title: pGAL-RNY1 tRF NEB with 5'+3' UMI Rep 2


title: pGAL-RNY1 tRF NEB with 5' UMI Rep 2

status: Public on Mar 06 2022

type: SRA

city: Worcester

first: Oliver

last: Rando

state: Massachusetts

address: 364 Plantation St

department: BMP

country: USA

institute: University of Massachusetts

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence with cutadapt v2.9, when UMI was present reads were deduplicated with seqkit v0.14.0 and UMI sequence was trimmed with cutadapt.
Trimmed reads where then mapped to sacCer3 or mm10 with tRAX using default settings.
Genome_build: mm10, sacCer3
Supplementary_files_format_and_content: Each processed data file contains information about read-start/stop site, coveage, and  misinicorporation rate.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: For full length tRNA experiments, yTG66 and yTG109 were grown overnight in selective synthetic media containing 2% dextrose, saturated cultures were diluted to OD600=0.1 and grown in selective synthetic media containing 2% dextrose until they reached OD600=0.5-07. For tRF experiments, yTG72 were grown overnight in selective synthetic media containing 2% raffinose. Saturated cultures were diluted to OD600=0.1 in selective synthetic media containing 2% raffinose and grown until early-midlog (OD600= 0.3-0.4). Cells were then centrifuged and diluted in selective synthetic media containing 2% galactose to an OD600 so that they reach OD600=0.5-0.7 in 360 minutes (“WT” samples were resuspended in selective synthetic media containing 2% galactose, centrifuged, and snap frozen immediately).

extract_protocol:
Mouse RNA was extracted using standard TRIZol protocol. Yeast RNA was extracted by beadbeating in TNE buffer (50 mM Tris-Cl pH7.4, 100 mM NaCl, 10 mM EDTA), followed by an acid Phenol extraction.
Libraries were constructed following published protocols.

tag: strain

tag: growth media

value: SC-Ura Galactose


title: mRNA_Skin4

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

country: Sweden

institute: Karolinska Institutet

data_processing:
Illumina Casava1.7 software used for basecalling.
miRNA-seq: The quality of raw data was assessed using FastQC v0.11.8 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used mapper.pl module in the miRDeep2 v0.1.3 package to filter low quality reads and remove sequencing adaptors and redundancies. Trimmed reads with length greater than 18 nt were mapped to GENCODE human reference genome (hg38) by the software Bowtie v1.2.2. The miRDeep2.pl module was then performed with default parameters to identify known miRNAs, which were compared to miRNAs in miRBase release 22.1. Counts of reads mapped to each known mature miRNAs were acquired from the quantifier.pl module output, without allowing mismatch.
Raw counts of  miRNAs were normalized for sequencing depth using TPM methods (transcript per million = mapped readcount / Total reads * 10e6).
mRNA-seq: Raw reads of mRNA sequencing were first trimmed for adaptors and low-quality bases using Trimmomatic v0.36 software. Clean reads were aligned to the human reference genome (GRCh38.p12), coupled with the comprehensive gene annotation file (GENCODEv31) using STAR v2.7.1a. Gene expression was then quantified by counting unique mapped fragments to exons using featureCount function from the Subread package.
Raw counts for each gene were normalized to fragments per kilobase of transcript, per million mapped reads (FPKM)-like values.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include miRNA TPM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw read counts for every miRNA and every sample
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw read counts for every gene and every sample

organism: Homo sapiens

source_name: Lower leg skin

extract_protocol:
The mRNA libraries were constructed with a total amount of 2 μg RNA per sample. Firstly, the ribosomal RNA was depleted by Epicentre Ribo-zero® rRNA Removal Kit (Epicentre). Subsequently, bulk strand-specific total-transcriptome RNA sequencing libraries were prepared by incorporating dUTPs in the second-strand synthesis step with NEB Next® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB). Finally, the libraries were sequenced on an Illumina Hiseq 4000 platform and 150 bp paried-end reads were generated for the following analysis.
paired-end 150bp

tag: tissue

value: Skin

tag: gender

value: Male

tag: age

tag: patients

tag: ethnicity

value: Caucasian

tag: groups

value: Intact skin

tag: librarytype

value: ribosomal RNA depletion


title: WT tRF NEB with 5'+3' UMI Rep 2


title: mRNA_Skin1

value: Female


title: WT tRF NEB with 5' UMI Rep 2


title: pGAL-RNY1 tRF NEB Rep 2


title: Pf4-Grin1-/- MKs, biological rep 4

type: RNA

city: Canberra

first: James

middle: Iain

last: Hearn

state: ACT

address: 131 Garran Rd

department: Division of Genome Sciences and Cancer

country: Australia

institute: Australian National University

description: Gene expression data from Grin1 deleted mouse bone marrow megakaryocytes

hyb_protocol: Hybridization to Clariom Mouse S arrays was done following the GeneChip 3' IVT Pico Kit manual using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) 4.0, using Affymetrix default analysis settings and Gene Level - SST-RMA as normalization.

label: Biotin

organism: Mus musculus

source_name: Pf4-Grin1-/- megakaryocytes

label_protocol: Microarray was performed at the Auckland Genomics facility at The University of Auckland, New Zealand. 10 ng of RNA was fragmented and labelled following the GeneChip 3' IVT Pico Kit (ThermoFisher Scientific) manual.

growth_protocol: C57BL/6 mice, of genotypes Pf4-Grin1-/- (Cre-loxP system directed deletion of Grin1 in megakaryocytes) and wildtype (Cre-negative littermates), were used at 8-12 weeks of age.

extract_protocol: Total RNA was isolated from magnetic bead isolated megakaryocytes using TRIzol and the MACHEREY-NAGEL NucleoSpin RNA XS kit with on-column DNase digestion. RNA yields were determined by Qubit 2.0 fluorometer using Qubit RNA HS assay kit.

treatment_protocol: Mice were killed by cervical dislocation and long bones were dissected. Bone marrow cells were isolated by gentle crushing in a mortar and pestle. The cell suspension was passed through a 100 µm filter, laid over a 1.050 gmL-1 Percoll, and spun at 400 g for 30 min. The interphase was labeled with anti-CD41-PE antibodies (BD Biosciences Cat# 558040), followed by Miltenyi anti-PE microbeads. Cells were passed twice through Miltenyi Large Cell columns on the Miltenyi MiniMACS Separator, and the positive fraction was collected.

tag: cell type

value: Magnetic bead isolated bone marrow megakaryocytes

tag: genotype


title: Pf4-Grin1-/- MKs, biological rep 5


title: pGAL-RNY1 tRF Fu16H ligation Rep 1


title: Pf4-Grin1-/- MKs, biological rep 6


title: WT tRF NEB Rep 2


title: Pf4-Grin1-/- MKs, biological rep 3


title: pGAL-RNY1 tRF Fu16H ligation Rep 2


title: Pf4-Grin1-/- MKs, biological rep 1


title: Wildtype MKs, biological rep 5

description: Gene expression data from wildtype mouse bone marrow megakaryocytes

source_name: Wild-type megakaryocytes

value: Wildtype


title: Wildtype MKs, biological rep 4


title: pGAL-RNY1 tRF OTTR with 5' UMI Rep 1


title: Wildtype MKs, biological rep 6


title: WT tRF Fu 2H ligation Rep 1


title: Pf4-Grin1-/- MKs, biological rep 2


title: pGAL-RNY1 tRF OTTR Rep 1


title: Wildtype MKs, biological rep 3


title: Wildtype MKs, biological rep 2


title: WT tRF OTTR Rep 1


title: Wildtype MKs, biological rep 1


title: WT tRF Fu 16H ligation Rep 1


title: pGAL-RNY1 tRF NEB with 5' UMI Rep 1


title: WT tRF OTTR with 5' UMI Rep 1


title: pGAL-RNY1 tRF NEB Rep 1


title: Hypothalamus_wild-type_rep2

city: shanghai

first: Wenbin

last: Liu

address: 500 Dongchuan Road

country: China

institute: East China Normal University

description:
WT3
Gene expression in the hypothalamus of wild-type mice.

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression V2.0（8*60K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0 (Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: Hypothalamus, wild-type

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice were obtained from Humangen Biotech Inc (Shanghai, China). ASMT-knockout mice (F0) were generated via co-injection of in vitro-synthesized ASMT sgRNA (5’-gCGCCTACACCAACTCCCCCC-3’), Cas9 mRNA and pMD19T-T7 vector into the zygotes of C57BL/6 mice. The founder mice test was analyzed with quantitative real-time polymerase chain reaction (qRT-PCR) using the set of primers (sense 5'-agggtcacagttcatggtgg-3' and antisense 5'-tcgacgcccacggccctcgcgta-3'). The originally produced ASMT-knockout mice (i.e., the positive founder mice with 20 bp deletion) were backcrossed with their wild-type littermates C57BL/6 mice for 3 generations. Genotyping was conducted with high resolution melting (HRM), which can distinguish three genotypes accurately.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: Mice were housed with a 12-hour light: dark cycle under controlled temperature (22 ± 2 °C) and humidity (50 ± 10%), and were given standard diet and water ad libitum. The breeding male mice (3-4-week old, 17-20g) were performed gene identification to select ASMT-knockout homozygous mice and wild-type littermate mice. All mice were adaptively reared for 3 weeks, and were then trained in a swimming program or not. Mice were randomly assigned to four groups: wild-type control group (WT), ASMT-knockout control group (KO), wild-type exercise group (WE), and ASMT-knockout exercise group (KE).

value: hypothalamus

value: WT

value: male

tag: treatment


title: pGAL-RNY1 tRF NEB with 5'+3' UMI Rep 1


title: pGAL-RNY1 tRF Fu 2H ligation Rep 1


title: WT tRF NEB with 5'+3' UMI Rep 1


title: Hypothalamus_wild-type_rep3

description:
WT4
Gene expression in the hypothalamus of wild-type mice.


title: WT tRF NEB with 5' UMI Rep 1


title: Hypothalamus_wild-type_rep1

description:
WT1
Gene expression in the hypothalamus of wild-type mice.


title: Hypothalamus_wild-type and swimming exercise_rep2

description:
WE3
Gene expression after swimming exercise in the hypothalamus of wild-type mice.

source_name: Hypothalamus, wild-type and swimming exercise

value: swimming exercise


title: Hypothalamus_wild-type and swimming exercise_rep1

description:
WE2
Gene expression after swimming exercise in the hypothalamus of wild-type mice.


title: Hypothalamus_wild-type and swimming exercise_rep3

description:
WE4
Gene expression after swimming exercise in the hypothalamus of wild-type mice.


title: WT tRF NEB Rep 1


title: WT Gel Purified Rep 2

value: SC-Ura Dextrose


title: WT mirVAna Porified Rep 2


title: WT mirVAna Porified Rep 1


title: Hypothalamus_ASMT knockout_rep2

description:
KO2
Gene expression in the hypothalamus of ASMT-knockout mice.

source_name: Hypothalamus, ASMT knockout

value: ASMT knockout


title: Hypothalamus_ASMT knockout_rep1

description:
KO1
Gene expression in the hypothalamus of ASMT-knockout mice.


title: TRM1Δ  Gel Purified Rep 2


title: WT Gel Purified Rep 1


title: MCF10A_ARID1A KO_Volasertib

city: Singapore

first: Anand

middle: D

last: Jeyasekharan

state: Outside US/Canada

address: 14 Medical Drive,  Centre for Translational Medicine, 13-02 Bench 13

country: Singapore

institute: Cancer Science Institute of Singapore

library_source: genomic

data_processing:
RNAseq: Data processing was performed using the CSI NGS Portal  (https://csibioinfo.nus.edu.sg/csingsportal).
Briefly, raw fastq files were trimmed by using Trimmomatic for adapter removal
The clean reads were aligned to the reference human genome (hg19) by using STAR (v2.7.3a) with default parameters.
The gene expression quantification was done by using HTSeq-count (v0.11.2) in strand-specific mode “-s reverse” to obtain raw read counts for each gene, and read counts only from the sense strand are used.
Differential gene expression analysis was performed by using DESeq2 (v1.24.0) starting from the raw read counts
For the mitochondrial encoded gene analysis the above procedure was followed bar these differences:  reads were aligned to the hg38 genomic build to ensure that mitochondrial DNA genes were included in the analysis; gene expression quantitation was performed using the HTSeq-count (v0.13.5) in strand specific mode (-s yes); and the differential gene expression analysis was performed by DESeq2 ( v 1.32.0).
CRISPR screen: raw data was processed and analysed by the MAGeCK-VISPR pipeline (https://doi.org/10.1186/s13059-015-0843-6)
Genome_build: RNAseq: hg19/hg38
Supplementary_files_format_and_content: RNAseq: csv files- differential expression data generated by DESeq2
Supplementary_files_format_and_content: CRISPR: xlsx files- normalised sgRNA counts,  sgRNA count summary, gene summary files for pairwise comparisons of conditions- all obtained through the MAGeCK-VISPR pipeline.

molecule: genomic DNA

source_name: MCF10A-normal breast epithelium

growth_protocol:
GES1: Grown in RPMI1640 supplemented with 20% FBS and 1% Pen/Strep
OVCAR3: grown in RPMI1640 with 10% FBS;
MCF10A:  grown in DMEM/F12 supplemented with 5% horse serum, 10µg/ml insulin, 20 ng/ml epithelial growth factor, 0.5 mg/ml hydrocortisone and 100 ng/ml cholera toxin.

extract_protocol:
RNA extracted using Qiagen RNeasy Mini Kit (RNAseq)
Gemonic DNA isolatied using Qiagen genomic DNA isolation kit (CRISPR screen)
RNA libraries and CRISPR sgRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
GES1/OVCAR3: 10nM Volasertib for 24 hours (RNAseq)
MCF10A: 10nM Volasertib for 23 days followed by 5 days at 1uM (CRISPR screen)

value: normal breast epithelium

value: ARID1A knockout


title: Brunello CRISPR sgRNA Library replicate 1 (L1)

source_name: Plasmid vectors containing sgRNA (Brunello library)


title: Brunello CRISPR sgRNA Library replicate 2 (L2)


title: MCF10A_WT_Volasertib

value: wild type

value: 10nM Volasertib for 23 days followed by 5 days at 1uM


title: TRM1Δ  mirVAna Purified Rep 1


title: TRM1Δ  Gel Purified Rep 1


title: MCF10A_ARID1A KO

value: untreated


title: miRNA_Wound7_5

extract_protocol:
Tissue samples were homogenized with the TissueLyser LT (Qiagen) and total RNA was isolated using the miRNeasy Mini kit (Qiagen) or Trizol reagent (ThermoFisher Scientific). RNA quality and quantity were determined by using Agilent 2100 Bioanalyzer (Agilent Technologies) and Nanodrop 1000 (Thermo Fisher Scientific Inc.), respectively.
The small RNA sequencing libraries were constructed using 3 μg total RNA per sample and NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendation. The library preparations were sequenced on an Illumina Hiseq 2500 platform (Illumina, Inc.) using single-end 50bp reads and all samples were run side by side.
single-end 50bp

value: Skin

value: Caucasian

value: Wound day 7

value: small RNA


title: MCF10A_WT


title: OVCAR3_ARID1A KO_rep2

source_name: OVCAR3-ovarian serous adenocarcinoma

value: ovarian serous adenocarcinoma


title: miRNA_Wound7_4

value: Male


title: Hypothalamus_ASMT knockout and swimming exercise_rep1

description:
KE3
Gene expression after swimming exercise in the hypothalamus of ASMT-knockout mice.

source_name: Hypothalamus, ASMT knockout and swimming exercise

value: hypothalamus


title: Hypothalamus_ASMT knockout and swimming exercise_rep3

description:
KE6
Gene expression after swimming exercise in the hypothalamus of ASMT-knockout mice.


title: Hypothalamus_ASMT knockout and swimming exercise_rep2

description:
KE4
Gene expression after swimming exercise in the hypothalamus of ASMT-knockout mice.


title: OVCAR3_ARID1A KO_rep1


title: miRNA_Wound7_3

value: Female


title: Hypothalamus_ASMT knockout_rep3

description:
KO3
Gene expression in the hypothalamus of ASMT-knockout mice.

value: male


title: OVCAR3_WT_rep2


title: miRNA_Wound7_2


title: miRNA_Wound7_1


title: GES1_ARID1A KO_Volasertib_rep2

source_name: GES1- normal gastric epithelium

value: normal gastric epithelium

value: 10nM Volasertib for 24 hours


title: miRNA_Wound1_4

value: Wound day 1


title: OVCAR3_WT_rep1


title: miRNA_Wound1_5


title: GES1_ARID1A KO_Volasertib_rep1


title: GES1_WT_Volasertib_rep2


title: GES1_ARID1A KO_rep2


title: miRNA_Wound1_2


title: miRNA_Skin5

value: Intact skin


title: GES1_ARID1A KO_rep1

value: ARID1A knockout


title: miRNA_Wound1_3


title: miRNA_Wound1_1


title: GES1_WT_rep2

value: wild type


title: miRNA_Skin3


title: miRNA_Skin4


title: GES1_WT_rep1


title: Cauda Sperm mirVana Purified OTTR pH6 Rep 2

source_name: Cauda Sperm

value: FVB/NJ


title: miRNA_VU5

value: Venous ulcer


title: Cauda Sperm mirVana Purified OTTR pH6 18H ligation Rep 1


title: miRNA_Skin2

value: Skin


title: Cauda Sperm mirVana Purified OTTR pH6 Rep 1


title: Cauda Sperm mirVana Purified OTTR pH6 18H ligation Rep 2


title: miRNA_VU3

value: Caucasian


title: miRNA_Skin1


title: Cauda Sperm mirVana Purified OTTR Rep 2


title: Vola-rep1

city: Shanghai

first: Mengying

last: Feng

address: no. 67 Chifeng road, Yangpu district

department: School of Life Sciences and Technology

institute: Tongji University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn6 or mm10 whole genome using hisat2 v2.1.0 with parameters -p 8 --dta -x -1 -2 -S
Raw transcripts were assembled using the StringTie (v1.3.4). Counts per million (cpm) were calculated by the edgeR (v3.20.9).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: human pluripotent stem cells derived cardiomyocytes

growth_protocol: hPSC-CMs were produced from ZSSY001 (Nuwacell) by regulating Wnt signaling pathway. hPSCs were grown on Matrigel (Corning, 354277) in Essential 8 TM Medium (Gibco, A15169-01, A15171-01). Cardiac differentiation was performed using dense monolayers of hPSCs treated with 6µM CHIR-99021 (Sellect, S1263) for 48 h and 5μM IWP-2 (Sellect, S7065) for 2 days in RPMI 1640 (Gibco, 11875-093)/B-27 minus insulin Medium (Gibco, A18956-01) previously described protocol . Spontaneously beating hPSC-CMs appeared after 7 days. Then the containing medium was replaced with RPMI 1640/B-27 Medium (Gibco, A17504-044). Metabolism selection was performed using Cardiomyocyte Selection Medium (ScienCell, 5911, 5962) for high purity cardiomyocytes.

extract_protocol:
The total RNA was extracted by TRIzol extraction reagent (Invitrogen, 15596018). Furthermore, the purity and concentration of RNA were examined by measuring the absorbance value at 260 and 280 nm.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hPSC-CMs were treated with Centrinone or Volasertib for 14 days.

value: cardiomyocytes

tag: agent

value: Volasertib


title: Cauda Sperm mirVana Purified OTTR 18H ligation Rep 2 (2)


title: CN-rep3

value: Centrinone


title: miRNA_VU4

value: small RNA


title: miRNA_VU2


title: Vola-rep3


title: Ctrl-rep3


title: G assay 2

type: genomic

city: São Paulo

first: José

middle: Franco

last: Da Silveira

state: São Paulo

address: Rua Botucatu, 862

department: Departamento de Microbiologia, Imunologia e Parasitologia

country: Brazil

institute: Universidade Federal de São Paulo

description: Second assay

hyb_protocol: After assembling the chamber the Hybridization was performed into the oven rotator rack at 67 ºC, 20 rpm for 24 hours, according to the manufacturer's instructions.

scan_protocol: The Scanning of the microarray slides was performed in a Agilent G2565CA Microarray Scanning System following the manufacturer's steps described in Oligonucleotide Array-Based CGH for Genomic DNA Analysis - Enzymatic Labeling (Agilent).

data_processing:
Raw data was first normalized using Feature Extraction software (Agilent).
Agilent Genomic Workbench Standard Edition 6.5 was then used to perform CNV interval detection. The QC metrics motif of Workbench 6.5 ensured adequate quality control of the hybridization data. In our study, an array signal which met the requirements if intensity value >50 and signal-to-noise ratio >25 was included in the analysis. The Aberration Detection Method 2 algorithm was used with a threshold of 6 and bin size of 10 to identify genomic variation. Additionally, we applied a relatively stringent post-analysis filter (4 probes, 0.5 log ratio) to ignore small, spurious or low-quality

organism: Trypanosoma cruzi

source_name: Epimastigotes

label_protocol: Fluorescent labeling of gDNA was performed with SureTag DNA Labeling kit (Agilent) following the manufacturer's instructions.

growth_protocol: Clone CL Brener (CLB) (T. cruzi Discrete Typing Unit (DTU) VI- lineage TcVI) and the G strain (T. cruzi DTU I - lineageTcI)  in axenic cultures at 28 °C in liver-infusion tryptose medium (LIT) containing 10% fetal calf serum.

extract_protocol: Genomic DNA extraction was performed with the Dneasy Blood & Tissue kit (Qiagen) using 5x107 cells/mL according to the manufacturer's instructions.

value: G


title: Vola-rep2


title: G assay 1

description: First assay


title: Cauda Sperm mirVana Purified OTTR Rep 1


title: Ctrl-rep2


title: D11 assay 1

description: First assay


title: GES1_WT_Volasertib_rep1


title: Cauda Sperm mirVana Purified OTTR ATP Rep 2


title: U87MG-R250 (Resistant)-1

city: Istanbul

first: Tugba

last: Bagci-Onder

state: Sariyer

address: Koc University School of Medicine

department: School of Medicine

country: Turkey

institute: Koc University

data_processing:
Mapping: Hisat2 v2.1.0
Rsubread(v.1.30.9)'s featureCountFunction was used to count reads. Subreads built-in hg19 used for counting. :
Gene Name Annotation: EnsDb.Hsapiens.v75 was used to get gene symbols that are corresponding to ensemble ID.
Differential Gene Expression: Count data was analysed using deseq2 1.20.0
Genome_build: hg19
Supplementary_files_format_and_content: Comma separated file - Raw Feature Count output

source_name: GBM cells

growth_protocol: Cells were grown in 10 cm tissue culture plates with DMEM supplemented with 10% FBS and 1% Pen/Strep at 37 C, 5%CO2 incubator for 24 hr.

extract_protocol: High quality total RNA was extracted from samples using Nucleospin RNA kit of Macherey-Nagel and eluted in RNAse free water.

tag: cell line

tag: passages

tag: condition

value: Resistant


title: Ctrl-rep1


title: miRNA_VU1

value: Male


title: CN-rep2


title: Cauda Sperm mirVana Purified OTTR ATP Rep 1


title: U87MG-R50 (Resistant)-2


title: Cauda Sperm mirVana Purified OTTR 18H ligation Rep 2


title: U87MG-R50 (Resistant)-1


title: QC11

city: Durham

first: Grace

middle: M

last: Lee

state: North Carolina

address: Box 3486, DUMC

institute: Duke University

data_processing:
RNA-seq data was processed using the TrimGalore toolkit1 which employs Cutadapt2 to trim low quality bases and Illumina sequencing adapters from the 3’ end of the reads.  Only reads that were 20nt or longer after trimming were kept for further analysis.  Reads were mapped to the GRCh38v93 version of the human genome and transcriptome3 using the STAR RNA-seq alignment tool4.  Reads were kept for subsequent analysis if they mapped to a single genomic location.   Gene counts were compiled using the HTSeq tool5.  Only genes that had at least 10 reads in any given library were used in subsequent analysis.  Normalization and differential expression was carried out using the DESeq26 Bioconductor7 package with the R statistical programming environment8.  The false discovery rate was calculated to control for multiple hypothesis testing.  Gene set enrichment analysis9 was performed to identify gene ontology terms and pathways associated with altered gene expression for each of the comparisons performed.
Genome_build: GRCh38v93
Supplementary_files_format_and_content: count

source_name: peripheral blood, isolated neutrophils

extract_protocol:
RNA was extracted from 107 neutrophils from 4 “low” and 3 ”high” subjects for RNA sequencing. Total RNA was extracted from 107 neutrophils using the NucleoSpin RNA Plus Mini Kit according to manufacturer’s directions.
Sequencing libraries were prepared for each sample using the Kapa Stranded mRNA-Seq Library Prep Kit followed by sequencing on the Illumina NovaSeq 6000 (Illumina, San Diego, CA) with a 50bp single end reads length. Library construction, RNA sequencing, and bioinformatic analysis was completed by the Duke University School of Medicine Sequencing and Genomic Technologies Shared Resource.

value: neutrophils

tag: disease

value: healthy


title: QC12


title: U87MG-S (Sensitive)-2

value: Sensitive


title: QC10


title: Cauda Sperm mirVana Purified OTTR 18H ligation Rep 1

tag: strain


title: QC8


title: D11 assay 2

description: Second assay


title: Cauda Sperm mirVana Purified OTTR 18H ligation Rep 1 (2)


title: QC6


title: Cauda Sperm mirVana Purified NEB Small RNA pH6 Rep 2


title: U87MG-S (Sensitive)-1


title: CN-rep1


title: QC4


title: U87MG-R250 (Resistant)-2


title: Cauda Sperm mirVana Purified NEB Small RNA pH6 18H ligation Rep 2


title: C1-sgEED-Epi_H3K27me3

city: Cambridge

first: Yun

last: Zhang

email: zhangyunbio@gmail.com, barc@wi.mit.edu

state: MA

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

data_processing:
library strategy: CUT&RUN
CUT&RUN paired-end reads were aligned using bowtie2 to the human genome (GRCh38), with the parameters: --very-sensitive --no-discordant -X 1000 --phred64
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files in counts per million (cpm) were generated using bamCoverage from deepTools

source_name: HMLER

growth_protocol: Cells were cultured in 2:1:1 MEGM (Lonza Bullet kit), DMEM and F12 media, supplemented with insulin (10 μg/ml), EGF (10 ng/ml), hydrocortisone (1 μg/ml), and 1x Pen/Strep (50 I.U./mL penicillin and 50 μg/mL streptomycin, Sigma-Aldrich #P4333).

extract_protocol: Libraries were prepared using Swift Science’s Accel-NGS Library Preparation Kit for Illumina Platforms according to manufacturer’s directions.

value: EED-KO

value: HMLER

tag: cut&run antibody


title: C1-sgControl_H3K27me3

value: wild type


title: Cauda Sperm mirVana Purified NEB Small RNA pH6 18H ligation Rep 1

value: FVB/NJ


title: Vero E6 cell replicate 3 DM(+)

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

data_processing:
Raw fastq files were demultiplexed based on a barcode on the first 4nt of read2. We used Je suite demultiplexer with the following parameters: je demultiplex F1=FastQ/$sample$R1 F2=FastQ/$sample$R2 BF=$bar_code_pathÂ Â BPOS=BOTH BM=READ_2 LEN=6:4 O=./0_barcode_read2/$sample FORCE=true C=false
Reads were then mapped to reference genome using bowtie2 and the following parameters: bowtie2 -x $reference -U $bar_directory$sample$in1Â Â Â -S ./3_bowtie2/$index_file/$sample_dir$underscore$sample$suffix -q -p 10 --local â€”no-unalÂ Â Several reference genomes were used, as indicated in the text and processed file descriptions
Sam files were used to generate several processed files using a variety of tools
For 'pileup' summary files, sam files were covered to bam files and sorted using samtools command samtools view -bS -o ./4_bam_sort_wig/$index_file/$base.bam ./3_bowtie2/$index_file/$filename and samtools sort ./4_bam_sort_wig/$index_file/$base.bam -o ./4_bam_sort_wig/$index_file/$base.sort.bam Next bam files were compressed with IGV command igvtools count -z 5 -w 1 -e 250 --bases 4_bam_sort_wig/$index_file/$base.sort.bam 4_bam_sort_wig/$index_file/$base.wig $reference to make summary .wig files. Wig files were reformatted with custom python scripts (available on GitHub)
For 'counts' reads, custom python script using the pysam python wra for samtools was used to tally the number of reads mapping to each reference sequence.
For tRNA fragment analysis, the pysam python package wrapper for samtools was used to determine the 3primeposition for each read and organize reads into separate sam files based on this position. These separate sam files were processed to generate pileup and count files as previously described
Genome_build: For Sars-Cov2 genome, we used NCBI NC_0455122_Wuhan_seafood_market_pneumonia_virus_isolate_Wuhan_Hu_1_complete_genome. For SRP mapping we used ensemble genome GCA_000409795.2. For vero cell tRNA refernce, we used tRNAs from RFAM set, then used tRNAscanSE to filter for tRNAs with scores > 70
Supplementary_files_format_and_content: see file: processed_data_file_names_and_descriptions.xlsx (available on the series record).
Supplementary_files_format_and_content: Some processed data files contain no data because we did not identify fragments from these tRNA positions present within our samples. However, we opted to include them still within our larger data set because when you run the custom python script and process step to identify these fragments, these are our files and we wanted to include our comprehensive result.

organism: Chlorocebus sabaeus

source_name: Host cell

extract_protocol: Extracted RNA was reverse transcribed. Following RT, products were ligated to adaptors. These adaptors were captured on beads and pooled and underwent demethylase and/or CMC treatment. Following this, samples were submitted for illumine sequencing.

tag: group

value: cell

value: Demethylase treated

tag: molecule subtype

value: ncRNA, tRNA


title: Vero E6 cell replicate 2 DM(+)


title: Cauda Sperm mirVana Purified NEB Small RNA Rep 2


title: Vero E6 cell replicate 1 DM(+)


title: QC14


title: Cauda Sperm mirVana Purified NEB Small RNA Rep 1


title: Cauda Sperm mirVana Purified NEB Small RNA 18H ligation Rep 2 (2)


title: Vero E6 cell replicate 3 DM(-)

value: Not demethylase treated


title: Vero E6 cell replicate 2 DM(-)


title: untransduced control (3)

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

source_name: untransduced control

label_protocol: Affymetrix protocol

extract_protocol: Total RNA from cells was isolated using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

tag: genotype/variation

value: untransduced control


title: RNF186_UN_3

city: Wuhan

first: Huazhi

address: Luoyu Road

institute: Huazhong University of Science and Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements

source_name: Ls174t cells

growth_protocol: Control Ls174t cells or RNF186-overexpressed Ls174t cells (stable cell line) were digested with trypsin,and then divided into three 6cm-dishes respectively. Cell were harvested after 48h culturing in DMEM medium plus 10% FBS and 1% Penicillin-Streptomycin.

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

treatment_protocol: untreated

value: untreated


title: Cauda Sperm mirVana Purified NEB Small RNA 18H ligation Rep 1 (2)


title: Cauda Sperm mirVana Purified NEB Small RNA ATP Rep 2


title: Vero E6 cell replicate 1 DM(-)


title: RNF186_UN_2


title: Cauda Sperm mirVana Purified NEB Small RNA ATP Rep 1


title: CXorf67-C (3)

value: transduced with lentiviral constructs expressing tuncated versions of CXorf67/EZHIP (C-terminal part)


title: RNF186_UN_1


title: CXorf67-M (3)

value: transduced with lentiviral constructs expressing tuncated versions of CXorf67/EZHIP (middle part)


title: untransduced control (2)


title: CXorf67-N (3)

value: transduced with lentiviral constructs expressing tuncated versions of CXorf67/EZHIP (N-terminal part)


title: Cauda Sperm mirVana Purified NEB Small RNA 18H ligation Rep 2


title: Vec_UN_3

value: Vector


title: Vec_UN_2


title: CXorf67-C (2)


title: Cauda Sperm mirVana Purified NEB Small RNA 18H ligation Rep 1


title: C1-sgKMT2D-Epi_H3K27me3


title: Cauda Sperm mirVana Purified NEB Small RNA pH6 Rep 1


title: CXorf67-full (2)

value: transduced with lentiviral constructs expressing full-length EZHIP/CXorf67


title: Vec_UN_1


title: untransduced control (1)


title: Cauda Sperm mirVana Purified Illumina TruSeq pH6 ATP 18H ligation Rep 1


title: CXorf67-full (3)


title: T98G-R (Resistant)-2

value: Resistant


title: CXorf67-N (2)


title: Cauda Sperm mirVana Purified Illumina TruSeq pH6 Rep 2


title: T98G-R (Resistant)-1


title: CXorf67-M (2)


title: CXorf67-full (1)


title: Cauda Sperm mirVana Purified Illumina TruSeq pH6 Rep 1


title: Cauda Sperm mirVana Purified Illumina TruSeq pH6 18H ligation Rep 2


title: Cauda Sperm mirVana Purified Illumina TruSeq pH6 18H ligation Rep 1


title: LN18-R (Resistant)-2


title: NR

city: Jena

first: Yu-Heng

last: Tseng

state: Thuringia

address: Dornburgerstr. 159

department: Plant Physiology

institute: Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller University Jena

data_processing:
Library strategy: WGS
Mapping was done with Samtools v 1.11
Comparison of SNPs found in the two samples were performed with SIMPLE v. 1.8.1, using bam files as input
Supplementary_files_format_and_content: frequency count of SNPs in csv format

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Seedlings were grown on agal plates with Hoagland′s No. 2 Basal Salt Mixture

extract_protocol: DNA from 50 seedlings per group was extracted and sequenced on Illumina sequencer by Novogene Co. UK (PE150).

treatment_protocol: 1mM cellobiose

tag: tissue

value: Root

tag: cytoplasmic calcium response

value: Non-responsive


title: T98G-S (Sensitive)-1

value: Sensitive


title: Cauda Sperm mirVana Purified Illumina TruSeq Rep 2


title: WT

value: responsive


title: LN18-R (Resistant)-1

value: wild type


title: Cauda Sperm mirVana Purified Illumina TruSeq Rep 1

value: FVB/NJ


title: LN18-S (Sensitive)-2


title: Cauda Sperm mirVana Purified Illumina TruSeq 18H ligation Rep 2


title: S38

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

data_processing:
Only the first read of the paired-end reads were used for data analysis, these were treated as single reads by our fastq file processing pipeline.
The quality of reads was assessed using FastQC version 0.11.5
Trimmed read sequences were mapped to the dog genome using STAR (version 2.5.3a)
The number of mapped reads were counted for each gene and compiled into an expression matrix using featureCounts (version 1.6.0)
Genome_build: CanFam3.1, release 97
Supplementary_files_format_and_content: Countdata.xlsx: count data per sample

molecule: polyA RNA

organism: Canis lupus

source_name: VaccineD_24h_dog cell line 030-D

growth_protocol: 030-D cell line, derived from a canine malignant histiocytosis, was cultured  at 37°C and 5% CO2 in RPMI-1640 (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS; Gibco), 100 U/ml penicillin, 100 µg/ml streptomycin and 300 ng/ml L-glutamine (all Gibco).

extract_protocol:
Cells were harvested and centrifuged 5 min at 300g. Pellet was suspended in 200 µl PBS and lysed in 550 µl Lysis/binding buffer (Roche) supplemented with 1% DTT (Sigma Aldrich). Cell lysates were stored at -80°C until RNA isolation with the MagNA Pure LC RNA isolation kit-High performance (Roche) on the MagNA Pure LC 2.0 instrument following the manufacturer’s protocol. Isolated RNA samples were quantified using UV spectroscopy (Take3 module, Synergy Mx, BioTek, Winooski, USA). RNA integrity was analysed by agarose gel electrophoresis using 2% E-Gel EX pre-stained gels (Thermo Fischer Scientific).
Library preparation and RNA sequencing was performed at MAD: Dutch Genomics Service & Support (University of Amsterdam, The Netherlands). Libraries were sequenced using an NextSeq 550 platform and 20 million reads per sample.

treatment_protocol: 4 x 10^6 030-D cells were stimulated with inactivated whole-cell preparations of L. interrogans serogroup Canicola or Icterohaemorrhagiae, excipient (non-antigen control) and two bivalent Leptospira vaccines.

value: dog cell line 030-D

tag: stimulus

value: VaccineD

tag: time

tag: replicate


title: CXorf67-M (1)


title: S39


title: Cauda Sperm mirVana Purified Illumina TruSeq pH6 ATP 18H ligation Rep 2


title: S37


title: Cauda Sperm mirVana Purified Illumina TruSeq 18H ligation Rep 1


title: S36

source_name: VaccineD_8h_dog cell line 030-D


title: Cauda Sperm mirVana Purified Illumina TruSeq ATP Rep 2


title: A172-R (Resistant)-1

tag: genotype


title: S35


title: S34


title: A172-S (Sensitive)-2


title: S33

source_name: VaccineB_24h_dog cell line 030-D

value: VaccineB


title: A172-S (Sensitive)-1


title: T98G-S (Sensitive)-2


title: Testis mirVana Purified Rep 2

source_name: Testis


title: S32


title: Testis Gel Purified Rep 2


title: Kidney ANRIL KO diabetic rep 3

city: London

first: Subrata

last: Chakrabarti

state: Ontario

address: 1151 Richmond St

department: Pathology and Lab Medicine

country: Canada

institute: Univeristy of Western Ontario

data_processing:
An average of 42 million (minimum of 27 million) paired-end reads were generated for each sample.
Samples were aligned using STAR version 2.7.3a to mouse genome mm10 with GENCODE M23 primary annotations.
An average of 30 million reads aligned uniquely (minimum 20 million).
Subsequent analysis was performed using R version 3.6.1. Count matrices were generated using the summarized overlaps function from the Genomic Alignments package version 1.20.1.
Differential expression analysis was performed using edgeR version 3.28.0 24.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with edgeR differential gene expression results (log-fold change and P values) for each comparison and every gene

source_name: Kidney

growth_protocol: The mice were kept in convention room, and give normal food and tap water

extract_protocol:
Three biological replicates were used for each of the four groups. Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, Toronto, ON).
The libraries were prepared by using the TruSeq RNA V2 kit. Sequencing was performed by Macrogen Corp. (Rockville, MD) on an Illumina sequencer with NovaSeq6000 S4 flow cell.

treatment_protocol: The mice were intraperitoneally injected streptozotocin (50 mg/kg body weight) for 5 consecutive days, then follow up 2 months

value: Kidney

tag: age

value: 8 weeks

value: ANRIL knockout


title: Cauda Sperm mirVana Purified Illumina TruSeq ATP Rep 1

extract_protocol:
Mouse RNA was extracted using standard TRIZol protocol. Yeast RNA was extracted by beadbeating in TNE buffer (50 mM Tris-Cl pH7.4, 100 mM NaCl, 10 mM EDTA), followed by an acid Phenol extraction.
Libraries were constructed following published protocols.


title: Kidney ANRIL KO diabetic rep 2


title: Testis mirVana Purified Rep 1


title: S31


title: Testis Gel Purified Rep 1


title: Kidney ANRIL KO diabetic rep 1


title: S30

source_name: VaccineB_8h_dog cell line 030-D


title: shCLCN3

city: Zhengzhou

first: Zhuoyu

last: Gu

address: Jianshe East Road

institute: The First Affiliated Hospital, Zhengzhou University

data_processing:
Illumina Casava1.7 software used for basecalling.
FPKM and count data

source_name: lung adenocarcinoma

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung adenocarcinoma

value: Fifth generation

value: CLCN3 knockdown


title: S29


title: Kidney ANRIL KO non-diabetic control rep 3


title: CXorf67-C (1)

value: transduced with lentiviral constructs expressing tuncated versions of CXorf67/EZHIP (C-terminal part)


title: shNC

value: CLCN3 shNC


title: Kidney ANRIL KO non-diabetic control rep 2


title: S28


title: CXorf67-N (1)

value: transduced with lentiviral constructs expressing tuncated versions of CXorf67/EZHIP (N-terminal part)


title: LN18-S (Sensitive)-1


title: Kidney ANRIL KO non-diabetic control rep 1


title: b6j 2 mg/kg rep6

city: SHANGHAI

first: XIAN

last: JIN

state: SHANGHAI

address: Cailun Road 720, 2-404

institute: ENNOVABIO

data_processing:
Original binary basecalling data obtained by sequencing was converted into sequence data by Illumina bcl2fastq software
Trimmomatic was used for removing adaptors, low-quality sequencing reads, and short sequences.
Read quality was checked for each sample using FastQC
Paired-end transcriptome reads were mapped to the mouse reference genome (GRCm38) using STAR spliced read aligner
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was isolated from the snap frozen kidney samples using the TRizol kit. The samples were then quantified and qualified by Agilent 2100 Bioanalyzer, NanoDrop  and 1% agrose gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

tag: type

tag: treatment

value: b6j:2 mg/kg CdCl2


title: S27

source_name: Ictero_24h_dog cell line 030-D

tag: cell line

value: Ictero


title: b6j 2 mg/kg rep5


title: SARS CoV 2 virion isolate 6 DM(+) CMC(+)

organism: Severe acute respiratory syndrome coronavirus 2

source_name: Virion isolate

value: isolate

value: demethylase treated; CMC treated

value: Genomic RNA, ncRNA, tRNA


title: Kidney WT diabetic rep 3

value: wilde type


title: A172-R (Resistant)-2

tag: passages

tag: condition

value: Resistant

value: wild type


title: S26

value: dog cell line 030-D


title: Kidney WT diabetic rep 2

value: Kidney

tag: strain

value: 8 weeks


title: SARS CoV 2 virion isolate 5 DM(+) CMC(+)


title: Kidney WT diabetic rep 1


title: b6j 2 mg/kg rep4


title: S25


title: SARS CoV 2 virion isolate 4 DM(+) CMC(+)


title: S24

source_name: Ictero_8h_dog cell line 030-D


title: SARS CoV 2 virion isolate 3 DM(+) CMC(+)


title: b6j 2 mg/kg rep2


title: S23


title: Kidney WT non-diabetic control rep 3


title: b6j 2 mg/kg rep1


title: Kidney WT non-diabetic control rep 2


title: b6j 0.5 mg/kg rep6

value: b6j:0.5 mg/kg CdCl2


title: S22


title: SARS CoV 2 virion isolate 1 DM(+) CMC(+)


title: SARS CoV 2 virion isolate 2 DM(+) CMC(+)


title: Kidney WT non-diabetic control rep 1


title: S21

source_name: Canicola_24h_dog cell line 030-D

value: Canicola


title: SARS CoV 2 virion isolate 6 DM(+) CMC(-)

value: demethylase treated; not CMC treated


title: Model of TAC mice treated with distilled water_rep3

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

institute: The Second Affiliated Hospital of Xinjiang Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Raw reads were processed using fastp version 0.20.0. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference  N. coloratarep genome using hisat2(v2.1.0) with parameters -p 8 --fr --dta-cufflinks
FPKM value of each gene was calculated using cufflinks(v2.2.1) with parameters --no-update-check -u -p 8 --library-type fr-firststrand, and the read counts of each gene were obtained by htseq-count(version 0.7.2) with parameters -i gene_id -f bam -s reverse -r name.
DEGs were identified using the Deseq library . P value < 0.05 and absolute value of foldchange >=2 was set as the threshold for significantly differential expression.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: heart

growth_protocol: C57BL/6J male mice (8-10 weeks old) and Sprague-Dawley rats (200-230g) were purchased from the Beijing Vital River Laboratory Animal Technology Co., Ltd. (certificate number: SCXK (JING) 2016-0006). All animals were housed in a temperature and humidity-controlled animal facility under 12-h light/ dark cycle and specific pathogen-free conditions, with free access to rodent chow and water.

extract_protocol:
The total RNA was extracted by trizol method from heart tissues of each sample using the three biological repeats.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments with right length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB,USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100system.

treatment_protocol: The tissue were immediately frozen in liquid nitrogen and stored at -80 °C.

value: heart

value: 18-20 weeks old

value: treated with distilled water


title: S20


title: b6j 0.5 mg/kg rep5

value: kidney


title: SARS CoV 2 virion isolate 5 DM(+) CMC(-)


title: S19


title: Model of TAC mice treated with distilled water_rep2


title: SARS CoV 2 virion isolate 4 DM(+) CMC(-)


title: b6j 0.5 mg/kg rep4


title: Model of TAC mice treated with distilled water_rep1


title: SARS CoV 2 virion isolate 3 DM(+) CMC(-)


title: b6j 0.5 mg/kg rep2


title: S17

source_name: Canicola_8h_dog cell line 030-D


title: SARS CoV 2 virion isolate 2 DM(+) CMC(-)


title: Sham operation group treated with distilled water_rep2


title: b6j 2 mg/kg rep3

value: b6j:2 mg/kg CdCl2


title: SARS CoV 2 virion isolate 1 DM(+) CMC(-)

value: isolate


title: S15

source_name: Excipient_24h_dog cell line 030-D

value: Excipient


title: b6j control rep5


title: SARS CoV 2 virion isolate 6 DM(-) CMC(+)

value: Not demethylase treated; CMC treated

value: Genomic RNA, ncRNA, tRNA


title: b6j control rep6


title: TAC mice treated with Lingguizhugan decoction_rep3

value: treated with Lingguizhugan decoction


title: S13


title: S14


title: SARS CoV 2 virion isolate 5 DM(-) CMC(+)


title: b6j control rep4


title: SARS CoV 2 virion isolate 4 DM(-) CMC(+)


title: SARS CoV 2 virion isolate 3 DM(-) CMC(+)


title: TAC mice treated with Lingguizhugan decoction_rep1


title: b6j control rep3


title: S11

source_name: Excipient_8h_dog cell line 030-D


title: b6j 0.5 mg/kg rep3


title: S18


title: HAP1_WT_2018-05-09_miRNAseq

city: Austin

first: Blerta

last: Xhemalce

state: Texas

address: 2500 Speedway

institute: University of Texas at Austin

data_processing:
For all datasets, sequence quality was verified by FastQC and reads were aligned using STAR.
For RNA-seq data, reads were aligned against the hg38 reference genome and counted using the FeatureCounts utility in the subread package with Gencode v21 annotation.
For miRNA-seq data, reads were adapter trimmed using cutadapt with the adapter sequence TGGAATTCTCGGGTGCCAAG and a minimum length of 16 nt, followed my alignment against mirbase v22 and counting with samtools idxstats with no additional filtering.
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited text fiels contain the total number of reads within each gene (for RNA-Seq) and within each miRNA (for miRNA-Seq).

source_name: HAP1 cell line

extract_protocol:
Norgen RNA/Protein purification kit plus
Illumina TruSeq Small RNA

tag: shRNA status

value: WT


title: SARS CoV 2 virion isolate 2 DM(-) CMC(+)

tag: group


title: SARS CoV 2 virion isolate 1 DM(-) CMC(+)

tag: molecule subtype


title: b6j control rep2


title: S10

value: dog cell line 030-D


title: Sham operation group treated with distilled water_rep3


title: S09

source_name: Unstimulated_24h_dog cell line 030-D

value: Unstimulated


title: S16


title: ob 2 mg/kg rep6

value: ob

value: ob:2 mg/kg CdCl2


title: b6j 0.5 mg/kg rep1

value: b6j:0.5 mg/kg CdCl2


title: HAP1_WT_2018-05-06_miRNAseq


title: SARS CoV 2 virion isolate 5 DM(-) CMC(-)

value: Not demethylase treated; not CMC treated


title: ob 2 mg/kg rep5


title: HAP1_KO_2018-05-06_miRNAseq

value: BCDIN3D KO clone 11


title: HAP1_KO_2018-05-09_RNAseq

extract_protocol:
Norgen RNA/Protein purification kit plus
Illumina TruSeq Stranded Total RNA


title: Sham operation group treated with distilled water_rep1

value: heart

value: 18-20 weeks old


title: S08


title: SARS CoV 2 virion isolate 6 DM(-) CMC(-)


title: TAC mice treated with Lingguizhugan decoction_rep2


title: SARS CoV 2 virion isolate 4 DM(-) CMC(-)


title: S07


title: ob 2 mg/kg rep3

value: kidney


title: S12


title: S06

source_name: Unstimulated_8h_dog cell line 030-D


title: ob 2 mg/kg rep2


title: b6j control rep1


title: SARS CoV 2 virion isolate 3 DM(-) CMC(-)


title: S05


title: HAP1_KO_2018-05-06_RNAseq


title: S04


title: HAP1_KO_2018-05-09_miRNAseq


title: SARS CoV 2 virion isolate 2 DM(-) CMC(-)


title: ob 0.5 mg/kg rep6

value: ob:0.5 mg/kg CdCl2


title: ob 2 mg/kg rep1


title: ob 2 mg/kg rep4


title: SARS CoV 2 virion isolate 1 DM(-) CMC(-)

value: isolate


title: S03

source_name: Unstimulated_0h_dog cell line 030-D


title: ob 0.5 mg/kg rep5


title: S02


title: ob 0.5 mg/kg rep4


title: S01


title: SARS CoV 2 virion isolate 6 DM(+)

value: Demethylase treated


title: SARS CoV 2 virion isolate 5 DM(+)


title: HAP1_WT_2018-05-09_RNAseq


title: ob 0.5 mg/kg rep3


title: ob 0.5 mg/kg rep2


title: SARS CoV 2 virion isolate 4 DM(+)


title: HAP1_WT_2018-05-06_RNAseq


title: SARS CoV 2 virion isolate 3 DM(+)


title: SKBR3r, biological rep2

city: Valencia

first: Pilar

last: Eroles

address: Menendez Pelayo acc4

country: Spain

institute: INCLIVA

description: miRNA expression data from SKBR3r cell line

hyb_protocol: The hybridization mixture was prepared with the reagents from the kit according to manufacturer’s instructions and added to the biotin labelled RNA sample for 5 minutes at 99ºC and 5 minutes at 45ºC. These reactions were injected in the microarray and incubated in the hybridization oven for 18h at 48ºC under agitation. After hybridising, microarrays were washed, and probes were stained for detection.

scan_protocol: Microarrays were scanned using the GeneChip Scanner GCS3000 with self-loading (Affymetrix Ltd., Santa Clara, CA)

data_processing: The data were analyzed with Transcriptome Analysis Console 3.0 (TAC 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: SKBR3r cell line

label_protocol: 300 ng of total RNA of each sample was labelled with biotin with a commercial Kit FlashTag ™ Biotin HSR RNA Labeling Kit

growth_protocol: Cell lines were grown in Dulbecco Modified Eagle medium nutrient mixture F-12 (DMEM/F12) with 2.5 mM L-Glutamine and 15 mM HEPES (Gibco), supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics (100 U/mL penicillin and 100 mg/L streptomycin). SKBR3r and BT474r cells were generated by culture with 15 μg/ml trastuzumab for 6–12 months86,  and cultured with that constant concentration of trastuzumab. Cells were maintained in a humidified atmosphere at 37ºC with 5% CO2.

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

treatment_protocol: Cell from 6-well plates were rinsed with PBS, scrapped, centrifuged and placed into the Trizol solution.

value: SKBR3r cell line


title: SKBR3r, biological rep1


title: SKBR3r, biological rep3


title: ob 0.5 mg/kg rep1


title: ob control rep6


title: SARS CoV 2 virion isolate 2 DM(+)

value: Genomic RNA, ncRNA, tRNA


title: ob control rep5


title: SARS CoV 2 virion isolate 1 DM(+)


title: SKBR3, biological rep3

description: miRNA expression data from SKBR3 cell line

source_name: SKBR3 cell line

value: SKBR3 cell line


title: SARS CoV 2 virion isolate 5 DM(-)

value: Not demethylase treated


title: SKBR3, biological rep2


title: ob control rep4

source_name: Kidney


title: SKBR3, biological rep1


title: BT474r, biological rep3

description: miRNA expression data from BT474r cell line

source_name: BT474r cell line

value: BT474r cell line


title: SARS CoV 2 virion isolate 6 DM(-)


title: ob control rep3


title: SARS CoV 2 virion isolate 4 DM(-)


title: Si-cTNFRSF21-3

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

institute: Karolinska Institutet

hyb_protocol: Standardized array processing procedures recommended by Affymetrix, including hybridization, fluidics processing, and scanning, were used

data_processing:
Expression data were analyzed by using Transcriptome Analysis Console 4.0. The follwoing criteria were used for data analysis:
Array Type: Clariom_S_Human
Analysis Type: Expression (Gene)
Analysis Version: version 2
Summarization Method: Gene Level - SST-RMA
Pos vs Neg AUC Threshold: 0,7
Genome Version: hg38 (Homo sapiens)
Annotation: Clariom_S_Human.r1.na36.hg38.a1.transcript.csv
Condition (Comparison): circRNA kd; ctr
Expression Analysis Settings:
• Gene-Level Fold Change < -2 or > 2
• Gene-Level P-Value < 0,05
• Anova Method: ebayes
• A Probeset (Gene/Exon) is considered expressed if ≥ 50% samples have DABG values below DABG Threshold.
• DABG < 0,05

source_name: Keratinocytes transfected with si-cTNFRSF21

label_protocol: One hundred fifty nanograms of total RNA was used to prepare cDNA following the GeneChip WT PLUS Reagent Kit labeling protocol

growth_protocol: Adult Human Epidermal Keratinocytes (HEKa) were cultured in EpiLife medium (Gibco™) supplemented with 10% Human Keratinocyte Growth Supplement (HKGS, Gibco™) and 1% penicillin/streptomycin (Gibco™) at 37°C in 5% CO2.

extract_protocol: Total RNA was extracted from the cells using TRIzol reagent (ThermoFisher Scientific).

treatment_protocol: Third passage HEKa cells were seeded in 24-well plates. At 60-70% confluence, cells were transfected with 20nM siRNA against cCHST15 or cTNFRSF21 or a non-targeting siRNA control (GE Healthcare Dharmacon) using Lipofectamine 3000 (ThermoFisher Scientific). After 24 hours, cells were harvested for RNA extraction.

value: HEKa

tag: tissue source

value: Skin

tag: cell type

value: Adult Human Epidermal Keratinocytes

value: si-cTNFRSF21 knockdown


title: BT474r, biological rep1


title: BT474r, biological rep2


title: Si-cTNFRSF21-1

scan_protocol: Standardized array processing procedures recommended by Affymetrix, including hybridization, fluidics processing, and scanning, were used


title: ob control rep2

tag: tissue

value: ob


title: SARS CoV 2 virion isolate 3 DM(-)


title: ob control rep1


title: Si-cTNFRSF21-2


title: Si-cCHST15-1

source_name: Keratinocytes transfected with si-cCHST15

value: si-cCHST15 knockdown


title: SARS CoV 2 virion isolate 2 DM(-)

source_name: Virion isolate


title: BT474, biological rep2

description: miRNA expression data from BT474 cell line

source_name: BT474 cell line

value: BT474 cell line


title: leaf, Zn_CMV_4

status: Public on Mar 05 2022

city: Kusatsu, Shiga

first: Midori

last: Tabara

address: 1-1-1, Noji-Higashi

country: Japan

institute: Ritsumeikan University

data_processing:
Illumina Casava ver.1.8.2 software was used for base calling.
Sequenced reads were mapped to the A. halleri genome (Briskine et al., 2017) using TopHat (ver. 2.0.13) in combination with Bowtie2 (ver. 2.2.3) (Langmead & Salzberg, 2012) and SAMtools (ver. 0.1.19).
The number of fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm ver. 2.2.1 (Trapnell et al., 2010).
We obtained the annotation data from Ensemblgenome (https://plants.ensembl.org/Arabidopsis_halleri/Info/Index).
Genome_build: A. halleri genome (Briskine et al., 2017)
Supplementary_files_format_and_content: counts

organism: Arabidopsis halleri

source_name: leaf

extract_protocol:
Total RNAs were extracted by using the Trizol reagent following the manufacturer’s protocol (Thermo Fisher Scientific, MA).
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: leaf

tag: cultivar

tag: infection

value: cucumber mosaic virus (CMV), Zn


title: leaf, Zn_CMV_3


title: leaf, Zn_CMV_2


title: BT474, biological rep3


title: leaf, Zn_Mock_3

value: Free Zn


title: SARS CoV 2 virion isolate 1 DM(-)

value: isolate


title: Si-ctrl-3

source_name: Keratinocytes transfected with siRNA control

value: Control


title: leaf, CMV_3

value: cucumber mosaic virus (CMV)


title: BT474, biological rep1


title: Si-cCHST15-2


title: Si-cCHST15-3


title: leaf, Zn_Mock_2


title: leaf, CMV_2


title: leaf, CMV_4


title: leaf, Mock_4

value: Free


title: leaf, Zn_Mock_4


title: leaf, Mock_3


title: Encapsulated mouse myoblasts implanted in a old mouse - Rep. 3

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

country: Switzerland

institute: Nestle Institute Of Health Sciences

description:
Myoblasts from a capsule implanted in a old mouse
htseq_GEO_2400.csv

data_processing:
Genome build: Mus musculus GRCm38
Sequencing raw data (bcl) were demultiplexed and transformed in fastq files using cassava v1.8.2.
The fastq files were aligned against the reference genome by RNAstar v2.5.3a.
The raw sequencing counts per gene were generated using htseq_count v2.16.2
Supplementary_files_format_and_content: comma separated value file including counts per gene (row)  for each sample (column)

source_name: Encapsulated mouse skeletal myoblasts

growth_protocol: Primary mouse myoblasts from 3-week-old C57Bl6/J (Charles River, C57BL/6NCrl) mice were maintained in Ham’s F10 media (Wisent, 318-051-CL) containing 20% FBS (Wisent, 80450, lot 115714), 1% Penicillin Streptomycin solution (Wisent, 450-201-EL) and 2,5 ng/mL bFGF (VWR, 10821-962) in a 37°C, 5% CO2 incubator at a confluence under 80%.

extract_protocol:
RNA was extracted using RNAdvance Tissue Kit (Beckman Coulter). Quality control was performed with Fragment Analyzer (Advanced Analytical).
Libraries were quantified with the Quant-iT Picogreen (Invitrogen, 10545213) on a FilterMax F3 (Molecular Devices, F3). Size pattern was assessed with Fragment Analyzer-96 with the DNF-474-0500 High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies, DNF-474-0500).
Libraries (Average size: 295 bp) were pooled at an equimolar ratio and clustered at a concentration of 9 pM on a single read sequencing flow cell.

value: C57BL/6J mice

value: Old

value: Primary myoblasts isolated from skeletal muscle


title: Encapsulated mouse myoblasts implanted in a old mouse - Rep. 4


title: leaf, Mock_2


title: Si-ctrl-2

value: HEKa


title: Encapsulated mouse myoblasts implanted in a old mouse - Rep. 5


title: Encapsulated mouse myoblasts implanted in a old mouse - Rep. 2


title: Encapsulated mouse myoblasts implanted in a young mouse - Rep. 5

description:
Myoblasts from a capsule implanted in a young mouse
htseq_GEO_2400.csv

value: Young


title: Encapsulated mouse myoblasts implanted in a young mouse - Rep. 3


title: Encapsulated mouse myoblasts implanted in a young mouse - Rep. 2


title: Encapsulated mouse myoblasts implanted in a young mouse - Rep. 4


title: Encapsulated mouse myoblasts implanted in a young mouse - Rep. 7


title: Encapsulated mouse myoblasts implanted in a young mouse - Rep. 6


title: Si-ctrl-1

value: Skin

value: Adult Human Epidermal Keratinocytes


title: Encapsulated mouse myoblasts implanted in a old mouse - Rep. 1


title: Encapsulated mouse myoblasts implanted in a young mouse - Rep. 1


title: LNCaP_Ctrl Prostate cancer cells_rep1 [Exome-Seq]

city: Philadelphia

first: Irfan

last: Asangani

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Library strategy: Exome-Seq
Illumina bcl2fastq for demultiplexing to generate fastq files
fastq files were aligned to hg19 reference genome using STAR aligner (2.7.3a) with non-splice aware settings
resulting bam files were filtered to remove PCR duplicates, sorted, and recalibrated using the Base Quality Score Recalibration metric defined in the Genome Analysis Toolkit (GATK)
Following the GATK best practices, we called per sample variants using the `GATK Haplotypecaller`  in the GVCF mode. The individual sample variants, generated in gvcf format, were combined using `GATK combineGVCFs` to create a master vcf file. We next used the GRCh37 exon coordinates  downloaded from the UCSC genome browser to only retain the combined variants associated with exons. The filtered variants were genotyped against the gnomad database using `GenotypeGVCFs`  and annotated using the `variant effect predictor` tool from Ensembl . We performed all further analysis of the variants using HAIL.
We further filtered variants to only retain high quality calls that satisfy the following filters: (i) call rate >95% in all samples, (ii) reads per allele > 5 in all samples, (iii) (alt allele frequency in resistant lines) >= 2x  (alt allele frequency in corresponding controls).
hg19

source_name: Prostate cancer

growth_protocol: Cells were grown in RPMI medium with 10% FBS and 1% Pen/Strep

extract_protocol:
Total DNA was extracted using Qiagen DNA extraction kit.
Illumina Nextera Flex Enrichment kit and IDT exome capture probes were used with 1 ug of total DNA for the construction of Exome sequencing libraries. Sequencing run was perfromed using NextSeq mid output 2x150 kit.

treatment_protocol: Cells were cultured with the drug Zenith-3694 for 16-20 weeks.

value: DMSO


title: 22RV1_Prostate cancer cells_rep1 [Exome-Seq]


title: 22RV1 ZenR_Prostate cancer cells_rep1 [Exome-Seq]

value: Zenith-3694 1uM


title: LNCaP ZenR_Prostate cancer cells_rep2

data_processing:
Illumina bcl2fastq for demultiplexing to generate fastq files
fastq files were aligned to hg19 reference genome using STAR aligner (2.7.3a) with default parameters
samtools (v1.9) was used to convert SAM to BAM and filter out duplicates and reads q<30
Cufflinks,cuffquant, and cuffnorm (v2.2.1) was used to quantify transcripts and construct the expression table
Genome_build: hg19
Supplementary_files_format_and_content: Comma separated text files including raw count values for each Sample …

extract_protocol:
Cells were cultured with the drug for 16-20 weeks and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat# ) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: agent

value: Zenith-3694 300nM


title: VCaP ZenR_Prostate cancer cells_rep2

value: Zenith-3694 200nM


title: LNCaP_Prostate cancer cells_rep1


title: 22RV1_Prostate cancer cells_rep2


title: LNCaP_Prostate cancer cells_rep2


title: LNCaP ZenR200nM_Prostate cancer cells_rep1 [Exome-Seq]


title: 22RV1_Prostate cancer cells_rep1


title: LNCaP ZenR_Prostate cancer cells_rep1


title: 22RV1 ZenR_Prostate cancer cells_rep1


title: 22RV1 ZenR_Prostate cancer cells_rep2


title: nonclassMO_P9

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

description: Each biological replicate was sequenced on two sequencing flow cells to achieve the intended sequencing depth. Each sequencing run is represented by a separate SRR.

data_processing:
Quality control FastQC Galaxy Version 0.72
Reads were mapped to the human reference genome (Gencode, GRCh38.p13, all regions, release 37) with RNA STAR (Galaxy Version 2.7.7a) using the Gencode main annotation file (Gencode, release 37).
Two BAM files for each sample (one for each lane) were combined in one BAM file per sample using Merge BAM Files (Galaxy Version 1.2.0).
Reads mapped to the human reference genome were counted with featureCounts (Galaxy Version 2.0.1) using the aforementioned annotation file.
The outputs of featureCounts were imported to RStudio (Version 1.4.1103, R Version 4.0.3). Gene symbols were determined based on the ENSEMBL database (release 103, download on 03/23/2021). Genes with 0 reads in all samples were removed from the analysis.
Expression profiles of all 5 cell types were adjusted for individual patients by the limma function removeBatchEffect and by consideration within the linear model of DESeq2. After principle component analysis, normalized reads and differential gene expression were calculated using the R package DESeq2 (version 1.30.1) with default parameters (Benjamini-Hochberg adjusted p-values).
Genome_build: hg38

source_name: Human non-classical monocytes

extract_protocol:
Total RNA was extracted from FACS sorted cells stabilized in RNAprotect buffer ac-cording to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Plus Micro Kit (QIAGEN, Hilden, Germany). In brief, cells were stored and shipped in buffer RNAprotect at 2-8 °C. After pelleting by centrifugation for 5 minutes at 5,000 x g, the RNAprotect was replaced by 350 µl buffer RLT Plus and the samples were homogenized by vortexing for 30 seconds. Genomic DNA con-tamination was removed by using gDNA Eliminator spin columns. Next, one volume of 70 % ethanol was added and the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Finally, the total RNA was eluted in 12 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA).
The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from approx-imately 1 ng total-RNA. Double stranded cDNA was amplified by LD PCR (12 cy-cles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and frag-mented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step, 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA Library Quantification Kit - Illumina/ABI Prism User Guide (Roche Sequencing Solutions, Inc., Pleasanton, CA, USA). Equimolar amounts of each library were sequenced on a NextSeq 500 instrument controlled by the NextSeq Control Software (NCS) v2.2.0, using two 75 Cycles High Output Kits with the dual index, single-read (SR) run parameters. Image analysis and base calling were done by the Real Time Analysis Software (RTA) v2.4.11. The resulting .bcl files were converted into .fastq files with the bcl2fastq v2.18 software. RNA extraction, library preparation and RNAseq were performed at the Genomics Core Facility “KFB - Center of Excellence for Fluorescent Bioanalytics” (University of Regensburg, Regensburg, Germany; www.kfb-regensburg.de).

value: non-classical monocytes


title: nonclassMO_P8


title: nonclassMO_P7


title: VCaP_Prostate cancer cells_rep2


title: VCaP ZenR_Prostate cancer cells_rep1


title: nonclassMO_P2


title: nonclassMO_P1


title: intermMO_P9

source_name: Human intermediate monocytes

value: intermediate monocytes


title: intermMO_P7


title: intermMO_P8


title: VCaP_Prostate cancer cells_rep1


title: intermMO_P1


title: intermMO_P2


title: classicMO_P9

source_name: Human classical monocytes

value: classical monocytes


title: classicMO_P7


title: classicMO_P8


title: classicMO_P2


title: MG P6

source_name: Human retinal microglia

value: retinal microglia


title: MG P4


title: classicMO_P5


title: HY P2

source_name: Human hyalocytes

value: hyalocytes


title: HY P5


title: HY P4


title: MG P3


title: MG P5


title: HY P1


title: HY P6


title: EBs.MUA_EV_004_X331

city: Utrecht

first: Isabel

last: Guerreiro

address: Uppsalalaan 8

institute: Hubrecht Institute

description: Transcriptome measurement of sample EBs.MUA_EV_004_X331

data_processing:
Demultiplexing of raw data (previously demultiplexed on Illumina index) was done using barcodes. Read1 measurements contained only the barcode and UMI followed by unalignable sequence , usually polyT and are therefore not included. Read2 of the transcriptomic measurements contains the mRNA sequence. All reads provided are read 2. The sequencing was run in 4 lanes: L001-L004.
mRNA reads (in read2) were aligned using tophat2 (v2.1.1) using parameters ‘--segment-length 22 --read-mismatches 4 --read-edit-dist 4 --min-anchor 6 --min-intron-length 25 --max-intron-length 25000 --no-novel-juncs --no-novel-indels --no-coverage-search --b2-very-sensitive --b2-N 1 --b2-gbar 200’ to a transcriptome (options ‘--GTF’ and ‘--transcriptome-index’) obtained from GENCODE (v26) supplemented with ERCC mRNA spike-in sequences.
Reads and unique UMIs were counted per gene (according to the “intersection-strict” algorithm of `htseq-count` [http://htseq.readthedocs.io/en/master/count.html]). For each gene, the number of unique observed UMIs was trimmed by starting at the UMI with highest read count and setting UMIs with Hamming distance of 1 to zero, and iteratively filtering all UMI sequences (in case of equal read counts for a UMI, ties were broking by lexicographic sorting of the UMIs). The number of observed distinct UMIs after trimming was taken as the transcript count for that gene.
Genome_build: mm10
Supplementary_files_format_and_content: Tables are provided with the number of transcripts per gene.

source_name: embryoid bodies from mouse ESCs

growth_protocol:
Advanced N2B27 medium was used as the basic medium consisting of 2% B27 (Gibco, 17504-044) and 1% N2 (Gibco, 17502-048), a 1/1 mixture of Advanced DMEM/F12 (ThermoFisher, 12634028) with Neurobasal (ThermoFisher, 12348017), 2 mM Glutamax (Gibco), 10mM NEAA (ThermoFisher, 11140050), 0.5% Bovine Serum Albumin (Sigma-Aldrich, A7979), 10 mM HEPES (Gibco, 15630056), 1 mM Sodium Pyruvate (ThermoFisher, 11360070). supplemented right before use with 10 ng/mL leukaemia inhibitory factor (Lif, Merck Millipore ESG1106), 1 ?M PD0325901 (AxonMed, 1408), 3 ?M CHIR99021 (AxonMed, 1386) and 50 ?M 2-mercaptoethanol (Gibco, 11528926). For ESC expansion the cells were expanded for minimally 2 passages on gelatin-coated tissue-culture plastic in advanced N2B27 medium was supplemented right before use with 3 ?M CHIR99021 (AxonMed 1386), 10 ng/mL Lif (Merck Millipore ESG1106), 1 ?M PD0325901 (AxonMed 1408) and 50 µM 2-mercaptoethanol (Gibco 11528926).
PrE-induction for Rosette formation was done by seeding an average of 14 ESC per microwell in Advanced B27N2 medium supplemented with 10 mM HEPES and penicillin/streptomycin, and the PrE-induction compounds 3 ?M CHIR99021 (AxonMed 1386), 50 ng/mL Fgf4 (RnD systems, 5846-F4-025), 10 nM RA (Sigma R2625), 1 mM 8Br-cAMP (Biolog, B007-50E), 1 µg/mL heparin (Sigma) and 50 µM 2-mercaptoethanol (Gibco 11528926). When seeding the cells in the microwells 2 µM Y27632 (AxonMed 1683) was added. Microwell arrays were pre-wetted in serum-medium containing 100U/ml penicillin/streptomycin before use. After 24 h or 48 h of culture, cells were washed once with advanced N2B27 medium and then refreshed with advanced N2B27 supplemented with 50 µM 2-mercaptoethanol. After 72 h EBs were flushed out and transferred into non-TCPS 6-well plates with 2 mL advanced N2B27 medium supplemented with 50 µM 2-mercaptoethanol.

extract_protocol:
EBs were washed twice in PBS before collagenase IV (600 U/ml) was added. Plates were shaken at 350 RPM for 30 minutes before being transferred to TrypLE 10X (Thermofisher, A1217701, no dilution) and shaken again for 20 minutes. EBs were dissociated into single cell suspensions using a small capillary. The resulting suspension was quenched using PBS with 50% FBS, centrifuged and resuspended in 230 µl of PBS with 10% FBS. Cells were stained with Pdgfr? antibody (1:150 dilution) for 30 min at 4°C followed by three PBS (+10%FBS) washes, secondary antibody incubation (1:400) for 30 min. Cells were washed three times in PBS and sorted for further processing.
Rosettes were manually picked and placed in a round-bottom 96wp-well containing 100 µl PBS + 0.5% BSA. When sufficient numbers were collected, they were transferred to an Eppendorf tube with 600 µl Accumax and incubated at 37 degree C for 30 min. Every 5-10 minutes the mixture was resuspended using a 200 µl pipette. When single cells were observed under the microscope the suspension was centrifuged at 200g for 4 min and, supernatant was removed and cells were resuspended in staining solution in PBS (2 µM Di-I + 0.1% Dead-stain-647 ) and incubated for 20 min at RT in the dark. Epiblast-only rosettes were washed once with PBS before domes were disrupted using 150 µl of a 1:1 DipaseII:N2B27 mixture and incubated for 20 min at 37 degree C in a 1.5ml Eppendorf tube (4 domes per tube). Solution was resuspended every 5-10 minutes using a 200 µl pipette tip. Finally, the cell suspension was resuspended in 700 µl Accumax with 100 µl of PBS with 0.5% BSA and incubated for 25 min at 37 degree C. Single cells were stained with 2 µM Di-I + 0.1% Dead-stain-647) and incubated for 20 min at RT in the dark.

tag: celseq2 adapter

tag: sample type

value: XEN


title: EBs.MUA_EV_004_X334

description: Transcriptome measurement of sample EBs.MUA_EV_004_X334


title: EBs.MUA_EV_004_X330

description: Transcriptome measurement of sample EBs.MUA_EV_004_X330


title: EBs.MUA_EV_004_X332

description: Transcriptome measurement of sample EBs.MUA_EV_004_X332


title: EBs.MUA_EV_004_X326

description: Transcriptome measurement of sample EBs.MUA_EV_004_X326


title: EBs.MUA_EV_004_X328

description: Transcriptome measurement of sample EBs.MUA_EV_004_X328


title: EBs.MUA_EV_004_X329

description: Transcriptome measurement of sample EBs.MUA_EV_004_X329


title: EBs.MUA_EV_004_X327

description: Transcriptome measurement of sample EBs.MUA_EV_004_X327


title: EBs.MUA_EV_004_X324

description: Transcriptome measurement of sample EBs.MUA_EV_004_X324


title: EBs.MUA_EV_004_X325

description: Transcriptome measurement of sample EBs.MUA_EV_004_X325


title: EBs.MUA_EV_004_X319

description: Transcriptome measurement of sample EBs.MUA_EV_004_X319


title: EBs.MUA_EV_004_X313

description: Transcriptome measurement of sample EBs.MUA_EV_004_X313


title: EBs.MUA_EV_004_X311

description: Transcriptome measurement of sample EBs.MUA_EV_004_X311


title: EBs.MUA_EV_004_X322

description: Transcriptome measurement of sample EBs.MUA_EV_004_X322


title: EBs.MUA_EV_004_X320

description: Transcriptome measurement of sample EBs.MUA_EV_004_X320


title: EBs.MUA_EV_004_X321

description: Transcriptome measurement of sample EBs.MUA_EV_004_X321


title: EBs.MUA_EV_004_X333

description: Transcriptome measurement of sample EBs.MUA_EV_004_X333


title: EBs.MUA_EV_004_X323

description: Transcriptome measurement of sample EBs.MUA_EV_004_X323


title: classicMO_P1

description: Each biological replicate was sequenced on two sequencing flow cells to achieve the intended sequencing depth. Each sequencing run is represented by a separate SRR.


title: EBs.MUA_EV_004_X318

description: Transcriptome measurement of sample EBs.MUA_EV_004_X318


title: MG P1


title: EBs.MUA_EV_004_X317

description: Transcriptome measurement of sample EBs.MUA_EV_004_X317


title: EBs.MUA_EV_004_X316

description: Transcriptome measurement of sample EBs.MUA_EV_004_X316


title: EBs.MUA_EV_004_X305

description: Transcriptome measurement of sample EBs.MUA_EV_004_X305


title: EBs.MUA_EV_004_X335

description: Transcriptome measurement of sample EBs.MUA_EV_004_X335


title: EBs.MUA_EV_004_X314

description: Transcriptome measurement of sample EBs.MUA_EV_004_X314


title: EBs.MUA_EV_004_X310

description: Transcriptome measurement of sample EBs.MUA_EV_004_X310


title: EBs.MUA_EV_004_X308

description: Transcriptome measurement of sample EBs.MUA_EV_004_X308


title: EBs.MUA_EV_004_X309

description: Transcriptome measurement of sample EBs.MUA_EV_004_X309


title: EBs.MUA_EV_004_X304

description: Transcriptome measurement of sample EBs.MUA_EV_004_X304


title: EBs.MUA_EV_004_X315

description: Transcriptome measurement of sample EBs.MUA_EV_004_X315


title: EBs.MUA_EV_004_X306

description: Transcriptome measurement of sample EBs.MUA_EV_004_X306


title: EBs.MUA_EV_004_X301

description: Transcriptome measurement of sample EBs.MUA_EV_004_X301


title: EBs.MUA_EV_004_X307

description: Transcriptome measurement of sample EBs.MUA_EV_004_X307


title: EBs.MUA_EV_004_X303

description: Transcriptome measurement of sample EBs.MUA_EV_004_X303


title: EBs.MUA_EV_004_X298

description: Transcriptome measurement of sample EBs.MUA_EV_004_X298


title: EBs.MUA_EV_004_X299

description: Transcriptome measurement of sample EBs.MUA_EV_004_X299


title: EBs.MUA_EV_004_X312

description: Transcriptome measurement of sample EBs.MUA_EV_004_X312


title: EBs.MUA_EV_004_X295

description: Transcriptome measurement of sample EBs.MUA_EV_004_X295


title: EBs.MUA_EV_004_X294

description: Transcriptome measurement of sample EBs.MUA_EV_004_X294


title: EBs.MUA_EV_004_X297

description: Transcriptome measurement of sample EBs.MUA_EV_004_X297


title: EBs.MUA_EV_004_X293

description: Transcriptome measurement of sample EBs.MUA_EV_004_X293


title: EBs.MUA_EV_004_X292

description: Transcriptome measurement of sample EBs.MUA_EV_004_X292


title: EBs.MUA_EV_004_X291

description: Transcriptome measurement of sample EBs.MUA_EV_004_X291


title: Encapsulated mouse myoblasts implanted in a young mouse - Rep. 8

description:
Myoblasts from a capsule implanted in a young mouse
htseq_GEO_2400.csv

value: C57BL/6J mice

tag: age


title: EBs.MUA_EV_004_X289

description: Transcriptome measurement of sample EBs.MUA_EV_004_X289


title: EBs.MUA_EV_004_X286

description: Transcriptome measurement of sample EBs.MUA_EV_004_X286


title: EBs.MUA_EV_004_X288

description: Transcriptome measurement of sample EBs.MUA_EV_004_X288


title: EBs.MUA_EV_004_X283

description: Transcriptome measurement of sample EBs.MUA_EV_004_X283


title: EBs.MUA_EV_004_X287

description: Transcriptome measurement of sample EBs.MUA_EV_004_X287


title: EBs.MUA_EV_004_X284

description: Transcriptome measurement of sample EBs.MUA_EV_004_X284


title: EBs.MUA_EV_004_X290

description: Transcriptome measurement of sample EBs.MUA_EV_004_X290


title: EBs.MUA_EV_004_X282

description: Transcriptome measurement of sample EBs.MUA_EV_004_X282


title: EBs.MUA_EV_004_X285

description: Transcriptome measurement of sample EBs.MUA_EV_004_X285


title: EBs.MUA_EV_004_X281

description: Transcriptome measurement of sample EBs.MUA_EV_004_X281


title: EBs.MUA_EV_004_X277

description: Transcriptome measurement of sample EBs.MUA_EV_004_X277


title: EBs.MUA_EV_004_X278

description: Transcriptome measurement of sample EBs.MUA_EV_004_X278


title: EBs.MUA_EV_004_X300

description: Transcriptome measurement of sample EBs.MUA_EV_004_X300


title: EBs.MUA_EV_004_X279

description: Transcriptome measurement of sample EBs.MUA_EV_004_X279


title: EBs.MUA_EV_004_X276

description: Transcriptome measurement of sample EBs.MUA_EV_004_X276


title: EBs.MUA_EV_004_X280

description: Transcriptome measurement of sample EBs.MUA_EV_004_X280


title: EBs.MUA_EV_004_X302

description: Transcriptome measurement of sample EBs.MUA_EV_004_X302


title: EBs.MUA_EV_004_X273

description: Transcriptome measurement of sample EBs.MUA_EV_004_X273


title: EBs.MUA_EV_004_X270

description: Transcriptome measurement of sample EBs.MUA_EV_004_X270


title: EBs.MUA_EV_004_X271

description: Transcriptome measurement of sample EBs.MUA_EV_004_X271


title: EBs.MUA_EV_004_X296

description: Transcriptome measurement of sample EBs.MUA_EV_004_X296


title: EBs.MUA_EV_004_X268

description: Transcriptome measurement of sample EBs.MUA_EV_004_X268


title: EBs.MUA_EV_004_X269

description: Transcriptome measurement of sample EBs.MUA_EV_004_X269


title: EBs.MUA_EV_004_X272

description: Transcriptome measurement of sample EBs.MUA_EV_004_X272


title: EBs.MUA_EV_004_X265

description: Transcriptome measurement of sample EBs.MUA_EV_004_X265


title: EBs.MUA_EV_004_X267

description: Transcriptome measurement of sample EBs.MUA_EV_004_X267


title: EBs.MUA_EV_004_X266

description: Transcriptome measurement of sample EBs.MUA_EV_004_X266


title: EBs.MUA_EV_004_X259

description: Transcriptome measurement of sample EBs.MUA_EV_004_X259


title: EBs.MUA_EV_004_X263

description: Transcriptome measurement of sample EBs.MUA_EV_004_X263


title: EBs.MUA_EV_004_X260

description: Transcriptome measurement of sample EBs.MUA_EV_004_X260


title: EBs.MUA_EV_004_X262

description: Transcriptome measurement of sample EBs.MUA_EV_004_X262


title: EBs.MUA_EV_004_X255

description: Transcriptome measurement of sample EBs.MUA_EV_004_X255


title: EBs.MUA_EV_004_X256

description: Transcriptome measurement of sample EBs.MUA_EV_004_X256


title: EBs.MUA_EV_004_X258

description: Transcriptome measurement of sample EBs.MUA_EV_004_X258


title: EBs.MUA_EV_004_X250

description: Transcriptome measurement of sample EBs.MUA_EV_004_X250


title: EBs.MUA_EV_004_X253

description: Transcriptome measurement of sample EBs.MUA_EV_004_X253


title: EBs.MUA_EV_004_X257

description: Transcriptome measurement of sample EBs.MUA_EV_004_X257


title: EBs.MUA_EV_004_X249

description: Transcriptome measurement of sample EBs.MUA_EV_004_X249


title: EBs.MUA_EV_004_X275

description: Transcriptome measurement of sample EBs.MUA_EV_004_X275


title: EBs.MUA_EV_004_X264

description: Transcriptome measurement of sample EBs.MUA_EV_004_X264


title: EBs.MUA_EV_004_X248

description: Transcriptome measurement of sample EBs.MUA_EV_004_X248


title: EBs.MUA_EV_004_X251

description: Transcriptome measurement of sample EBs.MUA_EV_004_X251


title: EBs.MUA_EV_004_X274

description: Transcriptome measurement of sample EBs.MUA_EV_004_X274


title: EBs.MUA_EV_004_X247

description: Transcriptome measurement of sample EBs.MUA_EV_004_X247


title: EBs.MUA_EV_004_X246

description: Transcriptome measurement of sample EBs.MUA_EV_004_X246


title: EBs.MUA_EV_004_X245

description: Transcriptome measurement of sample EBs.MUA_EV_004_X245


title: EBs.MUA_EV_004_X242

description: Transcriptome measurement of sample EBs.MUA_EV_004_X242


title: EBs.MUA_EV_004_X243

description: Transcriptome measurement of sample EBs.MUA_EV_004_X243


title: EBs.MUA_EV_004_X244

description: Transcriptome measurement of sample EBs.MUA_EV_004_X244


title: EBs.MUA_EV_004_X241

description: Transcriptome measurement of sample EBs.MUA_EV_004_X241


title: EBs.MUA_EV_004_X240

description: Transcriptome measurement of sample EBs.MUA_EV_004_X240


title: EBs.MUA_EV_004_X239

description: Transcriptome measurement of sample EBs.MUA_EV_004_X239


title: EBs.MUA_EV_004_X237

description: Transcriptome measurement of sample EBs.MUA_EV_004_X237


title: EBs.MUA_EV_004_X232

description: Transcriptome measurement of sample EBs.MUA_EV_004_X232


title: EBs.MUA_EV_004_X252

description: Transcriptome measurement of sample EBs.MUA_EV_004_X252


title: EBs.MUA_EV_004_X229

description: Transcriptome measurement of sample EBs.MUA_EV_004_X229


title: EBs.MUA_EV_004_X226

description: Transcriptome measurement of sample EBs.MUA_EV_004_X226


title: EBs.MUA_EV_004_X222

description: Transcriptome measurement of sample EBs.MUA_EV_004_X222


title: EBs.MUA_EV_004_X220

description: Transcriptome measurement of sample EBs.MUA_EV_004_X220


title: EBs.MUA_EV_004_X235

description: Transcriptome measurement of sample EBs.MUA_EV_004_X235


title: EBs.MUA_EV_004_X236

description: Transcriptome measurement of sample EBs.MUA_EV_004_X236


title: EBs.MUA_EV_004_X234

description: Transcriptome measurement of sample EBs.MUA_EV_004_X234


title: EBs.MUA_EV_004_X218

description: Transcriptome measurement of sample EBs.MUA_EV_004_X218


title: EBs.MUA_EV_004_X231

description: Transcriptome measurement of sample EBs.MUA_EV_004_X231


title: EBs.MUA_EV_004_X216

description: Transcriptome measurement of sample EBs.MUA_EV_004_X216


title: EBs.MUA_EV_004_X219

description: Transcriptome measurement of sample EBs.MUA_EV_004_X219


title: EBs.MUA_EV_004_X230

description: Transcriptome measurement of sample EBs.MUA_EV_004_X230


title: EBs.MUA_EV_004_X214

description: Transcriptome measurement of sample EBs.MUA_EV_004_X214


title: EBs.MUA_EV_004_X254

description: Transcriptome measurement of sample EBs.MUA_EV_004_X254


title: EBs.MUA_EV_004_X228

description: Transcriptome measurement of sample EBs.MUA_EV_004_X228


title: EBs.MUA_EV_004_X227

description: Transcriptome measurement of sample EBs.MUA_EV_004_X227


title: EBs.MUA_EV_004_X212

description: Transcriptome measurement of sample EBs.MUA_EV_004_X212


title: EBs.MUA_EV_004_X211

description: Transcriptome measurement of sample EBs.MUA_EV_004_X211


title: EBs.MUA_EV_004_X225

description: Transcriptome measurement of sample EBs.MUA_EV_004_X225


title: EBs.MUA_EV_004_X223

description: Transcriptome measurement of sample EBs.MUA_EV_004_X223


title: EBs.MUA_EV_004_X221

description: Transcriptome measurement of sample EBs.MUA_EV_004_X221


title: EBs.MUA_EV_004_X217

description: Transcriptome measurement of sample EBs.MUA_EV_004_X217


title: EBs.MUA_EV_004_X233

description: Transcriptome measurement of sample EBs.MUA_EV_004_X233


title: EBs.MUA_EV_004_X215

description: Transcriptome measurement of sample EBs.MUA_EV_004_X215


title: EBs.MUA_EV_004_X207

description: Transcriptome measurement of sample EBs.MUA_EV_004_X207


title: EBs.MUA_EV_004_X213

description: Transcriptome measurement of sample EBs.MUA_EV_004_X213


title: EBs.MUA_EV_004_X205

description: Transcriptome measurement of sample EBs.MUA_EV_004_X205


title: EBs.MUA_EV_004_X238

description: Transcriptome measurement of sample EBs.MUA_EV_004_X238


title: EBs.MUA_EV_004_X210

description: Transcriptome measurement of sample EBs.MUA_EV_004_X210


title: EBs.MUA_EV_004_X200

description: Transcriptome measurement of sample EBs.MUA_EV_004_X200


title: EBs.MUA_EV_004_X196

description: Transcriptome measurement of sample EBs.MUA_EV_004_X196


title: EBs.MUA_EV_004_X209

description: Transcriptome measurement of sample EBs.MUA_EV_004_X209


title: EBs.MUA_EV_004_X208

description: Transcriptome measurement of sample EBs.MUA_EV_004_X208


title: EBs.MUA_EV_004_X261

description: Transcriptome measurement of sample EBs.MUA_EV_004_X261


title: EBs.MUA_EV_004_X197

description: Transcriptome measurement of sample EBs.MUA_EV_004_X197


title: EBs.MUA_EV_004_X193

description: Transcriptome measurement of sample EBs.MUA_EV_004_X193


title: EBs.MUA_EV_004_X206

description: Transcriptome measurement of sample EBs.MUA_EV_004_X206


title: EBs.MUA_EV_004_X194

description: Transcriptome measurement of sample EBs.MUA_EV_004_X194


title: EBs.MUA_EV_004_X192

description: Transcriptome measurement of sample EBs.MUA_EV_004_X192


title: EBs.MUA_EV_004_X191

description: Transcriptome measurement of sample EBs.MUA_EV_004_X191


title: EBs.MUA_EV_004_X224

description: Transcriptome measurement of sample EBs.MUA_EV_004_X224


title: EBs.MUA_EV_004_X203

description: Transcriptome measurement of sample EBs.MUA_EV_004_X203


title: EBs.MUA_EV_004_X204

description: Transcriptome measurement of sample EBs.MUA_EV_004_X204


title: EBs.MUA_EV_004_X188

description: Transcriptome measurement of sample EBs.MUA_EV_004_X188


title: EBs.MUA_EV_004_X202

description: Transcriptome measurement of sample EBs.MUA_EV_004_X202


title: EBs.MUA_EV_004_X187

description: Transcriptome measurement of sample EBs.MUA_EV_004_X187


title: EBs.MUA_EV_004_X199

description: Transcriptome measurement of sample EBs.MUA_EV_004_X199


title: EBs.MUA_EV_004_X183

description: Transcriptome measurement of sample EBs.MUA_EV_004_X183


title: EBs.MUA_EV_004_X182

description: Transcriptome measurement of sample EBs.MUA_EV_004_X182


title: EBs.MUA_EV_004_X195

description: Transcriptome measurement of sample EBs.MUA_EV_004_X195


title: EBs.MUA_EV_004_X190

description: Transcriptome measurement of sample EBs.MUA_EV_004_X190


title: EBs.MUA_EV_004_X189

description: Transcriptome measurement of sample EBs.MUA_EV_004_X189


title: EBs.MUA_EV_004_X201

description: Transcriptome measurement of sample EBs.MUA_EV_004_X201


title: EBs.MUA_EV_004_X186

description: Transcriptome measurement of sample EBs.MUA_EV_004_X186


title: EBs.MUA_EV_004_X177

description: Transcriptome measurement of sample EBs.MUA_EV_004_X177


title: EBs.MUA_EV_004_X198

description: Transcriptome measurement of sample EBs.MUA_EV_004_X198


title: EBs.MUA_EV_004_X185

description: Transcriptome measurement of sample EBs.MUA_EV_004_X185


title: EBs.MUA_EV_004_X175

description: Transcriptome measurement of sample EBs.MUA_EV_004_X175


title: EBs.MUA_EV_004_X169

description: Transcriptome measurement of sample EBs.MUA_EV_004_X169


title: EBs.MUA_EV_004_X168

description: Transcriptome measurement of sample EBs.MUA_EV_004_X168


title: EBs.MUA_EV_004_X181

description: Transcriptome measurement of sample EBs.MUA_EV_004_X181


title: EBs.MUA_EV_004_X165

description: Transcriptome measurement of sample EBs.MUA_EV_004_X165


title: EBs.MUA_EV_004_X173

description: Transcriptome measurement of sample EBs.MUA_EV_004_X173


title: EBs.MUA_EV_004_X174

description: Transcriptome measurement of sample EBs.MUA_EV_004_X174


title: EBs.MUA_EV_004_X172

description: Transcriptome measurement of sample EBs.MUA_EV_004_X172


title: EBs.MUA_EV_004_X170

description: Transcriptome measurement of sample EBs.MUA_EV_004_X170


title: EBs.MUA_EV_004_X171

description: Transcriptome measurement of sample EBs.MUA_EV_004_X171


title: EBs.MUA_EV_004_X184

description: Transcriptome measurement of sample EBs.MUA_EV_004_X184


title: EBs.MUA_EV_004_X167

description: Transcriptome measurement of sample EBs.MUA_EV_004_X167


title: EBs.MUA_EV_004_X164

description: Transcriptome measurement of sample EBs.MUA_EV_004_X164


title: EBs.MUA_EV_004_X153

description: Transcriptome measurement of sample EBs.MUA_EV_004_X153


title: EBs.MUA_EV_004_X158

description: Transcriptome measurement of sample EBs.MUA_EV_004_X158


title: EBs.MUA_EV_004_X156

description: Transcriptome measurement of sample EBs.MUA_EV_004_X156


title: EBs.MUA_EV_004_X159

description: Transcriptome measurement of sample EBs.MUA_EV_004_X159


title: EBs.MUA_EV_004_X160

description: Transcriptome measurement of sample EBs.MUA_EV_004_X160


title: EBs.MUA_EV_004_X162

description: Transcriptome measurement of sample EBs.MUA_EV_004_X162


title: EBs.MUA_EV_004_X154

description: Transcriptome measurement of sample EBs.MUA_EV_004_X154


title: EBs.MUA_EV_004_X155

description: Transcriptome measurement of sample EBs.MUA_EV_004_X155


title: EBs.MUA_EV_004_X152

description: Transcriptome measurement of sample EBs.MUA_EV_004_X152


title: EBs.MUA_EV_004_X180

description: Transcriptome measurement of sample EBs.MUA_EV_004_X180


title: EBs.MUA_EV_004_X179

description: Transcriptome measurement of sample EBs.MUA_EV_004_X179


title: EBs.MUA_EV_004_X176

description: Transcriptome measurement of sample EBs.MUA_EV_004_X176


title: EBs.MUA_EV_004_X150

description: Transcriptome measurement of sample EBs.MUA_EV_004_X150


title: EBs.MUA_EV_004_X151

description: Transcriptome measurement of sample EBs.MUA_EV_004_X151


title: EBs.MUA_EV_004_X178

description: Transcriptome measurement of sample EBs.MUA_EV_004_X178


title: EBs.MUA_EV_004_X149

description: Transcriptome measurement of sample EBs.MUA_EV_004_X149


title: EBs.MUA_EV_004_X147

description: Transcriptome measurement of sample EBs.MUA_EV_004_X147


title: EBs.MUA_EV_004_X148

description: Transcriptome measurement of sample EBs.MUA_EV_004_X148


title: EBs.MUA_EV_004_X166

description: Transcriptome measurement of sample EBs.MUA_EV_004_X166


title: EBs.MUA_EV_004_X145

description: Transcriptome measurement of sample EBs.MUA_EV_004_X145


title: EBs.MUA_EV_004_X146

description: Transcriptome measurement of sample EBs.MUA_EV_004_X146


title: EBs.MUA_EV_004_X144

description: Transcriptome measurement of sample EBs.MUA_EV_004_X144


title: EBs.MUA_EV_004_X163

description: Transcriptome measurement of sample EBs.MUA_EV_004_X163


title: EBs.MUA_EV_004_X141

description: Transcriptome measurement of sample EBs.MUA_EV_004_X141


title: EBs.MUA_EV_004_X139

description: Transcriptome measurement of sample EBs.MUA_EV_004_X139


title: EBs.MUA_EV_004_X161

description: Transcriptome measurement of sample EBs.MUA_EV_004_X161


title: EBs.MUA_EV_004_X132

description: Transcriptome measurement of sample EBs.MUA_EV_004_X132


title: EBs.MUA_EV_004_X130

description: Transcriptome measurement of sample EBs.MUA_EV_004_X130


title: EBs.MUA_EV_004_X137

description: Transcriptome measurement of sample EBs.MUA_EV_004_X137


title: EBs.MUA_EV_004_X134

description: Transcriptome measurement of sample EBs.MUA_EV_004_X134


title: EBs.MUA_EV_004_X138

description: Transcriptome measurement of sample EBs.MUA_EV_004_X138


title: EBs.MUA_EV_004_X135

description: Transcriptome measurement of sample EBs.MUA_EV_004_X135


title: EBs.MUA_EV_004_X131

description: Transcriptome measurement of sample EBs.MUA_EV_004_X131


title: EBs.MUA_EV_004_X129

description: Transcriptome measurement of sample EBs.MUA_EV_004_X129


title: EBs.MUA_EV_004_X157

description: Transcriptome measurement of sample EBs.MUA_EV_004_X157


title: EBs.MUA_EV_004_X126

description: Transcriptome measurement of sample EBs.MUA_EV_004_X126


title: EBs.MUA_EV_004_X128

description: Transcriptome measurement of sample EBs.MUA_EV_004_X128


title: EBs.MUA_EV_004_X133

description: Transcriptome measurement of sample EBs.MUA_EV_004_X133


title: EBs.MUA_EV_004_X136

description: Transcriptome measurement of sample EBs.MUA_EV_004_X136


title: EBs.MUA_EV_004_X122

description: Transcriptome measurement of sample EBs.MUA_EV_004_X122


title: EBs.MUA_EV_004_X127

description: Transcriptome measurement of sample EBs.MUA_EV_004_X127


title: EBs.MUA_EV_004_X121

description: Transcriptome measurement of sample EBs.MUA_EV_004_X121


title: EBs.MUA_EV_004_X124

description: Transcriptome measurement of sample EBs.MUA_EV_004_X124


title: EBs.MUA_EV_004_X120

description: Transcriptome measurement of sample EBs.MUA_EV_004_X120


title: EBs.MUA_EV_004_X119

description: Transcriptome measurement of sample EBs.MUA_EV_004_X119


title: EBs.MUA_EV_004_X125

description: Transcriptome measurement of sample EBs.MUA_EV_004_X125