title: dgriZA27Z3_m_wb_R3.ERCC

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description: mixed-species RNA preparation

data_processing:
We performed single-end 76 bp sequencing on the HiSeq2000 Sequencing System (Illumina, San Diego, CA) according to the manufacturer. De-multiplexed reads (Chastity > 0.6) FASTQ output was from Illumina CASAVA v.1.8.2. For each mixed sample, the RNA-seq reads were first mapped to a merged genome and annotation including D. grimshawi (dgri_caf1 assembly; Drosophila_grimshawi.GCA_000005155.1.29.dna_sm.genome.fa), D. melanogaster (FlyBase release 6 version 04 ; FlyBase file: dmel-all-chromosome-r6.04.fasta), and A. stephensi (Anopheles-stephensi-Indian_SCAFFOLDS_AsteI2.fa), appended with updated ERCC sequences (Jiang et al., Genome Research, 2011, PMID21816910; Lee et al., J Genomics, 2016, PMID27512518) using STAR (v2.4.2a) (Doblin et al., Bioinformatics, 2012, PMID23104886) with default parameters or HiSAT2 (v2.0.5; --dta and -max-intronlen = 300,000) (Kim et al., 2015, Nature Methods, PMID25751142). All processed data for Hawaiian species was based on alignment to D. grimshawi (FlyBase version 2016_05). For each chromosome or scaffold in the merged annotation, we add a four letter prefix to identify the species (e.g., scaffold_15110 => dgri_ scaffold_15110) for bam file parsing using SAMtools (v0.1.19) (Li et al., 2009, PMID19505943). We used a demultiplexer (http://github.com/haiwangyang/demultiplexer) to fetch the prefix of read names in the bam alignments and obtained all uniquely-mapped and multi-hit (with < 10 hits, >10 hits are excluded) reads (in bam format) that mapped exclusively to a single species or exclusively to ERCC. We reconverted bam files for each species to raw read fastq files using BEDTools (2.25.0; bamtofastq) (Quinlan and Hall, 2010, Bioinformatics, PMID20110278).
After this step, reads of each multi-species sample were split into three categories based on the mapped genome– D. grimshawi, ERCC, and leftover, which includes unmapped reads, reads mapped to multiple species (or multiple species plus ERCC), and reads mapped to either D. melanogaster or A. stephensi. For multi-species samples, the original fastq file can be restored by merging the reads of D. grimshawi as well as the ERCC and leftover reads. We provide both STAR (SRR3355*) and HiSAT2 (SRR724* & SRR725*) fastq files in this GEO entry. We provided associated gene-level read count files based on HiSAT2 alignments, and the read count files have both FlyBase version (*htseq_reverse.HiSAT2.FB.txt) and YO version (*htseq_reverse.HiSAT2.YO.txt) in Supplementary files of this GEO. For the latter one, we also provide two extra columns in the expression matrix, showing the maximum exon-level overlap (Jaccard index) between YO gene ID and FlyBase gene ID. In addition, we provided bigWig tracks for all samples (replicated merged), YO annotation files (in both gtf and gff3 format), ortholog look up table (among YO gene ID, FlyBase gene ID, and dmel gene), gene-level normalized read counts based on either YO or FlyBase annotation, and transcript-level transcripts per million (TPM) based on YO or FlyBase annotation.

organism: synthetic construct

source_name: ERCC that merged to the multi-species sample (Drosophila grimshawi; Drosophila melanogaster; Anopheles stephensi)

growth_protocol: All lines were originated from a single wild-caught female (iso-female line) and were reared at the Hawaiian Drosophila Research Stock Center. For D. grimishawi, the G1 strain was isolated from the Auwahi dry forest of East Maui in July 1965, the ZA27Z2 and ZA27Z3 strains were isolated from the Makawao Forest Reserve of East Maui in March 2010, and Mo010 strain was isolated from the southeast of Kawela Gulch of Molokai Island in December 2010, and Wm1041 strain was isolated from the Iao Valley of West Maui in July 2014. For D. silvestris, Y11R6 strain was isolated from the Olaa Forest Reserve of Hawaii in December 1986, and U26B9 strain was isolated from the Kahuku Ranch of Hawaii in January 1997. The D. hemipeza strain W40B14 was isolated from the Palikea Ridge of Oahu in July 1983. The D. heteroneura W48B6 strain was isolated from the base of Hinakapoula of Hawaii in August 1983. The D. hawaiiensis Y17P5 strain was isolated from Kipuka Ki, Hawaii Volcano National Park in March 1987. 70-100 Flies were grown in gallon glass jars with a 5 cm bed of dry sterile sand. Flies were fed once a week with five vials containing ~3ml of Yeastless Wheeler Clayton medium (placed horizontally in each jar). A single batch of this media was prepared with: 16g each of agar, rice cereal, Kellogg’s Special K, and wheat germ powder, plus 400g Gerber’s banana baby food and 1400ml water. These ingredients were mixed, cooked to boil and cooled. After cooling (but still liquid), 6ml each of 95% ethanol and propionic acid was added and mixed and then used to fill glass dram vials, which were stored 4oC until needed. 1/5 sheet of folded non-bleached facial tissue paper saturated with a water extract of fermenting Clermontia sp. leaves was added to each vial. Females of each strain laid eggs onto the tissue. Vials with eggs were collected weekly. Eggs hatched in about one week. Larvae were fed weekly for 2 weeks (as needed based on density of larvae). The recipe for cornmeal paste larval food was: 800g cornmeal, 100g brewers yeast, 90g soybean meal, 90g agar, 133ml karo syrup, 45g molasses and 4L water. This mixture was boiled, cooled, and 45ml each of 95% ethanol and propionic acid was added. The cornmeal paste is mixed with the water extract of fermenting Clermontia sp. leaves. After 3 weeks the larval tubes were transferred to moist sterile sand jars. Larvae burrow into the sand for pupation. Adults eclosed after 6 weeks and were aged for dissection. Females of all sequenced species began laying eggs around 4 weeks. Males of some species tend to die much earlier than females, making it problematic to collect sexually mature flies of both sexes at the same age for dissection. All flies were grown at 18oC with a 12h/12h Day/Night cycle.

extract_protocol:
Flies were anesthetized by briefly chilling on a 0oC glass plate. All samples were dissected in Phosphate Buffered Saline solution pH7.4 and transferred to 112ul of RNA later (Life Technologies, Carlsbad, CA) in 96-well plates at room temperature after being macerated with forceps. After transport, plates were stored at -80oC. For D. grimshawi samples, we added 20-30 1.0mm glass beads (BioSpec Products, Bartlesville, OK) to each sample and added 600ul RLT buffer from the RNeasy 96 kit (Qiagen, Valencia, CA) to each well. We homogenized the samples three times for 60 seconds each with a mini-beadbeater (Biospec Products, Bartlesville, OK). Extraction of total RNA was performed using the RNeasy 96 kit according to manufacturer's guide (spin version), except that we used 712μl of 70% ethanol in each well to dilute the RNAlater and RLT buffer. D. grimshawi RNA was added to D. melanogaster RNA and A. stephensi embryos for homogenization and a second round of RNA extraction using the RNeasy kit. D. melanogaster and A. stephensi RNAseq will be reported elsewhere. Four head and gonad samples of Wm1041 were split into mixed-species and single-species RNA preparations. All other samples were prepared without mixing with other species using the same RNeasy protocol. RNA was quantified using the Quant-iT RiboGreen quantification kit Life Technologies, Carlsbad, CA).
We used the Truseq PolyA+ and stranded mRNA kit with half volumes (Illumina, San Diego, CA). 100ng total RNA was input for all samples. We also added 20pg Pool 78A or 78B ERCC spike-ins (Jiang et al., Genome Research, 2011, PMID 21816910) added to the Fragment-Prime-Finish Mix during mRNA fragmentation step. Libraries were quantified with Quant-iT PicoGreen (Life Technologies, Carlsbad, CA), and pooled for multiplexed sequencing.

tag: strain

value: not applicable

tag: Sex


title: dgriZA27Z3_m_wb_R4.ERCC

status: Public on Jun 01 2018

type: SRA

country: USA

description: mixed-species RNA preparation

library_source: transcriptomic

molecule: polyA RNA

tag: tissue

tag: replicate


title: control_cultivar4_timepoint1_rep2

type: RNA

city: Beaucouzé

first: Mathilde

last: ORSEL

address: 42, rue Georges Morel

country: France

institute: IRHS

hyb_protocol: The hybridization performed on a AryANE 12x135k array (NimbleGen Hybridization System, Roche) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532 and 635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. Pair-data files were extracted from the scanned images using DEVA 1.2 software (Roche).

data_processing: Statistical analyses were performed using R version 2.14.1 (R Development Core Team, 2011) and the package LIMMA 3.10.1 (Smyth G.K., 2005) from the Bioconductor project. Data were normalized by the lowess method from LIMMA.

molecule: total RNA

organism: Malus domestica

source_name: Apple 'Linda' fruit flesh

label_protocol: 200ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. Five µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5mmol of cyanine-3 (Cy3) or cyanine-5 (Cy5) (Interchim, France), then purified with QIAquick PCR Purification Kit (QIAGEN) according to manufacturer’s instructions. Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized.

growth_protocol: Apples fruits were harvested from a commercial orchard at a preclimatric stage.

extract_protocol: Total RNA was extracted from frozen samples as described by Gasic et al. (2004) and Chang et al. (1993)

treatment_protocol:
protocol 1: Harvested fruits were washed with tap water, surface-sterilized by 2% sodium hypochlorite for 2 min, and then washed with sterilized water, air-dried and finally inoculated with 20 µl (1×105 conidia mL-1) of P. expansum on opposite sides of each fruit, and stored in open-faced plastic boxes at 2°C.
protocol 2: Samples were then taken from each control and inoculated fruits at 3 time points. i.e. one hour, one week and six weeks post inoculation.

tag: organ

value: Mature fruit

tag: tissus

value: parenchyma

tag: genetic background

value: Linda

tag: phenotype

value: Susceptible

tag: treatment 1

tag: treatment 2

value: 1h cold storage 2°C


title: Inoculated_cultivar4_timepoint1_rep2

value: Inoculated with Penicillium expansum


title: control_cultivar4_timepoint1_rep1


title: wild type control rep1

city: Wuhan

first: Lingye

last: Su

address: Lumo Road, Moshan

country: China

institute: Wuhan Botanical Garden, Chinese Academy of Sciences

description: Gene expression data from wild type Arabdopsis leaf under normal conditon

hyb_protocol: 12.5 μg of labelled and fragmented cRNA probes were hybridized to the Arabidopsis arrays with the Hybridization, Wash and Stain Kit (Affymetrix, #900720) according to the manufacturer’s instructions

scan_protocol: The arrays were scanned using a GeneChip® Scanner 3000 (Affymetrix, #3000).

data_processing: The data were analyzed with Microarray Suite version 3.0 (MAS 3.0)

label: biotin

organism: Arabidopsis thaliana

source_name: wild type Arabdopsis leaf

label_protocol: The cRNA was labelled with a biotinylated ribonucleotide  analogue and was fragmented with fragmentation buffer using the MessageAmp™ Premier RNA Amplification Kit (Ambion, #1792).

growth_protocol: Plants were grown on soil in a greenhouse (16-h light/8-h dark) at 22 oC

extract_protocol: Total RNA was extracted from 100 mg samples by using the Column Plant RNAout 2.0 (Tiandz Inc., Beijing, China)

treatment_protocol: For cold treatment, seedlings of transgenic lines and wild-type Arabidopsis were grown in soil in 22 oC for 21 d. After irrigation, the phenotypes of plant were observed during the following 8 h 4℃ cold treatment.

value: leaf

tag: genotype/variation

value: wild type

tag: treatment

value: normal condition


title: dgriZA27Z3_m_wb_R2.ERCC

description: mixed-species RNA preparation


title: dgriZA27Z3_m_wb_R1.ERCC

description: mixed-species RNA preparation


title: dgriZA27Z3_f_wb_R4.ERCC

description: mixed-species RNA preparation


title: dgriZA27Z3_f_wb_R3.ERCC

description: mixed-species RNA preparation


title: dgriZA27Z3_f_wb_R2.ERCC

description: mixed-species RNA preparation


title: dgriZA27Z3_f_wb_R1.ERCC

description: mixed-species RNA preparation


title: dgriZA27Z2_m_wb_R4.ERCC

description: mixed-species RNA preparation


title: dgriZA27Z2_m_wb_R2.ERCC

description: mixed-species RNA preparation


title: dgriZA27Z2_m_wb_R3.ERCC

description: mixed-species RNA preparation


title: dgriZA27Z2_m_wb_R1.ERCC

description: mixed-species RNA preparation


title: Inoculated_cultivar4_timepoint1_rep3


title: VaMyb14OE control rep1

description: Gene expression data from VaNAC26 transgenic Arabdopsis leaf under normal conditon

source_name: VaMyb14 transgenic Arabdopsis leaf

value: VaMyb14 transgenic


title: dgriZA27Z2_f_wb_R3.ERCC

description: mixed-species RNA preparation


title: Inoculated_cultivar4_timepoint1_rep1


title: Inoculated_cultivar1_timepoint3_rep3

source_name: Apple 'Delorina' fruit flesh

value: Delorina

value: Resistant

value: 6 weeks cold storage 2°C


title: control_cultivar1_timepoint3_rep3


title: siNC_rep2

city: Beijing

first: Xuerui

last: Yang

address: Haidian District

department: School of Life Sciences

institute: Tsinghua University

data_processing:
Low-quality reads with Phred quality scores lower than 20 (50% of bases) were removed using fastq quality filter. Adapters cut.
STAR mapping software returns "toGenome.bam" files. Command: STAR --runThreadN 16 --quantTranscriptomeBan Singleend --outFilterType BySJout --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMunmapped Within --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --genomeDir $STARgenomeDir --readFilesIn $R1 $R2 --outFileNamePrefix $i --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM GeneCounts
Raw counts of sequencing reads for genes using HTSeq(uniq map)
Genome_build: Grch38
Supplementary_files_format_and_content: "counts.txt" files with 2 columns, i.e. "geneID" and "counts".

organism: Homo sapiens

source_name: Prostate cancer cells

growth_protocol: PC3 cells were purchased from the American Type Culture Collection (ATCC). PC3 cells were cultured in Roswell Park Memorial Institute 1640 (RPMI-1640), which were supplemented with 10% fetal bovine serum (HyClone)

extract_protocol:
RNA was isolated using Trizol reagent.
RNA library construction were performed by Next_Ultra_Directional RNA Library Prep kit (NEB #E7420L)

treatment_protocol: PC3 cells were transfected with siNC and siNEAT1_2, respectively.

tag: cell line

tag: transfection

value: siNC


title: dgriZA27Z2_f_wb_R4.ERCC

description: mixed-species RNA preparation


title: control_cultivar1_timepoint3_rep2


title: Inoculated_cultivar1_timepoint3_rep1


title: dgriZA27Z2_f_wb_R2.ERCC

description: mixed-species RNA preparation


title: siNEAT1_rep2


title: dgriZA27Z2_f_wb_R1.ERCC

description: mixed-species RNA preparation


title: siNC_rep1


title: siNEAT1_rep1


title: 3999215202_R02C01

type: genomic

city: Exeter

first: Therese

middle: M

last: Murphy

address: RILD building

department: University of Exeter Medical School

country: United Kingdom

institute: University of Exeter

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylation450K BeadChip (Illumina) protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing: Illumina Genome Studio software was used to extract the raw signal intensities of each probe (without background correction or normalization).   Probes containing a SNP with minor allele frequency (MAF) >5% within 10bp of the single base extension site based on   Illumina’s database and probes identified by Chen et al.* were removed. Data was then  pre-processed in the R package wateRmelon using the pfilter and dasen functions.

label: Cy3, Cy5

molecule: genomic DNA

source_name: whole blood

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit  (Zymo Research) according to the manufacturer’s standard protocol.

extract_protocol: Genomic DNA was isolated from whole blood  using a standard phenol-chloroform extraction method, and tested for degradation and purity before analysis.

treatment_protocol: Individuals with a self-reported history of doctor's diagnosed depression & a self-reported history of an inflammatory disorder (code = 1); Individuals with a self-reported history of doctor's diagnosed depression (code = 2); Individuals with a self-reported history of an inflammatory disorder (code = 3); Healthy controls (code = 4 )

tag: age

tag: groupid

tag: gender

value: F


title: 3999215202_R03C01


title: 3999215202_R01C01

value: M


title: dgriWm1041_f_rg_R2.ERCC

description: mixed-species RNA preparation

tag: strain

value: not applicable


title: control_cultivar1_timepoint3_rep1

value: Mature fruit


title: Inoculated_cultivar1_timepoint2_rep3

value: parenchyma

value: 1 week cold storage 2°C


title: dgriWm1041_f_hd_R2a.ERCC

description: mixed-species RNA preparation

tag: Sex


title: control_cultivar1_timepoint2_rep3


title: dgriWm1041_f_rg_R1.ERCC

description: mixed-species RNA preparation

tag: tissue


title: 3999215202_R04C01


title: Inoculated_cultivar1_timepoint2_rep2


title: 3999215194_R05C02


title: 3999215194_R06C02


title: 3999215194_R06C01


title: 3999215194_R01C02


title: control_cultivar1_timepoint2_rep2


title: Cx30_KO_MPTP

city: Fukuoka

first: Atsushi

last: Fujita

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Neurology

country: Japan

institute: Graduate School of Medical Sciences, Kyushu University

hyb_protocol: cDNA was hybridized to a SurePrint G3 Mouse Gene Expression Microarray 8x60K v2; Agilent Technologies according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

organism: Mus musculus

source_name: Cx30 KO, MPTP, striatum

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

tag: agent

value: MPTP

tag: genotype

value: Cx30 KO

value: Male

tag: tssue

value: striatum


title: Inoculated_cultivar1_timepoint2_rep1

tag: organ

tag: tissus

tag: genetic background

value: Inoculated with Penicillium expansum


title: dgriWm1041_f_hd_R1a.ERCC

description: mixed-species RNA preparation

tag: replicate


title: 3999215194_R02C02


title: 3999215194_R03C02


title: embryo_e9_rep2

city: Geneva

first: Leonardo

last: Beccari

address: 30 Quai Ernest Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

description: pool of 2-3 embryos

data_processing:
Illumina Casava1.8.2 software used for basecalling.Replicate data set was concatenated together.
Demultiplexed RNA-seq reads were mapped onto the public available GRCm38 (mm10). using TopHat release 2.0.9 (Kim et al., 2013). TopHat output files were processed with SAMTools (Li et al., 2009) and BedTools (Quinlan, 2014) to extract the unique read coverage along the genome. For visualisation and comparison across samples, the read coverage was divided by the number of millions of mapped reads in each sample.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph of the RNAseq read coverage, divided by the number of millions of mapped reads in each sample.

source_name: mouse embryo stage e9

growth_protocol: Mouse embryos form wild-type CD1 mothers were collected at different days post-coitum

extract_protocol:
The RNA was extracted using the RNAeasy mini kit (Qiagen) following the manufacturer’s instructions. Contaminant DNA was eliminated using the on-column DNAase digestion and RNA was eluted in RNAase free water. RNA was quantified with the Qubit HS RNA quantification kit (Thermo fisher) and the integrity assessed with bioanalyser.
RNA-seq libraries were prepared from 100ng of pure total RNA using the TruSeq Stranded mRNA protocol from Illumina with polyA selection

treatment_protocol: Embryos at similar developmental stages were collected and stored at -80 in RNA later solution

tag: developmental stage

tag: tissues

value: post-occipital region of the embryo


title: embryo_e9_rep1

description: pool of 2-3 embryos


title: dgriWm1041_f_go_R2a.ERCC

description: mixed-species RNA preparation


title: control_cultivar1_timepoint2_rep1

tag: phenotype

tag: treatment 1

tag: treatment 2


title: 3999215194_R04C01

tag: age

tag: groupid


title: 3999215194_R05C01

tag: gender


title: dgriWm1041_f_ca_R2.ERCC

description: mixed-species RNA preparation

tag: strain

tag: Sex


title: dgriWm1041_f_go_R1a.ERCC

description: mixed-species RNA preparation

tag: tissue


title: embryo_e7_rep3

description: pools of 10 embryos

source_name: mouse embryo stage e7

value: posterior portion of the embryo (excluding the anterior neural plate domain)


title: embryo_e8_rep2

description: pool of 2-3 embryos

source_name: mouse embryo stage e8

value: E8.5 (After turning 12-16somites)


title: dgriWm1041_m_rg_R2.ERCC

description: mixed-species RNA preparation


title: Inoculated_cultivar1_timepoint3_rep2

value: Delorina

value: Resistant


title: Inoculated_cultivar1_timepoint1_rep3

value: 1h cold storage 2°C


title: 3999431078_R04C02


title: embryo_e8_rep1

description: pool of 2-3 embryos


title: 3999215194_R02C01

value: F


title: WT_MPTP

source_name: WT, MPTP, striatum

tag: agent

tag: genotype

value: WT


title: dgriMo010_m_wb_R4.ERCC

description: mixed-species RNA preparation

value: not applicable


title: 3999215194_R03C01


title: dgriWm1041_f_ca_R1.ERCC

description: mixed-species RNA preparation


title: Inoculated_cultivar1_timepoint1_rep2

tag: organ

value: Mature fruit


title: control_cultivar1_timepoint1_rep3

tag: tissus

value: parenchyma


title: Inoculated_cultivar1_timepoint1_rep1

tag: genetic background


title: 3999215194_R01C01

value: M


title: dgriMo010_m_wb_R3.ERCC

description: mixed-species RNA preparation

tag: replicate


title: embryo_e7_rep2

description: pools of 10 embryos

tag: developmental stage


title: embryo_e7_rep1

description: pools of 10 embryos

tag: tissues


title: dgriMo010_m_wb_R1.ERCC

description: mixed-species RNA preparation


title: control_cultivar1_timepoint1_rep2

tag: phenotype


title: embryo_e6_rep3

description: pools of 10 embryos

source_name: mouse embryo stage e6

value: Whole embryo


title: embryo_e6_rep2

description: pools of 10 embryos


title: AortaPlus_RMM138

city: Singapore

first: Daniel

last: Carbajo

state: Singapore

address: 8A Biomedical Grove, Immunos Building levels 3 & 4

department: Bioinformatics

country: Singapore

institute: SIgN (A*STAR)

description: Aorta1 Lyve1+ macrophages

data_processing:
Paired-end reads were mapped to reference genome using STAR version 2.5.2b
Mapped paired-end reads were summarized to gene level using featureCounts v1.5.0 and with GENCODE GRCm38 vM7 gene annotation
Counts per million were calculated in R_3.3.0 using edgeR_3.14.0 over TMM-normalized read counts summarized at gene level; CPM values were log2-transformed
Genome_build: GRCm38
Supplementary_files_format_and_content: log2-transformed CPM values calculated on TMM-normalized read counts summarized at gene level; raw counts per sample

source_name: Aorta Lyve1+ macrophages

extract_protocol:
Total RNA was extracted using Arcturus PicoPure RNA Isolation kit (Thermofisher, KIT0204) according to manufacturer’s protocol.
cDNA libraries were prepared using 2ng of total RNA and 1ul of a 1:50,000 dilution of Ambion ERCC RNA Spike-in Controls (Thermofisher, 4456740) using the SMARTSeq v2 protocol described in Nature Protocols volume 9, pages 171-181 (Picelli et al., 2014) with the following modifications: 1. Use of 20mM TSO, 2. Use of 250pg of cDNA with 1/5 reaction of Nextera XT kit (Illumina, FC-131). 12 samples were subjected to an indexed PE sequencing run of 2x51 cycles on an Illumina HiSeq 2000 (20 samples/lane) and 1 sample was subjected to an indexed PE sequencing run of 2x51 cycles on an Illumina HiSeq 2500 Rapid mode (14 samples/lane).

tag: genotype/variation

value: wid type

value: Aorta

tag: cell type

value: sorted Lyve1+ macrophages


title: dgriMo010_f_wb_R3.ERCC

description: mixed-species RNA preparation


title: embryo_e6_rep1

description: pools of 10 embryos


title: 3999431078_R02C02

tag: age


title: dgriMo010_f_wb_R4.ERCC

description: mixed-species RNA preparation


title: control_cultivar1_timepoint1_rep1

tag: treatment 1

tag: treatment 2


title: 3999431078_R03C02

tag: groupid

tag: gender


title: DRR_ChIRP_input_rep2

city: Bethsda

first: Vittorio

last: Sartorelli

address: 50 South Dr.

department: NIAMS

institute: NIH

library_source: genomic

data_processing:
Library strategy: ChIRP-seq
Basecalls performed using CASAVA version 1.8.2 and bcl2fastq/2.17.1
ATAC-seq reads were processed with CASAVA 1.8.2 to generate FastQ files. The raw reads were trimmed with cutadapt/1.12 and redundant reads were removed using FastUniq at pair end  FastQ level.  Reads of 50 bases were aligned to mouse genome build mm9 with Bowtie 1.1.1, allowing two mismatches. Only uniquely mapped, non-redundant reads were used for peak calling after removing highly repetitive reads.
ChIP-seq reads were were processed with CASAVA 1.8.2 to generate FastQ files. Reads of 50 bases were aligned to mouse genome build mm9 with Bowtie 1.1.1, allowing two mismatches. Only uniquely mapped, non-redundant reads were used for peak calling.
ChIRP-seq reads were mapped to the mm9 genome assembly using Bowtie2 version 2.2.4 with the default configurations.
ChIP-seq reads were mapped to the mm9 genome assembly using Bowtie 1.1.1 with the default configurations.
peaks of ATAC-seq were called using MACS 1.4.2 ( Zhang et al., 2008) with the following setting: p-value cutoff of 1.0 E-03 .
peaks of ChIRP were called using MACS2 ( Zhang et al., 2008) with the following setting: p-value cutoff of 1.0E-05 .
peaks of ChIP were called using MACS 1.4.2 ( Zhang et al., 2008) with the following setting: p-value cutoff of 1.0E-05 .
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include peak values for each Sample

source_name: muscle

growth_protocol: C2C12 cells were cultured  in DMEM medium with 20% HyClone FBS. For differentiation, cells were cultured in differentiation medium (DMEM with 2% horse serum and 1x insulin-transferrin-selenium)

extract_protocol:
For ChIPSeq,cells were cross-linked in 1% formaldehyde and lysate to extract nuclei. The chromatin was sonicated to 250 bp fragments.  Lysates were cleared from sonicated nuclei and used for immunoprecipitation  For ChIRPseq, cells were cross-linked in 1% glutaraldehyde. Nuclei were sonicated and used for probe hybridization. For ATACseq, nucli were isolated and   treated with Tn5 transpoase.
For ChIPSeq,  10ng of immuno-precipitated DNA fragments were used to prepare ChIP-seq libraries with NEBNext Ultra DNA library prep kit for Illumina (New England BioLabs) following the manufacturer’s protocol.  NEBNext Ultra II RNA library prep kit (New England BioLabs) was used to process RNA-Seq libraries following the manufacturer’s protocol.

treatment_protocol: Cells were transfected with control and DRR or SMC3 siRNA with RNAiMAX according to manufacturer's protocol.

tag: differentiation stage

value: myotube (MT)

tag: probe/chip antibody

value: DRR probe input

tag: strain


title: Inoculated_cultivar4_timepoint2_rep3

tag: organ

value: Linda

value: Susceptible

value: Inoculated with Penicillium expansum

value: 1 week cold storage 2°C


title: LacZ_ChIRP_rep2

value: LacZ probe


title: dgriMo010_f_wb_R2.ERCC

description: mixed-species RNA preparation

tag: tissue

tag: Sex


title: 3999431078_R06C01


title: 3999431078_R01C02

value: F


title: dgriMo010_f_wb_R1.ERCC

description: mixed-species RNA preparation

tag: replicate


title: DRR_ChIRP_pool2_rep2

value: DRR probe pool2


title: control_cultivar4_timepoint2_rep2

tag: tissus

tag: genetic background


title: control_cultivar4_timepoint2_rep3

tag: phenotype


title: 3999431078_R05C01


title: Inoculated_cultivar4_timepoint2_rep2


title: DRR_ChIRP_pool1_rep2

value: DRR probe pool1


title: Inoculated_cultivar4_timepoint2_rep1

value: Mature fruit


title: Inoculated_cultivar2_timepoint3_rep3

source_name: Apple 'Ella' fruit flesh

value: parenchyma

value: Ella

value: 6 weeks cold storage 2°C


title: dgriG1_m_wb_R2.ERCC

description: mixed-species RNA preparation

value: not applicable


title: dgriG1_m_wb_R4.ERCC

description: mixed-species RNA preparation


title: DRR_ChIRP_input_rep1


title: dgriG1_m_wb_R1.ERCC

description: mixed-species RNA preparation


title: control_cultivar4_timepoint2_rep1


title: dgriG1_m_vs_R4.ERCC

description: mixed-species RNA preparation


title: DRR_ChIRP_pool2_rep1


title: 3999442083_R04C02


title: dgriG1_m_wb_R3.ERCC

description: mixed-species RNA preparation


title: DRR_ChIRP_pool1_rep1


title: control_cultivar2_timepoint3_rep3


title: 3999431078_R03C01


title: 3999431078_R01C01


title: Inoculated_cultivar2_timepoint3_rep2


title: control_cultivar2_timepoint3_rep2


title: 3999431078_R04C01


title: S4

city: Boston

first: Irene

last: Ghobrial

state: MA

address: 4 Blackfan Circle, 2nd Floor, Suite 240

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
We used Picard and STAR to process and align the RNA-seq reads with mouse reference genome (mm10) or human reference genome (GRCh37) and to compute a series of quality control metrics.
RNA-seq transcript abundances were estimated using RSEM.
Genes with low expression (RSEM expected counts) were filtered out and differential gene expression between different samples was determined using DESeq2.
Genome_build: Mus musculus mm10 for OBC
Genome_build: Human reference genome (GRCh37) for OPM2
Supplementary_files_format_and_content: RSEM output

source_name: OBCs from KaLwRij mice

extract_protocol:
Total RNA was isolated from flow-sorted OBCs (Lin-/CD45-/CD31-/CD51+/Sca-1-) aquired from femur bones and collected directly in lysis buffer from the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech TaKaRa cellartis) for RNA sequencing. Total RNA was extracted from ND-MSCs co-cultured with OPM2 cells using the TRIzol kit (Invitrogen)
Nextera XT DNA Library Preparation Kit (Illumina, Cat. Nos. FC-131-1024) for OBC
NEBNext® UltraTM RNA Library Prep Kit for OPM2 cells

tag: treatment

value: Scramble control

tag: genotype/variation

value: C57BL/KaLwRij (KaLwRij)


title: dgriG1_m_vs_R1.ERCC

description: mixed-species RNA preparation

source_name: ERCC that merged to the multi-species sample (Drosophila grimshawi; Drosophila melanogaster; Anopheles stephensi)


title: Inoculated_cultivar2_timepoint3_rep1


title: dgriG1_m_vs_R2.ERCC

description: mixed-species RNA preparation


title: dgriG1_m_tx_R4.ERCC

description: mixed-species RNA preparation


title: S2


title: 3999442083_R05C02

tag: age


title: 3999442083_R02C02


title: S3


title: dgriG1_m_tx_R3.ERCC

description: mixed-species RNA preparation


title: S1


title: Inoculated_cultivar2_timepoint2_rep3

tag: treatment 1


title: control_cultivar2_timepoint2_rep2

tag: treatment 2


title: dgriG1_m_tx_R2.ERCC

description: mixed-species RNA preparation


title: A6


title: LacZ_ChIRP_rep1

value: myotube (MT)


title: 3999442083_R06C01

tag: groupid


title: control_cultivar2_timepoint2_rep3


title: 3999442083_R03C02

tag: gender

value: M


title: 3999431078_R02C01


title: 3999442083_R01C02


title: dgriG1_m_tx_R1.ERCC

description: mixed-species RNA preparation


title: Inoculated_cultivar2_timepoint2_rep2


title: A4


title: A3


title: A1


title: 3999442083_R03C01


title: IFNb1_Li_Macr

first: Alexander

last: Poltorak

state: Massachusetts

address: 150 Harrison avenue

institute: Tufts University

data_processing:
The resulted data were demultiplexed using Illumina CASAVA 1.8 and fastq files for each initial sample were generated
Tophat2 alignment of raw single reads to UCSC mm10 genome
Cuffdids using the outputs from two previous steps with mm10 annotation
Genome_build: mm10

source_name: liver

growth_protocol:
Mice were euthanized, and alveolar macrophages were elicited via rinsing the lungs of the animals with sterile PBS; following isolation of macrophages, livers were excized and used for RNA preparation
Seven to fifteen week old mice were used for each experiment. Wild type C57BL/6 mice were purchased from The Jackson Laboratory (Bar Harbor Maine). STING-/- mice obtained from Dr. Glen Barber (University of Miami) and IFNAR-/- mice provided by Dr. Katherine Fitzgerald

extract_protocol:
RNA was prepared according to manufacture's instructions with 1 ml of Trizol being used per 5 million of cells or 50 µg of tissue
Library was prepared using Truseq pair-end Illumina kit. Briefly, 10-100 ng of total RNA was reconstituted in water, mixed with Ribosomal removal Buffer containing RNAClean XP beads, and depleted from rRNA. First strand was synthesized using RT, followed by a second strand synthesis, 3' ends were adenylated and ligated to the adaptors, followed by ligateion of the 5' adaptors; the library was purified and measured on DNA-concentration

treatment_protocol: there was no stimulation

tag: strain background

tag: genotype

value: liver


title: 3999442083_R01C01


title: 3999442083_R02C01


title: dgriG1_m_re_R4.ERCC

description: mixed-species RNA preparation

tag: strain


title: dgriG1_m_re_R3.ERCC

description: mixed-species RNA preparation


title: Inoculated_cultivar2_timepoint2_rep1

tag: organ

value: Susceptible


title: IFNAR_Li_Macr

value: IFNAR-KO

tag: tissue


title: 3999431010_R06C02


title: Inoculated_cultivar2_timepoint1_rep3

value: Inoculated with Penicillium expansum

value: 1h cold storage 2°C


title: 3999431010_R04C02


title: 3999442083_R04C01

value: F


title: 3999431010_R05C02


title: control_cultivar2_timepoint1_rep3


title: control_cultivar2_timepoint2_rep1

value: 1 week cold storage 2°C


title: IFNb_A_Macr

source_name: Alveolar macrophages

value: Alveolar macrophages


title: Inoculated_cultivar2_timepoint1_rep2

value: Mature fruit


title: control_cultivar2_timepoint1_rep2

value: parenchyma


title: dgriG1_m_hd_R3.ERCC

description: mixed-species RNA preparation

tag: Sex


title: dgriG1_m_re_R2a.ERCC

description: mixed-species RNA preparation

tag: replicate


title: dgriG1_m_re_R1.ERCC

description: mixed-species RNA preparation


title: 3999431010_R03C02


title: Inoculated_cultivar2_timepoint1_rep1

tag: tissus

value: Ella


title: control_cultivar2_timepoint3_rep1

tag: genetic background

value: 6 weeks cold storage 2°C


title: dgriG1_m_hd_R2.ERCC

description: mixed-species RNA preparation

value: not applicable


title: dgriG1_m_hd_R4.ERCC

description: mixed-species RNA preparation


title: IFNAR_A_Macr


title: dgriG1_m_vs_R3.ERCC

description: mixed-species RNA preparation


title: B6_A_Macr

value: WT


title: dgriG1_m_hd_R1.ERCC

description: mixed-species RNA preparation


title: dgriG1_m_go_R4.ERCC

description: mixed-species RNA preparation


title: control_cultivar2_timepoint1_rep1

tag: phenotype


title: dgriG1_m_go_R1.ERCC

description: mixed-species RNA preparation


title: dgriG1_m_go_R2.ERCC

description: mixed-species RNA preparation


title: dgriG1_m_go_R3.ERCC

description: mixed-species RNA preparation


title: 3999431010_R01C02


title: dgriG1_m_ge_R4.ERCC

description: mixed-species RNA preparation


title: 3999431010_R05C01


title: 3999431010_R02C02


title: dgriG1_m_ge_R3.ERCC

description: mixed-species RNA preparation


title: control_cultivar4_timepoint3_rep3

source_name: Apple 'Linda' fruit flesh

value: Linda


title: Inoculated_cultivar4_timepoint3_rep2


title: 3999431010_R02C01


title: B6_Li_Macr


title: control_cultivar4_timepoint3_rep2


title: 3999431010_R06C01


title: dgriG1_m_ge_R2.ERCC

description: mixed-species RNA preparation


title: Inoculated_cultivar4_timepoint3_rep3


title: 3999431010_R03C01


title: Inoculated_cultivar4_timepoint3_rep1


title: Inoculated_cultivar3_timepoint3_rep3

source_name: Apple 'Reglindis' fruit flesh

value: Reglindis

value: Resistant


title: dgriG1_m_ge_R1.ERCC

description: mixed-species RNA preparation


title: control_cultivar4_timepoint3_rep1


title: control_cultivar3_timepoint3_rep3


title: control_cultivar3_timepoint3_rep2


title: dgriG1_m_ac_R4.ERCC

description: mixed-species RNA preparation


title: dgriG1_m_ac_R3.ERCC

description: mixed-species RNA preparation


title: 3999431010_R01C01


title: 3999431077_R06C02


title: dgriG1_m_ac_R2.ERCC

description: mixed-species RNA preparation


title: dgriG1_m_ac_R1.ERCC

description: mixed-species RNA preparation


title: dgriG1_f_wb_R4.ERCC

description: mixed-species RNA preparation


title: Inoculated_cultivar3_timepoint3_rep2


title: dgriG1_f_wb_R3.ERCC

description: mixed-species RNA preparation


title: 3999431077_R06C01


title: control_cultivar3_timepoint2_rep2


title: dgriG1_f_wb_R2.ERCC

description: mixed-species RNA preparation


title: 3999431077_R03C02

value: M


title: dgriG1_f_wb_R1.ERCC

description: mixed-species RNA preparation


title: 3999431077_R04C02


title: 3999431077_R03C01


title: control_cultivar3_timepoint2_rep3


title: dgriG1_f_vs_R4.ERCC

description: mixed-species RNA preparation


title: 3999431077_R02C02


title: 3999431077_R01C02


title: 3999431077_R05C01


title: control_cultivar3_timepoint3_rep1


title: dgriG1_f_vs_R3.ERCC

description: mixed-species RNA preparation


title: 3999431077_R04C01


title: Inoculated_cultivar3_timepoint2_rep2


title: Inoculated_cultivar3_timepoint3_rep1


title: 3999431077_R05C02


title: control_cultivar3_timepoint2_rep1


title: Inoculated_cultivar3_timepoint2_rep3


title: dgriG1_f_vs_R2.ERCC

description: mixed-species RNA preparation


title: dgriG1_f_vs_R1.ERCC

description: mixed-species RNA preparation


title: dgriG1_f_tx_R4.ERCC

description: mixed-species RNA preparation


title: Inoculated_cultivar3_timepoint2_rep1


title: 3999431077_R02C01


title: dgriG1_f_tx_R3.ERCC

description: mixed-species RNA preparation


title: Inoculated_cultivar3_timepoint1_rep2


title: control_cultivar3_timepoint1_rep3


title: dgriG1_f_tx_R2.ERCC

description: mixed-species RNA preparation


title: 3999431002_R05C02


title: control_cultivar3_timepoint1_rep2


title: dgriG1_f_tx_R1.ERCC

description: mixed-species RNA preparation


title: 3999431002_R06C02


title: 3999431002_R04C02


title: AM from RB-ILD patient 4

city: Edinburgh

first: John

middle: Alexander

last: Marwick

address: 47 Little France Crescent

department: Center for Inflammation Research

institute: University of Edinburgh

description: RB-ILD 4

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip HuGene 2.1 ST  peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Signal was analyzed with Affymetrix Expression Console, v. 1.1, using an RMA normalization algorithm producing log base 2 results. Statistical analysis of the array data utilized Partek Genomic Suite (Partek, St. Louis, USA).

label: Biotin

source_name: AM from RB-ILD

label_protocol: Five hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974]

growth_protocol:
Experiment set 1: Peripheral blood mononuclear cells (PBMCs) were isolated from peripheral human blood (healthy volunteer) using discontinuous percol gradients. Monocytes were isolated from the PBMCs by negative selection using Miltenyi Biotec’s pan monocyte isolation kit. Purified monocytes were plated in 24 well plates and differentiated over 5 days in IMDM media containing 2% autologous serum, GM-CSF (5ng/ml) IL-6 (10ng/ml).
Experiment set 2: AM were isolated from bronchoalveolar lavage using cell sorting. BAL cells were stained with HLA-DR; HLA-DR +ve cells were gated by forward/side scatter which shows a clear defined population for macrophages.  After sorting, macrophage purity was assessed by morphological assessment of centrifugal cytospin preparations staining with DiffQuik stain.

extract_protocol: total RNA was extracted using Quiagen Rneasy kits as per manufacturers instructions

treatment_protocol: Experimental set 1: At day 5, MDM were washed with PBS and then either media (IMDM serum free) or apoptotic neutrophils (AN: human, isolated from peripheral blood, aged overnight, washed and re-suspended in IMDM serum free) added. The LPS (1ng/ml) was added to give 4 groups: MDM Control (no treatment), MDM with AN, MDM treated with LPS, MDM with AN and treated with LPS. Treatments were for 9 hours. Following treatment the plates were placed on ice and the MDM were washed with ice cold PBS to remove treatments. The MDM were then scrapped, pelleted (all performed on ice or at 4 degrees) and then the total RNA extracted.

tag: cell type

value: Alveolar macrophage

tag: disease state

value: RB-ILD

tag: individual

value: patient 4


title: 3999431002_R02C02

source_name: whole blood

tag: age


title: 3999431002_R03C02


title: dgriG1_f_re_R4.ERCC

description: mixed-species RNA preparation


title: Inoculated_cultivar3_timepoint1_rep1

tag: treatment 1

value: Inoculated with Penicillium expansum

tag: treatment 2

value: 1h cold storage 2°C


title: control_cultivar3_timepoint1_rep1


title: AM from RB-ILD patient 2

description: RB-ILD 2

value: patient 2


title: dgriG1_f_re_R2.ERCC

description: mixed-species RNA preparation


title: dgriG1_f_re_R3.ERCC

description: mixed-species RNA preparation


title: AM from RB-ILD patient 1

description: RB-ILD 1

value: patient 1


title: dgriG1_f_re_R1.ERCC

description: mixed-species RNA preparation


title: dgriG1_f_hd_R4.ERCC

description: mixed-species RNA preparation


title: 3999431002_R06C01

tag: groupid

tag: gender

value: F


title: dgriG1_f_hd_R3.ERCC

description: mixed-species RNA preparation


title: 3999431002_R05C01


title: 3999431002_R03C01


title: dgriG1_f_hd_R2.ERCC

description: mixed-species RNA preparation


title: AM from IPF patient 2

description: IPF 2

source_name: AM from IPF

value: IPF


title: AM from IPF patient 4

description: IPF 4


title: AM from RB-ILD patient 3

description: RB-ILD 3

value: patient 3


title: AM from IPF patient 1

description: IPF 1


title: Inoculated_cultivar3_timepoint1_rep3

value: Mature fruit

value: parenchyma


title: dgriG1_f_hd_R1.ERCC

description: mixed-species RNA preparation

value: not applicable


title: AM from IPF patient 3

description: IPF 3


title: MDM co-cultured with AN and treated with LPs replicate 4

description: LPS + AN 4

source_name: MDM co-cultured with apoptotic neutrophils and stimulated with LPS (1ng/ml) for 9h

value: monocyte-derived macrophage

tag: treatment


title: 3999431002_R04C01


title: dgriG1_f_go_R4.ERCC

description: mixed-species RNA preparation

tag: strain


title: 3999078062_R05C02


title: 3999431002_R02C01


title: 3999078062_R04C02


title: 3999431002_R01C01


title: dgriG1_f_go_R3.ERCC

description: mixed-species RNA preparation


title: MDM co-cultured with AN and treated with LPs replicate 2

description: LPS + AN 2

value: co-cultured with apoptotic neutrophils and stimulated with LPS


title: 3999078062_R06C02


title: dgriG1_f_go_R2.ERCC

description: mixed-species RNA preparation


title: dgriG1_f_go_R1.ERCC

description: mixed-species RNA preparation


title: dgriG1_f_ge_R4.ERCC

description: mixed-species RNA preparation


title: 3999078062_R02C02


title: 3999078062_R03C02


title: HCC2814-shTMPRSS11B + doxy rep 3

city: Dallas

first: Barrett

middle: Logan

last: Updegraff

state: TX

address: 5323 Harry Hines Blvd.

department: Molecular Biology

institute: Univ. of Texas Southwestern Medical Center at Dallas

description:
gencode.v19_GENES_counts_EV-VS-shT11B.glmLRT.txt
shT11B_3

data_processing:
Fastq files were checked for quality using fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and fastq screen (http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen) and were quality trimmed using fastq-mcf (Aronesty, 2013).
Trimmed fastq files were mapped to hg19 (UCSC version from igenomes) using TopHat (Kim and Salzberg, 2011)
Duplicates were marked using picard-tools (https://broadinstitute.github.io/picard/)
Read counts were generated using featureCounts (Liao et al., 2014)
Differential expression analysis was performed using edgeR (Robinson et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files of CPM RNA abundance of HBEC-shp53 cells with TMPRSS11B relative to GFP expression (Samples 1-6) and HCC2814 cells with knockdown of TMPRSS11B relative to control (Samples 7-12)

source_name: Human lung squamous cell carcinoma

growth_protocol: Samples 1-6: cultured in complete keratinocyte serum-free media; Samples 7-12: cultured in complete RPMI1640 with 5% serum and 2ug/mL doxycycline hyclate

extract_protocol:
Cells were plated in triplicate in 15cm2 dishes and allowed to reach 70% confluence. Cells were then washed in cold HBSS- twice and scraped on ice into HBSS-. Cells were pelleted at 1,500RPM for 5m at 4C and resuspended in 600μL RLT buffer with fresh b-mercaptoethanol, vortexed, transferred to a QiaShredder column, and centrifuged at max speed for 2m at 4C. RNA was then extracted according to the RNeasy protocol (Qiagen) with on-column DNase digest and resuspended in 50μL nuclease-free H2O.
Samples were run on the Agilent 2100 Bioanalyzer to evaluate RNA quality and were quantified by Qubit (Invitrogen) prior to staring library prep. Four micrograms of total DNAse treated RNA were prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina. Poly-A RNA was purified and fragmented before strand specific cDNA synthesis. cDNA were A-tailed and indexed adapters were ligated. Samples were then PCR amplified and purified with AmpureXP beads, and validated again on the Agilent 2100 Bioanalyzer. Sequencing was performed on an Illumina NextSeq 500 to generate 76-bp single-ended reads.

treatment_protocol: Samples 1-6: untreated; Samples 7-12: cultured for 3 days in the presence of 2ug/mL doxycycline hyclate

tag: lentiviral vector


title: dgriG1_f_ge_R3.ERCC

description: mixed-species RNA preparation

tag: tissue


title: HCC2814-shTMPRSS11B + doxy rep 2

description:
gencode.v19_GENES_counts_EV-VS-shT11B.glmLRT.txt
shT11B_2


title: dgriG1_f_ge_R2.ERCC

description: mixed-species RNA preparation

tag: Sex


title: HCC2814-shTMPRSS11B + doxy rep 1

description:
gencode.v19_GENES_counts_EV-VS-shT11B.glmLRT.txt
shT11B_1


title: MDM treated with LPS replicate 1

description: LPS 1

source_name: MDM stimulated with LPS (1ng/ml, 9h)

value: stimulated with LPS

tag: replicate


title: 3999431002_R01C02

value: M


title: 3999078062_R06C01


title: 3999078062_R05C01


title: MDM co-cultured with AN replicate 4

description: Ct + AN 4

source_name: MDM co-cultured with apoptotic neutrophils (9h)

value: co-cultured with apoptotic neutrophils


title: MDM co-cultured with AN and treated with LPs replicate 1

description: LPS + AN 1


title: dgriG1_f_ge_R1.ERCC

description: mixed-species RNA preparation


title: HCC2814-EV + doxy rep 3

description:
gencode.v19_GENES_counts_EV-VS-shT11B.glmLRT.txt
EV_3

value: pTRIPZ-EV


title: 3999078062_R01C02


title: MDM treated with LPS replicate 2

description: LPS 2


title: MDM treated with LPS replicate 4

description: LPS 4


title: HCC2814-EV + doxy rep 2

description:
gencode.v19_GENES_counts_EV-VS-shT11B.glmLRT.txt
EV_2


title: dgriG1_f_ac_R3.ERCC

description: mixed-species RNA preparation


title: 3999078062_R03C01


title: 3999078062_R04C01


title: MDM co-cultured with AN replicate 1

description: Ct + AN 1


title: 3999078062_R02C01


title: 3999078111_R06C02


title: 3999078111_R04C02


title: HBEC-shp53-TMPRSS11B rep 3

description:
gencode.v19_GENES_counts_GFP-VS-TMPRSS11B.glmLRT.txt
TMPRSS11B_3

source_name: Human bronchial epithelial cells


title: HBEC-shp53-TMPRSS11B rep 2

description:
gencode.v19_GENES_counts_GFP-VS-TMPRSS11B.glmLRT.txt
TMPRSS11B_2


title: 3999078111_R05C02


title: 3999078111_R03C02


title: dgriG1_f_ac_R2.ERCC

description: mixed-species RNA preparation


title: Control MDM replicate 4

description: Ct 4

source_name: MDM no treatment


title: dgriG1_f_ac_R1.ERCC

description: mixed-species RNA preparation


title: HBEC-shp53-TMPRSS11B rep 1

description:
gencode.v19_GENES_counts_GFP-VS-TMPRSS11B.glmLRT.txt
TMPRSS11B_1


title: MDM co-cultured with AN replicate 2

description: Ct + AN 2


title: HBEC-shp53-GFP rep 3

description:
gencode.v19_GENES_counts_GFP-VS-TMPRSS11B.glmLRT.txt
GFP_3


title: Control MDM replicate 3

description: Ct 3


title: HCC2814-EV + doxy rep 1

description:
gencode.v19_GENES_counts_EV-VS-shT11B.glmLRT.txt
EV_1


title: 3999078111_R02C02


title: 3999078111_R06C01


title: HBEC-shp53-GFP rep 2

description:
gencode.v19_GENES_counts_GFP-VS-TMPRSS11B.glmLRT.txt
GFP_2


title: upc2 ecm22 deletion, 240min 100% nitrogen gas (SW_1014_8)

city: Glassboro

first: Mark

last: Hickman

state: NJ

address: 201 Mullica Hill Road

department: Biological Sciences

institute: Rowan University

data_processing:
Each raw file is a de-multiplexed fastq file
FASTQ Quality Trimmer, 5' and 3' ends, window size=1,step size=1,min score=10
Reads aligned to yeast genome using TopHat2
Number of reads per feature was calculated using HTSeq,mode=union
When a sample was sequenced two times (e.g., NH_101_1_1.fastqsanger.gz and NH_101_1_2.fastqsanger.gz), then the FASTQ files were processed separately resulting in two HTSEQ files (e.g., NH_101_1_1.tabular and NH_101_1_2.tabular). The counts were then added to obtain the total counts for that sample.
Genome_build: saccharomyces_cerevisiae_R64-1-1_20110208.fasta
Supplementary_files_format_and_content: tab-delimited text files, first column= feature, second column=number of reads that overlap feature

organism: Saccharomyces cerevisiae

source_name: strain yMH936 (S288C background with repaired HAP1)

growth_protocol: A saturated culture was diluted and grown to mid-log phase (~1-2x10^7 cells/ml). Then the cells were diluted again and placed in 100% nitrogen gas for the indicated time, with the gas flowing through flasks.  Cells were collected in mid-log phase, filtered and frozen in liquid nitrogen.

extract_protocol:
The Qiagen RNeasy kit, using mechanical lysis with beads, to isolate total RNA. PolyA selection was done through oligo-dT capture
TruSeq RNA Sample Preparation Kit (Illumina).
Samples were multiplexed. Some of the libraries were sequenced in two different lanes (e.g., NH_91_8_1 and NH_91_8_2). These were processed separtely but then combined later at the HTSEQ step

tag: time in 100% n2

value: 240 minutes

tag: genotype

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 upc2D ecm22D


title: Control MDM replicate 2

description: Ct 2


title: Cultured cell line with HCV treated with brusatol  rep1

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: Total RNA was extracted

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: The cells were maintained in DMEM with 10% FBS for 1 dyay as precultue and for 2 days after the administration of brusatol prior to RNA extraction.

extract_protocol: Total RNA of the cultured cell was exracted by using RNaasy Mini Kit (QIAGEN) according to the pmanufacture's protocol.

treatment_protocol: Bruratol was administered at the concentration of GI50 after precultuted cell.

value: Hepatoma cell line


title: 3999078111_R01C02


title: 3999078111_R05C01


title: Cultured cell line with HCV control rep1

description: Total RNA was extracted

source_name: HPI


title: 3999078062_R01C01


title: Control MDM replicate 1

description: Ct 1


title: MDM co-cultured with AN and treated with LPs replicate 3

description: LPS + AN 3


title: upc2 ecm22 deletion, 180min 100% nitrogen gas (SW_1014_7)

value: 180 minutes


title: HBEC-shp53-GFP rep 1

description:
gencode.v19_GENES_counts_GFP-VS-TMPRSS11B.glmLRT.txt
GFP_1


title: 3999078111_R04C01


title: MDM treated with LPS replicate 3

description: LPS 3


title: ref3 vs. reb1-aa-30min-1-a

first: Slawomir

last: Kubik

address: quai Ernest-Ansermet 30

department: Molecular Biology Department

hyb_protocol: Tecan HS4800 hybridization: * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA  * Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan) * Priming: 5xSSC, 0.1%SDS * Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul * Hybridization: 45 min at 42C. * Wash 2x: milliQ * Wash: 5xSSC, 0.1%SDS * Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul) * Hybridization: 16 hours at 42C. * Wash 2x: 1xSSC, 0.2%SDS at 23C * Wash 2x: 0.1xSSC, 0.2%SDS at 23C * Wash 2x: 0.1xSSC at 23C * Drying: blow with nitrogen for 3min at 30C

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. Features were extracted using ImaGene software from Biodiscovery.

data_processing: Genes, no bg corr, dye corr: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), by estimating the LOESS curve for all gene probes using no background subtraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from a set of wild-type wild-type hybridizations, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009.

organism: Saccharomyces cerevisiae S288C

source_name: refpool

label_protocol: Robot amplification and labeling v1.0: All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrophotometer (Molecular Devices), and a magnetic bead-locator (Beckman).  mRNA amplification protocol description: * all RNAs are diluted to 0.6 ug/ul and 5 ul is put in a 96-wells plate (Abgene). All subsequent steps are performed by the robot script. * mix1 containing 100 ng T7 Mlu VN primer (custom mix) and EC-control RNA per 5 ul is added and mixed in each well. * plate is incubated @ 70C for 10 mins, cooled to 48C. * mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNase Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and  1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well. * plate is incubated @ 48C for 2 hours and cooled to room temperature. * 106 ul water and subsequently  mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul RNaseH  (Promega) is added and mixed in each well. * plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul . * 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3-aminoallyl)-UTP (Ambion, Applied Biosystems). * Plate is incubated @37C for 4 hours. * cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturers protocol.  * Concentration  is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot. * Resulting cRNA plates are sampled for Bioanalyzer QC, snap frozen and stored at -80C.  Labeling protocol description:  * NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10).  All subsequent steps are performed by the robot script : * 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines cy3 and cy5 labeled material ). * 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells. * 3 ul cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour. * 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes. * Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturers protocol. * RNA concentration and labeling incorporation are measured (SpectraMax 190). * 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C. * Samples are stored at -20C until hybridization.

extract_protocol: Yeast HTP RNA isolation for robot v2.0: Growth of deletion mutant is done using the 24-well Tecan Plate Reader and subsequent RNA extraction and cleanup for robotic amplification:  1. Take frozen cell pellets from 1.5 ml cultures(-80C) and resuspend in 500 ul Acid Phenol Chloroform (From Sigma, 5:1, pH 4.7). Immediately add the same volume TES-buffer (TES: 10 mM Tris pH 7.5, 10 mM EDTA, 0.5% SDS). Vortex very hard for 20 seconds to resuspend pellet. 2. Incubate in water bath for 10 minutes at 65C and vortex again.  3. Incubate tubes in the thermomixer (65C, 1400RPM) for 50 minutes. 4. Spin for 20 minutes at 14000 rpm at 4C. 5. Take new Eppendorf-tube, fill with 500 ul Phenol Chloroform (5:1, pH 4.7). Add water-phase from point 3. Vortex hard for 20 seconds. Spin down for 10 minutes at 14000 rpm at 4C. 6. Take new Eppendorf-tube, fill with 500 ul Chloroform:Isoamyl-alcohol (25:1). Add water-phase from point 4. Vortex hard for 20 seconds. Spin down for 10 minutes at 14000 rpm at 4C. 7. Take new Eppendorf-tube, fill with 50 ul Sodium Acetate (NaAc 3M, pH 5.2). Add water-phase from point 5. Fill tube with Ethanol (100%, -20C). Flip tubes three times. Incubate at -20C for longer than 30 minutes. 8. Spin tubes down for 5 minutes at room temperature, 14000 rpm. Remove fluid with pipette. Be careful not to touch RNA-pellet. 9. Wash pellet with Ethanol 500 ul (80%, -20C). Spin down shortly. 10. Remove Ethanol, do not air dry but directly proceed to 11. 11. Dissolve RNA-pellet in 93 ul sterile water (MQ, freshly tapped). Pipet until the pellet is released from the side of the tube. Wait 5 minutes and pipet up and down 5 more times. Yield will be around 150ug. (Make sure all RNA is dissolved completely!) 12. RNA solution is transferred to a 96 wells plate (4titude, Bioke).  Subsequent protocols are processed automatically on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrophotometer (Molecular Devices), and a magnetic bead-locator (Beckman).  RNA cleanup protocol description: * concentration of all RNAs is measured by diluting 5 ul RNA on the SpectraMax; * 12.5 ul DNaseI dilution (RNase-free DNase kit, Qiagen, nr 79254, diluted 1:5 in RDD)is mixed with remaining 87.5 ul RNA-solution and incubated @ 18C for 15 minutes; * RNA is purified and concentrated with RNAClean (Agencourt, Beckman) according to manufacturers protocol, to an end volume of 25 ul; * 4 ul cleaned RNA is diluted and measured on the SpectraMAX, concentrations are normalized to 0.2 ug/ul in each well; * 5 ul of cleaned and normalized RNA is used to set up a startplate for RNA amplification. * 1 ul of cleaned and normalized RNA is used to check integrity by running on a QiaXcel system. * All plates are snap frozen and stored at -80C until further use.

value: no rapamycin

tag: genotype/variation

value: BY4742 :MET15; his3-1; leu2; lys2; ura3; matalpha

value: 30 minutes rapamycin

value: reb1-aa :tor1-1; fpr1del; RPL13A-FKBP12-NAT; Reb1-FRB-yEGFP-3V5


title: upc2 ecm22 deletion, 120min 100% nitrogen gas (SW_1014_6)

value: 120 minutes


title: upc2 ecm22 deletion, 10min 100% nitrogen gas (SW_1014_3)

value: 10 minutes


title: upc2 ecm22 deletion, 30min 100% nitrogen gas (SW_1014_4)

value: 30 minutes


title: upc2 ecm22 deletion, 5min 100% nitrogen gas (SW_1014_2)

value: 5 minutes


title: upc2 ecm22 deletion, 0min 100% nitrogen gas (SW_1014_1)

value: 0 minutes


title: 3999078111_R03C01

value: F


title: ref3 vs. rap1-303-aa-30min-a

organism: Saccharomyces cerevisiae W303

value: rap1-303-aa :tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 RAP1-FRB-RAP1::LEU


title: ref3 vs. reb1-aa-0min-1-a


title: ecm22 deletion, 240min 100% nitrogen gas (SW_1008_8)

source_name: strain yMH931 (S288C background with repaired HAP1)

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 ecm22D


title: ref3 vs. abf1-aa-30min-1-a

value: abf1-aa :tor1-1; fpr1del; RPL13A-FKBP12-NAT; Abf1-FRB-yEGFP


title: MDM co-cultured with AN replicate 3

description: Ct + AN 3

tag: cell type

value: monocyte-derived macrophage

value: co-cultured with apoptotic neutrophils


title: 3999941048_R05C02

value: M


title: 3999078111_R01C01


title: 3999941048_R06C02


title: ecm22 deletion, 120min 100% nitrogen gas (SW_1008_6)


title: ecm22 deletion, 180min 100% nitrogen gas (SW_1008_7)

value: 180 minutes


title: ref3 vs. rap1-303-aa-0min-a

value: no rapamycin


title: reb1-aa-0min-6-b vs. ref3

value: BY4742 :MET15; his3-1; leu2; lys2; ura3; matalpha


title: 3999941048_R04C02


title: 3999078111_R02C01


title: ref3 vs. abf1-aa-0min-1-a


title: reb1-aa-30min-6-b vs. ref3

value: 30 minutes rapamycin


title: rap1-303-aa-30min-b vs. ref3


title: ecm22 deletion, 60min 100% nitrogen gas (SW_1008_5)

value: 60 minutes


title: ecm22 deletion, 30min 100% nitrogen gas (SW_1008_4)


title: upc2 ecm22 deletion, 60min 100% nitrogen gas (SW_1014_5)

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 upc2D ecm22D


title: IRF3-KO_rep3

city: Chapel Hill

first: Stanley

last: Lemon

state: NC

address: 8034 Burnett-Womack CB#7292

department: Division of Infectious Diseases

institute: University of North Carolina at Chapel Hill

data_processing:
fastq reads were aligned to hg38 using STAR version 2.4.2a (parameters: --outSAMunmapped Within --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM)
transcript abundance estimates were performed using Salmon version SalmonBeta-0.4.2
Genome_build: hg38
Supplementary_files_format_and_content: txt: transcript names and abundance estimates

source_name: PH5CH8 cells

growth_protocol: PH5CH8 cells were routinely cultured in Dulbecco’s modified Eagle’s medium (DMEM), High Glucose, supplemented with 10% fetal bovine serum, 1×Penicillin-Streptomycin, 1×GlutaMAX-I and 1×MEM Non-Essential Amino Acids Solution

extract_protocol:
Total RNA was extracted using RNeasy mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PH5CH8 cells were transduced with lentivirus expressing Cas9 and single-guide RNA (sgRNA) targeting IRF3, two independent sgRNAs targeting IRF1, or a non-targeting control sequence. The knockout cell lines were infected with hepatitis A virus HM-175/18f strain  in triplicate at a multiplicity of infection of 10 for 48 h.

value: immortalized primary adult human hepatocytes

tag: genotype/variations


title: ecm22 deletion, 10min 100% nitrogen gas (SW_1008_3)

value: 10 minutes


title: IRF1-KO-2_rep3


title: rap1-303-aa-0min-b vs. ref3


title: ecm22 deletion, 5min 100% nitrogen gas (SW_1008_2)

value: 5 minutes


title: abf1-aa-0min-1-b vs. ref3


title: abf1-aa-30min-1-b vs. ref3


title: IRF3-KO_rep2


title: IRF1-KO-1_rep3


title: mga2 deletion, 180min 100% nitrogen gas (SW_1007_7)

source_name: strain yMH932 (S288C background with repaired HAP1)

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 mga2D


title: ecm22 deletion, 0min 100% nitrogen gas (SW_1008_1)

value: 0 minutes


title: IRF1-KO-2_rep2


title: Control_rep3

value: wild type


title: 3999941048_R03C02


title: 3999941048_R02C02

value: F


title: 3999941048_R01C02


title: Control_rep2


title: IRF1-KO-1_rep2


title: 3999941048_R06C01


title: 3999941048_R02C01


title: mga2 deletion, 30min 100% nitrogen gas (SW_1007_4)

value: 30 minutes


title: IRF3-KO_rep1


title: IRF1-KO-2_rep1


title: 3999941037_R06C02


title: 3999941048_R03C01


title: 3999941048_R05C01


title: mga2 deletion, 60min 100% nitrogen gas (SW_1007_5)


title: mga2 deletion, 5min 100% nitrogen gas (SW_1007_2)


title: mga2 deletion, 0min 100% nitrogen gas (SW_1007_1)


title: Control_rep1


title: IRF1-KO-1_rep1


title: 3999941037_R04C02


title: 3999941048_R01C01


title: mga2 deletion, 120min 100% nitrogen gas (SW_1007_6)

value: 120 minutes


title: dgriG1_f_ac_R4.ERCC

first: Brian

last: Oliver

address: 50 South Drive

description: mixed-species RNA preparation

data_processing:
We performed single-end 76 bp sequencing on the HiSeq2000 Sequencing System (Illumina, San Diego, CA) according to the manufacturer. De-multiplexed reads (Chastity > 0.6) FASTQ output was from Illumina CASAVA v.1.8.2. For each mixed sample, the RNA-seq reads were first mapped to a merged genome and annotation including D. grimshawi (dgri_caf1 assembly; Drosophila_grimshawi.GCA_000005155.1.29.dna_sm.genome.fa), D. melanogaster (FlyBase release 6 version 04 ; FlyBase file: dmel-all-chromosome-r6.04.fasta), and A. stephensi (Anopheles-stephensi-Indian_SCAFFOLDS_AsteI2.fa), appended with updated ERCC sequences (Jiang et al., Genome Research, 2011, PMID21816910; Lee et al., J Genomics, 2016, PMID27512518) using STAR (v2.4.2a) (Doblin et al., Bioinformatics, 2012, PMID23104886) with default parameters or HiSAT2 (v2.0.5; --dta and -max-intronlen = 300,000) (Kim et al., 2015, Nature Methods, PMID25751142). All processed data for Hawaiian species was based on alignment to D. grimshawi (FlyBase version 2016_05). For each chromosome or scaffold in the merged annotation, we add a four letter prefix to identify the species (e.g., scaffold_15110 => dgri_ scaffold_15110) for bam file parsing using SAMtools (v0.1.19) (Li et al., 2009, PMID19505943). We used a demultiplexer (http://github.com/haiwangyang/demultiplexer) to fetch the prefix of read names in the bam alignments and obtained all uniquely-mapped and multi-hit (with < 10 hits, >10 hits are excluded) reads (in bam format) that mapped exclusively to a single species or exclusively to ERCC. We reconverted bam files for each species to raw read fastq files using BEDTools (2.25.0; bamtofastq) (Quinlan and Hall, 2010, Bioinformatics, PMID20110278).
After this step, reads of each multi-species sample were split into three categories based on the mapped genome– D. grimshawi, ERCC, and leftover, which includes unmapped reads, reads mapped to multiple species (or multiple species plus ERCC), and reads mapped to either D. melanogaster or A. stephensi. For multi-species samples, the original fastq file can be restored by merging the reads of D. grimshawi as well as the ERCC and leftover reads. We provide both STAR (SRR3355*) and HiSAT2 (SRR724* & SRR725*) fastq files in this GEO entry. We provided associated gene-level read count files based on HiSAT2 alignments, and the read count files have both FlyBase version (*htseq_reverse.HiSAT2.FB.txt) and YO version (*htseq_reverse.HiSAT2.YO.txt) in Supplementary files of this GEO. For the latter one, we also provide two extra columns in the expression matrix, showing the maximum exon-level overlap (Jaccard index) between YO gene ID and FlyBase gene ID. In addition, we provided bigWig tracks for all samples (replicated merged), YO annotation files (in both gtf and gff3 format), ortholog look up table (among YO gene ID, FlyBase gene ID, and dmel gene), gene-level normalized read counts based on either YO or FlyBase annotation, and transcript-level transcripts per million (TPM) based on YO or FlyBase annotation.

source_name: ERCC that merged to the multi-species sample (Drosophila grimshawi; Drosophila melanogaster; Anopheles stephensi)

extract_protocol:
Flies were anesthetized by briefly chilling on a 0oC glass plate. All samples were dissected in Phosphate Buffered Saline solution pH7.4 and transferred to 112ul of RNA later (Life Technologies, Carlsbad, CA) in 96-well plates at room temperature after being macerated with forceps. After transport, plates were stored at -80oC. For D. grimshawi samples, we added 20-30 1.0mm glass beads (BioSpec Products, Bartlesville, OK) to each sample and added 600ul RLT buffer from the RNeasy 96 kit (Qiagen, Valencia, CA) to each well. We homogenized the samples three times for 60 seconds each with a mini-beadbeater (Biospec Products, Bartlesville, OK). Extraction of total RNA was performed using the RNeasy 96 kit according to manufacturer's guide (spin version), except that we used 712μl of 70% ethanol in each well to dilute the RNAlater and RLT buffer. D. grimshawi RNA was added to D. melanogaster RNA and A. stephensi embryos for homogenization and a second round of RNA extraction using the RNeasy kit. D. melanogaster and A. stephensi RNAseq will be reported elsewhere. Four head and gonad samples of Wm1041 were split into mixed-species and single-species RNA preparations. All other samples were prepared without mixing with other species using the same RNeasy protocol. RNA was quantified using the Quant-iT RiboGreen quantification kit Life Technologies, Carlsbad, CA).
We used the Truseq PolyA+ and stranded mRNA kit with half volumes (Illumina, San Diego, CA). 100ng total RNA was input for all samples. We also added 20pg Pool 78A or 78B ERCC spike-ins (Jiang et al., Genome Research, 2011, PMID 21816910) added to the Fragment-Prime-Finish Mix during mRNA fragmentation step. Libraries were quantified with Quant-iT PicoGreen (Life Technologies, Carlsbad, CA), and pooled for multiplexed sequencing.

value: not applicable


title: MOLM13, sh-FIS1-#D, Rep 3 [RNA-seq]

city: Aurora

first: Shanshan

last: Pei

state: CO

institute: University of Colorado

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32
MAPPING - SHRiMP_2_2_3
Genome_build: hg19
Supplementary_files_format_and_content: A txt file containing fpkm values of all samples

source_name: Human leukemia cell line

extract_protocol:
QIAGEN RNeasy Plus
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina) was used for next generation sequencing library construction per manufacturer’s protocols.
mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3’-adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size.

treatment_protocol: shRNA-mediated knock-down

tag: cell line

tag: shRNA

tag: rep

value: Rep 3


title: upc2 deletion, 240min 100% nitrogen gas (SW_1004_8)

source_name: strain yMH928 (S288C background with repaired HAP1)

value: 240 minutes

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 upc2D


title: 3999941037_R05C02

source_name: whole blood

tag: age


title: mga2 deletion, 240min 100% nitrogen gas (SW_1007_8)


title: upc2 deletion, 180min 100% nitrogen gas (SW_1004_7)

value: 180 minutes


title: MOLM13, sh-FIS1-#D, Rep 2 [RNA-seq]

value: Rep 2


title: MOLM13, sh-FIS1-#B, Rep 3 [RNA-seq]


title: MOLM13, sh-FIS1-#D, Rep 1 [RNA-seq]

value: Rep 1


title: upc2 deletion, 60min 100% nitrogen gas (SW_1004_5)

value: 60 minutes


title: 3999941037_R03C01

tag: groupid


title: upc2 deletion, 120min 100% nitrogen gas (SW_1004_6)


title: 3999941037_R02C02

tag: gender

value: M


title: 3999941037_R04C01


title: 3999941037_R03C02


title: MOLM13, sh-FIS1-#B, Rep 2 [RNA-seq]


title: MOLM13, sh-FIS1-#B, Rep 1 [RNA-seq]


title: 3999941037_R06C01


title: 3999941037_R02C01


title: upc2 deletion, 10min 100% nitrogen gas (SW_1004_3)

value: 10 minutes


title: mga2 deletion, 10min 100% nitrogen gas (SW_1007_3)


title: upc2 deletion, 30min 100% nitrogen gas (SW_1004_4)


title: upc2 deletion, 5min 100% nitrogen gas (SW_1004_2)

value: 5 minutes


title: MOLM13, sh-RNA control, Rep 3 [RNA-seq]

value: sh-RNA Control


title: 3999941037_R01C02


title: MOLM13, sh-RNA control, Rep 2 [RNA-seq]


title: 4640_carcinoma

city: Shanghai

first: Wei

last: Sun

address: Dongan Road 270

department: Department of Musculoskeletal Surgery

institute: Fudan University Shanghai Cancer Center

hyb_protocol: Hybridization of ST cDNA was performed on Affymetrix GeneChip HTA 2.0 Array as per the manufacturers protocol.

scan_protocol: Arrays were then washed and stained using the FS450_0001 fluidics protocol and scanned using an Affymetrix 3000 7G scanner.

data_processing: Initial Data processign was done with Affymetrix Expression Command Console software. Background correction was done by composition based and normalisation was done by IterativeProbe Logarithmic Intensity Error Estimation (iterPLIER) summarization algorithm with Global Median method

source_name: carcinoma

label_protocol: Fragmentation and Biotin labelling and target preparation of the ST cDNA  were performed using the NuGEN Encore Biotin Module.

growth_protocol: Fresh frozon tissue samples were obtained after breast cancer surgery

extract_protocol: Tissues total RNA were extracted using RNeasy plus Mini Kit (QIAGEN) according to manufacturer's instructions.

treatment_protocol: Breast cancer surgery

tag: disease state

value: luminal (ER+) breast cancer

value: breast

value: female


title: ett1 deletion, 240min 100% nitrogen gas (NH_91_8_2)

source_name: strain yMH1016 (S288C background with repaired HAP1)

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 ett1d


title: 4640_para-carcinoma

source_name: para-carcinoma


title: 3998998246_R04C02

value: F


title: 3998998246_R06C02


title: upc2 deletion, 0min 100% nitrogen gas (SW_1004_1)

value: 0 minutes


title: 4632_para-carcinoma


title: AML 3, sh-FIS1-#D

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-2.19.0
CLEANING - Trimmomatic-0.36 "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15"
MAPPING - STAR_2.5.2b "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
REFERENCE - GRCh38.p7 + Gencode-25 Annotation
READ COUNTING - subread-1.5.0p3,  featurecounts, Unique "-s 2 -t exon -g gene_name'"
Multi-Mapping "-s 2 -M -t exon -g gene_name"
Genome_build: hg19
Supplementary_files_format_and_content: A txt file containing raw counts of all samples

source_name: AML Patient 3

growth_protocol: Serum free media with cytokines

value: Primary human AML patient specimen


title: 4618_carcinoma


title: ett1 deletion, 180min 100% nitrogen gas (NH_91_7_2)


title: AML 2, sh-FIS1-#D

source_name: AML Patient 2


title: 3998998246_R05C02

data_processing: Illumina Genome Studio software was used to extract the raw signal intensities of each probe (without background correction or normalization).   Probes containing a SNP with minor allele frequency (MAF) >5% within 10bp of the single base extension site based on   Illumina’s database and probes identified by Chen et al.* were removed. Data was then  pre-processed in the R package wateRmelon using the pfilter and dasen functions.


title: 4632_carcinoma


title: 3998998246_R03C02


title: ett1 deletion, 240min 100% nitrogen gas (NH_91_8_1)

value: 240 minutes


title: 4618_para-carcinoma


title: ett1 deletion, 180min 100% nitrogen gas (NH_91_7_1)


title: AML 1, sh-FIS1-#D

source_name: AML Patient 1


title: ett1 deletion, 120min 100% nitrogen gas (NH_91_6_2)

value: 120 minutes


title: 3998998246_R02C02


title: 3998998246_R01C02


title: MOLM13, sh-RNA control, Rep 1 [RNA-seq]


title: 4514_para-carcinoma


title: AML 2, sh-FIS1-#B


title: AML 3, sh-FIS1-#B


title: 4514_carcinoma


title: 4511_carcinoma


title: ett1 deletion, 60min 100% nitrogen gas (NH_91_5_1)


title: AML Patient 3, sh-RNA control


title: 3998998246_R03C01


title: ett1 deletion, 120min 100% nitrogen gas (NH_91_6_1)


title: 3998998240_R04C02


title: ett1 deletion, 30min 100% nitrogen gas (NH_91_4_2)

value: 30 minutes


title: 4511_para-carcinoma


title: AML 1, sh-FIS1-#B


title: 3998998246_R05C01


title: 4493_carcinoma


title: AML Patient 1, sh-RNA control


title: ett1 deletion, 60min 100% nitrogen gas (NH_91_5_2)


title: 4493_para-carcinoma


title: AML Patient 2, sh-RNA control


title: ett1 deletion, 30min 100% nitrogen gas (NH_91_4_1)


title: 3998998240_R05C02


title: 3998998240_R06C02


title: 3998998246_R02C01


title: 4486_carcinoma


title: 3998998240_R02C02


title: 3998998246_R06C01


title: ett1 deletion, 10min 100% nitrogen gas (NH_91_3_1)


title: AML 3, sh-AMPK(PRKAA1)

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13
ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:25"
PhiX Screen - Bowtie-2.2.1 "-N 1"
MAPPING - SHRiMP_2_2_3 "--qv-offset 33 --all-contigs"
Genome_build: hg19
Supplementary_files_format_and_content: txt file containing fpkm values of all samples


title: AML 1, sh-AMPK(PRKAA1)


title: 4486_para-carcinoma


title: ett1 deletion, 5min 100% nitrogen gas (NH_91_2_2)


title: ett1 deletion, 5min 100% nitrogen gas (NH_91_2_1)


title: AML 3, sh-RNA control


title: 3998998240_R03C02


title: ett1 deletion, 0min 100% nitrogen gas (NH_91_1_2)


title: 4473_carcinoma


title: ett1 deletion, 10min 100% nitrogen gas (NH_91_3_2)


title: 3998998240_R01C02


title: AML 2, sh-AMPK(PRKAA1)


title: AML 2, sh-RNA control


title: 3998998240_R06C01


title: 3998998240_R05C01


title: 4411_para-carcinoma


title: 4473_para-carcinoma


title: 4383_carcinoma


title: 4411_carcinoma


title: tpa1 deletion, 240min 100% nitrogen gas (NH_88_8_2)

source_name: strain yMH1014 (S288C background with repaired HAP1)

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 tpa1d


title: P55

source_name: ND-MSCs cocultured with OPM2

tag: treatment

value: BM-derived MSCs obtained from normal healthy donors (ND-MSCs) co-cultured with myeloma cells (OPM2)


title: 3998998240_R03C01


title: 3998998240_R04C01


title: 3998998240_R02C01


title: P54

value: Scramble control


title: AML 1, sh-RNA control


title: tpa1 deletion, 180min 100% nitrogen gas (NH_88_7_2)

value: 180 minutes


title: 3998998240_R01C01


title: P46


title: tpa1 deletion, 180min 100% nitrogen gas (NH_88_7_1)


title: P45


title: B19


title: ett1 deletion, 0min 100% nitrogen gas (NH_91_1_1)


title: B18


title: tpa1 deletion, 120min 100% nitrogen gas (NH_88_6_1)


title: 4315_para-carcinoma


title: 3998998195_R06C02

value: M


title: 3998998195_R03C02


title: 3998998195_R05C02


title: tpa1 deletion, 120min 100% nitrogen gas (NH_88_6_2)


title: 4290_para-carcinoma


title: 4288_carcinoma


title: 3998998195_R02C02


title: tpa1 deletion, 60min 100% nitrogen gas (NH_88_5_2)

value: 60 minutes


title: 4383_para-carcinoma


title: OVTOKO miR-508-3p inhibitor rep2

city: Chengdu

first: Shentao

last: Zhou

address: Chengdu

institute: West China Second University Hospital

data_processing:
Reads were aligned to the human genome (hg38) using STAR (v2.5) for RNA-Seq.
Gene expression counts were calculated by STAR with parameter: --quantMode GeneCounts
RNA-Seq expression file contains raw counts for all genes
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Sample.

source_name: ovarian cancer cell line, miR-508-3p inhibitor

growth_protocol: cells were cultured in RPMI-1640 containing 10% FBS and 100 U/ml penicillin-streptomycin mixture(both from Gibco-BRL, Grand Island, NY, USA).

extract_protocol:
Total RNA was extracted using the High Pure RNA paraffin kit (Roche Applied Science, Indianapolis, IN).
The libraries were sequenced on the Illumina HiSeq platform (Novogen, China).

treatment_protocol: miR-508-3p inhibitor and respective controls were obtained from RiboBio (Guangzhou, China). They were separately transfected into cells using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer's instructions.

value: OVTOKO

value: ovarian cancer cell line

value: miR-508-3p inhibitor


title: OVTOKO miR-508-3p inhibitor rep1


title: tpa1 deletion, 60min 100% nitrogen gas (NH_88_5_1)


title: tpa1 deletion, 30min 100% nitrogen gas (NH_88_4_2)


title: OVTOKO control rep2

source_name: ovarian cancer cell line, Treatment-naïve

value: Treatment-naive


title: 3998998195_R01C02

first: Therese

last: Murphy

extract_protocol: Genomic DNA was isolated from whole blood  using a standard phenol-chloroform extraction method, and tested for degradation and purity before analysis.


title: tpa1 deletion, 30min 100% nitrogen gas (NH_88_4_1)


title: OVTOKO control rep1


title: 4235_carcinoma

value: luminal (ER+) breast cancer

value: breast

value: female


title: 4232_carcinoma


title: 4232_para-carcinoma


title: OVISE miR-508-3p inhibitor rep2

value: OVISE


title: 4288_para-carcinoma


title: 4290_carcinoma


title: OVISE miR-508-3p inhibitor rep1


title: 4235_para-carcinoma


title: tpa1 deletion, 10min 100% nitrogen gas (NH_88_3_2)

value: 10 minutes


title: tpa1 deletion, 5min 100% nitrogen gas (NH_88_2_2)

value: 5 minutes


title: tpa1 deletion, 10min 100% nitrogen gas (NH_88_3_1)


title: tpa1 deletion, 240min 100% nitrogen gas (NH_88_8_1)

value: 240 minutes


title: OVISE control rep2


title: tpa1 deletion, 5min 100% nitrogen gas (NH_88_2_1)

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 tpa1d


title: 4230_para-carcinoma


title: OVISE control rep1


title: 4315_carcinoma


title: 3998998195_R04C01

value: F


title: 3998998195_R03C01


title: 4230_carcinoma


title: tpa1 deletion, 0min 100% nitrogen gas (NH_88_1_2)

value: 0 minutes


title: 3998998195_R06C01


title: 3998998195_R05C01


title: 3998998195_R01C01


title: tpa1 deletion, 0min 100% nitrogen gas (NH_88_1_1)


title: 3998998195_R02C01


title: 4198_para-carcinoma


title: 3998998207_R06C02


title: dsc1 dsc2 dsc3 dsc5 deletion, 240min 100% nitrogen gas (NH_86_8_2)

source_name: strain yMH1019 (S288C background with repaired HAP1)

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 dsc1d dsc2d dsc3d dsc5d


title: 4185_carcinoma


title: dsc1 dsc2 dsc3 dsc5 deletion, 240min 100% nitrogen gas (NH_86_8_1)


title: 4185_para-carcinoma


title: dsc1 dsc2 dsc3 dsc5 deletion, 180min 100% nitrogen gas (NH_86_7_2)

value: 180 minutes


title: 3998998207_R04C01


title: 3998998207_R03C02


title: 4171_para-carcinoma


title: 3998998207_R05C02

value: M


title: dsc1 dsc2 dsc3 dsc5 deletion, 120min 100% nitrogen gas (NH_86_6_2)

value: 120 minutes


title: 3998998207_R02C02


title: 3998998207_R01C02


title: dsc1 dsc2 dsc3 dsc5 deletion, 120min 100% nitrogen gas (NH_86_6_1)


title: 3998998207_R04C02


title: 4133_para-carcinoma


title: 4014_carcinoma


title: dsc1 dsc2 dsc3 dsc5 deletion, 60min 100% nitrogen gas (NH_86_5_2)

value: 60 minutes


title: 4133_carcinoma


title: 4171_carcinoma


title: 4198_carcinoma


title: dsc1 dsc2 dsc3 dsc5 deletion, 180min 100% nitrogen gas (NH_86_7_1)


title: 4014_para-carcinoma


title: 3998998207_R06C01


title: dsc1 dsc2 dsc3 dsc5 deletion, 30min 100% nitrogen gas (NH_86_4_2)

value: 30 minutes


title: dsc1 dsc2 dsc3 dsc5 deletion, 60min 100% nitrogen gas (NH_86_5_1)


title: 3998998207_R01C01


title: 3998998207_R02C01


title: Rice  K3K14cr replicate 2

city: Madison

first: Yufeng

last: Wu

state: WI

address: 1575 Linden Drive

institute: UW-Madison

data_processing:
The reads from the HiSeq analysis were mapped to the rice reference genome Tigr 7 (Kawahara et al. 2013) using the Bowtie program (Langmead et al. 2009). Only the reads mapped to unique positions in the genome were retained to identify histone Kcr-enriched regions using MACS with P-value <1e-5 (Zhang et al. 2008).
Genome_build: Rice Tigr 7
Supplementary_files_format_and_content: Processed data were stored in txt files, which included enriched regions from ChIP-seq.

organism: Oryza sativa Japonica Group

source_name: Rice Nipponbare Seedling

growth_protocol: Oryza sativa cultivar “Nipponbare” seeds were germinated at ambient temperature for 72h. Germinated seeds were then sowed in water under greenhouse conditions for further growth. Two-week-old rice seedling leaves were gathered for protein and ChIP-DNA isolation.

extract_protocol:
ChIP experiments were performed using a pan anti-Kcr antibody (PTM BioLabs, PTM-501) and H3K14cr antibody (PTM BioLabs, PTM-535) following a published protocol (Nagaki et al. 2003), including methods for nuclei extraction and cleaning, chromatin digestion, pre-cleaning of digested chromatin and evaluation of digested chromatin. Negative control is a mock treatment using normal rabbit serum.
The DNAs identified in ChIP experiments were then used for library construction according to the protocol provided by Illumina, and were sequenced using the HiSeq 2500 platform.

tag: cultivar

value: Nipponbare

tag: developmental stage

value: Seedling

tag: antibody

value: H3K14cr antibody (PTM BioLabs, PTM-535)


title: 3998998207_R03C01

address: RILD building


title: dsc1 dsc2 dsc3 dsc5 deletion, 10min 100% nitrogen gas (NH_86_3_1)


title: dsc1 dsc2 dsc3 dsc5 deletion, 10min 100% nitrogen gas (NH_86_3_2)


title: dsc1 dsc2 dsc3 dsc5 deletion, 5min 100% nitrogen gas (NH_86_2_2)


title: UFH-001-rep3

city: Gainesville

first: Susan

middle: Cooke

last: Frost

state: Florida

address: 1200 Newell Drive

department: Biochemistry and Molecular Biology

institute: University of Florida

description: gene expression data from UFH-001 cells in growth phase

hyb_protocol: Following fragmentation, 5.2 ug ss-cDNA was hybridized for 16  hours at 45 degrees C, with rotation, using the Affymetrix GeneChip Human Transcriptome 2.0 Array

scan_protocol: The arrays were washed and stained with the reagents supplied in the GeneChip Hybridization Wash and Stain Kit (Affymetrix, Inc) on an Affymetrix Fluidics Station 450, and scanned with a GeneChip 7G Scanner (Affymetrix, Inc)

data_processing: CEL files were processed with the limma package from R/Bioconductor.

label: biotine

source_name: 75-80% confluent UFH-001 cells

label_protocol: Biotinyhated cRNA was prepared from total RNA (200ng) using the protocol described in GeneChip WT PLUS Reagent Kit (ThermoFisher Catalog # 902280)

growth_protocol: Cells were plated at 10,000 cells/ml (UFH-001 cells) or 20,000 cells/mL (MCF10A) and grown for 3 to 5 days to 75-80% confluence.

extract_protocol: RNA was extracted using an Rnase Easy Plus Mini Kit, following manufacturers instructions

treatment_protocol: Cells were grown in an incubator containing 5% carbon dioxide, 95% oxygen and balanced nitrogen.

value: metastatic breast cancer cell line


title: Rice  H3K14cr replicate 1


title: MCF10A-rep2

description: gene expression data from MCF10A cells in growth phase

source_name: 75-80% confluent MCF10A cells

value: human mammary epithelial cells


title: MCF10A-rep3


title: UFH-001-rep2


title: Rice  Kcr replicate 2

description: Kcr.txt

value: pan anti-Kcr antibody (PTM BioLabs, PTM-501)


title: MCF10A-rep1


title: dsc1 dsc2 dsc3 dsc5 deletion, 5min 100% nitrogen gas (NH_86_2_1)

value: 5 minutes


title: dsc1 dsc2 dsc3 dsc5 deletion, 0min 100% nitrogen gas (NH_86_1_1)


title: 3998998192_R06C01

institute: University of Exeter


title: dsc1 dsc2 dsc3 dsc5 deletion, 0min 100% nitrogen gas (NH_86_1_2)


title: Trim27_MP_rep4

city: Guangzhou

first: Tongjie

last: Wang

address: No.190 Kaiyuan Road

institute: Guangzhou Institutes of Biomedicine and Health Chinese Academy of Sciences

data_processing:
Bcl2fastq convert .bcl files into fastq files
Fastq files were aligned to NCBIM37 genome files to generate sam files by Hisat2, and then featureCounts was used to calculate expression raw counts of all the genes.
Genome_build: NCBIM37
Supplementary_files_format_and_content: raw counts

source_name: Trim27 MP

growth_protocol: All mice in this study were kept in C57BL/6J backgroud. E14.5 fetal liver HSPCs were obtained and infected with Trim27 virus and GFP control virus.

extract_protocol:
The procedure of RNA extraction by Qiagen RNeasy Mini Kit (Cat. No. 74104) and reverse transcription into double-stranded DNA is based on published methods(PMID:20203668).
Libraries were prepared according to Illumina's instructions accompanying the  illumina Nextera XT DNA Sample Preparation Kit (FC-131-1096).

treatment_protocol: MPs were sorted from infected fetal liver cells.

tag: strain

value: fetal liver HSPCs

tag: infected with

value: Trim27 virus

tag: sorted cell type

value: myeloid progenitors (MPs)


title: Rice  Kcr replicate 1

description: Kcr.txt


title: UFH-001-rep1


title: 3998998192_R02C02

city: Exeter

value: F


title: 3998998192_R03C02


title: 3998998192_R06C02


title: dsc5 deletion, 180min 100% nitrogen gas (NH_84_7_2)

source_name: strain yMH951 (S288C background with repaired HAP1)

tag: time in 100% n2

tag: genotype

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 dsc5d


title: Trim27_MP_rep1

tag: cell type


title: dsc5 deletion, 240min 100% nitrogen gas (NH_84_8_1)

value: 240 minutes


title: dsc5 deletion, 180min 100% nitrogen gas (NH_84_7_1)

value: 180 minutes


title: Trim27_MP_rep2


title: 3998998192_R05C01

source_name: whole blood


title: 3998998192_R01C02


title: GFP_MP_rep3

source_name: GFP MP

value: GFP control virus


title: 3998998192_R05C02

value: M


title: 3998998192_R01C01


title: 3998998192_R04C01


title: dsc1 dsc2 dsc3 dsc5 deletion, 30min 100% nitrogen gas (NH_86_4_1)

value: 30 minutes

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 dsc1d dsc2d dsc3d dsc5d


title: dsc5 deletion, 120min 100% nitrogen gas (NH_84_6_1)

value: 120 minutes


title: GFP_MP_rep1


title: dsc5 deletion, 60min 100% nitrogen gas (NH_84_5_1)

value: 60 minutes


title: GFP_MP_rep4


title: dsc5 deletion, 240min 100% nitrogen gas (NH_84_8_2)


title: 3998998192_R02C01


title: 3998998192_R04C02


title: 3998998186_R05C02


title: LV23

city: Worcester

first: Ricardo

middle: Tostes

last: Gazzinelli

address: 364 Plantation Street

department: Medicine

institute: University of Massachusetts Medical School

description: Infected 2  18 Hours

data_processing:
Reads were trimmed with Trimmomatic and mapped to the Genome Reference Consortium Mouse Build 38 patch release 5 (GRCm38.p5) using STAR aligner
FPKM values were calculated with CUFFLINKS.
Data were then analyzed with the software Short Time-series Expression Miner (STEM, version 1.3.11) to identify genes with variable expression patterns along the period of 24h sampled at each 6 hours.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: Liver

growth_protocol: Mice were fed ad libitum and kept on a regular light cycle with lights on from 7:00 am (ZT 0) to 7:00 pm (ZT 12) and lights off from 7:00 pm (ZT 12) to 7:00 am (ZT 24)

extract_protocol:
Total RNA was harvested using Qiagen Rneasy mini kit following manufacturer's instructions.
Poly-A containing mRNA molecules were purified using poly-T oligo attached magnetic beads and fragmented using divalent cations. The RNA fragments were transcribed into cDNA using  II Reverse Transcriptase (Invitrogen), followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Finally, cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products were then purified and enriched by PCR using paired-end primers (Illumina) for 15 cycles to create the final cDNA library.
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.

treatment_protocol: Liver from C57BL/6 mice non-infected or after 8 days post infection with 10E5 P. chabaudi infected red blood

tag: tissue

value: Liver

tag: Sex

value: Female

value: 10 weeks

value: Wild Type

tag: agent

value: P. chabaudi

tag: time point

value: 18 Hours


title: dsc5 deletion, 30min 100% nitrogen gas (NH_84_4_2)


title: 3998998186_R06C02

tag: age

tag: groupid


title: 3998998186_R04C02

tag: gender


title: dsc5 deletion, 30min 100% nitrogen gas (NH_84_4_1)


title: 3998998186_R03C02


title: LV22

description: Infected 1  18 Hours


title: dsc5 deletion, 120min 100% nitrogen gas (NH_84_6_2)


title: LV21

description: Infected 3  12 Hours

value: 12 Hours


title: dsc5 deletion, 10min 100% nitrogen gas (NH_84_3_2)

value: 10 minutes


title: LV20

description: Infected 2  12 Hours


title: dsc5 deletion, 10min 100% nitrogen gas (NH_84_3_1)

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 dsc5d


title: 3998998174_R05C02

value: F


title: dsc5 deletion, 5min 100% nitrogen gas (NH_84_2_2)

value: 5 minutes


title: 3998998174_R06C02


title: dsc5 deletion, 60min 100% nitrogen gas (NH_84_5_2)


title: LV19

description: Infected 1  12 Hours


title: dsc5 deletion, 5min 100% nitrogen gas (NH_84_2_1)


title: dsc5 deletion, 0min 100% nitrogen gas (NH_84_1_2)

value: 0 minutes


title: 3998998174_R02C02


title: LV18

description: Infected 3  06 Hours

value: 06 Hours


title: 3998998174_R03C02

value: M


title: LV17

description: Infected 2  06 Hours


title: 3998998174_R01C02


title: dsc3 deletion, 240min 100% nitrogen gas (NH_82_8_2)

source_name: strain yMH949 (S288C background with repaired HAP1)

value: 240 minutes

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 dsc3d


title: 3998998174_R05C01


title: LV16

description: Infected 1  06 Hours


title: LV15

description: Infected 3  00 Hours

value: 00 Hours


title: GFP_MP_rep2

value: fetal liver HSPCs

value: GFP control virus

value: myeloid progenitors (MPs)


title: dsc3 deletion, 240min 100% nitrogen gas (NH_82_8_1)


title: 3998998174_R04C02


title: LV14

description: Infected 2  00 Hours

value: Liver

value: Female

value: 10 weeks

value: Wild Type


title: dsc3 deletion, 180min 100% nitrogen gas (NH_82_7_2)

value: 180 minutes


title: dsc3 deletion, 180min 100% nitrogen gas (NH_82_7_1)


title: LV13

description: Infected 1  00 Hours

value: P. chabaudi


title: LV12

description: Control 3  18 Hours

value: Control

value: 18 Hours


title: LV24

description: Infected 3  18 Hours


title: Trim27_MP_rep3

value: Trim27 virus


title: dsc3 deletion, 120min 100% nitrogen gas (NH_82_6_2)

value: 120 minutes


title: 3998998174_R04C01

value: F


title: LV10

description: Control 1  18 Hours


title: dsc3 deletion, 60min 100% nitrogen gas (NH_82_5_2)

value: 60 minutes


title: 3998998174_R01C01


title: dsc3 deletion, 120min 100% nitrogen gas (NH_82_6_1)

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 dsc3d


title: 3998998123_R05C02

value: M


title: LV9

description: Control 3  12 Hours

value: 12 Hours


title: 3998998174_R03C01


title: 3998998174_R02C01


title: dsc5 deletion, 0min 100% nitrogen gas (NH_84_1_1)

value: 0 minutes

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 dsc5d


title: LV8

description: Control 2  12 Hours

value: Liver


title: LV11

description: Control 2  18 Hours

value: Female


title: dsc3 deletion, 30min 100% nitrogen gas (NH_82_4_1)

value: 30 minutes


title: 3998998123_R02C02


title: 3998998123_R04C02


title: dsc3 deletion, 30min 100% nitrogen gas (NH_82_4_2)


title: LV7

description: Control 1  12 Hours

value: 10 weeks

value: Wild Type


title: LV6

description: Control 3  06 Hours

value: 06 Hours


title: dsc3 deletion, 10min 100% nitrogen gas (NH_82_3_1)

value: 10 minutes


title: dsc3 deletion, 10min 100% nitrogen gas (NH_82_3_2)


title: 3998998123_R03C01


title: 3998998123_R04C01


title: LV4

description: Control 1  06 Hours

value: Control


title: 3998998123_R05C01


title: 3998998123_R01C02


title: dsc3 deletion, 60min 100% nitrogen gas (NH_82_5_1)


title: dsc3 deletion, 5min 100% nitrogen gas (NH_82_2_1)

value: 5 minutes


title: LV3

description: Control 3  00 Hours

value: 00 Hours