the human transcriptome (Ensembl version 102) using kallisto.
Transcript counts are converted  to gene counts using tximport.
Genome_build: human transcriptome (Ensembl version 102)
Supplementary_files_format_and_content: count_table.csv

source_name: Endoc-bH1 cell line

growth_protocol: EndoC-bH1 cells were grown in conditioned media collected from HEK293 stable OE cells (media change everyday for 10 days).

extract_protocol:
Total RNA is isolated using Qiagen Kit.
TruSeq Stranded mRNA seq, NovaSeq 6000, 100PE, ~50M reads (25PR)

treatment_protocol: Conditioned media collected from EV, WT-CEL, MUT-CEL stable OE HEK293 cell line by culturing HEK293 cells in EndoC-bH1 media for 3 hours, filtered, and protein levels were normalized.

value: Endoc-bH1 cell line

value: Pancreatic beta cells

value: Treated with HEK293-MUT OE conditioned media for 10 days

tag: batch


title: Sample12_cDUXCinter_rep3_CnM


title: DDX5KO Tumor rep1

tag: sample type

value: Tumor excision_day 37 post TAM


title: MUT-1 (Sample 28)


title: Sample9_cDUXCintac_rep3_CnMb

description:
processed data file:
CinC.ens.dds.rda, rmsk.dds.rda
HinC-CinC-CALTinC-ENSEMBL-canFam3-genecounts.xlsx, HinC-CinC-CALTinC-rmsk-canFam3-counts.xlsx

value: pCW57.1 vector containing a doxycycline inducible DUXC


title: WT Tumor rep3

description:
Epithelial knockout of APC
tumor_colon.txt

value: APC(fl/fl), Cdx2Cre-ERT2(+), DDX5(fl/+)

value: Tumor excision_day 30 post TAM


title: WT-3 (Sample 27)

value: Treated with HEK293-WT OE conditioned media for 10 days


title: Control group 2

value: human aortic smooth muscle cells (HASMCs)

value: Normal culture for 4 days


title: wk12-1 [snATAC-seq]

description: single nucleus ATAC-Seq

value: Female

value: 58 years

value: caucasian


title: AD6716

description: PBS  at 48h after SCI - Microglia

source_name: Mouse 2 PBS Microglia

value: Mouse 2

value: Microglia

value: Injured spinal cord


title: Sibling 1 with no ID

description: Female with No Intellectual Disability and having OCA1

tag: Sex

value: Blood

tag: disease state

value: no ID

source_name: Reference gDNA

value: Reference gDNA


title: Sample7_cDUXCintac_rep1_CnMb

value: Immortalized canine myoblaste

tag: genotype/variation

value: DOXYCYCLINE


title: DDX5KO Tumor rep3

value: Large intestine-colon


title: MUT-3 (Sample 30)

value: Endoc-bH1 cell line

value: Pancreatic beta cells

value: Treated with HEK293-MUT OE conditioned media for 10 days


title: WT-2 (Sample 26)

value: Treated with HEK293-WT OE conditioned media for 10 days


title: Sample10_cDUXCinter_rep1_CnM

value: pCW57.1 vector containing a doxycycline inducible DUXC-ALT


title: AD6715

description: PBS  at 48h after SCI - Macrophages

source_name: Mouse 2 PBS Macrophage

value: Macrophage

value: PBS


title: AD6714

description: PBS  at 48h after SCI - Microglia

source_name: Mouse 1 PBS Microglia

value: Mouse 1


title: Sample5_hDUX4CA_rep2_CnMb

description:
processed data file:
HinC.ens.dds.rda, rmsk.dds.rda
HinC-CinC-CALTinC-ENSEMBL-canFam3-genecounts.xlsx, HinC-CinC-CALTinC-rmsk-canFam3-counts.xlsx

value: pCW57.1 vector containing a doxycycline inducible human DUX4


title: Sample6_hDUX4CA_rep3_CnMb


title: EV-3 (Sample 24)

value: Treated with HEK293-EV OE conditioned media for 10 days


title: WT Tumor rep1

value: APC(fl/fl), Cdx2Cre-ERT2(+), DDX5(fl/+)

value: Tumor excision_day 37 post TAM


title: AD6717

description: PBS  at 48h after SCI - Macrophages

source_name: Mouse 3 PBS Macrophage

value: Mouse 3

value: Injured spinal cord


title: EV-2 (Sample 23)


title: Sample8_cDUXCintac_rep2_CnMb

value: Immortalized canine myoblaste

value: pCW57.1 vector containing a doxycycline inducible DUXC


title: SS_MNUD2

city: Pittsburgh

first: Shivendra

middle: V

last: Singh

state: PA

address: 5117 Centre Avenue UPMC HCC Research Pavilion Suite 2.32A

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

data_processing:
Data filtering: (1 )Remove reads with adaptor contamination.  (2) Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%).  (3) Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Genome_build: ensembl_rattus_norvegicus_rnor_6_0_gca_000001895_4
Supplementary_files_format_and_content: FPKM represents summary of gene expression level analysis by FPKM

organism: Rattus norvegicus

source_name: rat mammary tumor

growth_protocol: 21-day old female Sprague-Dawley rats were injected intraperitoneally 50 mg/kg body weight of MNU. One week after MNU injection, the rats were randomly divided into two groups and treatment was started 5 times a week for 10 weeks.

extract_protocol:
Ttotal RNA was extracted using the Zymo Quick RNA Miniprep Plus kit (zymoresearch, Irvine, CA ).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Control group was given 100 µL of corn oil by oral gavage as a vehicle, while treatment group was received orally 50 mg/kg of DATS-contained corn oil.

value: rat mammary tumor tissue

value: DATS administration


title: Sample3_luciferase_rep3_CnMb

description:
processed data file:
HinC-CinC-CALTinC-ENSEMBL-canFam3-genecounts.xlsx, HinC-CinC-CALTinC-rmsk-canFam3-counts.xlsx

value: pCW57.1 vector containing a doxycycline inducible Luciferase


title: WT Tumor rep2

value: Large intestine-colon

value: Tumor excision_day 33 post TAM


title: SS_MNUD1


title: Sample2_luciferase_rep2_CnMb


title: EV-1 (Sample 22)

value: Endoc-bH1 cell line

value: Pancreatic beta cells


title: SS_MNUC3

value: vehicle administration


title: MUT-3 (Sample 21)

value: Treated with HEK293-MUT OE conditioned media for 10 days


title: TS188 TruSeq

city: Uchinada

first: Hiroki

last: Ura

state: Ishikawa

address: 1-1 Daigaku

institute: Kanazawa Medical University Hospital

data_processing:
The fastq fieles were generated using bcl2fastq software.
Sequenced reads were mapped to hg38 using HISAT2 (v2.1.0) with default parameter.
Reads Per Kilobase of exon per Megabase of library size (RPKM)  and Transcripts per Million (TPM) were calcurated by StringTie (v1.3.4d) with default parameter.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM and TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA of the peripheral blood mononuclear cells which were obtained from a patient with tuberous sclerosis complex was extracted with TRIzol reagent (Thermo Fisher Scientific) according to manufacturer instructions.
The libraries were constructed using the TruSeq stranded mRNA Library Prep Kit, SMART-Seq v4 ultra-low input RNA kit and TeloPrime Full-Lenth cDNA Amplification Kit V2 according to manufacturer instructions.

value: PBMC

tag: disease

value: Tuberous sclerosis complex

tag: library type

value: TruSeq


title: TS188 SMARTer

value: SMARTer


title: MUT-2 (Sample 20)


title: Sample7_ImmCnMb_CCH_mono

data_processing:
Illumina CASAVA software was used for basecalling and sample de-multiplexing.
Removed reads with the filter flag =Y indicated in the sequence ID
Trimed the adapter contamination
Aligned the processed reads to reference genome canFam3 using BWA-0.7.10
Called Peaks by MACS2-2.1.0 with Luciferase samples as negative controls. Only peaks with q-value < 0.01 were considered
Uesd MEME-5.1.1 to carry out de novo motif discovery based on the top 1000 peaks, ranked by q-value, with flanking sequences 50bps up/downstream from the peak summits.
Genome_build: canFam3
Supplementary_files_format_and_content: peaks_list.rda is an R compressed object containing a 'list' of three 'data.frame' of peaks of DUX4, DUXC, and DUXC-ALT transcription factors.

growth_protocol: Immortalized canine myoblastes were transduced  with the pCW57.1 vector containing a chimeric protein that substituted the human DUX4 carboxyterminal domain (CTD) for the canine CTD to permit use of rabbit antisera generated to the human DUX4 CTD and the protocol previously used for human DUX4 in human cells.

extract_protocol:
Briefly, ~6x10e7 cells were fixed in 1% formaldehyde for 11 minutes, quenched with glycine, lysed, and then sonicated to generate final DNA fragments of 150–600 bp. The soluble chromatin was diluted 1:10 and pre-cleared with protein A:G beads for 2 hours. Remaining chromatin was incubated with primary antibody overnight, then protein A:G beads were added for an additional 2 hours. Beads were washed and then de-crosslinked overnight.
Libraries were prepared according to Illumina's standard protocols.

treatment_protocol: Cells were  treated with (or without) 1 ug/ml doxycycline for 24 hours  with

value: Immortalized canine myoblastes

tag: transcription factor

value: DUXC

tag: chip antibody

value: DUXC monoclonal

value: doxycycline inducible


title: SS_MNUC2

value: rat mammary tumor tissue

tag: treatment


title: SS_MNUD3

value: DATS administration


title: TS178 TeloPrime

value: TeloPrime


title: SS_MNUC1


title: TS178 SMARTer


title: Sample6_ImmCnMb_hDUX4_mono

value: hDUX4 monoclonal


title: MUT-1 (Sample 19)

tag: cell line


title: TS178 TruSeq


title: WT-3 (Sample 18)

value: Treated with HEK293-WT OE conditioned media for 10 days


title: TS188 TeloPrime


title: Sample5_ImmCnMb_luc_mono

value: Luciferase

value: Luciferase monoclonal

value: not doxycycline inducible


title: Kidney_sunitinib_sensitive_tumor_01

city: Asan-si

first: Dayeon

last: Kang

address: 22, Soonchunhyang-ro, Sinchang-myeon

country: South Korea

institute: Soon Chun Hyang University

description:
9_254606411827_1_3.txt
miRNA
S1T

hyb_protocol: After purification, labeled samples were resuspended with Gene Expression blocking Reagent and Hi-RPM Hybridization buffer, followed by boiling for 5 min at 100 °C and 5 min chilled on ice. Finally, denatured labeled probes were pipetted onto assembled Agilent’s miRNA Microarray and hybridized for 20 hours at 55°C with 20 RPM rotating in Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

source_name: Kidney tumor tissue

label_protocol: For control and test RNAs, the synthesis of target miRNA probes and hybridization were performed using Agilent’s miRNA Labeling Reagent and Hybridization kit (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 100 ng of total RNA were dephosphorylated with ~15 Units of calf intestine alkaline phosphatase (CIP), followed by RNA denaturation with ~40% DMSO and 10 min incubation at 100 °C. Dephosphorylated RNA were ligated with pCp-Cy3 mononucleotide and purified with MicroBioSpin 6 columns (Bio-rad, USA).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

tag: tissue

value: kidney

tag: gender

value: male

value: Kidney tumor tissue


title: AD6713

description: PBS  at 48h after SCI - Macrophages

source_name: Mouse 1 PBS Macrophage

tag: mouse id

value: Mouse 1

tag: strain

value: Macrophage

value: Injured spinal cord

value: PBS


title: WT-2 (Sample 17)

value: Endoc-bH1 cell line

tag: cell type

value: Pancreatic beta cells


title: Sample4_ImmCnMb_CALTh_poly

value: Immortalized canine myoblastes

value: DUXC-ALT

value: DUXC-ALT polyclonal

value: doxycycline inducible


title: WT-1 (Sample 16)

value: Treated with HEK293-WT OE conditioned media for 10 days


title: Sample1_luciferase_rep1_CnMb

value: Immortalized canine myoblaste

value: pCW57.1 vector containing a doxycycline inducible Luciferase


title: Sample1_ImmCnMb_luc_poly

value: Luciferase

value: Luciferase polyclonal

value: not doxycycline inducible


title: Kidney_sunitinib_sensitive_tumor_02

description:
7_254606410806_2_2.txt
miRNA
S2T

value: kidney

value: male

tag: age

value: Kidney tumor tissue


title: Sample 6_MDA_Reb_5

city: Wuhan

first: xiao

last: Li

address: No. 115, Donghu Road

institute: Wuhan University

description:
processed data file:
MDA_Reb_counts
MDA_Reb_rpkm

data_processing:
Illumina Casava1.7 software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic , then mapped to the reference genome of Homo sapiens (Homo_sapiens. GRCh38; ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/) using STRA software (version 2.5.3a).
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor), and then RPKMs were calculated using a protocol from Mortazavi A. et al. 2008.
Genome_build: Homo_sapiens. GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for Sample 1-3 and Sample 4-6, respectively.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene of Sample 1-3 and Sample 4-6, respectively.

source_name: Breast

growth_protocol: MDA-MB-231 cells were cultured in DMEM mudium supplemented with 10% FBS and 1% PS.

extract_protocol:
Total RNA was extracted with RNAiso Plus (TaKaRa)，KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Sample 1-3: MDA-MB-231 cells were stably transfected with lentivirus-mediated scramble-shRNA, CDK16-sh1 and CDK16-sh2, respectively;
Sample 4-6: MDA-MB-231 cells were treated with vehicle (DMSO) or with Rebastinib at low (1 μM) or high (5 μM) doses for 48 h.

tag: tissue source

value: Breast

value: treated with Rebastinib at 5 μM


title: EV-3 (Sample 15)

value: Endoc-bH1 cell line

value: Treated with HEK293-EV OE conditioned media for 10 days

tag: batch


title: Kidney_sunitinib_sensitive_tumor_03

description:
4_254606410806_1_4.txt
miRNA
S3T

value: female


title: Sample 4_MDA_DMSO

value: treated with DMSO


title: Kidney_sunitinib_sensitive_normal_03

description:
6_254606410806_2_1.txt
miRNA
S3N

source_name: Noncancerous kidney tissue

value: Noncancerous kidney tissue


title: 6hpf_PACE_wildtype_MO_2

city: Kita-ku

first: Yuichiro

last: Mishima

state: Kyoto

address: Motoyama, Kamigamo,

department: Department of Frontier Life Sciences

institute: Kyoto Sangyo University

data_processing:
Illumina Casava1.8 software used for basecalling.
Quality was checked by FastQC 0.11.7 and low quality reads were discarded
Reads matched to the PACE reporter mRNA library were counted by Salmon 0.11.2
Supplementary_files_format_and_content: tab-delimited text files include read numbers for each codon tag reporters.

organism: Danio rerio

source_name: whole embryo

growth_protocol: fertilized eggs were obtained by natural breadings

extract_protocol:
Total RNA was extracted from 40–50 embryos using TRI Reagent (Molecular Research Center), treated with DNaseI (TAKARA) and purified with RNeasy Mini Kit (QIAGEN).
Libraries were prepared using TruSeq Stranded Total RNA with Ribo-Zero (Illumina).

treatment_protocol: PACE reporter mRNA library was injected at 1-cell stage

value: AB

tag: stages

value: 6 hpf

value: whole embryo

tag: experiments

value: PACE library and GFP MO injected


title: Kidney_sunitinib_sensitive_normal_01

description:
3_254606410806_1_3.txt
miRNA
S1N

tag: disease state


title: 6hpf_PACE_wildtype_MO_1


title: EV-1 (Sample 13)

value: Pancreatic beta cells


title: EV-2 (Sample 14)


title: Sample 2_MB231_CDK16_sh1

description:
processed data file:
MB231-CDK16_sh_counts
MB231-CDK16_sh_rpkm

value: transfected with CDK16-sh1


title: Sample 3_MB231_CDK16_sh2

value: transfected with CDK16-sh2


title: MUT-4 (Sample 12)

value: Treated with HEK293-MUT OE conditioned media for 10 days


title: Sample 1_MB231_SC

value: transfected with scramble-shRNA


title: 2hpf_PACE_wildtype_MO_1

value: 2 hpf


title: Kidney_sunitinib_resistance_tumor_03

description:
12_254606411827_2_1.txt
miRNA
R3T

value: kidney

value: male

value: Kidney tumor tissue


title: Sample 5_MDA_Reb_1

value: Breast

value: treated with Rebastinib at 1 μM


title: MUT-3 (Sample 11)

value: Endoc-bH1 cell line


title: 6hpf_PACE_wildtype_2

value: PACE library injected


title: Kidney_sunitinib_resistance_tumor_02

description:
8_254606411827_1_4.txt
miRNA
R2T


title: MUT-2 (Sample 10)


title: 6hpf_PACE_AnsB_H2

data_processing:
Illumina Casava1.8 software used for basecalling.
Quality was checked by FastQC 0.11.7 and low quality reads were discarded
Reads matched to the PACE reporter mRNA library were counted by Sailfish 0.10.1.1
Supplementary_files_format_and_content: tab-delimited text files include read numbers for each codon tag reporters.

value: AB

value: PACE library and AnsB injected


title: Kidney_sunitinib_resistance_tumor_01

description:
2_254606410806_1_2.txt
miRNA
R1T


title: MUT-1 (Sample 9)


title: 6hpf_PACE_wildtype_1

value: 6 hpf

value: whole embryo


title: 2hpf_PACE_AnsB_H2


title: 2hpf_PACE_wildtype_2


title: Kidney_sunitinib_resistance_normal_02

description:
10_254606411827_1_1.txt
miRNA
R2N

value: Noncancerous kidney tissue


title: Kidney_sunitinib_resistance_normal_03

description:
11_254606411827_2_4.txt
miRNA
R3N


title: 2hpf_PACE_AnsB_H1


title: 2hpf_PACE_wildtype_1


title: 2hpf_PACE_wildtype_MO_2

value: PACE library and GFP MO injected


title: WT-4 (Sample 8)

value: Pancreatic beta cells

value: Treated with HEK293-WT OE conditioned media for 10 days


title: WT-3 (Sample 7)


title: Verapamil_3

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

data_processing:
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Normalized counts files are comma separated value matrices containing the DESeq2 normalized counts for each of the samples.

source_name: human islets

extract_protocol: Libraries were prepared according to the Illumina TruSeq stranded mRNA sample preparation kit.

treatment_protocol: 24h incubation in 25mM glucose with or without verapamil

value: human islets

value: incubated with 25mM glucose + 100uM Verapamil for 24h


title: Verapamil_2


title: WT-2 (Sample 6)


title: WT_1884

description: 10x scRNAseq

data_processing:
Space v3.1.0 to align reads to mouse reference genome (mm10)
Used Loupe Browser to filter Atoh1, Sox4, Lgr5 high progenitor-containing spots and Dclk1, Klf4, Lyz1, Chga high mature secretory lineage-containing spots (Log2 expression > 0.5)
Differential gene expression analysis
Genome_build: mm10

source_name: small intestine_ileum

growth_protocol: All mice were raised in Specific Pathogen Free (SPF) facility on normal diet. 10-12 week old animals were used for experiments.

extract_protocol:
Mouse ileum samples were coiled into “Swiss rolls” and frozen immediately with chilled isopentane. The frozen tissues were then embedded into Optimal cutting temperature compound (OCT compound). Once OCT compound has solidified and turned white, intestinal tissue block was then processed by cryo-sectioning.
Tissue underwent permeabilization with permeabilization enzyme (24 minutes), reverse transcription and second strand synthesis performed on the slide.The following library construction was performed as per manufacturer’s instructions including fragmentation, end repair & A-tailing,  post fragmentation end repair & A-tailing double sided size selection(SPRIselect), adaptor ligation, post ligation cleanup, sample Index PCR, SPRIselect. The libraries were tested using the Agilent TapeStation.
The pooled libraries of each sample (100 million reads per tissue) ran on one lane of NovaSeq S4 following manufacturer’s recommendations.

treatment_protocol: No treatment. Steady state mice were harvest at around 8-week old.

value: 8wks old

value: steady state


title: 2hpf_PACE_control

value: 2 hpf


title: KO_1883

description: 10x scRNAseq


title: Kidney_sunitinib_resistance_normal_01

description:
1_254606410806_1_1.txt
miRNA
R1N

value: kidney

value: male


title: Verapamil_1


title: 6hpf_PACE_AnsB_H1


title: WT-1 (Sample 5)

value: Endoc-bH1 cell line


title: 6hpf_PACE_MZznf598_2

value: znf598 mutant

value: PACE library injected


title: EV-4 (Sample 4)

value: Treated with HEK293-EV OE conditioned media for 10 days


title: LEAN hashtag library

city: Farmington

first: William

middle: F

last: Flynn

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
FASTQ files for each library were generated and demultiplexed using Illumina bcl2fastq 2.20.0.422.
For all libraries, R1 (28bp) contains a 16bp cell barcode + 12bp UMI barcode and R2 (91bp) contains the biological reads.  If present, I1 contains the 8bp i7 index which is needed for 10X CellRanger pipelines.
An unfiltered digital gene expression matrix was generated for each gene expression library against the 10X Genomics mm10 reference build (version 3.0.0, GRCm38.93) using 10X Genomics CellRanger count version 3.1.0
A digital counts matrix was generated for each hashtag library using CITE-Seq-Count (https://github.com/Hoohm/CITE-seq-Count), version 1.4.3. This produces a matrix of counts with hashtag labels for rows (available via BioLegend https://www.biolegend.com/totalseq) and cell barcodes for columns.
The cell barcodes in LEAN-rna/LEAN-hto correspond to the same cells, similarly for HFD-rna/HFD-hto.  Note that gene expression barcodes (*-rna) have a "-1" appended to each barcode that is not present in the hashtag cell barcodes (*-hto).
Genome_build: GRCm38.93
Supplementary_files_format_and_content: Transcriptomic and HashTag (HTO) counts matrices in Matrix Market sparse CSC matrix format.  Rows correspond to genes in the order provided in features.tsv and columns correspond to cell-barcodes in the order provided in barcodes.tsv.

source_name: LEAN HTO

extract_protocol:
Sorted cells from each mouse sample were labeled with cell hashing antibodies (BioLegend TotalSeq anti-mouse Hashtag #3-5). 36,000 cells (12,000 cells from each hashtagged mouse) were loaded into one lane of a 10X Chromium microfluidic chip. Single cell capture, barcoding and library preparation were performed using the 10X Chromium platform, version 3 chemistry. cDNA and libraries were checked for quality on Agilent 4200 Tapestation, quantified by KAPA qPCR, and pooled using a ratio of 95% gene expression library and 5% hashtag library before sequencing on 50% of lane of an Illumina NovaSeq 6000 S2 flow cell, both targeting 18,000 barcoded cells with an average sequencing depth of 50,000 reads per cell.
Chromium System (10XGenomics) v3 chemistry

tag: number of organisms

tag: diet

value: normal chow

value: tamoxifen

value: visceral adipose tissue


title: Control_3

value: incubated with 25mM glucose for 24h


title: 6hpf_PACE_MZznf598_1

value: 6 hpf

value: whole embryo


title: LEAN gene expression library

source_name: LEAN GEX


title: Control_2

value: human islets


title: EV-3 (Sample 3)

value: Pancreatic beta cells


title: 2hpf_PACE_MZznf598_2


title: HFD hashtag library

source_name: HFD+PL HTO

value: high fat diet


title: EV-2 (Sample 31)

source_name: Endoc-bH1 cell line


title: 2hpf_PACE_MZznf598_1


title: 6hpf_PACE_control

value: AB


title: Control_1


title: HFD gene expression library

source_name: HFD+PL GEX


title: patient 7276 metastasis (mechanical fraction)

status: Public on Dec 02 2021

city: Stanford

first: Zinaida

last: Good

state: California

address: 265 Campus Drive, Room G2105

department: Stanford Cancer Institute, Department of Biomedical Data Science

institute: Stanford University School of Medicine

description: Human (HNSCC patient)

data_processing:
Cell Ranger pipeline v3.0.2 (10X Genomics) to align reads, and then extract and filter cell-gene matrix of UMI counts.
AbSeq Tools pipeline v0.3 (BD) to align reads, and then extact and filter UMI counts for AbSeq antibody oligos to generate UMI counts for the same cells as in the cell-gene matrix.
Genome_build: GRCh38
An h5 file for each sample containing Cell Ranger pipeline output for filtered cell-gene data: columns contain batch-normalized UMI counts across cells; rows contain genes.
Supplementary_files_format_and_content: An HTML file for each sample containing Cell Ranger alignment summary statistics.
Supplementary_files_format_and_content: A CSV file for each sample containing AbSeq oligo UMI counts for the same filtered cells as in the h5 cell-gene matrix.
Supplementary_files_format_and_content: 3 TXT files containing AbSeq panel information (protein.gene.oligoID.oligoType) for 36-plex, 44-plex, and 50-plex panels.
Data is paired-end, but read1 (26bp) only contains cell barcode and UMI data (sample index is 8 bp), and only read2 (98bp) contains transcript data.

source_name: Live tumor cells

extract_protocol:
Droplet-based single-cell RNA-sequencing on 10X Genomics Chromium platform.
10X Genomics Single Cell 3' v2 Kit

tag: location

value: lymph node metastasis

tag: digestion fraction

value: mechanical

tag: abseq panel

tag: abseq panel descriptor


title: patient 7276 metastasis (enzymatic fraction)

description: Human (HNSCC patient)

value: enzymatic


title: Lin- SVF cells from human: sample1

city: Los angeles

first: Gaoyan

address: 1929 beloit ave, apt315

institute: UCLA

data_processing:
The 10X Genomics Cell Ranger version 3.0.2 single-cell software was used to perform sample demultiplexing, sequence alignment to mouse genome mm10, filtering, and unique molecular identifier (UMI) counting to generate gene count matrices.
Data analysis was performed in R using Seurat v3 package.
Genome_build: mm10 for mouse cells and hg19 for human cells
Supplementary_files_format_and_content: Feature-barcode matrix. Each matrix is stored in the Market Exchange Format (MEX) for sparse matrices. It also contains gzipped TSV files with feature and barcode sequences corresponding to row and column indices.

source_name: peri-pancreatic adipose tissue

extract_protocol: Mouse epididymal adipose tissue (eWAT) was minced and transferred to a 50 mL Falcon tube containing 10 mL digestion buffer (100mM HEPES pH 7.4; 120mM NaCl; 50mM KCl; 5mM Glucose; 1mM CaCl2, 1.5% BSA, and 1 mg/mL collagenase D). The tissue was incubated in a 37℃ shaking water bath for 30 min. Digestion was stopped by adding 35 mL 2% FBS in PBS. The solution was passed through 100 µm and then 40 µm strainers, and centrifuged at 400 g for 5 min. The supernatant was aspirated, and SVF pellet was collected. Lin- SVFs was obtained by Multicolor Flow Cytometry (MACS) (Stemcell Technologies, Cat# 17656). To obtain Lin- SVFs, anti-mouse-CD45-PE, anti-mouse-CD31-PE, and anti-mouse-Ter119-PE (1:200, BioLegend) were used.  To obtain immune cells from eWAT, only anti-mouse-CD45-PE was used and isolated by MACS. Human peripancreatic white adipose tissue was minced and transferred to a 50 mL Falcon tube containing 10 mL digestion buffer (1 × PBS, and 10 mg/mL collagenase D). The tissue was incubated in a 37℃ shaking water bath for 45 min. Digestion was stopped by adding 35 mL 2% FBS in PBS. The solution was passed through a 250 µm mesh (Spectrum), and then 100 µm and 40 µm strainers, and centrifuged at 600 g for 5 min. The supernatant was aspirated, and SVF pellet was collected. To obtain Lin- SVF, cells were incubated with anti-human-CD45-PE, anti-human-CD31-PE, and anti-human-CD235a-PE (1:200, BioLegend), and isolated by MACS (Stemcell Technologies, Cat# 17654). To obtain immune cells, only anti-human-CD45-PE (1:200, BioLegend) was used and isolated by MACS.

tag: tissue

value: peri-pancreatic adipose tissue

value: Lin- SVF cells

tag: cell population

value: non-immune cells

value: 44 yrs

tag: Sex

value: M


title: Lin- SVF cells from human: sample4

value: 24 yrs


title: Lin- SVF cells from human: sample3

value: 42 yrs

value: F


title: Patient 1 tumor sample

city: Little Rock

first: Analiz

last: Rodriguez

state: AR

address: 4301 W. Markham St Slot 507

department: College of Medicine, Department of Neurosurgery

institute: University of Arkansas for Medical Sciences

data_processing:
RNA-Seq data were uniformly processed using the Toil RNA-Seq pipeline version 3.2 developed by the UCSC Computational Genomics Lab as described in the expression section of the pipelines repository https://github.com/UCSC-Treehouse/pipelines. These steps include:
Adapters are removed with CutAdapt v1.9 (Martin, 2011)
Reads are aligned by STAR v 2.4.2a using indices generated from the human reference genome GRCh38 and the human gene models Gencode 23 (Dobin et al., 2013)
RSEM 1.2.25 is used to quantify gene expression (Li and Dewey, 2011)
Gene level expression is in TPM
Genome_build: GRCh38
Genome_build: Gencode 23
Supplementary_files_format_and_content: Tab separated column of genes with the expression level estimate for each gene.

source_name: brain tumor

extract_protocol:
RNA was extracted with the Qiagen RNEasy kit.
A sequencing library was prepared with the Illumina TruSeq Stranded mRNA Library Preparation and sequenced on an Illumina HiSeq 2500 sequencer to obtain between 40-50 million reads.

tag: donor

value: Patient 1

tag: cell line

tag: sample type

value: fresh frozen tissue

tag: cancer predisposition

value: Li-Fraumeni syndrome

tag: diagnosis

value: glioma

tag: treehouse id

tag: tumor grade


title: Lin- SVF cells from human: sample5

tag: cell type

tag: age

value: 57 yrs


title: Lin- SVF cells from human: sample2

value: 21 yrs


title: patient 7275 primary tumor (enzymatic fraction)

description: Human (HNSCC patient)

value: primary tumor


title: patient 7275 primary tumor (mechanical fraction)

description: Human (HNSCC patient)

value: mechanical


title: patient 7268 primary tumor (enzymatic fraction)

description: Human (HNSCC patient)

value: enzymatic


title: patient 7268 primary tumor (mechanical fraction)

description: Human (HNSCC patient)


title: patient 7267 metastasis (mechanical fraction)

description: Human (HNSCC patient)

value: lymph node metastasis


title: patient 7240 metastasis (mechanical fraction)

description: Human (HNSCC patient)


title: patient 7267 metastasis (enzymatic fraction)

description: Human (HNSCC patient)


title: patient 7240 metastasis (enzymatic fraction)

description: Human (HNSCC patient)


title: patient 7240 primary tumor (mechanical fraction)

description: Human (HNSCC patient)


title: patient 7239 metastasis (mechanical fraction)

description: Human (HNSCC patient)


title: patient 7239 primary tumor (mechanical fraction)

description: Human (HNSCC patient)


title: patient 7239 metastasis (enzymatic fraction)

description: Human (HNSCC patient)


title: patient 7240 primary tumor (enzymatic fraction)

description: Human (HNSCC patient)


title: patient 7238 primary tumor (enzymatic fraction)

description: Human (HNSCC patient)


title: patient 7238 primary tumor (mechanical fraction)

description: Human (HNSCC patient)


title: patient 7239 primary tumor (enzymatic fraction)

description: Human (HNSCC patient)


title: Tumor_WNT-MB_FFPE_No.3

city: Hamburg

first: Julia

middle: Elisabeth

last: Neumann

state: Hamburg

address: Martinistr. 52

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: NanoString standard protocol

scan_protocol: NanoString standard protocol

data_processing: Raw expression data was processed using nSolverAnalysis Software 4.0.70: Background subtraction with geometric mean of negative controls; Normalization with geometric mean of positive controls and standard housekeeping genes; No ratios built

source_name: brain

label_protocol: NanoString standard protocol

extract_protocol: Protocol of the Roche High Pure RNA Isolation Kit (06650775001)

tag: origin

value: CNS

tag: disease state

tag: grading

tag: subgroup

value: WNT


title: Tumor_WNT-MB_FFPE_No.2


title: Tumor_WNT-MB_FFPE_No.4


title: GRDIM_NI-1

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

institute: VIB-UGent

description: run 1

data_processing:
Obtained reads were checked for quality and adapter contamination with fastqc
Reads were mapped to the mm10 reference genome using the ensembl structural annotation (release 100) using the hisat2 aligner (v 2.1.0) with additional options, next to index, splice sites and reads: --avoid-pseudogene and -p 8
A count matrix was made with featurecounts (v 2.0.0) wih extra options --primary and -T 8
The count matrix was processed using DESeq2 to obtain differentially expressed genes (v 1.26.0) according to a multifactorial model incorporating the condition and run (formula ~ run + condition)
Genome_build: mm10
Supplementary_files_format_and_content: count matrix

source_name: mouse embryonic fibroblast

extract_protocol:
Total RNA was isolated from solvent- or Dex-stimulated MEF cells with Aurum total RNA mini kit (732‐6820; Bio‐Rad) according to the manufacturer's instructions. RNA concentration was measured and RNA quality was checked with the Agilent RNA 6000 Pico Kit (Agilent Technologies)
Library preparation and sequencing was performed according to the manufacturer’s instruction with the illumina Truseq library prep kit

tag: strain

value: FVB/NJ

tag: genotype

value: GRD/D

tag: treatment

value: vehicle 5h


title: Tumor_WNT-MB_FFPE_No.1


title: Tumor_SHH-MB_FFPE_No.3

value: SHH


title: Tumor_SHH-MB_FFPE_No.2


title: Tumor_SHH-MB_FFPE_No.4


title: Sample 1_Wild-type zebrafish embryos 24 hours post-fertilisation

city: Sydney

first: Allegra

last: Angeloni

state: NSW

address: 384 Victoria St Darlinghurst

department: Genomics and Epigenetics Division

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Sample 1:
Base-calling was performed with Guppy (-x "cuda:0" -r -c dna_r9.4.1_450bps_hac_prom)
Pass fastq reads were mapped onto the GRCz10 reference (UCSC) using minimap2 (-x map-ont -a -t16 --secondary=no) and indexed using samtools 1.12
Methylation was called using nanopolish 0.13.2 call-methylation
Sample 2:
Bisulfite-converted (WGBS) sequence reads were trimmed with Trimmomatic 0.39 (ILLUMINACLIP:NEXTflex.fa:2:30:10 SLIDINGWINDOW:5:20 LEADING:5 TRAILING:5 MINLEN:50)
Reads were mapped using WALT v1.0 (-m 10 -t 24 N 10000000 -L 2000) onto the bisulphite-converted GRCz10 reference (UCSC) containing λ  added as a separate chromosome
The resulting alignments in BAM format were deduplicated using Picard 2.3.0
Methylation was called using MethylDackel 0.3.0 (--mergeContext --minOppositeDepth 5 --maxVariantFrac 0.5 --OT 10,0,10,130 --OB 10,140,30,145)
Genome_build: GRCz10/danRer10
Supplementary_files_format_and_content: tsv file containing genomic coordinates, number of alignments, number of alignments reporting methylated bases, methylation frequency (0.0-1.0)
Supplementary_files_format_and_content: bedGraph file containing genomic coordinates, methylation percentage rounded to an integer, number of alignments reporting methylated bases, number of alignments reporting unmethylated bases

source_name: Embryos 24 hours post-fertilisation

growth_protocol: Adult wild type (AB/Tubingen) Danio rerio (zebrafish) were bred in a 1 male:1 female ratio. Embryos were collected 0 hours post-fertilization (hpf) and incubated in 1X E3 medium (0.03% NaCl, 0.005% CaCl2, 0.0013% KCl, 99.9557% H2O, 0.008% H14MgO11S) for 24 hours at 28.5¡C.

extract_protocol:
24hpf embryos were snap frozen in liquid nitrogen and stored at -80°C prior to DNA extraction. Genomic DNA (gDNA) was extracted from 24hpf embryos using the QIAGEN DNeasy Blood & Tissue Kit (QIAGEN, Chadstone, VIC, Australia) according to manufacturer instructions in two biological replicates.
Oxford Nanopore Ligation 1D Kit (Native Barcoding); Zebrafish gDNA was prepared for Nanopore sequencing using the Oxford Nanopore Ligation 1D Kit including 1μL unmethylated lambda phage spike-in (concentration not disclosed by manufacturer) (Oxford Nanopore Technologies, Oxford, UK) according to manufacturer instructions. Briefly, 950ng of zebrafish gDNA was sheared to an average fragment size of 10kb using a Covaris G-Tube (Covaris, Woburn, MA, USA) at 6000rpm for one minute. Long fragment buffer was used to elute DNA fragments following the final AMpure clean-up step. In total, 250ng of the DNA library was loaded onto a PromethION flow cell (pore version 9.4.1, flow cell version FLO-PRO002) and run on a PromethION sequencing device for 64 hours.

value: AB/Tuebingen

value: Wild-type


title: Tumor_IOMEPL_FFPE_No.3

source_name: eye

value: eye


title: Tumor_IOMEPL_FFPE_No.5


title: Tumor_IOMEPL_FFPE_No.6


title: Tumor_IOMEPL_FFPE_No.8


title: Tumor_SHH-MB_FFPE_No.1


title: Sample 2_Wild-type zebrafish embryos 24 hours post-fertilisation

extract_protocol:
24hpf embryos were snap frozen in liquid nitrogen and stored at -80°C prior to DNA extraction. Genomic DNA (gDNA) was extracted from 24hpf embryos using the QIAGEN DNeasy Blood & Tissue Kit (QIAGEN, Chadstone, VIC, Australia) according to manufacturer instructions in two biological replicates.
1000ng of zebrafish gDNA and 5ng of unmethylated lambda phage DNA spike-in (Promega, Madison, WI, USA) was sonicated to an average insert size of 300bp. DNA was end repaired using Lucigen End-It DNA End-Repair Kit (LGC Biosearch Technologies, Novato, CA, USA) according to manufacturer instructions. Adapters were ligated to DNA overnight using NEXTFLEX Bisulfite-Seq Barcodes (PerkinElmer, Waltham, MA, USA). DNA was bisulfite converted using EZ DNA Methylation Kit (Zymo Research, Irvine, CA, USA) according to manufacturer instructions and PCR amplified (8 cycles). Library concentration was quantified through qPCR using KAPA Library Quantification Kit (Sigma-Aldrich, St. Louis, MO, USA) according to manufacturer instructions. The library was sequenced with 15% PhiX spike-in on Illumina HiSeq 10X platform using 150bp paired-end sequencing (high output mode).


title: Tumor_IOMEPL_FFPE_No.1


title: Tumor_G4-MB_FFPE_No.3


title: dominant 2

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

data_processing:
The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline (version 3.1.0). The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene-level counts were imported into R using the Seurat suite version 3.0
Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets, gene-level count values were summed to retain a final count matrix of 35,227 features across 39,424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: (1) >= 500 UMIs per cell; (2) >= 200 genes per cell; (3) >= 0.7 novelty score, calculated as log10(genes detected) / log10(UMI counts per cell); and (4) <= 10 percentage of reads mapping to mitochondrial genes.
Genome_build: Zebrafish Ensembl GRCz11 reference
Supplementary_files_format_and_content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms

source_name: dominant

growth_protocol: Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 months

extract_protocol:
After euthanasia, the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin, placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40-μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA (Gemini Bio-Products), then washed again after spinning down at 350 x g for 5 minutes at 4°C and counted after resuspension in DPBS/BSA to target 10,000 cells per reaction.
We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation
single-cell RNA sequencing, 10x genomics

treatment_protocol: No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample

value: sorted single color kidney marrow cells

tag: sorting

value: sorted

value: 8 months old

tag: genotype/variation

value: dominant Zebrabow color


title: dominant 3


title: dominant 1


title: Tumor_G4-MB_FFPE_No.2


title: Tumor_EMTR_FFPE_No.3


title: Tumor_G4-MB_FFPE_No.1


title: mutant 3

source_name: mutant

value: unsorted whole kidney marrow cells

value: unsorted

value: guide RNAs targeting 20 different genes and cas9 mRNA


title: Sample4_hDUX4CA_rep1_CnMb

city: Seattle

first: Stephen

address: 1100 Fairview N. Ave

data_processing:
Illumina CASAVA software was used for basecalling and sample de-multiplexing.
Removed reads with at least one "N" in the sequence from the raw FASTQ files.
Aligned FASTQ files against canFam3 using tophat-2.1.0 and bowtie2-2.2.6.
Counted gene (ENSEMBL 88) hits using Bioconductor's GenomicAlignments::summerizeOverlaps() function with "Intersection-Strict" mode.
Counted gene hits on canFam3 RMSK annotation; adjusted hits by the number of reported alignments.
Genome_build: canFam3
Supplementary_files_format_and_content: DESeq2's DESeqDataSet instances (*.dds.rda) and excel sheets (*.xlsx) containing gene counts on canFam3 ENSEMBL and RMSK annotations

source_name: cultured canine skeletal muscle

extract_protocol:
Total RNA was extracted from whole cells using NucleoSpin RNA kit (Macherey-Nagel) following the manufacturer's instructions.
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep v2 Kit (Illumina, Inc., San Diego, CA, USA) and a Sciclone  NGSx Workstation (PerkinElmer, Waltham, MA, USA).
RNA-seq libraries were pooled (14-plex) and clustered onto two flow cell lanes.

value: Immortalized canine myoblaste

value: pCW57.1 vector containing a doxycycline inducible human DUX4

value: DOXYCYCLINE


title: Tumor_IOMEPL_FFPE_No.7


title: Tumor_EMTR_FFPE_No.2

value: CNS


title: Tumor_SHH-MB_FFPE_No.5


title: Tumor_EMTR_FFPE_No.1


title: mutant 2


title: Tumor_IOMEPL_FFPE_No.4


title: Tumor_IOMEPL_FFPE_No.2


title: Tumor_G4-MB_FFPE_No.4


title: mutant 1


title: control 2

source_name: control

value: 2 control guide RNAs and cas9 mRNA