title: Kasumi-1_AE-FKBP_dTAG+LSD1i-24hr-2 [PRO-seq]

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave

department: Biochemistry

institute: Vanderbilt University

description:
24hr_500nM_dTAG_+_100nM_GSK2879552
Biotinylated RNA
processed data file: 24hr_dTAG_and_LSD1i_minus.ucsc.bedgraph.gz
processed data file: 24hr_dTAG_and_LSD1i_plus.ucsc.bedgraph.gz

data_processing:
Library strategy: PRO-seq
Adaptors were trimmed and short/low quality sequence filtered by Trimmomatic-0.32: ILLUMINACLIP:adaptor.txt:2:30:7 TRAILING:15 MINLEN:15.
Reverse complement sequence was generated using fastx_reverse_complement from the FASTX toolkit (v 0.0.13).
Reverse complement sequences were aligned to the human genome (hg19)+ spikein sequences using bowtie2 (v2.2.2).
Differential transcript analysis was carried out using the Nascent RNA Sequencing Analysis (NRSA) pipeline - pause_PROseq.pl.
Bedgraph files were generated by Homer makeUCSCfile.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.bedgraph: Homer-generated bedgraph files.
Supplementary_files_format_and_content: *_change.txt: Differential gene transcription analysis generated by NRSA.

source_name: Kasumi-1 cells

growth_protocol: Kasumi-1 cells were grown in RPMI +15% FBS + 50 U/ml penicillin, 50 μg/ml streptomycin, and 2mM L-glutamine.

extract_protocol:
Following nuclear run-on, total RNA was isolated by Trizol extraction and biotinylated RNA isolated by streptavidin bead binding.
Following hydrolysis of RNA, 3' adaptors were ligated to biotinylated RNA fragments. After 5'Cap removal and end repair, 5' adaptors were also ligated. Adaptor-ligated RNA fragments were reverse transcribed and cDNA libraries amplified using indexed primers.

treatment_protocol: Cells were treated with 500 nM dTAG-47 alone or in combination with 100 nM GSK2879552 for the indicated timepoints.

tag: genotype/variation

tag: time point


title: Basophils from infected patient 30894

status: Public on Dec 31 2020

type: SRA

city: New York

first: Juan-Jose

last: Garces

state: New York

address: 321 E 61st St

country: USA

institute: Memorial Sloan Kettering Cancer Center

description:
30894_basos
30894_S10_R*_001.basos
mRNA-3' from basophils sorted from infected patient

library_source: transcriptomic

data_processing:
FASTQ polyA trimming
STAR alignment (version 2.7.3a): outFilterMismatchNmax 1, alignEndsType EndToEnd
Gene counts performed using quant3p
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix counts. Each column corresponds to gene counts for each generated BAM (after merging all resequenced samples and downsampled to 10 millions of reads for each one).

molecule: total RNA

organism: Homo sapiens

source_name: Basophils from peripheral blood

extract_protocol:
Cells were FACSorted in Lysis Binding Buffer and mRNA was extracted through Dynabeads polyT
RNA was sample-barcodad by a RT reaction. After, cDNA was purified with SPRIselect and amplified using the T7 promotor as template. RNA molecules were fragmented and purified again. Afterwards, a ssRNA adaptor was ligated to the 3’-end of the RNA fragments and, finally, cDNA was amplified.

tag: covid status

value: Infected

tag: gender

value: Male

tag: age

tag: hospitalization

value: No

tag: exitus

tag: haematological tumor

tag: number of cells


title: Plasmacytoid dendritic cells from infected patient 30878

description:
30878_dendP
30878_S8_R*_001.dendP
mRNA-3' from plasmacytoid dendritic cells sorted from infected patient

source_name: Plasmacytoid dendritic cells from peripheral blood


title: Kasumi-1_AE-FKBP_dTAG+LSD1i-24hr-1 [PRO-seq]

tag: cell line

tag: treatment


title: Kasumi-1_AE-FKBP_LSD1i-24hr-2 [PRO-seq]

description:
24hr_100_nM_GSK2879552
Biotinylated RNA
processed data file: 24hr_LSD1i_minus.ucsc.bedgraph.gz
processed data file: 24hr_LSD1i_plus.ucsc.bedgraph.gz


title: Myeloid dendritic cells from infected patient 30872 (resequenced)

description:
30872_dendM_reseq420
30872_reseq418_S35_R*_001.dendM
mRNA-3' from myeloid dendritic cells sorted from infected patient

source_name: Myeloid dendritic cells from peripheral blood

value: Yes


title: Basophils from infected patient 30872

description:
30872_basos
30872_S11_R*_001.basos
mRNA-3' from basophils sorted from infected patient


title: Kasumi-1_AE-FKBP_dTAG-24hr-1 [PRO-seq]

description:
24hr_500_nM_dTAG-47
Biotinylated RNA
processed data file: 24hr_dTAG_minus.ucsc.bedgraph.gz
processed data file: 24hr_dTAG_plus.ucsc.bedgraph.gz

value: 500 nM dTAG-47


title: Plasmacytoid dendritic cells from infected patient 31037

description:
31037_dendP
31037_S21_R*_001.dendP
mRNA-3' from plasmacytoid dendritic cells sorted from infected patient

value: Female

value: Acute myeloid leukemia


title: Plasmacytoid dendritic cells from infected patient 30874

description:
30874_dendP
30874_S13_R*_001.dendP
mRNA-3' from plasmacytoid dendritic cells sorted from infected patient


title: Kasumi-1_AE-FKBP_LSD1i-24hr-1 [PRO-seq]


title: Plasmacytoid dendritic cells from infected patient 31037 (resequenced)

description:
31037_dendP_reseq420
31037_reseq417_S16_R*_001.dendP
mRNA-3' from plasmacytoid dendritic cells sorted from infected patient


title: Kasumi-1_AE-FKBP_dTAG-6hr-1 [PRO-seq]

description:
6hr_500_nM_dTAG-47
Biotinylated RNA
processed data file: 6hr_minus.ucsc.bedgraph.gz
processed data file: 6hr_plus.ucsc.bedgraph.gz
processed data file: 0hr_vs_6hr_gb_change.txt


title: Kasumi-1_AE-FKBP_dTAG-1hr-1 [PRO-seq]

description:
1hr_500 nM dTAG-47
Biotinylated RNA
processed data file: 1hr_minus.ucsc.bedgraph.gz
processed data file: 1hr_plus.ucsc.bedgraph.gz
processed data file: 0hr_vs_1hr_gb_change.txt


title: Kasumi-1_AE-FKBP_dTAG-24hr-2 [PRO-seq]


title: Kasumi-1_AE-FKBP_dTAG-2hr-1 [PRO-seq]

description:
2hr_500_nM_dTAG-47
Biotinylated RNA
processed data file: 2hr_minus.ucsc.bedgraph.gz
processed data file: 2hr_plus.ucsc.bedgraph.gz
processed data file: 0hr_vs_2hr_gb_change.txt


title: Kasumi-1_AE-FKBP_dTAG-6hr-2 [PRO-seq]


title: Kasumi-1_AE-FKBP_dTAG-30min-1 [PRO-seq]

description:
30min_500 nM dTAG-47
Biotinylated RNA
processed data file: 30min_minus.ucsc.bedgraph.gz
processed data file: 30min_plus.ucsc.bedgraph.gz
processed data file: 0hr_vs_30min_gb_change.txt


title: Kasumi-1_AE-FKBP_dTAG-30min-2 [PRO-seq]


title: Kasumi-1_AE-FKBP_dTAG-0hr-2 [PRO-seq]

description:
Biotinylated RNA
processed data file: 0hr_minus.ucsc.bedgraph.gz
processed data file: 0hr_plus.ucsc.bedgraph.gz

value: Untreated


title: Kasumi-1_parental-2 [PRO-seq]

description:
Biotinylated RNA
processed data file: wt_minus.ucsc.bedgraph.gz
processed data file: wt_plus.ucsc.bedgraph.gz
processed data file: wt_vs_0hr_gb_change.txt

value: Parental


title: Kasumi-1_parental-1 [PRO-seq]


title: Kasumi-1_AE-FKBP_dTAG-1hr-2 [PRO-seq]


title: Kasumi-1_AE-FKBP_dTAG_4hr-2 [RNA-seq]

description:
4hr_500 nM dTAG-47
processed data file: 0hr_v_4hr_gene_exp.diff

data_processing:
Adaptors were trimmed using trimmomatic (SE for Kasumi-1 cells, PE for CD34+ cells).
Trimmed reads were aligned to the human genome (hg19) with TopHat v2.0.11.
Differential gene expression was determined using Cuffdiff v.2.1.1.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_gene_exp.diff: Cuffdiff differential gene expression output; tab delimited text file.

molecule: polyA RNA

growth_protocol: Kasumi-1 cells were grown in RPMI +15% FBS +50 U/ml penicillin, 50 μg/ml streptomycin, and 2mM L-glutamine. CD34+ cells were cultured in IMDM + 20% FBS, 55 μM BME, 50 U/ml penicillin, 50 μg/ml streptomycin, 2mM L-glutamine, and 10 ng/mL SCF, Flt3-L, TPO, IL-3, and IL-6.

extract_protocol:
Total RNA was extracted by Trizol according to the manufacturer's protocol and precipitated with isopropanol.
Libraries were constructed on polyA selected transcript using standard Illumina protocol.

treatment_protocol: Cells were treated with 500 nM dTAG-47 for the indicated timepoints.


title: Kasumi-1_AE-FKBP_dTAG_24hr-2 [RNA-seq]

description:
24hr_500 nM dTAG-47
processed data file: 0hr_v_24hr_gene_exp.diff


title: Kasumi-1_AE-FKBP_dTAG_0hr-2 [RNA-seq]


title: Kasumi-1_AE-FKBP_dTAG_8hr-2 [RNA-seq]

description:
8hr_500 nM dTAG-47
processed data file: 0hr_v_8hr_gene_exp.diff


title: Kasumi-1_AE-FKBP_dTAG_24hr-1 [RNA-seq]


title: Kasumi-1_AE-FKBP_dTAG-2hr-2 [PRO-seq]


title: Kasumi-1_AE-FKBP_dTAG_8hr-1 [RNA-seq]


title: Kasumi-1_AE-FKBP_dTAG_4hr-1 [RNA-seq]


title: Kasumi-1_AE-FKBP_dTAG_2hr-1 [RNA-seq]

description:
2hr_500 nM dTAG-47
processed data file: 0hr_v_2hr_gene_exp.diff


title: Kasumi-1_AE-FKBP_dTAG_2hr-2 [RNA-seq]


title: Kasumi-1_parental-2 [RNA-seq]

description: processed data file: parental_v_0hr_gene_exp.diff


title: Kasumi-1_parental-1 [RNA-seq]


title: Kasumi-1_AE-FKBP_dTAG_0hr-1 [RNA-seq]


title: SMARTer_plasma_1

city: Vestec

first: Šárka

last: Benešová

address: Prumyslova 595

department: Institute of Biotechnology

country: Czech Republic

institute: Czech Academy of Science

description: processed data file: count_matrix_plasma.txt

data_processing:
Raw reads of all samples were trimmed with cutadapt tool (version 1.18) according to the respective library preparation manual and bases with phred 33 quality lower than 20 were trimmed.
Reads longer than 16 bp and shorter than 29 bp were kept.
Reads of all samples were aligned to rRNA and Univec database (obtained from sortmerna github repository) using bowtie aligner  (version 1.2.2) with one mismatch allowed and only reads which did not align were kept.
Reads of all samples were further aligned to synthetic spike-ins reference using bowtie aligner (version 1.2.2) with zero mismatch allowed and only reads which did not align were kept.
Reads of plasma samples were aligned with STAR (version 2.7.0c) to human genome GRCh38.95 and only mapped reads were aligned to mature miRNAs from miRBase v22 with following parameters --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 15 --outFilterScoreMinOverLread 0   --outFilterMatchNminOverLread 0 --alignIntronMax 1 --alignEndsType EndToEnd.
Reads of miRxplore samples were aligned to the reference obtained from Miltenyi Biotec using STAR (version 2.7.0c) with the same parameters as plasma samples.
Only uniquely mapped reads of both types of samples were counted using Rsubread package version 1.32.4.
Genome_build: miRBase v22  - hsa mature sequences (GRCh38)
Supplementary_files_format_and_content: tab delimited text files include raw count values generated with featureCounts function (package - Rsubread_1.32.4)

extract_protocol:
Blood samples were collected from four healthy volunteers into K2EDTA BD Vacutainer tubes (Beckman Dickinson) and centrifuged within 30 min from collection at 1500 x g for 15 min at room temperature. The plasma fraction was aspirated and transferred into 2 ml tubes and centrifuged again for 15 min at 3000 x g. The supernatant was transferred into new 2 ml tubes and stored at -80 °C until analysis. Total RNA was isolated starting from plasma aliquots of 250 µl using the miRNeasy Serum/Plasma Advanced Kit (Qiagen) according to manufacturer´s instructions. 1 µl of isolation spike-in mix and 1 µl of GlycoBlue Coprecipitant (Invitrogen) were added at the lysis step as described in (Androvic et al., 2019). RNA was eluted into 20 µl of nuclease-free water and stored at -80 °C. RNA eluates were then pooled together to produce standard plasma RNA sample used through the study.
Libraries were prepared in technical duplicates starting from 5 µl of plasma RNA pool and 5 µl of miRXplore Universal Reference (2x10^6 copies/µl) according to each manufacturer´s protocol using compatible set of sample indexes. Libraries generated by the same protocol were pooled and run on 5% TBE-PAGE on Mini-PROTEAN tetra cell (BioRad). A region representing fragments with RNA inserts of length 22 nt ± ~10 nt (i.e. fragments originating from miRNAs) was excised from the gel, DNA was eluted into nuclease-free water and purified with SPRIselect reagent (Beckman Coulter).

tag: sample type

value: Plasma

tag: library preparation protocol

value: Takara:SMARTer smRNA-Seq kit for Illumina

tag: technical replicate


title: SMARTer_plasma_2


title: Norgen_plasma _1

value: Norgen Biotek Copr.:Small RNA Library Prep Kit for Illumina


title: QIAseq_plasma_2

value: Qiagen:QIAseq miRNA Library Kit


title: Lexogen_plasma_2

value: Lexogen:Small RNA-Seq Library Prep Kit


title: Norgen_plasma _2


title: QIAseq_plasma_1


title: RealSeq_plasma_2

value: Somagenics:RealSeq Biofluids Plasma/Serum miRNA


title: EdgeSeq_plasma_2

value: HTG EdgeSeq miRNA Whole Transcriptome Assay


title: NEXTflex_plasma_2

value: Bioo Scientific Corp. NEXTflex Small RNA-Seq Library Prep Kit v3


title: EdgeSeq_plasma_1


title: NEXTflex_plasma_1


title: Lexogen_plasma_1


title: Kasumi-1_AE-FKBP_dTAG-0hr-1 [PRO-seq]


title: RealSeq_plasma_1


title: TFB2

city: Vienna

first: Smriti

last: Sharma

address: Spitalgasse 23

department: Internal Medicine II, Cardiology

country: Austria

institute: Medical University of Vienna

description: processed data file: DiffGene_results_AFB_vs_TFB.tsv

data_processing:
Illumina's bcl2fastq v2 was used for basecalling.
Single-end reads were subject to de-multiplexing and trimming of Illumina adaptor residuals using Illumina’s bcl2fastq software version 2.19.1.403.
The splice aware RNA mapping software STAR (version 2.6.0c) was used to map the reads to the reference genome. To count the uniquely mapped reads to annotated genes, the software htseq-count (HTSeq version 0.11.0) was used.
Normalization of the raw counts and differential gene expression analysis were carried out with help of the R software package DESeq2 (version 1.18.1).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: DiffGene_results_AFB_vs_TFB.tsv: Tab-delimited text file

source_name: Thrombus

extract_protocol:
Cellular RNA was extracted using ReliaPrep RNA Miniprep system (Promega).
Illumina’s TruSeq stranded RNA library preparation kit including polyA enrichment was used to construct libraries from total RNA.

tag: diagnosis

value: Chronic thromboembolic pulmonary hypertension (CTEPH)

tag: tissue

value: Thrombus

tag: cell type

value: Fibroblasts

tag: passage

tag: patient


title: TFB4


title: icLASER in vitro, Replicate 2

city: Irvine

first: Whitney

last: England

state: CA

address: 2403 Natural Sciences I

department: Pharmaceutical Sciences

institute: University of California Irvine

data_processing:
Adapters and barcodes were trimmed using Trimmomatic.
Reads were aligned to the ENSEMBL Release 88 GRCh38 transcriptome using Bowtie2.
Reverse transcription stops and enrichment scores were calculated using the icSHAPE pipeline.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt: Enrichment scores for each transcript. Format: transcript ID, length, RPKM, list of per-position enrichment scores

source_name: K562 cells

growth_protocol: K562 cells were grown in RPMI 1640 supplemented with 10% FBS, and 1% penicillin streptomycin

extract_protocol: RNA was harvested from cells using Trizol Reagent.  RNA was incubated with DBCO-Biotin, followed by bead enrichment for biotinylated RNA.  Samples were purified using the RNA Clean and Concentrator Kit (Zymo).

treatment_protocol: 5uL of 1M NAz-N3 (icLASER-treated) or DMSO (control) added to 45ul of sample.  Treated sample was then exposed to UV light for 10 min.

value: bone marrow chronic myelogenous leukemia

value: icLASER in vitro


title: TFB1


title: AFB4

source_name: Adventitia

value: Adventitia


title: AFB3


title: icLASER in vivo, Replicate 2

value: icLASER in vivo


title: No UV icLASER control, Replicate 2

description:
icLASER_invitro.out.txt
icLASER_invivo.out.txt

value: No UV icLASER control


title: AFB1


title: icLASER in vivo, Replicate 1


title: TFB3


title: AFB2


title: icSHAPE in vivo, Replicate 3

treatment_protocol: Incubated in 100 mM final concentration NAI-N3 solution (icSHAPE-treated) or 500 μl of DMSO solution (control) at 37 °C with rotation for 5 min.

value: icSHAPE in vivo


title: No UV icLASER control, Replicate 1


title: icLASER in vitro, Replicate 1


title: icSHAPE in vitro, Replicate 2

value: icSHAPE in vitro


title: icSHAPE in vivo, Replicate 2


title: HepaRG Treatment rep1 [HepaRG5_FA_S12]

city: Kingston

first: Fatemeh

last: Akhlaghi

state: RI

address: 7 Greenhouse Road

department: College of Pharmacy

institute: University of Rhode Island

description: Differentiated HepaRG treated with media containing 0.5 mM palmitate and oleate (1:2) conjugated to BSA (0.02%) for 72h

data_processing:
20 M 2x75 paired end reads were generated from an Illumina NextSeq 500 Platform
Following raw reads were filtered: reads containing adaptors
QuickRNASeq pipelin was used in reads mapping and counting: STAR 2.5.2.a was used for mapping; featureCounts subread-1.5.1 was used for counting; RSeQC was used for read QC; VarScan.v2.4.0 was used for SNP calling.
Genome_build: Genome fasta file is GRCh38.primary.genome.fa. Gene annotation file is GRCh38.gencode v25 annotation file. Gtf file is GRCh38.gencode.v25.gtf;  Bed file is GRCh38.gencode.v25.bed
Supplementary_files_format_and_content: Processed data is a tab delimited text file contains gene name as row, and the fpkm for that gene from each sample is the column.

source_name: HepaRG Treatment

growth_protocol: HepaRG cells were purchased from Biopredic International (Inserum, France) and were grown and differentiated in-house according to manufacturer’s instructions.  Following 14 days in growth phase and 14 days of differentiation, the cells in 24 well plate were treated with basal medium containing Williams E with Glutamax-I, 100 IU/ml of penicillin, 100 μg/ml of streptomycin, 4 μg/ml of bovine insulin and 5 × 10−5 M of hydrocortisone hemisuccinate for 5 days.  The cells were incubated at 37°C in 5% CO2 and the media was replenished every 2-3 days.

extract_protocol:
Total RNA samples were isolated using RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer’s instruction.  RNA integrity and quantity were measured using Agilent 2100 Bioanalyzer System (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina mRNA Stranded Neoprep Kit, RNA input was 100ng.

treatment_protocol: HepaRG cells were treated with fatty acids (1:2 palmitate: oleate) conjugated to 30% essentially fatty acid free (FAF) BSA solution (Invitrogen, Grand Island, NY), made up in Williams E media (Invitrogen).  The control cells were treated with 30% essentially fatty acid free (FAF) BSA solution alone.  The treatment was carried out for 72h.

value: HepaRG

value: Human Hepatocellular Carcinoma Cells

tag: passages


title: HepaRG control rep3 [HepaRG3_control_S11]

description: Differentiated HepaRG treated with media containing Bovine Serum Albumin (BSA) at 0.02% for 72 h

source_name: HepaRG control


title: DMSO icSHAPE control, Replicate 3

description:
icSHAPE_invitro.out.txt
icSHAPE_invivo.out.txt

value: DMSO icSHAPE control


title: icSHAPE in vitro, Replicate 1


title: HepaRG control rep1 [HepaRG1_control_S7]

value: media containing Bovine Serum Albumin (BSA) at 0.02% for 72 h


title: DMSO icSHAPE control, Replicate 2


title: DMSO icSHAPE control, Replicate 1


title: HepaRG control rep2 [HepaRG2_control_S10]


title: HepaRG Treatment rep3 [HepaRG7_FA_S14]

value: media containing 0.5 mM palmitate and oleate (1:2) conjugated to BSA (0.02%) for 72h


title: HepaRG Treatment rep2 [HepaRG6_FA_S13]


title: X102697.001.073

city: Amsterdam

first: Sanne

last: Hoefnagel

state: Noord-Holland

address: Meibergdreef 9

department: Gastroenterology

country: Netherlands

institute: Academic Medical Centre Amsterdam

description:
EAC.51.txt
TCCGCGAA-AGGCTATA

data_processing:
The reads were mapped to the reference sequence using a short read aligner based on Burrows—Wheeler Transform (Tophat v2.0.14) with default settings.
The alignment files (BAM files sorted on coordinates and indexed with the samtools v1.3 package) containing the mapping information were generated. Based on the mapped locations in the alignment file the frequency of how often a read was mapped on a transcript was determined using HTSeq v0.6.1p1.
FPKM (fragments per kilobase of exon per million reads mapped) values were calculated using Cufflinks v2.2.1and analyzed in R
Genome_build: Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
Supplementary_files_format_and_content: log2 transformed FPKM

source_name: pretreatment esophageal adenocarcinoma

extract_protocol:
Total RNA was isolated from EAC biopsies, previously stored in RNAlater RNA stabilization reagent (Qiagen), using the RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions. gDNA Eliminator columns from the same kit were used to eliminate genomic DNA contamination. RNA integrity was verified on the Fragment Analyzer (Advance Analytica) and, only samples with RNA Quality Number (RQN) ≥ 6 were selected for RNA-seq. A total of 500ng of purified total RNA per sample was used for Poly-A selection whole transcriptome analysis.
Single-Read sequencing libraries were prepared by the ServiceXS sequencing facility (BaseClear, Leiden, the Netherlands) using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB#E7420S/L) according to the protocol.  Libraries were sequenced on the Illumina NextSeq 500 platform according to manufacturer’s instructions. Image analysis, base calling and quality checks were performed with the Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.17.

value: esophageal adenocarcinoma


title: X102697.001.075

description:
EAC.51.txt
TCCGCGAA-AGGATAGG


title: X102697.001.071

description:
EAC.51.txt
CGGCTATG-ACGTCCTG


title: X102697.001.074

description:
EAC.51.txt
TCCGCGAA-GCCTCTAT


title: X102697.001.072

description:
EAC.51.txt
CGGCTATG-GTCAGTAC


title: X102697.001.069

description:
EAC.51.txt
CGGCTATG-CTTCGCCT


title: X102697.001.068

description:
EAC.51.txt
CGGCTATG-TCAGAGCC


title: X102697.001.067

description:
EAC.51.txt
CGGCTATG-AGGATAGG


title: X102697.001.061

description:
EAC.51.txt
TAATGCGC-CTTCGCCT


title: X102697.001.062

description:
EAC.51.txt
TAATGCGC-TAAGATTA


title: X102697.001.065

description:
EAC.51.txt
CGGCTATG-AGGCTATA


title: X102697.001.064

description:
EAC.51.txt
TAATGCGC-GTCAGTAC


title: X102697.001.060

description:
EAC.51.txt
TAATGCGC-TCAGAGCC


title: X102697.001.057

description:
EAC.51.txt
TAATGCGC-AGGCTATA


title: X102697.001.058

description:
EAC.51.txt
TAATGCGC-GCCTCTAT


title: X102697.001.059

description:
EAC.51.txt
TAATGCGC-AGGATAGG


title: icSHAPE in vivo, Replicate 1


title: X102697.001.052

description:
EAC.51.txt
CTGAAGCT-TCAGAGCC


title: X102697.001.056

description:
EAC.51.txt
CTGAAGCT-GTCAGTAC


title: X102697.001.048

description:
EAC.51.txt
GAATTCGT-GTCAGTAC


title: X102697.001.051

description:
EAC.51.txt
CTGAAGCT-AGGATAGG


title: X102697.001.050

description:
EAC.51.txt
CTGAAGCT-GCCTCTAT


title: X102697.001.055

description:
EAC.51.txt
CTGAAGCT-ACGTCCTG


title: X102697.001.054

description:
EAC.51.txt
CTGAAGCT-TAAGATTA


title: X102697.001.070

description:
EAC.51.txt
CGGCTATG-TAAGATTA


title: X102697.001.045

description:
EAC.51.txt
GAATTCGT-CTTCGCCT


title: X102697.001.040

description:
EAC.51.txt
ATTCAGAA-GTCAGTAC


title: X102697.001.046

description:
EAC.51.txt
GAATTCGT-TAAGATTA


title: X102697.001.036

description:
EAC.51.txt
ATTCAGAA-TCAGAGCC


title: X102697.001.041

description:
EAC.51.txt
GAATTCGT-AGGCTATA


title: X102697.001.044

description:
EAC.51.txt
GAATTCGT-TCAGAGCC


title: X102697.001.042

description:
EAC.51.txt
GAATTCGT-GCCTCTAT


title: X102697.001.035

description:
EAC.51.txt
ATTCAGAA-AGGATAGG


title: X102697.001.032

description:
EAC.51.txt
GAGATTCC-GTCAGTAC


title: X102697.001.029

description:
EAC.51.txt
GAGATTCC-CTTCGCCT


title: X102697.001.033

description:
EAC.51.txt
ATTCAGAA-AGGCTATA


title: X102697.001.030

description:
EAC.51.txt
GAGATTCC-TAAGATTA


title: X102697.001.026

description:
EAC.51.txt
GAGATTCC-GCCTCTAT


title: X102697.001.017

description:
EAC.51.txt
CGCTCATT-AGGCTATA


title: X102697.001.023

description:
EAC.51.txt
CGCTCATT-ACGTCCTG


title: X102697.001.016

description:
EAC.51.txt
TCCGGAGA-GTCAGTAC


title: X102697.001.018

description:
EAC.51.txt
CGCTCATT-GCCTCTAT


title: X102697.001.021

description:
EAC.51.txt
CGCTCATT-CTTCGCCT


title: X102697.001.015

description:
EAC.51.txt
TCCGGAGA-ACGTCCTG


title: X102697.001.020

description:
EAC.51.txt
CGCTCATT-TCAGAGCC


title: X102697.001.024

description:
EAC.51.txt
CGCTCATT-GTCAGTAC


title: X102697.001.011

description:
EAC.51.txt
TCCGGAGA-AGGATAGG


title: X102697.001.014

description:
EAC.51.txt
TCCGGAGA-TAAGATTA


title: X102697.001.002

description:
EAC.51.txt
ATTACTCG-GCCTCTAT


title: X102697.001.013

description:
EAC.51.txt
TCCGGAGA-CTTCGCCT


title: X102697.001.005

description:
EAC.51.txt
ATTACTCG-CTTCGCCT


title: GFP positive cells pWOX5:erGFP - Replicate 1

city: Raleigh

first: Lisa

last: Van den Broeck

state: NORTH CAROLINA

address: 112 Derieux Place

department: Plant and Microbial Biology

institute: North Carolina State University

description:
Named W5S in processed file
Supplemental_Table2_transc_cei.xlsx

data_processing:
Gene expression analysis of raw RNA-seq data was performed using the TuxNet interface (Spurney et al., 2019).
TuxNet uses ea-utils fastq-mcf (Aronesty, 2011, Aronesty, 2013) for preprocessing, hisat2 (Kim et al., 2015) for genome alignment, and Cufflinks (Trapnell et al., 2012) for differential expression analysis.
Genome_build: not provided
Supplementary_files_format_and_content: Supplemental_Table2_transc_cei.xlsx

organism: Arabidopsis thaliana

source_name: Root tip

extract_protocol:
RNA was extracted using the Qiagen RNeasy Micro kit.
Libraries were prepared using the SMART-Seq v3 Ultra Low RNA Input Kit for Sequencing and the Low Library Prep Kit v1 from Clontech.

value: Root tip

tag: genotype/variation

tag: gfp

value: positive


title: GFP positive cells pWOX5:erGFP - Replicate 2


title: GFP positive cells pWOX5:erGFP - Replicate 3


title: Leaf bulk RNA seq- Library 1

city: Düsseldorf

first: Jiyun

last: Kim

address: Universitätsstr. 1

department: Biology

country: Germany

institute: HHU

description:
Leaf bulk RNA seq- Replicate 1
L1

data_processing:
Paired-end reads (150 bp) were aligned to the Arabidopsis thaliana reference genome (Araport11) using STAR  (maximum intron length of 2 kbp).
Genome_build: Arabidopsis thaliana reference genome (Araport11)
Supplementary_files_format_and_content: deseq_genes_raw_counts.txt, DESeq_200628_sum_overlap.txt

source_name: Leaf

growth_protocol: Col-0 plants were grown under short-day (8 h light / 16 h dark) conditions at a PAR of 60 µmol m-2 s-1, 6 weeks.

extract_protocol:
Seven to nine abaxial epidermis-peeled and cut leaves attached to time tape were immediately immersed in the petri dish containing 15 mL freshly prepared protoplast isolation solution (1% Cellulase Onuzuka R-10 (Duchefa, Haarlem), 0.3% macerozyme R-10 (Duchefa, Haarlem), 0.6 M Mannitol, 20 mM MES pH 5.7, 20 mM KCL, 1 mM DTT, 10 mM CaCl2, and 0.1 % BSA). Dithiothreitol (DTT) and bovine serum albumin (BSA) were added to the enzyme solution to protect the protoplasts. Leaves were shaken at 30 rpm on a platform shaker for 2 hours. After confirming the release of the protoplasts into the solution, 10 mL of wash buffer (0.6 M Mannitol, 20 mM MES pH 5.7, 20 mM KCl, 1 mM DTT, 10 mM CaCl2, and 0.1 % BSA) was slowly added to the petri dish containing the protoplasts. The solution was filtered into a round bottom 20 mL tube using a 70 um pore size filter (Corning, New York). The protoplast solution was centrifuged at 100 x g for 3 min in a swinging rotor. The protoplasts were washed four times with 20 mL washing buffer. After the final wash step, protoplasts were slowly resuspended in 1 mL wash buffer and gently filtered twice using a 40 um Flowmi cell strainer (Bel-Art SP Scienceware, New Jersey). Total RNA was extracted from leaves (not protoplasted) and leaf protoplasts isolated.
For mRNA poly-A enrichment, 5 ug of total RNA was purified using the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Massachusetts). Libraries were constructed using the ULTRA II directional library kit (New England Biolab, Massachusetts), and size selection was done using SPRI beads (New England Biolab, Massachusetts) following the manufacturer manual with the following exceptions: 7 min of fragmentation time and 26.5 and 10 uL SPRI beads pre-PCR were used to enrich ~400 bp inserts. Library amplification included 10 PCR cycles, and 0.7 volumes of (35 uL) of SPRI beads were used for post-PCR purification. QC-tested libraries (Agilent Technologies, California) were sequenced on an Illumina HiSeq 2500 lane with 150 bp paired-end.

treatment_protocol: The adaxial side of the fully developed leaves was stabilized by placing on the time tape, and the abaxial side was adhered to the 3M Magic tape. The abaxial epidermis was removed by pulling off the 3 M Magic tape. Two cuts were made on each side of the major vein of the peeled leaves using a razor blade (Swann-Morton, Sheffield).

tag: ecotype

tag: genotype

value: Wild type

value: Leaf

tag: growth condition

value: Grown under SD conditions


title: Leaf protoplast bulk RNA seq- Library 1

description:
Leaf protoplast bulk RNA seq- Replicate 1
P1

source_name: Leaf protoplast

value: Leaf protoplast


title: Leaf bulk RNA seq- Library 2

description:
Leaf bulk RNA seq- Replicate 2
L2


title: GFP positive cells pWOX5:erGFP - Replicate 4


title: Leaf protoplast bulk RNA seq- Library 2

description:
Leaf protoplast bulk RNA seq- Replicate 2
P2


title: X102697.001.028

description:
EAC.51.txt
GAGATTCC-TCAGAGCC


title: GFP negative cells pWOX5:erGFP - Replicate 4

description:
Named W5NS in processed file
Supplemental_Table2_transc_cei.xlsx

value: negative


title: Col - meristematic root tissue - Replicate 3

description:
Named Col in processed file
Supplemental_Table9_transc_an3.xlsx

data_processing:
Gene expression analysis of raw RNA-seq data was performed using the TuxNet interface (Spurney et al., 2019).
TuxNet uses ea-utils fastq-mcf (Aronesty, 2011, Aronesty, 2013) for preprocessing, hisat2 (Kim et al., 2015) for genome alignment, and Cufflinks (Trapnell et al., 2012) for differential expression analysis.
Genome_build: not provided
Supplementary_files_format_and_content: Supplemental_Table9_transc_an3.xlsx

extract_protocol:
RNA was extracted using the Qiagen RNeasy Micro kit.
Libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs).

value: WT


title: GFP negative cells pWOX5:erGFP - Replicate 2


title: Col - meristematic root tissue - Replicate 2


title: an3 - meristematic root tissue - Replicate 3

description:
Named an3 in processed file
Supplemental_Table9_transc_an3.xlsx


title: GFP negative cells pWOX5:erGFP - Replicate 3


title: GFP positive cells wox5 x pCYCD6:GUS-GFP (CEI marker) - Replicate 2

description:
Named w5C6 in processed file
Supplemental_Table2_transc_cei.xlsx

value: wox5 x pCYCD6:GUS-GFP (CEI marker)


title: GFP negative cells pWOX5:erGFP - Replicate 1


title: GFP positive cells wox5 x pCYCD6:GUS-GFP (CEI marker) - Replicate 3


title: GFP positive cells wox5 x pCYCD6:GUS-GFP (CEI marker) - Replicate 1


title: Col - meristematic root tissue - Replicate 1


title: GFP positive cells pCYCD6:GUS-GFP (CEI marker) - Replicate 1

description:
Named C6 in processed file
Supplemental_Table2_transc_cei.xlsx

value: pCYCD6:GUS-GFP (CEI marker)


title: an3 - meristematic root tissue - Replicate 2


title: GFP positive cells pCYCD6:GUS-GFP (CEI marker) - Replicate 2


title: GFP positive cells pCYCD6:GUS-GFP (CEI marker) - Replicate 3


title: an3 - meristematic root tissue - Replicate 1


title: GFP positive cells wox5 x pCYCD6:GUS-GFP (CEI marker) - Replicate 4


title: GFP positive cells pCYCD6:GUS-GFP (CEI marker) - Replicate 4


title: Listeria monocytogenes_48C_v 2.0_biological3_tech rep1

type: RNA

city: Dallas

first: Palmy

middle: R

last: Jesudhasan

state: TX

department: Microbiology

institute: University of Texas Southwestern Medical Center

description: The slide was pre-hybridized following the TIGR SOP # M007

hyb_protocol: The labeling mixtures were further purified using a QIAquick PCR purification kit (Qiagen). Equal amounts of labeled cDNA from the treatment and control were used to hybridize on L. monocytogenes genome microarrays [version 2 arrays developed by JCVI and provided by the Pathogen Functional Genome Resource Center (PFGRC) of the National Institutes of Health]. These arrays were 70 mer-oligo arrays with 6347 oligonucleotides each, with 4 replicate spots per oligonucleotides. The labeled cDNA was applied to the above arrays. Hybridization was carried out overnight at 42°C in a water bath using Corning hybridization chamber. The pre-and post-hybridization was carried out using the the TIGR SOP #M008.

scan_protocol: The slides was washed and scanned using a GenePix 4100A scanner (Axon Instruments Inc., Union City, CA) at 532 nm (Cy3 channel) and 635 nm (Cy5 channel), and the image was stored for further analysis.

data_processing: The signal intensity of each gene was globally normalized using LOWESS within the R statistics package. (Normalizationfunctions.RData and R.2.5.1).

organism: Listeria monocytogenes

source_name: Listeria monocytogenes

label_protocol: Total RNA (10 µg) was used to synthesize cDNA using a random primer for reverse transcription (Invitrogen Life Technologies, Carlsbad, CA). The primer was annealed at 70°C for 10 min, followed by snap-freezing in a dry ice-ethanol bath for 30 s and centrifugation for 1 min. The reaction mixture (Superscript III buffer, 0.1 M dithiothreitol, and aminoallyl-deoxyuridine triphosphate mix) was then incubated overnight with Superscript III reverse transcriptase (Invitrogen) at 42°C. Residual RNA was removed by alkaline treatment followed by neutralization, and the cDNA was purified with a QIAquick PCR purification kit (Qiagen). Purified cDNAs from the mutant was labeled with Cy-5 mono-Reactive Dye (GE Health Care).

growth_protocol: Overnight cultures of L. monocytogenes were inoculated in fresh LB broth and the strain was incubated at 37°C with agitation at 100 rpm until OD600 0.5 (~ 108 CFU/mL) was reached. At this point, aliquots were placed into multiple 1.5 mL microfuge tubes for the different heat treatments. Heat treatments were performed in a calibrated water-bath (BOEKEL Grant ORS200, PA, USA) using temperature probes that facilitated temperature monitoring within the sample contained in the microfuge tubes.

extract_protocol: The total RNA was isolated from the samples using an RNeasy™ midi kit (Qiagen, Valencia, CA) according to the manufacturer's protocol. RNAprotect™ bacteria reagent (Qiagen) was added to the cultures to stabilize RNA before the isolation. The RNase-free DNase set (Qiagen) was used for on-column DNA digestion to remove residual genomic DNA. The quantity and quality of RNA was examined using the NanoDrop (ND-1000) spectrophotometer (NanoDrop® Technologies, Palo Alto, CA), and the Bioanalyzer 2100™ (Agilent Technologies, Santa Clara, CA), respectively.

treatment_protocol: Overnight cultures of L. monocytogenes were inoculated in fresh LB broth and the strain was incubated at 37°C with agitation at 100 rpm until OD600 0.5 (~ 108 CFU/mL) was reached (control).

tag: strain

tag: treatment group

value: control

treatment_protocol: Cells were incubated at 48°C for 30 minutes to induce thermo-tolerance.

value: thermo-tolerance


title: Listeria monocytogenes_48C_v 2.0_biological1_tech rep2


title: root of OsPI1 knockdown rice grown under phosphorus sufficiency, replication 2.

city: Higashi-Hiroshima

first: Jun

last: Wasaki

state: Hiroshima

address: Kagamiyama 1-7-1

department: Graduate School of Biosphere Science

country: Japan

institute: Hiroshima University

description:
Keyword = rice
Keyword = Phosphorus deficiency response
Keyword = knockdown line of OsPI1 (Oryza sativa Phosphate-limitation Inducible gene 1)

hyb_protocol: Standard protocol of In Situ Hybridization Kit Plus from Agilent Technologies.

scan_protocol: Standard protocol of Agilent DNA Microarray Scanner

data_processing: Feature Extraction software Version 8.5.1.1 from Agilent Technologies

organism: Oryza sativa

source_name: Root of ospi1-2 (OsPI1 knockdown line), replication 2

label_protocol: Standard Protocol of Agilent Low RNA Input Linear Amplification Kit

growth_protocol: Plants were grown in nutrient solutions with phosphorus. Root samples were harvested 9 d after the treatment.

extract_protocol: Plant RNA Isolation Mini Kit (Agilent Technologies) was used according to manufacturers protocol.

treatment_protocol: Phosphorus sufficiency (1 ppm)

tag: Root samples from ospi1-2 plants grown under phosphorus sufficiency.

source_name: Root of wild type (cv. Kitaake), replication 2

tag: Root samples from control plants grown under phosphorus sufficiency.


title: Listeria monocytogenes_48C_v 2.0_biological1_tech rep1


title: Listeria monocytogenes_48C_v 2.0_biological2_tech rep2


title: root of OsPI1 knockdown rice grown under phosphorus deficiency, replication 1.

source_name: Root of wild type (cv. Kitaake), replication 1

growth_protocol: Plants were grown in nutrient solutions without phosphorus. Root samples were harvested 9 d after the treatment.

treatment_protocol: Phosphorus deficiency (0 ppm)

tag: Root samples from control plants grown under phosphorus deficiency.

source_name: Root of ospi1-2 (OsPI1 knockdown line), replication 1

tag: Root samples from ospi1-2 plants grown under phosphorus deficiency.


title: shoot of OsPI1 knockdown rice grown under phosphorus sufficiency, replication 2.

source_name: Shoot of ospi1-2 (OsPI1 knockdown line), replication 2

growth_protocol: Plants were grown in nutrient solutions with phosphorus. Shoot samples were harvested 9 d after the treatment.

tag: Shoot samples from ospi1-2 plants grown under phosphorus sufficiency.

source_name: Shoot of wild type (cv. Kitaake), replication 2

tag: Shoot samples from control plants grown under phosphorus sufficiency.


title: Listeria monocytogenes_48C_v 2.0_biological2_tech rep1


title: Listeria monocytogenes_60C_9 min_v 2.0_biological1_tech rep1

data_processing: The signal intensity of each gene was globally normalized using LOWESS within the R  (Version R.2.5.1) statistics package.

label_protocol: Total RNA (10 µg) was used to synthesize cDNA using a random primer for reverse transcription (Invitrogen Life Technologies, Carlsbad, CA). The primer was annealed at 70°C for 10 min, followed by snap-freezing in a dry ice-ethanol bath for 30 s and centrifugation for 1 min. The reaction mixture (Superscript III buffer, 0.1 M dithiothreitol, and aminoallyl-deoxyuridine triphosphate mix) was then incubated overnight with Superscript III reverse transcriptase (Invitrogen) at 42°C. Residual RNA was removed by alkaline treatment followed by neutralization, and the cDNA was purified with a QIAquick PCR purification kit (Qiagen). Purified cDNAs was labeled with  mono-Reactive Cy Dye (GE Health Care).

extract_protocol: The total RNA was isolated from the samples using an RNeasyâ„¢ midi kit (Qiagen, Valencia, CA) according to the manufacturer's protocol. RNAprotectâ„¢ bacteria reagent (Qiagen) was added to the cultures to stabilize RNA before the isolation. The RNase-free DNase set (Qiagen) was used for on-column DNA digestion to remove residual genomic DNA. The quantity and quality of RNA was examined using the NanoDrop (ND-1000) spectrophotometer (NanoDropÂ® Technologies, Palo Alto, CA), and the Bioanalyzer 2100â„¢ (Agilent Technologies, Santa Clara, CA), respectively.

treatment_protocol: Cells were treated to a prolonged heat shock at 60 degrees C for 9 min

tag: treatment

value: 60 degrees C for 9 min

growth_protocol: Overnight cultures of L. monocytogenes were inoculated in fresh LB broth and the strain was incubated at 37Â°C with agitation at 100 rpm until OD600 0.5 (~ 108 CFU/mL) was reached. At this point, aliquots were placed into multiple 1.5 mL microfuge tubes for the different heat treatments. Heat treatments were performed in a calibrated water-bath (BOEKEL Grant ORS200, PA, USA) using temperature probes that facilitated temperature monitoring within the sample contained in the microfuge tubes.

treatment_protocol: Overnight cultures of L. monocytogenes were inoculated in fresh LB broth and the strain was incubated at 37 degrees C with agitation at 100 rpm until OD600 0.5 (~ 108 CFU/mL) was reached (control).

value: 37 degree control


title: Listeria monocytogenes_60C_9 min_v 2.0_biological2_tech rep2

treatment_protocol: Cells were treated to a prolonged heat shock at 60°C for 9 min.


title: shoot of OsPI1 knockdown rice grown under phosphorus sufficiency, replication 1.

source_name: Shoot of wild type (cv. Kitaake), replication 1

source_name: Shoot of ospi1-2 (OsPI1 knockdown line), replication 1


title: Listeria monocytogenes_60C_9 min_v 2.0_biological3_tech rep1


title: shoot of OsPI1 knockdown rice grown under phosphorus deficiency, replication 1.

growth_protocol: Plants were grown in nutrient solutions without phosphorus. Shoot samples were harvested 9 d after the treatment.

tag: Shoot samples from control plants grown under phosphorus deficiency.

tag: Shoot samples from ospi1-2 plants grown under phosphorus deficiency.


title: Listeria monocytogenes_60C_9 min_v 2.0_biological1_tech rep2


title: shoot of OsPI1 knockdown rice grown under phosphorus deficiency, replication 2.


title: Listeria monocytogenes_60C_9 min_v 2.0_biological2_tech rep1

treatment_protocol: Cells were treated to a prolonged heat shock at 60 degrees C for 9 min.


title: lymphoma 7050, ADR, rep1

city: Berlin

first: Maja

last: Milanovic

address: Augustenburgerplatz 1

department: Hematology and Oncology

institute: Charite University Medicine, Berlin

description:
7050 ADR
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
Reanalysis of GSM769986.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on MOE430 2.0 Arrays (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scanner G3000.

data_processing: Affymetrix CEL files were imported into Partek Genomics Suite Software (Version 6.5, Partek Inc., St. Louis, USA) and processed by the implemented RMA workflow (median polish probe set summarization, RMA background correction, quantile normalization).

label: biotin

organism: Mus musculus

source_name: primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice with palpable lymphadenopathy, Adriamycin treated

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (One Cycle Target labeling protocol) from 3 ug total RNA.

growth_protocol: Primary Emu-myc lymphoma cells were cultivated in B-cell medium (DMEM and IMDM in 1:1 ratio, 10%FBS, 4mM L-glutamine, 25µM beta-mercaptoethanol, 100U/ml penicilin/streptamycin) on gamma-irradiated (20Gy) NIH 3T3 cells as feeder.

extract_protocol: The total RNA from untreated or 5 days ADR-treated Myc;Bcl2 lymphomas was prepared using an RNeasy Mini kit (QIAGEN, Valencia, California) according to the manufacturer's instructions.

treatment_protocol: Freshly isolated lymphoma cells were retrovirally transduced by Bcl2 (MSCVpuro) and selected with Puromycin for 48h. These Myc;Bcl2 cells were either left untreated or treated in vitro with 0.05µg/ml Adriamycin for 5 days.

tag: strain/background

value: Emu-myc transgenic (Myc;Bcl2)

tag: cell type

value: primary lymphoma cells from lymph node

value: Adriamycin

tag: senescence induction

value: TIS

tag: lymphoma identifier


title: lymphoma 6054, ADR, rep1

description:
6054 ADR
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
Reanalysis of GSM769984.

tag: genotype


title: lymphoma 9584, untreated, rep1

description:
9584 untreated
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.

source_name: primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice with palpable lymphadenopathy, untreated

value: no


title: root of OsPI1 knockdown rice grown under phosphorus sufficiency, replication 1.


title: lymphoma 9584, ADR, rep1

description:
9584 ADR
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.


title: lymphoma 9583, ADR, rep1

description:
9583 ADR
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.


title: lymphoma 6054, untreated, rep1

description:
6054 untreated
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
Reanalysis of GSM769983.


title: lymphoma 7050, untreated, rep1

description:
7050 untreated
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
Reanalysis of GSM769985.


title: lymphoma 5766, untreated, rep1

description:
5766 untreated
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
Reanalysis of GSM769981.


title: lymphoma 9583, untreated, rep1

description:
9583 untreated
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.


title: root of OsPI1 knockdown rice grown under phosphorus deficiency, replication 2.


title: lymphoma 5560, untreated, rep1

description:
5560 untreated
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
Reanalysis of GSM769979.


title: lymphoma 5766, ADR, rep1

description:
5766 ADR
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
Reanalysis of GSM769982.


title: lymphoma 403, untreated, rep1

description:
403 untreated
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
Reanalysis of GSM769987.


title: lymphoma 5043, ADR, rep1

description:
5043 ADR
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.


title: VIS-EPA-9

city: Lubbock

first: Naima

last: Moustaid-Moussa

address: 1301 Human Sciences, Rm 402

department: Department of Nutritional Sciences

institute: Texas Tech University

data_processing:
Illumina small RNA adapter sequences were trimmed from the reads, and reads of length below 10nt or ending in homopolymers of length 9 nt or above were discarded.
Total usable number of reads for each sample was calculated.
The reads were mapped to the miRBase reference using BLAST; the abundance of each expressed microRNA was quantified as a fraction of the usable reads, and expressed as parts per million.
Genome_build: mm10
Supplementary_files_format_and_content: TAB-delimited text format, containing quantile normalized microRNA abundance

source_name: Visceral Adipose Tissue (VAT6: VIS-EPA-9)

extract_protocol:
At the end of 11 week feeding period, the mice were fasted for 4 hours and then euthanized by CO2 inhalation. Epidedimal (VAT), inguinal (SAT) and interscapular (BAT) adipose tissues were harvested, and snap frozen immediately in liquid N2, followed by storage at -80°C. Frozen adipose tissue samples (SAT, BAT, and VAT- 3 samples per group) were homogenized in QIAzol® (QIAGEN, Redwood City, CA).  Total RNA was isolated according to manufacturer’s protocol using RNeasy Mini Kit.
Small RNA libraries were prepared using the Illumina small RNA protocol (Illumina, Inc., San Diego, CA)

treatment_protocol: C57BL/6J mice aged 5-6 week were fed on a high fat diet which consisted of 45%, 20% and 35% of energy from fat, protein and carbohydrate respectively for 11 weeks.

tag: tissue

value: Visceral adipose


title: VIS-EPA-1

source_name: Visceral Adipose Tissue (VAT4: VIS-EPA-1)

tag: strain


title: VIS-EPA-3

source_name: Visceral Adipose Tissue (VAT5: VIS-EPA-3)


title: lymphoma 3769, ADR, rep1

description:
3769 ADR
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
Reanalysis of GSM769976.


title: lymphoma 5560, ADR, rep1

description:
5560 ADR
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
Reanalysis of GSM769980.


title: lymphoma 3594, untreated, rep1

description:
3594 untreated
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
Reanalysis of GSM769973.


title: lymphoma 5043, untreated, rep1

description:
5043 untreated
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.


title: lymphoma 2949, untreated, rep1

description:
2949 untreated
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
Reanalysis of GSM769971.


title: lymphoma 3769, untreated, rep1

description:
3769 untreated
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
Reanalysis of GSM769975.


title: lymphoma 3594, ADR, rep1

description:
3594 ADR
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
Reanalysis of GSM769974.


title: lymphoma 2581, ADR, rep1

description:
2581 ADR
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
Reanalysis of GSM769970.


title: lymphoma 2949, ADR, rep1

description:
2949 ADR
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
Reanalysis of GSM769972.


title: lymphoma 1570, untreated, rep1

description:
1570 untreated
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
Reanalysis of GSM769967.


title: lymphoma 1570, ADR, rep1

description:
1570 ADR
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
Reanalysis of GSM769968.


title: lymphoma 2581, untreated, rep1

description:
2581 untreated
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
Reanalysis of GSM769969.


title: lymphoma 1467, untreated, rep1

description:
1467 untreated
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
Reanalysis of GSM769965.


title: Mutant113A1

city: isehara

first: Akira

last: Oka

state: Kanagawa

address: 143 Shimokasuya

institute: Tokai university

description: Gene expression of normal skin

hyb_protocol: 600 ng of Cy3-labelled cRNA were hybridized using Gene Expression Hybridization Kit according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner ( G2600D SG13164306) using one color scan setting for 8x60k array slides using scan protocol AgilentG3_HiSen_GX_1Color.

data_processing: The scanned images were analyzed with Feature Extraction Software11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 028005_D_F_20110614) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Skin

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the LowInput QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop.

extract_protocol: Total RNA was isolated from sections of mouse skin using ISOGEN (Nippon Gene, Tokyo, Japan) in accordance with the manufacturer protocol and was treated twice with TURBO DNase (Ambion) to eliminate contaminating DNA. RNA was quantified using a NanoDrop 2000 (Thermo Fisher Scientific) and the quality of the extracted RNA was evaluated using a Bioanalyzer 2100 (Agilent Technologies).

value: Cchcr1 mutant

tag: hair phenotype

value: normal skin

value: skin


title: Mutant113B1

description: Gene expression of normal skin


title: Mutant097B1

description: Gene expression of normal skin


title: Mutant113S1

description: Gene expression of hair loss

value: hair loss


title: lymphoma 403, ADR, rep1

description:
403 ADR
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
Reanalysis of GSM769988.


title: Wild001B1

description: Gene expression of normal skin

value: Wild type


title: Wild001A1

description: Gene expression of normal skin


title: Mutant097A1

description: Gene expression of normal skin


title: lymphoma 1467, ADR, rep1

description:
1467 ADR
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
Reanalysis of GSM769966.


title: AFB1 72h 1

city: Kuopio

first: Markus

last: Storvik

address: University of Eastern Finland

department: Pharmacology

country: Finland

institute: University of Eastern Finland

description:
replicate 1
SAMPLE 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data between chips were normalised using to same distribution with Chipster

source_name: Primary cells

label_protocol: According to Illumina protocol

growth_protocol: The extraction of total RNA from human primary trophoblast was previously described in Huuskonen et al. (2016).

extract_protocol: The isolation and culture of primary placental trophoblast cells was conducted according to Petroff et al. (2006) with minor changes previously described by El Dairi et al. (2018)

treatment_protocol: Primary trophoblasts were treated with 1 µM AFB1 for 72 hours and the control was 0.25% DMSO

value: Trophoblast cells

value: AFB1 72h


title: AFB1 72h 3 rep 2

description:
replicate 2
SAMPLE 8


title: Control 2

description:
replicate 1
SAMPLE 3

value: control


title: AFB1 72h 3 rep 1

description:
replicate 1
SAMPLE 7


title: AFB1 72h 2

description:
replicate 1
SAMPLE 6


title: Notch3-/-_healthy_1

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: wild type UUO day 5 versus wild type healthy

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: kidney

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using Quiagen RNAeasy Kit.

treatment_protocol: Kidneys were collected and mechanical homogenized in TRIzol reagent and RNA was extracted using Quiagen RNAeasy Kit.

tag: genetic bkg


title: Control 1 rep2

description:
replicate 2
SAMPLE 2


title: Mutant097S1

description: Gene expression of hair loss


title: Notch3-/-_healthy_2


title: Control 3

description:
replicate 1
SAMPLE 4


title: wild_type_UUO_day_5_1

description: Notch3-/- UUO day 5 versus wild type UUO day 5

value: wild type


title: Notch3-/-_UUO_day_5_2


title: RNAseq_82494

city: Boston

first: Peter

last: Castaldi

state: Massachusetts

address: 181 Longwood Ave

institute: Brigham and Women's Hospital

description:
gene_TMM_counts.csv
exon_TMM_counts.csv
isoform_TMM_counts.csv

data_processing:
alignment: STAR, 2-pass
gene quantification: Salmon v0.12.0 and tximport
exon quantification: Rsubread v1.32.2
isoform quantification: Salmon v0.12.0
Genome_build: HG38 (GTF: Ensembl Homo_sapiens.GRCh38.94.gtf.gz)
Supplementary_files_format_and_content: count matrices

source_name: blood

extract_protocol:
Total RNA was extracted from PAXgene TM Blood RNA tubes using the Qiagen PreAnalytiX PAXgene Blood miRNA Kit (Qiagen, Valencia, CA).
Globin reduction and cDNA library preparation for total RNA was performed with the Illumina TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina, Inc., San Diego, CA).

tag: batch

tag: current smoker

tag: pack years

tag: age

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: RNAseq_72455


title: RNAseq_27582


title: RNAseq_31698


title: RNAseq_80550


title: RNAseq_75400


title: RNAseq_43691


title: RNAseq_79039


title: RNAseq_33481


title: RNAseq_19471


title: RNAseq_24420


title: Control 1 rep1

description:
replicate 1
SAMPLE 1

tag: cell type

tag: treatment


title: Notch3-/-_UUO_day_5_1


title: wild_type_UUO_day_5_2


title: Notch3-/-_UUO_day_5_3


title: wild_type_healthy_1


title: wild_type_healthy_2


title: RNAseq_61888


title: RNAseq_08852


title: RNAseq_39773


title: RNAseq_63111


title: RNAseq_70744


title: RNAseq_60652


title: RNAseq_04952


title: RNAseq_23192


title: RNAseq_92304


title: RNAseq_63979


title: RNAseq_03597


title: RNAseq_31014


title: RNAseq_22952


title: RNAseq_79842


title: RNAseq_20451


title: RNAseq_99528


title: RNAseq_67843


title: RNAseq_67896


title: RNAseq_53694


title: RNAseq_91069


title: RNAseq_89135


title: RNAseq_83405


title: RNAseq_70426


title: RNAseq_04670


title: RNAseq_18055


title: RNAseq_15261


title: RNAseq_34275


title: RNAseq_64556


title: RNAseq_83627


title: RNAseq_21974


title: RNAseq_76914


title: RNAseq_62968


title: RNAseq_71948


title: RNAseq_42321


title: RNAseq_08425


title: RNAseq_00792


title: RNAseq_54492


title: RNAseq_98746


title: RNAseq_38679


title: RNAseq_05693


title: RNAseq_42425


title: RNAseq_01869


title: RNAseq_69787


title: RNAseq_72497


title: RNAseq_94438


title: RNAseq_64376


title: RNAseq_93188


title: RNAseq_97194


title: RNAseq_69314


title: RNAseq_44853


title: RNAseq_59932


title: RNAseq_62648


title: RNAseq_70258


title: RNAseq_39032


title: RNAseq_97215


title: RNAseq_24380


title: RNAseq_85008


title: RNAseq_19586


title: RNAseq_04490


title: RNAseq_40510


title: RNAseq_21285


title: RNAseq_83164


title: RNAseq_06051


title: RNAseq_89375


title: RNAseq_14584


title: RNAseq_30192


title: RNAseq_55504


title: RNAseq_64161


title: RNAseq_21063


title: RNAseq_37504


title: RNAseq_03644


title: RNAseq_30283


title: RNAseq_09002


title: RNAseq_98545


title: RNAseq_21807


title: RNAseq_66007


title: RNAseq_43969


title: RNAseq_24647


title: RNAseq_17228


title: RNAseq_46109


title: RNAseq_18060


title: RNAseq_11803


title: RNAseq_19278


title: RNAseq_63617


title: RNAseq_52462


title: RNAseq_26244


title: RNAseq_72995


title: RNAseq_59843


title: RNAseq_11325


title: RNAseq_14735


title: RNAseq_05818


title: RNAseq_50907


title: RNAseq_90524


title: RNAseq_40565


title: RNAseq_70055


title: RNAseq_43811


title: RNAseq_86891


title: RNAseq_29264


title: RNAseq_13943


title: RNAseq_61486


title: RNAseq_88403


title: RNAseq_13776


title: RNAseq_48266


title: RNAseq_93969


title: RNAseq_93457


title: RNAseq_88501


title: RNAseq_33413


title: RNAseq_90820


title: RNAseq_71618


title: RNAseq_87062


title: RNAseq_37175


title: RNAseq_56856


title: RNAseq_08398


title: RNAseq_99625


title: RNAseq_57876


title: RNAseq_51304


title: RNAseq_54580


title: RNAseq_12394


title: RNAseq_54779


title: RNAseq_60052


title: RNAseq_55199


title: RNAseq_13877


title: RNAseq_94269


title: RNAseq_84354


title: RNAseq_57395


title: RNAseq_73057


title: RNAseq_20926


title: RNAseq_54322


title: RNAseq_02470


title: RNAseq_56899


title: RNAseq_74067


title: RNAseq_95355


title: RNAseq_76019


title: RNAseq_52362


title: RNAseq_44594


title: RNAseq_17038


title: RNAseq_22554


title: RNAseq_96039


title: RNAseq_15235


title: RNAseq_74904


title: RNAseq_85291


title: RNAseq_75118


title: RNAseq_88561


title: RNAseq_47575


title: RNAseq_94159


title: RNAseq_38437


title: RNAseq_36978


title: RNAseq_54729


title: RNAseq_29729


title: RNAseq_83639


title: RNAseq_22956


title: RNAseq_16388


title: RNAseq_96776


title: RNAseq_72754


title: RNAseq_78590


title: RNAseq_51061


title: RNAseq_89055


title: RNAseq_74668


title: RNAseq_79978


title: RNAseq_79674


title: RNAseq_93265


title: RNAseq_31767


title: RNAseq_48100


title: RNAseq_24493


title: RNAseq_67650


title: RNAseq_69767


title: RNAseq_64955


title: RNAseq_26846


title: RNAseq_85401


title: RNAseq_10453


title: RNAseq_16968


title: RNAseq_69702


title: RNAseq_68013


title: RNAseq_42289


title: RNAseq_04771


title: RNAseq_84874


title: RNAseq_64452


title: RNAseq_63813


title: RNAseq_65465


title: RNAseq_07661


title: RNAseq_65047


title: RNAseq_43492


title: RNAseq_27916


title: RNAseq_14507


title: RNAseq_52852


title: RNAseq_49177


title: RNAseq_41312


title: RNAseq_79445


title: RNAseq_27273


title: RNAseq_52727


title: RNAseq_20962


title: RNAseq_12545


title: RNAseq_61447


title: RNAseq_94211


title: RNAseq_98277


title: RNAseq_73645


title: RNAseq_97881


title: RNAseq_16351


title: RNAseq_63441


title: RNAseq_86586


title: RNAseq_64866


title: RNAseq_69678


title: RNAseq_34286


title: RNAseq_43059


title: RNAseq_90325


title: RNAseq_62956


title: RNAseq_04415


title: RNAseq_83784


title: RNAseq_80293


title: RNAseq_87137


title: RNAseq_40507


title: RNAseq_91067


title: RNAseq_97001


title: RNAseq_46358


title: RNAseq_01932


title: RNAseq_21981


title: RNAseq_64912


title: RNAseq_82215


title: RNAseq_04877


title: RNAseq_29908


title: RNAseq_38536


title: RNAseq_64240


title: RNAseq_51150


title: RNAseq_39249


title: RNAseq_38831


title: RNAseq_62706


title: RNAseq_63760


title: RNAseq_18575


title: RNAseq_22640


title: RNAseq_13631


title: RNAseq_12502


title: RNAseq_31027


title: RNAseq_31446


title: RNAseq_79519


title: RNAseq_04812


title: RNAseq_66955


title: RNAseq_92816


title: RNAseq_18864


title: RNAseq_15322


title: RNAseq_30415


title: RNAseq_82258


title: RNAseq_51813


title: RNAseq_04098


title: RNAseq_41307


title: RNAseq_21602


title: RNAseq_94782


title: RNAseq_98433


title: RNAseq_05735


title: RNAseq_24240


title: RNAseq_54852


title: RNAseq_12717


title: RNAseq_04377


title: RNAseq_97399


title: RNAseq_72543


title: RNAseq_52800


title: RNAseq_63084


title: RNAseq_67475


title: RNAseq_75657


title: RNAseq_04774


title: RNAseq_52860


title: RNAseq_24983


title: RNAseq_40664


title: RNAseq_62764


title: RNAseq_53700


title: RNAseq_13563


title: RNAseq_41861


title: RNAseq_03782


title: RNAseq_60493


title: RNAseq_95861


title: RNAseq_75185


title: RNAseq_64892


title: RNAseq_96965


title: RNAseq_55459


title: RNAseq_44877


title: RNAseq_18631


title: RNAseq_33307


title: RNAseq_71427


title: RNAseq_21768


title: RNAseq_29573


title: RNAseq_02083


title: RNAseq_55421


title: RNAseq_72451


title: RNAseq_52582


title: RNAseq_50426


title: RNAseq_25709


title: RNAseq_97293


title: RNAseq_39881


title: RNAseq_51472


title: RNAseq_84732


title: RNAseq_18962


title: RNAseq_37664


title: RNAseq_99899


title: RNAseq_31949


title: RNAseq_81704


title: RNAseq_25379


title: RNAseq_15249


title: RNAseq_88533


title: RNAseq_10762


title: RNAseq_16193


title: RNAseq_24887


title: RNAseq_91030


title: RNAseq_96228


title: RNAseq_84889


title: RNAseq_51518


title: RNAseq_35413


title: RNAseq_58581


title: RNAseq_49838


title: RNAseq_86302


title: RNAseq_11946


title: RNAseq_81333


title: RNAseq_21426


title: RNAseq_36281


title: RNAseq_03586


title: RNAseq_79783


title: RNAseq_30190


title: RNAseq_63654


title: RNAseq_85814


title: RNAseq_23580


title: RNAseq_75332


title: RNAseq_26296


title: RNAseq_18735


title: RNAseq_58399


title: RNAseq_52602


title: RNAseq_76707


title: RNAseq_33403


title: RNAseq_54644


title: RNAseq_93614


title: RNAseq_82559


title: RNAseq_34063


title: RNAseq_89577


title: RNAseq_58414


title: RNAseq_99119


title: RNAseq_29077


title: RNAseq_19117


title: RNAseq_25181


title: RNAseq_78449


title: RNAseq_36236


title: RNAseq_58323


title: RNAseq_86722


title: RNAseq_29619


title: RNAseq_52009


title: RNAseq_58009


title: RNAseq_35708


title: RNAseq_84059


title: RNAseq_56873


title: RNAseq_47281


title: RNAseq_61455


title: RNAseq_70322


title: RNAseq_05642


title: RNAseq_06486


title: RNAseq_44100


title: RNAseq_62296


title: RNAseq_12973


title: RNAseq_37982


title: RNAseq_63405


title: RNAseq_68450


title: RNAseq_78884


title: RNAseq_88576


title: RNAseq_86353


title: RNAseq_96131


title: RNAseq_07401


title: RNAseq_83312


title: RNAseq_48884


title: RNAseq_60638


title: RNAseq_50606


title: RNAseq_62237


title: RNAseq_61761


title: RNAseq_43704


title: RNAseq_16743


title: RNAseq_31049


title: RNAseq_11641


title: RNAseq_81930


title: RNAseq_44586


title: RNAseq_02513


title: RNAseq_68114


title: RNAseq_24332


title: RNAseq_06180


title: RNAseq_37829


title: RNAseq_01363


title: RNAseq_12370


title: RNAseq_89410


title: RNAseq_96960


title: RNAseq_55844


title: RNAseq_03878


title: RNAseq_49972


title: RNAseq_11169


title: RNAseq_84445


title: RNAseq_69614


title: RNAseq_21500


title: RNAseq_97732


title: RNAseq_25995


title: RNAseq_83494


title: RNAseq_00325


title: RNAseq_93775


title: RNAseq_33003


title: RNAseq_77693


title: RNAseq_02380


title: RNAseq_51618


title: RNAseq_71537


title: RNAseq_20884


title: RNAseq_76582


title: RNAseq_39968


title: RNAseq_86663


title: RNAseq_50652


title: RNAseq_93138


title: RNAseq_40641


title: RNAseq_92868


title: RNAseq_69766


title: RNAseq_80812


title: RNAseq_93860


title: RNAseq_70561


title: RNAseq_62948


title: RNAseq_22679


title: RNAseq_58540


title: RNAseq_95874


title: RNAseq_83208


title: RNAseq_26761


title: RNAseq_38345


title: RNAseq_22219


title: RNAseq_75730


title: RNAseq_20092


title: RNAseq_52661


title: RNAseq_02756


title: RNAseq_68340


title: RNAseq_51193


title: RNAseq_87155


title: RNAseq_47910


title: RNAseq_47913


title: RNAseq_55540


title: RNAseq_53586


title: RNAseq_41497


title: RNAseq_68733


title: RNAseq_70695


title: RNAseq_40947


title: RNAseq_38110


title: RNAseq_25431


title: RNAseq_86005


title: RNAseq_17860


title: RNAseq_90942


title: RNAseq_14203


title: RNAseq_63718


title: RNAseq_64238


title: RNAseq_91560


title: RNAseq_62494


title: RNAseq_83538


title: RNAseq_88625


title: RNAseq_79838


title: RNAseq_60504


title: RNAseq_13268


title: RNAseq_59807


title: RNAseq_59566


title: RNAseq_40646


title: RNAseq_88256


title: RNAseq_35890


title: RNAseq_28747


title: RNAseq_41871


title: RNAseq_86131


title: RNAseq_13804


title: RNAseq_17889


title: RNAseq_69073


title: RNAseq_87041


title: RNAseq_07662


title: RNAseq_94877


title: RNAseq_15679


title: RNAseq_02287


title: RNAseq_38368


title: RNAseq_54758


title: RNAseq_29877


title: RNAseq_03550


title: RNAseq_55666


title: RNAseq_58143


title: RNAseq_56565


title: RNAseq_15586


title: RNAseq_22481


title: RNAseq_46451


title: RNAseq_03401


title: RNAseq_55155


title: RNAseq_02226


title: RNAseq_17620


title: RNAseq_23250


title: RNAseq_14480


title: RNAseq_70857


title: RNAseq_93146


title: RNAseq_90490


title: RNAseq_24990


title: RNAseq_18085


title: RNAseq_72133


title: RNAseq_16205


title: RNAseq_12421


title: RNAseq_29207


title: RNAseq_63100


title: RNAseq_63208


title: RNAseq_85457


title: RNAseq_64209


title: RNAseq_74058


title: RNAseq_27656


title: RNAseq_75925


title: RNAseq_78056


title: RNAseq_90921


title: RNAseq_06218


title: RNAseq_30254


title: RNAseq_00849


title: RNAseq_76595


title: RNAseq_04404


title: RNAseq_86397


title: RNAseq_45351


title: RNAseq_32241


title: RNAseq_80329


title: RNAseq_91759


title: RNAseq_94898


title: RNAseq_74087


title: control_gDNA rep2

first: Sabrina

last: Jenull

address: Dr. Bohrgasse 9/2

institute: Max Perutz Labs

description:
gDNA from WT replicate2
processed data file:
used as background control during peak calling

library_source: genomic

data_processing:
Quality control of raw reads with fastQC (AndrewsS, 2010)
Reads were trimmed via cutadapt with a quality score threshold of 30.
Reads were mapped onto the Assembly 22 of the haploid C. albicans genome using NextGenMap (Sedlazeck, Bioinfromatics, 2013) with only keeping aligned reads with a mapping quality higher than 30.
Optical read duplicates were removed using the Picard tool and ribosomal RNA reads were removed with BEDtools intersect.
Reads per gene ID were counted using htseq count (AndersS, Bioinformatics, 2014) using the current C.albicans annotation file (.gff; C_albicans_SC5314_version_A22-s07-m01-r88; http://www.candidagenome.org) and used for differential gene analysis with edgeR (RobinsonMD, Bioinformatics, 2010). Peaks were annotated to the next downstream gene using the 'annotatePeak' function from the R ChIPseeker package (YuG, 2015, Bioinformatics).
Genome_build: Assembly 22
Supplementary_files_format_and_content: tab delimited .txt files containing the output of the htseq analysis (read counts) and Excel table (.xlsx) of the edgeR analysis result. Peaks were annotated to the next downstream gene.

molecule: genomic DNA

organism: Candida albicans

source_name: fungal cells

growth_protocol: Cells were either grown at YPD for approx. 16 hours at 30 °C with constant shaking (200 rpm) or washed 2 times with dH2O after overnight growth in YPD, re-inoculated in yeast carbon base (YCB) medium supplemented with 0.1 % BSA to a final OD600 of 0.5 and grown further for 4 hours (t4) or 8 hours (t8) at 30 °C with constant shaking (200 rpm). Cultures were then subjected to spheroplasting as described below.

extract_protocol:
Spheroplasts were generated by Zymolase treatment in Sorbitol buffer plus DTT for 5 minutes at 30 °C and then subjected to tagmentation by directly lysing the cell pellet in the tagmentation mix
Tagmented samples were subjected to ATAC-seq library prep based on the published protocol from the Greenleaf lab. Additionally, PCR-amplified libraires were purified with SPRI beads.

tag: growth condition

value: stationary phase cell

tag: strain background

tag: genotype

tag: sequenced molecule

value: genomic DNA


title: control_gDNA rep1

description:
gDNA from WT replicate1
processed data file:
used as background control during peak calling


title: RNAseq_13721

tag: batch

tag: current smoker


title: RNAseq_26001

tag: pack years

tag: age


title: RNAseq_65246

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: RNAseq_36259

tag: fev1 % predicted

tag: neutrophil percent


title: ATAC-seq_hir1_t8_2

description:
HIR1 KO t8 replicate2
processed data file:
raw_counts_all_samples.txt

value: YCB-BSA grown 8 hours

value: homozygous deletion of HIR1

value: chromatin


title: RNAseq_01592

tag: lymphocyte percent

tag: eosinophil percent


title: RNAseq_48921

tag: monocyte percent

tag: basophil percent


title: ATAC-seq_hir1_t8_1

description:
HIR1 KO t8 replicate1
processed data file:
raw_counts_all_samples.txt


title: RNAseq_84702


title: RNAseq_06640


title: ATAC-seq_wt_t8_3

description:
WT t8 replicate3
processed data file:
raw_counts_all_samples.txt


title: ATAC-seq_wt_t8_2

description:
WT t8 replicate2
processed data file:
raw_counts_all_samples.txt


title: RNAseq_07673


title: ATAC-seq_wt_t8_1

description:
WT t8 replicate1
processed data file:
raw_counts_all_samples.txt


title: RNAseq_29494


title: ATAC-seq_hir1_t4_3

description:
HIR1 KO t4 replicate3
processed data file:
raw_counts_all_samples.txt

value: YCB-BSA grown 4 hours


title: ATAC-seq_hir1_t4_2

description:
HIR1 KO t4 replicate2
processed data file:
raw_counts_all_samples.txt


title: ATAC-seq_wt_t4_3

description:
WT t4 replicate3
processed data file:
raw_counts_all_samples.txt


title: ATAC-seq_hir1_t4_1

description:
HIR1 KO t4 replicate1
processed data file:
raw_counts_all_samples.txt


title: ATAC-seq_wt_t4_2

description:
WT t4 replicate2
processed data file:
raw_counts_all_samples.txt


title: RNAseq_09990


title: ATAC-seq_hir1_t8_3

description:
HIR1 KO t8 replicate3
processed data file:
raw_counts_all_samples.txt


title: ATAC-seq_wt_t4_1

description:
WT t4 replicate1
processed data file:
raw_counts_all_samples.txt


title: RNAseq_04736


title: RNAseq_69340


title: RNAseq_45628


title: ATAC-seq_hir1_t0_1

description:
HIR1 KO t0 replicate1
processed data file:
raw_counts_all_samples.txt

value: YPD grown overnight


title: RNAseq_45232


title: ATAC-seq_hir1_t0_2

description:
HIR1 KO t0 replicate2
processed data file:
raw_counts_all_samples.txt


title: ATAC-seq_wt_t0_3

description:
WT t0 replicate3
processed data file:
raw_counts_all_samples.txt


title: ATAC-seq_hir1_t0_3

description:
HIR1 KO t0 replicate3
processed data file:
raw_counts_all_samples.txt


title: RNAseq_18968

description:
gene_TMM_counts.csv
exon_TMM_counts.csv
isoform_TMM_counts.csv


title: ATAC-seq_wt_t0_1

description:
WT t0 replicate1
processed data file:
raw_counts_all_samples.txt


title: RNAseq_64695


title: RNAseq_84369


title: RNAseq_13223


title: RNAseq_86406


title: RNAseq_37586


title: RNAseq_33463


title: RNAseq_30009


title: ICH_rep9

city: Cincinnati

first: Xiang

last: Zhang

state: OH

address: 160 Panzeca Way, Kettering Room 336

department: Environmental and Public Health Sciences

institute: University of Cincinnati

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq
using FASTQC, Phred scores and GC content were observed on a per base and per sequence level to trim reads accordingly
alignment and feature quantification steps were implemented with a modified QuickMIRSeq pipeline
sequence information was retrieved from Ensemble (release 99) and known mature miRNA from miRBase
index libraries were constructed for alignment with Bowtie and miRNA quantification was computed within QuickMIRSeq
Genome_build: Sscrofa11.1
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: matrix table including miRNA counts for every miRNA and every sample
Supplementary_files_format_and_content: Hsapiens.miR.Counts.csv:Raw counts - Human alignment
Supplementary_files_format_and_content: Hsapiens.miR.filter.Counts.csv:Filtered raw counts - Human alignment
Supplementary_files_format_and_content: Hsapiens.miR.filter.RPM.csv:Reads-per-million counts - Human alignment
Supplementary_files_format_and_content: Sscrofa.miR.Counts.csv:Raw counts - Swine alignment
Supplementary_files_format_and_content: Sscrofa.miR.filter.Counts.csv:Filtered raw counts - Swine alignment
Supplementary_files_format_and_content: Sscrofa.miR.filter.RPM.csv:Reads-per-million counts - Swine alignment

organism: Sus scrofa

source_name: PBMC

growth_protocol: Domestic pigs of the American Yorkshire breed, 80 to 90 days old and 36 to 41 kilograms.

extract_protocol:
PBMCs were separated from the whole blood by a density gradient centrifugation method; Total RNA was extracted using mirVana miRNA isolation kit (Thermo Fisher); miRNA library was constrcted using NEBNext Multiplex Small RNA Library Prep kit (cat. # E7560S) with 500 ng total RNA as input.
miRNA libraries were prepared for sequencing using modified NEB protocol.

treatment_protocol: To induce ICH, a single burr hole craniotomy was performed to pass an angiocatheter and to inject two to four milliliters of autologous blood under pressure control into the frontal white matter.

tag: sample collection

value: 6 hrs after ICH induction

tag: breed

value: American Yorkshire

tag: treatment

value: ICH

tag: weight

tag: Sex

value: female


title: ICH_rep10


title: Control_rep9

value: Prior to ICH induction

value: untreated


title: Control_rep10


title: RNAseq_89946

tag: batch


title: ICH_rep8


title: Control_rep8


title: RNAseq_11005

tag: current smoker


title: ICH_rep7


title: RNAseq_83369

tag: pack years


title: RNAseq_77991

tag: age


title: ATAC-seq_wt_t0_2

description:
WT t0 replicate2
processed data file:
raw_counts_all_samples.txt

tag: growth condition

tag: strain background

tag: genotype

tag: sequenced molecule


title: RNAseq_37530

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent


title: RNAseq_97675

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: Control_rep7

tag: sample collection

tag: breed

tag: treatment

tag: weight

tag: Sex


title: Control_rep6

tag: age


title: ICH_rep6


title: ICH_rep5


title: RNAseq_97005

tag: batch

tag: current smoker

tag: pack years


title: Control_rep5


title: RNAseq_00219

tag: gender (1=male, 2=female)


title: RNAseq_62614

tag: race (1=white, 2=black)


title: RNAseq_81393

tag: fev1 % predicted


title: RNAseq_13133

tag: neutrophil percent


title: ICH_rep3


title: RNAseq_01689

tag: lymphocyte percent


title: RNAseq_16365

tag: eosinophil percent


title: RNAseq_57821

tag: monocyte percent


title: ICH_rep2


title: Control_rep2


title: Control_rep4


title: RNAseq_05260

tag: basophil percent


title: ICH_rep1

tag: sample collection


title: Control_rep1

tag: breed


title: RNAseq_18905


title: RNAseq_68898


title: RNAseq_18560


title: RNAseq_34560


title: RNAseq_28337


title: RNAseq_88345


title: RNAseq_25809


title: ICH_rep4

tag: treatment


title: RNAseq_70880


title: RNAseq_85156


title: RNAseq_27973


title: RNAseq_78769


title: Control_rep3

tag: weight


title: RNAseq_91369


title: RNAseq_28620


title: RNAseq_30574


title: RNAseq_73734


title: RNAseq_41691


title: RNAseq_68672


title: RNAseq_87370


title: RNAseq_92938


title: RNAseq_79676


title: RNAseq_03248


title: RNAseq_96445


title: RNAseq_81614


title: RNAseq_43111


title: RNAseq_23492


title: RNAseq_82064


title: RNAseq_62171


title: RNAseq_13067


title: RNAseq_54391


title: RNAseq_95699


title: RNAseq_34003


title: RNAseq_53185


title: RNAseq_87874


title: RNAseq_84199


title: RNAseq_08895


title: RNAseq_24120


title: RNAseq_63155


title: RNAseq_71684


title: RNAseq_79599


title: RNAseq_35789


title: RNAseq_10826


title: RNAseq_79908


title: RNAseq_47812


title: RNAseq_44445


title: RNAseq_32222


title: RNAseq_24220


title: RNAseq_92562


title: RNAseq_62191


title: RNAseq_34933


title: RNAseq_39726


title: RNAseq_81769


title: RNAseq_19210


title: RNAseq_26378


title: RNAseq_77577


title: RNAseq_98465


title: RNAseq_69734


title: RNAseq_21011


title: RNAseq_52403


title: RNAseq_03157


title: RNAseq_56917


title: RNAseq_74426


title: RNAseq_43052


title: RNAseq_72577


title: RNAseq_63830


title: RNAseq_87682


title: RNAseq_03230


title: RNAseq_02337


title: RNAseq_04370


title: RNAseq_56020


title: RNAseq_46586


title: RNAseq_00586


title: WT_NF_12_Untx_M_1

city: Bethesda

first: Stephen

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

data_processing:
BCL conversion and demultiplex using bcl2fastq 2.17.1
Map to mm10 with Tophat 2.1.1
Calculate RPKM (Partek GS 7.0)
Transform to Log2 RPKM with 0.1 offset (Partek GS 7.0)
ANOVA comparison of Log2 RPKM (Partek GS 7.0)
Genome_build: genome build
Supplementary_files_format_and_content: Excel, RPKM table
Supplementary_files_format_and_content: Excel, ANOVA results

source_name: Liver

growth_protocol: 12h light:12 h dark ad libitum feeding

extract_protocol:
euthanasia 6h post LPS using CO2, liver removal and storage in RNAlater, Trizol RNA exraction
NEBNext Ulta II RNA Library Prep Kit for Illumina (New England BioLabs, Cat# E7770S)

treatment_protocol: 5 days time restricted feeding, LPS 20 mg/kg on day 5 at ZT0 or ZT12 i.p.

tag: tissue

value: Liver

tag: genotype

value: WT

tag: feeding (day or night)

value: NF

tag: zt

value: Untx

tag: Sex

value: M


title: WT_NF_12_LPS_M_2

value: LPS


title: WT_NF_12_LPS_M_1


title: WT_NF_12_Untx_M_2


title: WT_NF_12_Untx_F_2

value: F


title: RNAseq_49266

tag: batch

tag: current smoker

tag: pack years

tag: age

tag: gender (1=male, 2=female)


title: RNAseq_86607

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent


title: RNAseq_20295

tag: monocyte percent

tag: basophil percent


title: WT_NF_12_LPS_F_2

tag: tissue

tag: treatment


title: RNAseq_49645


title: WT_NF_0_Untx_M_1

tag: genotype

tag: feeding (day or night)


title: WT_NF_0_Untx_M_2

tag: zt

tag: Sex


title: RNAseq_10818

tag: batch

tag: current smoker


title: RNAseq_56200

tag: pack years

tag: age


title: WT_NF_12_LPS_F_1


title: RNAseq_34840

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: RNAseq_00405

tag: fev1 % predicted

tag: neutrophil percent


title: RNAseq_68781

tag: lymphocyte percent

tag: eosinophil percent


title: WT_NF_0_Untx_F_1


title: RNAseq_24190

tag: monocyte percent

tag: basophil percent


title: RNAseq_72277


title: WT_NF_0_LPS_M_2

tag: tissue

tag: treatment


title: RNAseq_50675


title: WT_NF_12_Untx_F_1

tag: genotype

tag: feeding (day or night)


title: WT_NF_0_LPS_M_1

tag: zt

tag: Sex


title: WT_NF_0_LPS_F_2


title: RNAseq_75010

tag: batch

tag: current smoker


title: WT_NF_0_LPS_F_1


title: RNAseq_24024

tag: pack years

tag: age


title: RNAseq_75466

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: WT_DF_12_Untx_M_1

value: DF


title: RNAseq_50345

tag: fev1 % predicted

tag: neutrophil percent


title: RNAseq_23183

tag: lymphocyte percent

tag: eosinophil percent


title: WT_DF_12_Untx_F_2


title: RNAseq_25649

tag: monocyte percent

tag: basophil percent


title: WT_NF_0_Untx_F_2

tag: tissue

tag: treatment


title: RNAseq_08616


title: RNAseq_99692


title: WT_DF_12_LPS_M_1

tag: genotype

tag: feeding (day or night)


title: WT_DF_12_LPS_M_2

tag: zt

tag: Sex


title: RNAseq_67907

tag: batch

tag: current smoker


title: RNAseq_39508

tag: pack years

tag: age


title: WT_DF_12_LPS_F_2


title: WT_DF_0_Untx_M_2


title: WT_DF_12_LPS_F_1


title: WT_DF_0_Untx_M_1


title: WT_DF_0_Untx_F_2


title: RNAseq_49178

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: WT_DF_0_Untx_F_1


title: RNAseq_62022

tag: fev1 % predicted

tag: neutrophil percent


title: WT_DF_12_Untx_F_1


title: WT_DF_0_LPS_M_2


title: RNAseq_72360

tag: lymphocyte percent

tag: eosinophil percent


title: RNAseq_55310

tag: monocyte percent

tag: basophil percent


title: RNAseq_25792


title: RNAseq_48721


title: WT_DF_0_LPS_F_2

tag: tissue

tag: treatment


title: WT_DF_0_LPS_F_1

tag: genotype

tag: feeding (day or night)


title: RNAseq_85050


title: KO_NF_12_Untx_M_2

value: BMAL1 KO

tag: zt

tag: Sex


title: RNAseq_13853

tag: batch

tag: current smoker


title: RNAseq_34073

tag: pack years

tag: age


title: RNAseq_76642

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: RNAseq_28706

tag: fev1 % predicted

tag: neutrophil percent


title: RNAseq_77668

tag: lymphocyte percent

tag: eosinophil percent


title: KO_NF_12_Untx_F_2


title: KO_NF_12_LPS_M_2


title: KO_NF_12_LPS_M_1


title: WT_DF_12_Untx_M_2


title: KO_NF_12_Untx_M_1


title: RNAseq_16246

tag: monocyte percent

tag: basophil percent


title: RNAseq_93556


title: KO_NF_12_Untx_F_1

tag: tissue

tag: treatment


title: RNAseq_04386


title: KO_NF_12_LPS_F_1

tag: genotype

tag: feeding (day or night)


title: WT_DF_0_LPS_M_1

tag: zt

tag: Sex


title: KO_NF_12_LPS_F_2


title: RNAseq_42483

tag: batch

tag: current smoker


title: RNAseq_82448

tag: pack years

tag: age


title: RNAseq_24721

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: RNAseq_65446

tag: fev1 % predicted

tag: neutrophil percent


title: KO_NF_0_Untx_M_1


title: KO_NF_0_Untx_M_2


title: KO_NF_0_Untx_F_2


title: RNAseq_31314

tag: lymphocyte percent

tag: eosinophil percent


title: KO_NF_0_LPS_M_2


title: RNAseq_11628

tag: monocyte percent

tag: basophil percent


title: KO_NF_0_LPS_M_1

tag: tissue

tag: treatment


title: RNAseq_95234


title: RNAseq_21207


title: KO_NF_0_LPS_F_1

tag: genotype

tag: feeding (day or night)


title: KO_NF_0_LPS_F_2

tag: zt

tag: Sex


title: KO_DF_12_Untx_M_2


title: RNAseq_79756

tag: batch

tag: current smoker


title: KO_DF_12_Untx_F_2


title: RNAseq_67900

tag: pack years

tag: age


title: KO_DF_12_Untx_F_1


title: RNAseq_64965

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: RNAseq_23043

tag: fev1 % predicted


title: RNAseq_10259

tag: neutrophil percent

tag: lymphocyte percent


title: KO_DF_12_Untx_M_1


title: RNAseq_97182

tag: eosinophil percent

tag: monocyte percent


title: RNAseq_92405

tag: basophil percent


title: RNAseq_71977


title: KO_DF_12_LPS_F_1

tag: tissue

tag: treatment


title: RNAseq_85901


title: KO_DF_12_LPS_F_3

tag: genotype

tag: feeding (day or night)


title: KO_DF_0_Untx_M_2

tag: zt

tag: Sex


title: RNAseq_32380

tag: batch

tag: current smoker


title: KO_NF_0_Untx_F_1


title: KO_DF_0_Untx_M_1


title: RNAseq_81975

tag: pack years

tag: age


title: KO_DF_0_Untx_F_2


title: RNAseq_33974

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: RNAseq_51702

tag: fev1 % predicted

tag: neutrophil percent


title: KO_DF_0_Untx_F_1


title: KO_DF_0_LPS_M_3


title: RNAseq_85566

tag: lymphocyte percent

tag: eosinophil percent


title: RNAseq_96951

tag: monocyte percent

tag: basophil percent


title: KO_DF_0_LPS_M_1

tag: tissue

tag: treatment


title: KO_DF_0_LPS_M_2

tag: genotype

tag: feeding (day or night)


title: RNAseq_19871


title: RNAseq_64858


title: RNAseq_67312


title: RNAseq_99069


title: KO_DF_12_LPS_M_1

tag: zt

tag: Sex


title: RNAseq_16208

tag: batch

tag: current smoker


title: RNAseq_59089

tag: pack years

tag: age


title: RNAseq_02363

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: RNAseq_67221

tag: fev1 % predicted

tag: neutrophil percent


title: Lumbar Spinal Cord Cells - Mouse E9

first: Ryan

middle: Barlow

last: Patterson-Cross

address: 9000 Rockville Pike

department: NINDS

institute: NIH

description: single-nucleus RNA

data_processing:
Samples were de-multiplexed and fastq files generated using cellranger mkfastq (v3.1.0)
Per-sample count matrices were generated against a mm10 pre-mRNA genome using cellranger count (v3.1.0) with the options --nosecondary --expect-cells=5000
Cells with fewer than 400 features or more than 5% of read mapping to mitochondrial genes were filtered out of the data
Samples were then merged to form a single, raw count matrix
Genome_build: mm10 pre-mRNA
Supplementary_files_format_and_content: A features x cell matrix files of all raw counts
Supplementary_files_format_and_content: A CSV of all feature names
Supplementary_files_format_and_content: A CSV of all cell names

source_name: Mouse - Lumbar Spinal Cord

growth_protocol: Nine week old mixed CB6F1/J wild-type mice

extract_protocol:
Detergent mechanical lysis and nuclei enrichment (as described in https://www.jove.com/t/58413/isolation-adult-spinal-cord-nuclei-for-massively-parallel-single)
10X Chromium Single Cell 3' Kit (v3 chemistry)

tag: strain

value: CB6F1/J wild-tyoe

value: Spinal Cord

value: Female

value: None/Control


title: RNAseq_94172

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: Lumbar Spinal Cord Cells - Mouse E6

description: single-nucleus RNA

tag: tissue

tag: treatment


title: Lumbar Spinal Cord Cells - Mouse E5

description: single-nucleus RNA

value: Male


title: Lumbar Spinal Cord Cells - Mouse E2

description: single-nucleus RNA


title: RNAseq_88354

tag: basophil percent


title: RNAseq_59742


title: RNAseq_27522


title: KO_DF_0_LPS_F_1

tag: genotype

tag: feeding (day or night)

tag: zt


title: RNAseq_52470

tag: batch

tag: current smoker


title: RNAseq_38285

tag: pack years

tag: age


title: RNAseq_48181

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: RNAseq_30331

tag: fev1 % predicted

tag: neutrophil percent


title: RNAseq_26707

tag: lymphocyte percent


title: RNAseq_95851

tag: eosinophil percent


title: RNAseq_45940

tag: monocyte percent


title: RNAseq_01697


title: RNAseq_62367


title: KO_DF_12_LPS_F_2

tag: tissue

tag: Sex


title: RNAseq_57477

tag: basophil percent


title: RNAseq_73609


title: RNAseq_85810


title: RNAseq_06949


title: RNAseq_82527


title: RNAseq_99286


title: RNAseq_59355


title: RNAseq_31631


title: RNAseq_95515


title: RNAseq_45887


title: RNAseq_70697


title: RNAseq_40780


title: RNAseq_50691


title: RNAseq_62807


title: RNAseq_55379


title: RNAseq_77793


title: RNAseq_80754


title: RNAseq_77155


title: RNAseq_34064


title: RNAseq_28628


title: RNAseq_79864


title: RNAseq_29759


title: RNAseq_25747


title: RNAseq_25700


title: RNAseq_59764


title: RNAseq_03065


title: RNAseq_36231


title: RNAseq_42329


title: RNAseq_65520


title: RNAseq_67564


title: RNAseq_79251


title: RNAseq_21949


title: RNAseq_99270


title: RNAseq_32082


title: RNAseq_62005


title: RNAseq_35541


title: RNAseq_51466


title: RNAseq_99437


title: RNAseq_76270


title: RNAseq_52992


title: RNAseq_18016


title: RNAseq_62945


title: RNAseq_17312


title: RNAseq_39428


title: RNAseq_10749


title: RNAseq_78486


title: RNAseq_08149


title: RNAseq_19819


title: RNAseq_94131


title: RNAseq_51390


title: RNAseq_93027


title: RNAseq_64719


title: RNAseq_16690


title: RNAseq_97441


title: RNAseq_44010


title: RNAseq_65955


title: RNAseq_42222


title: RNAseq_91966


title: RNAseq_04460


title: RNAseq_66081


title: RNAseq_26895


title: RNAseq_09891


title: RNAseq_54944


title: RNAseq_62190


title: RNAseq_11623


title: RNAseq_09147


title: RNAseq_75642


title: RNAseq_69268


title: RNAseq_17099


title: RNAseq_86103


title: RNAseq_94952


title: RNAseq_92885


title: RNAseq_99963


title: RNAseq_07933


title: RNAseq_18936


title: RNAseq_00802


title: RNAseq_24537


title: RNAseq_81482


title: RNAseq_88852


title: RNAseq_52094


title: RNAseq_92626


title: RNAseq_65787


title: RNAseq_17288


title: RNAseq_15876


title: RNAseq_82125


title: RNAseq_99856


title: RNAseq_50190


title: RNAseq_95843


title: RNAseq_34325


title: RNAseq_87411


title: RNAseq_60548


title: RNAseq_44575


title: RNAseq_82716


title: RNAseq_07466


title: RNAseq_15898


title: RNAseq_12772


title: RNAseq_76493


title: RNAseq_99631


title: RNAseq_35592


title: RNAseq_68776


title: RNAseq_13905


title: RNAseq_57400


title: RNAseq_42930


title: RNAseq_19862


title: RNAseq_42519


title: RNAseq_03061


title: RNAseq_90164


title: RNAseq_29403


title: RNAseq_67898


title: RNAseq_80257


title: RNAseq_25374


title: RNAseq_46112


title: RNAseq_80161


title: RNAseq_40941


title: RNAseq_34573


title: RNAseq_50727


title: RNAseq_57635


title: RNAseq_99519


title: RNAseq_92233


title: RNAseq_08576


title: RNAseq_87775


title: RNAseq_88453


title: RNAseq_72631


title: RNAseq_75445


title: RNAseq_71384


title: RNAseq_65244


title: RNAseq_32820


title: RNAseq_14324


title: RNAseq_05992


title: RNAseq_73686


title: RNAseq_70527


title: RNAseq_62573


title: RNAseq_08231


title: RNAseq_00278


title: RNAseq_82357


title: RNAseq_39801


title: RNAseq_24815


title: RNAseq_87734


title: RNAseq_53537


title: RNAseq_07596


title: RNAseq_29212


title: RNAseq_55276


title: RNAseq_60539


title: RNAseq_10007


title: RNAseq_66249


title: RNAseq_22684


title: RNAseq_69682


title: RNAseq_90958


title: RNAseq_05702


title: RNAseq_03262


title: RNAseq_62477


title: RNAseq_86614


title: RNAseq_42247


title: RNAseq_15216


title: RNAseq_47021


title: RNAseq_09117


title: RNAseq_79852


title: RNAseq_66064


title: RNAseq_21041


title: RNAseq_59190


title: RNAseq_62008


title: RNAseq_68386


title: RNAseq_43882


title: RNAseq_76132


title: RNAseq_52978


title: RNAseq_84961


title: RNAseq_25171


title: RNAseq_72209


title: RNAseq_47687


title: RNAseq_89439


title: RNAseq_55281


title: RNAseq_29715


title: RNAseq_86395


title: RNAseq_52222


title: RNAseq_85648


title: RNAseq_26830


title: RNAseq_84755


title: RNAseq_60600


title: RNAseq_47210


title: RNAseq_87340


title: RNAseq_51073


title: RNAseq_40474


title: RNAseq_66801


title: RNAseq_11192


title: RNAseq_23198


title: RNAseq_36609


title: RNAseq_26143


title: RNAseq_83564


title: RNAseq_23358


title: RNAseq_28309


title: RNAseq_25081


title: RNAseq_37837


title: RNAseq_97702


title: RNAseq_69241


title: RNAseq_24653


title: RNAseq_07078


title: RNAseq_72834


title: RNAseq_27290


title: RNAseq_03162


title: RNAseq_44819


title: RNAseq_01214


title: RNAseq_72996


title: RNAseq_10877


title: RNAseq_00943


title: RNAseq_06255


title: RNAseq_66209


title: RNAseq_79177


title: RNAseq_72877


title: RNAseq_21995


title: RNAseq_64635


title: RNAseq_74772


title: RNAseq_77265


title: RNAseq_67182


title: RNAseq_82081


title: RNAseq_74489


title: RNAseq_96818


title: RNAseq_28648


title: RNAseq_90731


title: RNAseq_52286


title: RNAseq_33041


title: RNAseq_07894


title: RNAseq_41950


title: RNAseq_03277


title: RNAseq_62861


title: RNAseq_25413


title: RNAseq_04270


title: RNAseq_40666


title: RNAseq_99696


title: RNAseq_34467


title: RNAseq_94732


title: RNAseq_98026


title: RNAseq_12358


title: RNAseq_93836


title: RNAseq_69535


title: RNAseq_84320


title: RNAseq_76452


title: RNAseq_95951


title: RNAseq_78712


title: RNAseq_04240


title: RNAseq_94056


title: RNAseq_52426


title: RNAseq_74391


title: RNAseq_08904


title: RNAseq_70348


title: RNAseq_30620


title: RNAseq_45057


title: RNAseq_39169


title: RNAseq_86991


title: RNAseq_66504


title: RNAseq_29860


title: RNAseq_69688


title: RNAseq_41057


title: RNAseq_30536


title: RNAseq_98847


title: RNAseq_39382


title: RNAseq_41598


title: RNAseq_43154


title: RNAseq_61425


title: RNAseq_48314


title: RNAseq_03192


title: RNAseq_40075


title: RNAseq_57443


title: RNAseq_75874


title: RNAseq_94766


title: RNAseq_52395


title: RNAseq_39903


title: RNAseq_76940


title: RNAseq_03525


title: RNAseq_24999


title: RNAseq_20976


title: RNAseq_05561


title: RNAseq_50204


title: RNAseq_15460


title: RNAseq_06242


title: RNAseq_97964


title: RNAseq_43035


title: RNAseq_30957


title: RNAseq_42408


title: RNAseq_23469


title: RNAseq_37321


title: RNAseq_77522


title: RNAseq_90943


title: RNAseq_34512


title: RNAseq_50866


title: RNAseq_34747


title: RNAseq_86165


title: RNAseq_21079


title: RNAseq_36860


title: RNAseq_71143


title: RNAseq_83026


title: RNAseq_01006


title: RNAseq_36629


title: RNAseq_14276


title: RNAseq_62400


title: RNAseq_37180


title: RNAseq_68689


title: RNAseq_11840


title: RNAseq_28085


title: RNAseq_83033


title: RNAseq_46537


title: RNAseq_77526


title: RNAseq_75712


title: RNAseq_83752


title: RNAseq_25053


title: RNAseq_49574


title: RNAseq_53998


title: RNAseq_49458


title: RNAseq_53164


title: RNAseq_34968


title: RNAseq_20149


title: RNAseq_46124


title: RNAseq_27504


title: RNAseq_11574


title: RNAseq_02932


title: RNAseq_57401


title: RNAseq_25779


title: RNAseq_23863


title: RNAseq_04197


title: RNAseq_25354


title: RNAseq_10709


title: RNAseq_48032


title: RNAseq_09241


title: RNAseq_47388


title: RNAseq_41282


title: RNAseq_44820


title: RNAseq_86953


title: RNAseq_92340


title: RNAseq_37399


title: RNAseq_85594


title: RNAseq_78961


title: RNAseq_42017


title: RNAseq_35248


title: RNAseq_07099


title: RNAseq_50712


title: RNAseq_34413


title: RNAseq_95601


title: RNAseq_04245


title: RNAseq_89174


title: RNAseq_08284


title: RNAseq_60618


title: RNAseq_10352


title: RNAseq_80155


title: RNAseq_21627


title: RNAseq_83621


title: RNAseq_91787


title: RNAseq_00254


title: RNAseq_45260


title: RNAseq_73058


title: RNAseq_85124


title: RNAseq_21648