title: th17N_96h_Dig_150812

description: 108h TCR stim; 96h polarization


title: Th17_RPMI_siEtv6_48h_SL11688

status: Public on Dec 16 2018

type: SRA

city: Cincinnati

first: Emily

middle: R

last: Miraldi

state: Ohio

address: 3333 Burnet Avenue, MLC 7038

department: Immunobiology and Biomedical Informatics

country: USA

institute: Cincinnati Children's Hospital Medical Center

description: 48h RPMI siEtv6; 48h

library_source: transcriptomic

data_processing:
Sequences were mapped to the murine genome (mm10) STAR aligner; only a single-end from paired-end samples were used
HTSeq-count was used to map reads to mm10 genes
Genes were normalized to account for 36bp vs. 50bp mappability (see manuscript Methods for details)
DESeq2 was used to normalize gene expression quantification
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2-normalized (VSD) gene quantification.

molecule: total RNA

organism: Mus musculus

source_name: Naive CD4+ T cells from spleen

extract_protocol:
Cells were lysed and snap-frozen in trizol, thawed for chloroform extraction and loaded onto a Qiagen RNEasy column
Libraries were constructed using Protocol 1 (poly-A selection, Nextera tagmentation) or Protocol 2 (Ribozero Gold, Illumina TruSeq Stranded Total RNA), as indicated in the characteristic: RNA library protocol

treatment_protocol: CD4+ T cells were purified from the spleen and polarized into Th0, Th2, Treg, and Th17

tag: strain

tag: tissue

value: spleen

tag: cell type

value: naive CD4+ T cell

tag: polarization

value: Th17, RPMI

tag: genotype

value: Wildtype

tag: time point (post tcr stimulation)

tag: rna library protocol


title: miRNA_2240T

city: Berlin

first: Robert

last: Altwasser

address: Robert-Rössle-Str. 10

department: AG Di Virgilio

country: Germany

institute: Max-Delbrück-centrum

description:
Sp2240T_GGCTAC_L002
processed data file: counts_miRNA_spalax.csv

data_processing:
FASTQ files were receiven from Mark Band, USA
repeated runs concatenated
Mapping of read pairs using TopHat (v1.4.1)
Read counting using HTSeq, annotation from BioMart mouse reference
Normalisation using R-package DESeq
Genome_build: Spalax genome: RefSeq/GenBank assembly accession GCF_000622305.1; mouse: GRCm38
Supplementary_files_format_and_content: comma seperated values (csv) with normalized read counts

organism: Nannospalax ehrenbergi

source_name: Spalax fibrosarcoma

extract_protocol:
1ug of total RNA was used to construct the libraries using the TruSeq Small RNA Sample Prep kit (Illumina).   The strand-specific RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNA Sample Prep kit'.
The libraries were pooled in equimolar concentration and the pool was quantitated by qPCR and sequenced on one lane (small RNAs) or two lanes (RNAseq) for 101 cycles on a HiSeq2500 using a TruSeq SBS sequencing kit version 4. Fastq files were generated and demultiplexed with with the bcl2fastq v1.8.4 Conversion Software (Illumina)

tag: diagnosis

value: fibrosarcoma

tag: Sex

value: F

tag: treatment

tag: time of operation after treatment

value: 18 months

value: muscle tissue

tag: sample side

value: injected side


title: 95097

type: RNA

city: Kuopio

first: Mikael

last: Marttinen

address: Yliopistonranta 1E

department: Biomedicine

country: Finland

institute: University of Eastern Finland

hyb_protocol: Cy-3 labeled with Agilent Low Input Quick Amp WT labeling kit, one-color (Prod. Num. 5190-2943)

scan_protocol: Scanned on Agilent Technologies scaner, model G2565CA (Scan profile: AgilentG3_GX_1color)

data_processing:
Data import was done with limma package version 3.16.7. The probe signal intensities were background-corrected using “normexp” method in limma package.
Quantile normalization was used to bring the array signal intensities to comparable levels between each other. Average expression levels between duplicate probes were used as the signal for the probe. For transcript expression analysis, 3′ untranslated region (UTR) probe signal was used as a measure of the respective transcript's global expression level. If multiple such probes targeted the same 3' UTR, average value of the probes was used. The expression level of each individual exon is affected by the global expression level of the transcript, and to adjust for this in the alternative splicing analysis, each exon signal was normalized by the respective transcript's global expression level (measured by 3′UTR probe). Probes that did not map to any known transcript were excluded, and in case of multiple probes mapping to a single transcript outside of the 3'UTR, the probe with the most interquartile-range (IRQ) variation across the samples, was retained in the analysis.  The sample tables include the normalized data filtered for these criteria and were the data used in this analysis. The quantile normalized values of the unfiltered probes are available in the file Data_matrix_full.csv on the series record.

organism: Homo sapiens

source_name: Inferior termporal cortex

label_protocol: RNA was extracted from frozen brain samples using Qiagen RNeasy Lipid Tissue Mini Kit (Qiagen) and RNA integrity number (RIN) was determined using 2100 Bioanalyzer

extract_protocol:
Post-mortem tissue extraction
grouping protocol: Assessment of the magnitude of AD-relatedneurofibrillary was performed via immunostaining of paraffin sections with AT8 antibody

tag: braak stage

value: brain

tag: brain region

value: Inferior termporal cortex

tag: age

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

tag: rna quality

tag: apoe (additive) (0=0 copies of apoee4, 1=1 copy of apoee4, 2=two copies of apoee4)

tag: gamma secretase activity

tag: alpha secretase activity

tag: beta secretase activity

tag: amyloid-beta 42 levels


title: Th17_RPMI_siRorc_48h_SL11691

description: 48h RPMI siRorc; 48h

tag: strain

tag: tissue

tag: cell type

tag: polarization

tag: genotype

tag: time point (post tcr stimulation)


title: Th17_RPMI_siCntl_48h_SL11687

description: 48h RPMI siCntl; 48h

tag: rna library protocol


title: miRNA_2240H

description:
Sp2240HM_CTTGTA_L002
processed data file: counts_miRNA_spalax.csv

tag: diagnosis

tag: Sex

tag: treatment

tag: time of operation after treatment

tag: sample side

value: uninjected side


title: th17N_96h_Dig_150729

description: 108h TCR stim; 96h polarization


title: Th17_Nrf2_pp_48h_SL12368

description: Nrf2 +/+; 48h


title: miRNA_976H

description:
Sp976HM_ACTTGA_L002
processed data file: counts_miRNA_spalax.csv

source_name: Spalax granuloma

value: granuloma

value: 16 months


title: Th17_Nrf2_mm_48h_SL12372

description: Nrf2 -/-; 48h


title: th17N_96h_Dig_150719

description: 108h TCR stim; 96h polarization


title: miRNA_976G

description:
Sp976G_CAGATC_L002
processed data file: counts_miRNA_spalax.csv


title: Th17_Nrf2_mm_48h_SL12370

description: Nrf2 -/-; 48h


title: Th17_IMDM_siRorc_24h_SL11676

description: 24h IMDM siRorc; 24h

value: Th17, IMDM


title: th17N_48h_Dig_150829

description: 60h TCR stim; 48h polarization


title: Th17_IMDM_siRorc_24h_SL11673

description: 24h IMDM siRorc; 24h


title: miRNA_600H

description:
Sp600HM_TAGCTT_L002
processed data file: counts_miRNA_spalax.csv

value: 14 months


title: Th17_IMDM_siNonTarget_2_24h_SL11674

description: 24h IMDM siNonTarget 2; 24h


title: Th17_IMDM_siJmjd3_24h_SL11675

description: 24h IMDM siJmjd3; 24h


title: miRNA_600G

description:
Sp600G_GATCAG_L002
processed data file: counts_miRNA_spalax.csv


title: th17N_48h_Dig_150817

description: 60h TCR stim; 48h polarization


title: 2230T

description:
Sp2230T
Sp2230T_AGTCAA_L00M
processed data file: counts_spalax_16samples.csv

extract_protocol:
1ug of total RNA was used to construct the libraries using the TruSeq Small RNA Sample Prep kit (Illumina).   The strand-specific RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNA Sample Prep kit'.
The libraries were pooled in equimolar concentration and the pool was quantitated by qPCR and sequenced on one lane (small RNAs) or two lanes (RNAseq) for 101 cycles on a Illumina HiSeq 2500 using a TruSeq SBS sequencing kit version 4. Fastq files were generated and demultiplexed with with the bcl2fastq v1.8.4 Conversion Software (Illumina)

value: M

value: 30 months

value: muscle


title: U2OS_ZBTB10_KO_ko3

city: Mainz

first: Falk

last: Butter

state: Germany

address: Ackermannweg 4

department: Quantitative Proteomics

institute: Institute of Molecular Biology gGmbH

description:
imb_butter_2017_08_Alina_29_U2OS_ZBTB10_KO4g3-IX_S19
processed data file: U2OS_KOvsWT_de_results.xls

data_processing:
Genome mapping using STAR version 2.5.2b, allowing up to 2 mismatches, a minimum intron length of 21 and keeping only uniquely aligned reads
Counting reads per gene using featureCounts from the subread package version 1.5.1, default parameters
Differential expression analysis using DESeq2 bioconductor package version 1.18.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file including rpkm values of all samples and differential expression changes statistics between wt and ko

growth_protocol: 37⁰C, 5% CO2, 80% humidity

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, 74104)
NGS libraries were prepared using Illuminas TruSeq stranded mRNA LT Sample Prep Kit with a starting amount of 250 ng. Libraries were pooled in equimolar amounts.

treatment_protocol: No treatment for WT and KO clones

tag: cell line

tag: genotype/vaiation

value: ZBTB10 knockout clone


title: Th17_IMDM_siJmjd3_24h_SL11672

description: 24h IMDM siJmjd3; 24h

value: spleen

value: naive CD4+ T cell

value: Wildtype


title: Th17_RPMI_siCntl_48h_SL11692

description: 48h RPMI siCntl; 48h

value: Th17, RPMI


title: Th0_Nrf2_mm_48h_SL12371

description: Nrf2 -/-; 48h


title: 2230H

description:
Sp2230H
Sp2230HM_AGTTCC_L00M
processed data file: counts_spalax_16samples.csv

value: fibrosarcoma


title: U2OS_ZBTB10_KO_ko2

description:
imb_butter_2017_08_Alina_27_U2OS_ZBTB10_KO2g2-12_S17
processed data file: U2OS_KOvsWT_de_results.xls


title: Th0_Nrf2_mm_48h_SL12369

description: Nrf2 -/-; 48h


title: U2OS_ZBTB10_KO_ko1

description:
imb_butter_2017_08_Alina_26_U2OS_ZBTB10_KO1g2-1_S16
processed data file: U2OS_KOvsWT_de_results.xls


title: CD4_T_cell_IRF4wt_48h_SL35247

description: IRF4wt; 48h

value: CD4 T cell


title: CD4_T_cell_IRF4wt_48h_SL35245

description: IRF4wt; 48h


title: WT_Th17_TGFb_IL6_IL1B_1

description:
accessible DNA
1_WT_Th17_TGFb_IL6_IL1B_CTCTCTAC

library_source: genomic

data_processing:
Sequences were mapped to the murine genome (mm10) with bowtie2 v2.2.3
Sequences were filtered (MAPQ>30) with Samtools
Duplicates were removed using Picard
Peakdeck (parameters -bin 75, -STEP 25, -back 10000, -npBack 100000) was used to call peaks (Praw < 1E-4)
A reference set of peaks was found by taking the union of peaks across samples
HTSeq-count was used to map reads to reference peaks
DESeq2 was used to quantify peak accessibility across samples and test for differential accessibility
Genome_build: mm10
Supplementary_files_format_and_content: Batch-corrected, DESeq2-normalized (RLOG) quantification for ATAC-seq peaks, peak annotations (nearest TSS, transcription factor motifs found within the peak, etc.)

molecule: genomic DNA

source_name: Naïve CD4+ T cells from spleen

extract_protocol:
Cells harvest was followed by a transposition reaction and purification (Buenrostro  et al. Curr Protoc Mol Biol. 2015)
Prepared as in Buenrostro  et al. Curr Protoc Mol Biol. 2015

treatment_protocol: CD4+ T cells were purified from the spleen and polarized into Th0, Th2, Treg, and Th17 according to (Ciofani et al., Cell. 2012)

value: naive CD4+ T cells

value: wild type

value: Th17 + IL1b

tag: batch


title: 2240T

description:
Sp2240T
Sp2240T_GGCTAC_L00M
processed data file: counts_spalax_16samples.csv

value: F

value: 18 months

value: injected side


title: CD4_T_cell_IRF4wt_48h_SL35243

description: IRF4wt; 48h


title: Th17_IMDM_siNonTarget_2_24h_SL11671

description: 24h IMDM siNonTarget 2; 24h

value: Th17, IMDM


title: 2240H

description:
Sp2240H
Sp2240HM_CTTGTA_L00M
processed data file: counts_spalax_16samples.csv

value: uninjected side


title: U2OS_ZBTB10_KO_wt2

description:
imb_butter_2017_08_Alina_23_U2OS_ZBTB10_WT11_S13
processed data file: U2OS_KOvsWT_de_results.xls

value: wildtype


title: CD4_T_cell_IRF4ko_48h_SL35248

description: IRF4ko; 48h


title: CD4_T_cell_IRF4wt_48h_SL35237

description: IRF4wt; 48h


title: 976G

description:
Sp976G
Sp976G_CAGATC_L00M
processed data file: counts_spalax_16samples.csv

value: granuloma

value: 16 months

value: muscle


title: U2OS_ZBTB10_KO_wt1

description:
imb_butter_2017_08_Alina_21_U2OS_ZBTB10_WT1_S11
processed data file: U2OS_KOvsWT_de_results.xls


title: 976H

description:
Sp976H
Sp979HM_ACTTGA_L00M
processed data file: counts_spalax_16samples.csv


title: HEK_ZBTB10_KO_ko5

description:
imb_butter_2017_05_HEK_zbtb10KO_20_g3cl36_S20
processed data file: HEK_KOvsWT_de_results.xls

value: ZBTB10 knockout clone


title: 98043

tag: braak stage

value: brain

tag: brain region

value: Inferior termporal cortex

tag: age

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

tag: rna quality

tag: apoe (additive) (0=0 copies of apoee4, 1=1 copy of apoee4, 2=two copies of apoee4)

tag: gamma secretase activity

tag: alpha secretase activity

tag: beta secretase activity


title: CD4_T_cell_IRF4ko_48h_SL35246

description: IRF4ko; 48h

tag: strain

tag: tissue

value: spleen

tag: cell type

value: naive CD4+ T cell

tag: polarization

tag: genotype

tag: time point (post tcr stimulation)

tag: rna library protocol


title: 600H

description:
Sp600H
Sp600HM_TAGCTT_L00M
processed data file: counts_spalax_16samples.csv

tag: diagnosis

tag: Sex

tag: treatment

tag: time of operation after treatment

value: 14 months

tag: sample side


title: Th0_Nrf2_pp_48h_SL12367

description: Nrf2 +/+; 48h

value: Wildtype


title: CD4_T_cell_IRF4ko_48h_SL35244

description: IRF4ko; 48h

value: CD4 T cell


title: CD4_T_cell_IRF4ko_48h_SL35242

description: IRF4ko; 48h


title: CD4_T_cell_IRF4ko_48h_SL35240

description: IRF4ko; 48h


title: CD4_T_cell_IRF4ko_48h_SL35238

description: IRF4ko; 48h


title: HEK_ZBTB10_KO_ko3

description:
imb_butter_2017_05_HEK_zbtb10KO_18_g3_cl13_S18
processed data file: HEK_KOvsWT_de_results.xls

tag: cell line

tag: genotype/vaiation


title: U2OS_ZBTB10_KO_wt3

description:
imb_butter_2017_08_Alina_24_U2OS_ZBTB10_WTg2-19_S14
processed data file: U2OS_KOvsWT_de_results.xls


title: 600G

description:
Sp600G
Sp600G_GATCAG_L00M
processed data file: counts_spalax_16samples.csv

value: F


title: CD4_T_cell_Batf_wt_48h_SL35235

description: Batf wt; 48h


title: 2375H

description:
SP2375
SP2375_S30MOH_TCTCGCGC-GTACTGAC_L00M
processed data file: counts_spalax_16samples.csv

source_name: Spalax tolerant

value: healthy

value: 30 months


title: CD4_T_cell_Batf_wt_48h_SL35233

description: Batf wt; 48h


title: CD4_T_cell_IRF4wt_48h_SL35239

description: IRF4wt; 48h


title: CD4_T_cell_Batf_wt_48h_SL35231

description: Batf wt; 48h


title: CD4_T_cell_IRF4wt_48h_SL35241

description: IRF4wt; 48h


title: 2218H

description:
SP2218
SP2218_S30MOH_TCTCGCGC-CAGGACGT_L00M
processed data file: counts_spalax_16samples.csv

value: M

value: injected side


title: HEK_ZBTB10_KO_ko1

description:
imb_butter_2017_05_HEK_zbtb10KO_16_g2cl16_S16
processed data file: HEK_KOvsWT_de_results.xls


title: CD4_T_cell_Batf_wt_48h_SL35227

description: Batf wt; 48h


title: 2261H

description:
SP2261
SP2261_3_S18MOH_TCTCGCGC-AGGCGAAG_L00M
processed data file: counts_spalax_16samples.csv

value: 18 months


title: CD4_T_cell_Batf_wt_48h_SL35229

description: Batf wt; 48h


title: HEK_ZBTB10_KO_ko4

description:
imb_butter_2017_05_HEK_zbtb10KO_19_g3cl28_S19
processed data file: HEK_KOvsWT_de_results.xls


title: HEK_ZBTB10_KO_wt5

description:
imb_butter_2017_05_HEK_zbtb10KO_15_wt7_S15
processed data file: HEK_KOvsWT_de_results.xls

value: wildtype


title: CD4_T_cell_Batf_ko_48h_SL35236

description: Batf ko; 48h

value: Batf-/-


title: CD4_T_cell_Batf_wt_48h_SL35225

description: Batf wt; 48h


title: 2251H

description:
SP2251
SP2251_2_S18MOH_TCTCGCGC-TAATCTTA_L00M
processed data file: counts_spalax_16samples.csv

value: muscle


title: CD4_T_cell_Batf_ko_48h_SL35232

description: Batf ko; 48h


title: CD4_T_cell_Batf_ko_48h_SL35234

description: Batf ko; 48h


title: HEK_ZBTB10_KO_wt4

description:
imb_butter_2017_05_HEK_zbtb10KO_14_wt6_S14
processed data file: HEK_KOvsWT_de_results.xls


title: 6038H

description:
SP6038
SP6038_S0_CGGCTATG-GGCTCTGA_L00M
processed data file: counts_spalax_16samples.csv

source_name: Spalax control

value: uninjected side


title: HEK_ZBTB10_KO_wt3

description:
imb_butter_2017_05_HEK_zbtb10KO_13_wt5_S13
processed data file: HEK_KOvsWT_de_results.xls


title: 2095H

description:
SP2095
SP2095_S0_AGCGATAG-AGGCGAAG_L00M
processed data file: counts_spalax_16samples.csv


title: CD4_T_cell_Batf_ko_48h_SL35228

description: Batf ko; 48h


title: HEK_ZBTB10_KO_ko2

description:
imb_butter_2017_05_HEK_zbtb10KO_17_g1_2cl19_S17
processed data file: HEK_KOvsWT_de_results.xls

value: ZBTB10 knockout clone


title: CD4_T_cell_Batf_ko_48h_SL35226

description: Batf ko; 48h


title: 1075H

description:
SP1075
SP1075_S0_AGCGATAG-GGCTCTGA_L00M
processed data file: counts_spalax_16samples.csv


title: 1042H

description:
SP1042
SP1042_S0_AGCGATAG-CCTATCCT_L00M
processed data file: counts_spalax_16samples.csv


title: HEK_ZBTB10_KO_wt1

description:
imb_butter_2017_05_HEK_zbtb10KO_11_wt1_S11
processed data file: HEK_KOvsWT_de_results.xls


title: HEK_ZBTB10_KO_wt2

description:
imb_butter_2017_05_HEK_zbtb10KO_12_wt2_S12
processed data file: HEK_KOvsWT_de_results.xls


title: healthy peripheral 2 (Cd1c+ DC)

status: Public on Dec 15 2018

city: la jolla

first: vipul

last: bhargava

state: California

address: 9500 gilman drive

institute: ucsd

description:
GEO_count_matrix.txt
CD1cHC02

data_processing:
Reads were trimmed for adaptors and sequence quality. Trimmed reads were aligned to human b37.3 reference genome using omicsoft sequence aligner (Hu et al., 2012).
Aligned reads were quantified using EM algorithm with RefSeq transcriptome model accessed on September 26, 2014 (Li et al., 2010).
Genome_build: b37.3
Supplementary_files_format_and_content: tab-delimited processed data matrix file contains feature counts for all samples and features

source_name: peripheral blood

growth_protocol: Synovial fluid was isolated from patients and synovial fluid mononuclear cells were isolated using a density gradient seperation. CD141+DC were magnetically sorted using CD141 antibody conjugated microbeads and used for RNA isolation

extract_protocol:
Total RNA was extracted from CD141+DCs from peripheral blood and synovial fluid of inflammatory arthritis and healthy control peripheral blood. RNA from CD1c+ DCs from peripheral blood of healthy control was also extracted. The quality of all RNA samples was evaluated using an Agilent Bioanalyzer.
RNA samples were reverse transcribed and sequencing libraries constructed using NuGen Ovation Universal RNA-Seq System (CAT# 0402-A01) according to the manufacturer’s protocol.  The resulting sequencing libraries were analyzed using the Caliper LabChip GX and quantified using KAPA qPCR.  Libraries were then normalized and pooled in one batch of 6 and one batch of 5.  Each pool was clustered and sequenced on an Illumina NextSeq500 instrument using 2x100 bp paired-end reads, following the manufacturer’s protocols.

tag: disease state

value: peripheral blood

value: Cd1c+ DC


title: healthy peripheral 1 (Cd1c+ DC)

description:
GEO_count_matrix.txt
CD1cHC01


title: healthy peripheral 3 (Cd1c+ DC)

description:
GEO_count_matrix.txt
CD1cHC03


title: IA peripheral 7 (CD141+ DC)

description:
GEO_count_matrix.txt
IAPBMC07

value: inflammatory arthritis

value: CD141+ DC


title: IA peripheral 5 (CD141+ DC)

description:
GEO_count_matrix.txt
IAPBMC05


title: IA peripheral 6 (CD141+ DC)

description:
GEO_count_matrix.txt
IAPBMC06


title: IA peripheral 3 (CD141+ DC)

description:
GEO_count_matrix.txt
IAPBMC03


title: IA synovial 3 (CD141+ DC)

description:
GEO_count_matrix.txt
IASF03

source_name: synovial fluid

value: synovial fluid


title: IA peripheral 1 (CD141+ DC)

description:
GEO_count_matrix.txt
IAPBMC01


title: IA synovial 6 (CD141+ DC)

description:
GEO_count_matrix.txt
IASF06


title: IA synovial 1 (CD141+ DC)

description:
GEO_count_matrix.txt
IASF01


title: IA synovial 2 (CD141+ DC)

description:
GEO_count_matrix.txt
IASF02


title: healthy peripheral 2 (CD141+ DC)

description:
GEO_count_matrix.txt
HC2


title: healthy peripheral 4 (CD141+ DC)

description:
GEO_count_matrix.txt
HC4


title: IA peripheral 4 (CD141+ DC)

description:
GEO_count_matrix.txt
IAPBMC04


title: IA peripheral 2 (CD141+ DC)

description:
GEO_count_matrix.txt
IAPBMC02


title: CD4_T_cell_Batf_ko_48h_SL35230

description: Batf ko; 48h

value: spleen

value: naive CD4+ T cell

value: CD4 T cell


title: IA synovial 4 (CD141+ DC)

description:
GEO_count_matrix.txt
IASF04


title: Saline

city: West Lafayette

first: Evan

last: Phillips

state: IN

address: 206 S. Martin Jischke Dr

department: Weldon School of Biomedical Engineering

institute: Purdue University

description: Suprarenal aortas harvested 10 days after implantation of saline-filled pumps

data_processing:
Illumina HiSeq 2500 reads were trimmed for adaptor sequence using FastQC and mapped to mm9 whole genome using HISAT2.
We assembled transcripts using the Cufflinks protocol including Cuffmerge and Cuffquant as detailed by Trapnell et al (PMID 22383036). Differential expression valves were calculated as RPKM usng Cuffdiff.
Genome_build: mm9
Supplementary_files_format_and_content: Three tab-delimited text files including RPKM values and log2-transformed fold change values

source_name: Suprarenal aorta

extract_protocol:
Half of dissecting AAA / suprarenal aorta was removed, flash frozen in liquid nitrogen, and 15 microliters of total RNA was extracted using Trizol reagent. Zymo Directzol RNA MiniPrep was used with columns from the Zymo RNA Clean and Concentrator 5 (RCC-5) kit followed by in-tube DNAse treatment. RNAse inhibitor was added to sample volume and samples were stored at -80 Celsius. Biological samples were diluted to have equal amounts of RNA within each treatment group pool. For each pooled sample, 10 to 100 ng of total RNA was used for library sample construction.
Libraries were prepared according to NuGEN's instructions accompanying the Ovation RNA-Seq System 1-16 for Mouse (Part# 0348). We used three unique 6-nt index adaptors.

treatment_protocol: In vivo infusion of either solubilized angiotensin II or saline

value: Suprarenal aorta

value: Saline

value: apoE null

tag: age at surgery

value: post natal 12 weeks

value: male


title: AngII No AAA

description: Suprarenal aortas harvested 10 days after implantation of angiotensin II-filled pumps

value: Angiotensin II


title: AngII AAA

description: Dissecting abdominal aortic aneurysms harvested within 24 hours of diagnosis

value: Suprarenal aorta and aneurysm tissues


title: MF-DC

city: Toronto

first: Slava

last: Epelman

state: Ontario

address: 101 College St

department: Cardiology, University Health Network

country: Canada

institute: Toronto General Hospital Research Institute

data_processing:
The sequenced data was processed into expression matrices with the Cell Ranger Single Cell Software Suite 1.3.1 by 10X Genomics (http://10xgenoics.come/).
Raw base call files from HiSeq2500 sequencer were demultiplexed into library specific FASTQ files.
Sequencing reads were aligned to the mouse transcriptome using STAR aligner
Subsequently, cell barcodes and Unique Molecular Identifiers (UMIs), underwent filtering and correction.
Reads associated with the retained barcodes were quantified and used to build a transcript count table.
Genome_build: mm10
Supplementary_files_format_and_content: Barcode, gene and expression matrix

source_name: Heart macrophages and dendritic cells

extract_protocol:
Mouse hearts were isolated and enzymatically digested in DMEM containing collagenase I (450 U/mL), DNase I (60 U/mL), and hyaluronidase (60 U/mL) and 1mM Flavopiridol in the digestion buffer. Digestions were stopped after 20min and cells were processed into a single cell suspension on ice. Cells were stained with CD45 magnetic beads (Miltenyi Biotec) and subsequently fluorescently tagged antibodies against CD45, CD64 and CD11b. Hematopoietic cells were positively enriched using the AutoMacs instrument (Miltenyi Biotec) and live MFs (CD45+, CD64+, CD11b+, DAPINeg) were sorted on the Aria Fusion (BD Bioscience) under low pressure into DMEM containing 50% FCS  10X single cell RNA sequencing.Cardiac MFs were identified as live, CD45+CD64low-hiCD11b+ and DCs as live,  CD45+CD64-CD11c+MHCIIInt-high.
Libraries were prepared as outlined by the Chromium Single Cell 3’ Reagent Kits v2 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics).

value: Heart macrophages and dendritic cells

value: wild Type

tag: age

tag: description

value: Steady state


title: MF-MI

source_name: Heart macrophages

tag: tissue

value: Heart macrophages

tag: strain

value: Post Myocardial Infarction day 11


title: Library 11010

city: Carlsbad

first: Christine

last: Cho

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

data_processing:
Transcript quantitation was performed with Salmon (ver 0.7.1) using quasi-mapping based mode with automated libtype detection.
Gene level TPM was computer by summing read counts of all associated transcript isoforms and normalizing by total number of mapped reads.
Genome_build: mm8
Supplementary_files_format_and_content: comma separated files (csv) contain TPM values for each sample

source_name: microglia, in vivo

extract_protocol:
Cells were lysed in RLT buffer containing 1% BME. RNA extraction was performed using Qiagen RNeasy kits.
Total RNA was used as template for the initial reverse transcription, which included 0.27 uM of barcoded primer, containing a T7 promoter sequence. 48-96 cDNA samples were pooled, followed by a 8 h T7 amplification. 50 ng of the resulting aRNA was used as input for library generation using the Quantseq aRNA kit (Lexogen, Cat #043.24.V0.1).

tag: cell type

value: microglia, in vivo

value: Naive

tag: duration

value: 22 months old


title: Library 11009


title: Library 11006


title: Library 11007


title: Library 11004


title: Library 11003


title: Library 11005


title: healthy peripheral 5 (CD141+ DC)

description:
GEO_count_matrix.txt
HC5

value: healthy

value: peripheral blood

value: CD141+ DC


title: SC02

city: Chicago

first: Alexander

middle: V

last: Misharin

state: IL

address: 240 E Huron

department: Pulmonary and Critical Care

institute: Northwestern University

data_processing:
BaseCalls: NextSeq Control/RTA2 software.
Fastq files were generated using bcl2fastq software (Illumina) as part of CellRanger V1.3 pipeline (10x Genomics) using mkfastq command.
Fastq files processed using CellRanger V1.3 pipeline (10x Genomics), mapping was done to mm10 version of mouse genome.
Sample SC02 was sequenced 3 times to achieve sequencing depth compartible with sample SC01. FASTQ files from 3 runs were processed using muli-run Cell Ranger workflow to generate single counts matrix.
Genome_build: mm10
Supplementary_files_format_and_content: Filtered Gene-Barcode Matrices, containing the number of UMIs associated with a gene and barcode in Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively. Raw and filtered matrices in HDF5 format are provided as an alternative to MEX format.

source_name: Lung

growth_protocol: C57Bl/6J male mice, 4 months old were maintaned at the barier facility at the Center for Comparative Medicine at Northwestern University using standard rodent diet (Teklad LM-485 mouse diet, irradiated) and normal day-night cycle.

extract_protocol:
Mice were euthanized with sodium pentobarbital overdose. Chest cavity was opened and lungs were perfused through the right ventricle with 10 ml of HBSS. The lungs were removed and, using 30G needle, infused with 1 mL dispase (Corning) with DNase I (Sigma). Lungs were incubated at room temperature with gentle agitation for 45 minutes, followed by gentle teasing using forceps into small (1-2 mm) fragments and incubation in digestion buffer for another 15 minutes. Resulting suspension was passed through passed through 70 μm cell strainer (Falcon), washed with DMEM (Corning) supplemented with 5% FBS (Corning), pelleted by centrifugation and erythrocytes were lysed using BD Pharm Lyse (BD Biosciences). Resulting single cell suspension was kept in DMEM/FBS and passed through 40 μm cell strainer (Falcon) two times. Cells were counted using Cellometer K2 (Nexcelom) with nucleic acid binding dyes acridine orange (AO) to calculate total number of nucleated cells and propidium iodide (PI) to count dead cells. All manipulations were performed using wide bore tips (Axygen).
10x Genomics, 3' single-cell RNA-seq, V2 chemistry (Protocol CG00052 Rev B). Read 1 (26 cycles) corresponds to cell barcode and UMI, Read 2 (98 cycles) corresponds to 3'-end of RNA molecule. Index 1 (8 cycles) is single cell library barcode.

tag: replicate

value: Mouse #2

tag: mouse strain

value: C57Bl/6j (Jax stock 000664)

value: 4 months

value: Male


title: SC01

value: Mouse #1


title: Library 11002


title: healthy peripheral 6 (CD141+ DC)

description:
GEO_count_matrix.txt
HC6


title: Library 7447


title: Library 7445


title: Library 7448


title: Library 10999

value: 2 month old


title: Library 11001


title: Library 10998


title: Library 10997


title: Library 10995


title: MF_SS

tag: genotype


title: Library 7442


title: Library 7444


title: Library 7443


title: Library 10994


title: Library 7441


title: Library 6689

value: LPS, 2 mg/kg

value: 4 hrs


title: Library 6687


title: Library 6685

value: PBS


title: Library 6688


title: Library 6683


title: Library 6682


title: Library 7662

source_name: microglia, in vitro

value: microglia, in vitro

value: IFNg, 0.0001 ug/ul

value: 72 hrs


title: Library 7661


title: Library 7660


title: Library 7446

value: microglia, in vivo

value: Naive


title: Library 7656


title: Library 6684


title: Library 10996


title: Library 7657


title: Library 7649

value: LiA, 150 uM


title: Library 7650


title: Library 7654


title: Library 11008

value: 22 months old


title: Library 7647

value: PA, 150 uM


title: Library 7646


title: Library 7648


title: Library 7645

value: TNFa + P3C + PGE2 + IFNb, 0.000004 ug/ul


title: Library 7639


title: Library 7636

value: LPS_hi, 0.0001 ug/ul


title: Library 7637


title: Library 7642


title: Library 7638


title: Library 7644


title: Library 6686


title: Library 7634

value: GABA, 100 uM


title: Library 7633


title: Library 7652

value: norepinephrine, 1 uM


title: Library 7628

value: LPS_lo + eotaxin, 0.00001 ug/ul


title: Library 7625


title: Library 7624


title: Library 7619


title: Library 7620

value: None, 0 ug/ul


title: Library 7655


title: Library 7611


title: Library 7621


title: Library 7631


title: Library 7607

value: estradiol, 1 nM


title: Library 7608


title: Library 7612


title: Library 7604

value: OA, 150 uM


title: Library 7606


title: Library 7610


title: Library 7602


title: Library 7603


title: Library 7601

value: IC, 0.2 ug/ul


title: Library 7635

value: microglia, in vitro


title: Library 7596


title: Library 7595


title: Library 7593


title: Library 7591

value: MPP, 100 uM


title: Library 7589

value: 72 hrs


title: Library 7588


title: Library 7584

value: LPS_lo + estradiol, 0.00001 ug/ul


title: Library 7581


title: Library 7586


title: Library 7609


title: Library 7580


title: Library 7605


title: Library 7578


title: Library 7250


title: Library 7576


title: Library 7574


title: Library 7577


title: Library 7573


title: Library 7243

value: eotaxin, 0.00005 ug/ul


title: Library 7248


title: Library 7249


title: Library 7594


title: Library 7246


title: Library 7244


title: Library 7241


title: Library 7592


title: Library 7237


title: Library 7238


title: Library 7236


title: Library 7240


title: Library 7590

value: TNFa + IFNg, 0.000004 ug/ul


title: Library 7235


title: Library 7575


title: Library 7234


title: Library 7231


title: Library 7230


title: Library 7232


title: Library 7228


title: Library 7225

value: LPS_lo + IFNg, 0.00001 ug/ul


title: Library 7226


title: Library 7229


title: Library 7224


title: Library 7222

value: LPS_lo + TGFb, 0.00001 ug/ul


title: Library 7220


title: Library 7219


title: Library 7218


title: Library 7216

value: LPS_lo + IC, 0.00001 ug/ul


title: Library 7202


title: Library 7201


title: Library 7200


title: Library 7242


title: Library 7217


title: Library 7195


title: Library 7204


title: Library 7198


title: Library 7190


title: Library 7194


title: Library 7188


title: Library 7189


title: Library 7196


title: Library 7191


title: Library 7185


title: Library 7186


title: Library 7184


title: Library 7223


title: Library 7180


title: Library 7179


title: Library 7178


title: Library 7177


title: Library 7176


title: Library 7172


title: Library 7174


title: Library 7161

value: IFNa, 0.0008 ug/ul


title: Library 7158

value: HDL, 2 ug/ul


title: Library 7159


title: Library 7156


title: Library 7150

value: LiA, 150 uM


title: Library 7170


title: Library 7144


title: Library 7157


title: Library 7160


title: Library 7138

value: LPS_hi, 0.0001 ug/ul


title: Library 7119


title: Library 7117

value: None, 0 ug/ul


title: Library 7114


title: Library 7183


title: Library 7115


title: Library 7116


title: Library 7112

value: CRH, 10 nM


title: Library 7113


title: Library 7111


title: Library 7110


title: Library 7173


title: Library 7171


title: Library 7091


title: Library 7072


title: Library 7071


title: Library 7070


title: Library 7182


title: Library 7067

value: LPS_hi + nicotine, 0.0001 ug/ul

value: 4 hrs


title: Library 7097

value: microglia, in vitro

value: OA, 150 uM


title: Library 7066


title: Library 7064


title: Library 7063

value: LPS_hi + ATP, 0.0001 ug/ul


title: Library 7061

value: IFNb, 0.0001 ug/ul

value: 24 hrs


title: Library 7062


title: Library 7065


title: Library 7058


title: Library 7060


title: Library 7055

value: IC, 0.2 ug/ul


title: Library 7056


title: Library 7059


title: Library 7054


title: Library 7052


title: Library 7047


title: Library 7049


title: Library 7051


title: Library 7046


title: Library 7048


title: Library 7045


title: Library 7042


title: Library 7038


title: Library 7044


title: Library 7040


title: Library 7050


title: Library 7039


title: Library 7036

value: nicotine, 1000 uM


title: Library 7034


title: Library 7069

value: 72 hrs


title: Library 7035


title: Library 7033


title: Library 7041


title: Library 7028

value: LPS_hi + norepinephrine, 0.0001 ug/ul


title: Library 7026


title: Library 7027


title: Library 7025


title: Library 7023


title: Library 7018


title: Library 7019


title: Library 7024


title: Library 7020


title: Library 7030


title: Library 7021


title: Library 7016

value: Valproic Acid, 1000 uM


title: Library 7017

value: HDL, 2 ug/ul


title: Library 7004


title: Library 7003


title: Library 7002


title: Library 7000


title: Library 7001


title: Library 7015


title: Library 6999

value: ATP, 1000 uM


title: Library 6994

value: norepinephrine, 1 uM


title: Library 7005


title: Library 6992


title: Library 6996


title: Library 6990


title: Library 7029


title: Library 6989


title: Library 6991


title: Library 6986


title: Library 6988


title: Library 6985


title: Library 6987


title: Library 6981

value: IFNa, 0.0008 ug/ul


title: Library 6982


title: Library 6978


title: Library 6980


title: Library 6995


title: Library 6976

value: GABA, 100 uM


title: Library 6972


title: Library 6970


title: Library 6968


title: Library 6967


title: Library 6969


title: Library 6974


title: Library 6965


title: Library 6964


title: Library 6961


title: Library 6960


title: Library 6971


title: Library 6962


title: Library 6984


title: Library 6955


title: Library 6954


title: Library 6959

value: LiA, 150 uM


title: Library 6958


title: Library 6979


title: Library 6956


title: Library 6973


title: Library 6949

value: None, 0 ug/ul


title: Library 6948

value: microglia, in vitro

value: LPS_hi, 0.0001 ug/ul


title: Library 6977


title: Library 6952

value: CRH, 10 nM


title: Library 6946


title: Library 6945

value: minocycline, 20 uM


title: Library 6966


title: Library 6944

value: 24 hrs


title: Library 6940

value: estradiol, 1 nM


title: Library 6939

value: LPS_hi + minocycline, 0.0001 ug/ul


title: Library 6942


title: Library 6937


title: Library 6936


title: Library 6934

value: LPS_hi + estradiol, 0.0001 ug/ul


title: Library 6943


title: Library 6933


title: Library 6938


title: Library 6931


title: Library 6929


title: Library 6932


title: Library 6930


title: Library 6953

value: 72 hrs


title: Library 6926

value: resveratrol, 50 uM


title: Library 6928


title: Library 6925


title: Library 6950


title: Library 6927


title: Library 6951


title: Library 6921

value: LPS_lo + resveratrol, 0.00001 ug/ul


title: Library 6924


title: Library 6922

value: rapamycin, 5 nM


title: Library 6923


title: Library 6918


title: Library 6919


title: Library 6917

value: LPS_lo + rapamycin, 0.00001 ug/ul


title: Library 6916


title: Library 6915


title: Library 6911

value: IFNa, 0.0008 ug/ul


title: Library 6913


title: Library 6914


title: Library 6910


title: Library 6908


title: Library 6907


title: Library 6905

value: IC, 0.2 ug/ul


title: Library 6904


title: Library 6906


title: Library 6900


title: Library 6896

value: substance P, 59.3 uM


title: Library 6895


title: Library 6947

value: Valproic Acid, 1000 uM


title: Library 6903

value: microglia, in vitro


title: Library 6902

value: LPS_hi, 0.0001 ug/ul


title: Library 6899

value: None, 0 ug/ul


title: Library 6920


title: Library 6891

value: AEA, 1 nM


title: Library 6892

value: 24 hrs


title: Library 6889

value: nicotine, 1000 uM


title: Library 6893


title: Library 6894


title: Library 6886

value: 2AG, 1 nM


title: Library 6885


title: Library 6883


title: Library 6912


title: Library 6882


title: Library 6880

value: LiA, 150 uM


title: Library 6879


title: Library 6875

value: OA, 150 uM


title: Library 6881


title: Library 6874


title: Library 6873


title: Library 6872

value: eotaxin, 0.00005 ug/ul


title: Library 6871


title: Library 6890


title: Library 6887


title: Library 6859

value: HDL, 2 ug/ul


title: Library 6862


title: Library 6861


title: Library 6857


title: Library 6863


title: Library 6866

value: norepinephrine, 1 uM


title: Library 6856


title: Library 6865


title: Library 6867

value: PA, 150 uM


title: Library 6864


title: Library 6860


title: Library 6884


title: Library 6854


title: Library 6853


title: Library 6851


title: Library 6852


title: Library 6876


title: Library 6877


title: Library 6850


title: Library 6849


title: Library 6848


title: Library 6846


title: Library 6845


title: Library 6843


title: Library 6844


title: Library 6858


title: Library 6841


title: Library 6842


title: Library 6840


title: Library 6839


title: Library 6837


title: Library 6832

value: glutamate, 500 uM


title: Library 6834


title: Library 6827

value: ATP, 1000 uM


title: Library 6835


title: Library 6828


title: Library 6830

value: IFNb, 0.0001 ug/ul


title: Library 6824

value: IFNg, 0.0001 ug/ul


title: Library 6833

value: microglia, in vitro


title: Library 6838


title: Library 6831


title: Library 6823


title: Library 6829


title: Library 6826


title: Library 6822

value: TGFb, 0.0001 ug/ul


title: Library 6820


title: Library 6836


title: Library 6818

value: dopamine, 100 uM


title: Library 6816

value: MPP, 100 uM


title: Library 6817

value: 24 hrs


title: Library 6819


title: Library 6815


title: Library 6812

value: 72 hrs


title: Library 6811

value: LPS_lo + norepinephrine, 0.00001 ug/ul


title: Library 6810


title: Library 6806


title: Library 6825


title: Library 6807


title: Library 6804


title: Library 6803


title: Library 6805


title: Library 6802


title: Library 6799


title: Library 6798


title: Library 6794


title: Library 6796


title: Library 6800

value: GABA, 100 uM


title: Library 6795


title: Library 6813


title: Library 6809


title: Library 6787


title: Library 6780


title: Library 6781


title: Library 6791


title: Library 6779


title: Library 6783

value: LiA, 150 uM


title: Library 6788


title: Library 6786


title: Library 6801


title: Library 6797


title: Library 6774


title: Library 6773


title: Library 6771

value: Valproic Acid, 1000 uM


title: Library 6769

value: LPS_hi, 0.0001 ug/ul


title: Library 6772

value: HDL, 2 ug/ul


title: Library 6789


title: Library 6793


title: Library 6792


title: Library 6763


title: Library 6765

value: estradiol, 1 nM


title: Library 6761


title: Library 6768

value: None, 0 ug/ul


title: Library 6764


title: Library 6782


title: Library 6760

value: LPS_hi + estradiol, 0.0001 ug/ul


title: Library 6766


title: Library 6762


title: Library 6785

value: PA, 150 uM


title: Library 6759


title: Library 6758

value: LPS_hi + GABA, 0.0001 ug/ul


title: Library 6757

value: microglia, in vitro


title: Library 6755


title: Library 6756


title: Library 6754


title: Library 6770


title: Library 6752


title: Library 6753


title: Library 6749


title: Library 6750


title: Library 6747

value: rapamycin, 5 nM


title: Library 6743


title: Library 6744


title: Library 6748


title: Library 6745


title: Library 6746


title: Library 6742

value: LPS_lo + rapamycin, 0.00001 ug/ul


title: Library 6739

value: LPS_lo + CCL2, 0.00001 ug/ul


title: Library 6738

value: 24 hrs


title: Library 6737


title: Library 6736

value: IFNa, 0.0008 ug/ul


title: Library 6733


title: Library 6732


title: Library 6731


title: Library 6575

value: LPS_hi + nicotine, 0.0001 ug/ul

value: 4 hrs


title: Library 6741


title: Library 6574


title: Library 6751


title: Library 6571


title: Library 6572


title: Library 6569

value: LPS_hi + ATP, 0.0001 ug/ul


title: Library 6565


title: Library 6570


title: Library 6567


title: Library 6734


title: Library 6561


title: Library 6559


title: Library 6735


title: Library 6557


title: Library 6563

value: LPS_hi + norepinephrine, 0.0001 ug/ul


title: Library 6562


title: Library 6558

value: LPS_hi, 0.0001 ug/ul


title: Library 6553


title: Library 6556


title: Library 6555


title: Library 6551


title: Library 6546


title: Library 6547


title: Library 6548


title: Library 6544

value: LPS_hi + minocycline, 0.0001 ug/ul


title: Library 6573


title: Library 6564


title: Library 6542


title: Library 6540


title: Library 6539


title: Library 6537


title: Library 6550


title: Library 6543


title: Library 6536


title: Library 6538


title: Library 6533

value: estradiol, 1 nM


title: Library 6534


title: Library 6554


title: Library 6549


title: Library 6532

value: GABA, 100 uM


title: Library 6530

value: minocycline, 20 uM


title: Library 6529


title: Library 6531


title: Library 6535


title: Library 6465

value: nicotine, 1000 uM


title: Library 6463


title: Library 6462


title: Library 6464


title: Library 6461


title: Library 6460


title: Library 6452

value: norepinephrine, 1 uM


title: Library 6454

value: microglia, in vitro


title: Library 6459

value: ATP, 1000 uM


title: Library 6457


title: Library 6456


title: Library 6458


title: Library 6451


title: Library 6453


title: Library 6440

value: LPS_lo + resveratrol, 0.00001 ug/ul


title: Library 6439


title: Library 6450


title: Library 6441


title: Library 6448


title: Library 6447


title: Library 6449


title: Library 6442


title: Library 6444


title: Library 6443


title: Library 6445


title: Library 6446


title: Library 6436

value: LPS_lo + CCL2, 0.00001 ug/ul


title: Library 6435

value: LPS_hi + estradiol, 0.0001 ug/ul

value: 24 hrs


title: Library 6438


title: Library 6430

value: LPS_hi + GABA, 0.0001 ug/ul


title: Library 6432


title: Library 6434


title: Library 6431


title: Library 6428

value: None, 0 ug/ul


title: Library 6429


title: Library 6426


title: Library 6425


title: Library 6427


title: Library 6433


title: Library 6420


title: Library 6423

value: resveratrol, 50 uM


title: Library 6418

value: rapamycin, 5 nM


title: Library 6307

value: TNFa + P3C + PGE2 + IFNb, 0.000004 ug/ul

value: 72 hrs


title: Library 6305


title: Library 6304


title: Library 6303


title: Library 6302


title: Library 6419


title: Library 6422


title: Library 6437


title: Library 6306


title: T422-1

city: Harbin

first: Yue

last: Leng

address: Xiangfang District Timber Street

country: China

institute: Northeast Agricultural University

data_processing:
The libraries were submitted for 125 base pair (bp) paired-end sequencing on the Illumina HiSeq 2500 platform
Paired-end clean reads were aligned to the reference genome using TopHat (v2.0.9). The mapped reads of each sample were assembled using both Scripture (beta2) and Cufflinks (v2.1.1).
The assembled transcripts were annotated using the Cuffcompare program from the Cufflinks package.
Genome_build: http://rice.plantbiology.msu.edu/index.shtml
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa

growth_protocol: growth in the natural environment

extract_protocol:
after treatment, one leaf was randomly collected per bucket , and the sample leaves were frozen immediately in liquid nitrogen. High-quality total RNA from sample leaves was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
The total amount of 3 μg RNA per sample was used as input material for RNA sample preparations. First, ribosomal RNA was removed and sequencing libraries were generated using a NEBNext® Ultra™ Directional RNA Library Prep Kit following user's manual. After synthesizing first-strand cDNA and second-strand cDNA, the library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, USA) to select 150~200 bp cDNA fragments. The cDNA library was obtained by PCR amplification.

treatment_protocol: in the incubator and treated with 17℃ temperature with 16 h illumination of full light intensity and 8 h dark for 13 days

value: leaf

tag: Stage

value: the booting stage


title: T422-2

tag: treatment


title: T422-3


title: Library 6300


title: CK422-3

value: control


title: Library 6299


title: CK422-2


title: Library 6297


title: Library 6424


title: CK422-1


title: Library 6296

value: LPS_lo + IFNg, 0.00001 ug/ul


title: Library 6295


title: Library 6301


title: T131-3


title: T131-2


title: Library 6292

value: LPS_lo + TGFb, 0.00001 ug/ul


title: Library 6293

value: microglia, in vitro


title: Library 6288

value: LPS_lo + eotaxin, 0.00001 ug/ul


title: Library 6291


title: CK131-2


title: CK131-3


title: CK131-1


title: Library 6290


title: Library 6287


title: Library 6286

value: LPS_lo + IC, 0.00001 ug/ul


title: Library 6284

value: LPS_hi, 0.0001 ug/ul


title: SMSNor1_152_S54_L006_R1_001_125_160

city: San Diego

first: Louise

last: Laurent

state: CA

address: 9500 Gilman Drive

institute: UC San Diego

description: sample_SMSNor1_152_S54_L006_R1_001_125_160_fastq

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with an adapter sequence of AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC. Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data archive contains RPM read counts for miRNAs, piRNAs, tRNAs, Y RNAs, lincRNAs, snoRNAs, and snRNAs.

extract_protocol:
Three "Core" RNA isolation methods (ExoRNeasy (Qiagen), miRNeasy (Qiagen), and miRCury Biofluids (Exiqon)) were tested in all labs, and 7 methods (Exosomal RNA Purification Kit (Norgen Biotek) w/o Amicon 3K, Exosomal RNA Purification Kit (Norgen Biotek) w/ Amicon 3K, Ultracentrifugation + miRNeasy, Millipore + miRNeasy, ME Kit (New England Peptide) + miRNeasy, Exoquick+Seramir (SBI), miRcury Exosome Isolation + miRcury Biofluids (Exiqon)) were tested in a subset of labs. RNA isolation was performed in triplicate for each method in each lab. Input volume for RNA isolation experiments was 500 uL. One can visit https://exrna.org/resources/protocols/ to see more information about the RNA isolation protocols used.
1.2 uL of each RNA sample was used for a first batch of small RNAseq library construction. The resulting initial dataset was analyzed to determine the total input read (TIR) count and the total miRNA read (TMR) count. Libraries that yielded <10,000 TIRs were considered to have failed library preparation. Libraries that yielded >10,000 TIRs and <100,000 TMRs were handled in one of three ways: 1. Libraries for which the percent TMR > 0.08% and for which there was sufficient material (small RNA library or isolated exRNA sample) to obtain 100,000 TMRs were re-run, and the data from the two runs were combined. 2. Libraries in which the percent TMR (TMR/TIR x 100) < 0.08% were not prepared again, as it would require >12.5 million TIR to obtain 100,000 TMRs. 3. Libraries for which the percent TMR > 0.08% and for which there was insufficient material (small RNA library or isolated exRNA sample) to obtain 100,000 TMRs were not re-run.

treatment_protocol: Serum and plasma were collected from healthy adult donors, 10 female and 10 male. Cells and cell debris were removed by centrifugation at 2,000 xg for 10 minutes, and the resulting cell-free serum and plasma were pooled using equal volumes from each donor to make four pools: female serum, male serum, female plasma, and male plasma. These pools were split into 1 mL aliquots and stored at -80 oC. In addition, serum and plasma from one female and one male donor were also aliquoted and stored. Aliquots of these standardized samples were distributed to each of three (for serum) or four (for plasma) labs.

tag: donor status

value: healthy adult donor control

tag: donor gender

value: Male

tag: tissue/cell type

value: Serum

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: Norgen


description: sample_SMSmiRNeasy2_150_S52_L006_R1_001_125_160_fastq

value: miRNeasy


title: SMSNor_Ami2_154_S56_L006_R1_001_125_160

description: sample_SMSNor_Ami2_154_S56_L006_R1_001_125_160_fastq


title: Library 6283

value: None, 0 ug/ul

value: 72 hrs


description: sample_SMSExoQuick1_158_S13_L005_R1_001_125_160_fastq

value: Exoquick


title: Library 6294


description: sample_SMSExoQuick2_159_S14_L005_R1_001_125_160_fastq


title: Library 6281


title: Library 6280


title: Library 6279


description: sample_SMPNor_Ami2_170_S161_L008_R1_001_125_160_fastq

value: Plasma


description: sample_SMPExoRNeasy1_162_S17_L005_R1_001_125_160_fastq

value: Exorneasy


title: Library 6278

value: IFNg, 0.0001 ug/ul


title: T131-1

value: leaf

value: the booting stage


title: Library 6277

value: microglia, in vitro


title: Library 6276


description: sample_SMPExoQuick2_175_S30_L005_R1_001_125_160_fastq


description: sample_SMPExoQuick3_176_S123_L007_R1_001_125_160_fastq


description: sample_SMPExoRNeasy1_162_S143_L004_R1_001_115_180_fastq


title: Library 6274

value: IFNb, 0.0001 ug/ul


description: sample_SMPExoQuick2_175_S153_L004_R1_001_115_180_fastq

value: healthy adult donor control


title: Library 6272


title: SMPExiqon1_164_S157_L008_R1_001_125_160

description: sample_SMPExiqon1_164_S157_L008_R1_001_125_160_fastq

value: Male

value: Exiqon


title: SFSNor_Ami2_153_S55_L006_R1_001_125_160

description: sample_SFSNor_Ami2_153_S55_L006_R1_001_125_160_fastq

value: Female

value: Serum

value: Entire cardiovascular system


title: SFSNor1_151_S53_L006_R1_001_125_160

description: sample_SFSNor1_151_S53_L006_R1_001_125_160_fastq

value: total cell-free biofluid RNA

value: Norgen


title: Library 6273

value: 72 hrs


title: Library 6268


title: Library 6270


description: sample_SFSExoRNeasy1_145_S48_L006_R1_001_125_160_fastq


title: SMPExiqon1_164_S145_L004_R1_001_115_180

description: sample_SMPExiqon1_164_S145_L004_R1_001_115_180_fastq


description: sample_SFSmiRNeasy2_149_S142_L008_R1_001_125_160_fastq

value: miRNeasy


description: sample_SFSExoQuick3_157_S12_L005_R1_001_125_160_fastq

value: Exoquick


title: Library 6266

value: eotaxin, 0.00005 ug/ul


title: Library 6267


title: SMPNor1_168_S159_L008_R1_001_125_160

description: sample_SMPNor1_168_S159_L008_R1_001_125_160_fastq

value: Plasma


description: sample_SFSExoQuick1_155_S57_L006_R1_001_125_160_fastq


description: sample_SFSExoQuick2_156_S58_L006_R1_001_125_160_fastq


title: Library 6282

value: None, 0 ug/ul


title: SMPNor1_168_S147_L004_R1_001_115_180

description: sample_SMPNor1_168_S147_L004_R1_001_115_180_fastq


title: Library 6264


title: Library 6263


title: SFSExiqon1_147_S50_L006_R1_001_125_160

description: sample_SFSExiqon1_147_S50_L006_R1_001_125_160_fastq


description: sample_SMSExoQuick3_160_S15_L005_R1_001_125_160_fastq


title: Library 6271


title: SFPNor1_167_S146_L004_R1_001_115_180

description: sample_SFPNor1_167_S146_L004_R1_001_115_180_fastq


title: Library 6258


title: Library 6265


title: Library 6269


title: Library 6254


title: Library 6256


description: sample_SFPNor_Ami2_169_S160_L008_R1_001_125_160_fastq


description: sample_SFPExoRNeasy1_161_S142_L004_R1_001_115_180_fastq

value: Exorneasy


title: Library 6252

value: microglia, in vitro


description: sample_SFPExoRNeasy1_161_S16_L005_R1_001_125_160_fastq


description: sample_SFPExoQuick3_173_S75_L006_R1_001_125_160_fastq


description: sample_SFPExoQuick3_173_S152_L004_R1_001_115_180_fastq


title: Library 6251


title: Library 6545

value: LPS_hi + GABA, 0.0001 ug/ul

value: 24 hrs


description: sample_SFPExoQuick2_172_S163_L008_R1_001_125_160_fastq

value: healthy adult donor control


title: Library 6249

value: TNFa + IFNg, 0.000004 ug/ul


title: Library 6248


description: sample_SFPExoQuick1_171_S162_L008_R1_001_125_160_fastq

value: Female


title: Library 6247


title: SFPExiqon1_163_S156_L008_R1_001_125_160

description: sample_SFPExiqon1_163_S156_L008_R1_001_125_160_fastq

value: Exiqon


title: SFPExiqon1_163_S144_L004_R1_001_115_180

description: sample_SFPExiqon1_163_S144_L004_R1_001_115_180_fastq

value: Entire cardiovascular system


title: Library 6245

value: LPS_lo + TGFb, 0.00001 ug/ul


title: GMSNor1_112_S62_L006_R1_001_125_160

description: sample_GMSNor1_112_S62_L006_R1_001_125_160_fastq

value: Male

value: Serum

value: total cell-free biofluid RNA

value: Norgen


title: GMSNor_Ami3_120_S70_L006_R1_001_125_160

description: sample_GMSNor_Ami3_120_S70_L006_R1_001_125_160_fastq


title: Library 6250

value: 72 hrs


title: Library 6257


title: SFPNor1_167_S158_L008_R1_001_125_160

description: sample_SFPNor1_167_S158_L008_R1_001_125_160_fastq

value: Plasma


title: Library 6243

value: LPS_lo + estradiol, 0.00001 ug/ul


title: Library 6255


title: Library 6241


title: Library 6242


title: GMSME1_108_S149_L008_R1_001_125_160

description: sample_GMSME1_108_S149_L008_R1_001_125_160_fastq

value: ME


title: GMSNor_Ami1_118_S68_L006_R1_001_125_160

description: sample_GMSNor_Ami1_118_S68_L006_R1_001_125_160_fastq


description: sample_GMSMillipore1_104_S145_L008_R1_001_125_160_fastq

value: Millipore


description: sample_GMSExoRNeasy1_98_S140_L008_R1_001_125_160_fastq

value: Exorneasy


title: Library 6246

value: microglia, in vitro


title: GMSUltra1_106_S147_L008_R1_001_125_160

description: sample_GMSUltra1_106_S147_L008_R1_001_125_160_fastq

value: healthy adult donor control

value: Ultra


title: GMPUltra1_130_S167_L008_R1_001_125_160

description: sample_GMPUltra1_130_S167_L008_R1_001_125_160_fastq


title: Library 6239

value: LPS_lo + IC, 0.00001 ug/ul


title: GMPNor1_136_S171_L008_R1_001_125_160

description: sample_GMPNor1_136_S171_L008_R1_001_125_160_fastq


title: GMPNor2_137_S160_L004_R1_001_115_180

description: sample_GMPNor2_137_S160_L004_R1_001_115_180_fastq


title: Library 6238


title: Library 6240


title: GMPNor2_137_S87_L006_R1_001_125_160

description: sample_GMPNor2_137_S87_L006_R1_001_125_160_fastq


title: Library 6235


description: sample_GMPNor_Ami3_144_S129_L003_R1_001_115_180_fastq


title: GMSNor_Ami2_119_S69_L006_R1_001_125_160

description: sample_GMSNor_Ami2_119_S69_L006_R1_001_125_160_fastq


title: Library 6236


title: Library 6244


title: Library 6237


title: GMPNor3_138_S173_L008_R1_001_125_160

description: sample_GMPNor3_138_S173_L008_R1_001_125_160_fastq


title: GMPNor_Ami1_142_S92_L006_R1_001_125_160

description: sample_GMPNor_Ami1_142_S92_L006_R1_001_125_160_fastq


title: Library 6233

value: None, 0 ug/ul


description: sample_GMPNor_Ami2_143_S128_L003_R1_001_115_180_fastq

value: Entire cardiovascular system


title: Library 6234


title: Library 6232


title: Library 6231


description: sample_GMPNor_Ami1_142_S164_L004_R1_001_115_180_fastq


title: Library 6230


description: sample_GMPmiRNeasy1_126_S121_L007_R1_001_125_160_fastq

value: miRNeasy


title: Library 6229

value: LPS_hi, 0.0001 ug/ul


description: sample_GMPMillipore1_128_S165_L008_R1_001_125_160_fastq

value: Male


title: Library 6228

value: IFNb, 0.0001 ug/ul


title: GMPME1_132_S168_L008_R1_001_125_160

description: sample_GMPME1_132_S168_L008_R1_001_125_160_fastq

value: total cell-free biofluid RNA


title: Library 6227

value: 72 hrs


description: sample_GMPExoRNeasy1_122_S72_L006_R1_001_125_160_fastq

value: Plasma


title: Library 6226

value: TGFb, 0.0001 ug/ul


title: Library 6225


title: GMPExiqon1_124_S74_L006_R1_001_125_160

description: sample_GMPExiqon1_124_S74_L006_R1_001_125_160_fastq

value: Exiqon


title: Library 6223


title: Library 6224


title: GMPExiqon1_124_S151_L004_R1_001_115_180

description: sample_GMPExiqon1_124_S151_L004_R1_001_115_180_fastq


title: Library 6221


title: Library 6222


title: GFSNor2_110_S60_L006_R1_001_125_160

description: sample_GFSNor2_110_S60_L006_R1_001_125_160_fastq

value: Female

value: Serum

value: Norgen


title: Library 6220

value: microglia, in vitro

value: estradiol, 1 nM


title: GFSNor1_109_S59_L006_R1_001_125_160

description: sample_GFSNor1_109_S59_L006_R1_001_125_160_fastq

value: healthy adult donor control


title: GFSNor3_111_S106_L007_R1_001_125_160

description: sample_GFSNor3_111_S106_L007_R1_001_125_160_fastq


title: GFSUltra1_105_S146_L008_R1_001_125_160

description: sample_GFSUltra1_105_S146_L008_R1_001_125_160_fastq

value: Ultra


title: Library 6219


title: GFSNor_Ami2_116_S66_L006_R1_001_125_160

description: sample_GFSNor_Ami2_116_S66_L006_R1_001_125_160_fastq

value: Entire cardiovascular system


title: Library 6213

value: IC, 0.2 ug/ul


title: Library 6217


description: sample_GFSNor_Ami3_117_S112_L007_R1_001_125_160_fastq


title: Library 6212


title: GFSME1_107_S148_L008_R1_001_125_160

description: sample_GFSME1_107_S148_L008_R1_001_125_160_fastq

value: ME


title: GFPUltra1_129_S166_L008_R1_001_125_160

description: sample_GFPUltra1_129_S166_L008_R1_001_125_160_fastq


description: sample_GMPExoRNeasy1_122_S149_L004_R1_001_115_180_fastq

value: Male

value: Exorneasy


title: GFPNor2_134_S84_L006_R1_001_125_160

description: sample_GFPNor2_134_S84_L006_R1_001_125_160_fastq

value: total cell-free biofluid RNA


title: Library 6181

value: 24 hrs


title: GFPNor2_134_S159_L004_R1_001_115_180

description: sample_GFPNor2_134_S159_L004_R1_001_115_180_fastq

value: Plasma


title: GFPNor3_135_S170_L008_R1_001_125_160

description: sample_GFPNor3_135_S170_L008_R1_001_125_160_fastq


title: GFPNor1_133_S83_L006_R1_001_125_160

description: sample_GFPNor1_133_S83_L006_R1_001_125_160_fastq


title: Library 6179

value: GABA, 100 uM


title: GFPNor1_133_S158_L004_R1_001_115_180

description: sample_GFPNor1_133_S158_L004_R1_001_115_180_fastq


title: Library 6178


title: Library 6177


title: Library 6176

value: MPP, 100 uM


title: GFPNor_Ami3_141_S91_L006_R1_001_125_160

description: sample_GFPNor_Ami3_141_S91_L006_R1_001_125_160_fastq

value: Female


title: Library 6218

value: 72 hrs


title: Library 6175


title: GFPNor_Ami2_140_S43_L005_R1_001_125_160

description: sample_GFPNor_Ami2_140_S43_L005_R1_001_125_160_fastq


title: Library 6174


title: GFSNor_Ami1_115_S65_L006_R1_001_125_160

description: sample_GFSNor_Ami1_115_S65_L006_R1_001_125_160_fastq

value: Serum


description: sample_GFPNor_Ami3_141_S163_L004_R1_001_115_180_fastq


title: Library 6173

value: microglia, in vitro

value: ATP, 1000 uM


title: GFPNor_Ami1_139_S42_L005_R1_001_125_160

description: sample_GFPNor_Ami1_139_S42_L005_R1_001_125_160_fastq

value: healthy adult donor control


description: sample_GFPNor_Ami2_140_S162_L004_R1_001_115_180_fastq


title: Library 6172


title: Library 6170


title: Library 6171


description: sample_GFPNor_Ami1_139_S161_L004_R1_001_115_180_fastq


description: sample_GFPmiRNeasy1_125_S164_L008_R1_001_125_160_fastq

value: miRNeasy


title: Library 6182

value: estradiol, 1 nM


title: GFPME1_131_S156_L004_R1_001_115_180

description: sample_GFPME1_131_S156_L004_R1_001_115_180_fastq

value: Entire cardiovascular system


title: Library 6180


title: Library 6168


description: sample_GFPExoRNeasy1_121_S71_L006_R1_001_125_160_fastq


title: Library 6167

value: OA, 150 uM


title: Library 6166


title: GFPExiqon1_123_S73_L006_R1_001_125_160

description: sample_GFPExiqon1_123_S73_L006_R1_001_125_160_fastq

value: Exiqon


title: Library 6164

value: TGFb, 0.0001 ug/ul


title: GFPExiqon1_123_S150_L004_R1_001_115_180

description: sample_GFPExiqon1_123_S150_L004_R1_001_115_180_fastq

value: total cell-free biofluid RNA


title: Library 6165

value: 24 hrs


title: Library 6161

value: None, 0 ug/ul


title: DMPExiqon1_180_S82_L006_R1_001_125_160

description: sample_DMPExiqon1_180_S82_L006_R1_001_125_160_fastq

value: Male

value: Plasma


description: sample_DMPExoRNeasy1_178_S155_L004_R1_001_115_180_fastq

value: ExoRNeasy


title: DMPExiqon1_180_S157_L004_R1_001_115_180

description: sample_DMPExiqon1_180_S157_L004_R1_001_115_180_fastq


title: Library 6160


description: sample_DMPExoRNeasy1_178_S80_L006_R1_001_125_160_fastq


description: sample_DFPmiRNeasy1_181_S169_L008_R1_001_125_160_fastq

value: Female


description: sample_DFPExoRNeasy1_177_S79_L006_R1_001_125_160_fastq


title: GFPME1_131_S81_L006_R1_001_125_160

description: sample_GFPME1_131_S81_L006_R1_001_125_160_fastq

value: ME


title: Library 6163

value: microglia, in vitro


description: sample_DFPExoRNeasy1_177_S154_L004_R1_001_115_180_fastq


title: Library 6155

value: LPS_hi, 0.0001 ug/ul


title: Library 6156


title: Library 6159


title: BMSUltra3_30_S29_L005_R1_001_125_160

description: sample_BMSUltra3_30_S29_L005_R1_001_125_160_fastq

value: healthy adult donor control

value: Serum

value: Ultra


title: Library 6169


title: BMSUltra2_29_S28_L005_R1_001_125_160

description: sample_BMSUltra2_29_S28_L005_R1_001_125_160_fastq

value: Entire cardiovascular system


description: sample_BMSmiRNeasy3_18_S155_L008_R1_001_125_160_fastq

value: miRNeasy


title: Library 6154


description: sample_GFPExoRNeasy1_121_S148_L004_R1_001_115_180_fastq

value: Exorneasy


title: Library 6153


title: BMSUltra1_28_S27_L005_R1_001_125_160

description: sample_BMSUltra1_28_S27_L005_R1_001_125_160_fastq


title: Library 6151

value: norepinephrine, 1 uM


title: Library 6162

value: TGFb, 0.0001 ug/ul


title: Library 6150

value: 24 hrs


description: sample_BMSmiRNeasy2_17_S108_L007_R1_001_125_160_fastq

value: total cell-free biofluid RNA


title: Library 6149

value: nicotine, 1000 uM


title: BMSmiRCury2_47_S178_L008_R1_001_125_160

description: sample_BMSmiRCury2_47_S178_L008_R1_001_125_160_fastq

value: Male

value: MiRCury


title: Library 6157


title: Library 6148


description: sample_BMSMillipore3_24_S23_L005_R1_001_125_160_fastq

value: Millipore


title: BMSmiRCury1_46_S45_L005_R1_001_125_160

description: sample_BMSmiRCury1_46_S45_L005_R1_001_125_160_fastq


title: Library 6147


title: Library 6146

value: minocycline, 20 uM


description: sample_BMSMillipore2_23_S22_L005_R1_001_125_160_fastq


description: sample_BMSMillipore1_22_S21_L005_R1_001_125_160_fastq


title: Library 6144

value: microglia, in vitro


title: Library 6145


title: BMSME2_35_S34_L005_R1_001_125_160

description: sample_BMSME2_35_S34_L005_R1_001_125_160_fastq

value: ME


title: BMSME3_36_S35_L005_R1_001_125_160

description: sample_BMSME3_36_S35_L005_R1_001_125_160_fastq

value: healthy adult donor control


title: Library 6143

value: rapamycin, 5 nM


title: Library 6142


title: Library 6141


title: BMSME1_34_S33_L005_R1_001_125_160

description: sample_BMSME1_34_S33_L005_R1_001_125_160_fastq

value: Serum


title: BMSExoRNeasy3_6_S5_L005_R1_001_125_160

description: sample_BMSExoRNeasy3_6_S5_L005_R1_001_125_160_fastq

value: Entire cardiovascular system

value: ExoRNeasy


title: Library 6140


title: BMSExoRNeasy2_5_S4_L005_R1_001_125_160

description: sample_BMSExoRNeasy2_5_S4_L005_R1_001_125_160_fastq


title: Library 6139


title: BMSExoQuick2_41_S40_L005_R1_001_125_160

description: sample_BMSExoQuick2_41_S40_L005_R1_001_125_160_fastq

value: Exoquick


title: BMSExoQuick3_42_S41_L005_R1_001_125_160

description: sample_BMSExoQuick3_42_S41_L005_R1_001_125_160_fastq


title: Library 6137


description: sample_BMSmiRNeasy1_16_S153_L008_R1_001_125_160_fastq

value: miRNeasy


title: BMSExoQuick1_40_S39_L005_R1_001_125_160

description: sample_BMSExoQuick1_40_S39_L005_R1_001_125_160_fastq


title: Library 6135


title: BMSExiqon2_11_S10_L005_R1_001_125_160

description: sample_BMSExiqon2_11_S10_L005_R1_001_125_160_fastq

value: Exiqon


title: Library 6036

value: glutamate, 500 uM

value: 24 hrs


title: Library 6037


title: Library 6035

value: ATP, 1000 uM


title: BMSExiqon1_10_S9_L005_R1_001_125_160

description: sample_BMSExiqon1_10_S9_L005_R1_001_125_160_fastq

value: Male

value: total cell-free biofluid RNA


title: BMPUltra2_77_S120_L007_R1_001_125_160

description: sample_BMPUltra2_77_S120_L007_R1_001_125_160_fastq

value: Plasma

value: Ultra


title: BMPUltra3_78_S111_L003_R1_001_115_180

description: sample_BMPUltra3_78_S111_L003_R1_001_115_180_fastq


title: Library 6136

value: microglia, in vitro


title: Library 6034


title: BMPUltra1_76_S110_L003_R1_001_115_180

description: sample_BMPUltra1_76_S110_L003_R1_001_115_180_fastq


description: sample_BMPmiRNeasy3_66_S109_L007_R1_001_125_160_fastq


title: Library 6032

value: MPP, 100 uM


description: sample_BMPmiRNeasy2_65_S154_L008_R1_001_125_160_fastq

value: healthy adult donor control


title: BMPmiRCury2_95_S138_L007_R1_001_125_160

description: sample_BMPmiRCury2_95_S138_L007_R1_001_125_160_fastq

value: MiRCury


title: Library 6031


title: Library 6030


title: Library 6033


title: Library 6138


title: Library 6029

value: rapamycin, 5 nM


title: BMPmiRCury1_94_S127_L003_R1_001_115_180

description: sample_BMPmiRCury1_94_S127_L003_R1_001_115_180_fastq

value: Entire cardiovascular system


title: Library 6027


description: sample_BMPMillipore3_72_S106_L003_R1_001_115_180_fastq

value: Millipore


title: Library 6026

value: dopamine, 100 uM


description: sample_BMPMillipore2_71_S105_L003_R1_001_115_180_fastq


title: Library 6025


title: BMSExiqon3_12_S11_L005_R1_001_125_160

description: sample_BMSExiqon3_12_S11_L005_R1_001_125_160_fastq

value: Serum


description: sample_BMPMillipore1_70_S104_L003_R1_001_115_180_fastq


title: BMPME3_84_S117_L003_R1_001_115_180

description: sample_BMPME3_84_S117_L003_R1_001_115_180_fastq

value: ME


title: Library 6024


title: BMPME2_83_S116_L003_R1_001_115_180

description: sample_BMPME2_83_S116_L003_R1_001_115_180_fastq


title: Library 6021


description: sample_BMPExoRNeasy3_54_S91_L003_R1_001_115_180_fastq

value: ExoRNeasy


title: Library 6019

value: 24 hrs


title: BMPME1_82_S115_L003_R1_001_115_180

description: sample_BMPME1_82_S115_L003_R1_001_115_180_fastq


title: Library 6023


description: sample_BMPExoRNeasy2_53_S90_L003_R1_001_115_180_fastq


title: Library 6018


title: Library 6017

value: IFNg, 0.0001 ug/ul


title: Library 6016


title: Library 6020


title: Library 6014


title: Library 6015


title: Library 6013


description: sample_BMPExoQuick2_89_S122_L003_R1_001_115_180_fastq

value: Male

value: Exoquick


description: sample_BMPExoQuick3_90_S123_L003_R1_001_115_180_fastq

value: Plasma

value: total cell-free biofluid RNA


description: sample_BMPExoQuick1_88_S121_L003_R1_001_115_180_fastq


title: BMPExiqon1_58_S95_L003_R1_001_115_180

description: sample_BMPExiqon1_58_S95_L003_R1_001_115_180_fastq

value: Exiqon


title: BFSUltra3_27_S26_L005_R1_001_125_160

description: sample_BFSUltra3_27_S26_L005_R1_001_125_160_fastq

value: Female

value: Ultra


title: BMPExiqon2_59_S96_L003_R1_001_115_180

description: sample_BMPExiqon2_59_S96_L003_R1_001_115_180_fastq

value: healthy adult donor control


title: BMPExiqon3_60_S97_L003_R1_001_115_180

description: sample_BMPExiqon3_60_S97_L003_R1_001_115_180_fastq


title: Library 6012

value: microglia, in vitro


title: Library 6011


title: BFSUltra1_25_S24_L005_R1_001_125_160

description: sample_BFSUltra1_25_S24_L005_R1_001_125_160_fastq

value: Entire cardiovascular system


description: sample_BFSmiRNeasy2_14_S151_L008_R1_001_125_160_fastq

value: miRNeasy


title: BFSUltra2_26_S25_L005_R1_001_125_160

description: sample_BFSUltra2_26_S25_L005_R1_001_125_160_fastq


title: Library 6010


title: BFSmiRCury3_45_S44_L005_R1_001_125_160

description: sample_BFSmiRCury3_45_S44_L005_R1_001_125_160_fastq

value: MiRCury


title: Library 6009


title: Library 6007

value: OA, 150 uM


title: BFSmiRCury2_44_S175_L008_R1_001_125_160

description: sample_BFSmiRCury2_44_S175_L008_R1_001_125_160_fastq

value: Serum


title: BFSmiRCury1_43_S174_L008_R1_001_125_160

description: sample_BFSmiRCury1_43_S174_L008_R1_001_125_160_fastq


description: sample_BFSMillipore3_21_S20_L005_R1_001_125_160_fastq

value: Millipore


description: sample_BFSMillipore2_20_S19_L005_R1_001_125_160_fastq


title: Library 6005

value: LiA, 150 uM

value: 24 hrs


title: Library 6006


title: Library 6003


description: sample_BFSMillipore1_19_S18_L005_R1_001_125_160_fastq


title: Library 6002

value: norepinephrine, 1 uM


title: Library 6000


title: Library 6001


title: Library 5999

value: eotaxin, 0.00005 ug/ul


title: Library 5998


title: Library 5996


title: BFSME1_31_S122_L007_R1_001_125_160

description: sample_BFSME1_31_S122_L007_R1_001_125_160_fastq

value: ME


title: BFSExoRNeasy1_1_S1_L005_R1_001_125_160

description: sample_BFSExoRNeasy1_1_S1_L005_R1_001_125_160_fastq

value: total cell-free biofluid RNA

value: ExoRNeasy


title: BFSExoRNeasy2_2_S2_L005_R1_001_125_160

description: sample_BFSExoRNeasy2_2_S2_L005_R1_001_125_160_fastq

value: Female


title: BFSExoQuick3_39_S38_L005_R1_001_125_160

description: sample_BFSExoQuick3_39_S38_L005_R1_001_125_160_fastq

value: Exoquick


title: Library 5995


title: BFSExoRNeasy3_3_S3_L005_R1_001_125_160

description: sample_BFSExoRNeasy3_3_S3_L005_R1_001_125_160_fastq

value: healthy adult donor control


title: Library 5997

value: microglia, in vitro


title: BFSME2_32_S78_L006_R1_001_125_160

description: sample_BFSME2_32_S78_L006_R1_001_125_160_fastq

value: Entire cardiovascular system


title: BFSExoQuick2_38_S37_L005_R1_001_125_160

description: sample_BFSExoQuick2_38_S37_L005_R1_001_125_160_fastq


title: Library 5993

value: nicotine, 1000 uM


title: Library 5992


title: BFSExiqon3_9_S8_L005_R1_001_125_160

description: sample_BFSExiqon3_9_S8_L005_R1_001_125_160_fastq

value: Exiqon


title: BFSExoQuick1_37_S36_L005_R1_001_125_160

description: sample_BFSExoQuick1_37_S36_L005_R1_001_125_160_fastq


title: Library 6004


title: Library 5991


title: Library 5990

value: TGFb, 0.0001 ug/ul


title: Library 5989


title: BFSExiqon1_7_S6_L005_R1_001_125_160

description: sample_BFSExiqon1_7_S6_L005_R1_001_125_160_fastq

value: Serum


title: Library 5988


title: BFPUltra3_75_S109_L003_R1_001_115_180

description: sample_BFPUltra3_75_S109_L003_R1_001_115_180_fastq

value: Plasma

value: Ultra


title: BFSME3_33_S32_L005_R1_001_125_160

description: sample_BFSME3_33_S32_L005_R1_001_125_160_fastq


title: BFPUltra2_74_S108_L003_R1_001_115_180

description: sample_BFPUltra2_74_S108_L003_R1_001_115_180_fastq


title: Library 5987

value: estradiol, 1 nM

value: 24 hrs


title: Library 5986


title: Library 5985


description: sample_BFPmiRNeasy3_63_S152_L008_R1_001_125_160_fastq

value: miRNeasy


title: Library 5984

value: GABA, 100 uM


title: BFPmiRNeasy2_62_S98_L003_R1_001_115_180

description: sample_BFPmiRNeasy2_62_S98_L003_R1_001_115_180_fastq

value: total cell-free biofluid RNA


title: Library 5983


description: sample_BFPmiRNeasy1_61_S104_L007_R1_001_125_160_fastq


title: Library 5980

value: minocycline, 20 uM


title: BFSExiqon2_8_S7_L005_R1_001_125_160

description: sample_BFSExiqon2_8_S7_L005_R1_001_125_160_fastq

value: Female


title: Library 5981


title: Library 5979


title: BFPmiRCury1_91_S124_L003_R1_001_115_180

description: sample_BFPmiRCury1_91_S124_L003_R1_001_115_180_fastq

value: MiRCury


title: BFPmiRCury2_92_S125_L003_R1_001_115_180

description: sample_BFPmiRCury2_92_S125_L003_R1_001_115_180_fastq

value: healthy adult donor control


description: sample_BFPMillipore3_69_S103_L003_R1_001_115_180_fastq

value: Millipore


title: Library 5982

value: microglia, in vitro


title: Library 5978

value: resveratrol, 50 uM


title: Library 5977


title: Library 5976


description: sample_BFPMillipore2_68_S102_L003_R1_001_115_180_fastq

value: Entire cardiovascular system


title: Library 5975


title: BFPUltra1_73_S107_L003_R1_001_115_180

description: sample_BFPUltra1_73_S107_L003_R1_001_115_180_fastq


title: Library 5974


title: Library 5973


description: sample_BFPExoRNeasy3_51_S89_L003_R1_001_115_180_fastq

value: ExoRNeasy


title: BFPME1_79_S112_L003_R1_001_115_180

description: sample_BFPME1_79_S112_L003_R1_001_115_180_fastq

value: ME


description: sample_BFPMillipore1_67_S101_L003_R1_001_115_180_fastq

value: Plasma


title: BFPME3_81_S114_L003_R1_001_115_180

description: sample_BFPME3_81_S114_L003_R1_001_115_180_fastq


description: sample_BFPExoRNeasy1_49_S87_L003_R1_001_115_180_fastq


title: Library 5972

value: IFNb, 0.0001 ug/ul


title: BFPmiRCury3_93_S126_L003_R1_001_115_180

description: sample_BFPmiRCury3_93_S126_L003_R1_001_115_180_fastq


description: sample_BFPExoQuick1_85_S118_L003_R1_001_115_180_fastq

value: Exoquick


title: BFPExiqon3_57_S94_L003_R1_001_115_180

description: sample_BFPExiqon3_57_S94_L003_R1_001_115_180_fastq

value: Exiqon


title: Library 5970

value: 24 hrs


title: Library 5966


title: Library 5968


title: BFPExiqon2_56_S93_L003_R1_001_115_180

description: sample_BFPExiqon2_56_S93_L003_R1_001_115_180_fastq


title: Library 5965


title: Library 5967


title: Library 5971


title: Library 5964


title: BFPExiqon1_55_S92_L003_R1_001_115_180

description: sample_BFPExiqon1_55_S92_L003_R1_001_115_180_fastq


title: Library 5963

value: PA, 150 uM


title: BFPME2_80_S113_L003_R1_001_115_180

description: sample_BFPME2_80_S113_L003_R1_001_115_180_fastq

value: total cell-free biofluid RNA


title: 531_serum_Idx32_S80_L006

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with an adapter sequence of AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC. Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data archive contains RPM read counts for miRNAs / piRNAs / tRNAs / GENCODE annotations / circular RNAs.

extract_protocol:
250 ml whole blood was collected from five adult female and five adult male donors using 19G needles using 60 mL syringes containing either no additive (for serum) or 440 uL 0.5 M K2EDTA pH 8. The blood was then transferred into 50 mL polypropylene tubes and allowed to sit at room temperature 10-60 minutes. The tubes were then spun at 2,000 xg for 20 minutes at room temperature. The clear supernatant was transferred to a fresh tube and centrifuged again at 2000 xg for 10 min at room temperature. The serum or plasma was then aliquoted into 1.5ml tubes and stored at -80 degrees C. A volume of 0.8 mL of each serum and plasma sample was individually mixed with 38 mL of PBS, placed into a 40 mL ultracentrifuge tube, and underlaid with 2 mL 60% iodixanol. The tubes were spun at 100,000 xg for 2 hours at 4 degrees C. The bottom 3 mL (2 mL iodixanol cushion + 1 mL supernatant was removed, mixed, and underlaid under a step gradient of iodixanol (5%-10%-20% iodixanol in PBS). This was spun at 100,000 xg for 18 hours at 4 degrees C. RNA from unfractionated serum and plasma samples (500 uL each) was isolated using the miRNeasy micro kit (Qiagen) and concentrated using a Zymo RNA clean and concentrator-5 kit with a final elution volume of 7 uL. From each OptiPrepTM gradient, we combined fractions 1-3 (numbered from the top of the gradient) to form the light fraction, fractions 4-7 for the low-density fraction, and 9-12 for the high-density fraction. RNA was isolated from 500 uL of each of these combined fractions using the miRNeasy micro kit (Qiagen) and concentrated using a Zymo RNA clean and concentrator-5 kit with a final elution volume of 7 uL.
4 uL of each RNA sample was dried in a SpeedVacTM. The dried RNA was then resuspended in 1.2 uL of water and used to generate a small RNAseq library using the NEBNext Multiplex small RNA Library Prep kit. The library reactions were performed at ⅕ scale using a Mosquito HTS liquid handler. The 80 libraries were combined into 2 pools, which were size-selected using a Pippen Prep with a cutoff of 117-180 bp. Each size-selected pool was run on one lane of a HiSeq4000.

value: Male

value: Serum

value: miRNeasy micro kit (Qiagen)

tag: used in analysis

value: TRUE


description: sample_BFPExoRNeasy2_50_S88_L003_R1_001_115_180_fastq

value: healthy adult donor control

value: Female


title: 531_serum_Fxn_4_7_Idx26_S26_L005


title: Library 5961

value: microglia, in vitro


title: 531_serum_Fxn_1_3_Idx25_S25_L005

value: Entire cardiovascular system


title: Library 5960

value: 2AG, 1 nM


title: 531_serum_Fxn_9_12_Idx27_S27_L005

description: 531_serum_Fxn_9_12_Idx27_S27_L005_R1_001


title: 531_plasma_Idx22_S70_L006


title: Library 5959


title: Library 5958


title: 531_plasma_Fxn_9_12_Idx15_S15_L005

description: 531_plasma_Fxn_9_12_Idx15_S15_L005_R1_001


title: 531_plasma_Fxn_4_7_Idx14_S14_L005

description: 531_plasma_Fxn_4_7_Idx14_S14_L005_R1_001


description: sample_BFPExoQuick3_87_S120_L003_R1_001_115_180_fastq


title: Library 5969


title: 531_plasma_Fxn_1_3_Idx13_S13_L005

description: 531_plasma_Fxn_1_3_Idx13_S13_L005_R1_001


description: sample_BFPExoQuick2_86_S119_L003_R1_001_115_180_fastq


title: Library 5957

value: AEA, 1 nM


title: Library 5954

value: LPS_hi, 0.0001 ug/ul


title: 528_serum_Fxn_9_12_Idx33_S33_L005

description: 528_serum_Fxn_9_12_Idx33_S33_L005_R1_001


title: Library 5952


title: 528_plasma_Idx21_S69_L006

value: Plasma


title: 528_serum_Fxn_1_3_Idx31_S31_L005


title: Library 5951

value: CRH, 10 nM


title: Library 5953


title: 528_plasma_Fxn_9_12_Idx18_S18_L005

description: 528_plasma_Fxn_9_12_Idx18_S18_L005_R1_001


title: Library 5950


title: Library 5949


title: Library 5947

value: substance P, 59.3 uM


title: 528_plasma_Fxn_4_7_Idx17_S17_L005

description: 528_plasma_Fxn_4_7_Idx17_S17_L005_R1_001


title: 528_plasma_Fxn_1_3_Idx16_S16_L005

description: 528_plasma_Fxn_1_3_Idx16_S16_L005_R1_001


title: Library 5948

value: 24 hrs


title: 524_serum_Fxn_9_12_Idx36_S36_L005

description: 524_serum_Fxn_9_12_Idx36_S36_L005_R1_001


title: 524_serum_Fxn_4_7_Idx35_S35_L005


title: Library 5945

value: None, 0 ug/ul


title: Library 5944


title: 524_plasma_Idx20_S68_L006

value: total cell-free biofluid RNA


title: 524_plasma_Fxn_9_12_Idx21_S21_L005

description: 524_plasma_Fxn_9_12_Idx21_S21_L005_R1_001

value: Male


title: Library 5584

value: glutamate, 500 uM


title: Library 5956


title: 528_serum_Idx31_S79_L006

value: Serum

value: miRNeasy micro kit (Qiagen)


title: Library 5585


title: 528_serum_Fxn_4_7_Idx32_S32_L005

value: healthy adult donor control

value: TRUE


title: 524_plasma_Fxn_4_7_Idx20_S20_L005

description: 524_plasma_Fxn_4_7_Idx20_S20_L005_R1_001


title: Library 5583

value: microglia, in vitro


title: 524_plasma_Fxn_1_3_Idx19_S19_L005

description: 524_plasma_Fxn_1_3_Idx19_S19_L005_R1_001

value: Entire cardiovascular system


title: 524_serum_Idx30_S78_L006


title: 517_serum_Idx29_S77_L006

value: Female


title: Library 5946


title: Library 5581


title: Library 5582


title: 517_serum_Fxn_9_12_Idx39_S39_L005

description: 517_serum_Fxn_9_12_Idx39_S39_L005_R1_001


title: 517_serum_Fxn_1_3_Idx37_S37_L005


title: Library 5579

value: resveratrol, 50 uM


title: Library 5578


title: 517_serum_Fxn_4_7_Idx38_S38_L005


title: 517_plasma_Fxn_9_12_Idx3_S51_L006

description: 517_plasma_Fxn_9_12_Idx3_S51_L006_R1_001


title: 524_serum_Fxn_1_3_Idx34_S34_L005


title: Library 5943


title: Library 5577


title: Library 5576


title: 517_plasma_Fxn_4_7_Idx2_S50_L006


title: Id1V_2iLIF_b

city: Edinburgh

first: Sally

last: Lowell

address: SCRM Building, 5 Little France Drive

department: MRC Cente for Regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

description: Unsorted sample, replicate B

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Raw data was processed in R using the beadarray (Dunning et al., 2007) package from the Bioconductor suite (Gentleman et al., 2004). Data was quantile-normalised.

label: Biotin

source_name: Unsorted sample, replicate B

label_protocol: 100 ng of total RNA were reverse transcribed into double-stranded cDNA and transcribed/amplified into biotin labelled cRNA using an Illumina TotalPrep RNA Amplification Kit (AMIL1791, Ambion).

extract_protocol: RNA was prepared using Absolutely RNA Purification Kits (Agilent).

value: Embryonic stem cells

tag: cell line


title: 517_plasma_Fxn_1_3_Idx1_S49_L006

tag: tissue

value: Plasma


title: Library 5575


title: Id1V_2i_b

description: Unsorted sample, replicate B

tag: strain


title: Library 5574

tag: cell type

value: LiA, 150 uM


title: Id1V_2iLIF_a

description: Unsorted sample, replicate A

source_name: Unsorted sample, replicate A


title: 515_serum_Idx28_S76_L006


title: 515_serum_Fxn_9_12_Idx45_S45_L005

description: 515_serum_Fxn_9_12_Idx45_S45_L005_R1_001


title: Library 5572

tag: duration


title: Library 5573


title: IVNR_Unsorted_b

description: Unsorted sample, replicate B

growth_protocol: GMEM+LIF+FCS

value: IVNR

value: Id1-Venus Nanog-tagRFP


title: 515_serum_Fxn_4_7_Idx44_S44_L005


title: Library 5571

value: PA, 150 uM

value: 24 hrs


title: MG tumor, Lsd1 ChIP, biological replicate 1

city: HEIDELBERG

first: Paul

middle: A.

last: Northcott

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

data_processing:
Sequence quality was assessed by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequence reads from ChIP-Seq were  aligned  to the mouse reference genome (mm10, chromosomes 1-19, X, Y and M) using the ‘Burrow-Wheeler Transformation’ based aligner BWA (version 0.6.2, arguments -q20).
BAM files were merged using Picard (http://picard.sourceforge.net) and duplicate reads were removed.
Peak calling for Gfi1 and Lsd1 in MG tumors was done using MACS with default parameters and using the appropriate input chromatin controls, used in the preparation of the respective factor ChIPs.
To identify the high confidence peak set for each factor, initially the peaks with the upper 20th percentile enrichments were identified separately for the two replicates of the respective factor. Afterwards, resulting peaks were overlapped (at least 50% overlap) and the overlapping peaks were referred as the high confidence peak set of the respective factor.
Genome_build: mm10
Supplementary_files_format_and_content: TDF files for visualization in IGV; BED files containing peak calls as determined by MACS.

source_name: Lsd1 ChIP-seq data derived from murine MG (Myc/Gfi1) medulloblastoma tumor

growth_protocol: Mouse cerebellar stem cells (isolated from cerebella at P5-P7) were purified by sorting cells that expressed prominin-1 (detected with antibody 13A4) and lacked the lineage markers O4, polysialated (PSA)-NCAM (Chemicon) and TAPA-1 (eBioscience). Prominin+lin− cells were sorted into Neurobasal medium with B27 supplement (NB-B27, Invitrogen) containing 10 mg ml−1 BSA (Sigma), washed and resuspended in NB-B27 with appropriate growth factors.

extract_protocol:
To isolate NSCs, Prominin1+, Lineage-negative (lin-) cells were FACS-sorted from cerebella of 5-7-day-old WT mice. Tumor cells were isolated by enzymatic dissociation of cerebella from adult tumor-bearing mice. All cells were snap-frozen in liquid nitrogen. Frozen tumor tissue was processed for ChIP at ActiveMotif (Carlsbad, CA) according to proprietary protocols.
According to Illumina protocols.

tag: tissue type

value: murine medulloblastoma tumor

tag: chip antibody

value: Rabbit polyclonal, anti-Lsd1, Abcam #ab17721 (4ug)


title: Pooled MGB tumor, input control

source_name: Input ChIP-seq control derived from pooled murine MGB (Myc/Gfi1b) medulloblastoma tumor

tag: mouse strain


title: IVNR_NR-LO_IdV-LO_a

description: Sorted sample, Nanog-tagRFP-low Id1-Venus-low, replicate A

tag: genotype


title: Library 5570

tag: treatment


title: MG tumor, Lsd1 ChIP, biological replicate 2


title: 515_plasma_Fxn_9_12_Idx12_S60_L006

description: 515_plasma_Fxn_9_12_Idx12_S60_L006_R1_001

tag: donor status

value: total cell-free biofluid RNA


title: IVNR_NR-LO_IdV-LO_b

description: Sorted sample, Nanog-tagRFP-low Id1-Venus-low, replicate B


title: IVNR_NR-HI_IdV-LO_a

description: Sorted sample, Nanog-tagRFP-high Id1-Venus-low, replicate A


title: IVNR_Unsorted_a

description: Unsorted sample, replicate A


title: IVNR_NR-LO_IdV-HI_b

description: Sorted sample, Nanog-tagRFP-low Id1-Venus-high, replicate B


title: Library 5569


title: 515_plasma_Fxn_4_7_Idx11_S59_L006

description: 515_plasma_Fxn_4_7_Idx11_S59_L006_R1_001

tag: donor gender

value: miRNeasy micro kit (Qiagen)


title: MG tumor, Gfi1 ChIP, biological replicate 2

source_name: Gfi1 ChIP-seq data derived from murine MG (Myc/Gfi1) medulloblastoma tumor

value: Rabbit polyclonal, anti-Gfi1 antibody, GNE-CJS-2 (4ug)


title: 515_plasma_Fxn_1_3_Idx10_S58_L006

description: 515_plasma_Fxn_1_3_Idx10_S58_L006_R1_001

value: healthy adult donor control

value: TRUE


title: 515_serum_Fxn_1_3_Idx43_S43_L005

value: Serum

value: Entire cardiovascular system


title: Library 5568

value: microglia, in vitro

value: IFNg, 0.0001 ug/ul


title: MG tumor, Gfi1 ChIP, biological replicate 1


title: Cortex_dbdb-Pio_5

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then processed using the Tuxedo suite of sequence analysis programs. Reads were mapped to the NCBI reference mouse transcriptome (NCBI 37) to identify transcripts.
Mapped reads were processed using the Cufflinks algorithm to calculate fragments per kilobase of exon per million mapped reads (FPKM), as presented in Trapnell et al., Nature Protocol 2012, which accurately reflects the RNA transcript number normalized for RNA length and total number of mapped reads.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: kidney cortex

extract_protocol:
Tissues [sciatic nerve (SCN), dorsal root ganglia (DRG), kidney glomerui, and kidney cortex] were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS‐122‐2001, RS‐122‐2002; Illumina, San Diego, CA, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney cortex

tag: agent

value: pioglitazone

tag: diabetes-type

value: dbdb

value: BKS.Cg-m +/+ Leprdb/J

tag: age

value: 16-week old


title: Cortex_dbdb_6


title: Cortex_dbdb-Pio_4


title: Cortex_dbdb-Pio_2


title: Cortex_dbdb-Pio_6


title: Library 5566

value: 24 hrs


title: Cortex_dbdb-Pio_1


title: IVNR_NR-LO_IdV-HI_a

description: Sorted sample, Nanog-tagRFP-low Id1-Venus-high, replicate A

value: Embryonic stem cells

value: IVNR

value: Id1-Venus Nanog-tagRFP


title: IVNR_NR-HI_IdV-LO_b

description: Sorted sample, Nanog-tagRFP-high Id1-Venus-low, replicate B


title: Cortex_dbdb-Pio_3


title: 514_serum_Fxn_9_12_Idx48_S48_L005

description: 514_serum_Fxn_9_12_Idx48_S48_L005_R1_001

value: Female

tag: anatomical location

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: miRNeasy micro kit (Qiagen)


title: Cortex_dbdb_5

tag: tissue


title: 514_serum_Idx27_S75_L006

value: healthy adult donor control

tag: used in analysis

value: TRUE


title: Library 5565

tag: cell type

value: eotaxin, 0.00005 ug/ul


title: Cortex_dbdb_4

tag: strain


title: Cortex_dbdb_3


title: 514_serum_Fxn_4_7_Idx47_S47_L005

value: Serum

value: Entire cardiovascular system


title: 514_serum_Fxn_1_3_Idx46_S46_L005


title: Cortex_dbdb_2

value: kidney cortex


title: Cortex_dbdb_1


title: Cortex_Cont-Pio_6

value: pioglitazone

value: db+


title: Library 5563

value: microglia, in vitro

tag: duration


title: Library 5567

value: IFNg, 0.0001 ug/ul


title: Cortex_Cont-Pio_5

value: BKS.Cg-m +/+ Leprdb/J

value: 16-week old


title: 514_plasma_Idx17_S65_L006

value: Plasma


title: Cortex_Cont-Pio_4


title: Id1V_2i_a

description: Unsorted sample, replicate A

value: Embryonic stem cells

tag: cell line


title: 514_plasma_Fxn_9_12_Idx9_S57_L006

description: 514_plasma_Fxn_9_12_Idx9_S57_L006_R1_001

value: Female


title: Library 5561

value: 24 hrs


title: Cortex_Cont-Pio_1


title: Cortex_Cont_4


title: Cortex_Cont_6


title: Library 5562


title: Cortex_Cont-Pio_3


title: 510_serum_Idx26_S74_L006

value: Male

value: total cell-free biofluid RNA

value: miRNeasy micro kit (Qiagen)


title: Cortex_Cont_3


title: 514_plasma_Fxn_1_3_Idx7_S55_L006

value: healthy adult donor control

value: TRUE


title: Cortex_Cont_5


title: Cortex_Cont_2


title: Library 5558


title: Cortex_Cont-Pio_2


title: 510_serum_Fxn_9_12_Idx30_S30_L005

description: 510_serum_Fxn_9_12_Idx30_S30_L005_R1_001

value: Serum

value: Entire cardiovascular system


title: 514_plasma_Fxn_4_7_Idx8_S56_L006


title: Library 5560


title: Library 5564

value: eotaxin, 0.00005 ug/ul


title: Library 5557


title: 510_serum_Fxn_4_7_Idx29_S29_L005


title: Cortex_Cont_1

value: kidney cortex

value: db+


title: Glom_dbdb-Pio_5

source_name: kidney glomeruli

value: kidney glomeruli

value: pioglitazone

value: dbdb


title: Glom_dbdb-Pio_4

value: BKS.Cg-m +/+ Leprdb/J

value: 16-week old


title: Library 5556

value: microglia, in vitro

value: dopamine, 100 uM


title: Glom_dbdb-Pio_3


title: Library 5555

value: 24 hrs


title: 510_serum_Fxn_1_3_Idx28_S28_L005

value: Male

value: total cell-free biofluid RNA


title: Library 5559


title: 510_plasma_Idx16_S64_L006

value: healthy adult donor control

value: Plasma

value: miRNeasy micro kit (Qiagen)


title: 510_plasma_Fxn_9_12_Idx24_S24_L005

description: 510_plasma_Fxn_9_12_Idx24_S24_L005_R1_001

value: Entire cardiovascular system

value: TRUE


title: Glom_dbdb_4


title: Glom_dbdb_6


title: Glom_dbdb-Pio_6


title: Glom_dbdb_5


title: 510_plasma_Fxn_4_7_Idx23_S23_L005

description: 510_plasma_Fxn_4_7_Idx23_S23_L005_R1_001


title: Library 5551

value: substance P, 59.3 uM


title: Glom_dbdb-Pio_1


title: Glom_dbdb-Pio_2


title: 509_serum_Idx25_S73_L006

value: Female

value: Serum


title: 510_plasma_Fxn_1_3_Idx22_S22_L005

description: 510_plasma_Fxn_1_3_Idx22_S22_L005_R1_001


title: Glom_dbdb_2

value: kidney glomeruli


title: Glom_dbdb_1

value: dbdb


title: Library 5552


title: Library 5550

value: 2AG, 1 nM


title: Glom_Cont-Pio_6

value: pioglitazone

value: db+

value: BKS.Cg-m +/+ Leprdb/J

value: 16-week old


title: Glom_Cont-Pio_5


title: Glom_Cont-Pio_4


title: Glom_Cont-Pio_2


title: 509_serum_Fxn_9_12_Idx42_S42_L005

description: 509_serum_Fxn_9_12_Idx42_S42_L005_R1_001


title: Library 5549

value: microglia, in vitro

value: 24 hrs


title: Glom_Cont-Pio_1


title: Library 5548


title: 509_serum_Fxn_4_7_Idx41_S41_L005

value: healthy adult donor control

value: total cell-free biofluid RNA


title: Library 5554

value: dopamine, 100 uM


title: Glom_dbdb_3


title: Library 5553


title: Glom_Cont-Pio_3


title: Glom_Cont_5


title: Library 5547

value: AEA, 1 nM


title: 509_plasma_Fxn_9_12_Idx6_S54_L006

description: 509_plasma_Fxn_9_12_Idx6_S54_L006_R1_001

value: Plasma

value: Entire cardiovascular system

value: miRNeasy micro kit (Qiagen)

value: TRUE


title: 509_serum_Fxn_1_3_Idx40_S40_L005

value: Female

value: Serum


title: Glom_Cont_1

value: kidney glomeruli


title: Glom_Cont_3


title: Library 5544

value: None, 0 ug/ul


title: DRG_dbdb-Pio_4

source_name: dorsal root ganglia

value: dorsal root ganglia

value: pioglitazone

value: dbdb


title: DRG_dbdb-Pio_5

value: BKS.Cg-m +/+ Leprdb/J

value: 16-week old


title: DRG_dbdb-Pio_6


title: 509_plasma_Fxn_1_3_Idx4_S52_L006

value: healthy adult donor control


title: Glom_Cont_2

value: db+


title: DRG_dbdb-Pio_2


title: Library 5546

value: microglia, in vitro

value: 24 hrs


title: Library 5545

value: AEA, 1 nM


title: DRG_dbdb-Pio_3


title: DRG_dbdb-Pio_1


title: Glom_Cont_6


title: 508_serum_Idx24_S72_L006

value: Entire cardiovascular system

value: total cell-free biofluid RNA


title: Library 5543


title: Glom_Cont_4


title: 509_plasma_Fxn_4_7_Idx5_S53_L006

value: Plasma

value: miRNeasy micro kit (Qiagen)

value: TRUE


title: Library 5542


title: 508_serum_Fxn_9_12_Idx6_S6_L005

value: Female

value: Serum


title: 509_plasma_Idx15_S63_L006


title: Library 5541

value: LPS_hi, 0.0001 ug/ul


title: DRG_dbdb_1

value: dorsal root ganglia


title: 508_serum_Fxn_4_7_Idx5_S5_L005


title: Library 5540


title: DRG_Cont-Pio_6

value: pioglitazone


title: DRG_dbdb_3

value: dbdb

value: BKS.Cg-m +/+ Leprdb/J


title: DRG_Cont-Pio_4

value: 16-week old


title: 508_plasma_Idx14_S62_L006

value: healthy adult donor control


title: DRG_dbdb_2


title: DRG_Cont-Pio_5

value: db+


title: 508_serum_Fxn_1_3_Idx4_S4_L005


title: Library 5539

value: microglia, in vitro

value: 24 hrs


title: 508_plasma_Fxn_9_12_Idx3_S3_L005

value: Entire cardiovascular system


title: DRG_Cont-Pio_2


title: DRG_Cont_6


title: DRG_dbdb_4


title: DRG_Cont_5


title: 508_plasma_Fxn_4_7_Idx2_S2_L005

value: total cell-free biofluid RNA


title: CD31+CD105neg

city: Tianjin

first: Jiaxi

last: Zhou

state: Tianjin

address: 288# Nanjing Road, He ping district

institute: PUMC

data_processing:
Illumina GA Pipeline v1.5 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then use BWA (Li, H. and Durbin, R., 2009) to map clean reads to genome reference and use Bowtie (Langmead B, et al., 2009) to gene reference
We provide genome alignment data in BAM format and recommend using IGV(Ietegrative Genomics Viewer) tool to visualize BAM file in different scales.
Genes expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). RSEM (Li B and Dewey C N., 2011)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: H1 cell line

growth_protocol: H1 were induced for stepwise hematopoietic differentiation. First, cells were cultured in Custom mTeSR1 medium supplemented with 40 ng/ml activinA (Peprotech) and 50 ng/ml BMP4 (Peprotech) for 2 days. Second, cells were incubated with Custom mTeSR1 medium supplemented with 40 ng/ml VEGF (Peprotech) and 50 ng/ml bFGF (Peprotech) for 3 days.

extract_protocol:
H1 drived cells was collected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD31+CD34+CD105negHEPs derived from day4 of hematopoietic differentiation


title: DRG_Cont_4


title: DRG_Cont-Pio_1


title: CD31+CD105high

value: CD31+CD34+CD105highHEPs derived from day4 of hematopoietic differentiation


title: DRG_Cont-Pio_3


title: 508_plasma_Fxn_1_3_Idx1_S1_L005

value: Plasma

value: miRNeasy micro kit (Qiagen)

value: TRUE


title: DRG_Cont_2


title: DRG_Cont_3


title: DRG_Cont_1


title: 505_serum_Idx23_S71_L006

value: Male

value: Serum


title: SCN_dbdb-Pio_6

source_name: sciatic nerve

value: sciatic nerve

value: pioglitazone


title: SCN_dbdb-Pio_5

value: dbdb

value: BKS.Cg-m +/+ Leprdb/J


title: 505_serum_Fxn_9_12_Idx9_S9_L005

value: healthy adult donor control


title: 505_serum_Fxn_4_7_Idx8_S8_L005


title: SCN_dbdb-Pio_4

value: 16-week old


title: SCN_dbdb-Pio_2


title: SCN_dbdb-Pio_3


title: 505_serum_Fxn_1_3_Idx7_S7_L005


title: 505_plasma_Idx13_S61_L006


title: SCN_dbdb_5


title: SCN_dbdb-Pio_1


title: SCN_dbdb_2


title: 505_plasma_Fxn_9_12_Idx12_S12_L005

description: 505_plasma_Fxn_9_12_Idx12_S12_L005_R1_001


title: SCN_dbdb_3


title: SCN_dbdb_4


title: DRG_dbdb_5

value: dorsal root ganglia


title: 505_plasma_Fxn_4_7_Idx11_S11_L005

description: 505_plasma_Fxn_4_7_Idx11_S11_L005_R1_001


title: SCN_dbdb_1


title: SCN_Cont-Pio_6

value: db+


title: 505_plasma_Fxn_1_3_Idx10_S10_L005

description: 505_plasma_Fxn_1_3_Idx10_S10_L005_R1_001

value: Entire cardiovascular system


title: SCN_Cont-Pio_5


title: SCN_Cont-Pio_4