title: 7.KO1.Tb: NMuMG_RREB1_KO_TGFb_1

first: Jie

last: Su

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

data_processing:
QC: FastQC v0.11.5
Alignment: STAR2.5.2b
RNAseq annotation: HTSeq v0.6.1p1
RNAseq normalization: DESeq2 v3.4
Genome_build: mm10
Supplementary_files_format_and_content: RNASeq: Normalized Counts in .csv

source_name: mouse mammary gland epithelial cells

growth_protocol: NMuMG mouse mammary epithelial cells were cultured in DMEM supplemented with 10% FBS, 10μg/mL insulin, 2 mM L-glutamine, 100 units/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
Total RNA was collected using Qiagen's Rneasy Mini Kit (74106) and assessed for RNA integrity number >9.5.
For RNASeq, library construction was performed using TruSeq RNA Sample Prep Kit v2 (Illumina) following manufacturer’s instructions.

treatment_protocol: Cells were serum starved for 6 h and treated with 2.5 µM SB505124 (Sigma S4696) for 6 h or 100 pM TGFβ (R&D 101-B1) for 1.5 h.

value: mouse mammary gland epithelial cells

tag: cell line

value: NMuMG

value: TGFβ

tag: timepoint


title: MEF-TC1

status: Public on Jan 09 2020

type: SRA

city: Guangzhou

first: Xiaodong

last: Ma

state: Guangdong

address: Rm406,Building 29, South China Normal University

country: China

institute: South China Normal University

library_source: transcriptomic

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 v2.1.0 with default parameters. The number of reads mapped to each gene was calculated by Htseq.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and counts for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Mouse embryonic fibroblast

extract_protocol:
Cell RNA were harvested using Trizol reagent. Poly(A) RNAs were purified by using the Dynabeads mRNA purification kit and Poly(A) RNAs were fragmented at 94C for 5 min before reverse transcribed to cDNA with random primers. cDNA fragments were blunted and ligated to sequencing adaptors. Libraries were sequenced with the High-Seq 2000 Illumina sequencing platform
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MEF treated with PBS (control), TNF-ɑ + Cycloheximide (TC) or TNF-ɑ + Cycloheximide+ z-VAD-fmk (TCZ).

tag: strain

tag: cell type

value: Mouse embryonic fibroblast

tag: passages


title: MEF-TCZ2


title: MEF-ctl2


title: MM4831_Lung

city: London

first: Anne

last: OGarra

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Insititue

description:
HN878_A_High_C57Bl6
GRA502A201

data_processing:
Trimmomatic v0.36 was used to remove the adapters and filter raw reads below 36 bases long. The filtered reads were aligned to the Mus musculus genome Ensembl GRCm38 (release 86) using HISAT2 v2.0.4 with default settings and RF rna-strandedness. The mapped and aligned reads were quantified to obtain the gene-level counts using HtSeq v0.6.1 with default settings and reverse strandedness
Raw counts were processed using the bioconductor package DESeq2 v1.12.4 in R v3.3.1, and normalized using the DESeq method to remove the library-specific artefacts. Variance stabilizing transformation was applied to obtain normalized log2 gene expression values.
Genome_build: Ensembl GRCm38 (release 86)
Supplementary_files_format_and_content: VST log2 normalised expression values. Rows = genes; Columns = samples.

source_name: Lung

extract_protocol:
Total RNA was extracted using the PerfectPure RNA Blood Kit (5 PRIME). Globin RNA was depleted from total RNA (1.5–2 µg) using the Mouse GLOBINclear kit (Thermo Fisher Scientific)
RNA (200 ng) was used to prepare cDNA libraries using the TruSeq Stranded mRNA HT Library Preparation Kit (Illumina). Libraries were normalized, pooled and then clustered using the HiSeq® 3000/4000 PE Cluster Kit (Illumina). The libraries were imaged and sequenced on an Illumina HiSeq 4000 sequencer using the HiSeq® 3000/4000 SBS kit (Illumina) at a minimum of 25 million paired-end reads (75 bp/100 bp) per sample.

treatment_protocol: Blood and whole lung samples obtained from C57Bl/6 and C3HeB/FeJ mice infected with low and high doses of Mycobacterium tuberculosis

tag: dose

value: High

tag: day

tag: gender

value: Female


title: 8.KO1.Tb: NMuMG_RREB1_KO_TGFb_2

city: New York

state: NY

country: USA

tag: tissue

tag: treatment


title: MEF-TCZ1


title: MEF-ctl1


title: BAL_Post_IP_10_RNA_Post_IP_1_01_18_19

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm9 version of the mouse genome using Tophat2 and the UCSC mm9 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique RefSeq gene using the GenomicRanges package in R/Bioconductor and the UCSC mm9 KnownGene table. Reads overlapping exons were normalized to reads per kilobase per million (RPKM)
Genome_build: mm9
Supplementary_files_format_and_content: Annotation file containing RPKM normalized read counts for all detected genes for each sample.

molecule: polyA RNA

source_name: Spleen CD8 memory T cells transferred into the peritoneum of congenic mice

extract_protocol:
1000 cells were FACS sorted into RLT+1%Bme using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
All purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara). Final libraries were constructed using 200 pg of cDNA as input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

tag: sorting markers

value: Live/Dead- CD8+ CD44hi FluNP366-374Db+ CD45.2+

tag: organ

value: Peritoneum

tag: stimulation

value: 35 days post Influenza X31 infection, 2 days post-transfer

tag: pre-transfer matched sample


title: MEF-TC2


title: 4.WT.Tb: NMuMG_RREB1_WT_TGFb_2


title: 5.KO1.SB: NMuMG_RREB1_KO_SB_1


title: MM4829_Lung

description:
HN878_A_Low_C57Bl6
GRA502A199

value: Low


title: 3.WT.Tb: NMuMG_RREB1_WT_TGFb_1


title: MM4830_Lung

description:
HN878_A_Low_C57Bl6
GRA502A200


title: 6.KO1.SB: NMuMG_RREB1_KO_SB_2


title: BAL_Post_IP_11_RNA_Post_IP_1_01_22_19


title: MM4832_Lung

description:
HN878_A_High_C57Bl6
GRA502A202


title: MM4828_Lung

description:
HN878_A_Low_C57Bl6
GRA502A198


title: 1.WT.SB: NMuMG_RREB1_WT_SB_1


title: Cohort2_SPL_rep2_RNA-seq

source_name: Spleen CD8 memory T cells

value: Spleen CD8 memory T cells

value: Live/Dead- CD8+ CD44hi FluNP366-374Db+ CD45.2(IV label)+/-

value: Spleen

value: 35 days post Influenza X31 infection


title: ATAC_EB_D3

library_source: genomic

data_processing:
QC: FastQC v0.11.5
Alignment: STAR2.5.2b for RNASeq, Bowtie2 for ChIPseq
RNAseq annotation: HTSeq v0.6.1p1
RNAseq normalization: DESeq2 v3.4
ChIPseq sorting, normalization, and visualization: Sam Tools & HOMER
Genome_build: mm10
Supplementary_files_format_and_content: RNASeq: Normalized Counts in .csv; ChIPSeq/ATACSeq: genome browser tracks in .bedGraph

molecule: genomic DNA

source_name: embryonic stem cells

growth_protocol: CIY_organoids are grown in pancreatic organoid medium; KSIC-806 are grown in DMEM with 10% FBS; E14 are grown in mouse embryonic stem cell medium.

extract_protocol:
Total RNA was collected using Qiagen's Rneasy Mini Kit (74106) and assessed for RNA integrity number >9.5. For ChIP-seq, cells were fixed, quenched, sonicated to ~250 bp in 1% SDS lysis buffer, and incubated with Protein A Dynabeads (Novex 10008) and 5 µg of the indicated antibody. 2% pre-cleared chromatin prior to primary antibody addition was kept as input DNA. After wash, treatment with RNAse A and Proteinase K, DNA was eluted and purified with Qiagen's PCR purification kit (28106).For ATACSeq, cell nuclei were prepared from 5x10^4 cells and incubated with 2.5 μL transposase (Illumina) in a 50 μL reaction for 30 minutes at 37°C.
For RNASeq, library construction was performed using TruSeq RNA Sample Prep Kit v2 (Illumina) following manufacturer’s instructions. For ChIPSeq, DNA quality was checked using Agilent Technologies 2200 TapeStation and quantified using PicoGreen. Library construction was performed using the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina  according to manufacturer's conditions. Samples were pooled and submitted to New York Genome Center for SE50 sequencing. For ATACSeq, following purification of transposase-fragmented DNA, the library was amplified by PCR and subjected to PE50 high-throughput sequencing.

treatment_protocol: Cells were treated with 2.5 µM SB505124 (Sigma S4696) or 100 pM TGFβ (R&D 101-B1). Where indicated, doxycycline at 1 µg/mL at plating.

value: EB

tag: time


title: EB_D3_RREB1

tag: chip antibody

value: Anti-HA (Cell signaling, catalog# 3724, lot# 8)


title: MM4827_Lung

description:
HN878_A_Low_C57Bl6
GRA502A197


title: MM4826_Lung

description:
HN878_A_Low_C57Bl6
GRA502A196


title: EB_D3_Input


title: Cohort2_LV_rep3_RNA-seq

source_name: lung vasculature CD8 memory T cells

value: lung vasculature CD8 memory T cells

value: Live/Dead- CD8+ CD44hi FluNP366-374Db+ CD45.2(IV label)+

value: Lung


title: EB_RREB1_KO_D4_2

description:
Processed data file: 15_EB_RREB1_WT_KO_D0_D4_normalized_counts.csv
Column header: 8_KO_D4


title: Cohort2_LV_rep2_RNA-seq


title: EB_D3_SMAD23

value: Anti-Smad2/3 (Cell signaling, catalog# 8685, lot# 4)


title: Cohort2_LV_rep1_RNA-seq


title: MM4680_blood

description:
HN878_D_Uninfected_C3HeBFeJ
GRA502A565

source_name: Blood

value: Uninfected


title: Cohort2_LR_rep3_RNA-seq

source_name: lung intersitium resident CD8 memory T cells

value: Live/Dead- CD8+ CD44hi FluNP366-374Db+ CD45.2(IV label)-


title: 2.WT.SB: NMuMG_RREB1_WT_SB_2

value: mouse mammary gland epithelial cells

value: NMuMG


title: EB_RREB1_KO_D0_2

description:
Processed data file: 15_EB_RREB1_WT_KO_D0_D4_normalized_counts.csv
Column header: 6_KO_D0


title: EB_RREB1_WT_D4_2

description:
Processed data file: 15_EB_RREB1_WT_KO_D0_D4_normalized_counts.csv
Column header: 4_WT_D4


title: Cohort2_SPL_rep1_RNA-seq


title: EB_RREB1_KO_D4_1

description:
Processed data file: 15_EB_RREB1_WT_KO_D0_D4_normalized_counts.csv
Column header: 7_KO_D4


title: EB_RREB1_KO_D0_1

description:
Processed data file: 15_EB_RREB1_WT_KO_D0_D4_normalized_counts.csv
Column header: 5_KO_D0


title: MM4678_blood

description:
HN878_D_Uninfected_C3HeBFeJ
GRA502A563

value: Female


title: Cohort2_SPL_rep3_RNA-seq


title: MM4677_blood

description:
HN878_D_Uninfected_C3HeBFeJ
GRA502A562


title: EB_RREB1_WT_D4_1

description:
Processed data file: 15_EB_RREB1_WT_KO_D0_D4_normalized_counts.csv
Column header: 3_WT_D4


title: EB_RREB1_WT_D0_2

description:
Processed data file: 15_EB_RREB1_WT_KO_D0_D4_normalized_counts.csv
Column header: 2_WT_D0


title: MM4679_blood

description:
HN878_D_Uninfected_C3HeBFeJ
GRA502A564


title: EB_RREB1_WT_D0_1

description:
Processed data file: 15_EB_RREB1_WT_KO_D0_D4_normalized_counts.csv
Column header: 1_WT_D0


title: MM4676_blood

description:
HN878_D_Uninfected_C3HeBFeJ
GRA502A561


title: 806_S4_RREB1_KO_TGFb_2

description:
Processed data file: 14_806_S4_RREB1_WT_KO_normalized_counts.csv
Column header: 8.KO.TGFB

source_name: pancreatic ductal adenocarcinoma

value: TGFβ


title: Cohort2_LR_rep2_RNA-seq

value: lung intersitium resident CD8 memory T cells


title: 806_S4_RREB1_KO_TGFb_1

description:
Processed data file: 14_806_S4_RREB1_WT_KO_normalized_counts.csv
Column header: 7.KO.TGFB


title: Cohort2_LR_rep1_RNA-seq


title: MM4675_blood

description:
HN878_D_High_C3HeBFeJ
GRA502A560

value: High


title: 806_S4_RREB1_KO_SB_2

description:
Processed data file: 14_806_S4_RREB1_WT_KO_normalized_counts.csv
Column header: 6.KO.SB


title: 806_S4_RREB1_KO_SB_1

description:
Processed data file: 14_806_S4_RREB1_WT_KO_normalized_counts.csv
Column header: 5.KO.SB


title: 806_S4_RREB1_WT_TGFb_2

description:
Processed data file: 14_806_S4_RREB1_WT_KO_normalized_counts.csv
Column header: 4.WT.TGFB


title: Cohort2_BAL_rep2_RNA-seq

source_name: airway resident CD8 memory T cells

value: airway resident CD8 memory T cells

value: Lung Airway


title: MM4673_blood

description:
HN878_D_High_C3HeBFeJ
GRA502A558


title: 806_S4_RREB1_KO_Input


title: 806_S4_RREB1_KO_SB_SMAD23


title: 806_S4_RREB1_WT_SB_SMAD23


title: Cohort2_SPL_rep2

data_processing:
Raw sequencing reads were mapped to the mm9 version of the mouse genome using Bowtie-1.1.1 with the default settings.
For each sample peaks of accessibility were identified and annotated using MACS2 with the default settings
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files are normalized to reads per million (rpm) using R/Bioconductor
Supplementary_files_format_and_content: tab delimited text file containing rpm normalized data for all peaks and all samples as well as peak annotations and locations.

extract_protocol: 1,000 cells were centrifuged for 10 minutes at 500xg and resuspended in 25 ul of Tagmentation Reaction mix (1x TD Buffer, 2.5 ul Tn5 Transpoase, 0.2% Digitonin) and incubating for 60 minutes at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

value: Spleen CD8 memory T cells

value: Live/Dead- CD8+ CD44hi FluNP366-374Db+ CD45.2(IV label)+/-

value: Spleen

value: 35 days post Influenza X31 infection


title: 806_S4_RREB1_WT_TGFb_SMAD23


title: MM4672_blood

description:
HN878_D_High_C3HeBFeJ
GRA502A557


title: Cohort2_SPL_rep1


title: Cohort2_BAL_rep3_RNA-seq


title: MM4671_blood

description:
HN878_D_High_C3HeBFeJ
GRA502A556


title: 806_S4_RREB1_WT_SB_2

description:
Processed data file: 14_806_S4_RREB1_WT_KO_normalized_counts.csv
Column header: 2.WT.SB


title: Cohort2_BAL_rep1_RNA-seq


title: 806_S4_RREB1_WT_Input


title: 806_S4_RREB1_TGFb_HA

value: Anti-HA (Cell signaling, catalog# 3724, lot# 8)


title: Cohort2_SPL_rep3


title: MM4670_blood

description:
HN878_D_Low_C3HeBFeJ
GRA502A555

value: Low


title: 806_S4_RREB1_WT_SB_1

description:
Processed data file: 14_806_S4_RREB1_WT_KO_normalized_counts.csv
Column header: 1.WT.SB


title: Cohort2_LV_rep3

value: lung vasculature CD8 memory T cells

value: Live/Dead- CD8+ CD44hi FluNP366-374Db+ CD45.2(IV label)+

value: Lung


title: MM4669_blood

description:
HN878_D_Low_C3HeBFeJ
GRA502A554


title: 806_S4_RREB1_KO_TGFb_SMAD23

value: Anti-Smad2/3 (Cell signaling, catalog# 8685, lot# 4)


title: 806_S4_RREB1_SB_HA


title: MM4668_blood

description:
HN878_D_Low_C3HeBFeJ
GRA502A553


title: Cohort2_LV_rep2


title: 806_S4_RREB1_WT_TGFb_1

description:
Processed data file: 14_806_S4_RREB1_WT_KO_normalized_counts.csv
Column header: 3.WT.TGFB


title: 806_S4_SB_SMAD23


title: 806_S4_Input


title: MM4666_blood

description:
HN878_D_Low_C3HeBFeJ
GRA502A551


title: Cohort2_LV_rep1


title: Cohort2_LR_rep3

value: Live/Dead- CD8+ CD44hi FluNP366-374Db+ CD45.2(IV label)-


title: Organoid_PlusDOX_SB

description:
Processed data file: 01_Organoid_normalized_counts.csv
Column header: 3.PlusDox.SB

source_name: pancreatic epithelial cells


title: MM4667_blood

description:
HN878_D_Low_C3HeBFeJ
GRA502A552

value: Female


title: Organoid_PlusDOX_TGFb

description:
Processed data file: 01_Organoid_normalized_counts.csv
Column header: 4.PlusDox.TGFb

value: TGFβ


title: Cohort2_BAL_rep3


title: Cohort2_LR_rep2

value: lung intersitium resident CD8 memory T cells


title: 806_S4_RREB1_Input


title: Organoid_NoDOX_SB

description:
Processed data file: 01_Organoid_normalized_counts.csv
Column header: 1.NoDox.SB


title: MM4664_blood

description:
HN878_A_Uninfected_C57Bl6
GRA502A549

value: Uninfected


title: MM4674_blood

description:
HN878_D_High_C3HeBFeJ
GRA502A559

value: High


title: MM4663_blood

description:
HN878_A_Uninfected_C57Bl6
GRA502A548


title: Cohort2_BAL_rep2

value: airway resident CD8 memory T cells

value: Lung Airway


title: MM4662_blood

description:
HN878_A_Uninfected_C57Bl6
GRA502A547


title: 806_S4_TGFb_SMAD23


title: MM4661_blood

description:
HN878_A_Uninfected_C57Bl6
GRA502A546


title: MM4665_blood

description:
HN878_A_Uninfected_C57Bl6
GRA502A550


title: Cohort2_LR_rep1


title: Cohort2_BAL_rep1


title: Organoid_NoDOX_TGFb

description:
Processed data file: 01_Organoid_normalized_counts.csv
Column header: 2.NoDox.TGFb


title: U251-WT

city: Tianjin

first: Xuexia

last: Zhou

address: 154 Anshan Road

department: Tianjin Neurological Institute

institute: Tianjin Medical University General Hospital

data_processing:
Illumina GA Pipeline v1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The stat of mapped reads was list in WT.gene.MapReadsStat.xls and KO.gene.MapReadsStat.xls
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi, 2008.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample

organism: Homo sapiens

growth_protocol: Human GBM cells U87MG and U251 cells were cultured in Dulbecco's modified eagle medium (DMEM),supplemented with 10% fetal bovine serum(FBS), 100 U/mL penicillin, and 100 μg/mL streptomycin.

extract_protocol:
Cells were harvested and total RNA was extracted by Trizol reagent. Beads with oligo(dT) were used to isolate poly(A) containing mRNA and ncRNAs after total RNA was collected.
Libraries for paired-end sequencing were prepared using mRNA-Seq Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: sh-NC (for WT) and sh-SRSF1 (for KD) lentiviruses were ordered from Gene Pharma (Shanghai, China). Infection (MOI=20) was performed in both U87MG and U251 cells. Stable WT and KD cell lines were generated by puromycin selection for one week.

value: human GBM cells

value: Brain

tag: genotype

value: WT


title: U251-KD

tag: cell line

value: SRSF1 KD


title: MM4660_blood

description:
HN878_A_High_C57Bl6
GRA502A545


title: MM4658_blood

description:
HN878_A_High_C57Bl6
GRA502A543


title: U87MG-KD


title: 5222446030_A

type: RNA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: raw illumina text files were read into R (v3.5) and normalised using the neqc function from limma package (v3.38.3), with default parameters

label: biotin

label_protocol: cRNA was prepared from 200 ng globin-reduced blood RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion). Quality was checked using an RNA 6000 Nano kit (Agilent) using a BioAnalyzer 2100 (Agilent). Biotinylated cRNA samples were randomized.

extract_protocol: Blood was collected in Tempus reagent (Life Technologies) at 1:2 ratio. Total RNA was extracted using the PerfectPure RNA Blood Kit (5 PRIME). Globin RNA was depleted from total RNA (1.5–2 µg) using the Mouse GLOBINclear kit (Ambion).

value: uninfected

value: BALB


title: 5222446016_A

tag: agent

value: Mycobacterium tuberculosis H37Rv


title: 5222446017_C

tag: strain


title: MM4657_blood

description:
HN878_A_High_C57Bl6
GRA502A542


title: U87MG-WT

tag: cell type


title: 5222446016_C


title: 5222446027_A


title: 5222446018_C


title: 5222446016_B


title: MM4656_blood

description:
HN878_A_High_C57Bl6
GRA502A541


title: MM4659_blood

description:
HN878_A_High_C57Bl6
GRA502A544


title: 5222446028_A


title: 5222446015_E


title: 5222446015_A


title: MM4655_blood

description:
HN878_A_Low_C57Bl6
GRA502A540

value: Low


title: 5222446014_A


title: 5222446015_B


title: 5222446014_E


title: 5222446015_C


title: 5216898007_F


title: MM4654_blood

description:
HN878_A_Low_C57Bl6
GRA502A539


title: 5216898006_F


title: 5222446014_C


title: 5216898007_E


title: 5222446014_B


title: MM4653_blood

description:
HN878_A_Low_C57Bl6
GRA502A538


title: mESCs, BR2_KO_10min_tot

city: Lausanne

first: Ana

last: Marques

address: Rue du Bugnon 27

department: Department of Computational Biology

country: Switzerland

institute: University of Lausanne

description:
BR2_KO_10min_tot
4sU_TPM_table.txt

data_processing:
4sU sequencing reads were first mapped to mouse ribosomal RNA sequences with STAR v2.5.0. Reads that do not map to ribosomal RNA were then aligned to intronic and exonic sequences using STAR and quantified using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: 4sU_TPM_table.txt contains the expression levels of transcript exons and introns (Transcripts Per Million, TPM).

source_name: mESC (conditional Dicer mutant)

growth_protocol: Mouse DTCM23/49 XY embryonic stem cell lines (mESCs) were cultured in Knockout Dulbecco’s Modified Eagle Medium (D-MEM, Thermo Fisher, #10829-018) supplemented with 15% fetal bovine serum (FBS, Thermo Fisher, #16000-044), 1% antibiotic penicillin/streptomycin (Thermo Fisher, 15070063), Recombinant mouse LIF protein to a final concentration of 0.01% (Merck, #ESG1107) and 0.06 mM 2-Mercaptoethanol (Thermo Fisher, #31350-010), on 0.1% gelatin-coated cell culture dishes.

extract_protocol: RNA was extracted using Trizol, according to manufacturer instructions. RNA was DNAse treated using RNeasy on column digestion according to manufacturer’s instructions. Total RNA libraries were prepared from 10 ng of DNase-treated preexisting and newly transcribed RNA using Ovation® RNA-Seq. reads were first mapped to mouse ribosomal RNA sequences with STAR v2.5.0. Reads that do not map to ribosomal RNA were then aligned to intronic and exonic sequences using STAR and quantified using RSEM.

treatment_protocol:
Loss of Dicer1 function was induced by culturing cells in mESC growth media supplemented with 800 nM tamoxifen ([Z]-4-Hydroxytamoxifen [4-OHT]).
Five million DTCM23/49 XY mESCs (WT and miRNA depleted) were seeded and allowed to grow to 70-80% confluency (approximately 1 day). 4sU was added to the growth medium (final concentration of 200 µM) and the cells were incubated at 37 ºC for 10 and 15 minutes

tag: treatment duration (days)

tag: rna fraction

value: 4sU preexisting (10 minutes)

tag: biological replicate number

value: mESC

value: Dicer depleted


title: mESCs, BR2_WT_15min_tot

description:
BR2_WT_15min_tot
4sU_TPM_table.txt

value: 4sU preexisting (15 minutes)


title: mESCs, BR2_KO_15min_tot

description:
BR2_KO_15min_tot
4sU_TPM_table.txt


title: 5216513054_E

tag: day


title: mESCs, BR1_KO_15min_tot

description:
BR1_KO_15min_tot
4sU_TPM_table.txt


title: MM4652_blood

description:
HN878_A_Low_C57Bl6
GRA502A537

tag: dose

tag: gender

value: Female


title: MM4651_blood

description:
HN878_A_Low_C57Bl6
GRA502A536


title: mESCs, BR1_KO_10min_tot

description:
BR1_KO_10min_tot
4sU_TPM_table.txt


title: mESCs, BR1_WT_15min_tot

description:
BR1_WT_15min_tot
4sU_TPM_table.txt


title: mESCs, BR2_WT_10min_tot

description:
BR2_WT_10min_tot
4sU_TPM_table.txt


title: 5216898006_E


title: MM4945_Lung

description:
H37RV_G_Uninfected_C3HeBFeJ
sample name in processed data file:
GRA502A315

tag: tissue

value: lung

value: Uninfected


title: mESCs, BR1_WT_10min_tot

description:
BR1_WT_10min_tot
4sU_TPM_table.txt


title: MM4943_Lung

description:
H37RV_G_Uninfected_C3HeBFeJ
sample name in processed data file:
GRA502A313


title: day 56 -5

source_name: Whole blood


title: day 138 -1


title: day 138 -3


title: day 56 -2


title: day 56 -3


title: mESCs, BR2_KO_15min_lab

description:
BR2_KO_15min_lab
4sU_TPM_table.txt

value: 4sU labelled (15 minutes)


title: MM4942_Lung

description:
H37RV_G_Uninfected_C3HeBFeJ
sample name in processed data file:
GRA502A312


title: MM4941_Lung

description:
H37RV_G_Uninfected_C3HeBFeJ
sample name in processed data file:
GRA502A311


title: mESCs, BR2_WT_15min_lab

description:
BR2_WT_15min_lab
4sU_TPM_table.txt


title: MM4944_Lung

description:
H37RV_G_Uninfected_C3HeBFeJ
sample name in processed data file:
GRA502A314


title: day 28 -3


title: day 28 -5


title: MM4940_Lung

description:
H37RV_G_High_C3HeBFeJ
sample name in processed data file:
GRA502A310

value: High


title: mESCs, BR2_WT_10min_lab

description:
BR2_WT_10min_lab
4sU_TPM_table.txt

value: 4sU labelled (10 minutes)


title: day 28 -2


title: day 21 -5


title: 5216513054_F


title: day 28 -1


title: day 21 -3


title: day 28 -4


title: day 56 -1


title: MM4939_Lung

description:
H37RV_G_High_C3HeBFeJ
sample name in processed data file:
GRA502A309


title: mESCs, BR2_KO_10min_lab

description:
BR2_KO_10min_lab
4sU_TPM_table.txt


title: MM4938_Lung

description:
H37RV_G_High_C3HeBFeJ
sample name in processed data file:
GRA502A308


title: mESCs, BR1_KO_15min_lab

description:
BR1_KO_15min_lab
4sU_TPM_table.txt


title: mESCs, BR1_KO_10min_lab

description:
BR1_KO_10min_lab
4sU_TPM_table.txt


title: MM4937_Lung

description:
H37RV_G_High_C3HeBFeJ
sample name in processed data file:
GRA502A307


title: MM4936_Lung

description:
H37RV_G_High_C3HeBFeJ
sample name in processed data file:
GRA502A306


title: day 14-4


title: day 14-5


title: day 14-3


title: mESCs, BR1_WT_10min_lab

description:
BR1_WT_10min_lab
4sU_TPM_table.txt


title: day 14-2


title: mESCs, BR1_WT_15min_lab

description:
BR1_WT_15min_lab
4sU_TPM_table.txt


title: mESCs, smallRNA_KO_d12_3

description:
KO_d12_3
smallRNAseq_counts_table.txt

data_processing:
Sequencing adapters were removed from fifty nucleotides long single-end reads using cutadapt (v1.8) and reads  aligned to the mouse genome (mm10) using bowtie2. The levels of miRNA ( miRBase v21) were quantified using HTseq.
Genome_build: mm10
Supplementary_files_format_and_content: smallRNAseq_counts_table.txt contains the counts of miRNAs levels of transcript exons and introns (Transcripts Per Million, TPM).

extract_protocol: Small RNA extraction following 0, 4, 8, 10 and 12 days of 4-OHT treatment was performed using the Qiagen miRNEasy Mini Kit according to manufacturer instructions. Small RNA sequencing libraies were prepared using Illumina TruSeq samll RNA library prep kit and sequenced in a Illumina 2500. Sequencing adapters were removed from fifty nucleotides long single-end reads using cutadapt (v1.8) and reads  aligned to the mouse genome (mm10) using bowtie2. The levels of miRNA ( miRBase v21) were quantified using HTseq.

value: total RNA


title: day 138 -2


title: day 21 -1


title: day 21 -2


title: MM4933_Lung

description:
H37RV_G_Low_C3HeBFeJ
sample name in processed data file:
GRA502A303


title: mESCs, smallRNA_KO_d12_2

description:
KO_d12_2
smallRNAseq_counts_table.txt


title: HepG2_C_rep2

city: Palo Alto

first: Baoxu

last: Pang

state: CALIFORNIA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

description:
Amplification of virus inserts
HepG2_FDR_0.01.bed

data_processing:
Sequence reads were aligned using bowtie.
A GFF file was made from aligned reads pooled from all experiments. Then read counts were calculated using HTSeq.
Final enrichment was calculated by MAGeCK.
Genome_build: hg19
Supplementary_files_format_and_content: .bed file reports significantly enriched fragments

growth_protocol: K562 cells were cultured in RPMI 1640 with Lglutamine, 10% FBS and Pen-Strep. HepG2 cells were cultured in DMEM, 10% FBS and Antibiotic-Antimycotic. Cell density and culture conditions were maintained according to the ENCODE Cell Culture Guidelines.

extract_protocol:
Genomic DNA was extracted using QIAamp DNA Blood Maxi Kit.
Genome DNA was amplified using Illumina PCR primer 1.0 and 2.0 using PCR. PCR products were then size-selected and purified. Final products were sequenced by Illumina MiSeq platform. Sequence reads were aligned using bowtie.

treatment_protocol: K562 cells and HepG2 cells were infected with the virus library at MOI 0.5 by spin infection. Two days after infection, cells were selected by 2mg/ml puromycin for another 5 days. K562 cells infected with virus library and selected with puromycin were divided into two portions. The genomic DNA was isolated from one half of the cells and these genomic DNA fragments were the control library representation. For the other half of the cells, 1nM AP20187 was added to induce apoptosis. 1 day later, dead cell removal kit (Miltenyi Biotec) was used to deplete the apoptotic cells, and live cells were further cultured for another 5 days. Genomic DNA was extracted from these cells. For HepG2 cells, the experiment procedures were similar except that dead cells were removed by taking away the media, because HepG2 cells are adherent cells and live cells remained attached to the tissue culture flasks.

value: hepatocellular carcinoma

tag: treatment

value: control


title: K562_1nM_AP_rep2

description:
Amplification of virus inserts
K562_FDR_0.01.bed

value: chronic myelogenous leukemia


title: HepG2_C_rep1


title: day 56 -4

value: BALB


title: MM4934_Lung

description:
H37RV_G_Low_C3HeBFeJ
sample name in processed data file:
GRA502A304


title: day 14-1

value: Mycobacterium tuberculosis H37Rv


title: K562_1nM_AP_rep1


title: K562_C_rep2


title: uninfected-3

value: uninfected


title: uninfected-1


title: mESCs, smallRNA_KO_d12_1

description:
KO_d12_1
smallRNAseq_counts_table.txt


title: uninfected-2


title: MM4932_Lung

description:
H37RV_G_Low_C3HeBFeJ
sample name in processed data file:
GRA502A302

value: Low


title: day 21 -4


title: K562_C_rep1


title: HepG2_1nM_AP_rep1


title: MM4935_Lung

description:
H37RV_G_Low_C3HeBFeJ
sample name in processed data file:
GRA502A305


title: HepG2_1nM_AP_rep2


title: MM4931_Lung

description:
H37RV_G_Low_C3HeBFeJ
sample name in processed data file:
GRA502A301


title: MM4930_Lung

description:
H37RV_C_Uninfected_C57Bl6
sample name in processed data file:
GRA502A300


title: Cf_24h_2

city: Stanford

first: Elizabeth

last: Sattely

state: California

address: 443 Via Ortega

department: Shriram Center for Biological and Chemical Engineering

data_processing:
The FASTX-toolkit was used for quality assessment and cleaning of reads
The reference fasta files (SL2.50) were pre-processed into an index using Bowtie 2
Quality reads were aligned to the Heinz tomato genome using TopHat 2
Aligned sequence pairs were counted with HTSeq
Reads counts were analyzed  using edgeR to identify differentially expressed genes between treatments, resulting in counts per million (CPM) mapped reads
Genome_build: SL2.50
Supplementary_files_format_and_content: counts files include CPM values for each Sample

organism: Solanum lycopersicum

source_name: leaf tissue

growth_protocol: Tomato (Solanum lycopersicum) plant cultivar VF36 was grown in a greenhouse (16h light, 25-28°C). For experiments, 4.5 week-old tomato was used.

extract_protocol:
cDNA library was prepared from RNA isolated from the elicited tomato leaves (two biological replicates for each treatment per time point, 54 samples total) using the NEBNext mRNA Library Prep Master Mix Set for Illumina.
A multiplexed RNA-Seq cDNA library was PCR amplified using NEBNext Multiplex Oligos for Illumina according to the manufacturer’s instructions (New England  Biolabs). The quality  and average length (insert size was approximately 200 bp) of cDNAs in the library were determined using a High Sensitivity DNA chip on a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Leaflets of tomato VF36 plants were hand-inoculated using a needleless 1 mL syringe with: 1) fungal  elicitors:  chitin  (0.5  mg/mL  in  water), M.  restricta(OD600=  0.5  in  water)  or C.  fulvum(OD600= 1.0 in water); 2) bacterial elicitors: flg22 (1 μM in water), S. epidermidis(OD600= 1.0 in water), P. acnes(OD600= 1.0 in water) or X. euvesicatoria(OD600= 0.2 in 10mM MgCl2); or 3) mock (water, control) (FigureS1). After treatment, leaves (one leaf from three individual plants per treatment, n=3) were collected at 12, 24, and 48 hours post-inoculation (hpi) using a razor, flash frozen by liquid nitrogen, and stored at -80°C for gene profiling and RNA-Sequencing (RNA-Seq).

tag: cultivar

tag: age

value: 4.5 week-old

tag: elicitor

value: Cladosporium fulvum

tag: time point (hour post inoculation)


title: mESCs, smallRNA_KO_d10_3

description:
KO_d10_3
smallRNAseq_counts_table.txt

value: mESC

tag: genotype

value: Dicer depleted


title: ECM55

city: Homburg

first: Nicole

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

country: Germany

institute: Saarland University

description:
miRNAs in embryonic culture medium
1_55

scan_protocol: Array´s were scanned with the Agilent Scanner with default settings.

data_processing: Raw expression values were extracted using the Feature Extraction Software of Agilent. Raw signal intensities were quantil-normalized and log2 transformed.

source_name: Embryonic culture media

label_protocol:
using miRNA Complete Labeling and Hyb Kit (Agilent, Cat. No 5190-0456),  Cyanine 3-pcp
The expression profile of 2549 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations

extract_protocol: Total RNA including miRNAs was isolated using the Qiagen miRNeasy Kit according to manufacturers recommendations.

tag: pregnancy (y/n)

value: y


title: mESCs, smallRNA_KO_d10_2

description:
KO_d10_2
smallRNAseq_counts_table.txt


title: mESCs, smallRNA_KO_d8_2

description:
KO_d8_2
smallRNAseq_counts_table.txt


title: MM4929_Lung

description:
H37RV_C_Uninfected_C57Bl6
sample name in processed data file:
GRA502A299

value: lung

value: Uninfected

value: Female


title: Cf_24h_1


title: ECM54

description:
miRNAs in embryonic culture medium
1_54

hyb_protocol: The expression profile of 2549 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations


title: MM4927_Lung

description:
H37RV_C_Uninfected_C57Bl6
sample name in processed data file:
GRA502A297


title: Cf_48h_2


title: mESCs, smallRNA_KO_d8_3

description:
KO_d8_3
smallRNAseq_counts_table.txt


title: MM4928_Lung

description:
H37RV_C_Uninfected_C57Bl6
sample name in processed data file:
GRA502A298


title: mESCs, smallRNA_KO_d4_3

description:
KO_d4_3
smallRNAseq_counts_table.txt


title: ECM56

description:
miRNAs in embryonic culture medium
1_56

value: n


title: Xe_48h_2

value: Xanthomonas euvesicatoria


title: MM4926_Lung

description:
H37RV_C_Uninfected_C57Bl6
sample name in processed data file:
GRA502A296


title: mESCs, smallRNA_KO_d8_1

description:
KO_d8_1
smallRNAseq_counts_table.txt

value: total RNA


title: Cf_12h_1


title: Cf_12h_2


title: MM4925_Lung

description:
H37RV_C_High_C57Bl6
sample name in processed data file:
GRA502A295

value: High


title: ECM53

description:
miRNAs in embryonic culture medium
1_53


title: Xe_48h_1


title: MM4924_Lung

description:
H37RV_C_High_C57Bl6
sample name in processed data file:
GRA502A294


title: mESCs, smallRNA_KO_d4_1

description:
KO_d4_1
smallRNAseq_counts_table.txt


title: ECM52

description:
miRNAs in embryonic culture medium
1_52


title: mESCs, smallRNA_KO_d10_1

description:
KO_d10_1
smallRNAseq_counts_table.txt


title: Cf_48h_1


title: Xe_24h_2


title: MM4923_Lung

description:
H37RV_C_High_C57Bl6
sample name in processed data file:
GRA502A293


title: ECM51

description:
miRNAs in embryonic culture medium
1_51


title: mESCs, smallRNA_KO_d0_3

description:
KO_d0_3
smallRNAseq_counts_table.txt


title: Xe_24h_1


title: ECM50

description:
miRNAs in embryonic culture medium
1_50


title: MM4921_Lung

description:
H37RV_C_High_C57Bl6
sample name in processed data file:
GRA502A291


title: mESCs, smallRNA_KO_d0_2

description:
KO_d0_2
smallRNAseq_counts_table.txt


title: MM4920_Lung

description:
H37RV_C_Low_C57Bl6
sample name in processed data file:
GRA502A290


title: Xe_12h_2


title: ECM49

description:
miRNAs in embryonic culture medium
1_49


title: ECM46

description:
miRNAs in embryonic culture medium
1_46


title: ECM47

description:
miRNAs in embryonic culture medium
1_47


title: Mk2_48h_1

description: (-) control for Xe and Cf-treated samples

value: water


title: Xe_12h_1


title: MM4918_Lung

description:
H37RV_C_Low_C57Bl6
sample name in processed data file:
GRA502A288


title: mESCs, smallRNA_KO_d0_1

description:
KO_d0_1
smallRNAseq_counts_table.txt


title: mESCs, smallRNA_KO_d4_2

description:
KO_d4_2
smallRNAseq_counts_table.txt


title: MM4919_Lung

description:
H37RV_C_Low_C57Bl6
sample name in processed data file:
GRA502A289


title: AG_EC-LPS rep1

city: Dresden

first: Lan-Sun

last: Chen

address: Fetscherstraße 74

institute: TU Dresden

data_processing:
Raw reads in fastq format were trimmed using trim-galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the mouse genome, mm10, using HISAT2 (Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements.) with default parameters. htseq-count (Anders, S., Pyl, P. T. & Huber, W. HTSeq--a Python framework to work with high-throughput sequencing data.) was used to assign reads to exons thus eventually getting counts per gene.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include read counts and log2foldchange

source_name: sorted adrenal endothelial cells

extract_protocol:
For isolation of endothelial cells, adrenal glands were digested using a solution containing collagenase I and bovine serum albumin (both at 1.6 mg/ml concentration, Sigma-Aldrich, Germany) dissolved in the phosphate-buffered saline (PBS). Digestion was performed for a total of 30 minutes at 37°C in a thermomixer with shaking. After digestion, cells were dissociated using a 1 ml tuberculin syringe and 20 Gauge needle (Braun, Germany) and by subsequent passing through 100 µm-pore size strainers. Resulting cell suspensions were centrifuged at 2900 RPM for 8 minutes at 4°C. Next pellets were resuspended in 100 µl of 1x red blood cell (RBC) lysis buffer (eBioscience, Thermo Fisher Scientific, USA) to remove erythrocytes, and washed in a FACS buffer (PBS solution containing 5% of foetal calf serum). Afterward, cells were incubated for 60 minutes at 4°C with a mixture of conjugated antibodies in the FACS buffer: including rat against mouse CD45-PE antibody (immune cells), rat against mouse CD31-PE/CY7 antibody (endothelial cells) and rat against mouse Ter119-APC (erythrocytes) antibody. All those monoclonal antibodies were purchased from BD Bioscience (BD Biosciences, USA). Dead cells were excluded using Hoechst 33258 (Invitrogen, Thermo Fisher Scientific). Populations of single, alive, CD31 positive endothelial cells were subsequently isolated by BD FACSAria III sorter (BD Biosciences). From each adrenal gland, 30.000 endothelial cells were sorted out and used for further analysis.
After verification of RNA integrity by 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany), RNA was subjected to the amplification workflow of the SMARTer Ultra HV v2 kit (Takara Bio Europe SAS, Saint-Germain-en-Laye, France). Amplified cDNA was successively converted into short read sequencing libraries using the NEBnext Ultra DNA library preparation chemistry (New England Biolabs, Frankfurt am Main, Germany). Libraries were equimolarly pooled and sequenced on an Illumina HiSeq 2500, resulting in ∼30 million single end reads per library in the Deep Sequencing Group, BIOTEC/Center for Regenerative Therapies Dresden.

value: adrenal gland endothelial cells

value: 8 weeks

tag: agent

value: LPS


title: ECM45

description:
miRNAs in embryonic culture medium
1_45


title: Mk2_24h_2


title: AG_EC-Saline rep3

tag: strain

value: Saline


title: Mk2_24h_1

value: 4.5 week-old


title: MM4917_Lung

description:
H37RV_C_Low_C57Bl6
sample name in processed data file:
GRA502A287

value: Low


title: MM4916_Lung

description:
H37RV_C_Low_C57Bl6
sample name in processed data file:
GRA502A286


title: ECM44

description:
miRNAs in embryonic culture medium
1_44


title: MM4922_Lung

description:
H37RV_C_High_C57Bl6
sample name in processed data file:
GRA502A292


title: AG_EC-Saline rep2

tag: cell type


title: ECM43

description:
miRNAs in embryonic culture medium
1_43


title: Mk2_48h_2


title: Mk2_12h_2


title: AG_EC-LPS rep3


title: ECM48

description:
miRNAs in embryonic culture medium
1_48


title: AG_EC-LPS rep2


title: ECM42

description:
miRNAs in embryonic culture medium
1_42


title: MM4914_Lung

description:
HN878_E_Uninfected_C3HeBFeJ
sample name in processed data file:
GRA502A284


title: ECM41

description:
miRNAs in embryonic culture medium
1_41


title: Fg_48h_2


title: Mk2_12h_1


title: ECM40

description:
miRNAs in embryonic culture medium
1_40


title: OFT_16_6 [S37]

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

description: S37__GhislaineLioux_RNA_Seq_NEBNext_TTAGGC_L004

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2.
Illumina adapter contaminations were removed from reads using Cutadapt v1.3.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3.
Genome_build: GRCm38 assembly, Ensembl genebuild 76
Supplementary_files_format_and_content: Matrix_table.xls file contains ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

source_name: Epicardium, OFT

growth_protocol: Hearts from E16.5 mouse embryos were dissected in cold PBS and mesothelial+sub-mesothelial or epicardial+sub-epicardial layers were peeled off using forceps

extract_protocol:
Upon dissection epicardial and arterial mesothelial tissues were snap-frozen in Eppendorf tubes placed on dry ice. For each mouse litter, the epicardium+subepicardium and the arterial mesothelium + submesothelium samples were pooled separately. RNA was then purified from each population using the RNeasy Micro kit (Qiagen).
RNA-seq libraries were generated with the NEBNext Ultra RNA Library preparation kit (New England Biolabs).
Libraries were sequenced (single-end mode and length of 50 bp) on the Illumina HiSeq 2500 system.

value: wild type

tag: developmental stage

value: dissected mesothelial + sub-mesothelial layers of the base of the great arteries

tag: litter


title: MM4913_Lung

description:
HN878_E_Uninfected_C3HeBFeJ
sample name in processed data file:
GRA502A283


title: MM4912_Lung

description:
HN878_E_Uninfected_C3HeBFeJ
sample name in processed data file:
GRA502A282


title: VENT_16_5 [S32]

description: S32__GhislaineLioux_RNA_Seq_NEBNext_ACTGAT_L002

source_name: Epicardium, ventricle

value: dissected epicardium + sub-epicardiom of the heart ventricles


title: VENT_16_6 [S38]

description: S38__GhislaineLioux_RNA_Seq_NEBNext_TGACCA_L001


title: ECM39

description:
miRNAs in embryonic culture medium
1_39

value: y


title: MM4911_Lung

description:
HN878_E_Uninfected_C3HeBFeJ
sample name in processed data file:
GRA502A281

source_name: Lung

value: lung

value: Uninfected


title: MM4910_Lung

description:
HN878_E_High_C3HeBFeJ
sample name in processed data file:
GRA502A280

value: Female


title: Fg_24h_1


title: ECM38

description:
miRNAs in embryonic culture medium
1_38

value: n


title: Fg_48h_1


title: OFT_16_5 [S31]

description: S31__GhislaineLioux_RNA_Seq_NEBNext_GAGTGG_L002


title: MM4915_Lung

description:
HN878_E_Uninfected_C3HeBFeJ
sample name in processed data file:
GRA502A285


title: AG_EC-Saline rep1


title: VENT_16_4 [S27]

description: S27__GhislaineLioux_RNA_Seq_NEBNext_GTTTCG_L002


title: Fg_12h_2


title: ECM37

description:
miRNAs in embryonic culture medium
1_37


title: OFT_16_4 [S26]

description: S26__GhislaineLioux_RNA_Seq_NEBNext_GTGGCC_L002


title: ECM36

description:
miRNAs in embryonic culture medium
1_36


title: VENT_16_3 [S17]

description: S17__GhislaineLioux_RNA_Seq_NEBNext_AGTCAA_L001


title: MM4909_Lung

description:
HN878_E_High_C3HeBFeJ
sample name in processed data file:
GRA502A279


title: MM4908_Lung

description:
HN878_E_High_C3HeBFeJ
sample name in processed data file:
GRA502A278


title: ECM35

description:
miRNAs in embryonic culture medium
1_35


title: Pb_48h_2

value: Propionibacterium acnes


title: Pb_48h_1


title: ECM34

description:
miRNAs in embryonic culture medium
1_34


title: Fg_24h_2


title: MM4907_Lung

description:
HN878_E_High_C3HeBFeJ
sample name in processed data file:
GRA502A277

value: High


title: Pb_24h_2


title: MM4906_Lung

description:
HN878_E_High_C3HeBFeJ
sample name in processed data file:
GRA502A276


title: OFT_16_2 [S6]

description: S6__GhislaineLioux_RNA_Seq_NEBNext_TGACCA_L002


title: Pb_24h_1


title: ECM32

description:
miRNAs in embryonic culture medium
1_32


title: MM4904_Lung

description:
HN878_E_Low_C3HeBFeJ
sample name in processed data file:
GRA502A274


title: VENT_16_1 [S2]

description: S2__GhislaineLioux_RNA_Seq_NEBNext_CGATGT_L002


title: Pb_12h_2


title: ECM31

description:
miRNAs in embryonic culture medium
1_31


title: OFT_16_1 [S1]

description: S1__GhislaineLioux_RNA_Seq_NEBNext_ATCACG_L001


title: Fg_12h_1


title: Pb_12h_1


title: 5.SP_RNAseq

data_processing:
Raw sequencing reads were mapped to the mm9 version of the mouse genome using Tophat2 and the UCSC mm9 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique RefSeq gene using the GenomicRanges package in R/Bioconductor and the UCSC mm9 KnownGene table.  Reads overlapping exons were normalized to reads per kilobase per million (RPKM)
Genome_build: mm9
Supplementary_files_format_and_content: Annotation file containing RPKM normalized read counts for each sample.

source_name: circulating CD8 memory T cells

extract_protocol:
1000 cells were FACS sorted into RLT+1%Bme using the indicated markers.  Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
All purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara).  Final libraries were constructed using 200 pg of cDNA as input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

value: circulating CD8 memory T cells

tag: Sex

value: female

tag: sorting markers

value: Live/Dead- CD8+ CD44hi FluNP366-374Db+ CD62L-

tag: organ

value: Spleen

tag: stimulation

value: 35 days post Influenza X31 infection


title: ECM30

description:
miRNAs in embryonic culture medium
1_30


title: MM4900_Lung

description:
HN878_B_Uninfected_C57Bl6
sample name in processed data file:
GRA502A270

tag: tissue

tag: dose

tag: day

tag: gender


title: ECM33

description:
miRNAs in embryonic culture medium
1_33


title: VENT_16_2 [S7]

description: S7__GhislaineLioux_RNA_Seq_NEBNext_ACAGTG_L002


title: MM4905_Lung

description:
HN878_E_Low_C3HeBFeJ
sample name in processed data file:
GRA502A275


title: OFT_16_3 [S16]

description: S16__GhislaineLioux_RNA_Seq_NEBNext_CTTGTA_L001


title: MM4902_Lung

description:
HN878_E_Low_C3HeBFeJ
sample name in processed data file:
GRA502A272


title: 4.SP_RNAseq


title: Ct_48h_2

tag: cultivar

tag: age

value: 4.5 week-old

tag: elicitor

value: chitin


title: Ct_48h_1

tag: time point (hour post inoculation)


title: MM4899_Lung

description:
HN878_B_Uninfected_C57Bl6
sample name in processed data file:
GRA502A269


title: MM4898_Lung

description:
HN878_B_Uninfected_C57Bl6
sample name in processed data file:
GRA502A268


title: 5.Lung_RNAseq

source_name: parenchyma resident CD8 memory T cells

value: parenchyma resident CD8 memory T cells

value: Live/Dead- CD8+ CD44hi FluNP366-374Db+ CD45.2(IV label)-

value: Lung Parenchyma


title: Sc_48h_2

value: Staphylococcus epidermidis


title: 3.Sp_RNAseq


title: ECM28

description:
miRNAs in embryonic culture medium
1_28

tag: pregnancy (y/n)

value: y


title: ECM27

description:
miRNAs in embryonic culture medium
1_27


title: MM4897_Lung

description:
HN878_B_Uninfected_C57Bl6
sample name in processed data file:
GRA502A267

value: lung

value: Uninfected


title: Sc_48h_1


title: MM4896_Lung

description:
HN878_B_Uninfected_C57Bl6
sample name in processed data file:
GRA502A266

value: Female


title: 3.Lung_RNAseq

tag: strain


title: ECM26

description:
miRNAs in embryonic culture medium
1_26

value: n


title: Mz_48h_2

value: Malassezia restricta


title: MM4895_Lung

description:
HN878_B_High_C57Bl6
sample name in processed data file:
GRA502A265

value: High


title: ECM25

description:
miRNAs in embryonic culture medium
1_25


title: ECM29

description:
miRNAs in embryonic culture medium
1_29


title: 5.BAL_RNAseq

value: airway resident CD8 memory T cells

value: female

value: Lung Airway


title: Mz_48h_1


title: MM4894_Lung

description:
HN878_B_High_C57Bl6
sample name in processed data file:
GRA502A264


title: ECM24

description:
miRNAs in embryonic culture medium
1_24


title: Mk_48h_2

description: (-) control for Mz, Sc, Ct-treated samples

value: water


title: ECM22

description:
miRNAs in embryonic culture medium
1_22


title: MM4893_Lung

description:
HN878_B_High_C57Bl6
sample name in processed data file:
GRA502A263


title: MM4892_Lung

description:
HN878_B_High_C57Bl6
sample name in processed data file:
GRA502A262


title: ECM23

description:
miRNAs in embryonic culture medium
1_23


title: 3.BAL_RNAseq

value: 35 days post Influenza X31 infection


title: JK002_pre4_RNAseq

source_name: Splenocytes pre-transfer

value: circulating CD8 memory T cells

value: Live/Dead- CD45.2+ CD8+ CD44hi FluNP366-374Db+ CD62L-


title: ECM21

description:
miRNAs in embryonic culture medium
1_21


title: Ct_24h_2

value: 4.5 week-old

value: chitin


title: JK002_pre3_RNAseq


title: MM4890_Lung

description:
HN878_B_Low_C57Bl6
sample name in processed data file:
GRA502A260

value: Low


title: MM4889_Lung

description:
HN878_B_Low_C57Bl6
sample name in processed data file:
GRA502A259


title: Ct_24h_1


title: ECM19

description:
miRNAs in embryonic culture medium
1_19


title: ECM20

description:
miRNAs in embryonic culture medium
1_20


title: Mk_48h_1


title: Sc_24h_2

value: Staphylococcus epidermidis


title: Sc_24h_1


title: ECM18

description:
miRNAs in embryonic culture medium
1_18


title: JK002_post2_RNAseq

source_name: Splenocytes post-transfer into airways


title: JK002_post1_RNAseq


title: JK001_pre2_RNAseq


title: Mz_24h_2


title: 4.BAL_RNAseq

value: Live/Dead- CD8+ CD44hi FluNP366-374Db+ CD45.2(IV label)-


title: MM4887_Lung

description:
HN878_B_Low_C57Bl6
sample name in processed data file:
GRA502A257

value: lung


title: JK001_pre1_RNAseq


title: ECM17

description:
miRNAs in embryonic culture medium
1_17


title: Mz_24h_1


title: ECM16

description:
miRNAs in embryonic culture medium
1_16


title: MM4886_Lung

description:
HN878_B_Low_C57Bl6
sample name in processed data file:
GRA502A256

value: Female


title: 6.BAL_ATACseq

data_processing:
Raw sequencing reads were mapped to the mm9 version of the mouse genome using Bowtie-1.1.1
For each sample peaks of accessibility were identified and annotated using MACS2 with the default settings
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files are normalized to reads per peak million (rpm) using R/Bioconductor.  Peak file is annotated with reads per million (rpm) normalized read counts for each sample, overlap with genomic features, and distance to closest gene

extract_protocol:
Cells were FACS sorted into purified populations.
2000-4000 cells were centrifuged for 10 minutes at 500xg, resuspended in 50 ul of Lysis Buffer (contents), and immediately centrifuged for 30 minutes at 500xg. Tagmentation was performed by resuspending cells in 25 ul of Tagmentation mix (1x TD Buffer, 2.5 ul Tn5 Transpoase) and incubating for 60 minutes at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

treatment_protocol: Mice were infected with 30,000 EID50 of influenza x31 intranasally and rested for 35 days.

value: F


title: MM4770_Blood

description:
H37RV_G_Uninfected_C3HeBFeJ
GRA502A655

source_name: Blood

value: Uninfected

tag: mouse strain


title: Mk_24h_1


title: 4.BAL_ATACseq


title: ECM15

description:
miRNAs in embryonic culture medium
1_15

value: n


title: Mk_24h_2


title: ECM14

description:
miRNAs in embryonic culture medium
1_14


title: ECM13

description:
miRNAs in embryonic culture medium
1_13

value: y


title: 3.BAL_ATACseq

value: airway resident CD8 memory T cells


title: Ct_12h_2


title: ECM12

description:
miRNAs in embryonic culture medium
1_12


title: MM4767_Blood

description:
H37RV_G_Uninfected_C3HeBFeJ
GRA502A652

value: blood


title: MM4769_Blood

description:
H37RV_G_Uninfected_C3HeBFeJ
GRA502A654


title: Ct_12h_1


title: MM4891_Lung

description:
HN878_B_High_C57Bl6
sample name in processed data file:
GRA502A261

value: High


title: 1.BAL_ATACseq

value: Lung Airway

value: 35 days post Influenza X31 infection


title: MM4888_Lung

description:
HN878_B_Low_C57Bl6
sample name in processed data file:
GRA502A258


title: MM4766_Blood

description:
H37RV_G_Uninfected_C3HeBFeJ
GRA502A651


title: 5.Lung_ATACseq

value: parenchyma resident CD8 memory T cells

value: Lung Parenchyma


title: ECM11

description:
miRNAs in embryonic culture medium
1_11


title: Sc_12h_2

value: 4.5 week-old


title: 4.Lung_ATACseq


title: MM4765_Blood

description:
H37RV_G_High_C3HeBFeJ
GRA502A650


title: Sc_12h_1


title: Mz_12h_2

value: Malassezia restricta


title: ECM9

description:
miRNAs in embryonic culture medium
1_9


title: MM4764_Blood

description:
H37RV_G_High_C3HeBFeJ
GRA502A649


title: 6.SP_ATACseq

value: circulating CD8 memory T cells

value: Live/Dead- CD8+ CD44hi FluNP366-374Db+ CD62L-

value: Spleen


title: 3.Lung_ATACseq

value: Live/Dead- CD8+ CD44hi FluNP366-374Db+ CD45.2(IV label)-


title: Mz_12h_1


title: ECM8

description:
miRNAs in embryonic culture medium
1_8


title: MM4763_Blood

description:
H37RV_G_High_C3HeBFeJ
GRA502A648

value: Female


title: MM4762_Blood

description:
H37RV_G_High_C3HeBFeJ
GRA502A647


title: 5.SP_ATACseq

value: F


title: MM4761_Blood

description:
H37RV_G_High_C3HeBFeJ
GRA502A646


title: ECM5

description:
miRNAs in embryonic culture medium
1_5


title: ECM7

description:
miRNAs in embryonic culture medium
1_7

value: n


title: ECM6

description:
miRNAs in embryonic culture medium
1_6


title: 4.SP_ATACseq


title: 2.SP_ATACseq


title: MM4759_Blood

description:
H37RV_G_Low_C3HeBFeJ
GRA502A644

value: Low


title: Mk_12h_1

value: water


title: Mk_12h_2


title: ECM4

description:
miRNAs in embryonic culture medium
1_4


title: ECM10

description:
miRNAs in embryonic culture medium
1_10


title: MM4758_Blood

description:
H37RV_G_Low_C3HeBFeJ
GRA502A643

value: blood


title: ECM3

description:
miRNAs in embryonic culture medium
1_3


title: MM4757_Blood

description:
H37RV_G_Low_C3HeBFeJ
GRA502A642


title: ECM2

description:
miRNAs in embryonic culture medium
1_2


title: MM4756_Blood

description:
H37RV_G_Low_C3HeBFeJ
GRA502A641


title: 2017 9pm Replicate 11

city: Baltimore

first: Diego

middle: Rivera

last: Gelsinger

state: MD

address: 910 Light Street, Apartment 2

department: Biology

institute: The Johns Hopkins Univeristy

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9pm11
sample name in processed data file (antisense to asRNA):
g2017-9pm11

data_processing:
An analytic pipeline, Snap-T for  Small ncRNA annotation pipeline for Transcriptomic or metatranscriptomic data, was developed to find, annotate, and quantify intergenic and anti-sense sRNA transcripts from transcriptomic or metatranscriptomic data.
Intergenic transcripts were at least 30 nt away from any gene or ORF on both strands; Antisense transcripts were 30 nt away from any gene on their strand, but overlapped with a gene on the opposite strand by at least 10 nt; small peptides (<100 nt) were not counted as genes if they were encoded in a transcript that was more than 3 times their length; non-coding transcripts could not contain any reading frame greater than 1/3 of their lengths; predicted non-coding transcripts near contig edges were discarded and the minimum distance to the edge of a contig was dynamically computed such that the tips of contigs were not statistically enriched in annotated ncRNAs; small ncRNAs were between 50 nt and 500 nt in length; sRNA transcripts could not have significant homology with any protein in the NCBI_nr database (query cover>30%, Bitscore>50, evalue<0.0001, and identity>30%) and with any tRNA or RNase P model in the Rfam non-coding RNA database.
The taxonomic origin of each annotated ncRNA was taken to be as that of the contig on which it lay. The taxonomy of each contig was estimated by taking the weighted average of the taxonomic assignment of the genes encoded on it, as determined through the JGI IMG functional and taxonomic annotation service.
Small RNA expression values were calculated using the program stringtie which were tabulated in transcripts per million (TPM)
We used a read count-based differential expression analysis to identify differentially expressed sRNA and mRNA transcripts. The program featureCounts was used to rapidly count reads that map to the assembled RNA transcripts. The read counts were used in the R differential expression software package DESeq2 to calculate differential expression by determining the difference in read counts between one condition normalized read counts from the other condition normalized read counts. The differentially expressed RNAs were filtered based on the statistical parameter of False Discovery Rate (FDR) and those that were equal to or under a FDR of 5% were classified as true differentially expressed transcripts. We carried out differential expression analysis between all conditions, using a likelihood ratio test, and between conditions, using a pairwise Wald test to find any possible differences.
Genome_build: halite metagenome [Taxonomy ID: 1319833]
Supplementary_files_format_and_content: gff, txt; Note: the s (eg *s*9b1) corresponds to the asRNA expression, while the g (eg *g*9b1) corresponds to    the gene expression that is antisense to the asRNA. The expressions for    both asRNA and gene were calculated from the same .fastq

organism: halite metagenome

source_name: Environmental sample

extract_protocol:
Total RNA was extracted from the fixed samples by first isolating the cells through gradual dissolving of the salt particles and lysing them through mechanical bead beating with the RNAeasy PowerSoil RNA extraction kit (QIAGEN). Total RNA was then extracted from the lysate with a Quick-RNA miniprep kit (Zymo Research).
Total RNAseq libraries were prepared with the SMARTer Stranded RNA-seq kit (TaKaRa), using 25ng of RNA input and 12 cycles for library amplification. We sequenced 22 libraries from replicate samples from 2016 and 24 libraries from replicate samples from 2017.

treatment_protocol: Halite nodules were harvested in Salar Grande, an ancient evaporated lake in the Northern part of the Atacama Desert in February 2016 and 2017. All nodules were harvested within a 50m2 area by scraping colonization zone. The colonization zone of each nodule was grounded into a powder, pooling from 1-3 nodules until sufficient material was collected, and stored in the dark in dry conditions until DNA extraction in the lab. Samples used for RNA were stored in RNAlater at 4°C until RNA extraction in the lab.

tag: collection year

tag: collection time


title: 2017 9pm Replicate 12

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9pm12
sample name in processed data file (antisense to asRNA):
g2017-9pm12


title: MM4755_Blood

description:
H37RV_C_Uninfected_C57Bl6
GRA502A640

value: Uninfected


title: ECM1

description:
miRNAs in embryonic culture medium
1_1


title: 3.SP_ATACseq

tag: Sex


title: 2017 9pm Replicate 10

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9pm10
sample name in processed data file (antisense to asRNA):
g2017-9pm10


title: MM4752_Blood

description:
H37RV_C_Uninfected_C57Bl6
GRA502A637


title: 1.SP_ATACseq

tag: sorting markers


title: MM4754_Blood

description:
H37RV_C_Uninfected_C57Bl6
GRA502A639


title: 2017 9pm Replicate 6

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9pm6
sample name in processed data file (antisense to asRNA):
g2017-9pm6


title: 2017 9pm Replicate 7

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9pm7
sample name in processed data file (antisense to asRNA):
g2017-9pm7


title: 2017 9pm Replicate 9

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9pm9
sample name in processed data file (antisense to asRNA):
g2017-9pm9


title: 2017 9pm Replicate 8

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9pm8
sample name in processed data file (antisense to asRNA):
g2017-9pm8


title: MM4753_Blood

description:
H37RV_C_Uninfected_C57Bl6
GRA502A638


title: MM4750_Blood

description:
H37RV_C_High_C57Bl6
GRA502A635

value: High


title: MM4751_Blood

description:
H37RV_C_Uninfected_C57Bl6
GRA502A636


title: REF rep3

city: Istanbul

first: Halil

middle: ibrahim

last: KISAKESEN

state: Istanbul

address: ITU MOBGAM, SARIYER

department: Molecular Biology, Genetics and Biotechnology

country: Turkey

institute: Istanbul Technical University

description: Gene expression at log-phase in Yeast Minimal Medium

hyb_protocol: 0.6 µg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Yeast V2 Oligo Microarrays (G4813A-016322) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 016322_D_F_20070321). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Saccharomyces cerevisiae

source_name: Reference strain

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 0.2 µg RNA using the One-color Low Input Quick Amp Kit (Agilent) according to the manufacturer's instructions, followed by Agilent Nano-prep RNA purification (Agilent, Santa Clara, CA). Dye incorporation and cRNA yield were checked with the NanoDrop-2000 spectrophotometer.

growth_protocol: Precultures of silver-resistant Saccharomyces cerevisiae (2E) mutant strain and reference strain were prepared in yeast minimal medium (2% glucose and 0.67% yeast nitrogen base without amino acid (Difco)) by incubating at 30°C and 150 rpm for about ~ 16 hour. Precultures were inoculated into fresh yeast minimal medium to an initial OD600 of 0.1. Then, cultures were incubated at 30°C and 150 rpm. When cultures OD600 value reach the of about 1.0 (correspoinding to mid-exponential phase). Cells were harvested and total RNA extraction was done.

extract_protocol: Total RNA of yeast cells were extracted by using RNeasy Mini Kit supplied from QIAGEN according to the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: There is no treatment protocol in this study.

tag: strain background

value: Reference strain

tag: genotype/variation

value: wild type; reference

tag: growth phase

value: log phase


title: 2017 9pm Replicate 5

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9pm5
sample name in processed data file (antisense to asRNA):
g2017-9pm5


title: REF rep2


title: REF rep1


title: MM4749_Blood

description:
H37RV_C_High_C57Bl6
GRA502A634

data_processing:
Trimmomatic v0.36 was used to remove the adapters and filter raw reads below 36 bases long. The filtered reads were aligned to the Mus musculus genome Ensembl GRCm38 (release 86) using HISAT2 v2.0.4 with default settings and RF rna-strandedness. The mapped and aligned reads were quantified to obtain the gene-level counts using HtSeq v0.6.1 with default settings and reverse strandedness
Raw counts were processed using the bioconductor package DESeq2 v1.12.4 in R v3.3.1, and normalized using the DESeq method to remove the library-specific artefacts. Variance stabilizing transformation was applied to obtain normalized log2 gene expression values.
Genome_build: Ensembl GRCm38 (release 86)
Supplementary_files_format_and_content: VST log2 normalised expression values. Rows = genes; Columns = samples.

extract_protocol:
Total RNA was extracted using the PerfectPure RNA Blood Kit (5 PRIME). Globin RNA was depleted from total RNA (1.5–2 µg) using the Mouse GLOBINclear kit (Thermo Fisher Scientific)
RNA (200 ng) was used to prepare cDNA libraries using the TruSeq Stranded mRNA HT Library Preparation Kit (Illumina). Libraries were normalized, pooled and then clustered using the HiSeq® 3000/4000 PE Cluster Kit (Illumina). The libraries were imaged and sequenced on an Illumina HiSeq 4000 sequencer using the HiSeq® 3000/4000 SBS kit (Illumina) at a minimum of 25 million paired-end reads (75 bp/100 bp) per sample.

tag: tissue

tag: dose


title: 2E-Log phase-Rep 3

description: Gene expression in the log phase of cell growth

source_name: Silver-resistant Saccharomyces cerevisiae, log. Phase

value: CEN.PK 113.7D (MATa)

value: silver-resistant 2E mutant


title: 2E-Log phase-Rep 2


title: 2017 9pm Replicate 4

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9pm4
sample name in processed data file (antisense to asRNA):
g2017-9pm4


title: MM4748_Blood

description:
H37RV_C_High_C57Bl6
GRA502A633

tag: day

tag: gender


title: MM4747_Blood

description:
H37RV_C_High_C57Bl6
GRA502A632


title: 2E-Log phase-Rep 1


title: MM4745_Blood

description:
H37RV_C_Low_C57Bl6
GRA502A630


title: 2017 9pm Replicate 2

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9pm2
sample name in processed data file (antisense to asRNA):
g2017-9pm2


title: MM4746_Blood

description:
H37RV_C_High_C57Bl6
GRA502A631


title: 2017 9pm Replicate 1

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9pm1
sample name in processed data file (antisense to asRNA):
g2017-9pm1


title: MM4768_Blood

description:
H37RV_G_Uninfected_C3HeBFeJ
GRA502A653


title: 2017 9am Replicate 12

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9am12
sample name in processed data file (antisense to asRNA):
g2017-9am12


title: MM4744_Blood

description:
H37RV_C_Low_C57Bl6
GRA502A629


title: 2017 9am Replicate 11

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9am11
sample name in processed data file (antisense to asRNA):
g2017-9am11


title: 2017 9pm Replicate 3

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9pm3
sample name in processed data file (antisense to asRNA):
g2017-9pm3


title: 2017 9am Replicate 9

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9am9
sample name in processed data file (antisense to asRNA):
g2017-9am9


title: 2017 9am Replicate 8

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9am8
sample name in processed data file (antisense to asRNA):
g2017-9am8


title: MM4743_Blood

description:
H37RV_C_Low_C57Bl6
GRA502A628


title: 2017 9am Replicate 7

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9am7
sample name in processed data file (antisense to asRNA):
g2017-9am7


title: 2017 9am Replicate 10

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9am10
sample name in processed data file (antisense to asRNA):
g2017-9am10


title: MM4740_Blood

description:
HN878_E_Uninfected_C3HeBFeJ
GRA502A625


title: MM4739_Blood

description:
HN878_E_Uninfected_C3HeBFeJ
GRA502A624


title: M(LPS)_input Data rep2

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

data_processing:
Trimmed sequence was examined for its quality by FastQC.
ChIP-seq reads were aligned to the mm10 genome by Bowtie2.
Peaks were called using MACS14 and MACS2
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using MACS14
Supplementary_files_format_and_content: bgd files were generated using MAC2

source_name: Bone marrow

growth_protocol: Bone–marrow derived Macrophages (BMDMs) were isolated from tibias and femurs by flushing with Dulbecco's Modified Eagle Medium (DMEM) (HyClone, Logan, UT, USA) supplementing with 10% (v/v) fetal bovine serum (GIBCO, Grand Island, NY, USA), 1% (w/v) sodium pyruvate (Hyclone), 1% (w/v) HEPES (Hyclone), 100 U/ml penicillin, 0.25 mg/ml streptomycin (Hyclone), 20% L929 cell–conditioned media and 5% horse serum (Hyclone). Cells were cultured for a week while the media were changed every 3 days. BMDMs were plated 24 hr before use.

extract_protocol:
Lysates were clarified from nuclease and histone-DNA complexes were isolated with antibody.
ChIP data were generated using SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) (Cell Signaling Technology) following the manufacturer's protocol. The antibody used in the ChIP assay was anti-H3K4me3 antibody (Cell Signaling Technology), The ChIP-seq data were generated using 50 bp single-end sequencing reads by BGI (Beijing, China).

treatment_protocol: BMDMs were primed with 10 ng/ml recombinant mouse IFN-γ (BioLegend, San Diego, CA, USA) for 18 hr before stimulation. M(LPS) and M(IC) were generated by adding 100 ng/ml Sallmonella LPS (Sigma-Aldrich, St Louis, MO, USA) or 100 ng/ml of LPS in combination with immune complex. Immune complex were prepared in 10-fold molar excess of rabbit anti-OVA IgG (Sigma-Aldrich) to OVA incubated 30 minutes at RT(16) and used 1:100 volume ratio of the immune complex to media for stimulation.

tag: treatment

value: LPS

tag: cell type

value: Bone marrow derived macrophages

value: Bone marrow

tag: age

value: 7-8 weeks old

tag: genotype

value: wild type

tag: chip antibody


title: MM4741_Blood

description:
H37RV_C_Low_C57Bl6
GRA502A626

tag: mouse strain

value: Female


title: MM4742_Blood

description:
H37RV_C_Low_C57Bl6
GRA502A627


title: 2017 9am Replicate 6

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9am6
sample name in processed data file (antisense to asRNA):
g2017-9am6

tag: collection year


title: M(IC)_input Data rep2

value: LPS/IC

tag: strain


title: 2017 9am Replicate 5

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9am5
sample name in processed data file (antisense to asRNA):
g2017-9am5

tag: collection time


title: M(IC)_H3K4me3 rep2

value: anti-H3K4me3 antibody (Cell Signaling Technology)


title: genomic DNA from whole blood 45

type: genomic

city: Boston

first: Sarah

last: Booth

state: Massachusetts

address: 711 Washington St.

institute: JM-USDA Human Nutrition Research Center on Aging at Tufts University

description: whole blood

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina MethylationEPIC Beadchip using standard Illumina protocol (performed at Yale Center for Genome Analysis)

scan_protocol: Standard YCGA procedure

data_processing: Noob + BMIQ normalization

label: Cy3 and Cy5

source_name: whole blood 45

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: responder

value: FALSE

tag: Sex

value: M


title: genomic DNA from whole blood 48

description: whole blood

source_name: whole blood 48

value: F


title: genomic DNA from whole blood 42

description: whole blood

source_name: whole blood 42


title: MM4738_Blood

description:
HN878_E_Uninfected_C3HeBFeJ
GRA502A623

value: blood

value: Uninfected


title: genomic DNA from whole blood 47

description: whole blood

source_name: whole blood 47


title: genomic DNA from whole blood 39

description: whole blood

source_name: whole blood 39


title: unstimulation_input Data rep2

value: unstimulated


title: genomic DNA from whole blood 43

description: whole blood

source_name: whole blood 43


title: genomic DNA from whole blood 44

description: whole blood

source_name: whole blood 44


title: genomic DNA from whole blood 40

description: whole blood

source_name: whole blood 40


title: MM4736_Blood

description:
HN878_E_Uninfected_C3HeBFeJ
GRA502A621


title: MM4737_Blood

description:
HN878_E_Uninfected_C3HeBFeJ
GRA502A622


title: genomic DNA from whole blood 41

description: whole blood

source_name: whole blood 41


title: genomic DNA from whole blood 35

description: whole blood

source_name: whole blood 35


title: 2017 9am Replicate 2

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9am2
sample name in processed data file (antisense to asRNA):
g2017-9am2


title: unstimulation_H3K4me3 rep2


title: MM4735_Blood

description:
HN878_E_High_C3HeBFeJ
GRA502A620

value: High


title: genomic DNA from whole blood 34

description: whole blood

source_name: whole blood 34


title: genomic DNA from whole blood 32

description: whole blood

source_name: whole blood 32


title: genomic DNA from whole blood 38

description: whole blood

source_name: whole blood 38


title: genomic DNA from whole blood 37

description: whole blood

source_name: whole blood 37


title: 2017 9am Replicate 4

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9am4
sample name in processed data file (antisense to asRNA):
g2017-9am4

source_name: Environmental sample


title: M(IC)_input Data rep1


title: genomic DNA from whole blood 33

description: whole blood

source_name: whole blood 33


title: genomic DNA from whole blood 46

description: whole blood

source_name: whole blood 46


title: 2017 9am Replicate 1

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9am1
sample name in processed data file (antisense to asRNA):
g2017-9am1


title: genomic DNA from whole blood 31

description: whole blood

source_name: whole blood 31


title: genomic DNA from whole blood 29

description: whole blood

source_name: whole blood 29


title: 2016 5pm Day 2 Replicate 3

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s17b3
sample name in processed data file (antisense to asRNA):
g17b3


title: 2017 9am Replicate 3

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s2017-9am3
sample name in processed data file (antisense to asRNA):
g2017-9am3


title: M(LPS)_input Data rep1

source_name: Bone marrow


title: genomic DNA from whole blood 36

description: whole blood

source_name: whole blood 36


title: genomic DNA from whole blood 30

description: whole blood

source_name: whole blood 30


title: MM4734_Blood

description:
HN878_E_High_C3HeBFeJ
GRA502A619

source_name: Blood


title: M(LPS)_H3K4me3 rep1


title: M(LPS)_H3K4me3 rep2


title: M(IC)_H3K4me3 rep1


title: MM4731_Blood

description:
HN878_E_High_C3HeBFeJ
GRA502A616


title: 2016 5pm Day 2 Replicate 1

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s17b1
sample name in processed data file (antisense to asRNA):
g17b1


title: unstimulation_H3K4me3 rep1


title: MM4733_Blood

description:
HN878_E_High_C3HeBFeJ
GRA502A618


title: MM4728_Blood

description:
HN878_E_Low_C3HeBFeJ
GRA502A613

value: Low


title: MM4732_Blood

description:
HN878_E_High_C3HeBFeJ
GRA502A617


title: 2016 5pm Day 1 Replicate 1

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s17a1
sample name in processed data file (antisense to asRNA):
g17a1


title: 2016 5pm Day 2 Replicate 2

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s17b2
sample name in processed data file (antisense to asRNA):
g17b2


title: N7

city: Jouy-en-Josas

first: Sandrine

last: Le Guillou

address: Domaine de Vilvert Bat.440

department: Animal Genetics

country: France

institute: INRAE

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
After adapters cleaning and filtering for their size (17-28 nt) with Cutadapt, the RNA-seq data were analysed using miRDeep2 software, with bovine reference genome bosTau8 and miRBase release 22 (all species). The quantification results generated by the quantifier.pl miRDeep2 module were filtered with a custom perl script parse_miRDeep2_outputs.pl (https://forgemia.inra.fr/sylvain.marthey/paqmir/blob/master/paqmir_postprocess_quantifier/parse_miRDeep2_output.pl) to eliminate any redundancy between mature microRNAs by assigning them to the precursors in the following order of priority: 1) mature known in the bovine species, 2) mature known in another species then 3) mature predicted unknown. Additionally, microRNAs of the last two categories were faced with the new RumimiR database (v. June 2019) in order to identify ruminant microRNAs already described in literature but not in the last version of miRBase (v.22), and this information was included for the annotation of quantified microRNAs.
Genome_build: bosTau8

organism: Bos taurus

source_name: Whole milk

extract_protocol:
Total RNA were isolated from whole milk using RNA NOW kit (Ozyme) with overnight precipitation
Illumina TruSeq Small RNA Library Prep Kit

tag: breed

value: Normande


title: MM4726_Blood

description:
HN878_E_Low_C3HeBFeJ
GRA502A611


title: unstimulation_input Data rep1


title: N6


title: 2016 1pm Day 2 Replicate 2

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s13b2
sample name in processed data file (antisense to asRNA):
g13b2


title: 2016 5pm Day 1 Replicate 3

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s17a3
sample name in processed data file (antisense to asRNA):
g17a3


title: MM4730_Blood

description:
HN878_E_Low_C3HeBFeJ
GRA502A615


title: genomic DNA from whole blood 26

description: whole blood

source_name: whole blood 26


title: genomic DNA from whole blood 28

description: whole blood

source_name: whole blood 28


title: MM4729_Blood

description:
HN878_E_Low_C3HeBFeJ
GRA502A614


title: N5


title: 2016 1pm Day 2 Replicate 1

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s13b1
sample name in processed data file (antisense to asRNA):
g13b1


title: MM4725_Blood

description:
HN878_B_Uninfected_C57Bl6
GRA502A610


title: 2016 5pm Day 1 Replicate 2

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s17a2
sample name in processed data file (antisense to asRNA):
g17a2


title: N8


title: 2016 1pm Day 2 Replicate 3

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s13b3
sample name in processed data file (antisense to asRNA):
g13b3


title: genomic DNA from whole blood 27

description: whole blood

source_name: whole blood 27


title: 2016 1pm Day 1 Replicate 2

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s13a2
sample name in processed data file (antisense to asRNA):
g13a2


title: 2016 1pm Day 1 Replicate 1

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s13a1
sample name in processed data file (antisense to asRNA):
g13a1


title: MM4722_Blood

description:
HN878_B_Uninfected_C57Bl6
GRA502A607


title: MM4723_Blood

description:
HN878_B_Uninfected_C57Bl6
GRA502A608


title: N4


title: MM4724_Blood

description:
HN878_B_Uninfected_C57Bl6
GRA502A609


title: 2016 1pm Day 1 Replicate 3

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s13a3
sample name in processed data file (antisense to asRNA):
g13a3


title: N3


title: N1


title: MM4720_Blood

description:
HN878_B_High_C57Bl6
GRA502A605


title: MM4721_Blood

description:
HN878_B_Uninfected_C57Bl6
GRA502A606


title: N2


title: genomic DNA from whole blood 25

description: whole blood

source_name: whole blood 25


title: H9

value: Holstein


title: 2016 9am Day 2 Replicate 3

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s9b3
sample name in processed data file (antisense to asRNA):
g9b3


title: 2016 9am Day 2 Replicate 2

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s9b2
sample name in processed data file (antisense to asRNA):
g9b2


title: genomic DNA from whole blood 24

description: whole blood

source_name: whole blood 24

value: TRUE


title: MM4718_Blood

description:
HN878_B_High_C57Bl6
GRA502A603


title: 2016 9am Day 2 Replicate 1

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s9b1
sample name in processed data file (antisense to asRNA):
g9b1


title: H8


title: MM4719_Blood

description:
HN878_B_High_C57Bl6
GRA502A604


title: genomic DNA from whole blood 22

description: whole blood

source_name: whole blood 22


title: MM4717_Blood

description:
HN878_B_High_C57Bl6
GRA502A602


title: H7


title: 2016 1am Day 2 Replicate 3

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s1b3
sample name in processed data file (antisense to asRNA):
g1b3


title: MM4716_Blood

description:
HN878_B_High_C57Bl6
GRA502A601


title: genomic DNA from whole blood 21

description: whole blood

source_name: whole blood 21


title: 2016 1am Day 2 Replicate 2

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s1b2
sample name in processed data file (antisense to asRNA):
g1b2

source_name: Environmental sample


title: H6


title: genomic DNA from whole blood 15

description: whole blood

source_name: whole blood 15


title: 2016 1am Day 2 Replicate 1

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s1b1
sample name in processed data file (antisense to asRNA):
g1b1


title: MM4715_Blood

description:
HN878_B_Low_C57Bl6
GRA502A600


title: H5


title: H4


title: MM4713_Blood

description:
HN878_B_Low_C57Bl6
GRA502A598


title: MM4714_Blood

description:
HN878_B_Low_C57Bl6
GRA502A599


title: H3


title: 2016 1am Day 1 Replicate 2

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s1a2
sample name in processed data file (antisense to asRNA):
g1a2


title: MM4712_Blood

description:
HN878_B_Low_C57Bl6
GRA502A597


title: genomic DNA from whole blood 17

description: whole blood

source_name: whole blood 17


title: 2016 1am Day 1 Replicate 1

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s1a1
sample name in processed data file (antisense to asRNA):
g1a1


title: genomic DNA from whole blood 16

description: whole blood

source_name: whole blood 16


title: genomic DNA from whole blood 19

description: whole blood

source_name: whole blood 19


title: genomic DNA from whole blood 20

description: whole blood

source_name: whole blood 20


title: H1


title: H2


title: 2016 1am Day 1 Replicate 3

description:
Metatranscriptomic total RNA-seq
2016vs2017_all_asRNAs_non-normalized_TPM_table.txt; 2016vs2017_all_itsRNAs_non-normalized_TPM_table.txt; all_small_ncRNAs.gff
sample name in processed data file (asRNA):
s1a3
sample name in processed data file (antisense to asRNA):
g1a3


title: genomic DNA from whole blood 13

description: whole blood

source_name: whole blood 13


title: genomic DNA from whole blood 14

description: whole blood

source_name: whole blood 14


title: 100116 iMK input

status: Public on Jan 08 2020

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

data_processing:
Mapping to reference genome with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2  --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle generated with MACS using parameters --nomodel --shiftsize=120--format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Peaks called with Sicer V1.1 using parameters mm10 1 200 150 0.74 600 0.01
Filter blacklist regions from peaks, and convert to broadpeak format (see UCSC Genome Browser for format specs)
UCSC's wigToBigWig to convert wiggle track
Genome_build: mm10
Supplementary_files_format_and_content: bigWig, signal from Macs
Supplementary_files_format_and_content: broadpeak, peaks from Sicer

source_name: bone marrow

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying TruSeq ChIP-seq Sample Preparation Kit. (Part#  IP-202-1012). In brief, ChIP-enriched, fragmented DNA was subjected to end repair to generate blunt-end double stranded DNA, adenylation of 3’ ends, and adaptor ligation. Following ligation, SPRIselect (Beckman Coulter) beads were used at 0.9X and 0.6X for left and right side selection, respectively, to obtain an average library target size of ~300 bp. After size selection, fragments were amplified for 16 cycles, and PCR products were purified using Agencourt AMPureXP beads (Beckman Coulter).

tag: chip ab

tag: developmental stage

value: adult

tag: cell isolation markers

value: megakaryocyte


title: 100022 iMK input


title: 100168 ERY input

value: erythroblast


title: 100003 ERY input


title: 100004 ERY input


title: 100169 ERY input


title: 100117 iMK H3K27ac

value: H3K27ac (Abcam, ab4729)


title: 100118 iMK input


title: 100008 Ery H3K27ac


title: 100007 Ery H3K27ac


title: 100126 iMK H3K4me3

value: H3K4me3 (Millipore, 07-473)


title: genomic DNA from whole blood 10

description: whole blood

source_name: whole blood 10


title: 100010 ERY H3K4me3


title: 100016 iMK H3K4me3


title: genomic DNA from whole blood 12

description: whole blood

source_name: whole blood 12


title: genomic DNA from whole blood 7

description: whole blood

source_name: whole blood 7


title: MM4711_Blood

description:
HN878_B_Low_C57Bl6
GRA502A596

source_name: Blood

tag: tissue

tag: dose

tag: day

value: Female


title: 100009 ERY H3K4me3 (Millipore, 07-473)

tag: cell type


title: IMJCKO6: Nrl-KO replicate 6 mRNA-seq

city: Chicago

first: Ivan

last: Moskowitz

state: IL

address: 900 E 57th St

department: Pediatrics, Pathology, and Human Genetics

institute: University of Chicago

description: mRNAseq

data_processing:
Reads were mapped to mouse genome with TopHat2 (v 2.1.1). Reads mapped to the mitochondrial genome, and with phred score < 30 were excluded. Counts were retrieved with HTseq (v.0.6.0)60 in union mode.  Lastly, counts were analyzed for differential expression with R (3.4) package DEseq
Genome_build: mm9

source_name: Retina

extract_protocol: Libraries were prepared from this RNA starting with 1 g per sample and using the mRNA‐seq Sample Prep Kit (Illumina) as per recommended instructions. After Ribozero purification and removing only ribosomal RNA, barcoded libraries were prepared according to Illumina's instructions (2013) accompanying the TruSeq RNA Sample prep kit v2 (Part# RS‐122‐2001). Libraries were quantitated using the Agilent Bio‐analyzer (model 2100) and pooled in equimolar amounts. The pooled libraries were sequenced with stranded 50-bp single-end reads on the HiSeq2500 in Rapid Run Mode

value: retina

tag: age

value: post natal day 21

tag: genotype/variation

value: Nrl knock-out


title: 100083 iMK input


title: IMJCKO5: Nrl-KO replicate 5 mRNA-seq

description: mRNAseq


title: IMJCKO4: Nrl-KO replicate 4 mRNA-seq

description: mRNAseq


title: genomic DNA from whole blood 23

description: whole blood

source_name: whole blood 23

value: F


title: IMJCKO3: Nrl-KO replicate 3 mRNA-seq

description: mRNAseq


title: IMJCKO1: Nrl-KO replicate 1 mRNA-seq

description: mRNAseq


title: IMJCWT5: Wild-type replicate 5 mRNA-seq

description: mRNAseq

value: wild-type


title: IMJCWT3: Wild-type replicate 3 mRNA-seq

description: mRNAseq


title: IMJCWT4: Wild-type replicate 4 mRNA-seq

description: mRNAseq


title: genomic DNA from whole blood 4

description: whole blood

source_name: whole blood 4


title: 100170 iMK input


title: NOD.B10 Rep 3

city: Buffalo

first: Jill

last: Kramer

address: 3435 Main Street

institute: State University of New York at Buffalo

data_processing:
illumina Bcl2fastq
hisat2/2.0.5
featureCoutns v1.5.1
Genome_build: Grcm38
Supplementary_files_format_and_content: a text file includes raw counts

source_name: Spleen

extract_protocol:
Spleens were isolated from NOD.B10 females at 26 weeks of age and from age and gender-matched BL/10 controls. RNA was isolated according to standard protocols using a Qiagen RNeasy kit. RNA meeting quality standards (>8.0) were used as input for RNA-seq using Illumina’sTru-seq low-throughput multiplex protocol. Three biological replicates for each strain were sequenced in parallel using an Illumina HiSeq 2500, with 50 cycle single-end read reactions.
TruSeq RNA Library Prep

value: 36 weeks

tag: gender

value: female


title: genomic DNA from whole blood 5

description: whole blood

source_name: whole blood 5


title: genomic DNA from whole blood 2

description: whole blood

source_name: whole blood 2

value: M


title: genomic DNA from whole blood 6

description: whole blood

source_name: whole blood 6


title: NOD.B10 Rep 1

value: 26 weeks


title: BL/10 Rep 3


title: BL/10 Rep 2


title: BL/10 Rep 1


title: 100023 iMK input


title: 308 cell  S100a4 exon2 KO

city: South San Francisco

first: Steffen

last: Durinck

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
Illumina Casava 1.8
Sequencing reads were filtered to have at least an average base quality of 23 and were then aligned to GRCm38  using GSNAP
Expression counts per gene were obtained by counting the number of reads aligned uniquely to each gene locus as defined by NCBI and Ensembl gene annotations and RefSeq mRNA sequences
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file with gene expression counts

source_name: mammary tumor cell line

extract_protocol:
RNeasy Kit (Qiagen, Hilden, Germany)
TruSeq Stranded Total RNA Library Prep Kit
following manufacturer user guide from Illumina

tag: celltype

value: mammary tumor primary cell line


title: 307 cell  S100a4 exon3 KO


title: 307 cell


title: IMJCWT1: Wild-type replicate 1 mRNA-seq

description: mRNAseq


title: genomic DNA from whole blood 8

description: whole blood

source_name: whole blood 8

value: TRUE