title: dis2Δ Rhn1-TAP_IP_1 ChIP-seq

value: h+:leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; dis2::ura4+; Rhn1-3XHA-TAP::kanMX


title: dis2Δ Pcf11-TAP_IP_1 ChIP-seq

status: Public on Dec 26 2018

type: SRA

city: Oxford

first: Tea

last: Kecman

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

library_source: genomic

data_processing:
ChIP-seq: Single end reads with a Phred score of less than 20 were removed using the the program Trimmomatic (version 0.36) and the remaining reads were aligned to the S. pombe genome (ASM294v2.25 from Pombase.org) using the short read aligner Bowtie (version 2.2.6).
Genome_build: S. pombe genome version ASM294v2.28
Supplementary_files_format_and_content: ChIP-Seq: the data is provided as bigwig files

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: Yeast cell extract

growth_protocol: S. pombe were grown in YES medium to exponential phase at 30°C

extract_protocol:
Cells were grown to mid-log phase and crosslinked using 11% formaldehyde. Cells were lysed by vortexing with glass beads and chromatin was extracted by two consecutive ultra-centrifugation steps. The DNA was sheared by sonication and DNA was extracted by ChIP DNA Clean & Concentrator (Zymo Research).
Libraries were generated using the NEBNext fast DNA library Prep set for Ion Torrent (E6270).

tag: genotype

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; dis2::ura4+; Pcf11-TAP::kanMX

tag: antibody

value: Rabbit IgG Agarose, Sigma-Aldrich, Cat# A2909

tag: molecule

value: Crosslinked DNA


title: res tomato mutant, leaflets, salt stress condition, rep. 1

type: RNA

city: Espinardo

first: Irene

last: Albaladejo

state: Murcia

address: Campus Universitario Espinardo

country: Spain

institute: CEBAS-CSIC

description: res tomato mutant, leaflets, salt stress condition, replicate 1

hyb_protocol: Following fragmentation and labeling, 3.5 ug of cDNA was hybridized for 20 hr at 48ºC on TomGene-1-1-st-v1 array using the GeneAtlas Hybridization Station. After hybridization, arrays were washed and stained in the GeneAtlas Fluidics Station (GeneAtlasTM System, Affymetrix)

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station (GeneAtlasTM System, Affymetrix)

data_processing: Data were analyzed with RMA (Robust Multiarray Analysis) using Affymetrix default analysis settings and global scaling as normalization method. Non-supervised Principal Components Analysis (PCA) and hierarchical clustering were performed and they showed that samples tend to separate according to genotype and condition. Partek Genomics Suite and Partek Pathways software (Partek Incorporated, St. Louis, USA) were used for obtaining the annotation of probesets and performing the statistical analysis. An ANOVA test was applied with a restrictive threshold at p-value ≤ 0.05, and multiple test corrections was performed using the FDR (Benjamini and Hochberg, 1995).

label: Biotin

molecule: total RNA

organism: Solanum lycopersicum

source_name: res mutant leaflets, salt stress condition

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 100ng of total RNA (GeneChip WT Plus Reagent Kit. Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays).

growth_protocol: Plants of the res mutant and Solanum lycopersicum L. cv. Moneymaker (background genotype), were used. Seeds were germinated in darkness, in a 8:3 (v/v) mixture of peat:perlite, at 28ºC temperature and 90% of relative humidity (RH). After emergence, plants were grown in a controlled growth chamber with 16 h light/8 h darkness photoperiod, with light of a photosynthetic photon flux (400-700 nm) of 350 µmol m-2 s-1 at the plant level, provided by fluorescent tubes (Philips Master TL-D 58W/840 REFLEX, Holland), and 25 ºC and 50-60% of temperature and RH, respectively. Two-week old plantlets were transferred to hydroponics. The hydroponic system consisted in tanks of 50 L volume (219 x 20 x 17 cm) filled with half-strength (½) Hoagland nutritive solution (Hoagland and Arnon, 1950), which was continuously aerated by means of a compressor (Puska N-150-150, with a 115 L min-1 flow, 10 Kg cm-2 maximum pressure). The nutritive solution was controlled by monitoring pH and electrical conductivity (EC), renewing it at least once per week.

extract_protocol: Total RNA from 24 samples was extracted by means of Rneasy Mini Kit (Qiagen) according to instrutions from manufacturer.The amount and quality of the RNA was checked by Bioanalyzer and spectrophotometrically by Nanodrop.

treatment_protocol: Salt stress was applied in hydroponics to six-week old WT and res plants, and consisted in ½ Hoagland plus 200 mM NaCl for 5 days. Leaflets from the first fully-expanded leaf and roots were harvested and immediately frozen in liquid N2 prior to stress application (control) and after 5 days of salt treatment. Three biological replicates (each one including three plants) were considered for each genotype and treatment.

tag: tissue

value: leaflet

value: res mutant

tag: background cultivar

value: Moneymaker

tag: age

value: six-week old plants

tag: condition

value: salt stress (200 mM NaCl for 5 days)


title: res tomato mutant, leaflets, control condition, rep. 1

description: res tomato mutant, leaflets, control condition, replicate 1

source_name: res mutant leaflets, control condition

value: control (optimal growth condition)


title: WT Pcf11-TAP_input_2 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; Pcf11-TAP::kanMX

value: genomic DNA


title: res tomato mutant, leaflets, control condition, rep. 2

description: res tomato mutant, leaflets, control condition, replicate 2


title: dis2Δ, Spt5-T1A Seb1-TAP_input_2 ChIP-seq

growth_protocol:
S. pombe were grown in YES medium to exponential phase at 30°C
S. pombe were grown in YES medium to exponential phase at 30°C

extract_protocol:
Cells were grown to mid-log phase and crosslinked using 11% formaldehyde. Cells were lysed by vortexing with glass beads and chromatin was extracted by two consecutive ultra-centrifugation steps. The DNA was sheared by sonication and DNA was extracted by ChIP DNA Clean & Concentrator (Zymo Research).
Libraries were generated using the NEBNext fast DNA library Prep set for Illumina (E7335).
Cells were grown to mid-log phase and crosslinked using 11% formaldehyde. Cells were lysed by vortexing with glass beads and chromatin was extracted by two consecutive ultra-centrifugation steps. The DNA was sheared by sonication and DNA was extracted by ChIP DNA Clean & Concentrator (Zymo Research).
Libraries were generated using the NEBNext fast DNA library Prep set for Ion Torrent (E6270) or Illumina (E7335).

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; dis2::ura4+;Seb1-3XHA-TAP::kanMX; Spt5-T1A-3xFlag::natMX

tag: method

value: ChIP-Seq


title: Tomato (S. lycopersicum) cv. Moneymaker, roots, salt stress condition, rep. 3

description: Tomato (S. lycopersicum) cv. Moneymaker, roots, salt stress condition, replicate 3

source_name: WT roots, salt stress condition

value: root

value: WT


title: dis2Δ, Spt5-T1A Seb1-TAP_input_4 ChIP-seq


title: WT Pcf11-TAP_IP_2 ChIP-seq


title: WT Pcf11-TAP_input_1 ChIP-seq


title: Tomato (S. lycopersicum) cv. Moneymaker, roots, salt stress condition, rep. 2

description: Tomato (S. lycopersicum) cv. Moneymaker, roots, salt stress condition, replicate 2


title: WT Pcf11-TAP_IP_1 ChIP-seq


title: dis2Δ, Spt5-T1A Seb1-TAP_input_3 ChIP-seq


title: dis2Δ, Spt5-T1A Seb1-TAP_IP_2 ChIP-seq

description: Crosslinked DNA


title: dis2Δ, Spt5-T1A Seb1-TAP_IP_3 ChIP-seq

description: Crosslinked DNA


title: dis2Δ Seb1-TAP_IP_2 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; dis2::ura4+; Seb1-3XHA-TAP::kanMX


title: dis2Δ Seb1-TAP_input_2 ChIP-seq


title: dis2Δ, Spt5-T1A Seb1-TAP_IP_4 ChIP-seq

description: Crosslinked DNA


title: dis2Δ Seb1-TAP_IP_1 ChIP-seq


title: dis2Δ Seb1-TAP_input_1 ChIP-seq


title: dis2+, Spt5-WT total-Pol II_IP_1 ChIP-seq

description: Crosslinked DNA

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; Seb1-3XHA-TAP::kanMX; Spt5-wt-3xFlag::natMX

value: RNAPII (8WG16) antibody, Millipore, Cat#05-952


title: dis2Δ, Spt5-T1E Seb1-TAP_input_3 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; dis2::ura4+;Seb1-3XHA-TAP::kanMX; Spt5-T1E-3xFlag::natMX


title: Tomato (S. lycopersicum) cv. Moneymaker, roots, control condition, rep. 2

description: Tomato (S. lycopersicum) cv. Moneymaker, roots, control condition, replicate 2

source_name: WT roots, control condition


title: FANTOM6_5-30125351

city: GLASGOW

first: Simon

last: Milling

address: 120 UNIVERSITY PLACE, ROOM B421, Sir Graeme Davies Building

department: Immunobiology

institute: University of Glasgow

library_source: transcriptomic

data_processing:
the sequencing was done on the Illumina NextSeq 500 using High Throughput flow-cells multiplexing eight samples per flow cell to produce 50M read-pairs per sample on average.
Sample-specific fastq files were generated using bcl2fastq software.
Statistical analysis: Data was aligned using HISAT2 and the reads summarised and normalised using the Feature Counts tool.
Differential expression was performed using the DESeq2 R package. Significant differential expression was defined as adjusted P-value < 0.05.
Supplementary_files_format_and_content: Deseq files contain abundance table comparisons

organism: Homo sapiens

source_name: Colonic macrophages

extract_protocol:
Sample preparation: Histologically normal margins of healthy colonic resections were processed, digested and stained for FACS analysis as previously described. CD45+ CD64+ HLA-DR+ CD206+ and CD45+ CD64+ HLA-DR+ CD206- cells were sorted using a FACSAria II/III. Cells were sorted into 300 μl RLT buffer (Qiagen) and stored at -80°C prior to RNA extraction using a MicroRNA kit (Qiagen).
Sequencing libraries were prepared using the SMARTer Stranded Total RNA-Seq kit-Pico Input Mammalian (Clontech), starting with 1ng of RNA and following the manufactures protocol with 15 cycles of PCR.

treatment_protocol: Intestinal tissue processing. To remove the epithelial layer from biopsies, tissue was incubated in 2 mM EDTA/HBSS (Gibco) for three minutes at 37°C in a shaking incubator.  For resected tissue samples, fat and muscle layers were first removed; tissue was washed in HBSS and subsequently dissected into 0.5 cm pieces. To remove the epithelial layer from resections, tissue was incubated in 2 mM EDTA/HBSS for 15 minutes at 37°C in a shaking incubator. Tissue was vigorously shaken; supernatant discarded and the process was repeated three times. After the final EDTA step, all samples were washed in HBSS and resuspended in 2 ml (20 ml for resections) of pre-warmed 10% complete media (RPMI 1640 supplemented with 10% foetal calf serum (FCS), 100 U ml-1 penicillin, 100 U ml-1 streptomycin, 2 mM L-glutamine and 50 μM 2-mercaptoethanol) containing: Collagenase VIII (1 mg/ml, Sigma-Aldrich), Collagenase D (1.25 mg/ml, Roche), Dispase (1 mg/ml, Gibco) and DNase. Samples were returned to the shaking incubator (37°C) for 30-40 minutes; additional vigorous shaking was performed every 10 minutes to aid digestion. Cell suspension was first filtered through a 100 μM then a 40 μM cell strainer (BD Falcon) and washed in PBS containing 2 mM EDTA and 2% FCS.

tag: cell type


title: Tomato (S. lycopersicum) cv. Moneymaker, roots, salt stress condition, rep. 1

description: Tomato (S. lycopersicum) cv. Moneymaker, roots, salt stress condition, replicate 1


title: Tomato (S. lycopersicum) cv. Moneymaker, roots, control condition, rep. 3

description: Tomato (S. lycopersicum) cv. Moneymaker, roots, control condition, replicate 3


title: dis2Δ, Spt5-T1E Seb1-TAP_input_2 ChIP-seq


title: WT Seb1-TAP_input_2 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; Seb1-3XHA-TAP::kanMX


title: dis2Δ, Spt5-T1E Seb1-TAP_input_4 ChIP-seq


title: dis2Δ, Spt5-T1E Seb1-TAP_IP_4 ChIP-seq

description: Crosslinked DNA

value: Rabbit IgG Agarose, Sigma-Aldrich, Cat# A2909


title: WT Seb1-TAP_input_1 ChIP-seq


title: res tomato mutant, roots, salt stress condition, rep. 3

description: res tomato mutant, roots, salt stress condition, replicate 3

source_name: res mutant roots, salt stress condition

value: res mutant


title: res tomato mutant, roots, salt stress condition, rep. 1

description: res tomato mutant, roots, salt stress condition, replicate 1

value: Moneymaker


title: dis2Δ, Spt5-T1E Seb1-TAP_IP_2 ChIP-seq

description: Crosslinked DNA


title: WT Seb1-TAP_IP_1 ChIP-seq

value: Crosslinked DNA


title: dis2Δ, Spt5-T1E Seb1-TAP_IP_3 ChIP-seq

description: Crosslinked DNA


title: res tomato mutant, roots, salt stress condition, rep. 2

description: res tomato mutant, roots, salt stress condition, replicate 2

value: six-week old plants

value: salt stress (200 mM NaCl for 5 days)


title: res tomato mutant, roots, control condition, rep. 3

description: res tomato mutant, roots, control condition, replicate 3

source_name: res mutant roots, control condition

value: control (optimal growth condition)


title: res tomato mutant, roots, control condition, rep. 2

description: res tomato mutant, roots, control condition, replicate 2


title: dis2Δ, Spt5-WT Seb1-TAP_input_4 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; dis2::ura4+;Seb1-3XHA-TAP::kanMX; Spt5-wt-3xFlag::natMX


title: Tomato (S. lycopersicum) cv. Moneymaker, roots, control condition, rep. 1

description: Tomato (S. lycopersicum) cv. Moneymaker, roots, control condition, replicate 1


title: res tomato mutant, roots, control condition, rep. 1

description: res tomato mutant, roots, control condition, replicate 1


title: dis2Δ, Spt5-WT Seb1-TAP_input_2 ChIP-seq


title: WT total-Pol II_input_2 ChIP-seq

value: genomic DNA


title: dis2Δ total-Pol II_IP_1 ChIP-seq


title: dis2Δ total-Pol II_input_1 ChIP-seq


title: dis2Δ, Spt5-WT Seb1-TAP_IP_4 ChIP-seq

description: Crosslinked DNA

value: ChIP-Seq


title: WT total-Pol II_input_1 ChIP-seq


title: dis2Δ, Spt5-WT Seb1-TAP_IP_2 ChIP-seq

description: Crosslinked DNA


title: MCF_7_3

city: Shenzhen

first: Qiangzu

last: Zhang

address: Nan Hai Da Dao Chuang Shi Ji Bin Hai Hua Yuan Building9 9A , Nanshan District, Shenzhen City, Guangdong Province

country: China

institute: Lemondata BioTechnology Limited

data_processing:
Illumina hiseq4000 used for basecalling.
Sequence reads were trimmed for adaptor sequence and 3'-end was trimmed by quality, reads were filtered by quality and mapped to GRCh37 using the HISAT2 software
mapping QC by samtools and picard software
Quantification was done by using Cufflinks to produce gene-level expression values (FPKMs)
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: breast cancer cell

growth_protocol: cells were cultured in DMEM with 10% FBS.

extract_protocol:
The total RNA was extracted from cells by the qiagen RNA exaction kit
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Part# 0801-0303).

tag: cell line

tag: passage

value: 15-18 passage


title: WT total-Pol II_IP_1 ChIP-seq


title: dis2Δ, Spt5-WT Seb1-TAP_IP_3 ChIP-seq

description: Crosslinked DNA


title: dis2Δ, Spt5-WT Seb1-TAP_input_3 ChIP-seq


title: WT Seb1-TAP_IP_2 ChIP-seq


title: dis2+, Spt5-T1A Seb1-TAP_input_4 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; Seb1-3XHA-TAP::kanMX; Spt5-T1A-3xFlag::natMX


title: MCF_7_2


title: dis2Δ total-Pol II_input_2 ChIP-seq


title: dis2+, Spt5-T1A Seb1-TAP_input_2 ChIP-seq


title: dis2Δ Thr4P-CTD_input_2 ChIP-seq


title: MCF_7_1


title: dis2Δ total-Pol II_IP_2 ChIP-seq


title: dis2Δ Thr4P-CTD_input_1 ChIP-seq


title: dis2+, Spt5-T1A Seb1-TAP_input_3 ChIP-seq


title: dis2+, Spt5-T1A Seb1-TAP_IP_4 ChIP-seq

description: Crosslinked DNA


title: LCC2_3


title: dis2Δ Thr4P-CTD_IP_2 ChIP-seq

value: RNA pol II CTD phospho Thr4 antibody, Clone 6D7, Active Motif, Cat#61361


title: WT total-Pol II_IP_2 ChIP-seq


title: LCC2_2


title: dis2+, Spt5-T1A Seb1-TAP_IP_2 ChIP-seq

description: Crosslinked DNA


title: dis2+, Spt5-T1A Seb1-TAP_IP_3 ChIP-seq

description: Crosslinked DNA


title: LCC2_1


title: dis2Δ Thr4P-CTD_IP_1 ChIP-seq


title: WT Thr4P-CTD_input_2 ChIP-seq


title: ZR-75-1_20percentO2

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

country: USA

institute: University of Maryland, Baltimore

data_processing:
Transcript quantification with Salmon version 0.8.2
Estimation of gene level counts from transcript quantification with R/Bioconductor package tximport version 1.2.0 using the Gencode v26 gene annotations
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Comma delimited text file containing gene-level counts

source_name: breast cancer cell line

growth_protocol: All cell lines except SUM159 and SUM149 were obtained directly from the ATCC or Asterand (SUM lines). Cells were cultured as described by the ATCC or Asterand and experiments were conducted on early passage cells within 2-3 passages after receipt.

extract_protocol:
Total RNA was extracted from cells using TRIzol (Invitrogen) and treated with DNase I (Ambion). All samples had a RIN value of >9.0 when measured on an Agilent Bioanalyzer.
Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit. The workflow consisted of mRNA enrichment, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation and 12 cycles of PCR amplification. Unique adaptors were used for each sample in order to multiplex samples into several lanes. Sequencing was performed on Illumina Hiseq 3000/4000 with a 150bp pair-end run. A data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

treatment_protocol: Hypoxic cells (1% O2 treatment) were maintained at 37°C in a modular incubator chamber (Billups–Rothenberg) flushed with a gas mixture containing 1% O2, 5% CO2, and 94% N2 for 24h.

tag: breast cancer subtype

value: Luminal

tag: o2 concentration (percent)


title: dis2+, Spt5-T1E Seb1-TAP_input_4 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; Seb1-3XHA-TAP::kanMX; Spt5-T1E-3xFlag::natMX


title: dis2+, Spt5-T1E Seb1-TAP_input_2 ChIP-seq


title: ZR-75-1_1percentO2


title: WT Thr4P-CTD_IP_2 ChIP-seq


title: dis2+, Spt5-T1E Seb1-TAP_input_3 ChIP-seq


title: WT Thr4P-CTD_input_1 ChIP-seq


title: dis2+, Spt5-T1E Seb1-TAP_IP_4 ChIP-seq

description: Crosslinked DNA


title: WT Thr4P-CTD_IP_1 ChIP-seq


title: WT Ser5P-CTD_IP_1 ChIP-seq

value: RNA pol II CTD phospho Ser5 antibody, Clone 3E8, Millipore, Cat#04-1572-I


title: WT Ser5P-CTD_WCE_1 ChIP-seq


title: T47D_20percentO2


title: SUM229_20percentO2

value: Basal B


title: T47D_1percentO2


title: liver_MCD+DDC_rep3

city: Beijing

first: Tianhui

last: Liu

address: No. 95 Yong-an Road, Xi-cheng District

institute: Beijing Friendship Hospital, Capital Medical University

hyb_protocol: MOA2.1 arrays were pre-heat at 60°C for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on MOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: The arrays were scanned by GenePix 4000B scanner (635nm power 100 PMT 520 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by Rosetta Resolver   (Rosetta Biosoftware). The probes <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

organism: Mus musculus

source_name: NASH mice with MCD diet and DDC treatment

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: Eight-week-old male C57BL/6 mice were kept on MCD or MCS control diet for eight weeks.

extract_protocol: RNA extraction by Trizol Reagent. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: MCD group were treated either with vehicle (1×PBS) or 450 mg/kg DDC via daily gavage for eight weeks.

tag: Sex

value: male

tag: strain

value: liver


title: liver_MCD+DDC_rep2


title: liver_MCD_rep3

source_name: NASH mice with MCD diet


title: liver_MCD_rep2


title: liver_MCD_rep1


title: liver_control_rep2

source_name: control mice with the methionine and choline sufficient diet


title: dis2+, Spt5-T1E Seb1-TAP_IP_3 ChIP-seq

description: Crosslinked DNA

value: Rabbit IgG Agarose, Sigma-Aldrich, Cat# A2909


title: Sum225CWN_20percentO2

value: Basal A


title: WT Ser2P-CTD_WCE_1 ChIP-seq


title: WT Ser2P-CTD_IP_2 ChIP-seq

value: RNA pol II CTD phospho Ser2 antibody, Clone 3E10, Millipore, Cat#04-1571-I

value: Crosslinked DNA


title: dis2+, Spt5-WT Seb1-TAP_input_4 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; Seb1-3XHA-TAP::kanMX; Spt5-wt-3xFlag::natMX


title: liver_MCD+DDC_rep1


title: liver_control_rep1


title: Sum225CWN_1percentO2


title: dis2+, Spt5-WT Seb1-TAP_input_2 ChIP-seq


title: AML patient #9, before therapy

first: Hanna

middle: A

last: Knaus

state: Maryland

address: 1650 Orleans St

department: Oncology

institute: Johns Hopkins

description: Gene expression data from AML patient of CD8+ T cells in the peripheral blood (PB) at diagnosis before chemotherapy (PRE)

hyb_protocol: Hybridization with Human PrimeView expression arrays (Affymetrix) as per manufacturer’s instructions.

scan_protocol: Scanning was performed with M10 scanner using AGCC ScanCom software.

data_processing: R/Bioconductor package 'affy' and  RMA for background processing (PM-MM model), quantile normalization, probe summarization

label: biotin

source_name: AML patient

label_protocol: Total RNA was amplified with the NuGEN™ Ovation Pico WTA system and biotin labelled according manufacturer’s instructions (Affymetrix)

extract_protocol: Total RNA was isolated using TRIzol (Life Techologies) and purified using the RNA Clean&Concentrator Kit (Zymo Research). Sample quality was checked using the Agilent Bioanalyzer Nano kit, and concentrations were verified using the Nanodrop spectrophotometer (Thermo Fisher Scientific). Only specimens with a high RNA integrity (RIN >9) were used for analyses.

treatment_protocol: PBMCs were first separated by T-cell negative selection with a custom made kit (Stem Cell Technologies) containing Abs against CD33, CD34, CD123, CD11c, and CD36. CD3+CD8+ T-cells were sorted on a FACSAria II (BSL-2) (BD) to high purity (>98%)

value: peripheral blood (PB)

value: CD8+ T-cells

tag: pre or post therapy

value: Pre

tag: chemotherapy response

value: Responder (CR)

tag: pairs


title: SUM185_20percentO2


title: dis2+, Spt5-T1E Seb1-TAP_IP_2 ChIP-seq

description: Crosslinked DNA

tag: genotype

value: ChIP-Seq

tag: antibody


title: dis2+, Spt5-WT Seb1-TAP_input_3 ChIP-seq


title: WT Tyr1P-CTD_WCE_2 ChIP-seq

tag: molecule

value: genomic DNA


title: AML patient #8, before therapy

tag: tissue


title: dis2+, Spt5-WT Seb1-TAP_IP_4 ChIP-seq

description: Crosslinked DNA


title: SUM159_20percentO2


title: dis2+, Spt5-WT Seb1-TAP_IP_2 ChIP-seq

description: Crosslinked DNA


title: SUM229_1percentO2


title: WT Ser2P-CTD_IP_1 ChIP-seq


title: WT Tyr1P-CTD_IP_2 ChIP-seq

value: RNA pol II CTD phospho Tyr1 antibody, Clone 3D12, Active Motif, Cat#61383


title: WT Tyr1P-CTD_IP_1 ChIP-seq


title: dis2+, Spt5-WT Seb1-TAP_IP_3 ChIP-seq

description: Crosslinked DNA


title: WT Tyr1P-CTD_WCE_1 ChIP-seq


title: SUM149_20percentO2


title: dis2Δ, Spt5-T1A  Seb1-TAP_input_1 ChIP-seq

extract_protocol:
Cells were grown to mid-log phase and crosslinked using 11% formaldehyde. Cells were lysed by vortexing with glass beads and chromatin was extracted by two consecutive ultra-centrifugation steps. The DNA was sheared by sonication and DNA was extracted by ChIP DNA Clean & Concentrator (Zymo Research).
Libraries were generated using the NEBNext fast DNA library Prep set for Illumina (E7335).

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; dis2::ura4+; Seb1-3XHA-TAP::kanMX; Spt5-T1A-3xFlag::natMX


title: SUM159_1percentO2


title: SUM149_1percentO2


title: dis2Δ, Spt5-T1E  Seb1-TAP_input_1 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; dis2::ura4+; Seb1-3XHA-TAP::kanMX; Spt5-T1E-3xFlag::natMX


title: fresh-to-saltwater 24hr arsenic, rep 4

city: Orono

first: Benjamin

middle: L

last: King

state: ME

address: 5735 Hitchner Hall

department: Molecular and Biomedical Sciences

institute: University of Maine

data_processing:
Read quality control diagnostic analyses using FastQC version 0.11.2.
Small RNA-Seq reads were adapter clipped using FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
MicroRNA were annotated using the miRMiner software (Tarver et al., 2013; Wheeler et al., 2009) and the killifish genome assembly (Reid et al., 2017). Using miRMiner, the clipped and length-filtered reads from all samples were collapsed into unique sequence tags. Sequence tags were aligned to miRBase stem-loop precursors in miRBase (version 21) (Kozomara and Griffiths-Jones, 2014) using NCBI BLAST (Altschul et al., 1990) to identify tags with high similarity to previously annotated miRNAs . Next, sequence tags were aligned to the genome assembly using BLAT (Kent, 2002). Alignment coordinates were analyzed to generate multiple sequence alignments of the mature miRNA products along genomic segments predicted to form stable stem-loop secondary structures by RNAFold from within the ViennaRNA Package version 1.7 (Lorenz et al., 2011). These multiple sequence alignments were examined to annotate miRNA where at least one sequence tag mapped to both the mature and star mature arms consistent with miRNA in other animals (Fromm et al, 2016). Each annotated miRNA was assigned a stem-loop precursor sequence, mature and star sequences according to the evidence in the multiple sequence alignments. miRNA homologs were identified in zebrafish (Danio rerio) miRNA families compared with eight other vertebrates in miRGeneDB (http://mirgenedb.org/) (Fromm et al., 2015)
Following miRNA annotation, the expression level of miRNAs, expressed as read counts, in each sample was calculated by aligning clipped and length filtered sequences to the annotated stem-loop precursor sequences using CLCBio Genomics Workbench version 9.0 (QIAGEN Bioinformatics, Aarhus, Denmark).
Genome_build: GCA_000826765.1 Fundulus_heteroclitus-3.0.2
Supplementary_files_format_and_content: Tab-delimited text files with mapped read counts for microRNAs. A FASTA file with miRNA sequences is included.

organism: Fundulus heteroclitus

source_name: gill

growth_protocol: Killifish, Fundulus heteroclitus, were collected from Northeast Creek, Bar Harbor, ME and acclimated to fresh water at the MDI Biological Laboratory by gradually reducing the salinity to 10% seawater,  followed by “soft” freshwater for 2 week intervals as described previously (Shaw 2007).

extract_protocol:
Total RNA was isolated using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) following manufacturer’s protocol.
Illumina TruSeq small RNA libraries.

treatment_protocol: Male killifish were exposed to 100 ug/L total arsenic, as sodium (meta)arsenite (Sigma-Aldrich, St. Louis, MO) or control for 48 hours, and then transferred to seawater containing the same levels of arsenic. Fish were euthanized at 0, 1 and 24 hours post-transition to seawater and gills dissected for RNA isolation.

value: gill

tag: hours post-transition to seawater

tag: arsenic


title: fresh-to-saltwater 24hr arsenic, rep 3

value: male


title: SUM185_1percentO2

value: Luminal


title: fresh-to-saltwater 24hr arsenic, rep 2


title: SUM1315_20percentO2

value: Basal B


title: dis2Δ, Spt5-WT  Seb1-TAP_input_1 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; dis2::ura4+; Seb1-3XHA-TAP::kanMX; Spt5-wt-3xFlag::natMX


title: SUM1315_1percentO2


title: Healthy control #4

description: Gene expression data from healthy controls (HC) of CD8+ T cells in the peripheral blood

source_name: Healthy controls

value: Healthy control (HC)


title: AML patient #7, before therapy


title: Healthy control #2


title: Healthy control #1


title: dis2+, Spt5-T1E  Seb1-TAP_input_1 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; Seb1-3XHA-TAP::kanMX; Spt5-T1E-3xFlag::natMX


title: Healthy control #3


title: AML patient #6, before therapy

value: Non-responder (NR)


title: AML patient #5, after therapy

description: Gene expression data from AML patient of CD8+ T cells in the peripheral blood(PB) at full recovery after chemotherapy (POST)

value: peripheral blood (PB)

value: Post


title: AML patient #6, after therapy

value: CD8+ T-cells


title: SKBR3_20percentO2


title: fresh-to-saltwater 24hr arsenic, rep 1


title: dis2+, Spt5-WT  Seb1-TAP_input_1 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; Seb1-3XHA-TAP::kanMX; Spt5-wt-3xFlag::natMX


title: fresh-to-saltwater 1hr arsenic, rep 4


title: AML patient #5, before therapy

value: Pre


title: SKBR3_1percentO2


title: dis2Δ, Spt5-T1A  Seb1-TAP_IP_1 ChIP-seq

value: Rabbit IgG Agarose, Sigma-Aldrich, Cat# A2909

value: Crosslinked DNA


title: fresh-to-saltwater 1hr arsenic, rep 2


title: dis2Δ, Spt5-T1E  Seb1-TAP_IP_1 ChIP-seq


title: fresh-to-saltwater 1hr arsenic, rep 3


title: MDA-MB-468_1percentO2

value: Basal A


title: MDA-MB-468_20percentO2


title: AML patient #4, after therapy


title: dis2Δ, Spt5-WT  Seb1-TAP_IP_1 ChIP-seq


title: fresh-to-saltwater 1hr arsenic, rep 1


title: MDAMB436_20percentO2


title: dis2+, Spt5-T1E  Seb1-TAP_IP_1 ChIP-seq


title: freshwater arsenic, rep 4


title: dis2+, Spt5-WT  Seb1-TAP_IP_1 ChIP-seq


title: freshwater arsenic, rep 3


title: AML patient #3, before therapy

value: Responder (CR)


title: AML patient #4, before therapy


title: MDA-MB-231-PSOC_20percentO2


title: MDAMB436_1percentO2


title: AML patient #3, after therapy


title: MDA-MB-231-PSOC_1percentO2


title: dis2Δ Rhn1-TAP_input_2 ChIP-seq

value: h+:leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; dis2::ura4+; Rhn1-3XHA-TAP::kanMX

value: genomic DNA


title: freshwater arsenic, rep 1

value: gill

value: male


title: dis2Δ Rhn1-TAP_IP_2 ChIP-seq


title: MDA-MB-175_20percentO2

value: Luminal


title: WT Rhn1-TAP_input_2 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; Rhn1-3XHA-TAP::kanMX


title: fresh-to-saltwater 24hr control, rep 4


title: WT Rhn1-TAP_IP_2 ChIP-seq


title: MDA_MB_175_1percentO2


title: AML patient #2, before therapy


title: fresh-to-saltwater 24hr control, rep 3


title: AML patient #1, before therapy


title: AML patient #1, after therapy

description: Gene expression data from AML patient of CD8+ T cells in the peripheral blood (PB) at full recovery after chemotherapy (POST)


title: MDA-MB-157_20percentO2

value: Basal B


title: WT Ser5P-CTD_WCE_2 ChIP-seq


title: MG cells, control

city: Tokushima

first: Kensei

last: Nishida

state: Tokushima

address: 3-18-15 Kuramoto-cho

country: Japan

institute: Tokushima University Graduate school

hyb_protocol: Hybridizations were performed using GE Hybridization Kit (P/N 5188-5242) and GE Wash Buffer 1 and 2 (P/N 5188-5325, -5326) as following Agilent's protocol. The fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4858A) for 17 hours at 65C in a rotating Agilent hybridization oven.

scan_protocol: Microarrays were scanned using Agilent’s DNA Microarray Scanner (P/N G2600D).

data_processing: Data extracted using Agilent's Feature Extraction software. Raw data output was imported into Genespring GX14.9 (Agilent) and normalized each chip to the 75th percentile of all measurements (per chip normalization).

source_name: colon cancer cell line

label_protocol: Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis’ Protocol. These protocols are available for download from Agilent's DNA Microarray Manuals website. For microarray analysis, total RNA (400 ng) was used for amplification and labeling of complementary RNA (cRNA) using a Low RNA Input Liner Amplification Kit PLUS and a succinimide-containing fluorescent dye (Cy3)-CTP according to the manufacturer’s protocol (Agilent).

extract_protocol: The total RNA was extracted using RNAiso Plus reagent (Takara).

treatment_protocol: HCT116 cells (non-MG cells or MG cells) were treated with 5 μM of 5-azacytidine for 48 hours.

tag: treatment

value: control


title: AML patient #2, after therapy

value: peripheral blood (PB)

tag: cell type


title: freshwater arsenic, rep 2


title: MG cells, 5-azacytidine

tag: cell line


title: fresh-to-saltwater 24hr control, rep 2


title: fresh-to-saltwater 24hr control, rep 1


title: WT Ser5P-CTD_IP_2 ChIP-seq

source_name: Yeast cell extract

value: RNA pol II CTD phospho Ser5 antibody, Clone 3E8, Millipore, Cat#04-1572-I


title: non-MG cells, 5-azacytidine


title: fresh-to-saltwater 1hr control, rep 4


title: MDA-MB-157_1percentO2


title: MCF-7_20percentO2


title: MCF-7_1percentO2


title: MCF12A_1percentO2


title: MCF12A_20percentO2


title: MCF10A_20percentO2


title: freshwater control, rep 4


title: freshwater control, rep 3


title: fresh-to-saltwater 1hr control, rep 3


title: MCF10A_1percentO2


title: freshwater control, rep 2


title: non-MG cells, control


title: CD8_KOd22_3

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

country: France

institute: Institut Curie

hyb_protocol: Hybridization performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

scan_protocol: Scanning were performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

data_processing: Arrays were normalized by the RMA procedure using Brainarray annotations (V.22.0.0, ENTREZG)

label_protocol: According to the standard Affymetrix protocol

extract_protocol: Total RNAs were collected from samples using the miRNeasy kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: B6/c57 mice infected with Trypanosoma cruzi. d0: Without infection; d14: 14 days post-infection with 5000 tripomastigotes of Tulahuén strain; d22: 22 days post-infection with 5000 tripomastigotes of Tulahuén strain

tag: strain background

tag: genotype/variation

value: IL-17RA KO

tag: infected with

value: Trypanosoma cruzi

tag: time point

value: day 22 post infection

value: spleen

value: sorted CD8 T cell


title: fresh-to-saltwater 1hr control, rep 2

tag: Sex


title: CD8_KOd22_2


title: CD8_KOd22_1


title: fresh-to-saltwater 1hr control, rep 1


title: CD8_KOd14_3

value: day 14 post infection


title: CD8_KOd0_3

value: day 0 post infection


title: htert-HME_1percentO2

value: htert-HME

tag: breast cancer subtype

value: Normal

tag: o2 concentration (percent)


title: CD8_KOd14_2


title: freshwater control, rep 1

value: gill


title: HS578T_20percentO2


title: OV-VC_2

city: London

first: Daniela

last: Loessner

address: Mile End Rd

institute: Queen Mary University of London

hyb_protocol: 1650 ng of the labeled cRNA were hybridized onto a custom Agilent oligo micrarray at 65⁰C for 17 hours.

scan_protocol: Arrays were scanned on an Agilent scanner (G2565CA) using the Agilent Scan Control Software (A.8.4.1) and feature extraction was performed using the Agilent Feature Extraction Software (10.7).

data_processing: A quantile between array normalization was applied and differential expression was determined using the Baysian adjusted t-statistic linear model of the ‘Linear Models for Microarray Data’ (LIMMA) package in R. Annotation of the data in the study is based on Gencode v21/Ensembl 77 (GRCh38).

source_name: Ovarian Cancer Cell line OV-MZ-6 expressing empty vector

label_protocol: 100 ng of total RNA was amplified and labelled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's protocol.

growth_protocol: OV-MZ-6 ovarian cancer cells were cultured in DMEM + 10% FBS at 37°C in a humidified incubator at 5% CO2.

extract_protocol: Total cellular RNA was extracted using the Qiagen RNeasy Kit including on-column DNAse-I treatment.

treatment_protocol: Cells were stably co-transfected with an expression vector harboring human full-length cDNAs of KLK4-7, resulting in OV-KLK4-7 cells. Cells transfected with the vector only were used as controls (OV-VC cells). 3 biological repeats of each condition were processed for microarray analysis.

value: Ovarian Cancer Cell line OV-MZ-6

value: vehicle control


title: htert-HME_20percentO2


title: OV-VC_1


title: OV-KLK4-7_3

source_name: Ovarian Cancer Cell line OV-MZ-6 overexpressing KLK4-7

value: KLK4-7 overexpression


title: OV-VC_3


title: HS578T_1percentO2

value: Basal B


title: OV-KLK4-7_2


title: Cp_3_240

city: Jena

first: Philipp

last: Kämmer

address: Adolf-Reichwein-Straße 23

department: Microbial Pathogenicity Mechanisms

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI)

data_processing:
RTA software version 1.18.64 were used for basecalling.
Read quality were checked with Fastqc. Reads were trimmed with trimmomatic version 0.32 and following parameters: SE threads 5 -phred33 FILE LEADING: 3 TRAILING: 3 SLIDINGWINDOW: 15:20 MINLEN 30
Trimmed reads were mapped to reference genome of Candida parapsilosis CDC317_version_s01-m03-r10_features and of Homo sapiens GRCh38.77 using tophat2 with following parameters: -p 10 -g 1 --no-mixed --no-discordant --b2-very-sensitive --max-intron-length 100000 -o OUTDIR -G ANNOTATION INDEX FASTQFILE > OUTFILE
Mapped reads were counted using featureCounts version 1.4.5 and DeSeq2 were used for differential expression filtering.
Genome_build: GRCh38.77, CDC317_version_s01-m03-r10_features
Supplementary_files_format_and_content: Comma-delimited text files include counts for each gene per sample

molecule: polyA RNA

organism:
Candida parapsilosis
Homo sapiens

source_name: whole blood, all

growth_protocol: Candida parapsilosis cells grew at 37°C in Homo sapiens whole blood.

extract_protocol:
To isolate human RNA aliquots of infected or mock infected samples were added to a PAXgene® Blood RNA Tube (PreAnalytiX) and processed with the PAXgene® Blood RNA Kit (PreAnalytiX) according to the manufacturer’s protocol. For fungal RNA isolation aliquots were added to ice-cold water, centrifuged and immediately frozen in liquid nitrogen. The cell pellet was further processed with the RiboPure™-Yeast Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol. RNA quantity was determined with NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific) and RNA quality was verified with an Agilent 2100 Bioanalyzer (Agilent Technologies). Fungal and human RNA samples were pooled subsequently in a quantitative ratio of 1:10.
Library Preperation was performed by GATC Biotech using validated  standard procedures modified to optimize the method for automated  Preperation. Library Preparation consisted of the following steps:  Purification of poly-A containing mRNA molecules, mRNA fragmentation, Random primed cDNA synthesis (strand specific), Adapter ligation and adapter specific PCR amplification

treatment_protocol: Homo sapiens whole blood cells were treated with Candida parapsilosis GA-1.

tag: c. parapsilosis strain

value: 240 minutes


title: HME2_20percentO2


title: Cp_3_30

value: 30 minutes


title: OV-KLK4-7_1

tag: genotype


title: CD8_KOd0_1


title: CD8_KOd14_1


title: CD8_KOd0_2


title: Cp_3_120

value: 120 minutes


title: HME2_1percentO2


title: Cp_3_15

value: 15 minutes


title: HCC1954_20percentO2

value: Basal A


title: HCC38_1percentO2


title: Cp_3_0

value: 0 minutes


title: Cp_2_60

value: 60 minutes


title: Cp_2_30


title: HCC1937_20percentO2


title: 4-3: XUSE rep3

city: Seoul

first: Ja Kyong

last: Ko

address: Seongbuk-gu, Wharang-ro, 14 gil 5

department: Clearn Energy Research Center

country: South Korea

institute: Korea Institute of Science and Technology (KIST)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to sacCer3 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: After the 20-h microaerobic fermentations with xylose as the sole carbon source, yeast cells were harvested by centrifugation at 500×g and 4 °C for 5 min.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

value: yeast cells

tag: strain

value: XUSE

tag: phase

value: Exponential phase

value: BY4741; xylA3*, TAL1, XKS1, {delta}gre3, {delta}pho13, Evolved


title: Cp_3_60


title: 4-1: XUSE rep1

tag: tissue


title: HCC38_20percentO2


title: Cp_2_240


title: CD8_WTd14_2

value: wild type

value: Trypanosoma cruzi

value: day 14 post infection

value: spleen

value: sorted CD8 T cell


title: 3-3: XUS rep3

value: XUS

value: BY4741; xylA3*, TAL1, XKS1, {delta}gre3, {delta}pho13


title: Cp_2_15


title: CD8_WTd14_3


title: CD8_WTd22_1

value: day 22 post infection


title: HCC1806_20percentO2

value: Basal B


title: HCC1937_1percentO2


title: HCC1954_1percentO2


title: Cp_2_120

value: 120 minutes


title: CD8_WTd22_2


title: CD8_WTd22_3


title: CD8_WTd0_3

value: day 0 post infection


title: CD8_WTd0_2


title: 3-1: XUS rep1


title: 4-2: XUSE rep2


title: HCC1806_1percentO2


title: 3-2: XUS rep2


title: Cp_2_0

value: 0 minutes


title: X7D_C

city: Shanghai

first: Qingjian

last: Ou

address: Siping Rd

department: Medical

institute: Tongji University

data_processing:
SOAPnuke used for filtering with parameters  -l 15 -q 0.2 -n 0.1
RNA-seq reads  mapped to Mus musculus whole genome using BOWTIE2 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Fragments Per Kilobase per Million mapped fragments of library size (FPKM) were calculated using RSEM with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: text files include FPKM values for each Sample.

source_name: Retina

growth_protocol: mouse retinal progenitor cells cultured with or without bFGF and CHIR99021 after 1,3,5,7 days.

extract_protocol:
RNA was harvested using Trizol reagent and extracted with phenol:chloroform:isoamyl alcohol.
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature.We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

treatment_protocol: The mouse retinal progenitor cells culture with or without bFGF,CHIR99021

value: Mouse retinal progenitor cells

tag: time course


title: X7D_BM


title: X7D_B

value: bFGF


title: CeA.16.Day35.Meth

city: New York

first: Hannah

middle: M

last: Cates

state: NY

address: 1425 Madison Ave, Box 6052

institute: Icahn School of Medicine at Mt. Sinai

description:
HMC16_CCGTCC_L005
processed data file: Table S2.xlsx, CeA expression_log2CPM.xls

data_processing:
Sequence reads were aligned to the rn4 genome using Tophat with parameters of “--no-novel-juncs –b2-very-sensitive”
QC assessment was done using the SPEctRA pipeline (https://github.com/shenlab-sinai/SPEctRA)
HtSeq was used to calculate gene read counts
Differential analysis was performed using Voom-Limma
Genome_build: rn4
Supplementary_files_format_and_content: The bedGraph files are the RNAseq data for the OFC aligned to the rn4  genome, showing normalized reads for each sample.
Supplementary_files_format_and_content: raw count files for the OFC dataset, and an excel spreadsheet of log2CPM for the CeA dataset.

organism: Rattus norvegicus

extract_protocol:
We took the rats directly from home cage and performed live decapitation. We obtained a 2-mm coronal section using a brain matrix (ASI Instruments), and punched CeA or OFC with a 14- or 12-gauge metal needle as shown in Fig.1c, respectively. We froze tissue punches in Eppendorf tubes on dry ice and stored tissue at -80 °C. For RNA isolation, we pooled tissue punches from two rats to reduce biological variability without increasing library number. Based on previous RNA-seq studies in micro-dissected brain tissue from rodents {Feng, 2014 #492;Bagot, 2017 #491;Bagot, 2016 #494}, we chose to use 3 to 4 independent biological replicates for each group. We isolated RNA using Trizol (Invitrogen) and purified RNA with RNeasy Micro columns (Qiagen). We confirmed the RNA purity by spectroscopy at 260/280 and 260/230>1.8.
We used Agilent 2100 Bioanalyzer (Agilent RNA 6000 Pico Kit, 5067-1511) to assess RNA integrity. We confirmed that the average of mRNA RIN (RNA integrity number) was above 8. We used total RNA (1 µg) for mRNA library construction following TruSeq RNA sample Pre Kit v2 protocol (Illumina). Briefly, we purified poly-A containing mRNA using Oligo(dT) magnetic beads. We fragmented mRNA using divalent cations under elevated temperature. Then we synthesized cDNA from poly-A containing and fragmented mRNA using random hexamer, followed by end-repair and ligation with sequencing adaptors. We selected the final library based on size and purified the library using AMPure XP beads (Beckman). We introduced barcode bases (6 bp) at one end of the adaptors during amplification steps. We used a Bioanalyzer to verify the library size and concentration before sequencing libraries on the Illumina HiSeq 2000 machine at Mount Sinai’s Genomic Core facility.

value: Sprague Dawley

value: Methamphetamine

value: brain

tag: brain region

value: Central Amygdala


title: CD8_WTd14_1

value: wild type

value: Trypanosoma cruzi


title: HCC1569_1percentO2

value: Basal A


title: HCC1569_20percentO2


title: Cp_1_60

value: 60 minutes


title: X7D_BC

tag: treatment

value: bFGF and CHIR99021


title: CD8_WTd0_1

value: spleen

tag: cell type

value: sorted CD8 T cell


title: Cp_1_30

value: 30 minutes


title: CeA.15.Day35.Meth

description:
HMC15_ATGTCA_L005
processed data file: Table S2.xlsx, CeA expression_log2CPM.xls


title: HCC1428_20percentO2

tag: cell line

value: Luminal


title: X5D_C


title: CeA.14.Day35.Meth

description:
HMC14_AGTTCC_L005
processed data file: Table S2.xlsx, CeA expression_log2CPM.xls


title: Cp_1_240

value: 240 minutes


title: Cp_1_15

value: 15 minutes


title: CeA.12.Day35.Sal

description:
HMC12_CTTGTA_L005
processed data file: Table S2.xlsx, CeA expression_log2CPM.xls

value: Saline


title: HBL100_20percentO2

value: Basal B


title: HCC1428_1percentO2


title: CeA.10.Day35.Sal

description:
HMC10_TAGCTT_L005
processed data file: Table S2.xlsx, CeA expression_log2CPM.xls

value: Sprague Dawley


title: X5D_BM

value: Mouse retinal progenitor cells


title: CeA.11.Day35.Sal

description:
HMC11_GGCTAC_L005
processed data file: Table S2.xlsx, CeA expression_log2CPM.xls

value: brain


title: HBL100_1percentO2


title: X3D_C


title: Cp_1_0

value: 0 minutes


title: DU4475_20percentO2

value: Unknown


title: CeA.8.Day2.Meth

description:
HMC8_ACTTGA_L004
processed data file: Table S2.xlsx, CeA expression_log2CPM.xls

value: Methamphetamine

value: Central Amygdala


title: Cp_1_120

value: 120 minutes


title: X5D_BC

value: bFGF and CHIR99021


title: X3D_BM


title: CeA.7.Day2.Meth

description:
HMC7_CAGATC_L004
processed data file: Table S2.xlsx, CeA expression_log2CPM.xls


title: Cg_3_30

data_processing:
RTA software version 1.18.64 were used for basecalling.
Read quality were checked with Fastqc. Reads were trimmed with trimmomatic version 0.32 and following parameters: SE threads 5 -phred33 FILE LEADING: 3 TRAILING: 3 SLIDINGWINDOW: 15:20 MINLEN 30
Trimmed reads were mapped to reference genome of Candida glabrata s02-m05-r02_features and of Homo sapiens GRCh38.77 using tophat2 with following parameters: -p 10 -g 1 --no-mixed --no-discordant --b2-very-sensitive --max-intron-length 100000 -o OUTDIR -G ANNOTATION INDEX FASTQFILE > OUTFILE
Mapped reads were counted using featureCounts version 1.4.5 and DeSeq2 were used for differential expression filtering.
Genome_build: GRCh38.77, CBS138_s02-m05-r02_features
Supplementary_files_format_and_content: Comma-delimited text files include counts for each gene per sample

organism:
Nakaseomyces glabratus
Homo sapiens

growth_protocol: Candida glabrata cells grew at 37°C in Homo sapiens whole blood.

treatment_protocol: Homo sapiens whole blood cells were treated with Candida glabrata CBS138 (ATCC 2001).

tag: c. glabrata strain


title: Cg_3_240


title: CAMA1_20percentO2


title: CAMA1_1percentO2


title: X3D_BC


title: X5D_B

value: bFGF


title: Cg_3_15


title: CeA.5.Day2.Meth

description:
HMC5_ACAGTG_L004
processed data file: Table S2.xlsx, CeA expression_log2CPM.xls


title: BT549_20percentO2


title: CeA.4.Day2.Sal

description:
HMC4_TGACCA_L004
processed data file: Table S2.xlsx, CeA expression_log2CPM.xls


title: X1D_C


title: X1D_B


title: CeA.1.Day2.Sal

description:
HMC1_ATCGACG_L003
processed data file: Table S2.xlsx, CeA expression_log2CPM.xls


title: X1D_BM


title: Cg_3_0


title: Cg_3_120


title: Cg_3_60

value: 60 minutes


title: X3D_B


title: BT549_1percentO2


title: CeA.3.Day2.Sal

description:
HMC3_TTAGGC_L004
processed data file: Table S2.xlsx, CeA expression_log2CPM.xls


title: Cg_2_60


title: X1D_BC


title: CeA.6.Day2.Meth

description:
HMC6_GCCAAT_L004
processed data file: Table S2.xlsx, CeA expression_log2CPM.xls


title: DU4475_1percentO2


title: BT474_1percentO2


title: OFC_short_sal_16

description:
OFC_short_sal_16_RNAseq_GATCAG_L004
processed data file: Table S2.xlsx

value: Orbitofrontal Cortex


title: OFC_short_sal_15

description:
OFC_short_sal_15_RNAseq_GATCAG_L003
processed data file: Table S2.xlsx


title: Cg_2_240


title: X0D


title: OFC_short_sal_13

description:
OFC_short_sal_13_RNAseq_GATCAG_L001
processed data file: Table S2.xlsx


title: rice_RSV.rep2 (sRNA-Seq)

city: Fuzhou

first: Liu

last: Renyi

state: Fujian Province

address: Shangxiadian Road 15, Fujian University of Agriculture and Forestry, Fuzhou, Fujian, P.R.China

institute: Fujian Agriculture and Forestry University

data_processing:
Illumina Casava1.7 software used for basecalling.
The adapter sequence was removed using cutadapt (v1.16) (Martin, 2011). Reads that are 18-30 nt in length and contain no ambiguous nucleotide (‘N’) were retained as clean reads, which were clustered into unique reads with an in-house python script.
For rice sRNAs datasets, clean reads were then mapped to the ncRNA reference (ftp://ftp.ensemblgenomes.org/pub/plants/release-31/fasta/oryza_sativa/ncrna/Oryza_sativa.IRGSP-1.0.31.ncrna.fa.gz) downloaded from ensemble database to remove reads mapped to known rice rRNA, tRNA, snRNAs using bowtie software (Langmead et al., 2009) with perfect match. For planthopper sRNAs datasets, cleans reads mapped to the rRNAs, tRNAs, snoRNAs, snRNAs resolved by our lab (Zhu et al., 2017) with perfect match were discarded.
The remaining sRNA reads were then mapped to the host genome (rice or planthopper genome, depending on the sample source) with perfect match or the RSV genome (MF287953-MF287956), allowing up to one mismatch. Only sRNAs reads with at least one mapping location were regarded as genuine sRNAs and retained for down-stream analyses
Genome_build: MSU7 for rice and in-house assmbly genome for planthopper (Zhu, J.J., Jiang, F., Wang, X.H., Yang, P.C., Bao, Y.Y., Zhao, W., Wang, W., Lu, H., Wang, Q.S., Cui, N., Li, J., Chen, X.F., Luo, L., Yu, J.T., Kang, L., and Cui, F. (2017). Genome sequence of the small brown planthopper, Laodelphax striatellus. Gigascience 6.)
Supplementary_files_format_and_content: Tab-delimited text file include RPM (Reads per Million) values

organism: Oryza sativa

source_name: Leaves

growth_protocol: The viruliferous and non-viruliferous small brown planthopper strains used in this work were derived from a rice field population in Hai'an, Jiangsu Province, China, and maintained in the laboratory for nearly nine years. The planthoppers were reared on 2 cm to 3 cm seedlings of rice (Oryza sativa Huangjinqing) in glass incubators, which were sealed with a nylon mesh, at 25 ± 1°C, 80% relative humidity, and 16 h of light per day. The planthoppers were transferred to fresh rice seedlings every 8 days to ensure sufficient nutrition.

extract_protocol:
Total RNA was isolated from rice plants or planthoppers by using the TRIzol Reagent (Invitrogen) according to manufacturer’s instructions. Approximately 100 mg rice leaves or 10 small brown planthoppers were ground in liquid nitrogen and mixed with 1 ml of TRIzol Reagent for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 4th instar nymphs of viruliferous planthoppers were transferred to fresh rice seedlings for RSV inoculation. After 24 h feeding, the planthoppers were removed and the inoculated seedlings were cultured at 25 ± 1°C with 16 h of light daily for 20 d until disease symptom appeared. Each rice seedling was fed by three viruliferous planthoppers, and three seedlings were used as a replicate. Meanwhile, healthy rice seedlings without inoculation were prepared and maintained at the same condition as the negative control. Leaves with typical disease symptoms from RSV-infected rice plants and leaves from healthy rice plants were collected at the same time and three biological replicates for each group were prepared for sequencing analysis

tag: infection

value: RSV

tag: treatment time

value: Leaves

tag: genome build


title: OFC_short_sal_14

description:
OFC_short_sal_14_RNAseq_GATCAG_L002
processed data file: Table S2.xlsx


title: Cg_2_15

tag: time point

value: 15 minutes


title: BT20_1percentO2

tag: breast cancer subtype

value: Basal A


title: rice_RSV.rep1 (sRNA-Seq)


title: BT474_20percentO2

value: Luminal

tag: o2 concentration (percent)


title: Cg_2_30

value: 30 minutes


title: Cg_2_120


title: BT20_20percentO2


title: rice_mock.rep2 (sRNA-Seq)

value: control


title: OFC_long_sal_12

description:
OFC_long_sal_12_RNAseq_ACTTGA_L004
processed data file: Table S2.xlsx

value: Sprague Dawley

value: Saline

value: brain


title: Cg_2_0

value: 0 minutes


title: OFC_long_sal_11

description:
OFC_long_sal_11_RNAseq_ACTTGA_L003
processed data file: Table S2.xlsx


title: rice_mock.rep1 (sRNA-Seq)


title: Cg_1_30


title: Cg_1_240

value: 240 minutes


title: OFC_long_sal_10

description:
OFC_long_sal_10_RNAseq_ACTTGA_L002
processed data file: Table S2.xlsx


title: OFC_long_sal_9

description:
OFC_long_sal_9_RNAseq_ACTTGA_L001
processed data file: Table S2.xlsx


title: esophageal squamous cell carcinoma_biological rep29

city: Guangzhou

first: Jing

last: Wen

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

hyb_protocol: 100 ng of Cy3-labelled RNA was hybridized using Agilent’s miRNA Complete Labeling and Hyb Kit (Agilent). Prepare hybridization samples by resuspending the dried Cy3-labelled samples in nuclease-free water, and adding proper amount of 10×GE Blocking Agent and 2× Hi-RPM Hybridization Buffer. Then the sample was hybridized to Agilent human miRNA microarrays based on miRBase (release 18.0) GeneChip for 20 hours at 55°C in a rotating hybridization oven set. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Scanner (G2505C) using one color scan setting for 8x15K array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel was set to Green and Green PMT was set as XDR Hi 100% and XDR Lo 5%).

data_processing: The microarray image information was converted in to spot intensity values using Feature Extraction Software version 10.7.3 (Agilent). The raw miRNA array data were imported into Genespring 12.0, and were log2-transformed and quantile normalized without baseline transformation.

source_name: tumor tissues from patient with esophageal squamous cell carcinoma

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from100 ng RNA using Agilent’s miRNA Complete Labeling and Hyb Kit (Agilent) according to the manufacturer's instructions. The labeled miRNA was purified using the Micro Bio-spin 6 colums and completely dried.

extract_protocol: Total RNA were isolated using mirVana miRNA Isolation Kit (Ambion) according to the manufacture's instruction.

treatment_protocol: Tissue specimens from each patients were snap frozen in liquid nitrogen and stored at -80℃ until RNA isolation.

value: tumor tissue

tag: disease state

value: esophageal squamous cell carcinoma

tag: age

tag: gender

value: Male

tag: tumor stage


title: Cg_1_120

value: 120 minutes


title: OFC_long_meth_8

description:
OFC_long_meth_8_RNAseq_TTAGGC_L004
processed data file: Table S2.xlsx

tag: strain

value: Methamphetamine

tag: tissue

value: Orbitofrontal Cortex


title: OFC_long_meth_6

description:
OFC_long_meth_6_RNAseq_TTAGGC_L002
processed data file: Table S2.xlsx

tag: brain region


title: esophageal squamous cell carcinoma_biological rep28


title: Cg_1_15


title: OFC_long_meth_5

description:
OFC_long_meth_5_RNAseq_TTAGGC_L001
processed data file: Table S2.xlsx

tag: treatment


title: esophageal squamous cell carcinoma_biological rep27


title: Ca_3_60

data_processing:
RTA software version 1.18.64 were used for basecalling.
Read quality were checked with Fastqc. Reads were trimmed with trimmomatic version 0.32 and following parameters: SE threads 5 -phred33 FILE LEADING: 3 TRAILING: 3 SLIDINGWINDOW: 15:20 MINLEN 30
Trimmed reads were mapped to reference genome of Candida albicans A22-s05-m04-r04_features and of Homo sapiens GRCh38.77 using tophat2 with following parameters: -p 10 -g 1 --no-mixed --no-discordant --b2-very-sensitive --max-intron-length 100000 -o OUTDIR -G ANNOTATION INDEX FASTQFILE > OUTFILE
Mapped reads were counted using featureCounts version 1.4.5 and DeSeq2 were used for differential expression filtering.
Genome_build: GRCh38.77, SC5314_A22-s05-m04-r04_features
Supplementary_files_format_and_content: Comma-delimited text files include counts for each gene per sample

organism:
Candida albicans
Homo sapiens

growth_protocol: Candida albicans cells grew at 37°C in Homo sapiens whole blood.

treatment_protocol: Homo sapiens whole blood cells were treated with Candida albicans SC5314.

tag: c. albicans strain

value: 60 minutes


title: OFC_long_meth_7

description:
OFC_long_7_RNAseq_TTAGGC_L003
processed data file: Table S2.xlsx


title: OFC_short_meth_4

description:
OFC_short_meth_4_RNAseq_ATCACG_L004
processed data file: Table S2.xlsx


title: Ca_3_30


title: Cg_1_0


title: esophageal squamous cell carcinoma_biological rep26


title: Cg_1_60


title: OFC_short_meth_3

description:
OFC_short_meth_3_RNAseq_ATCACG_L003
processed data file: Table S2.xlsx


title: Ca_3_240


title: esophageal squamous cell carcinoma_biological rep25


title: Ca_3_15

value: 15 minutes


title: esophageal squamous cell carcinoma_biological rep24


title: esophageal squamous cell carcinoma_biological rep23


title: LRDD_M3

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

data_processing:
Adaptors were trimmed
Alignment was performed using the STAR algorithm v2.4.1d
Unaligned reads were then aligned using Bowtie 2 v 2.1.0
Aligned reads from both alignment steps were then combined
Transcripts were then quantified using a modified version of the expectation-maximization (E/M) algorithm in the Partek Flow software
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with RPKM values for each sample. Data from all 12 samples are in one file

source_name: Mouse lung

extract_protocol:
RNA was isolated using the RNeasy kit from Qiagen according to the manufacturer's protocol. Purified RNA samples were then cleaned and resuspended in nuclease-free water. RNA quantity was measured using the Nanodrop 1000. Quality of RNA samples was quantitatively assessed by computation of RNA integrity numbers (RINs) using the Agilent RNA 6000 Pico kit (Agilent) following the manufacturer’s protocol.
Total RNA (~800ng) was ribosomal RNA (rRNA) depleted using the Low Input RiboMinus™ Eukaryote System v2 (Thermofisher) according to the manufacturer’s instructions. Samples were then vacuum concentrated and whole-transcriptome and barcoded libraries were prepared using the Ion Total RNA-Seq Kit v2 (Thermofisher) according to the manufacturer’s instructions. Size distribution of samples was assessed using the Agilent 2100 Bioanalyzer and 6000 RNA Pico kit. Library concentrations were quantified using the Agilent DNA 1000 assay and the 2100 Bioanalyzer according to the manufacturer’s instructions. Barcoded whole-transcriptome libraries were diluted to a 66 pM concentration and combined in equal volumes (13 µl each, 26 µl total) for sequencing with two samples per template preparation. All template reactions were performed on the Ion Chef Instrument using the Ion PI Hi-Q Chef kit (Thermofisher) according to the manufacturer’s instructions. Reactions were loaded onto Ion PI Chips v3 (Thermofisher) for sequencing on an Ion Proton sequencer according to the manufacturer’s protocol.

value: lung

tag: genotype

value: CC-LR/Stat3 knockout

tag: mouse

value: CC-LR/Stat3 knockout_male_3


title: Ca_3_120


title: esophageal squamous cell carcinoma_biological rep30


title: esophageal squamous cell carcinoma_biological rep21


title: esophageal squamous cell carcinoma_biological rep22


title: LRDD_M1

value: CC-LR/Stat3 knockout_male_1


title: Ca_2_30

value: 30 minutes


title: Ca_2_60


title: LRDD_M2

value: CC-LR/Stat3 knockout_male_2


title: Ca_3_0


title: esophageal squamous cell carcinoma_biological rep20


title: LRDD_F3

value: Female

value: CC-LR/Stat3 knockout_female_3


title: LRDD_F1

value: CC-LR/Stat3 knockout_female_1


title: Ca_2_240

value: 240 minutes


title: LRDD_F2

value: CC-LR/Stat3 knockout_female_2


title: OFC_short_meth_2

description:
OFC_short_meth_2_RNAseq_ATCACG_L002
processed data file: Table S2.xlsx

value: Sprague Dawley

value: brain


title: esophageal squamous cell carcinoma_biological rep17

value: tumor tissue

value: esophageal squamous cell carcinoma

value: Male


title: esophageal squamous cell carcinoma_biological rep19


title: Ca_2_15

value: 15 minutes


title: esophageal squamous cell carcinoma_biological rep18


title: CCLR_M3

value: lung

value: CC-LR


title: esophageal squamous cell carcinoma_biological rep15


title: Ca_2_120

value: 120 minutes


title: OFC_short_meth_1

description:
OFC_short_meth_1_RNAseq_ATCACG_L001
processed data file: Table S2.xlsx

value: Methamphetamine

value: Orbitofrontal Cortex


title: esophageal squamous cell carcinoma_biological rep16


title: esophageal squamous cell carcinoma_biological rep14


title: Ca_1_60

value: 60 minutes


title: CCLR_M2


title: CCLR_M1


title: Ca_1_30

value: 30 minutes


title: CCLR_F3

value: Female


title: CCLR_F2


title: esophageal squamous cell carcinoma_biological rep13


title: esophageal squamous cell carcinoma_biological rep12


title: Ca_1_15


title: CCLR_F1


title: Ca_1_120


title: Ca_1_0

value: 0 minutes


title: Ca_2_0


title: planthopper_RSV.rep3 (sRNA-Seq)

organism: Nilaparvata lugens

source_name: nymphs

tag: infection

value: RSV

value: nymphs

value: in house assembly


title: esophageal squamous cell carcinoma_biological rep10


title: esophageal squamous cell carcinoma_biological rep9


title: esophageal squamous cell carcinoma_biological rep11


title: planthopper_RSV.rep2 (sRNA-Seq)

tag: treatment time


title: planthopper_RSV.rep1 (sRNA-Seq)

tag: genome build


title: esophageal squamous cell carcinoma_biological rep8


title: planthopper_mock.rep3 (sRNA-Seq)

value: control


title: planthopper_mock.rep2 (sRNA-Seq)


title: esophageal squamous cell carcinoma_biological rep7

value: tumor tissue


title: esophageal squamous cell carcinoma_biological rep6

value: esophageal squamous cell carcinoma


title: Ca_1_240

tag: time point

value: 240 minutes


title: esophageal squamous cell carcinoma_biological rep5


title: Citrobacter rodentium ΔcpxP grown in DMEM to OD600 of 0.5-0.6, biological replicate 3

type: mixed

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

description: ΔcpxP

hyb_protocol: Hybridization was performed as previously described (Hovel-Miner, G 2009. JB, 191:2461).

scan_protocol: Scanning and image acquisition was performed on a InnoScan 710 using the mapix software. Spot intensity an local background was measured.

data_processing: Data were processed with the mapix software. Values from each channel were background substracted and the % contribution of each sopts to the total fluorsecence in each channel was calculated. Then the ratio Ch1/Ch2 was calculated. We used gDNA for data normalization accross slides.

label: Alexa Fluor 647

organism: Citrobacter rodentium

source_name: CpxP

label_protocol: RNA: 15 ug of Total RNA was labeled with amino-allyl dUTP during reverse transcriptase and subsequently coupled with the succinimidyl ester fluorescent dye AlexaFluor 546 as previously described (Hovel-Miner, G 2009. JB, 191:2461). Genomic DNA: 5 ug of genomic DNA was labeled with amino-allyl dUTP with klenow fragment and random hexamer as previously described (Porwollik, S. 2001. Mutat Res 483:1). Subsequently, the resulting DNA was coupled to the succinimidyl ester fluorescent dye AlexaFluor 647.

growth_protocol: DMEM to exponential phase (OD600 = 0.5-0.6).

extract_protocol: RNA: TRIzol reagent (Invitrogen), reverse-transcribed into cDNA. Genomic DNA: QIAamp kit (QIAgen).

treatment_protocol: No treatment

tag: genotype/variation

value: CpxP

tag: growth protocol

value: DMEM broth, 37°C shaking

label: Alexa Fluor 546

source_name: genomic DNA, reference channel

value: WT

value: LB broth, 37°C shaking


title: planthopper_mock.rep1 (sRNA-Seq)


title: esophageal squamous cell carcinoma_biological rep4

tag: disease state


title: planthopper_RSV.rep2 (RNA-Seq)

data_processing:
Illumina Casava1.7 software used for basecalling.
The quality of raw RNA sequencing reads was evaluated with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). To obtain clean reads, low quality regions and adapter sequences were removed using SolexQA (v2.2) (Cox et al., 2010) and cutadapt, respectively. Reads shorter than 25 bases were discarded
Clean reads were mapped to the host (rice or planthopper, depending on the sample source) genome sequence using HISAT2 (Kim et al., 2015).
Read counts of the annotated genes were summarized by HTSeq-count (Anders et al., 2015)
Genome_build: MSU7 for rice and in-house assmbly genome for planthopper (Zhu, J.J., Jiang, F., Wang, X.H., Yang, P.C., Bao, Y.Y., Zhao, W., Wang, W., Lu, H., Wang, Q.S., Cui, N., Li, J., Chen, X.F., Luo, L., Yu, J.T., Kang, L., and Cui, F. (2017). Genome sequence of the small brown planthopper, Laodelphax striatellus. Gigascience 6.)
Supplementary_files_format_and_content: Tab-delimited text file include RPM(Reads per Million) values


title: esophageal squamous cell carcinoma_biological rep1

tag: age

value: Male


title: esophageal squamous cell carcinoma_biological rep3

tag: gender


title: Col-0 WT TRAP 2

city: University Park

first: Hardik

last: Kundariya

state: PA

address: 361 N. Frear

institute: The Pennsylvania State University

data_processing:
Illumina for basecalling
Alignments were performed using RUM 2.0.4 (--min-length 70) (Grant et al., 2011) keeping only uniquely mapped reads
The read count data were generated from the SAM files by using QoRTs software package (Hartley and Mullikin, 2015) --stranded --minMAPQ 25 --dropChrom Pt,Mt
DESeq2 (Love, M.I., Huber, W., Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Genome Biology 15(12):550 2014) was used for gene count normalization and to identify differentially expressed genes (FDR < 0.05, |log2FC| > 0.5. GTF file TAIR10.31
Genome_build: TAIR 10
Supplementary_files_format_and_content: Text file with GENEID and COUNTS to be used with DESeq2

organism: Arabidopsis thaliana

growth_protocol: Seeds were sown on peat mix in square pots in reach-in chambers at 16hrs daylenght (22 °C, 120-150 μmol/(m^2*s) light)

extract_protocol:
total RNA from each sample was extracted by NucleoSpin RNA Plant kit (Macherey-Nagel, Germany) following manufacturer’s protocol, including genomic DNA removal.
RNA libraries were constructed as described in the TruSeq RNA Sample Preparation v2 Guide.
These libraries were sequenced with the 100-bp paired-end reads option, in Hi-Seq 4000 analyzer (Illumina, USA) at BGI-Tech (Shenzhen, China).

treatment_protocol: Two samples from each Col-0 wild type TRAP, msh1 TRAP, Col-0 Total, and msh1 Total. Floral stem tissue was used.

tag: replicate

value: biological rep 2

value: floral stem

value: wild type TRAP


title: esophageal squamous cell carcinoma_biological rep2

tag: tumor stage


title: Citrobacter rodentium ΔnlpE grown in DMEM to OD600 of 0.5-0.6, biological replicate 3

description: ΔnlpE

source_name: NlpE

value: NlpE

tag: strain


title: Citrobacter rodentium ΔcpxP grown in DMEM to OD600 of 0.5-0.6, biological replicate 1

description: ΔcpxP


title: Citrobacter rodentium ΔnlpE grown in DMEM to OD600 of 0.5-0.6, biological replicate 2

description: ΔnlpE


title: Col-0 WT TRAP 1

value: biological rep 1

tag: tissue


title: normal esophageal epithelia_biological rep9

source_name: normal esophageal epithelium from patient with esophageal squamous cell carcinoma

value: normal esophageal epithelium


title: planthopper_RSV.rep1 (RNA-Seq)

value: RSV

value: nymphs


title: planthopper_mock.rep3 (RNA-Seq)

value: control

value: in house assembly


title: Citrobacter rodentium ΔnlpE grown in DMEM to OD600 of 0.5-0.6, biological replicate 1

description: ΔnlpE


title: normal esophageal epithelia_biological rep10

value: esophageal squamous cell carcinoma


title: msh1 TRAP 2

value: msh1 TRAP


title: planthopper_mock.rep2 (RNA-Seq)


title: Citrobacter rodentium ΔcpxP grown in DMEM to OD600 of 0.5-0.6, biological replicate 2

description: ΔcpxP

value: CpxP


title: msh1 Total 2


title: planthopper_RSV.rep3 (RNA-Seq)


title: normal esophageal epithelia_biological rep8


title: normal esophageal epithelia_biological rep7

value: Female


title: AB4

city: Louisville

first: Daniel

last: Miller

state: KY

address: 570 South Preston Street, Baxter 1, Room 224

institute: University of Louisville

description:
ribo-depleted RNA
AB_vs_ABPG.txt

data_processing:
Raw Fastq data was processed using the SPARTA (1.0) pipeline. (BMC Bioinformatics, 2016, Volume 17, Number 1, Page 1,  Benjamin K. Johnson et al.)
Briefly, reads were trimmed to remove adaptors and low quality bases using Trimmomatic, and read quality was assessed by FastQC.  Reads were mapped to the references genomes with Bowtie, transcript abundance was determined using HTSeq, and differential gene expression was determined using edgeR.
Reference genomes and gtf files were downloaded from ensemble.
Genome_build: Gene annotation from http://csbl.bmb.uga.edu/DOOR/.  For Ab (NC_011585 and NC_011586) and Pg (NC_010729) were used for read alignment.
Supplementary_files_format_and_content: Tab-delimted text files, for PG_v_PGAB the RPKM adundance value for the 4 biological samples is shown along with the log2 fold change, p- and q- value. For AB_vs_ABPG the RPKM abundance values for each sample is shown along with the log2 fold change, the p-value and FDR.

organism: Acinetobacter baumannii

source_name: A. baumannii monotypic community

growth_protocol: P. gingivalis was grown in TSB broth supplemented with hemin and menadione under anaerobic conditions. A. baumannii was grown in BHI under aerobic conditions

extract_protocol:
Total RNA was isolated using the Qiagen RNAeasy kit according to manufacturers protocol
RNA libraries were prepared according to manufacturers protocols using the Ilumina Ribo-zero kit for rRNA depletion and the TruSeq kits

treatment_protocol: 1x10^9 cells of P. gingivalis and A. baumannii were washed two time in PBS and finally resuspended in 500 ul of PBS, pelleted by gentle centrifugation to force community  development, and incubated aerobically for 3 hrs

tag: strain(s)

tag: community

value: mono-typic


title: normal esophageal epithelia_biological rep6


title: Citrobacter rodentium ΔcpxRA grown in DMEM to OD600 of 0.5-0.6, biological replicate 1

description: ΔcpxRA

source_name: CpxRA

value: CpxRA

value: DMEM broth, 37°C shaking

tag: genotype

value: WT

value: LB broth, 37°C shaking


title: Citrobacter rodentium wild-type grown in DMEM to OD600 of 0.5-0.6, biological replicate 2

description: WT

source_name: WT


title: Citrobacter rodentium wild-type grown in DMEM to OD600 of 0.5-0.6, biological replicate 3

description: WT


title: Col-0 WT Total 2

value: biological rep 2

value: floral stem

value: wild type


title: Citrobacter rodentium ΔcpxRA grown in DMEM to OD600 of 0.5-0.6, biological replicate 2

description: ΔcpxRA


title: Citrobacter rodentium wild-type grown in DMEM to OD600 of 0.5-0.6, biological replicate 1

description: WT


title: drnB- 16h a sRNA

city: Uppsala

first: Erik

last: Holmqvist

state: Uppland

address: Husargatan 3, Box 596, Uppsala University, Dept. of Cell and Molecular Biology

country: Sweden

institute: Uppsala University

description:
drnB-16h-A
miRNA_counts.txt

data_processing:
Demultiplexing and conversion using CASAVA v1.8.2
Illumina small RNA adapter trimming using cutadapt (1.0) discarding reads <18nt after trimming
Alignment of poly(A) RNA-seq reads using TopHat v.2.0.8b.
Poly(A) RNA-seq read count performed with HTSeq-count v. 0.6.1p1 using gene annotations generated 06-03-2015 from ww.dictybase.org
Genome_build: D. discoideum (05-13-2009)
Supplementary_files_format_and_content: tab-delimited raw read count tables

organism: Dictyostelium discoideum AX2

source_name: 16h developed cells

growth_protocol: D. discoideum AX2 wild-type (wt) and drnB knock out (drnB-) cells were grown axenically in HL5 medium supplemented with 10 ml/mL Penicillin Streptomycin (ThermoFisher Scientific) at 22°C. For each development, approximately 5x10^7 cells were collected and washed twice with PDF buffer (20mM KCl, 5mM MgCl2, 20mM KPO4, pH at 6.2), resuspended in 500ul PDF buffer and spread on a nitrocellulose membrane (Millipore) followed by incubation at 22°C.

extract_protocol:
Total RNA was isolated from 1x10^8 cells using TRIzol (Thermo Scientific) according to the manufacturer's recommendation
poly(A)-enriched sample libraries were created using TruSeq RNA Library Prep Kit (Illumina). small RNA libraries (18-40nt) were prepared using TruSeq Small RNA Library Preparation Kit (Illumina).

value: drnB-

tag: background strain

tag: developmental stage

value: 16h developed cells


title: msh1 Total 1

value: biological rep 1


title: AB2

description:
ribo-depleted RNA
AB_vs_ABPG.txt


title: drnB- 0h b sRNA

description:
drnB-0h-B
miRNA_counts.txt

source_name: Vegetative growing cells

value: Vegetative growing cells


title: AB3

description:
ribo-depleted RNA
AB_vs_ABPG.txt


title: normal esophageal epithelia_biological rep5

value: normal esophageal epithelium

value: Male


title: Col-0 WT Total 1


title: drnB- 16h b sRNA

description:
drnB-16h-B
miRNA_counts.txt


title: AB1

description:
ribo-depleted RNA
AB_vs_ABPG.txt


title: msh1 TRAP 1

value: msh1 TRAP


title: PG4

description:
ribo-depleted RNA
PG_v_PGAB.txt

organism: Porphyromonas gingivalis

source_name: P. gingivalis monotypic community


title: drnB- 0h a sRNA

description:
drnB-0h-A
miRNA_counts.txt


title: normal esophageal epithelia_biological rep4

value: esophageal squamous cell carcinoma


title: planthopper_mock.rep1 (RNA-Seq)

tag: infection

value: control

tag: treatment time

value: nymphs

value: in house assembly


title: normal esophageal epithelia_biological rep3

value: Female


title: PG3

description:
ribo-depleted RNA
PG_v_PGAB.txt

value: mono-typic


title: blastocyst

city: Nanning

last: Chen

state: GuangXi

address: No. 100, East University Road

department: Animal Science and Technology

institute: Guangxi University

data_processing:
Illumina Hiseq Xten platform and paired-end reads were generated
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq Xten platform and paired-end reads were generated.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.

organism: Bubalus bubalis

source_name: blastocyst stage embryo

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: blastocyst


title: wt 16h b sRNA

description:
WT16h-B
miRNA_counts.txt

value: wt


title: normal esophageal epithelia_biological rep2


title: PG2

description:
ribo-depleted RNA
PG_v_PGAB.txt


title: wt 16h a sRNA

description:
WT16h-A
miRNA_counts.txt


title: normal esophageal epithelia_biological rep1


title: morula

source_name: morula stage embryo

value: morula


title: PG1

description:
ribo-depleted RNA
PG_v_PGAB.txt


title: 16cells

source_name: 16-cell stage embryo

value: 16 cells embryo


title: wt 0h b sRNA

description:
WT0h-B
miRNA_counts.txt


title: drnB- 16h b mRNA

description:
drnB-16h-B
mRNA_counts.txt

value: drnB-


title: 8cells

source_name: 8-cell stage embryo

value: 8 cells embryo


title: drnB- 16h a mRNA

description:
drnB-16h-A
mRNA_counts.txt

value: 16h developed cells


title: 4cells

source_name: 4-cell stage embryo

value: 4 cells embryo


title: 2cells

source_name: 2-cell stage embryo

value: 2 cells embryo


title: drnB- 0h b mRNA

description:
drnB-0h-B
mRNA_counts.txt

value: Vegetative growing cells


title: MII

source_name: mature oocyte

value: mature oocyte


title: drnB- 0h a mRNA

description:
drnB-0h-A
mRNA_counts.txt


title: GV

source_name: Immature oocyte

value: Immature oocyte


title: wt 16h b mRNA

description:
WT-16h-B
mRNA_counts.txt


title: wt 16h a mRNA

description:
WT-16h-A
mRNA_counts.txt


title: Citrobacter rodentium ΔcpxRA grown in DMEM to OD600 of 0.5-0.6, biological replicate 3

description: ΔcpxRA

value: CpxRA

value: DMEM broth, 37°C shaking

source_name: genomic DNA, reference channel

value: WT

value: LB broth, 37°C shaking


title: wt 0h b mRNA

description:
WT-0h-B
mRNA_counts.txt


title: wt 0h a mRNA

description:
WT-0h-A
mRNA_counts.txt


title: wt 0h a sRNA

description:
WT0h-A
miRNA_counts.txt


title: ABPG2

description:
ribo-depleted RNA
AB_vs_ABPG.txt

organism:
Acinetobacter baumannii
Porphyromonas gingivalis

source_name: A. baumannii and P. gingivalis heterotypic community

value: P. gingivalis 33277 and A. baumannii AB0057

value: hetero-typic


title: ABPG3

description:
ribo-depleted RNA
AB_vs_ABPG.txt


title: ABPG1

description:
ribo-depleted RNA
AB_vs_ABPG.txt


title: PGAB4

description:
ribo-depleted RNA
PG_v_PGAB.txt

source_name: P. gingivalis and A. baumannii heterotypic community


title: PGAB3

description:
ribo-depleted RNA
PG_v_PGAB.txt


title: ABPG4

description:
ribo-depleted RNA
AB_vs_ABPG.txt


title: PGAB2

description:
ribo-depleted RNA
PG_v_PGAB.txt


title: PGAB1

description:
ribo-depleted RNA
PG_v_PGAB.txt


title: benzo(a)pyrene, biological replicate 2

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

institute: Inserm U1085-Irset

description: Gene expression data from benzo(a)pyrene

hyb_protocol: Each RNA pools were hybridized to Human Clariom™ S GeneChip (ThermoFischer Scientific).

scan_protocol: Arrays were immediately scanned, and images were analyzed and rigorously quality controlled for hybridization artefacts.

data_processing: The resulting CEL files were processed using the oligo package available performed in R/Bioconductor (Gentleman et al., 2004). Data were then normalized and background corrected using the SCAN.UPC package (Piccolo et al., 2013) with the Brainarray custom CDF file for directly mapping Affymetrix probe to Entrez gene identifiers (hta20_Hs_ENTREZG version 22.0.0) (Dai et al., 2005).

organism: Homo sapiens

source_name: T lymphocytes

label_protocol: Total RNA was amplified and labelled using the Gene Chip™ WT PLUS Reagent Kit according to the manufacturer’s instructions (ThermoFischer Scientific).

growth_protocol: Peripheral blood mononuclear cells were isolated from blood donor buffy coats (written consent for the use of blood samples for the research protocol obtained according to the regulation for blood transfusion of the French blood organization Etablissement Français du Sang, Rennes (France)) by Ficoll (Thermofischer Scientific, Braunschweig, Germany) gradient centrifugation. After separation of monocytes by a 1-h adhesion step, T lymphocytes were purified from nonadherent cells by negative selection using Dynabeads® Untouched™ Human T Cells Kit (Thermofischer Scientific). T lymphocytes were cultured in RPMI medium (Eurobio, Les Ulis, France) supplemented with 20 IU/mL penicillin, 20 μg/mL streptomycin, and 10% decomplemented fetal calf serum (Thermofischer Scientific), and stimulated with Dynabeads® T-Expander beads coated with anti-CD3 and anti-CD28 antibodies (Thermofischer Scientific).

extract_protocol: Total RNA was isolated from T lymphocytes using the TRIzol method (Thermofischer Scientific) and then purified using a RNeasy Mini Kit with on-column RNAse-free DNAse digestion (Qiagen, Courtaboeuf, France), according to the manufacturer’s protocol.

treatment_protocol: Primary activated human T lymphocytes were treated with with 2 µM B[a]P (Sigma-Aldrich, St. Louis, MO, USA) for 48 h as previously reported (Liamin et al., 2017). B[a]P was used as stock solutions in dimethylsulfoxide (DMSO). The final concentration of DMSO in culture medium was always < 0.2% v/v and control cultures received vehicle containing the same dose of DMSO (CTR) as treated cultures.

tag: sample type

value: primary culture from blood donors


title: benzo(a)pyrene, biological replicate 4


title: infection WT 6hr

status: Public on Dec 25 2018

city: Suwon

first: Seungyeop

last: Lee

address: Seobu-ro 2066

department: School of Pharmacy

institute: Sungkyunkwan University

description: mice infected with 2x10^8 CFU of  S. pneumoniae

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Mus musculus

source_name: lung

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: lung

value: 2x10^8 CFU of  S. pneumoniae


title: Non infection WT group 0hr


title: benzo(a)pyrene, biological replicate 3


title: CTR (dimethylsulfoxide), biological replicate 4

description: Gene expression data from CTR


title: benzo(a)pyrene, biological replicate 1


title: CTR (dimethylsulfoxide), biological replicate 3

description: Gene expression data from CTR


title: CTR (dimethylsulfoxide), biological replicate 1

description: Gene expression data from CTR


title: CTR (dimethylsulfoxide), biological replicate 2

description: Gene expression data from CTR


title: infection activating 7days


title: infection activating 6hr


title: Non infection activating group 0hr


title: HDL_SRBIKO_13

city: Nashville

first: Ryan

last: Allen

state: TN

address: 2220 Pierce Ave

department: Medicine

institute: Vanderbilt University Medical Center

description:
Small RNA Seq-fastq, demultiplexed, NextFlex V3
processed data file:
ENV_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
Fungus_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
HMB_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
ex_rRNA_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
ex_tRNA_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
isomiR_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
miRNA_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
othersRNA_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
rRNA_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
snoRNA_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
snRNA_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
tRNA_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
bacteria_group1_pm_KCV_3018_77_78_79.category.count.txt
bacteria_group1_pm_KCV_3018_77_78_79.read.count.txt
bacteria_group2_pm_KCV_3018_77_78_79.category.count.txt
bacteria_group2_pm_KCV_3018_77_78_79.read.count.txt
fungus_group4_pm_KCV_3018_77_78_79.category.count.txt
fungus_group4_pm_KCV_3018_77_78_79.read.count.txt
KCV_3018_77_78_79.Category.Table.csv
rRNA_pm_KCV_3018_77_78_79.count.txt
tRNA_pm_KCV_3018_77_78_79.read.count.txt
tRNA_pm_KCV_3018_77_78_79.category.count.txt
tRNA_pm_KCV_3018_77_78_79.count.txt
miRBase_pm_KCV_3018_77_78_79.count.txt
miRBase_pm_KCV_3018_77_78_79.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.isomiR.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.NTA.base.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.NTA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.other.count.txt
smallRNA_1mm_KCV_3018_77_78_79.other.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.rRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.rRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snoRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snoRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.aminoacid.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.aminoacid.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.NTA.count.txt
rRNA_pm_KCV_3018_77_78_79.read.count.txt

data_processing:
Analysis Pipeline: TIGER
https://www.biorxiv.org/content/early/2018/01/23/246900
Step 1: Pre-processing
To assess raw data quality, FastQC was performed at the raw read level to check for base quality, total read counts, and adapter identification. Cutadapt was then used to trim 3’ adapters from processed reads (-a TGGAATTCTCGGGTGCCAAGG). Cutadapt was then used to remove the first and last 4 bases from the trimmed reads and all trimmed reads <16 nts in length were removed (-m 16 -u 4 -u -4). After trimming, read length distributions were plotted and FastQC was performed on trimmed reads to validate the efficiency of adapter trimming. To generate identical read files, trimmed reads in each sample were collapsed into non-redundant “identical” reads in FASTQ format and copy numbers were recorded for downstream analysis.
Step 2: Host-Genome Alignment (Mouse)
In the Host Genome & Database alignment module, bowtie (v1.1.2) was used to map reads to a costumed database with option (-a -m 100 --best - strata -v 1) which allows 1 mismatch (MM) and 100 multi-mapped loci, and only the best matches were recorded. The costumed database was constructed by the host genome and known sequences of host mature transcripts curated in specific library databases – tRNAs (http://gtrnadb.ucsc.edu/GtRNAdb2/) and rRNA (http://archive.broadinstitute.org/cancer/cga/rnaseqc_download). Counting and differential expression analysis of miRNAs, tDRs, rDRs, snDRs, snoDRs, and other miscellaneous sRNAs (miscRNA), including yDRs and lincDRs, were performed. All prepossessed quality reads were assigned to different classes of annotated sRNAs using distinct rules -- miRNA: 1 MM, ≥16nt, offset -2, -1, 0, 1, 2 and tDR, snDRs, snoDRs, yDRs, and miscRNAs: 1 MM, ≥16nt, overlap ≥0.9 overlap. Based on the extensive genomic coverage of lncRNAs and repetitive elements and conservation of rRNAs, the TIGER pipeline applies more stringent assignment rules for lncDRs and rDRs – perfect match, ≥20 nt, and ≥90% overlap with parent lncRNAs or rRNAs. Furthermore, reads assigned to lncDRs must only be aligned to lncRNA coordinates and not to any other loci in the genome. All reads ≥20 nts in length and not aligned to the costumed database were extracted and tested for alignment as non-host reads. Differential expression of tabulated read counts were performed by DEseq2.
Step 3: Non-Host Alignment Module
Non-host reads were then analyzed using the Non-Host Genome and Non-Host Library modules in parallel. In the Non-Host Genome module, reads were aligned in parallel to two collections of bacterial genomes: a human microbiome (HMB) collection and a hand-curated list of environmental bacteria observed during sequencing of human and mouse lipoproteins. Due to high conservation between bacterial genomes and multi-mapping issues, a different bowtie option (-a -m 1000 --best -strata -v 0) was used which allowed perfect match only and 1000 multi-mapped loci. Reads were aligned to the HMB, ENV, and fungal groups in parallel and, thus, the same reads could have been counted in multiple groups. The fraction of reads that align to both databases (HMB, ENV) and the reads that are unique to specific databases were plotted. Differential expression and high-end analyses, as described above, were performed at the genome level (total normalized read count for each genome) and at the individual read level. In parallel, non-host reads were also analyzed by the Non-Host Library (Gold) module where they were aligned to non-coding RNA databases with same bowtie option as non-host genome analysis. To identify possible non-host miRNAs (xenomiRs) in sRNA-seq datasets, all non-host reads were aligned perfectly to annotated miRNAs in miRBase (miRBase.org) and tabulated. Similarly, non-host reads were aligned to all tRNAs in the GtRNAdb database (GtRNAdb2). Extensive categorical analysis of parent non-host tRNAs were performed at the kingdom, genome (species), amino acid, anti-codon, and fragment (read) levels. All assigned non-host tDRs underwent differential expression analysis, high-end analysis, and data visualization, as described above. Non-host reads were also aligned to prokaryotic and eukaryotic rRNA transcripts in SILVA database (https://www.arb-silva.de). TIGER limits the analysis of non-host rDR to the kingdom level for counting, differential expression analysis and high- end analysis.
Genome_build: mm9
Supplementary_files_format_and_content:
Identical.fastq files are fastq files that contain all reads that survive processing (Step 1),
Count files are comma separated value spreadsheets that list all annotated features (.count.txt) or fragment reads (read.count.txt) or total categorical counts (category.count.txt) for associated with a given category
CSV files are outputs from differential expression analysis using DeSeq2 comparing Wild-type vs SRBIKO

growth_protocol: Conventional Housing

extract_protocol:
Plasma, basal bile, urine, and livers were collected from wild-type (WT) and SR-BI-deficient (B6;129S2-Scarb1tm1Kri/J, SR-BI KO) mice. Mice were anesthetized with urethane (1g/kg, i.p.). The common bile duct was ligated and the gall bladder cannulated to divert bile into collection tubes. Basal bile was collected for a period of 30 min. Mice were then exsanguinated, blood was collected from the abdominal aorta in EDTA coated tubes and placed on wet ice, and tissues were dissected and snap frozen in liquid nitrogen. Plasma and tissues were stored at -80oC prior to analysis.  All animal procedures were completed under active and approved IACUC protocols. To separate HDL and apolipoprotein B (APOB)-containing lipoproteins from mouse plasma, 200 µL of 0.22-µm filtered-plasma samples were diluted to 500 µL in size-exclusion chromatography (SEC) running buffer (10 mM Tris-HCl, 0.15 M NaCl, 0.2% NaN3) and injected an ÄKTA SEC system (GE Healthcare) with three in-series Superdex-200 Increase gel filtration columns (10/300 GL; GE Healthcare). Samples were applied to the column with a flow rate of 0.3 mL/min at room temperature and eluate collected as 72 x 1.5 mL fractions using a F9-C 96-well plate fraction collector (GE Healthcare). Each fraction was analyzed for total protein (BCA; Pierce), total cholesterol (Raichem), and triglycerides (Raichem) to identify fractions corresponding with HDL and APOB particles. Due to the SEC set-up, we were not able to separate VLDL from LDL particles, and thus, we collected fractions covering both lipoprotein classes, referred to here as APOB. Fractions corresponding with each lipoprotein group were pooled, concentrated with Amicon Ultra-4 10 kDa centrifugal filters (Millipore) to <200 µL volume, and protein concentrations were quantified by BCA assays (Pierce). Based on the distribution of total cholesterol, triglycerides, and protein, fractions corresponding to HDL and APOB were collected, pooled, and concentrated. To differentiate lipoprotein sRNA signatures from liver and biofluids, and determine the impact of SR-BI-deficiency, samples were collected from Scarb1-/- (SR-BI KO) and wild-type (WT) mice. Total RNA was extracted from HDL (WT N=7, SR-BI KO N=7) and APOB (WT N=7, SR-BI KO N=7) particles, as well as livers (WT N=7, SR-BI KO N=7), bile (WT N=7, SR-BI KO N=6), and urine (WT N=5, SR-BI KO N=6). RNA was isolated from equal inputs of either bile (volume), liver (mg), HDL (protein) or APOB (protein) using miRNAEasy Mini kits (Qiagen). Specifically, 30 µL of primary bile, 120 μg of APOB, 180 μg of HDL or 20 mg of liver were added to 1 mL of Qiazol. Livers were homogenized in Qiazol with High-Impact Zirconium beads using a Bead Bug Homogenizer (Benchmark Scientific).  After removal of beads, subsequent steps for liver RNA extraction were followed according to manufacturer’s protocol. Bile, APOB and HDL RNA isolations were processed according to manufacturer’s protocol, except that after addition of ethanol, samples were incubated at -80oC overnight before application to isolation columns, and were eluted with a volume of 50 μL. Liver RNA samples were quantified by Take3 plates (BioTek).
NEXTflex Small RNA Library Preparation Kits v3 for Illumina® Platforms (BioO Scientific) were used to generate cDNA libraries for sRNA-seq. Briefly, 1 µg of liver total RNA was used as input for adapter ligation, as per manufacturer’s protocol. For bile, APOB and HDL RNA, 10.5 μL (21%) of the RNA isolation eluate was used as input for adapter ligation. Library generation was performed according to manufacturer’s protocol (BioO Scientific) with a modification to the amplification step, as liver libraries received 18 cycles and bile, APOB and HDL libraries received 25 cycles. After amplification, samples were size-selected using a Pippin-Prep (Sage Science) -- set for a range of 135-200 nts in length -- and subsequently purified and concentrated using DNA Clean and Concentrator 5 kit (Zymo). Individual libraries were then screened for quality by High-Sensitivity DNA chips using a 2100 Bioanalyzer (Agilent) and quantified using High-Sensitivity DNA assays with Qubit (Life Technologies). Equal concentrations of all individual libraries were pooled for multiplex sequencing runs, and concentrated using DNA Clean and Concentrator 5 kit (Zymo). For rigor in down-stream comparisons, all 66 sequencing libraries were randomized and run independently on three individual sequencing lanes. Single-end sequencing (75 cycles) of multiplexed libraries were performed on an Illumina NextSEQ 500 at the Vanderbilt Technologies for Advanced Genomics (VANTAGE) core laboratory. Each library was sequenced at an average depth of 16.28 million reads/sample.

tag: strain background

tag: genotype/variation

value: SRBIKO; Srbi-/-

tag: animal id#

value: HDL

tag: barcode


title: infection WT 7days


title: HDL_WT_12