title: P19_14388 Run1

source_name: P19_14388_endometrial cells


title: Scripps registry control_82

status: Public on Dec 04 2021

type: genomic

city: La Jolla

first: Hiroshi

last: Deguchi

state: Ca

address: 10550 N Torrey pines Rd

country: USA

institute: The Scripps Research Institute

hyb_protocol: Samples were hybridized with Axiom® Exome Genotyping Array (Affymetrix) and scanned at DNA Core Laboratory of the Scripps Research Institute.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: The genotype for each SNP for each subject was determined using the Affymetrix Genotyping Console (version 4.1.4)

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: control

label_protocol: not provided

growth_protocol: EDTA Blood was collected and white blood cells were separated by centrifuge in the presence of Ficol

extract_protocol: DNA were extracted from white blood cells using commercial kit.

tag: sample id

tag: diagnosis

value: healthy


title: P18_14331 Run1

type: SRA

city: Coventry

first: Jan

middle: J

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

country: United Kingdom

institute: University of Warwick

library_source: transcriptomic

data_processing:
Transcriptomic maps of paired-end reads were generated using bowtie-2.2.3, samtools-0.1.19, and tophat-2.0.12 against the hg19 reference genome (2014)
Transcript counts were assessed by HTSeq-0.6.1 using the reverse strand setting and intersection-non-empty mode and counts were assigned to gene ids.
Genome_build: hg19
Supplementary_files_format_and_content: Count and TPM data in .XLS format

molecule: total RNA

source_name: P18_14331_endometrial cells

extract_protocol:
RNA was purified using RNA STAT-60 (AMS Bio) according to manufacturer's instructions and treated using Amplification Grade DNase I (Invitrogen) followed by ethanol precipitation and clean-up. Quality control, library preparation and sequencing were performed by the Wellcome Trust Centre for Human Genetics.
Libraries were prepared using the Illumina TruSeq Stranded mRNA sample prep kit according to manufacturer's instructions.  Paired-end 75bp sequencing was performed on Illumina HiSeq4000.

tag: age

tag: lh+

tag: nk

tag: previous losses

tag: previous live births

tag: outcome after biopsy

value: Live birth

tag: cell type

value: Endometrial cells


title: Scripps registry control_69


title: Tau-GFP Plus MG_2 [E3_S3]

city: Hangzhou

first: DANYANG

last: HE

state: Zhejiang

address: 600 Dunyu Road Sandun Town

department: School of Life Sciences

country: China

institute: Westlake Univeristy

description:
E3_S3_R1_001
processed data file:
rsem.genes.counts.matrix

data_processing:
bulk RNAseq: map to mm10 using Bowtie 2 with default parameters
bulk RNAseq: RSEM were used for calculating counts
scRNA-seq data: the 10x Genomics Cell Ranger Single Cell Software Suite 2.0.1 was used to perform sample demultiplexing and single cell UMI counting
Genome_build: mm10
Supplementary_files_format_and_content:
For bulkRNAseq data: tab-delimited text files include counts values for each sample.
For scRNA-seq data:
mtx, a gene by cell count matrix in the sparse matrix market format
barcodes.tsv, cell names (colname names of the count matrix)
genes.tsv, gene names (row names of the count matrix)
matrix.tsv, the coordinates of cells form projecting cells measured from single-cell RNA-sequencing to the bulk ImmGen dataset

organism: Mus musculus

source_name: Tau-GFP Plus MG

growth_protocol: Briefly, brains were digested enzymatically with papain then mechanically dissociated to generate a single cell suspension, followed by density gradient separation with 40% Percoll. Cell suspensions were then positively selected for CD11b expression by CD11b magnetic bead (Miltenyi) separation using the MACS system. CD11b purified mouse microglia were cultured in PDL-coated plates at in a defined culture media containing DMEM/F-12 (Thermo Fisher Scientific, 11320033), 100U/ml penicillin, 100ug/ml streptomycin, 5 ug/ml N-acetyl cysteine, 1X N-2 Supplement (Gibco), and 10ng/ml M-CSF (R&D) with 2.5% heat inactivated FCS (Sigma).

extract_protocol:
RNA were extracted from cells using RNAClean XP beads (Backman)
10x single cell RNA-seq, Smart-seq 2

treatment_protocol: For IL33 stimulation and compound treatment assays, microglia at 7-9 days in vitro (DIV) were pretreated with 0.2uM GSK-J4 (Cayman Chemicals) for 1h and then stimulated with 200ng/ml IL33 (Biolegend) for 3hrs.

tag: strain background

value: postnatal day 10

tag: genotype/variation

value: Mapttm1(EGFP)Klt carrier

tag: tissue/cell type

value: Cortex

tag: experiment type

value: full length bulk RNA-seq


title: Scripps registry control_70


title: P17_14292 Run1

source_name: P17_14292_endometrial cells


title: P16_14263 Run1

source_name: P16_14263_endometrial cells


title: Scripps registry control_68


title: Tau-GFP Neg MG_1 [E2_S2]

description:
E2_S2_R1_001
processed data file:
rsem.genes.counts.matrix

source_name: Tau-GFP Neg MG


title: Scripps registry control_67


title: P15_14248 Run1

source_name: P15_14248_endometrial cells


title: Scripps registry control_65


title: Tau-GFP Plus MG_1 [E1_S1]

description:
E1_S1_R1_001
processed data file:
rsem.genes.counts.matrix


title: Tau-GFP Plus MG_3 [E5_S5]

description:
E5_S5_R1_001
processed data file:
rsem.genes.counts.matrix


title: Scripps registry control_62


title: Scripps registry control_63


title: Scripps registry control_64


title: P13_14226 Run1

source_name: P13_14226_endometrial cells

value: Miscarriage


title: TIC004

city: Washington

first: Timothy

last: McCaffrey

state: DC

address: 2300 I St NW, Ross 203

department: Medicine

institute: George Washington University

data_processing:
Galaxy Project was used to align reads to the reference genome hg38. The Galaxy Project modules used were Cat1 (concatenation), trimmomatic 0.36.5 (filtering), hisat2 v2.1.0+galaxy3 (alignment), featureCounts 1.6.2 (counting), Samtools v1.9, and seqtk v1.30.
Agilent GeneSpring GX (version 14.9) was used for DEG analysis.
Supplementary_files_format_and_content: The Excel Workbook (XLSX) file includes RPKM values for each gene for each patient with their clinical data and viremia data.

source_name: Peripheral venous blood

growth_protocol: Not applicable.

extract_protocol:
The Tempus Spin RNA Isolation Kit's protocol was used with a TurboDNase step and elution into DEPC-treated nuclease-free molecular-grade water. RNA integrity was analyzed on an Agilent BioAnalyzer.
cDNA library synthesis was perfomred using an Illumina TruSeq Stranded Total RNA Prep with H/M/R kit. H/M/R denotes the human, mouse, and rat rRNA baits that were used to deplete the eukaryotic cytoplasmic ribosomal RNA.
RNA-Seq was perfomed using an Illumina NextSeq 500 using a High-Output v2.5 150 cycle kit.

treatment_protocol: 3mL of peripheral blood from venepuncture was collected into Tempus Blood RNA Tubes (Applied Biosystems) and frozen at -80 Celsius.

tag: clinical diagnosis

value: CONTROL

tag: covid-19 titer

tag: covid-19 viremia diagnosis

value: NEG

tag: vasopressor

value: no

tag: mortality

value: ok


title: TIC001


title: Scripps registry control_61

tag: sample id

tag: diagnosis


title: P12_14221 Run1

source_name: P12_14221_endometrial cells

tag: age

tag: lh+


title: Scripps registry control_60


title: TIC003


title: P11_14180 Run1

source_name: P11_14180_endometrial cells

tag: nk

tag: previous losses


title: Scripps registry control_58


title: Scripps registry control_59


title: Scripps registry control_56


title: Scripps registry control_55


title: TID026

value: Critical

value: POS

value: vas


title: Scripps registry control_54


title: Scripps registry control_57


title: TID020

value: fatal


title: P9_14120 Run1

source_name: P9_14120_endometrial cells

tag: previous live births

tag: outcome after biopsy


title: Scripps registry control_66


title: P10_14131 Run1

source_name: P10_14131_endometrial cells

tag: cell type


title: P8_14114 Run1

source_name: P8_14114_endometrial cells


title: P14_14231 Run1

source_name: P14_14231_endometrial cells


title: Scripps registry control_52


title: Scripps registry control_51


title: TIC005


title: P7_14060 Run1

source_name: P7_14060_endometrial cells

value: Ongoing


title: Scripps registry control_50

value: healthy


title: TID018


title: P6_14056 Run1

source_name: P6_14056_endometrial cells


title: TID017


title: P5_14046 Run1

source_name: P5_14046_endometrial cells

value: Live birth


title: Scripps registry control_45

source_name: control


title: TID016

value: Incidental


title: Scripps registry control_47


title: Scripps registry control_46


title: Scripps registry control_53


title: P4_14043 Run1

source_name: P4_14043_endometrial cells

value: Endometrial cells


title: P3_14033 Run1

source_name: P3_14033_endometrial cells


title: TID014


title: Scripps registry control_41


title: P2_13244 Run1

source_name: P2_13244_endometrial cells


title: Scripps registry control_43


title: Scripps registry control_42


title: Scripps registry control_44


title: TID013


title: TID015

value: Moderate


title: Scripps registry control_40


title: Scripps registry control_38


title: TID019


title: P1_13063 Run1

source_name: P1_13063_endometrial cells


title: Scripps registry control_49


title: Scripps registry control_37


title: TID012


title: TID011


title: Bc-ML-WT-RNA_3

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

country: France

institute: INRAE

data_processing:
Sequenced reads were mapped to BcinB0510 Botrytis cinerea genome (fungi.ensembl.org/Botrytis_cinerea/) using STAR-2.5.1b with parameters --alignIntronMax 10000 --alignMatesGapMax 10000 --quantMode GeneCounts
Genome_build: BcinB0510 Botrytis cinerea genome (fungi.ensembl.org/Botrytis_cinerea/)
Supplementary_files_format_and_content: The matrix table (tab-delimited text file) with raw values for all features.

organism: Botrytis cinerea

source_name: B. cinerea B0510_wild-type

growth_protocol: Botrytis cinerea strain B05.10 was grown for two days on Malt Medium (MM, 20 g/L malt extract, 5 g/L yeast extract and 15 g/L agar) covered with a cellophane layer. The plates were incubated in a growth chamber (Sanyo MLR-350H) at 23°C with an alternation of 14 h of white light and 10 h of darkness.

extract_protocol:
Total RNA was extracted according to the total RNA isolation protocol described by Reid et al. (2006), but with 10M rather than 8M LiCl, and resuspended in RNAse/DNAse-free water. The total RNA was then treated with a DNA-freeTM kit to remove any trace of DNA (Ambion – Applied Biosystems).
The NEBNext Ultra Directional RNA Library Prep Kit for Illumina (cat. # E7420L New England BioLabs) was used to prepare all RNA-seq libraries, following the manufacturer’s instructions. Sequencing was performed by the GenomEast platform, a member of the ‘France Génomique’ consortium (ANR-10-INBS-0009). Samples were run in 9-plex on an Illumina HiSeq 4000 in paired mode, 2x50 bp.

tag: strain

tag: genotype/variation

value: wild type


title: Scripps registry control_48


title: Scripps registry control_36


title: Scripps registry control_33


title: Bc-ML-WT-RNA_2


title: TID010


title: Scripps registry control_32


title: Scripps registry control_35


title: TID009


title: Scripps registry control_31


title: Scripps registry control_39


title: Scripps registry control_30


title: TID008


title: Scripps registry control_29


title: TID006


title: Scripps registry control_27


title: Scripps registry control_25


title: TID007


title: TID005


title: San1 null mutant TBP ChIP-seq Biological replicate 2

city: Carbondale

first: Sukesh

middle: R.

last: Bhaumik

state: IL

address: 1245 Lincoln Drive, Neckers Building, Rm 229

department: Biochemistry and Molecular Biology

institute: Southern Illinois University School of Medicine

description:
S10
Biological replicate 2

library_source: genomic

data_processing:
Paired-end sequences of immunoprecipited DNA were aligned to the yeast genome (SacCer3) using Bowtie2 with parameters -X 1000 --very-sensitive --no-mixed --no-unal, to map sequences up to 1 kb with maximum accuracy.
The PCR duplicates were removed by Samtool Rmdup tool
The .Bam files after removing duplicates were converted to bed files using BedTools.
The .Bam files were used to generate the profiles using BamR (https://github.com/rchereji/bamR)

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae

growth_protocol: Cells were grown up to an OD at 600 nm of 1.0 prior to formaldehyde-based crosslinking and harvesting.

extract_protocol:
sonicated lysates were used to ChIP using either Pol II or TBP antibody. ChIPs and corresponding inputs were reverse-crosslinked, extracted with phenol:chloroform:IAA, then precipitated with ethanol.
ChIP DNA samples (7-14 ng) were processed for library preparation at the Genome Technology Access Center at the McDonnell Genome Institute of Washington University, St. Louis, USA. ChIP DNA was blunt ended, had addition of “A” base to 3’ end, and had sequencing adapters ligated to the ends. The fragments were size selected to 200-600 base pairs, and underwent amplification for 15 cycles with primers incorporating p5 and p7 sequences and dual unique index tags for multiplexing. The resulting libraries were sequenced were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.  The raw data was demultiplexed and aligned to the reference genome using Novoalign.

tag: antibody

value: TBP ChIP-seq

tag: strain genotype


title: WT Pol II_ChIP-seq Biological replicate 2

description:
S7
Biological replicate 2

treatment_protocol: sonicated lysates were used to ChIP using either Pol II or TBP antibody. ChIPs and corresponding inputs were reverse-crosslinked, extracted with phenol:chloroform:IAA, then precipitated with ethanol.

value: Pol II_ChIP-seq


title: San1 null mutant Pol II_ChIP-seq Biological replicate 2

description:
S9
Biological replicate 2


title: WT TBP_ChIP-seq Biological replicate 2

description:
S8
Biological replicate 2


title: San1 null mutant TBP ChIP-seq Biological replicate 1

description:
S6
Biological replicate 1


title: TID003

source_name: Peripheral venous blood

tag: clinical diagnosis

tag: covid-19 titer


title: Scripps registry control_22


title: Scripps registry control_34


title: Scripps registry control_24


title: Bc-ML-WT-RNA_1


title: TID002

tag: covid-19 viremia diagnosis

tag: vasopressor


title: Scripps registry control_19

tag: sample id


title: Scripps registry control_20

tag: diagnosis


title: San1 null mutant Pol II_ChIP-seq Biological replicate 1

description:
S5
Biological replicate 1


title: Scripps registry control_18


title: Scripps registry control_26


title: Scripps registry control_17


title: Scripps registry control_28


title: TID001

tag: mortality


title: Scripps registry control_16


title: San1 null mutant Input DNA Biological replicate 1

description:
S4
Biological replicate 1

value: Input DNA


title: WT TBP_ChIP-seq Biological replicate 1

description:
S3
Biological replicate 1


title: Scripps registry control_15


title: Scripps registry control_14


title: WT Pol II_ChIP-seq Biological replicate 1

description:
S2
Biological replicate 1


title: T47D-P/PalboR_LM rep3

city: Boston

first: Rinath

last: Jeselsohn

state: MD

address: 450 Brookline Ave, D728

department: Medical Oncology

institute: DFCI

data_processing:
Illumina Casava software used for basecalling
Reads were aligned to hg19 using Bowtie
Differential gene expression was calculated using Cuffdiff program of Cufflinks v2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: Comma-delimited csv file includes cufflink output of gene read counts

source_name: breast cancer T47D cells

growth_protocol: Estrogen deprivation-resistant cells were kept in phenol-red free (PRF) RPMI medium supplemented with 10% heat-inactivated charcoal-stripped (CS)-fetal bovine serum (FBS) and 1% penicillin/streptomycin/glutamine (PSG). Tamoxifen- or fulvestrant-resistant cells were kept in PRF RPMI medium supplemented with 10% heat-inactivated CS-FBS and 1% PSG, with the addition of 100 nM 4-OH-tamoxifen (H7904, Sigma) or 100nM fulvestrant (I4409, Sigma), respectively. To generate resistant derivatives to palbociclib (SelleckChem), MCF7-P, MCF7-EDR, T47D-P, and T47D-EDR cells were exposed to progressively increasing doses of palbociclib up to 1 µM. The obtained resistant derivatives were maintained under 1 µM of palbociclib.

extract_protocol:
Total RNA isolation was performed using the RNeasy Mini Kit (Qiagen). DNA was degraded on columns with DNase I (Qiagen).
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina) adapted for use on the Sciclone (Perkin-Elmer) liquid handler.

treatment_protocol: Cells were maintained in their original media and harvested for RNA extraction.

value: palbociclib-resistant derivative


title: Scripps registry control_23


title: T47D-P/PalboR_LM rep2


title: Scripps registry control_13


title: WT Input DNA Biological replicate 1

description:
S1
Biological replicate 1


title: Scripps registry control_12


title: T47D-P/PalboR_LM rep1


title: Scripps registry control_10


title: Scripps registry control_9


title: T47D-P_LM rep2

value: endocrine-sensitive parental


title: Scripps registry control_8


title: Scripps registry control_21


title: IL-4 Stimulated Eosinophils 2

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

data_processing:
RNA-Seq data was trimmed using fastp 0.20.1
RNA-Seq data was aligned using STAR 2.7.2a. CEL-Seq data was aligned using Tophat2 version 2.1.0
CEL-Seq transcript quantification was performed using HTSeq-count 0.6.1 on union mode. RNA-Seq quantification was performed by STAR 2.7.2a.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw gene abundance for each sample

source_name: Eosinophils

extract_protocol: The CEL-Seq library was ran on an Illumina NextiSeq550 instrument. The RNASeq experiment ran on the HISEQ platform

tag: treatment


title: IL-4 Stimulated Eosinophils 3


title: Scripps registry control_7


title: Scripps registry control_6


title: Scripps registry control_5


title: IL-4 Stimulated Eosinophils 1


title: Unstimulaetd eosinophils f

value: unstimulated


title: ZR75-1-TamR rep2

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to hg19 using Bowtie
For peak calling STAR was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using STAR using the VIPER pipeline

source_name: breast cancer ZR75-1 cells

value: tamoxifen-resistant derivative


title: T47D-P_LM rep1


title: Scripps registry control_3


title: Scripps registry control_4


title: Unstimulaetd eosinophils e


title: iPSC_iMN3_sh_shTDP-43_rep2

city: Stanford

first: Rosa

last: Ma

address: 279 Campus Dr.

department: Genetics

institute: Stanford University

data_processing:
Adaptors in FASTQ files were removed using trimmomatic (0.39) (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
The quality of the resulting files was then evaluated using FastQC (v0.11.9)
The sequencing reads were then mapped to the human (hg38) using STAR v2.7.3a following ENCODE standard option.
Uniquely mapped reads were then filtered for using the command “samtools view -b -q 255”.
The bigwig files were generated from the bam files using deeptools(3.3.1) "bamCovereage  --binSize 1 --region chr19:17640000:17649000"
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated from the corresponding bam files using deepTools

growth_protocol: iPSC lines were obtained from public biobanks (GM25256-Corriell Institute (iPSC-MN1); NDS00209-NINDS(iPSC-MN2); NDS00262-NINDS(iPSC-MN3)) and maintained in mTeSR1 media (StemCell Technologies) on matrigel (Corning). iPSCs were fed daily and split every 4-7 days using ReLeSR (StemCell Technologies) according to manufacturer's instructions. iPSCs were dissociated and placed in ultra-low adhesion flasks (Corning) to form 3D spheroids in media containing DMEMF12/Neurobasal (Thermo Fisher), N2 supplement (Thermo Fisher), and B-27 supplement-Xeno free (Thermo Fisher). Small molecules were added to induce neuronal progenitor patterning of the spheroids, (LDN193189, SB-431542, Chir99021), followed by motor neuron induction (RA, SAG, DAPT). After 14 days, neuronal spheroids were dissociated with Papain and DNAse (Worthington Biochemical) and plated on Poly-D-Lysine/Laminin coated plates in Neurobasal medium (Thermo Fisher) containing neurotrophic factors (BDNF, GDNF, CNTF; R&D Systems). The shRNA sequences used for the shRNA lentivirus were originated from the Broad GPP Portal (TDP-43: AGATCTTAAGACTGGTCATTC, scramble: GATATCGCTTCTACTAGTAAG). To clone, complementary oligos were synthesized to generate 4 nt overhangs, annealed, and ligated into pRSITCH (Tet inducible U6) or pRSI16 (constitutive U6) (Cellecta).  Ligations were transformed into Stbl3 chemically competent cells (Thermo Scientific) and grown at 30 °C.  Large scale plasmid generation was performed using Maxiprep columns (Promega), with purified plasmid used as input for lentiviral packaging with second generation packaging plasmids psPAX2 and pMD2.G (Cellecta), transduced with Lipofectamine 2000 (Invitrogen) in Lenti-X 293T cells (Takara).  Viral supernatant was collected at 48 and 72 hours post transfection and concentrated using Lenti-X Concentrator (Takara).  Viral titer was established by serial dilution in relevant cell lines and readout of %BFP+ by flow cytometry, with a dilution achieving a minimum of 80% BFP+ cells selected for experiments.

extract_protocol:
Neuronal cultures were analyzed for RNA and protein 7 days post transduction. Total RNA was extracted 7 days post transduction using RNeasy Micro kit (Qiagen) per manufacturer's instructions, with lysate passed through a QIAshredder column (Qiagen) to maximize yield. RNA was quantified by Nanodrop (Thermo Scientific), with 75ng used for cDNA synthesis with SuperScript IV VILO Master Mix (Thermo Scientific).
Splice variants in iPSC-derived motor neuron cells were established by PCR amplification from UNC13A exon 19 to exon 21 (UNC13A_19_21 FWD 5'-3'= CAACCTGGACAAGCGAACTG, UNC13A_19_21 RVS 5'-3'= GGGCTGTCTCATCGTAGTAAAC). Resulting products were purified using Wizard SV Gel and PCR Clean-Up columns (Promega) and submitted for Sanger and NGS (Amplicon EZ) (Genewiz).

treatment_protocol: For viral transductions, neuronal cultures were incubated for 18 hr with media containing lentivirus particles for shScramble, or shTDP-43. Infection efficiency of over 90% was assessed by RFP expression.

tag: cell line

value: iPSC-derived motor neurons (iPSC-MNs)


title: Unstimulaetd eosinophils d


title: ZR75-1-P rep2


title: iPSC_iMN3_sh_shTDP-43_rep1


title: iPSC_iMN3_sh_shScramble_rep2

value: shScramble


title: Scripps registry control_11


title: ZR75-1-P rep1


title: iPSC_iMN3_sh_shScramble_rep1


title: ZR75-1-FulR rep2

value: fulvestrant-resistant derivative


title: IFNγ+E. coli Stimulated Eosinophils 3

value: IFN[gamma] + E. coli


title: IFNγ+E. coli Stimulated Eosinophils 2


title: iPSC_iMN2_sh_shTDP-43_rep2


title: ZR75-1-FulR rep1


title: IFNγ+E. coli Stimulated Eosinophils 1


title: ZR75-1-EDR rep2


title: iPSC_iMN1_sh_shTDP-43_rep2

value: GM25256-Corriell Institute


title: iPSC_iMN2_sh_shScramble_rep2


title: ZR75-1-TamR rep1


title: IFNγ Stimulated Eosinophils 3

value: IFN[gamma]


title: ZR75-1-EDR rep1


title: iPSC_iMN2_sh_shScramble_rep1


title: IFNγ Stimulated Eosinophils 2


title: iPSC_iMN1_sh_shScramble_rep2


title: iPSC_iMN1_sh_shScramble_rep1


title: Scripps registry control_1

value: healthy


title: IFNγ Stimulated Eosinophils 1


title: iPSC_iMN1_sh_shTDP-43_rep1


title: Scripps registry control_2


title: T47D-TamR rep1


title: iPSC_iMN2_sh_shTDP-43_rep1


title: T47D-FulR rep2


title: E. coli Stimulated Eosinophils 3

value: E. coli


title: y2

city: Jinan

first: jianhua

last: zhang

address: gongyebei street No. 23788

institute: Shandong Academy of Agricultural Sciences

description: MicroRNAs sequencing

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: excel,expression profiles

organism: Spodoptera frugiperda

source_name: 3rd-instar S. frugiperda

growth_protocol: Spodoptera frugiperda were reared in an illumination incubator at 26 ± 1 °C with 60-70% humidity and 16 h light: 8 h dark photoperiod

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: Cyantraniliprole, spinetoram, emamectin benzoate and tetraniliprole treatment

tag: development stage

value: 3rd-instar S. frugiperda

value: Spinetoram treatment


title: y3

description: MicroRNAs sequencing


title: y1

description: MicroRNAs sequencing


title: E. coli Stimulated Eosinophils 2


title: x3

description: MicroRNAs sequencing

value: Cyantraniliprole treatment


title: E. coli Stimulated Eosinophils 1


title: T47D-FulR rep1


title: T47D-EDR rep2


title: x1

description: MicroRNAs sequencing


title: Unstimulaetd eosinophils c


title: s3

description: MicroRNAs sequencing

value: Tetraniliprole  treatment


title: x2

description: MicroRNAs sequencing


title: s2

description: MicroRNAs sequencing


title: s1

description: MicroRNAs sequencing


title: T47D-TamR rep2


title: T47D-EDR rep1


title: j3

description: MicroRNAs sequencing

value: Emamectin benzoate  treatment


title: j1

description: MicroRNAs sequencing


title: Unstimulaetd eosinophils b


title: 95R-GFP-neg

city: Raleigh

first: Jorge

last: Piedrahita

state: North Carolina

address: 1060 William Moore Drive, BPC Suite 200

institute: North Carolina State University

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mappedto the Sus scrofa reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Genome_build: Sus scrofa 11.1
Supplementary_files_format_and_content: matrix file of raw counts for each gene for each sample

organism: Sus scrofa

source_name: epidermal cells

extract_protocol:
Juvenile or adult porcine skin was cut into 5mm2 pieces and incubated with 10mg/mL Dispase II (Sigma) in PBS without calcium and magnesium (Corning) for 1.5 hours at 37℃ or overnight at 4℃. Hair and epidermis were manually removed from dermis and incubated in 0.05% trypsin for 5-10 minutes at 37°C with shaking. Suspension was vortexed and strained with 70µm cell strainer (BD Falcon). Cells were resuspended in PBS with 10% fetal bovine serum (Corning) and 1% antibiotic-antimycotic (Corning). 250ng/mL propidium iodide (Biotium) was added to cells for live/dead detection and samples were sorted by Beckman Coulter MoFlo XPD.
RNA libraries were prepared for sequencing using standard Illumina protocols with poly(A) selection

value: epidermal cells

tag: population

value: LGR5-GFP- sorted epidermis

tag: age

value: juvenile


title: j2

description: MicroRNAs sequencing


title: T47D-EDR/PalboR rep2

value: estrogen deprivation and palbociclib-resistant derivative


title: Fg349-MS2-WT-RNA_2

data_processing:
Sequenced reads were mapped to Fusarium graminearum CBS185.32 genome (FungiDB v44) using STAR-2.5.1b with parameters --alignIntronMax 10000 --alignMatesGapMax 10000 --quantMode GeneCounts
Genome_build: Fusarium graminearum CBS185.32 genome (FungiDB v44)
Supplementary_files_format_and_content: The matrix table (tab-delimited text file) with raw values for all features.

organism: Fusarium graminearum

source_name: F. graminearum CBS185.32 wild-type

growth_protocol: Fusarium graminearum CBS185.32 was grown for three days in modified liquid MS (glucose was substituted with sucrose).

extract_protocol:
Mycelia were harvested by filtering, rinsed twice with sterile deionized water, and flash frozen in liquid nitrogen. One milliliter of TRIzolTM Reagent (Thermo Fischer Scientific) was added to 200 mg of mycelium before grinding for 1.5 min at 30 Hz using a TissueLyzer (Qiagen). Total RNA was then extracted using a previously published protocol (Hallen et al., 2007).
The NEBNext Ultra Directional RNA Library Prep Kit for Illumina (cat. # E7420L New England BioLabs) was used to prepare all RNA-seq libraries, following the manufacturer’s instructions. Sequencing was performed by the GenomEast platform, a member of the ‘France Génomique’ consortium (ANR-10-INBS-0009). Samples were run in 9-plex on an Illumina HiSeq 4000 in paired mode, 2x50 bp.

value: wild type


title: MCF7-TamR rep1

source_name: breast cancer MCF7 cells

value: tamoxifen-resistant derivative


title: ck2

description: MicroRNAs sequencing

value: Acetone treatment


title: ck1

description: MicroRNAs sequencing


title: 88R-GFP-hi

tag: cell type

value: LGR5-GFP+ sorted epidermis


title: iKD-PT2+ATc_3

city: Wuhan

first: Bang

last: Shen

address: No. 1 SHizishan St

institute: Huazhong Agricultural University

data_processing:
Illumina Casava software (v 1.6) was used for basecalling
sequenced reads were trimmed  for adaptor sequence, reads containing ploy-N and low quality reads. Then clean reads were mapped to Toxoplasma GT1 reference genome by  using (TopHat v2.1.1).
The transcripts per million reads (TPM) of each transcript was calculated using RSEM(v1.3.3)
Genome_build: https://toxodb.org/toxo/app/downloads/release-52/TgondiiGT1/
Supplementary_files_format_and_content: tab-delimited text files include reads counts values for each sample

organism: Toxoplasma gondii

source_name: TgPT2 knockdown strain

growth_protocol: The Toxoplasma tachyzoites were cultured in DMEM with 2% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin, respectively. Both maintained in incubator with 5% CO₂ and kept 37℃.  ATc (0.5 μg/ml) was added where indicated.

extract_protocol:
The samples were collected and  total RNA was harvested using Trizol reagent.  RNA-seq transcriptome library was prepared using TrueSeqTM RNA sample preparation kit (San Diego, USA) from Illumina with 1 ug total RNA .
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Each parasite strain was maintained under same conditions and the newly egressed Toxoplasma tachyzoites from HFFs were  washed three times with pre-coldPBS.

tag: parasite strain or treatment

tag: culture conditions

value: 37C, 5% CO₂ in incubator

tag: culture time

value: newly egressed Toxoplasma tachyzoites

tag: type

value: TgPT2 experimental sample


title: iKD-PT2+ATc_2


title: Lymph node control [LN_CTR]

city: Seoul

first: Jungmin

last: Choi

state: Seoul

address: 73, Goryeodae-ro, Seongbuk-gu

department: Department of Biomedical Sciences

country: South Korea

institute: Korea University College of Medicine

data_processing:
Standard 10x Genomics Cell Ranger Pipeline, cellranger-3.1.0, and bcl2fastq (v2.20.0.422)
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: output files from the Cell Ranger pipeline, including filtered count matrices in tsv

molecule: polyA RNA

source_name: Lymph node control

extract_protocol:
Peripheral lymph node stromal cell suspensions were prepared from lymph node slices digested with 900 U/ml Collagenase IV and 40 μg/ml Dnase1 for  30 min at 37°C. Cells from 2 mice per genotype were pooled. CD45 and Ter119+ cell were magnetically depleted. The leftover cells were stained with antibodies against CD45, Ter119, CD71, CD31 and GP38. Lymph node stromal cells were sorted as CD45- Ter119- CD71- CD31- cells into 350 μL DMEM with 20% FBS. Splenic stromal cells suspensions were prepared the same way. Cells from 3 mice per genotype were pooled. CD45 and Ter119+ cell were magnetically depleted.The leftover cells were stained for CD45, Ter119, CD71, LIN (CD3e, B220, CD19), CD31, GP38 and PDGFRa. Splenic stromal cells were sorted as CD45- Ter119- LIN- CD71- CD31- into 350 μL DMEM with 20% FBS.
The libraries were prepared using the Chromium Single Cell 3ʹ Reagent Kits v3.0 and run on an Illumina NovaSeq system with 100-bp paired-end reads to a coverage of ~ 65,000 mean reads per cell and > 90% saturation for lymph node stromal cells and to a coverage of ~ 30,000 - 57,000 mean reads per cell and > 80% saturation for splenic stromal cells. The sequencing reads were aligned onto the Mus musculus GRCm38 (mm10) reference genome.

value: Peripheral lymph node stromal cells

tag: tissue

value: peripheral lymph node

tag: strain

tag: genotype

value: untreated


title: MCF7-P/PalboR rep2

value: palbociclib-resistant derivative


title: MCF7-P rep1

value: endocrine-sensitive parental


title: iKD-PT2+ATc_1


title: Spleen WHIM [SP_WHIM]

source_name: Spleen WHIM

value: Splenic stromal cells

value: spleen


title: MCF7-P/PalboR rep1


title: ck3

description: MicroRNAs sequencing

value: 3rd-instar S. frugiperda


title: Sedentary corrected-delEx44 DMD  [Run552_DK_EO_10-20-21_Corrected-2]

city: Dallas

first: Jiwoong

last: Kim

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used for quality and adapter trimming. The mouse reference genome sequence and gene annotation data, mm10, were downloaded from Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html). The qualities of RNA-sequencing libraries were estimated by mapping the reads onto mouse transcript and ribosomal RNA sequences (Ensembl release 89) using Bowtie (v2.3.4.3) (Langmead and Salzberg, 2012). STAR (v2.7.2b) (Dobin et al., 2013) was employed to align the reads onto the mouse genome, SAMtools (v1.9) (Li et al., 2009) was employed to sort the alignments, and HTSeq Python package (Anders et al., 2015) was employed to count reads per gene. edgeR R Bioconductor package (Gentleman et al., 2004; Robinson et al., 2010; McCarthy et al., 2012) was used to normalize read counts and identify differentially expressed (DE) genes. KEGG (Kanehisa et al., 2017) pathway data was downloaded using KEGG API (https://www.kegg.jp/kegg/rest/keggapi.html) and gene ontology (GO) data was downloaded from NCBI FTP (ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz). The enrichment of DE genes to pathways and GOs were calculated by Fisher's exact test in R statistical package.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Sedentary corrected-delEx44 DMD

extract_protocol:
Quadriceps muscle was harvested and flash frozen in liquid nitrogen. RNA was extracted using miRNAeasy mini kit (Cat#217004).
Libraries were constructed using the Illumina TruSeq RNA Sample Prep Kit.

treatment_protocol: DelEx44 DMD mice were injected intraperitoneally with ssAAV9-sgRNA (2.5 x 10^14 vg/kg) and ssAAV9-SpCas9 (5 x 10^13 vg/kg) on day P4. At 18 months of age, tissue was harvested.

tag: strain background

value: 18 months

value: CRISPR-Cas9 treated delEx44

value: Quadriceps Muscle


title: T47D-EDR/PalboR rep1

value: estrogen deprivation and palbociclib-resistant derivative


title: iKD-PT2-ATc_3

source_name: TgPT2 wild type

value: TgPT2 control


title: Fg349-MS2-WT-RNA_3

tag: genotype/variation

value: wild type


title: 95R-GFP-hi

value: epidermal cells

value: LGR5-GFP+ sorted epidermis

value: juvenile


title: MCF7-FulR rep2

value: fulvestrant-resistant derivative


title: MCF7-TamR rep2

value: tamoxifen-resistant derivative


title: Fg349-MS2-WT-RNA_1


title: 88R-GFP-neg

value: LGR5-GFP- sorted epidermis


title: Unstimulaetd eosinophils a

value: unstimulated


title: Sedentary corrected-delEx44 DMD  [Run552_DK_EO_10-20-21_Corrected-1]


title: Sedentary corrected-delEx44 DMD  [Run552_DK_EO_10-20-21_Corrected-3]


title: Sedentary delEx44 DMD [Run552_DK_EO_10-20-21_Ex44-2]

source_name: Sedentary delEx44 DMD


title: MCF7-P rep2

value: endocrine-sensitive parental


title: MCF7-FulR rep1


title: Sedentary delEx44 DMD [Run552_DK_EO_10-20-21_Ex44-1]


title: BM MSC and endothelial cells - Cxcr4WHIM/+ [WHIM-1]

data_processing:
Cellranger (v4.0) count function with the default parameters was run to generate single cell feature counts from FASTQ files.
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated file, feature counts amd indexes

source_name: BM MSC and endothelial cells

extract_protocol:
Long bones were flushed with HBSS supplemented with 2% heat-inactivated FBS, 1% Penicillin/Streptomycin, 1% L-glutamine, 1% HEPES and 200 U/ml Collagenase IV. The flush out was digested for 30 min at 37C. Flushed bones were cut into bone chips and digested separately for 45 min at 37°C under agitation (120rpm) and washed with HBSS 2% FBS, 1% Penicillin /Streptomycin, 1% L-glutamine, 1% HEPES. Both cell suspensions were filtered through cell strainers and combined. Cells from 2 mice per genotype were pooled. Cells were stained with antibodies against Ter119, CD45, lineage (LIN) (B220, CD19, CD11b, CD3e), CD31, CD144, LEPR and CD71. CD45- Ter119- CD71- LIN- LEPR+ and CD45- Ter119- CD71- LIN- CD31+ CD144+ cells were sorted into the same tube with 350 μL DMEM with 20% FBS.
The libraries were prepared using the Chromium Single Cell 3ʹ Reagent Kits v3.0 and run on an Illumina NovaSeq system with 100-bp paired-end reads to a coverage of ~ 40,000 - 44,000 mean reads per cell and ~ 80% saturation. The sequencing reads were aligned onto the Mus musculus GRCm38 (mm10) reference genome.

value: BM MSC and endothelial cells

value: bone marrow

value: untreated


title: iKD-PT2-ATc_2

value: 37C, 5% CO₂ in incubator

value: newly egressed Toxoplasma tachyzoites


title: iKD-PT2-ATc_1


title: Sedentary WT [Run552_DK_EO_10-20-21_WT-3]

source_name: Sedentary WT

value: 18 months

value: WT

value: Quadriceps Muscle


title: RHΔpit_3

source_name: TgPiT knockout strain

value: RH-delta-pit

value: TgPiT experimental sample


title: MCF7-EDR rep2


title: BM MSC and endothelial cells - Cxcr4+/+ [CTR-1]


title: Sedentary delEx44 DMD [Run552_DK_EO_10-20-21_Ex44-3]


title: MCF7-EDR/PalboR rep2

value: estrogen deprivation and palbociclib-resistant derivative


title: RHΔpit_2


title: long day IP rep2

city: Liverpool

first: Mirko

last: Pegoraro

state: Liverpool

address: Byrom Street

department: School of Natural Science and Psychology

institute: Liverpool John Moores University

data_processing:
Adapter sequences and poor quality readings were trimmed from the RNA-seq data with trimmomatic (version 0.32) 39. The quality of the resulting trimmed libraries was checked with fastQC (0.11.2)
For the alignment we used the software STAR (version 2.5.2b) 41 with these options --runMode alignReads -genomeDir genomeIndex (this contain the index for the reference genome) --sjdbGTFfile genes.gtf (from NCBI_build5.41) as gene annotation reference --sjdbOverhang 100 --outSAMstrandField IntronMotif --outFilterIntronMotifs RemoveNoncanonical.
Samtools (version 1.3.2) 42 was used to convert sam to bam files to sort them and index them
To quantify the expression of transcripts (genes) of the aligned RNA we initially used cufflinks (vrsion 2.2.1), cuffmerge and cuffquant 43-46 with these options: -u --library-type fr-unstranded -g genes.gtf (from NCBI_build5.41) as gene annotation reference -N -b genome.fa (from NCBI_build5.41/Bowtie2Index) as reference genome -M Mask_sequences.fa (including mitochondrial and ribosomal RNA as well as polyA and polyC sequences).
The expression was expressed in Fragments Per Kilobase of transcript per Million fragments mapped (FPKM). Finally, to calculate enriched transcripts in IP (Input vs IP) and differences between samples (long vs short day) we used cuffdiff with a geometric method of normalization
Genome_build: D. melanogaster transcriptome (NCBI_build5.41) downloaded from the illumina igenome website
Supplementary_files_format_and_content: expression data for all individual samples and Ratio RIP/IN per treatment (LD and SD)
Supplementary_files_format_and_content: expression data for all samples (gropued by treatment_input_RIP), including all pairwise comparison and associated qvalues

organism: Drosophila melanogaster

source_name: heads

growth_protocol: ~40 eggs of OR-R flies maintained at 25ºC LD 12:12 were collected and placed either in long (LD 16:8) or short (LD 8:16) day (18ºC). The flies developed in these conditions for 20 days and the heads of emerging females (3-4 days old) were collected at ZT3.5 (3.5 hours after light on) in liquid nitrogen

extract_protocol:
Two-hundred µl (volume) of frozen fly heads where homogenized in 600 µl of lysis buffer (30 mM HEPES KOH pH 7.4, 100 mM KAcetate, 2 mM MgAcetate, 5% glycerol, 0.1% Triton X-100, 1 mM EGTA, 5 mM DTT, 0.4 U/ul RNAse OUT [Invitrogen], 25 mM EDTA). The lysate was incubated in ice for 10min and centrifuge at 14000rpm for 15min at 4ºC. 100 µl of the supernatant was isolate as input while the rest (~450 µl) was used for the immunoprecipitation. 15 µl of anti-AGO-1 antibody 38 was added to the supernatant and incubated at 4ºC O/N with rotation. 100 µl of protein-G plus beads slurry (MERCK, IP04-1.5ML) was washed trice with 250 µl of lysis buffer and then added to the lysate and incubated at 4ºC for 4 hours. The beads were recovered by a 2min centrifugation at 8000rcf and washed 5 times in 500 µl lysis buffer at 4ºC with rotation. Finally, the RNA in the immunoprecipitation and input was isolated with TRIzol (Thermo-Fisher Scientific) following manufacture instructions.
The RNA-seq library preparation and sequencing was carried by Glasgow polyomics (http://www.polyomics.gla.ac.uk/) using an IlluminaNextseq500 platform. Two independent libraries (pair-end) for long day and one for short day (input and IP) were generated.

treatment_protocol: One group was exposed to lond days (LD16:8) and a second gropu was exposed to short days (LD8:16) during the development and until tissue (heads) collection.

value: Oregon-R

tag: developmental stage

value: Adult

value: long day(16:8)

tag: antibody

value: AGOI


title: Sedentary WT [Run552_DK_EO_10-20-21_WT-2]


title: Sedentary WT [Run552_DK_EO_10-20-21_WT-1]


title: PBMCs-Y_3

first: Siji

last: Chen

address: Qingchun East road

institute: Department of Dermatology and Venereology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Supplementary_files_format_and_content: Tab-delimited text files include FPKM and count values for each Sample

source_name: PBMCs

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

tag: Sex

value: male

tag: Stage

value: one-week follow-up

tag: clinical diagnosis

value: Pemphigus Vulgaris Complicated with Pulmonary Tuberculosis


title: RH_3

source_name: RH wild type

value: RH

value: RH control


title: long day input rep2

tag: treatment


title: METTL8-His6-2xFLAG

city: Goettingen

first: Markus

middle: T.

last: Bohnsack

address: Humboldtallee 23

department: Institute for Molecular Biology

country: Germany

institute: Goettingen University

description: enrichment from total RNA

data_processing:
Sequencing reads for each experimental sample were demultiplexed using their 5' barcode sequences NNNNNAGC. Using pyBarcode Filter (pyCRAC version 1.4.5).
3' adaptor sequences (TGGAATTCTCGGGTGCCAAGG) were removed using Flexbar (version 3.5.0).   flexbar', '-r', , '-t', '-q', 'TAIL', '-qf', u'i1.8', '-qt', '13', '-u', '0', '-m', '21', '-n', '8', '-at', 'RIGHT', '-z', 'GZ', '-o', '-ao', '2', '-ae', '0.1', '-as'
Identical sequence reads containing the same UMI were collapsed using pyFastqDuplicateRemover (PyCRAC version 1.4.5).
STAR (version 2.7.0d):
STAR --genomeLoad LoadAndKeep
--quantMode TranscriptomeSAM
--limitBAMsortRAM 21470000000
--outFilterMultimapNmax 20
--outFilterMismatchNmax 4
--outSAMmultNmax 1
--scoreDelOpen -2
--scoreDelBase -2
--outFilterMismatchNoverReadLmax 0.04
--outSAMtype BAM SortedByCoordinate
--outReadsUnmapped Fastx
--outMultimapperOrder Random
--outFilterType BySJout
--alignSJoverhangMin 8
--alignSJDBoverhangMin 1
--outSJfilterOverhangMin -1 -1 -1 -1
--outSJfilterCountTotalMin -1 -1 -1 -1
--outSAMattributes NH HI AS MD nM
--alignEndsType EndToEnd)
Aligned reads were counted using feature counts (version 1.6.3).   featureCounts -a -s 1 -T 8 -f -t gene -O -M –largestOverlap
The EdgeR package (version 3.34.1) was used for TMM normalization and to calculate fold changes.
Nucleotide substitutions within mapped reads were counted using a cutom Python script available in the manuscript associated with the entry.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Processed data are provided as .txt and .bedgraph files.

source_name: HEK293 cell culture

growth_protocol: HEK293 Flp-In T-Rex cell lines expressing METTL8-His6-Prescission protease cleavage site-2xFLAG (His6-2xFLAG) or the His6-2xFLAG tag alone were grown at 37°C in 5% CO2 in high glucose DMEM supplemented with 10% foetal calf serum. Cells from 3x 90% confluent 15 cm dishes were used per experiment.

extract_protocol:
Crosslinked RNA-protein complexes were enriched on anti-FLAG beads (Sigma) and eluted using 3x FLAG peptide. RNAs associated with His6-2xFLAG-tagged proteins were subjected to partial RNase digestion using 1 U RNace-It ribonuclease cocktail for 3 min at 37°C. Complexes were immobilized on NiNTA under denaturing conditions (6 M guanidium hydrochloride).
Illumina TruSeq RA3 and RA5 adapters were ligated to the 3' and 5' ends of the RNA fragments enriched on the matrix. Complexes were eluted using immidazole and precipitated using trichloroacetic acid. Protein-RNA complexes were separated by NuPAGE and transfered to a nitrocellulose membrane. Relevant regions of the membrane containing complexes of interest were excised and RNAs eluted by Proteinase K treatment. RNAs were isolated, and reverse transcribed using Superscript III reverse transcriptase to produce a cDNA library that was amplified by PCR (Haag et al., 2017).

treatment_protocol: Expression of tagged proteins was induced by addition of 1 ug/ml tetracycline for 24 h before crosslinking. Cells were UV crosslinked three times with 800 mJ/cm2 light at 254 nm as described in detail in Haag et al., 2017 Crosslinking methods to identify RNA methyltransferase targets in vivo. Meth. Mol. Biol. 1562, 269-281.

tag: cell line

value: HEK293 Flp-In T-Rex cells


title: MCF7-EDR/PalboR rep1


title: short day IP

value: short day(8:16)


title: RH_2

value: 37C, 5% CO₂ in incubator

value: newly egressed Toxoplasma tachyzoites


title: PBMCs-Y_2

tag: age

value: discharge


title: His6-2xFLAG

description: enrichment from total RNA


title: short day input


title: RH_1

tag: parasite strain or treatment


title: RHΔpit_1

value: RH-delta-pit

tag: culture conditions


title: long day input rep1


title: PBMCs-Y_1

value: hospitalization


title: long day IP rep1


title: spatialRNAseq_T1L_Heart_D7PI

status: Public on Dec 03 2021

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: Weill Hall, 237 Tower Road

department: Meinig School of Biomedical Engineering

institute: Cornell University

description: Spatial RNA sequencing of heart tissue from T1L-infected neonatal mice at 7 dpi

data_processing:
Sequencing data was then aligned to a combined mouse and reovirus reference genome using the Space Ranger 1.0.0 (10x Genomics) pipeline to derive a feature spot-barcode expression matrix.
Mus musculus genome and gene annotations (assembly: GRCm38) were downloaded from the Ensembl genome browser, and Reovirus strain Type 1 lang genome and gene annotations were downloaded from the NCBI browser. Genomes were processed using the Cell Ranger (10x Genomics) pipeline’s mkref command.
Genome_build: GRCm38
Supplementary_files_format_and_content: HDF5 file containing filtered feature barcode expression matrix (UMI counts)

source_name: Neonatal murine heart

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

extract_protocol:
Whole hearts were isolated using aseptic technique and placed in ice cold sterile Hank’s Balanced Salt Solution, HBSS.  Blood and other contamination were carefully removed by perfusing the tissues with fresh HBSS. Fresh tissues were immediately embedded in Optimal Cutting Compound (OCT) media and frozen in a liquid-nitrogen-cooled isopentane (EMD Millipore, MX0760) bath for spatial transcriptomics experiments. The tissue blocks were cut into 10µm sections using Thermo Scientific CryoStar NX50 cryostat, and mounted on Visium Gene Expression slides (10x Genomics), which were pre-cooled to -20°C and used for the Visium Spatial Gene Expression experiment.
10x Genomics Fresh Frozen Visium Spatial Gene Expression 3’ Library Construction V1 Kit

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

value: Heart

tag: infection state

tag: days post infection (dpi)

value: 7 dpi


title: spatialRNAseq_Mock_Heart_D7PI

description: Spatial RNA sequencing of heart tissue from mock-infected neonatal mice at 7 dpi

tag: tissue

value: Mock-infected


title: MCF7-EDR rep1

tag: strain


title: spatialRNAseq_Mock_Heart_D4PI

description: Spatial RNA sequencing of heart tissue from mock-infected neonatal mice at 4 dpi

value: 4 dpi


title: spatialRNAseq_T1L_Heart_D4PI

description: Spatial RNA sequencing of heart tissue from T1L-infected neonatal mice at 4 dpi


title: Low miR-125b rep 3

city: Kent Ridge

first: Sai Mun

last: Leong

address: Lvl 3, NUH Main Building, 5 Lower Kent Ridge Road

department: Pathology

country: Singapore

institute: National University of Singapore

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads containing adapter or low quality sequences were removed, and the quality of the reads was determined by their error rate, Q20, Q30, and GC-contents. The clean reads were mapped with the TopHat package against hg19 human DNA reference
Alignments were sorted with Integrative Genomics Viewer. The read counts of each gene were summarized by HTSeq and DESeq2 R package was used to detect differentially expressed genes (DEGs)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files for Read Counts and Normalized Abundance Measurements

source_name: Breast cancer cells

extract_protocol:
MDA-MB-231(miR-125b-promo-EGFP) cells were flow sorted, immediately lysed and whole-transcriptome amplified using SMARTer Ultra Low RNA kit for Illumina (Clontech). A total of 3 ug of RNA per sample was used for the construction of sequencing libraries
Single-cell cDNA libraries were constructed with NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) according to manual instructions

tag: sorted cells

value: low

tag: cell type

value: Triple negative breast cancer cell

tag: passages

value: Breast


title: Low miR-125b rep 9


title: Low miR-125b rep 1


title: Low miR-125b rep 6


title: Low miR-125b rep 7


title: Low miR-125b rep 8


title: Low miR-125b rep 5


title: Low miR-125b rep 4


title: Low miR-125b rep 2


title: High miR-125b rep 8

value: high


title: High miR-125b rep 10


title: High miR-125b rep 12


title: High miR-125b rep 11


title: High miR-125b rep 5


title: High miR-125b rep 6


title: High miR-125b rep 7


title: Synovial tissues_AIA_H_BHGZD_NS_rep2

type: RNA

city: Beijing

first: Weijie

last: LI

address: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, China

description: Gene expression in synovial tissues of BHGZD treatment rats

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

organism: Rattus norvegicus

source_name: Synovial tissues_AIA_H_BHGZD

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Synovial tissues were collected, immersed in Trizol (Invitrogen, CA, USA) and transferred immediately into liquid nitrogen for microarray detection.

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Briefly, male Lewis rats were injected intradermally at the base of tail with 10mg/mL M tuberculosis H37 Ra (Difco, BD company, New Jersey, US) suspended in liquid paraffin (Freund's complete adjuvant, CFA). From the day of primary immunization, male Lewis rats were kept in the artificial climate box (production license no. RXZ-380A-LED) for 2 hours daily with certain wind velocity (6m/s), temperature (37℃) and humidity (90%) for a period of 15 days.  In AIA_H_BHGZD treatment group, the dosage selection for BHGZD was 21.4 g/kg, nearly equivalent two times of the daily dosage of RA patients in clinics.

tag: strain background

value: Lewis

tag: strain/genotype

value: BHGZD treatment rats

value: Synovial tissues


title: Synovial tissues_Con_NS_rep3

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

description: Gene expression in synovial tissues of normal control rats

source_name: Synovial tissues_normal control

value: normal control rats


title: Synovial tissues_Con_NS_rep1


title: Synovial tissues_AIA_H_NS_rep3

description: Gene expression in synovial tissues of AIA_H model rats

source_name: Synovial tissues_AIA_H

value: AIA_H model rats


title: Synovial tissues_AIA_H_NS_rep1


title: Synovial tissues_AIA_H_BHGZD_NS_rep1


title: High miR-125b rep 3


title: High miR-125b rep 4


title: Synovial tissues_Con_NS_rep2


title: Synovial tissues_AIA_H_NS_rep2


title: Synovial tissues_AIA_H_BHGZD_NS_rep3


title: High miR-125b rep 9


title: M3LV1

city: Kuopio

first: Andrea

last: Hanel

address: Yliopistonranta 1E, POB 1627

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

data_processing:
Read alignment via STAR version 2.6.0c (no trimming step performed)
Read quantification via STAR version 2.6.0c (--quantMode GeneCounts)
Read counts normalization via EdgeR (TMM)
Differential gene expression analysis via EdgeR
Genome_build: hg38, Ensembl annotation version 93
Supplementary_files_format_and_content: Excel tables of normalized read counts and statistical metrics

source_name: PBMC

growth_protocol: RPMI 1640 medium supplemented with 10% charcoal-depleted fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and were at 37 °C in a humidified 95% air/5% CO2 incubator.

extract_protocol:
extraction of total RNA using High Pure RNA Isolation kit (Roche)
rRNA-deplete cDNA library following NEB protocols

treatment_protocol: In Model 1 (M1) treatment with 10 ng/ml lipopolysaccharide (L), 5 µg/ml beta-glucan (B) or 0.1% DMSO (D) for 24 h, then for another 24 h with 10 nM 1,25(OH)2D3 (V) or 0.1% ethanol (E). In Model 2 (M2) treatment order was reversed and in Model 3 (M3) treatment was with both type of stimuli in parallel for 24 h.

value: peripheral blood mononuclear cells

tag: agent

value: LV


title: ControlChIP

city: Singapore

first: Muhammad Sufyan

last: Bin Masroni

address: Special Histopathology Laboratory, Level 3, Main Building, 5 Lower Kent Ridge Road, National University Hospital

institute: National University Singapore

data_processing:
Sequencing quality check was performed using FastQC and Trimmomatic (for trimming and removal of adapters).
Bowtie was used to align sequencing reads to the human UCSC hg19 genome.
MACS2 was used to perform peak calling. ChIPseeker was used for peak annotation.
command for MACS2 $ macs2 callpeak -t ChIP.bam -q 0.05 -g species --keep-dup 1 -B --call-summits -n SAMPLE
MAnorm (Genome Biol. Mar 16;13(3):R16) was used for comparative analysis to generate unique peaks for the respective samples
Genome_build: UCSC hg19 genome
Supplementary_files_format_and_content: tab-delimited txt files and bed files for peak calling, bedGRAPH files for visualisation

source_name: MDA-MB-231 breast cancer cells

growth_protocol: MDA-MB-231 cells are cultured in EMEM medium supplemented with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
Cells were mechanically broken up, nuclei/DNA was enzymatically sheared and dCas9-DNA complexes were isolated with dCas9 antibody (by Active Motif, cat no: 61757).
Libraries prepared according to Illumina's protocol (TruSeq ChIP-seq library)

treatment_protocol: MDA-MB-231 cells are lentivirally transduced with CRISPRi (CRISPR-dCas9) targeting copGFP sequences (as control) or KL2-binding site 1 on the miR-125b-1 promoter

tag: cell line background

value: triple-negative breast cancer cells

value: control CRISPRi (targeting copGFP sequences)

tag: chip antibody

value: dCas9 antibody (Active Motif, cat no. 61757)


title: M3LV3


title: High miR-125b rep 2


title: M3LE2

value: LE


title: M3DE2

value: DE


title: M3LE3


title: M3DV1

value: DV


title: M3LV2


title: M3DE3


title: R536ChIP

tag: treatment

value: targeted CRISPRi (KLF2 binding site 1 on the miR-125b-1 promoter)


title: M3DV2


title: M3DV3


title: M3LE1


title: M3BV3

value: BV


title: M3BV2


title: M3BE1

value: BE


title: M2VL2

value: VL


title: M3BE3


title: M3BV1


title: M3BE2


title: M2VL3


title: M2VL1


title: M2VD2

value: VD


title: M2VD3


title: M2VD1


title: M3DE1


title: High miR-125b rep 1

value: high

value: Triple negative breast cancer cell

value: Breast


title: M2EL2

value: EL


title: M2VB1

value: peripheral blood mononuclear cells

value: VB


title: M2VB2


title: M2ED3

value: ED


title: M2EB1

value: EB


title: M2EB3


title: M2ED1


title: M2EL3


title: M2VB3


title: M1LV3

value: LV


title: M1LV2


title: M1LV1


title: M2ED2


title: M2EL1


title: M1LE3

value: LE


title: M1LE1


title: M1DV3


title: M1LE2


title: M1DV1


title: M1DE3

value: DE


title: M1DV2

value: DV


title: M1DE2


title: M1BV3


title: M1DE1


title: M1BV2


title: M2EB2


title: M1BE3


title: M1BV1


title: M1BE1


title: M1BE2


title: spatialRNAseq_Mock_Ileum_D1PI

description: Spatial RNA sequencing of ileum tissue from mock-infected neonatal mice at 1 dpi

source_name: Neonatal murine ileum

extract_protocol:
Intestinal ileum were isolated using aseptic technique and placed in ice cold sterile Hank’s Balanced Salt Solution, HBSS.  Blood and other contamination were carefully removed by perfusing the tissues with fresh HBSS. Fresh tissues were immediately embedded in Optimal Cutting Compound (OCT) media and frozen in a liquid-nitrogen-cooled isopentane (EMD Millipore, MX0760) bath for spatial transcriptomics experiments. The tissue blocks were cut into 10µm sections using Thermo Scientific CryoStar NX50 cryostat, and mounted on Visium Gene Expression slides (10x Genomics), which were pre-cooled to -20°C and used for the Visium Spatial Gene Expression experiment.
10x Genomics Fresh Frozen Visium Spatial Gene Expression 3’ Library Construction V1 Kit

value: Ileum

value: Mock-infected

value: 1 dpi


title: scRNAseq_T1L_Heart_D7PI_reovirus_xGen

description: Single-cell reoviral RNA sequencing of heart tissue from T1L-infected neonatal mice at 7 dpi

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

extract_protocol:
Hearts from respective stages were isolated aseptically, washed with ice-cold Hank’s Balanced Salt Solution, HBSS (with calcium and magnesium chloride), and minced into 1-2mm pieces. Cardiac tissue pieces were then digested in tissue dissociation media with 200U/mL collagenase type II (Gibco17100-015), 1 mg/ml dispase (Sigma D4693), and 3mM calcium chloride in HBSS for four cycles of 10 minutes under mild agitation at 37°C in 1.5 ml eppendorf tubes. After every 10 minute cycle, cell suspension was collected, added to ice-cold phosphate buffered saline, PBS with 0.04% bovine serum albumin, BSA (Sigma A3803) and new dissociation media was added to the tubes. At the end of the digestion, the cells were passed through a 70µm filter and centrifuged into a pellet. To remove most blood contaminants, samples were resuspended in an ammonium-chloride-potassium (ACK) lysis buffer (Lonza #10-548E) for 3-5 minutes and centrifuged. Samples were then washed again in PBS with 0.04% BSA and then resuspended at 1 × 106 cells per ml. Cells from each sample were stained with Trypan Blue and cell viability was calculated on automated cell counters before loading the cells on 10x Chromium. We used these cell viabilities to adjust the number of cells loaded on 10x Chromium to get the desired number of transcriptomes from viable cells.
10x Genomics Chromium Next GEM Single Cell 3’ RNA-seq Library Construction V3 Kit followed by IDT xGen Hybridization Capture Kit

value: Heart

value: 7 dpi


title: scRNAseq_K287T_Heart_D10PI

description: Single-cell RNA sequencing of heart tissue from K287T-infected neonatal mice at 10 dpi

extract_protocol:
Hearts from respective stages were isolated aseptically, washed with ice-cold Hank’s Balanced Salt Solution, HBSS (with calcium and magnesium chloride), and minced into 1-2mm pieces. Cardiac tissue pieces were then digested in tissue dissociation media with 200U/mL collagenase type II (Gibco17100-015), 1 mg/ml dispase (Sigma D4693), and 3mM calcium chloride in HBSS for four cycles of 10 minutes under mild agitation at 37°C in 1.5 ml eppendorf tubes. After every 10 minute cycle, cell suspension was collected, added to ice-cold phosphate buffered saline, PBS with 0.04% bovine serum albumin, BSA (Sigma A3803) and new dissociation media was added to the tubes. At the end of the digestion, the cells were passed through a 70µm filter and centrifuged into a pellet. To remove most blood contaminants, samples were resuspended in an ammonium-chloride-potassium (ACK) lysis buffer (Lonza #10-548E) for 3-5 minutes and centrifuged. Samples were then washed again in PBS with 0.04% BSA and then resuspended at 1 × 106 cells per ml. Cells from each sample were stained with Trypan Blue and cell viability was calculated on automated cell counters before loading the cells on 10x Chromium. We used these cell viabilities to adjust the number of cells loaded on 10x Chromium to get the desired number of transcriptomes from viable cells.
10x Genomics Chromium Next GEM Single Cell 3’ RNA-seq Library Construction V3 Kit

value: 10 dpi


title: spatialRNAseq_T1L_Ileum_D1PI

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


title: scRNAseq_Mock_Heart_D10PI

description: Single-cell RNA sequencing of heart tissue from mock-infected neonatal mice at 10 dpi


title: scRNAseq_T1L_Heart_D10PI_reovirus_xGen

description: Single-cell reoviral RNA sequencing of heart tissue from T1L-infected neonatal mice at 10 dpi


title: scRNAseq_T1L_Heart_D10PI

description: Single-cell RNA sequencing of heart tissue from T1L-infected neonatal mice at 10 dpi


title: scRNAseq_K287T_Heart_D7PI

description: Single-cell RNA sequencing of heart tissue from K287T-infected neonatal mice at 7 dpi


title: Spleen control [SP_CTR]

source_name: Spleen control

value: Splenic stromal cells

value: spleen

tag: genotype

value: untreated


title: scRNAseq_T1L_Heart_D4PI_reovirus_xGen

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

value: 4 dpi


title: scRNAseq_Mock_Heart_D4PI

description: Single-cell RNA sequencing of heart tissue from mock-infected neonatal mice at 4 dpi


title: scRNAseq_T1L_Ileum_D4PI

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

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


title: scRNAseq_Mock_Ileum_D4PI

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


title: scRNAseq_K287T_Heart_D4PI_reovirus_xGen

description: Single-cell reoviral RNA sequencing of heart tissue from K287T-infected neonatal mice at 4 dpi


title: scRNAseq_T1L_Ileum_D1PI

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


title: scRNAseq_K287T_Heart_D10PI_reovirus_xGen

description: Single-cell reoviral RNA sequencing of heart tissue from K287T-infected neonatal mice at 10 dpi


title: spatialRNAseq_T1L_Ileum_D4PI

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


title: scRNAseq_K287T_Heart_D4PI

description: Single-cell RNA sequencing of heart tissue from K287T-infected neonatal mice at 4 dpi


title: scRNAseq_K287T_Heart_D7PI_reovirus_xGen

description: Single-cell reoviral RNA sequencing of heart tissue from K287T-infected neonatal mice at 7 dpi


title: scRNAseq_Mock_Ileum_D1PI

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


title: scRNAseq_T1L_Heart_D7PI

description: Single-cell RNA sequencing of heart tissue from T1L-infected neonatal mice at 7 dpi


title: spatialRNAseq_Mock_Ileum_D4PI

description: Spatial RNA sequencing of ileum tissue from mock-infected neonatal mice at 4 dpi


title: scRNAseq_Mock_Heart_D7PI

description: Single-cell RNA sequencing of heart tissue from mock-infected neonatal mice at 7 dpi


title: Lymph node WHIM [LN_WHIM]

source_name: Lymph node WHIM

value: Peripheral lymph node stromal cells

value: peripheral lymph node


title: Inma98

city: La Tronche

first: Nathanaël

last: Lemonnier

address: Allée des Alpes

department: Institute for Advanced Biosciences

institute: University Grenoble Alpes

description: Total RNA from whole blood from Inma98

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

scan_protocol: 7000G scanner (Affymetrix)

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

source_name: whole blood

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

growth_protocol: whole blood drawn from INMA subjects

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

treatment_protocol: not applicable

tag: gender

tag: age

tag: allergy

tag: asthma

tag: dermatitis

tag: rhinitis

value: whole blood


title: Inma94

description: Total RNA from whole blood from Inma94

tag: tissue


title: Inma95

description: Total RNA from whole blood from Inma95


title: Inma96

description: Total RNA from whole blood from Inma96


title: Inma99

description: Total RNA from whole blood from Inma99


title: Inma93

description: Total RNA from whole blood from Inma93


title: Inma92

description: Total RNA from whole blood from Inma92


title: Inma97

description: Total RNA from whole blood from Inma97


title: Inma87

description: Total RNA from whole blood from Inma87


title: Inma9

description: Total RNA from whole blood from Inma9


title: Inma89

description: Total RNA from whole blood from Inma89


title: Inma77

description: Total RNA from whole blood from Inma77


title: Inma86

description: Total RNA from whole blood from Inma86


title: scRNAseq_T1L_Heart_D4PI

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

tag: infection state

tag: days post infection (dpi)


title: Inma8

description: Total RNA from whole blood from Inma8


title: Inma74

description: Total RNA from whole blood from Inma74


title: Inma90

description: Total RNA from whole blood from Inma90


title: Inma83

description: Total RNA from whole blood from Inma83


title: Inma81

description: Total RNA from whole blood from Inma81


title: Inma76

description: Total RNA from whole blood from Inma76


title: Inma73

description: Total RNA from whole blood from Inma73


title: Inma91

description: Total RNA from whole blood from Inma91


title: Inma78

description: Total RNA from whole blood from Inma78


title: Inma79

description: Total RNA from whole blood from Inma79


title: Inma84

description: Total RNA from whole blood from Inma84


title: Inma88

description: Total RNA from whole blood from Inma88


title: Inma75

description: Total RNA from whole blood from Inma75


title: Inma85

description: Total RNA from whole blood from Inma85


title: Inma82

description: Total RNA from whole blood from Inma82


title: Inma80

description: Total RNA from whole blood from Inma80


title: Inma70

description: Total RNA from whole blood from Inma70


title: Inma68

description: Total RNA from whole blood from Inma68


title: Inma69

description: Total RNA from whole blood from Inma69


title: Inma66

description: Total RNA from whole blood from Inma66


title: Inma71

description: Total RNA from whole blood from Inma71


title: Inma72

description: Total RNA from whole blood from Inma72


title: Inma67

description: Total RNA from whole blood from Inma67


title: Inma64

description: Total RNA from whole blood from Inma64


title: Inma47

description: Total RNA from whole blood from Inma47


title: Inma60

description: Total RNA from whole blood from Inma60


title: Inma52

description: Total RNA from whole blood from Inma52


title: Inma61

description: Total RNA from whole blood from Inma61


title: Inma65

description: Total RNA from whole blood from Inma65


title: Inma6

description: Total RNA from whole blood from Inma6


title: Inma5

description: Total RNA from whole blood from Inma5


title: Inma50

description: Total RNA from whole blood from Inma50


title: Inma43

description: Total RNA from whole blood from Inma43


title: Inma58

description: Total RNA from whole blood from Inma58


title: Inma48

description: Total RNA from whole blood from Inma48


title: Inma7

description: Total RNA from whole blood from Inma7


title: Inma62

description: Total RNA from whole blood from Inma62


title: Inma53

description: Total RNA from whole blood from Inma53


title: Inma51

description: Total RNA from whole blood from Inma51


title: Inma45

description: Total RNA from whole blood from Inma45


title: Inma57

description: Total RNA from whole blood from Inma57


title: Inma54

description: Total RNA from whole blood from Inma54


title: Inma55

description: Total RNA from whole blood from Inma55


title: Inma63

description: Total RNA from whole blood from Inma63


title: Inma56

description: Total RNA from whole blood from Inma56


title: Inma59

description: Total RNA from whole blood from Inma59


title: Inma46

description: Total RNA from whole blood from Inma46


title: Inma4

description: Total RNA from whole blood from Inma4


title: Inma44

description: Total RNA from whole blood from Inma44


title: Inma40

description: Total RNA from whole blood from Inma40


title: Inma26

description: Total RNA from whole blood from Inma26


title: Inma49

description: Total RNA from whole blood from Inma49


title: Inma30

description: Total RNA from whole blood from Inma30


title: Inma33

description: Total RNA from whole blood from Inma33


title: Inma39

description: Total RNA from whole blood from Inma39


title: Inma20

description: Total RNA from whole blood from Inma20


title: Inma35

description: Total RNA from whole blood from Inma35


title: Inma42

description: Total RNA from whole blood from Inma42


title: Inma25

description: Total RNA from whole blood from Inma25


title: Inma31

description: Total RNA from whole blood from Inma31


title: Inma27

description: Total RNA from whole blood from Inma27


title: Inma23

description: Total RNA from whole blood from Inma23


title: Inma38

description: Total RNA from whole blood from Inma38


title: Inma32

description: Total RNA from whole blood from Inma32


title: Inma36

description: Total RNA from whole blood from Inma36


title: Inma41

description: Total RNA from whole blood from Inma41


title: Inma24

description: Total RNA from whole blood from Inma24


title: Inma28

description: Total RNA from whole blood from Inma28


title: Inma37

description: Total RNA from whole blood from Inma37


title: Inma201

description: Total RNA from whole blood from Inma201


title: Inma34

description: Total RNA from whole blood from Inma34


title: Inma22

description: Total RNA from whole blood from Inma22


title: Inma29

description: Total RNA from whole blood from Inma29


title: Inma3

description: Total RNA from whole blood from Inma3


title: Inma21

description: Total RNA from whole blood from Inma21


title: Inma200

description: Total RNA from whole blood from Inma200


title: Inma197

description: Total RNA from whole blood from Inma197


title: Inma185

description: Total RNA from whole blood from Inma185


title: Inma19

description: Total RNA from whole blood from Inma19


title: Inma189

description: Total RNA from whole blood from Inma189


title: Inma199

description: Total RNA from whole blood from Inma199


title: Inma192

description: Total RNA from whole blood from Inma192


title: Inma181

description: Total RNA from whole blood from Inma181


title: Inma180

description: Total RNA from whole blood from Inma180


title: Inma196

description: Total RNA from whole blood from Inma196


title: Inma188

description: Total RNA from whole blood from Inma188


title: Inma195

description: Total RNA from whole blood from Inma195


title: Inma186

description: Total RNA from whole blood from Inma186


title: Inma184

description: Total RNA from whole blood from Inma184


title: Inma194

description: Total RNA from whole blood from Inma194


title: Inma187

description: Total RNA from whole blood from Inma187


title: Inma190

description: Total RNA from whole blood from Inma190


title: Inma2

description: Total RNA from whole blood from Inma2


title: Inma175

description: Total RNA from whole blood from Inma175


title: Inma182

description: Total RNA from whole blood from Inma182


title: Inma193

description: Total RNA from whole blood from Inma193


title: Inma183

description: Total RNA from whole blood from Inma183


title: Inma198

description: Total RNA from whole blood from Inma198


title: Inma176

description: Total RNA from whole blood from Inma176


title: Inma179

description: Total RNA from whole blood from Inma179


title: Inma191

description: Total RNA from whole blood from Inma191


title: Inma18

description: Total RNA from whole blood from Inma18


title: Inma177

description: Total RNA from whole blood from Inma177


title: Inma178

description: Total RNA from whole blood from Inma178


title: Inma174

description: Total RNA from whole blood from Inma174


title: Inma172

description: Total RNA from whole blood from Inma172


title: Inma16

description: Total RNA from whole blood from Inma16


title: Inma168

description: Total RNA from whole blood from Inma168


title: Inma171

description: Total RNA from whole blood from Inma171


title: Inma165

description: Total RNA from whole blood from Inma165


title: Inma164

description: Total RNA from whole blood from Inma164


title: Inma160

description: Total RNA from whole blood from Inma160


title: Inma157

description: Total RNA from whole blood from Inma157


title: Inma161

description: Total RNA from whole blood from Inma161


title: Inma17

description: Total RNA from whole blood from Inma17


title: Inma169

description: Total RNA from whole blood from Inma169


title: Inma166

description: Total RNA from whole blood from Inma166


title: Inma158

description: Total RNA from whole blood from Inma158


title: Inma167

description: Total RNA from whole blood from Inma167


title: Inma170

description: Total RNA from whole blood from Inma170


title: Inma162

description: Total RNA from whole blood from Inma162


title: Inma156

description: Total RNA from whole blood from Inma156


title: Inma150

description: Total RNA from whole blood from Inma150


title: Inma155

description: Total RNA from whole blood from Inma155


title: Inma154

description: Total RNA from whole blood from Inma154


title: Inma163

description: Total RNA from whole blood from Inma163


title: Inma153

description: Total RNA from whole blood from Inma153


title: Inma151

description: Total RNA from whole blood from Inma151


title: Inma173

description: Total RNA from whole blood from Inma173


title: Inma159

description: Total RNA from whole blood from Inma159


title: Inma15

description: Total RNA from whole blood from Inma15


title: Inma148

description: Total RNA from whole blood from Inma148


title: Inma149

description: Total RNA from whole blood from Inma149


title: Inma141

description: Total RNA from whole blood from Inma141


title: Inma152

description: Total RNA from whole blood from Inma152


title: Inma140

description: Total RNA from whole blood from Inma140


title: Inma143

description: Total RNA from whole blood from Inma143


title: Inma136

description: Total RNA from whole blood from Inma136


title: Inma144

description: Total RNA from whole blood from Inma144


title: Inma139

description: Total RNA from whole blood from Inma139


title: Inma145

description: Total RNA from whole blood from Inma145


title: Inma142

description: Total RNA from whole blood from Inma142


title: Inma146

description: Total RNA from whole blood from Inma146


title: Inma135

description: Total RNA from whole blood from Inma135


title: Inma13

description: Total RNA from whole blood from Inma13


title: Inma138

description: Total RNA from whole blood from Inma138


title: Inma14

description: Total RNA from whole blood from Inma14


title: Inma134

description: Total RNA from whole blood from Inma134


title: Inma147

description: Total RNA from whole blood from Inma147


title: Inma126

description: Total RNA from whole blood from Inma126


title: Inma131

description: Total RNA from whole blood from Inma131


title: Inma129

description: Total RNA from whole blood from Inma129


title: Inma133

description: Total RNA from whole blood from Inma133


title: Inma130

description: Total RNA from whole blood from Inma130


title: Inma137

description: Total RNA from whole blood from Inma137


title: Inma128

description: Total RNA from whole blood from Inma128


title: Inma132

description: Total RNA from whole blood from Inma132


title: Inma124

description: Total RNA from whole blood from Inma124


title: Inma125

description: Total RNA from whole blood from Inma125


title: Inma127

description: Total RNA from whole blood from Inma127


title: Inma123

description: Total RNA from whole blood from Inma123


title: Inma122

description: Total RNA from whole blood from Inma122


title: Inma120

description: Total RNA from whole blood from Inma120


title: Inma119

description: Total RNA from whole blood from Inma119


title: Inma12

description: Total RNA from whole blood from Inma12


title: Inma118

description: Total RNA from whole blood from Inma118


title: Inma115

description: Total RNA from whole blood from Inma115


title: Inma114

description: Total RNA from whole blood from Inma114


title: Inma116

description: Total RNA from whole blood from Inma116


title: Inma113

description: Total RNA from whole blood from Inma113


title: Inma110

description: Total RNA from whole blood from Inma110


title: Inma112

description: Total RNA from whole blood from Inma112


title: Inma111

description: Total RNA from whole blood from Inma111


title: Inma121

description: Total RNA from whole blood from Inma121


title: Inma107

description: Total RNA from whole blood from Inma107


title: Inma106

description: Total RNA from whole blood from Inma106


title: Inma104

description: Total RNA from whole blood from Inma104


title: Inma102

description: Total RNA from whole blood from Inma102


title: Inma101

description: Total RNA from whole blood from Inma101


title: Inma103

description: Total RNA from whole blood from Inma103


title: Inma108

description: Total RNA from whole blood from Inma108


title: Inma11

description: Total RNA from whole blood from Inma11


title: Inma105

description: Total RNA from whole blood from Inma105


title: Inma109

description: Total RNA from whole blood from Inma109


title: Inma117

description: Total RNA from whole blood from Inma117


title: Inma1

description: Total RNA from whole blood from Inma1


title: Inma100

description: Total RNA from whole blood from Inma100


title: Bamse98

description: Total RNA from whole blood from Bamse98

growth_protocol: whole blood drawn from BAMSE subjects

tag: age (months)


title: Bamse99

description: Total RNA from whole blood from Bamse99


title: Bamse97

description: Total RNA from whole blood from Bamse97


title: Bamse89

description: Total RNA from whole blood from Bamse89


title: Bamse95

description: Total RNA from whole blood from Bamse95


title: Bamse94

description: Total RNA from whole blood from Bamse94


title: Bamse91

description: Total RNA from whole blood from Bamse91


title: Bamse93

description: Total RNA from whole blood from Bamse93


title: Bamse87

description: Total RNA from whole blood from Bamse87


title: Bamse9

description: Total RNA from whole blood from Bamse9


title: Bamse86

description: Total RNA from whole blood from Bamse86


title: Bamse92

description: Total RNA from whole blood from Bamse92


title: Inma10

description: Total RNA from whole blood from Inma10


title: Bamse82

description: Total RNA from whole blood from Bamse82


title: Bamse88

description: Total RNA from whole blood from Bamse88


title: Bamse90

description: Total RNA from whole blood from Bamse90


title: Bamse80

description: Total RNA from whole blood from Bamse80


title: Bamse81

description: Total RNA from whole blood from Bamse81


title: Bamse8

description: Total RNA from whole blood from Bamse8


title: Bamse84

description: Total RNA from whole blood from Bamse84


title: Bamse78

description: Total RNA from whole blood from Bamse78


title: Bamse77

description: Total RNA from whole blood from Bamse77


title: Bamse85

description: Total RNA from whole blood from Bamse85


title: Bamse79

description: Total RNA from whole blood from Bamse79


title: Bamse96

description: Total RNA from whole blood from Bamse96


title: Bamse76

description: Total RNA from whole blood from Bamse76


title: Bamse83

description: Total RNA from whole blood from Bamse83


title: Bamse70

description: Total RNA from whole blood from Bamse70


title: Bamse66

description: Total RNA from whole blood from Bamse66


title: Bamse71

description: Total RNA from whole blood from Bamse71


title: Bamse69

description: Total RNA from whole blood from Bamse69


title: Bamse72

description: Total RNA from whole blood from Bamse72


title: Bamse62

description: Total RNA from whole blood from Bamse62


title: Bamse73

description: Total RNA from whole blood from Bamse73


title: Bamse68

description: Total RNA from whole blood from Bamse68


title: Bamse67

description: Total RNA from whole blood from Bamse67


title: Bamse74

description: Total RNA from whole blood from Bamse74


title: Bamse65

description: Total RNA from whole blood from Bamse65


title: Bamse64

description: Total RNA from whole blood from Bamse64


title: Bamse6

description: Total RNA from whole blood from Bamse6


title: Bamse63

description: Total RNA from whole blood from Bamse63


title: Bamse59

description: Total RNA from whole blood from Bamse59


title: Bamse7

description: Total RNA from whole blood from Bamse7


title: Bamse75

description: Total RNA from whole blood from Bamse75


title: Bamse53

description: Total RNA from whole blood from Bamse53


title: Bamse60

description: Total RNA from whole blood from Bamse60


title: Bamse56

description: Total RNA from whole blood from Bamse56


title: Bamse61

description: Total RNA from whole blood from Bamse61


title: Bamse57

description: Total RNA from whole blood from Bamse57


title: Bamse55

description: Total RNA from whole blood from Bamse55


title: Bamse54

description: Total RNA from whole blood from Bamse54


title: Bamse58

description: Total RNA from whole blood from Bamse58


title: Bamse49

description: Total RNA from whole blood from Bamse49


title: Bamse44

description: Total RNA from whole blood from Bamse44


title: Bamse45

description: Total RNA from whole blood from Bamse45


title: Bamse43

description: Total RNA from whole blood from Bamse43


title: Bamse51

description: Total RNA from whole blood from Bamse51


title: Bamse48

description: Total RNA from whole blood from Bamse48


title: Bamse5

description: Total RNA from whole blood from Bamse5


title: Bamse42

description: Total RNA from whole blood from Bamse42


title: Bamse46

description: Total RNA from whole blood from Bamse46


title: Bamse38

description: Total RNA from whole blood from Bamse38


title: Bamse47

description: Total RNA from whole blood from Bamse47


title: Bamse52

description: Total RNA from whole blood from Bamse52


title: Bamse37

description: Total RNA from whole blood from Bamse37


title: Bamse4

description: Total RNA from whole blood from Bamse4


title: Bamse34

description: Total RNA from whole blood from Bamse34


title: Bamse39

description: Total RNA from whole blood from Bamse39


title: Bamse36

description: Total RNA from whole blood from Bamse36


title: Bamse31

description: Total RNA from whole blood from Bamse31


title: Bamse50

description: Total RNA from whole blood from Bamse50


title: Bamse29

description: Total RNA from whole blood from Bamse29


title: Bamse40

description: Total RNA from whole blood from Bamse40


title: Bamse35

description: Total RNA from whole blood from Bamse35


title: Bamse41

description: Total RNA from whole blood from Bamse41


title: Bamse30

description: Total RNA from whole blood from Bamse30


title: Bamse252

description: Total RNA from whole blood from Bamse252


title: Bamse3

description: Total RNA from whole blood from Bamse3


title: Bamse33

description: Total RNA from whole blood from Bamse33


title: Bamse27

description: Total RNA from whole blood from Bamse27


title: Bamse255

description: Total RNA from whole blood from Bamse255


title: Bamse254

description: Total RNA from whole blood from Bamse254


title: Bamse26

description: Total RNA from whole blood from Bamse26


title: Bamse250

description: Total RNA from whole blood from Bamse250


title: Bamse32

description: Total RNA from whole blood from Bamse32


title: Bamse251

description: Total RNA from whole blood from Bamse251


title: Bamse253

description: Total RNA from whole blood from Bamse253


title: Bamse249

description: Total RNA from whole blood from Bamse249


title: Bamse248

description: Total RNA from whole blood from Bamse248


title: Bamse256

description: Total RNA from whole blood from Bamse256


title: Bamse247

description: Total RNA from whole blood from Bamse247


title: Bamse244

description: Total RNA from whole blood from Bamse244


title: Bamse246

description: Total RNA from whole blood from Bamse246


title: Bamse245

description: Total RNA from whole blood from Bamse245


title: Bamse25

description: Total RNA from whole blood from Bamse25


title: Bamse28

description: Total RNA from whole blood from Bamse28


title: Bamse243

description: Total RNA from whole blood from Bamse243


title: Bamse242

description: Total RNA from whole blood from Bamse242


title: Bamse238

description: Total RNA from whole blood from Bamse238


title: Bamse241

description: Total RNA from whole blood from Bamse241


title: Bamse230

description: Total RNA from whole blood from Bamse230


title: Bamse233

description: Total RNA from whole blood from Bamse233


title: Bamse235

description: Total RNA from whole blood from Bamse235


title: Bamse24

description: Total RNA from whole blood from Bamse24


title: Bamse234

description: Total RNA from whole blood from Bamse234


title: Bamse237

description: Total RNA from whole blood from Bamse237


title: Bamse240

description: Total RNA from whole blood from Bamse240


title: Bamse226

description: Total RNA from whole blood from Bamse226


title: Bamse229

description: Total RNA from whole blood from Bamse229


title: Bamse239

description: Total RNA from whole blood from Bamse239


title: Bamse231

description: Total RNA from whole blood from Bamse231


title: Bamse232

description: Total RNA from whole blood from Bamse232


title: Bamse236

description: Total RNA from whole blood from Bamse236


title: Bamse228

description: Total RNA from whole blood from Bamse228


title: Bamse23

description: Total RNA from whole blood from Bamse23


title: Bamse223

description: Total RNA from whole blood from Bamse223


title: Bamse227

description: Total RNA from whole blood from Bamse227


title: Bamse221

description: Total RNA from whole blood from Bamse221


title: Bamse220

description: Total RNA from whole blood from Bamse220


title: Bamse218

description: Total RNA from whole blood from Bamse218