title: ATAC-Seq in Sox2 KO Mouse E16 Stomach

description: ATAC-Seq in Sox2 KO Mouse E16 Stomach

data_processing:
After removing adaptors by Cutadapt, pair-end ATAC-Seq reads were aligned to mouse reference genome (GRCm38) using Bowtie2 with parameter “-X 2000”. ATAC-Seq peaks were then called by MACS2 -callpeak with parameters “--keep-dup=1” and “--SPMR”. ENCODE mm10 blacklist regions (https://www.encodeproject.org/annotations/ENCSR636HFF/) were excluded from the called peaks for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated txt files containing ATAC-Seq peak regions.

extract_protocol:
For E13.5 mouse experiments, ShhCre; R26YFP/+ embryos were used for downstream high-throughput experiments. After dissection, the stomach and intestinal organs were isolated, separated, washed in cold PBS and digested in 4ml of a 3:1 solution of Trypsin LE: 1x PBS at 37˚C. After 10 minutes, tissue was vigorously pipetted, until the organs broke down into a single cell suspension, which was confirmed using brightfield microscopy. The enzymatic reaction was then inhibited with 10% FBS. After washing cells in cold PBS, the single cells were re-suspended in 400µl of 1:5000 Sytox Blue (ThermoFisher Scientific, S34857) in cold 1x PBS, filtered through a 30µm mesh and submitted for sorting. Sorted cells were washed again and processed for ATAC-seq (50,000 cells from 3-4 YFP+ embryos) using the previously published protocol (44).    For E16.5 experiments, whole organ digestion using Trypsin was detrimental to epithelial cell viability; thus, an alternative isolation approach was employed. Given strict cell numbers are required for ATAC-seq, gut epithelium was isolated from ShhCre;R26YFP/+ embryos prior to single cell dissociation. In more detail, the E16.5 embryonic stomach, the proximal small intestine and the colon were dissected and opened longitudinally using a 0.5 cm tungsten needle. The forestomach was separated from the hindstomach along the squamous-glandular border under a dissecting microscope, and incubated in Dispase solution for 15 minutes at 37˚C. Following, the epithelial layer was manually separated from the mesenchyme and flash frozen for RNA isolation or collagenase digested for sorting. The hindstomach, proximal small intestine and colon were incubated in 10mM EDTA, 5mM EDTA and 5mM EDTA in 1x PBS, respectively, for 30-40 minutes at 4˚C on a shaker. Tissues were then moved to fresh 1x PBS and shaken vigorously for 2-3 minutes, or until epithelial glands/villi/crypts were observed in suspension. Isolated epithelial cells were immediately frozen and RNA isolation was conducted using an RNA isolation kit (Qiagen, Cat No. 74104). To prepare for sorting for ATAC-seq experiments, the fresh epithelial pellets of the forestomach, hindstomach, intestine and colon were then digested in collagenase-based solution for 20 mins at 37˚C. The resulting single cell suspension was washed in cold 1x PBS, re-suspended in 500µl of 1:5000 Sytox Blue and submitted for sorting. Sorted cells were then used for ATAC-seq using the same protocol as mentioned above.
Nextera DNA Flex Library Prep Kit


title: 4-V-16-4-6 [MS_238]

status: Public on Dec 31 2019

type: SRA

city: Fort Pierce

first: Joshua

last: Voss

state: FL

address: 5600 N US Highway 1

country: USA

institute: Florida Atlantic University at Harbor Branch Oceanographic Institute

library_source: transcriptomic

data_processing:
Data processing was completed using the analysis pipeline available on GitHub:
https://github.com/mstudiva/tagseq-modified-scripts
Genome_build: concatenated M. cavernosa (https://github.com/mstudiva/Mcav-Annotated-Transcriptome.git) and Symbiodinium Clade C (ftp://marchanon:anon@rc-ns-ftp.its.unc.edu/CladeC_Symbiodinium_transcriptome.zip) transcriptomes
Supplementary_files_format_and_content: tab-delimited text file containing gene counts per sample and isogroup annotations

molecule: total RNA

organism: Montastraea cavernosa

tag: site

value: WFGB

tag: depth

value: mesophotic


title: E_air_2

city: Biberach

first: Karsten

last: Quast

address: Birkendorfer Str. 65

department: Computational Biology

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

data_processing:
Sequenced read quality was checked with FastQC v0.11.2
RNA-Seq reads from all samples were aligned to the genome using the STAR Aligner v2.5.2a11
Duplication rates of the RNA-Seq samples were computed with bamUtil v1.0.11 to mark duplicate reads and the dupRadar v1.4 Bioconductor R package for assessment
The gene expression profiles were quantified using Cufflinks software version 2.2.1 to get the Reads Per Kilobase of transcript per Million mapped reads (RPKM) as well as read counts from the feature counts software package
Genome_build: ensembl70
Supplementary_files_format_and_content: tab-delimited text file contains RPKM values for each sample

organism: Homo sapiens

source_name: Air Liquid Interface culture

growth_protocol: Human Small Airway Epithelial Cells (SAEC, CC-2547, Lonza, Basel, Switzerland) were thawed and approximately one million cells were seeded into a T175 cell culture flask with 50 ml pre-warmed PneumaCult™-Ex Plus Medium (Stemcell Technologies, Vancouver, Canada). On the following day, the medium was exchanged, to remove residuals from the cryoprotectant cocktail. On the fourth day after seeding, the cells were sufficiently confluent (max. 80 %) to be harvested for seeding onto transwell inserts. The Transwells (#3460, Corning Life Sciences B.V., Amsterdam, the Netherlands) were coated with 300 µl rat tail collagen type 1 solution (Corning Life Sciences B.V., Amsterdam, the Netherlands, 30µg/ml in phosphate buffered saline) for 45 minutes at 37 °C. Collagen solution was aspirated and transwell inserts were washed with phosphate buffered saline. The basolateral compartments of the transwells were filled with 1.5 ml PneumaCult™-Ex Plus Medium. Dissociation of SAEC was performed using the Animal Component-Free Cell Dissociation Kit (Stemcell Technologies, Vancouver, Canada) according to the manufacturer’s instructions. Subsequently, 100.000 cells per insert were seeded in 300 µl on the transwell membrane. On the following day, apical and basolateral media was exchanged using PneumaCult™-Ex Plus Medium. On day three after the transfer to transwell inserts, when the cells were fully confluent, the apical and basolateral medium was removed and 1.5 ml Pneumacult-ALI-S Medium (Stemcell Technologies, Vancouver, Canada) was added basolaterally. The apical compartment was washed with phosphate buffered saline to remove residual growth factors of the media. The cells were from then on grown in air-liquid interface (day 0). Medium exchanges were performed three times a week. The cells were fully differentiated 28 days post air-lift.   As stated by Lonza, the cells were isolated from donated human tissue after obtaining permission for their use in research applications by informed consent or legal authorization.

extract_protocol:
Total RNAs were individually extracted using the Ambion Magmax™-96 total RNA isolation kit (Life Sciences) according to the manufacturer’s instructions. Briefly, 5 mg of tissue was placed in the lysis solution and homogenised in Qiagen Tissuelyzer™ for a period of 30 sec. Nucleic acids were captured onto magnetic beads, washed and treated with DNase. Total RNA was then eluted in 50 μl elution buffer. RNA quality and concentration was measured using an RNA Pico chip on an Agilent Bioanalyzer.
The Sequencing library preparation has been done using 200 ng of total RNA input with the TrueSeq RNA Sample Prep Kit v2-Set B (RS-122-2002, Illumina Inc, San Diego, CA) producing a 275bp fragment including adapters in average size. Libraries have  been clustered on the cBot Instrument from Illumina using the TruSeq SR Cluster Kit v3 - cBot - HS(GD-401-3001, Illumina Inc, San Diego, CA)  sequencing was then performed on an Illumina HiSeq3000 instrument

treatment_protocol: SAECs were exposed to whole cigarette smoke of K3R4F reference cigarettes (University of Kentucky, Lexington, KY, USA) using an automated cigarette smoking machine (In-Expose smoking robot, Scireq Montreal, QC, Canada) and the P.R.I.T. (Professional In-Vitro Technologies) ExpoCube in the experimental setup developed by Fraunhofer Institute for Toxicology and Experimental Medicine. Four cigarettes were smoked in parallel in compliance to ISO 3308, drawing every 15 seconds a puff from the sequentially smoked cigarettes (9 puffs per cigarette). The smoke was diluted with ambient air (dilution rate: 0.5 l/min). The cells were exposed to CS three times a week during the differentiation phase (28 days) beginning on day 0 (= day of air-lift). Readouts were performed 24 hours post last exposure.

tag: donor

tag: lonza id

tag: disease state

value: COPD

tag: age

tag: Sex

value: F

tag: ethnicity

value: Caucasian

tag: smoker

value: Y

tag: treatment

value: air

tag: cigarettes per treatment

tag: dilution rate (l/min)

tag: number of treatments a week

tag: cell type

value: Small Airway Epithelial Cells (SAECs)


title: BA10_AUD_rep8

type: genomic

city: Chicago

first: Subhash

middle: C

last: Pandey

state: IL

address: 1601 West Taylor Street

department: Psychiatry

institute: University of Illinois at Chicago & Jesse Brown VA Medical Center

description:
8A
A.8

hyb_protocol: DNA was bisulfite converted (EZ DNA methylation kit, Zymo Research, Irvine, CA) then amplified, fragmented and hybridised to Illumina Infinium® MethylationEPICBeadChip  using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan Reader using standard recommended Illumina scanner setting

data_processing:
R (v 3.4.3) and the minfi package (v 1.22.1) were used to read the idat files and compute methylated,  unmethylated, detection p-values, and normalized beta values per probe
Unmethylated and methylated signal intensities (methValues.txt)

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol, taking place after hybridization

extract_protocol: DNA was extracted using QIAamp® DNA Mini Kit (Qiagen, Valencia, CA)

tag: group

value: AUD

tag: tissue

value: brain, prefrontal cortex BA10

value: male

tag: postmortem interval (h)

tag: total drinking years

tag: etoh daily use (g)

tag: drinks per week

tag: cigarette packs per year

tag: age of drinking onset


title: ATAC-Seq in Mouse E16 Intestine

city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

country: Canada

institute: UNIV HEALTH NETWORK

description: ATAC-Seq in Mouse E16 Intestine

library_source: genomic

organism: Mus musculus

source_name: Mouse E16 embryonic tissue

growth_protocol: All animal husbandry was conducted in adherence to the standards proposed by the Canadian Council on Animal care and approved by the institutional animal care committees, The Centre for Phenogenomics, Toronto.

treatment_protocol: No treatment

tag: age


title: BA10_AUD_rep10

description:
10A
A.10

tag: Sex


title: 26-X-14-1-6 [MS_236]

tag: site

value: EFGB

tag: depth

value: shallow


title: BA10_AUD_rep15

description:
15A
A.15


title: E_CS_3

tag: donor

tag: lonza id

tag: disease state

tag: ethnicity

tag: smoker

tag: treatment

value: CS


title: E_air_1

tag: cigarettes per treatment

tag: dilution rate (l/min)

tag: number of treatments a week

tag: cell type


title: ATAC-Seq in Mouse E16 Forestomach

description: ATAC-Seq in Mouse E16 Forestomach


title: E_CS_2


title: ATAC-Seq in Mouse E16 Colon

description: ATAC-Seq in Mouse E16 Colon


title: 25-X-14-2-4 [MS_235]


title: BA10_AUD_rep11

description:
11A
A.11

tag: group

tag: tissue

tag: postmortem interval (h)

tag: total drinking years

tag: etoh daily use (g)

tag: drinks per week


title: EB 3001 [MS_234]

tag: site

tag: depth


title: F_CS_1

tag: donor

tag: lonza id

tag: age

tag: Sex

value: Black


title: ATAC-Seq in Mouse E13 Stomach

description: ATAC-Seq in Mouse E13 Stomach

source_name: Mouse E13 embryonic tissue


title: E_CS_1

tag: disease state

tag: ethnicity

tag: smoker

tag: treatment


title: BA10_AUD_rep1

description:
1A
A.1

value: female

tag: cigarette packs per year

tag: age of drinking onset


title: BA10_AUD_rep14

description:
14A
A.14

tag: group

tag: tissue


title: 25-X-14-2-2 [MS_233]


title: ATAC-Seq in Mouse E16 Hindstomach

description: ATAC-Seq in Mouse E16 Hindstomach


title: EB 60 [MS_232]


title: D_air_3

tag: cigarettes per treatment

tag: dilution rate (l/min)

tag: number of treatments a week

tag: cell type


title: BA10_control_rep24

description:
24C
C.24

value: control

tag: postmortem interval (h)

tag: total drinking years

tag: etoh daily use (g)

tag: drinks per week


title: 5-V-16-1-3 [MS_231]

tag: site

value: WFGB

tag: depth


title: D_air_2

tag: donor

tag: lonza id

tag: disease state

tag: age

tag: Sex

tag: ethnicity


title: D_air_1

tag: smoker

tag: treatment


title: D_CS_3

tag: cigarettes per treatment

tag: dilution rate (l/min)


title: 26-IX-16-4-2-118 [MS_237]

tag: time

value: twelve


title: 25-X-14-3-4 [MS_229]


title: D_CS_2

value: COPD

tag: number of treatments a week

tag: cell type


title: D_CS_1

value: F


title: C_air_3

value: healthy

value: M

value: Caucasian

value: N


title: BA10_AUD_rep2

description:
2A
A.2

tag: group

value: AUD

tag: tissue

tag: postmortem interval (h)

tag: total drinking years

tag: etoh daily use (g)

tag: cigarette packs per year

tag: age of drinking onset


title: BA10_control_rep23

description:
23C
C.23

value: brain, prefrontal cortex BA10

tag: drinks per week


title: BA10_AUD_rep5

description:
5A
A.5

tag: Sex


title: WB 121 [MS_227]

tag: site

tag: depth


title: 5-V-16-2-2-54 [MS_226]

value: transplant

value: six


title: 25-X-14-3-5 [MS_225]

value: shallow


title: BA10_control_rep25

description:
25C
C.25

value: male


title: C_air_2

tag: donor

tag: lonza id

tag: disease state

tag: age

tag: ethnicity

tag: smoker

tag: treatment

value: air

value: Small Airway Epithelial Cells (SAECs)


title: C_air_1

tag: cigarettes per treatment

tag: dilution rate (l/min)

tag: number of treatments a week

tag: cell type


title: YN14_248_RheMac_NeuN

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description: Protocol 1

data_processing:
Single-end reads were aligned with STAR 2.5.2b using options "“--outFilterMultimapNmax 10 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 3 --twopassMode Basic" to the reference sequence (hg19, PanTro5, RheMac8 from UCSC)
Crossmap and Liftover tools were used to translate non-human priamte coordinates into human coordinates. Human reference was used for gene annotation and counting (gencode v19). Uniquely mapped reads were quantified using HTSeq python suite using high-scored orthologs' protein coding genes by exons.
Genome_build: Human hg19, Chimpanzee PanTro5, Rhesus Macaque RheMac8
Supplementary_files_format_and_content: tab separated files with raw counts

organism: Macaca mulatta

source_name: brain

extract_protocol:
nuclear extraction protocol: Tissue isolated from Brodmann Area 46 from 27 healthy humans, 11 healthy chimpanzee and 15 healthy rhesus macaque.700 mg of frozen postmortem brain was homogenized with lysis buffer using a dounce homogenizer. Brain lysate was placed on a sucrose solution to create a concentration gradient. Ultracentrifuge was used to separate nuclei and cytoplasmic fraction.
FANS protocol: Nuclei were resuspended in PBS plus RNase inhibitors and incubated with mouse Alexa488 conjugated anti-NeuN (1:200) (#MAB377X, Millipore, Billerica, MA) and rabbit Alexa555 conjugated anti-OLIG2 (1:75) (#AB9610-AF555, Millipore) antibodies with 0.5% BSA. Immuno-labeled nuclei were collected as NeuN-positive or OLIG2-positive populations by fluorescence-activated cell sorting (FACS).
total RNA extraction protocol: Total RNA were purified from each nuclei population using a ZR-Duet DNA/RNA MiniPrep (Plus) kit according to the manufacturer's instruction. 200 ng total RNA from each sample was treated for ribosomal RNA (rRNA) removal using the Low Input RiboMinus Eukaryote System v2 (#A15027, ThermoFisher) according to the manufacturer's instruction.
Total RNAs with an average RIN value of 7.5±0.16 were used for RNA-seq library preparation. 50 ng of total RNA after rRNA removal was subjected to fragmentation, first and second strand syntheses, and clean up by EpiNext beads (#P1063, EpiGentek, Farmingdale, NY). Second strand cDNA was adenylated, ligated and cleaned up twice by EpiNext beads. cDNA libraries were amplified by PCR, and cleaned up twice by EpiNext beads. cDNA library quality was quantified by a 2100 Bioanalyzer using an Agilent High Sensitivity DNA Kit (#5067-4626, Agilent, Santa Clara, CA). Barcoded libraries were pooled and underwent 75 bp single-end sequencing on an Illumina NextSeq 500.

tag: tissue

value: brain

tag: nuclei

value: NeuN

tag: tissue preparation

value: Frozen Brain Tissue

tag: region

value: Brodmann Area 46

tag: sample id

tag: gender

tag: humanized age

tag: hemisphere

value: R

tag: pmi

tag: rin


title: 4-V-16-1-11-189 [MS_228]

tag: site

value: EFGB

tag: depth

tag: time


title: BA10_control_rep22

description:
22C
C.22

tag: group

value: control

tag: Sex

tag: postmortem interval (h)

tag: total drinking years

tag: etoh daily use (g)

tag: drinks per week

tag: cigarette packs per year

tag: age of drinking onset


title: BA10_control_rep21

description:
21C
C.21

tag: tissue


title: YN12_654_RheMac_Olig2

description: Protocol 1

tag: nuclei

tag: tissue preparation

tag: region

tag: sample id

tag: gender

value: F

tag: age


title: PBS_rep3

city: Irvine

first: Marian

middle: L.

last: Waterman

state: CA

address: Rm B251 Medical Sciences I, School of Medicine

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

data_processing:
Adapter sequences and low quality base pairs from the 5’ and 3’ ends of the paired-ends reads were trimmed using Trimmomatic v. 0.35 (Bolger et al, 2014) using the following parameters: “PE read1.fastq read2.fastq pe_read1.fastq.gz se_read1.fastq.gz pe_read2.fastq.gz se_read2.fastq.gz ILLUMINACLIP:NexteraPE-PE.fa:2:30:8:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:17 MINLEN:30”.
Reads from the host (mouse) and the graft (human) were classified and separated using Xenome (Conway et al, 2012).
Reads for each sample were mapped to the reference transcriptome (GENCODE v. 28 for human and v. M18 for mouse) using Bowtie v. 1.2 (Langmead et al, 2009) with the following parameters: “-X 2000 -a -m 200 -S --seedlen 25 -n 2 -v 3”.
Gene expression levels and read counts were obtained using RSEM v. 1.2.31 (Li & Dewey, 2011).
Genome_build: hg38
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM values of host (mouse) and graft (human).

source_name: Mock xenograft (PBS-injected mouse caecum)

growth_protocol: Cell lines were cultured in Dulbecco’s Modification of Eagle’s Medium (DMEM, Hyclone) or RPMI-1640 (Hyclone) supplemented with 10% Fetal Bovine Serum (Atlas Biologicals), 1% Penicillin/Streptomycin (Mediatech), and 2mM Glutamine (Mediatech).

extract_protocol:
Mouse caecums were excised and rinsed with PBS prior to flash freezing in liquid nitrogen. Tissue was fragmented using a mortar and pestle, and approximately 1 mg tissue was collected into Precellys (Bertin) tubes with TRIzol. Following tissue homogenization, RNA was extracted from cells using TRIzol (Invitrogen) and DirectZol RNA Extraction Kit following the manufacturer’s instructions (Zymo Research). RNA quality was checked with Agilent Bioanalyzer. Samples with RNA Integrity Number (RIN) scores ≥ 9 were used for RNA-seq library construction.
RNA-seq libraries were built using the Smart-seq2 protocol (Picelli et al, 2014) with modifications according to (Serra et al, 2018).

treatment_protocol: dnLEF1 cell lines were prepared as previously described (Pate et al, 2014). LRP6 knockout (LRP6KO) cell lines were created by co-transfecting cell lines with 3 μg LRP6 CRISPR and 300 ng eGFP-Puro using BioT transfection reagent (Bioland Scientific, B01). After selection with Puromycin, cells were sorted for LRP6 knockdown using flow cytometry (anti-human LRP6-APC, R&D Systems MAB1505). Immuno-deficient NSG mice (Jackson labs) were anaesthetized with 300μl of 100mg/kg ketamine/10mg/kg xylazine. The surgical site was shaved and cleaned with ethanol. After an incision was made, the caecum was drawn out and washed with sterile PBS. Cells (5*10^5) were injected in the caecum wall at six to eight sites using a Hamilton syringe (Hamilton 80301), three to four injections per side. The peritoneal wall and skin were sutured separately, the former with resorbable sutures, the latter with nylon. 5mg/kg carprofen was injected as an analgesic. Mice health was monitored for 28 days prior to harvest.

value: caecum

tag: transduction

value: Mock (PBS injection)


title: WB 176 [MS_230]

tag: site

value: WFGB

tag: depth

value: mesophotic


title: WB 2001 [MS_223]


title: C_CS_3

tag: donor

tag: lonza id

tag: disease state

value: healthy

tag: Sex

value: M

tag: ethnicity

value: Caucasian

tag: smoker

value: N

tag: treatment

value: CS

tag: cigarettes per treatment

tag: dilution rate (l/min)

tag: number of treatments a week

tag: cell type


title: C_CS_2

value: Small Airway Epithelial Cells (SAECs)


title: PBS_rep2

tag: tissue


title: YN12_654_RheMac_NeuN

description: Protocol 1

value: brain

tag: nuclei

value: NeuN

tag: tissue preparation

tag: region

tag: sample id

tag: gender

tag: humanized age

tag: hemisphere

tag: pmi

tag: rin


title: ATAC-Seq in Mouse E13 Intestine

description: ATAC-Seq in Mouse E13 Intestine

tag: age


title: 26-X-14-3-7 [MS_222]

tag: site

tag: depth

value: shallow


title: 25-X-14-2-7 [MS_221]


title: PBS_rep1

tag: transduction


title: YN12_409_RheMac_NeuN

description: Protocol 1

value: Frozen Brain Tissue

value: Brodmann Area 46

value: R


title: ATAC_Mono_STAT1-KO_BM_Toxo

city: Gosselies

first: Stanislas

last: Goriely

address: Rue Adrienne Bolland 8

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Reads were aligned to mm10 by Bowtie2
Reads with quality lesser than 1 (=mapping to multiple locations and/or insufficient mapping quality) were filtered out with samtools view
Reads in ENCODE blacklist were removed with bedtools intersect
Reads mapping in chrM were removed with a custom script and samtools view
Duplicate reads were filtered out using MarkDuplicate tool from Picard suite
Peak calling was performed with MACS2 callpeak, using standard parameters for paired-end reads and q-value threshold=0.05
Genome_build: mm10
Supplementary_files_format_and_content: Bed: peaks ; bigwig: signal

source_name: Bone Marrow

extract_protocol:
20000 sorted monocytes were washed with cold PBS and resuspended in cold lysis buffer (10 mM Tris·Cl, pH 7.4, 10 mM NaCl,3 mM MgCl2, 0.1% (v/v) Igepal CA-630).
Nuclei were subject to transposition reaction in 1x TD Buffer containing 2.5 μl transposase Nextera enzyme and DNA was purified. Purified DNA was amplified by PCR with 10-12 cycles. Amplified libraries were purified and quality controlled.

tag: strain

value: Bone Marrow

value: Monocyte

tag: infection

value: Toxoplasma gondii infection

tag: genotype


title: YN12_335_RheMac_Olig2

description: Protocol 1

tag: tissue

value: F


title: B_air_3

tag: donor

tag: lonza id

tag: disease state

tag: Sex

tag: ethnicity

value: Hispanic

tag: smoker

tag: treatment

value: air

tag: cigarettes per treatment

tag: dilution rate (l/min)

tag: number of treatments a week

tag: cell type


title: WB 195 [MS_220]

tag: site

value: WFGB

tag: depth


title: BA10_control_rep18

description:
18C
C.18

tag: group

value: control

value: brain, prefrontal cortex BA10

value: male

tag: postmortem interval (h)

tag: total drinking years

tag: etoh daily use (g)

tag: drinks per week

tag: cigarette packs per year

tag: age of drinking onset


title: B_air_2

tag: donor

tag: lonza id

tag: disease state

value: healthy

tag: age

tag: Sex

value: N

value: Small Airway Epithelial Cells (SAECs)


title: BA10_control_rep19

description:
19C
C.19

tag: tissue


title: C_CS_1

value: M

tag: ethnicity

value: Caucasian

tag: smoker

tag: treatment

value: CS

tag: cigarettes per treatment

tag: dilution rate (l/min)

tag: number of treatments a week


title: BA10_control_rep20

description:
20C
C.20

tag: group

tag: postmortem interval (h)

tag: total drinking years


title: YN12_335_RheMac_NeuN

description: Protocol 1

value: brain

tag: nuclei

value: NeuN

tag: tissue preparation

value: Frozen Brain Tissue

tag: region

value: Brodmann Area 46

tag: sample id

tag: gender

tag: humanized age

tag: hemisphere

value: R

tag: pmi

tag: rin


title: EB 7003 [MS_219]

tag: site

value: EFGB

tag: depth

value: mesophotic


title: EB 192 [MS_218]


title: ATAC_Mono_WT_BM_Toxo

tag: strain

tag: tissue

value: Bone Marrow

tag: cell type

value: Monocyte

tag: infection

value: Toxoplasma gondii infection

tag: genotype


title: 4-V-16-4-8 [MS_224]

value: WFGB


title: YN11_78_RheMac_Olig2

description: Protocol 1

value: F

tag: age


title: BA10_control_rep16

description:
16C
C.16

tag: group

value: control

value: brain, prefrontal cortex BA10

tag: Sex

value: male

tag: postmortem interval (h)

tag: total drinking years

tag: etoh daily use (g)

tag: drinks per week

tag: cigarette packs per year

tag: age of drinking onset


title: BA10_control_rep15

description:
15C
C.15


title: ATAC_Mono_WT_Spleen_Toxo

source_name: Spleen

value: Spleen


title: WB 1006 [MS_217]


title: B_CS_3

tag: donor

tag: lonza id

tag: disease state

value: healthy

tag: ethnicity

value: Hispanic

tag: smoker

value: N

tag: treatment

value: CS

tag: cigarettes per treatment

tag: dilution rate (l/min)

tag: number of treatments a week

value: Small Airway Epithelial Cells (SAECs)


title: B_CS_2

tag: age

tag: cell type


title: ATAC_Mono_BM_SteadyState

tag: strain

tag: tissue

tag: infection

value: Steady State


title: YN11_77_RheMac_Olig2

description: Protocol 1

value: brain

tag: nuclei

tag: tissue preparation

value: Frozen Brain Tissue

tag: region

value: Brodmann Area 46

tag: sample id

tag: gender

value: M

tag: humanized age

tag: hemisphere

value: R

tag: pmi

tag: rin


title: ATAC_Mono_STAT1-KO_Spleen_Toxo

value: Monocyte

value: Toxoplasma gondii infection

tag: genotype


title: 5-V-16-2-4-53 [MS_216]

tag: site

value: WFGB

tag: depth

value: transplant

tag: time

value: six


title: YN11_77_RheMac_NeuN

description: Protocol 1

value: NeuN

tag: age


title: ATAC_Mono_Spleen_SteadyState_rep2

tag: strain

value: Spleen

tag: cell type


title: B_air_1

tag: donor

tag: lonza id

tag: disease state

value: healthy

tag: Sex

value: F

tag: ethnicity

value: Hispanic

tag: smoker

tag: treatment

value: air

tag: cigarettes per treatment

tag: dilution rate (l/min)

tag: number of treatments a week


title: ATAC_Mono_BM_Toxo

tag: tissue

value: Bone Marrow

tag: infection


title: 26-X-14-3-4 [MS_215]

tag: site

value: EFGB

tag: depth

value: shallow


title: BA10_control_rep17

description:
17C
C.17

tag: group

value: control

value: brain, prefrontal cortex BA10

value: male

tag: postmortem interval (h)

tag: total drinking years

tag: etoh daily use (g)

tag: drinks per week

tag: cigarette packs per year

tag: age of drinking onset


title: 4-V-16-1-1-74 [MS_214]

value: mesophotic


title: ATAC_Mono_Spleen_Toxo

tag: strain

tag: cell type

value: Monocyte

value: Toxoplasma gondii infection


title: A_air_3

tag: donor

tag: lonza id

tag: disease state

tag: age

tag: Sex

tag: ethnicity

value: Caucasian

tag: smoker

value: N

tag: treatment

value: Small Airway Epithelial Cells (SAECs)


title: A_air_2

tag: cigarettes per treatment

tag: dilution rate (l/min)

tag: number of treatments a week


title: YN11_64_RheMac_NeuN

description: Protocol 1

tag: tissue

value: brain

tag: nuclei

value: NeuN

tag: tissue preparation

value: Frozen Brain Tissue

tag: region

value: Brodmann Area 46

tag: sample id

tag: gender

tag: humanized age

tag: hemisphere

value: R

tag: pmi

tag: rin


title: 27-IX-16-4-5-72 [MS_213]

tag: site

tag: depth

value: transplant

tag: time

value: twelve


title: BA10_control_rep12

description:
12C
C.12

tag: group

tag: Sex

tag: postmortem interval (h)

tag: total drinking years

tag: etoh daily use (g)

tag: drinks per week

tag: cigarette packs per year

tag: age of drinking onset


title: BA10_control_rep9

description:
9C
C.9

tag: tissue


title: A_air_1

tag: donor

tag: lonza id

tag: disease state

value: healthy

tag: age

value: F

tag: ethnicity

tag: smoker

tag: treatment

value: air

tag: cigarettes per treatment

tag: dilution rate (l/min)

tag: number of treatments a week

tag: cell type


title: YN11_300_RheMac_Olig2

description: Protocol 1

tag: nuclei

tag: tissue preparation

tag: region

tag: sample id

tag: gender

value: M

tag: humanized age

tag: hemisphere

tag: pmi

tag: rin


title: B_CS_1

tag: donor

tag: lonza id

tag: disease state

tag: age

tag: Sex

value: Hispanic

value: CS


title: ATAC_Mono_LP_Toxo

source_name: Lamina Propria

tag: strain

tag: tissue

value: Lamina Propria

value: Monocyte

tag: infection

value: Toxoplasma gondii infection


title: 26-X-14-3-1 [MS_212]

tag: site

value: EFGB

tag: depth

value: shallow


title: BA10_control_rep10

description:
10C
C.10

tag: group

value: control

value: brain, prefrontal cortex BA10

value: male

tag: postmortem interval (h)

tag: total drinking years

tag: etoh daily use (g)

tag: drinks per week

tag: cigarette packs per year

tag: age of drinking onset


title: ATAC_Mono_Spleen_SteadyState_rep1

value: Spleen

tag: cell type

value: Steady State


title: BA10_control_rep11

description:
11C
C.11


title: BA10_control_rep14

description:
14C
C.14


title: EB 7002 [MS_211]

value: mesophotic


title: A_CS_2

tag: donor

tag: lonza id

value: healthy

tag: ethnicity

value: Caucasian

tag: smoker

value: N

tag: treatment

tag: cigarettes per treatment

tag: dilution rate (l/min)

tag: number of treatments a week

value: Small Airway Epithelial Cells (SAECs)


title: BA10_control_rep8

description:
8C
C.8

tag: tissue

tag: Sex


title: BA10_control_rep6

description:
6C
C.6

tag: group

tag: postmortem interval (h)


title: A_CS_3

tag: disease state

tag: age

value: F


title: YN09_72_RheMac_Olig2

description: Protocol 1

value: brain

tag: nuclei

tag: tissue preparation

value: Frozen Brain Tissue

tag: region

value: Brodmann Area 46

tag: sample id

tag: gender

tag: humanized age

tag: hemisphere

value: R

tag: pmi

tag: rin


title: BA10_control_rep7

description:
7C
C.7

tag: total drinking years

tag: etoh daily use (g)

tag: drinks per week

tag: cigarette packs per year

tag: age of drinking onset


title: 25-X-14-1-6 [MS_210]

tag: site

value: WFGB

tag: depth


title: ATAC_MonoLow_Spleen_Toxo

tag: strain

tag: tissue

tag: cell type

value: Monocyte

tag: infection

value: Toxoplasma gondii infection


title: YN09_59_RheMac_NeuN

description: Protocol 1

tag: nuclei

value: NeuN

tag: tissue preparation

tag: region

tag: sample id

tag: age


title: Med1_ChIP_Esrrb_KO_rep2

city: London

first: Ed

last: Curry

address: Hammersmith Hospital, Du Cane Road

country: United Kingdom

institute: Imperial College London

data_processing:
Adapter removal, low-quality read trimming and filtering using Trimmomatic
alignment to mm9 reference genome with Bowtie2
duplicate read marking and removal with Picard Tools
replicates were merged
Genome_build: mm9
Supplementary_files_format_and_content: bed files contain counts of deduplicated reads from each ChIPseq library, for each SE sub-region described in the Bell et al manuscript

source_name: Esrrb -/- embryonic stem cells

growth_protocol: Mouse ESCs were routinely cultured on 0.1% gelatin coated plates and maintained in GMEM media supplemented with 10% FBS (serum), MEM non-essential amino acids, beta-mercaptoethanol, L-glutamine, sodium pyruvate, sodium bicarbonate, penicillin/streptomycin, LIF prepared in-house and the appropriate drug selection. Mouse ESRRB KO ESCs (Martello G et al. 2012) and control populations have been previously described.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as previously described (Frank et al., 2001) with minor modifications outlined below. Chromatin was fixed with 1% Formaldehyde (Sigma-Aldrich) for 10 minutes and sonicated on a bioruptor (Diagenode) to produce fragments of 100-500 bp, and ChIPs performed with Protein G-coupled magnetic Dynabeads (Invitrogen) and the following antibodies : 8 µg MED1 (A300-793A Bethyl Laboratories). The amounts of chromatin (protein) used in each ChIP were as follows: 800 µg (Med1).  Following washes of bound DNA-protein complexes, DNA was eluted in 1% SDS and treated with 40 ng/µl RNaseA following 0.2 µg/µl Proteinase K. After phenol/chloroform purification, DNA was then precipitated at -20°C with 20-30 μg GlycoBlue carrier (Invitrogen), 1/10 volumes of 3 M NaAc and 2 volumes of 100% ethanol.
Sequencing libraries were prepared using the NEBNext® UltraTM DNA Library Prep Kit and Multiplex Oligos (New England Biolabs) from 5 ng of DNA. Following analysis on an Agilent Bioanalyzer, libraries were pooled and sequenced on an Illumina NextSeq500.

tag: chip antibody

tag: genotype/variation

value: Esrrb knock-out


title: EB 7008 [MS_208]

value: EFGB


title: BA10_control_rep2

description:
2C
C.2

tag: group

value: control

value: brain, prefrontal cortex BA10

tag: Sex

value: female

tag: postmortem interval (h)

tag: total drinking years

tag: etoh daily use (g)


title: siRNA-PiHL_rep3

city: shanghai

first: Xuan

last: Deng

address: No.512 Huashan Road

country: China

institute: Huashan Hospital

description:
siRNA-NC_rep3 vs. siRNA-PiHL_rep3
siRNA-PiHL treated HCT116 cells, replicate 3

data_processing:
HiSeq 3000 software was used for basecalling
Sequenced reads were mapped human transcriptome hg19 using TopHat 2.0.2 module
Transcripts were assembled and tested for abundance using Cufflinks 2.0.2 module
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM value for each sample

source_name: Colon cancer

growth_protocol: HCT116 cells were maintained at 37 °C in a humidified incubator containing 5% CO2 in Dulbecco’s modified Eagle medium (DMEM) (Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (Gibco).

extract_protocol:
Total RNA from each sample was extracted using Trizol reagent (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA purity was assessed by using an ND-1000 NanoDrop (Thermo Scientific, Wilmington, DE, USA). Each RNA sample had an A260:A280 ratio above 1.8 and an A260:A230 ratio above 2.0. RNA integrity was evaluated using the Agilent 2200 Tape Station (Agilent Technologies, Santa Clara, CA, USA), and all samples had an RNA integrity value above 7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HCT116 cells were treated with siRNA-NC or siRNA-PiHL

tag: cell line

value: siRNA-PiHL treatment


title: BA10_control_rep5

description:
5C
C.5

tag: drinks per week

tag: cigarette packs per year

tag: age of drinking onset


title: EB 190 [MS_207]

tag: site

tag: depth

value: shallow


title: YN11_78_RheMac_NeuN

description: Protocol 1

tag: tissue

tag: nuclei

tag: tissue preparation

tag: gender

tag: humanized age

tag: hemisphere

tag: pmi

tag: rin


title: H3K27ac_ChIP_Esrrb_KO_rep2

tag: chip antibody

tag: genotype/variation


title: siRNA-PiHL_rep2

description:
siRNA-NC_rep2 vs. siRNA-PiHL_rep2
siRNA-PiHL treated HCT116 cells, replicate 2


title: YN09_72_RheMac_NeuN

description: Protocol 1

tag: region

tag: sample id

tag: age


title: A_CS_1

tag: donor

tag: lonza id

tag: disease state

value: healthy

tag: Sex

tag: ethnicity

value: Caucasian

tag: smoker

value: N

tag: treatment

value: CS

tag: cigarettes per treatment

tag: dilution rate (l/min)

tag: number of treatments a week

tag: cell type

value: Small Airway Epithelial Cells (SAECs)


title: InputDNA_Esrrb_KO_rep2

description:
EsrrbKO_Med1_RPKM_per_SElet.bed
EsrrbKO_H3K27ac_RPKM_per_SElet.bed


title: YN09_179_RheMac_Olig2

description: Protocol 1

tag: tissue

value: brain

tag: nuclei

tag: tissue preparation

value: Frozen Brain Tissue

value: Brodmann Area 46

tag: gender

value: F

tag: humanized age

tag: hemisphere

value: R

tag: pmi

tag: rin


title: YN11_300_RheMac_NeuN

description: Protocol 1

value: NeuN

tag: region

tag: sample id

value: M

tag: age


title: YN09_179_RheMac_NeuN

description: Protocol 1


title: siRNA-PiHL_rep1

description:
siRNA-NC_rep1 vs. siRNA-PiHL_rep1
siRNA-PiHL treated HCT116 cells, replicate 1

tag: cell line

tag: genotype/variation


title: YN11_64_RheMac_Olig2

description: Protocol 1


title: siRNA-NC_rep3

description:
siRNA-NC_rep3 vs. siRNA-PiHL_rep3
siRNA-NC treated HCT116 cells, replicate 3

value: siRNA-NC treatment


title: YN09_173_RheMac_Olig2

description: Protocol 1


title: siRNA-NC_rep2

description:
siRNA-NC_rep2 vs. siRNA-PiHL_rep2
siRNA-NC treated HCT116 cells, replicate 2


title: 5-V-16-4-2-120 [MS_205]

tag: site

value: WFGB

tag: depth

tag: time

value: six


title: H3K27ac_ChIP_Esrrb_KO_rep1

tag: chip antibody

value: Esrrb knock-out


title: WB 1010 [MS_206]

value: mesophotic


title: Med1_ChIP_Esrrb_KO_rep1


title: BA10_control_rep1

description:
1C
C.1

tag: group

value: control

tag: tissue

value: brain, prefrontal cortex BA10

tag: Sex

value: female

tag: postmortem interval (h)

tag: total drinking years

tag: etoh daily use (g)

tag: drinks per week

tag: cigarette packs per year

tag: age of drinking onset


title: YN09_173_RheMac_NeuN

description: Protocol 1

tag: nuclei

tag: tissue preparation

tag: region

tag: sample id

tag: gender

tag: humanized age

tag: hemisphere

tag: pmi

tag: rin


title: siRNA-NC_rep1

description:
siRNA-NC_rep1 vs. siRNA-PiHL_rep1
siRNA-NC treated HCT116 cells, replicate 1

tag: cell line

tag: genotype/variation


title: InputDNA_Esrrb_KO_rep1

tag: chip antibody


title: YN09_122_RheMac_NeuN

description: Protocol 1

tag: tissue

tag: age


title: EB 7009 [MS_202]

tag: site

value: EFGB

tag: depth


title: 26-X-14-3-6 [MS_201]

value: shallow


title: Med1_ChIP_Esrrb_wt_rep2

source_name: Esrrb fl/fl embryonic stem cells

value: wild-type


title: EB 188 [MS_203]


title: H3K27ac_ChIP_Esrrb_wt_rep2


title: 4-V-16-2-3 [MS_198]


title: H3K27ac_ChIP_Esrrb_wt_rep1


title: YN08_380_RheMac_NeuN

description: Protocol 1

value: brain

value: Frozen Brain Tissue


title: Med1_ChIP_Esrrb_wt_rep1


title: RNA-seq_vehicle_replicate5

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

data_processing:
The SOLiD 5500xl sequencer-generated raw binary files (XSQ format) were converted into csfasta/QV.qual color-space ASCII text raw read files using the ABI XSQ tool.
The csfasta/QV.qual files were mapped to Xenopus laevis v9.1 reference genome sequence (fasta) using TopHat. Color-space alignment engine was Bowtie with the "-C" option.
The TopHat output bam files were subjected to RNA expression analysis using Cufflinks.
Genome_build: Xla v9.1
Supplementary_files_format_and_content: Matrix table holding the FPKM values for annotated gene models for each replicate

organism: Xenopus laevis

source_name: vehicle, whole embryo

growth_protocol: Xenopus laevis eggs were fertilized in vitro.

extract_protocol:
Each dish of embryos were harvested at stage 18 in five, 5-embryo aliquots, each of which was designated as one replicate. Each replicate embryos were homogenized in 200 uL/aliquot of TriPure. Total RNA was Dnase-treated, LiCl precipitated.
Total RNA (100 ng) was reverse transcribed into cDNA using Nugen Ovation RNA Amplification System V2. The cDNA was converted to ABI SOLiD 5500xl deep sequencing libraries using SOLiD Fragment Library Core Kit with barcodes.
RNA-seq, single read (50 nt), non-directional

treatment_protocol: Stage 6-7 embryos were exposed in groups of 25 in 60-mm glass Petri dishes with 10 mL of 0.1X MBS containing NRX204647 (10 nM or 1 microM) or 0.1% EtOH vehicle until stage 18.

tag: protocol

value: Vehicle (0.1% EtOH)

tag: time

value: exposed between stage 6 until 18

value: whole embryo


title: WB 1003 [MS_196]


title: YN04_200_RheMac_NeuN

description: Protocol 1

tag: nuclei

value: NeuN

tag: tissue preparation

value: Brodmann Area 46

value: M

value: R


title: BA10_control_rep13

description:
13C
C.13

tag: group

tag: Sex

value: male

tag: postmortem interval (h)

tag: total drinking years

tag: etoh daily use (g)

tag: drinks per week

tag: cigarette packs per year

tag: age of drinking onset


title: 27-IX-16-4-2-71 [MS_195]

value: transplant

value: six


title: RNA-seq_vehicle_replicate4


title: RNA-seq_vehicle_replicate3


title: InputDNA_Esrrb_wt_rep1

description:
Esrrbflfl_Med1_RPKM_per_SElet.bed
Esrrbflfl_H3K27ac_RPKM_per_SElet.bed

tag: chip antibody

tag: genotype/variation


title: 4-V-16-1-4 [MS_193]


title: WB 120 [MS_192]

value: WFGB


title: RNA-seq_10nM_replicate5

source_name: 10nM, whole embryo

value: NRX204647 low dose (specifically activates RARgamma)

tag: tissue


title: RNA-seq_vehicle_replicate1


title: 4-V-16-3-4 [MS_209]

tag: site

value: EFGB


title: 4-V-16-4-1-176 [MS_191]

tag: depth

value: mesophotic


title: 25-X-14-1-2 [MS_188]

value: shallow


title: 26-X-14-1-4 [MS_189]


title: RNA-seq_10nM_replicate1

tag: protocol


title: InputDNA_Esrrb_wt_rep2

value: wild-type


title: YN08_380_RheMac_Olig2

description: Protocol 1

value: brain

value: Frozen Brain Tissue

tag: region

tag: sample id

tag: gender

value: F

tag: age

tag: humanized age

tag: hemisphere

tag: pmi

tag: rin


title: control OL rep3, input

first: Huan

last: Xu

state: Illinois

address: 5841 S. Maryland Ave MC2030, Ab514

department: Neurology

institute: University of Chicago

data_processing:
Library strategy: m6A-Seq
Adapters and low quality reads trimmed: Trimmomatic V0.32
Gapped mapping to reference genome: STAR V2.6.1
Modeling and quantification of m6A peaks: Magenta V0.3.13
Expression Quantification: Subread V1.6.3 Bioconductor Packages:  featuresCounts, GRanges, DEseq2
Data visualization: R V3.5.1 Packages:  venn.diagram, plotly, ggplot2
Genome_build: UCSC mouse genome mm10
Supplementary_files_format_and_content: Z_score_m6A.csv
Supplementary_files_format_and_content: OL.3 and OPC.3 were omitted from analysis in paper due to discordance observed in PCA analsysis; files included in GEO for completeness

source_name: Brain

growth_protocol: Using an immunopanning approach, we purified OPCs from neonatal mouse pups. These cells were maintained under proliferating conditions with the addition of the OPC mitogen PDGFα. We obtained mature oligodendrocytes by promoting OPC differentiation via removal of PDGFα and addition of the T3 hormone to the culture media

extract_protocol:
Lysis buffer (Bio-Rad Aurum total RNA Mini Kit , Cat# 732-6820) was added to culture dishes, cells were then removed by cell scrapers, and flash frozen on dry ice. RNA was extracted using the Bio-Rad Aurum total RNA Mini Kit (Cat# 732-6820) .
The equivalent amount of input and m6A-imunoprecipitated RNA were prepared for library generation using the SMART-seq protocol as described (Picelli et al., 2014)

tag: genotype

tag: strain

value: C57BL/6 background

tag: cell type

value: mature oligodendrocytes


title: RNA-seq_10nM_replicate4

tag: time

value: exposed between stage 6 until 18

value: whole embryo


title: control OL rep1, input


title: RNA-seq_10nM_replicate2


title: RNA-seq_1microM_replicate5

source_name: 1microM, whole embryo

value: NRX204647 high dose (activates RARalpha, beta, and gamma)


title: 5-V-16-4-3-119 [MS_194]


title: 4-V-16-1-3-169 [MS_190]


title: control OL rep2, input


title: RNA-seq_vehicle_replicate2

value: Vehicle (0.1% EtOH)


title: WB 179 [MS_185]


title: WB 178 [MS_187]


title: 26-X-14-3-5 [MS_184]


title: RNA-seq_10nM_replicate3


title: control OPC rep2, input

value: oligodendrocyre precursor cell


title: control OPC rep1, input


title: RNA-seq_1microM_replicate3


title: RNA-seq_1microM_replicate4


title: 5-V-16-2-1-68 [MS_182]

value: transplant

value: six


title: control OL rep3

description: m6A-imunoprecipitated RNA


title: RNA-seq_1microM_replicate1


title: WB 1004 [MS_181]

value: WFGB


title: control OPC rep3, input


title: control OL rep2

description: m6A-imunoprecipitated RNA


title: 26-X-14-3-2 [MS_180]

value: EFGB


title: 25-X-14-1-4 [MS_179]


title: 1493_THD_RNA

city: Beaverton

first: Charles

last: Keller

state: OR

address: 12655 SW Beaverdam Rd. West

institute: Children's Cancer Therapy Development Institute

data_processing:
raw reads aligned to CanFam3.1 canine reference genome or GRCHM38 mouse reference genome using STAR
aligned transcripts were quantified using RSEM
Genome_build: GEMM and the mouse cell line were aligned to GRCHM38 mouse genome
Genome_build: Canine samples were aligned to CanFam3.1 canine genome
Supplementary_files_format_and_content: result files are in tabular format. These files have quantified TPM data with addional information.

organism: Canis lupus familiaris

source_name: tumor

growth_protocol: the mouse cell line C2C12 was grown in DMEM + 10% FBS + 1% P/S, while all other samples had no growth conditions

extract_protocol:
RNA was isolated from preserved clinical tissue stored as cryopreserved tissue or FFPE tissue (except C2-C12, isolated from snap frozen cells folllowing harvesting from plateware). RNA isolation was performed at Beijing Genomics Institute
library construction was performed at Beijing Genomics Institute
Paired-End RNA sequencing of GEMM (mouse samples)
Single-End RNA sequencing (canine samples)

tag: tumor type

value: non-rhabdomyosarcoma soft tissue sarcoma

tag: sample type

value: primary tumor tissue; frozen tumor


title: 1494_TTJ_RNA


title: 1492_TCM_RNA


title: RNA-seq_1microM_replicate2

tag: tissue


title: control OPC rep3

description: m6A-imunoprecipitated RNA


title: control OL rep1

description: m6A-imunoprecipitated RNA


title: 26-X-14-2-6 [MS_177]

tag: site

tag: depth

value: shallow


title: 26-X-14-1-10 [MS_183]


title: 1491_TCC_RNA


title: 1489_FFU_RNA


title: control OPC rep1

description: m6A-imunoprecipitated RNA


title: control OPC rep2

description: m6A-imunoprecipitated RNA


title: WB 1 [MS_178]


title: 4-V-16-3-1 [MS_176]


title: 1487_684M_RNA


title: 26-X-14-1-1 [MS_175]


title: 26-IX-16-2-2-68 [MS_174]

value: twelve


title: 1484_1908A_RNA


title: WB 3 [MS_173]


title: WB 124 [MS_172]


title: 1482_1433B_RNA


title: 1481_1419B_RNA


title: WB 69 [MS_171]

value: mesophotic


title: 1480_1238B_RNA


title: 1479_684B_RNA


title: 26-X-14-2-1 [MS_170]


title: 25-X-14-2-1 [MS_169]


title: 1488_694M_RNA


title: 26-X-14-1-7 [MS_168]


title: D42_T3 RNA-seq

city: Qingdao

last: Wang

state: Shandong

address: 106 Nanjing Road

institute: Yellow Sea Fisheries Research Institute, Chinese Academy Fishery Science

data_processing:
Raw reads of RNA-seq were treated by removing reads that contained adapters, poly-N, and low quality reads. At the same time, Q20, Q30, and GC contents were calculated. All downstream analyses were based on clean data with high quality.
Clean reads were subsequently aligned to the Japanese flounder reference genome via TopHat v2.0.12. HTSeq v0.6.1 was used to count the read numbers mapped to each gene. The fragments per kilobase of transcript sequence per million base pairs (FPKM) of each gene was calculated based on the length of the gene and the reads count was mapped to this gene. Prior to analysis of differential gene expression, read counts were adjusted for each sequenced library via the edgeR program package using one scaling normalized factor.
Genome_build: Paralichtys olivaceus genome
Supplementary_files_format_and_content: readcount and FPKM of genes.xls

organism: Paralichthys olivaceus

source_name: 42 DAH larvae of T3 treated Paralichtys olivaceus

extract_protocol:
Total amounts of 3 μg RNA per sample were used for sequencing libraries via the NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer’s recommendations. Briefly, mRNA was purified with poly-T oligo-attached magnetic beads and fragmented using divalent cations under elevated temperature in the NEBNext First Strand Synthesis Reaction Buffer (5X). Then, the first and second strand cDNA were separately synthesized using random hexamer primer and M-MuLV reverse transcriptase (RNase H-), DNA polymerase I, and RNase H. After adenylation of the 3’ ends of DNA fragments, a NEBNext Adaptor with hairpin loop structure was ligated to prepare for hybridization. To select cDNA fragments of preferentially 150-200 bp in length, library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 μl USER Enzyme (NEB, USA) was incubated with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C prior to PCR. The subsequent PCR was performed with Phusion High-Fidelity DNA polymerase, universal PCR primers, and Index (X) Primer. Finally, PCR products were purified (with the AMPure XP system) and the library was assessed on the Agilent Bioanalyzer 2100 system and sequenced on the Illumina Hiseq 4000 platform, generating 150 bp paired-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At the beginning of the experiment, 1000 individual larvae of the Japanese flounder at 16 DAH were separately treated with 0.01 mg/L thyroid hormone T3 (3,3′,5-triiodo-L-thyronine, sigma), 0.05 mg/L thyroid hormone T4 (levothyroxine sodium hydrate, sigma), or 20 mg/L TU (thiourea, sigma) for 10 continuous days. 1000 untreated individuals were used as control group. At 17, 20, 23, 28, 42, 47, and 57 DAH, four groups of fishes were sampled and body color were measured. The period with the maximal difference in body color was submitted for high-throughput mRNA sequencing analysis.

value: the whole body

value: 42 DAH (days after hatchery)

tag: treatment

value: T3 treatment


title: WB 199 [MS_166]


title: D42_Con RNA-seq

source_name: 42 DAH larvae of control Paralichtys olivaceus

value: No treatment


title: 26-X-14-2-2 [MS_165]


title: 1483_1853B_RNA


title: HFD_peptide

city: Singapore

first: Benson

last: Chen

address: 60 Biopolis Street, Genome, #04-01

department: Genome Institute of Singapore

country: Singapore

institute: A*STAR

data_processing:
The sequences were aligned to a curated bacterial reference database, downloaded from the NCBI NR sequence database, using BWA (version 0.7.12-r1039) “mem” command.
The sam alignment files thus created were used to count the reads aligned to individual bacterial genes using the program HTSeq count (version 0.6.0)
The counts were further normalized based on size factors estimated using median of the ratios of observed counts method as described in [https://www.ncbi.nlm.nih.gov/pubmed/20979621]
Genome_build: bacterial reference genome from NCBI NR sequence database
Supplementary_files_format_and_content: The normalized counts for each gene are tabulated in flat format (*.txt). 1. Gene ID 2. Reference genome 3. Normalized counts from CHD_control 4. Normalized counts from HFD_control 5. Normalized counts from HFD_peptide

organism: feces metagenome

source_name: gut microbiome from LDLr -/- mice_high fat diet with peptide treatment

growth_protocol: Regular chow diet (Harlan Teklad 7019) and high-fat diet (Harlan Teklad 94059) were used in this study

extract_protocol:
Total bacterial RNA from feces sample was isolated with ZR Soil/Fecal RNA MicroPrep (Zymo research). Briefly, the sample was suspended in RNA lysis buffer and lysed by the mixer (Retsch). The supernatant was transferred to RNA-binding column and washed several times with RNA wash buffer. In-column DNaseI digestion at 25°C for 15 min was performed to eliminate DNA contamination in the sample. The presence of genomic DNA contamination was assessed by PCR with universal 16S rRNA gene primers.
Before RNA-seq library preparation, rRNA was removed from 2 µg of total bacterial RNA with Ribo-Zero Bacteria kit (Illumina). 100 ng of purified RNA was used for RNA-seq library preparation and the cDNA was synthesized from reverse transcription with SuperScript III (Life technologies) and second-strand synthesis (New England Biolabs). The sequencing library was generated from purified cDNA with Nextera XT DNA library preparation kit (Illumina) and amplified by PCR. Cycling conditions were 72°C for 3 min, 95°C for 30 s, followed by 16 cycles of 95°C for 10 s, 55°C for 30 s, and 72°C for 30 s. A condition of 72°C for 5 min was used for the final elongation step. Libraries with different indexes were pooled and single-end sequencing (75bp) was performed on an Illumina NextSeq at the Scripps Research Institute next generation sequencing core.

treatment_protocol: The lyophilized peptide was dissolved in PBS (pH 7.4) containing 1% sucrose, resulting in a clear solution. The drinking water solution was replaced with fresh solution every other day. The mice were fed CHD or HFD with control (PBS with 1% sucrose) drinking water or peptide at a dose of 180 μM (200 μg/mL) for two weeks.

tag: host organism

value: Mus musculus

tag: bacterial metagenome source

value: feces

tag: mouse genotype

value: LDLr -/-

value: peptide

tag: mouse diet

value: HFD


title: ATAC_MonoHigh_Spleen_Toxo

value: Spleen

value: Monocyte

tag: infection

value: Toxoplasma gondii infection


title: HFD_control

source_name: gut microbiome from LDLr -/- mice_high fat diet

value: control


title: 25-X-14-3-3 [MS_164]

value: WFGB


title: 25-X-14-2-5 [MS_162]

value: shallow


title: EB 7016 [MS_163]

value: EFGB


title: Rose-leaf-degradome

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

data_processing:
Remove low quality reads with nucleotides of scores lower than 30 in the first 25 nucleotides
Cut the first 20 nucleotides in the remaining reads
Sort and remove repetitive sequences
Calculate the counts of unique sequences
Supplementary_files_format_and_content: sequences and count values

organism: Rosa rugosa

source_name: leaf

growth_protocol: The rose were grown in greenhouse, Kunming university of science and technology, Kunming, Yunnan, China

extract_protocol:
Total RNA was isolated from selected tissues using TRIzol reagent with the manufacture's protocol.
Degradome or PARE library was prepared by following the protocol reported in Li et al. 2010 (The Plant Journal 2010, 62:742-759).

value: leaf


title: 25-X-14-1-1 [MS_161]


title: CHD_control

source_name: gut microbiome from LDLr -/- mice_control diet

value: CHD


title: Rose-leaf-sample-1

data_processing:
Remove low quality reads with nucleotides of scores lower than 30 in the first 25 nucleotides
Keep the sequences whose lengths are greater than or equal to 18 bp (the 3' adapter sequences of reads had been removed by the sequencing facility)
Sort and remove repetitive sequences
Calculate the counts of unique sequences
The unique sequences were aligned to a self-assembled transcriptome with SOAP2
Supplementary_files_format_and_content: sequences and count values

extract_protocol:
Total RNA was isolated from selected tissues using TRIzol reagent with the manufacture's protocol.
Small RNA libraries were prepared by following the Illumina's protocol.

treatment_protocol: no treatment


title: WB 1005 [MS_160]

value: mesophotic


title: Rose-stamen-sample2

source_name: stamen

value: stamen


title: 9: NOX5+BAY87-2243-3

type: RNA

city: Beijing

first: Jie

address: No. 52 Fucheng Road Haidian District Beijing

institute: Peking University Cancer Hospital

description: Total RNA uses ULS tagging on cy5. The chips were removed and washed with 6X SSPET, 3X SSPET, 0.5X SSPET, and 0.5X SSPET in order to remove the non-specific hybridization background. The developing solution and cover glass were added to the hybridization area for scanning.

hyb_protocol: Hybridization was performed in Agilent Hybridization System.

scan_protocol: After washing, slides were scanned with Axon GenePix 4000B scanner.

data_processing: Data was extracted and normalized using the Agilent 2200 Bioanalyzer-related software. Further Data analysis was performed using Agilent GeneSpring GX v11.5.1 software.

source_name: KYSE410 NOX5 cells treated with BAY87-2243

label_protocol: RiboArray Human mRNA Array One-Color DNA Labeling Kit was used for sample labeling.

growth_protocol: KYSE410 cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), penicillin (100 U/ml), and streptomycin (100 μg/ml).

extract_protocol: Total RNA was isolated using RNA isolation kit (QIAGEN) and was verified with RNA integrity number.

treatment_protocol: KYSE410 cells were transfected with NOX5 plasmids in the presence or absence of BAY87-2243.

tag: cell line


title: B6N_mature_oocyte_02

city: New Haven

first: Akiko

last: Iwasaki

state: CT

address: 300 Cedar Street

institute: Yale University School of Medicine

description:
processed data file:
Oocyte_normalized_count.txt
Oocute_normalized_count_ERV.txt

data_processing:
RNA-seq of cellular genes:
Btrim to trim adapters and low-quality read
Tophat2 to map reads
DEseq2 to analyze differential gene expression
RNA-seq of ERV or VL30:
Btrim to trim adapters and low-quality read
BWA-mem to map reads
SAMtools processing of unmapped reads
BEDTools to read mapping counts to ERV
DEseq2 to analyze differential gene expression
RNA-seq RepEnrich:
Btrim to trim adapters and low-quality read
Bowtie to map reads
SAMtools processing of uniquely mapped reads
RepEnrich analysis of non-uniquely mapped reads
DEseq2 to analyze differential gene expression
ChIP-seq:
Bowtie2
Picard to remove duplicates
deepTools to count reads and generate bigWig files
Genome_build: mm10
Genome_build: ChIP-seq: Unique ERV and VL30 loci
Supplementary_files_format_and_content: RNA-seq of cellular genes: Excel spreadsheet of Deseq output
Supplementary_files_format_and_content: RNA-seq of ERV or VL30: Excel spreadsheet of Deseq output
Supplementary_files_format_and_content: RNA-seq RepEnrich: Excel spreadsheet of Deseq output
Supplementary_files_format_and_content: ChIP-seq: bigWig files of normalized reads mapped to unique ERV and VL30 loci

molecule: polyA RNA

source_name: ovary

extract_protocol:
Immature (M1 prophase-arrested) oocytes were harvested from super-ovulated (PMSG + hCG) ovaries of 6 B6J female mice. Denuded oocytes were isolated into Qiagen RLT buffer and RNA was isolated using Qiagen RNA Micro kit.
Full length RNAseq (SMART-Seq2)

value: mature oocyte


title: WB 1008 [MS_159]

address: 5600 N US Highway 1

institute: Florida Atlantic University at Harbor Branch Oceanographic Institute

data_processing:
Data processing was completed using the analysis pipeline available on GitHub:
https://github.com/mstudiva/tagseq-modified-scripts
Genome_build: concatenated M. cavernosa (https://github.com/mstudiva/Mcav-Annotated-Transcriptome.git) and Symbiodinium Clade C (ftp://marchanon:anon@rc-ns-ftp.its.unc.edu/CladeC_Symbiodinium_transcriptome.zip) transcriptomes
Supplementary_files_format_and_content: tab-delimited text file containing gene counts per sample and isogroup annotations


title: 5--6--7--8: NOX5+BAY87-2243-2


title: Rose-stamen-sample1


title: WB 177 [MS_167]


title: 26-X-14-2-8 [MS_158]


title: 5--6--7--8: NOX5+BAY87-2243-1


title: Rose-pollen-sample-2

source_name: pollen

value: pollen


title: B6N_immature_oocyte_02

extract_protocol:
Immature (M1 prophase-arrested) oocytes were harvested from ovaries of 4 B6J female mice 48hr after injection with pregnant mare serum gonadotopin. Denuded oocytes were isolated into Qiagen RLT buffer and RNA was isolated using Qiagen RNA Micro kit.
Full length RNAseq (SMART-Seq2)

value: immature oocyte


title: 5--6--7--8: NOX5-3

source_name: KYSE410 NOX5 cells


title: WB 1011 [MS_157]


title: Rose-pollen-sample-1


title: Rose-leaf-sample-2


title: B6J_mature_oocyte_02


title: 5--6--7--8: NOX5-2


title: 1--2--3--4: NOX5-1


title: Rose-petal-sample-1

source_name: petal

value: petal


title: EB 7004 [MS_155]


title: B6J_mature_oocyte_01


title: 27-IX-16-4-3-74 [MS_154]

value: transplant

value: six


title: B6J_immature_oocyte_02


title: 1--2--3--4: vector-3

source_name: KYSE410 vector cells


title: Rose-root-sample-2

source_name: root

value: root


title: Rose-root-sample-1


title: WB 1012 [MS_153]


title: B6N_mature_oocyte_01


title: EB 189 [MS_152]


title: 1--2--3--4: vector-1


title: B6J_immature_oocyte_01


title: B6N_BMDM_02

description:
processed data file:
NJ_normalized_count.txt
NJ_normalized_count_ERV.txt

source_name: bone marrow-derived macrophage

extract_protocol:
Bone marrow was isolated and pooled from 3 B6J mice and cultured for 7 days in L-929 conditioned media. Replicate cultures were harvested in Qiagen RLT buffer and RNA was isolated using Qiagen RNeasy Mini kit
NEBNext® Ultra RNA Library Prep Kit for Illumina (E7530) was used with 250ng of total RNA for the construction of sequencing libraries

value: bone marrow-derived macrophage


title: WB 1002 [MS_156]


title: WB 1007 [MS_151]


title: Rose-petal-sample-2


title: B6N_immature_oocyte_01


title: U37125_RNA

tag: strain background

value: Mixed (predominately SvJ/129)

tag: genotype/variation

value: rhabodmyosarcoma, embryonal

value: primary tumor tissue; frozen tumor


title: U57810_RNA

value: Myf6(ICNm/ICNm) Trp53(F2-10/F2-10) ROSA26(LUSAPm/WT) Hairless(SKH1/SKH1)


title: B6N_BMDM_01

tag: strain


title: B6J_BMDM_02

tag: cell type


title: U35545_RNA

value: rhabodmyosarcoma, pleomorphic


title: WB 68 [MS_149]

value: WFGB


title: B6J_BMDM_01


title: 4-V-16-3-3 [MS_150]

value: EFGB

value: shallow


title: Hu_58_H3N2

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

data_processing:
Illumina RTA v3.1.5 was used for basecalling and Illumina bcl2fastq2 was used for fastq file generation
PE100 reads (Seq1) were quality checked with package FastQC, then trimmed using Trimgalore (with default settings). Trimmed reads were mapped to human genome annotation and H3N2 virus using STAR with default settings. PE150 reads (Seq2) were first cut down to PE 100 reads, quality checked with package FastQC and then trimmed using Trimgalore (with default settings).  Trimmed reads were mapped to human genome annotation and H3N2 virus using STAR with default settings.
Seq1 and Seq2 reads were mapped separatly to human and virus genome. Mapped reads were then counted using RsubRead. Raw counts from human genome and virus mapping were then combined resulting in two raw count tables (for Seq1 and Seq2).  The two raw count tables from Seq1 and Seq2 were then combined to one and further analyzed. Normalization was done with DESeq2.
Genome_build: hg38 (ENSMBL hg38 release 91) and H3N2 virus (gb:CY034100|A/Panama/2007/1999)
Supplementary_files_format_and_content: txt files containing normalized reads per sample

source_name: lung

extract_protocol:
Tissue blocks were transferred to Lysing Matrix A tubes (MP Biomedicals, Germany) in 600 µl RLT buffer supplemented with 1% β-Mercapthoethanol (Sigma, Germany). Tissue was lysed using FastPrep®-24 (MP Biomedicals, Germany) applying six rounds of tissue lysis at default settings (4 m/s, 20 s). Homogenates were centrifuged for 5 min full speed at 4°C and RNA was purified from the supernatant. Total RNA was reverse transcribed with oligo (dT) primers and RevertAid H Minus Reverse Transcriptase (Thermo Fisher Scientific, USA).
The RNA sequencing library was generated from 500ng total RNA using Dynabeads® mRNA DIRECT™ Micro Purification Kit (Thermo Fisher) for mRNA purification followed by NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England BioLabs) according to manufacture´s protocols.

value: lung

tag: donor


title: WB 180 [MS_148]

city: Fort Pierce

first: Joshua

last: Voss

value: mesophotic


title: Hu_58_Mock

value: Mock


title: U34279 _RNA

source_name: tumor

tag: tumor type


title: 1--2--3--4: vector-2


title: WB 53 [MS_186]


title: Hu_53_Mock


title: U33915_RNA

value: Pax7(CREERp/WT) Trp53(F2-10/F2-10) PTC1(F1-2m/WT) ROSA26(LUSAPp/WT)

tag: sample type


title: WB 1001 [MS_147]


title: Hu_53_H3N2

tag: tissue


title: B6N_nCD4_01

description:
processed data file:
B6JN_normalized_count.txt
B6JN_normalized_count_ERV.txt

source_name: naïve CD4 T cells (spleen)

extract_protocol:
Naïve CD4 T cells were obtained from splenocytes using an EasySep negative isolation kit and RNA was isolated using Qiagen RNeasy Mini Kit.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500ng of total RNA for the construction of sequencing libraries.

value: naive CD4 T cell


title: 25-X-14-2-8 [MS_145]

tag: site


title: B6J_nCD4_02


title: U29415_RNA


title: WB 1009 [MS_146]

tag: depth


title: B6J_nCD4_01


title: FXN vs EMPTY (slide A)

city: Rome

first: Silvia

last: Gioiosa

address: Via dei Tizii,6

department: Supercomputing Applications and Innovation

country: Italy

institute: CINECA

description: frataxin-deficient lymphoblastoid cells derived from a FRDA patient stably reconstituted with wild type frataxin (FTX) vs frataxin-deficient lymphoblastoid cells derived from a FRDA patients stably reconstituted with an empty vector

hyb_protocol: Hybridization was performed in duplicate, with one dye swap. Microarray slides were incubated in a water bath at 42°C for an overnight in the dark.

scan_protocol: Each slide was scanned on the GenePix 4000B Microarray Scanner at the optimal wavelength for the Alexa555 (F532) and Alexa647 (F635) dyes.

data_processing: Flagged spots were filtered and systematic bias in the data was removed by applying dye-swap and printiploess intra-array normalization followed by inter-array quantile normalization.

label: Alexa647, Alexa555 dyes

label_protocol: Direct labelling of second strand (ss) cDNA was conducted according to manufacturer’s instructions (Invitrogen) with starting material of 5 µg of total RNA. Briefly, the amino-allyl labeled dNTP mix was added to the reaction to generate amino-allyl labelled second strand cDNA. PCR purification kit (Qiagen) was used to remove unincorporated dNTPs, fluorescent dyes and primer. Alexa555- and Alexa647-labelled cDNA was then combined in one tube and evaporated almost to dryness. The combined labelled cDNAs were stored on ice protected from light until hybridization.

extract_protocol: Total RNA of HEK-293 and HEK-293 Flp-In was extracted and purified using TriZol reagent (Invitrogen). RNA quality and quantity was assessed using a Nanodrop spectrophotometer (Thermo Scientific) and agarose gel electrophoresis.

tag: condition

value: FRDA

label: Alexa-555, Alexa-647


title: U35855_RNA

value: undifferentiated pleomorphic sarcoma (mixed epithelioid and spindle)


title: 27-IX-16-4-4-57 [MS_144]

value: transplant

tag: time

value: twelve


title: Hu_44_H3N2


title: Hu_41_Mock


title: U28285 _RNA

value: Mixed (predominately SvJ/129)

value: Pax7(CREERp/WT) Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10) ROSA26(LUSAPp/WT)


title: B6N_nCD4_02


title: [delta]nctA_0.5mg_mL_Itra_Rep3

city: Manchester

first: Michael

middle: J

last: Bromley

state: Greater Manchester

address: 46 Grafton Street

department: Division of Infection, Immunity, and Respiratory mediciney

institute: The University of Manchester

data_processing:
Raw sequencing reads were quality controlled with Illumina chastity filter and fastqc v0.11.3.
Illumina adapters were trimmed from them using Trimmomatic v0.30.
The resulting reads were aligned to the Aspergillus fumigatus A1163 CADRE genome from Ensemble fungi, version 24 using Bowtie version 0.12.9
Differential expression analysis was performed using DESeq version 1.9.12
Genome_build: Aspergillus fumigatus A1163 CADRE genome from Ensemble fungi, version 24
Supplementary_files_format_and_content: tab-delimited text files include normalized abundance measurements for each sample.

organism: Aspergillus fumigatus

source_name: Mycelia

growth_protocol: 1x10^6 spores/ml of A. fumigatus strains were grown in 50 ml of Vogel’s minimal medium containing 1.0 % glucose for 18 h at 37 °C with constant  shaking at 180 rpm.

extract_protocol:
Total RNA was extracted using TRI Reagent (Sigma-Aldrich) according to the manufacture’s instructions. The extracted RNA samples were treated with RQ1 RNase-Free DNase I (Promega) and further purified using the RNeasy Mini Kit (Qiagen).
Libraries were constructed using the TruSeq RNA Sample Prep kit (Illumina, Inc.) according to the manifactures instruction.

treatment_protocol: The pre-cultured mycelia were collected by filtration, and washed twice with RPMI-1640 medium.  About 1.0 g of wet mycelia were transferred into 50 ml of RPMI-1640 medium containing 2.0 % glucose and 165 mM MOPS (pH7.), and the cells were incubated for 4 hours in the absence and the presence (0.5 mg/mL) of  itraconazole at 37 °C with shaking.

tag: genomtype

value: A1160 pyrG+, [delta]nctA::hph


title: 26-X-14-1-3 [MS_142]


title: 25-X-14-1-3 [MS_143]


title: deltaGm_deltaRik_CD4_01

source_name: CD4 T cells (spleen)

extract_protocol:
Bulk CD4 T cells were obtained from splenocytes using an EasySep negative isolation kit and RNA was isolated using Qiagen RNeasy Mini Kit.
NEBNext® Ultra RNA Library Prep Kit for Illumina (E7530) was used with 250ng of total RNA for the construction of sequencing libraries

value: CD4 T cell


title: [delta]nctA_0.5mg_mL_Itra_Rep2


title: C2-C12_RNA

value: normal tissue

value: established cell line; cell culture


title: deltaGm_deltaRik_CD4_02


title: B6N_CD4_02


title: Hu_40.1_Mock


title: [delta]nctA_0.5mg_mL_Itra_Rep1


title: B6N_CD4_01


title: EB 169 [MS_141]

value: EFGB


title: Hu_44_Mock


title: Hu_40.1_H3N2


title: 27-VIII-13-2-012 [MS_140]

value: PRTER


title: B6J_CD4_02


title: B6J_CD4_01


title: [delta]nctA_NoDrug_Rep3


title: [delta]nctA_NoDrug_Rep2


title: RCMB45

city: St. Petersburg

first: Piyush

last: Joshi

address: 600 5th St S

department: Oncolog/JHACH

institute: Johns Hopkins University

data_processing:
For RNA-seq, Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped using HISAT2 v2.1.0, with --rna-strand -RF option. StringTIe was used to quantify obtained alignment that was converted into read counts.
Genome_build: hg38
Supplementary_files_format_and_content: comma-delimited csv files include reads counts for each sample

source_name: PDX sample from RCMB45 patient

growth_protocol: PDX samples were initially generated by implanting patient cells  orthotopically in  cerebellum of immuno-compramised SCID mouse. Subsequent passage of PDX was done by implanting PDX tissue directly into mouse cerebellum without in vitro propogation.

extract_protocol: RNA-Seq libraries were prepared using Truseq Stranded Total RNA Library preparation kit (Illumina, San Diego, CA) with 1 ug of total RNA.

value: Medulloblastoma PDX


title: 29-VIII-13-1-006 [MS_138]

value: shallow


title: RCMB51

source_name: PDX sample from RCMB51 patient


title: PR 223 [MS_139]


title: [delta]nctA_NoDrug_Rep1


title: WB 54 [MS_197]

value: WFGB

value: mesophotic


title: PR 245 [MS_137]


title: [delta]nctB_0.5mg_mL_Itra_Rep3

value: A1160 pyrG+, [delta]nctB::hph


title: Hu_41_H3N2

value: lung


title: RCMB40

source_name: PDX sample from RCMB40 patient


title: PR 214 [MS_136]


title: PR 246 [MS_135]


title: [delta]nctB_0.5mg_mL_Itra_Rep2


title: [delta]nctB_0.5mg_mL_Itra_Rep1


title: 19139 BrKo_ TdT-positiv

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
3085
norm_gene_counts_Cxcr4CreKO

data_processing:
bcl2fastq2 v2.20
Kallisto
DESeq2

source_name: brain

extract_protocol:
SMART-Seq2
Qiagen miRNeasy

value: Cxcr4CreER KO

tag: population

value: monocytes


title: RCMB32

source_name: PDX sample from RCMB32 patient


title: 19010 BrKo_ TdT-positiv

description:
3083
norm_gene_counts_Cxcr4CreKO


title: 19010 BrKo_ TdT-negativ

description:
3082
norm_gene_counts_Cxcr4CreKO

value: microglia


title: RCMB28

source_name: PDX sample from RCMB28 patient


title: 19417 BrKo_ TdT-positiv

description:
3087
norm_gene_counts_Cxcr4CreKO


title: [delta]nctB_NoDrug_Rep3


title: 27-VIII-13-2-019 [MS_134]


title: MED1712FH

source_name: PDX sample from MED1712FH patient


title: [delta]nctB_NoDrug_Rep2


title: 27-VIII-13-3-012 [MS_133]


title: 19131 BrKo_ TdT-negativ

description:
3080
norm_gene_counts_Cxcr4CreKO


title: MB511H

source_name: PDX sample from MB511H patient


title: PR 148 [MS_132]


title: 19446 BrC_ TdT-positiv

description:
3079
norm_gene_counts_Cxcr4CreKO

value: Cxcr4CreER contol


title: RCMB38

source_name: PDX sample from RCMB38 patient


title: 19417 BrKo_ TdT-negativ

description:
3086
norm_gene_counts_Cxcr4CreKO


title: MB002

source_name: PDX sample from MB002 patient


title: [delta]nctB_NoDrug_Rep1


title: WT_0.5mg_mL_Itra_Rep3

description: 0.5mg_mL_Itra_Wt_vs_nctA.txt, 0.5mg_mL_Itra_Wt_vs_nctB.txt

value: A1160 pyrG+


title: PR 215 [MS_130]


title: DMB006

source_name: PDX sample from DMB006 patient


title: 27-VIII-13-3-015 [MS_129]


title: 19439 BrC_ TdT-negativ

description:
3076
norm_gene_counts_Cxcr4CreKO


title: 19446 BrC_ TdT-negativ

description:
3078
norm_gene_counts_Cxcr4CreKO


title: WT_0.5mg_mL_Itra_Rep1


title: WT_0.5mg_mL_Itra_Rep2


title: PR 166 [MS_128]


title: BT084

source_name: PDX sample from BT084 patient


title: DMB012

source_name: PDX sample from DMB012 patient


title: 19448 BrC_ TdT-positiv

description:
3075
norm_gene_counts_Cxcr4CreKO


title: WT_NoDrug_Rep3

description: NoDrug_Wt_vs_nctA.txt, NoDrug_Wt_vs_nctB.txt


title: 19447 BrC_ TdT-positiv

description:
3073
norm_gene_counts_Cxcr4CreKO


title: 19447 BrC_ TdT-negativ

description:
3072
norm_gene_counts_Cxcr4CreKO


title: 27-VIII-13-2-015 [MS_126]


title: ANK-MCM_ko2_22

city: Dresden

first: Attila

last: Toth

state: Saxony

address: Fiedlerstr. 42

department: Faculty of Medicine

institute: TU Dresden

description:
L26992_ANK-MCM_ko2_22
RNA-seq of Ankrd31-/- replicate B

data_processing:
Bcl2fastq 2.19.1
Alignment to mouse (mm10) reference with GSNAP (2018-03-11) and support of Ensembl 87 annotation to detect splice sites
FeatureCounts (1.6.0) was used to create fragment to gene counts; mm10 and Ensembl 87 annotation was used
Genome_build: mm10
Supplementary_files_format_and_content: the output of FeatureCounts; the first columns are geneid, chromosom, start, end, strand and length, followed by the raw counts for the 6 samples

source_name: KO_Mouse testis

extract_protocol:
RNA was extracted using the commercial available kit RNeasy Mini (Qiagen)
Strand specific RNA-Seq library preparation was performed with Ultra II Directional RNA Library Prep (New England Biolabs)

value: KO; 3xAnkrd31-/-

tag: age

value: 12 days post-partum

value: whole-testis


title: ANK-MCM_ko3_24

description:
L26994_ANK-MCM_ko3_24
RNA-seq of Ankrd31-/- replicate C


title: PR 233 [MS_131]


title: PR 132 [MS_124]


title: WT_NoDrug_Rep2


title: WT_NoDrug_Rep1


title: 27-VIII-13-2-010 [MS_125]


title: PR 229 [MS_123]


title: ANK-MCM_ko1_20

description:
L26990_ANK-MCM_ko1_20
RNA-seq of Ankrd31-/- replicate A


title: 27-VIII-13-2-017 [MS_122]


title: WT4_Q_LPS

city: Castellana Grotte (BA)

first: Grazia

last: Serino

address: Via Turi, 27

institute: National Institute of Gastroenterology “S. de Bellis”, Research Hospital

data_processing:
Basecalls performed using RTA version 2 (standard parameters)
Adapter cleavage was performed using (TGGAATTCTCGGGTGCCAAGG) using cutadapt tool
Read alignment was performed using iSmaRT (standard parameters)
Genome_build: mm9
Supplementary_files_format_and_content: File named "rawCount all samples" is a matrix table that contains data about miRNA raw count  for all samples

source_name: Bone marow dendritic cells

extract_protocol:
Total RNA including miRNAs were extracted using Qiagen miRNeasy mini kit according to the manufacturer's instructions.
Small RNA libraries were prepared using the TruSeq Small RNA Sample Preparation kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.

value: Dendritic cells from bone marrow

tag: growth protocol

value: Bone marrow cells from the tibiae and femurs of 7-week-old male mouse were flushed with PBS with 0.5mM EDTA (Thermo Fisher Scientific, MA, USA), and depleted of red blood cells with ACK (Ammonium-Chloride-Potassium) lysing buffer (Thermo Fisher Scientific, MA, USA). Cells were plated in a 10 ml dish (1x106 cells/mL) in RPMI-1640 (Thermo Fisher Scientific, MA, USA) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Thermo Fisher Scientific, MA, USA), 2mM L-glutamine, 1mM sodium pyruvate, 1 mM nonessential amino acids, 25 mM HEPES, 100 U/mL penicillin (Thermo Fisher Scientific, MA, USA), 100 mg/mL streptomycin (Thermo Fisher Scientific, MA, USA), 25 μg/mL rmGM-CSF (Miltenyi Biotec, Bergisch Gladbach, Germany), and 25 μg/mL rmIL-4 (Miltenyi Biotec, Bergisch Gladbach, Germany) at 37°C in a humidified 5% CO2 atmosphere. On day 5 cells were harvested, restimulated with new growth factors and plated 1x106 cells/mL on 12-well culture plate.

tag: treatment protocol

value: On day 5 and day 7, cells were treated with 25µM of aglycone quercetin powder (Farmalabor Srl, Italy). On day 8 BMDCs were stimulated with 1 μg/mL of LPS (Sigma-Aldrich, St Louis, MO, USA) for 6 hours.


title: WT4_Q

value: On day 5 and day 7, cells were treated with 25µM of aglycone quercetin powder (Farmalabor Srl, Italy).


title: PR 236 [MS_120]

value: PRTER

value: shallow


title: 27-VIII-13-2-005 [MS_118]

value: mesophotic


title: WT4_LPS

value: On day 8 BMDCs were stimulated with 1 μg/mL of LPS (Sigma-Aldrich, St Louis, MO, USA) for 6 hours.


title: ANK-MCM_wt2_21

description:
L26991_ANK-MCM_wt2_21
RNA-seq of Ankrd31+/+ replicate B

source_name: WT_Mouse testis

tag: strain background

value: wild type; 3xAnkrd31+/+


title: PR 244 [MS_117]


title: WT4_CTRL

value: no stimulation


title: S_late3

city: Wuhan

first: Bo

last: Du

state: Hubei

address: Luojiashan

institute: Wuhan University

data_processing:
The clean reads were compared to GenBank (release 209.0) and Rfam (release 11.0) to move other types of RNA (rRNA, snRNA, snoRNA, tRNA). Also, the clean tags were aligned with rice genome. Those mapped to exons or introns were removed, and the tags mapped to repeat sequences were also removed.
The rest of the unique sequences were used to search against the miRBase database (release 21, http://www.mirbase.org/) for known rice miRNA identification.

organism: Oryza sativa Japonica Group

source_name: Nippnbare

growth_protocol: BPH6-transgenic line and Nipponbare were sown in plastic cups (9 cm in diameter and 15 cm in height), with 15 plants per cup in a greenhouse, which was controlled to have 30 ± 2 °C/14 h light (07:00–21:00) and 28 ± 2 °C/10 h dark (21:00–07:00) cycles.

extract_protocol:
Total RNA was extracted from infested and mock the leaf sheathes using a RNAiso Plus kit (TaKaRa, code no. 9109) according to the manufacturer’s instructions.
The cDNA libraries were constructed for each sample using Ion Total RNA-Seq Kit v2.0  (Thermo Fisher, code no. 4475936) according to the manufacturer’s instructions.

treatment_protocol: At the four-leaf stage, the seedlings were infested with eight second-instar BPH per plant from 0 to 72 hours, and divided into non-infested control (0), early feeding stage including 6, 12 and 24 hours, and late feeding stage including 48, 60 and 72 hours. All treatments, each with three biological replicates, with each biological replicate having 15 seedlings per rice line used for analysis.

tag: cultivar

value: Nippnbare

tag: bph feeding status

value: late

value: Leaf sheath

tag: development stage

value: Four-leaf stage


title: PR 243 [MS_127]


title: S_late2-2


title: WT3_Q

tag: cell type

tag: strain

value: Bone marrow cells from the tibiae and femurs of 8-week-old male mouse were flushed with PBS with 0.5mM EDTA (Thermo Fisher Scientific, MA, USA), and depleted of red blood cells with ACK (Ammonium-Chloride-Potassium) lysing buffer (Thermo Fisher Scientific, MA, USA). Cells were plated in a 10 ml dish (1x106 cells/mL) in RPMI-1640 (Thermo Fisher Scientific, MA, USA) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Thermo Fisher Scientific, MA, USA), 2mM L-glutamine, 1mM sodium pyruvate, 1 mM nonessential amino acids, 25 mM HEPES, 100 U/mL penicillin (Thermo Fisher Scientific, MA, USA), 100 mg/mL streptomycin (Thermo Fisher Scientific, MA, USA), 25 μg/mL rmGM-CSF (Miltenyi Biotec, Bergisch Gladbach, Germany), and 25 μg/mL rmIL-4 (Miltenyi Biotec, Bergisch Gladbach, Germany) at 37°C in a humidified 5% CO2 atmosphere. On day 5 cells were harvested, restimulated with new growth factors and plated 1x106 cells/mL on 12-well culture plate.


title: WT3_Q_LPS


title: 28-VIII-13-2-004 [MS_116]


title: WT3_LPS


title: 27-VIII-13-2-013 [MS_113]


title: 27-VIII-13-3-013 [MS_115]


title: WT3_CTRL


title: WT2_Q_LPS


title: S_early3

value: before


title: 27-VIII-13-2-006 [MS_114]


title: S_late1


title: S_early2


title: 24-VIII-13-9-005 [MS_121]


title: ANK-MCM_wt1_19

description:
L26989_ANK-MCM_wt1_19
RNA-seq of Ankrd31+/+ replicate A

tag: genotype/variation

value: 12 days post-partum

value: whole-testis


title: PR 144 [MS_119]


title: PR 189 [MS_112]


title: PR 170 [MS_111]


title: WT2_LPS

value: Dendritic cells from bone marrow

value: Bone marrow cells from the tibiae and femurs of 8-week-old mouse mice were flushed with PBS with 0.5mM EDTA (Thermo Fisher Scientific, MA, USA), and depleted of red blood cells with ACK (Ammonium-Chloride-Potassium) lysing buffer (Thermo Fisher Scientific, MA, USA). Cells were plated in a 10 ml dish (1x106 cells/mL) in RPMI-1640 (Thermo Fisher Scientific, MA, USA) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Thermo Fisher Scientific, MA, USA), 2mM L-glutamine, 1mM sodium pyruvate, 1 mM nonessential amino acids, 25 mM HEPES, 100 U/mL penicillin (Thermo Fisher Scientific, MA, USA), 100 mg/mL streptomycin (Thermo Fisher Scientific, MA, USA), 25 μg/mL rmGM-CSF (Miltenyi Biotec, Bergisch Gladbach, Germany), and 25 μg/mL rmIL-4 (Miltenyi Biotec, Bergisch Gladbach, Germany) at 37°C in a humidified 5% CO2 atmosphere. On day 5 cells were harvested, restimulated with new growth factors and plated 1x106 cells/mL on 12-well culture plate.


title: 29-VIII-13-1-001 [MS_108]


title: 27-VIII-13-2-016 [MS_110]


title: WT2_CTRL


title: S_late2-1

tag: tissue


title: WT1_Q_LPS

value: On day 5 and day 7, cells were treated with 25µM of aglycone quercetin powder (Farmalabor Srl, Italy). On day 8 BMDCs were stimulated with 1 μg/mL of LPS (Sigma-Aldrich, St Louis, MO, USA) for 6 hours.


title: WT1_Q

value: On day 5 and day 7, cells were treated with 25µM of aglycone quercetin powder (Farmalabor Srl, Italy).


title: PR 224 [MS_105]

tag: site

value: PRTER

value: shallow


title: WT1_LPS

value: On day 8 BMDCs were stimulated with 1 μg/mL of LPS (Sigma-Aldrich, St Louis, MO, USA) for 6 hours.


title: PR 146 [MS_104]

tag: depth

value: mesophotic


title: 27-VIII-13-3-011 [MS_103]


title: PR 147 [MS_102]


title: PR 222 [MS_101]


title: WT2_Q


title: PR 163 [MS_100]


title: PR 234 [MS_099]


title: PR 228 [MS_098]


title: 27-VIII-13-3-016 [MS_107]


title: PR 235 [MS_097]


title: HFD_ileum_Treatment3

data_processing:
Barcode sequences were trimmed and rRNA reads were removed by aligning to the mm9 genome assembly using Bowtie 2-2.1.0
Non-rRNA reads were aligned to mm9 genome using Tophat 2.1.0
Transcript quantification using HOMER 4.8.3
Differentially expressed genes were identified by DESeq2 (Bioconductor-package)
Genome_build: mm9
Supplementary_files_format_and_content: Output from DESeq2. 1. Gene ID 2. baseMean 3. Log2FoldChange 4. lfcSE 5. stat 6. pvalue 7. padj. Log2FoldChange was calculated by comparing the treated samples to control samples at each indicated condition differentiation.

source_name: LDLr -/- mice

extract_protocol:
RNA was isolated with TRIzol reagent, as per the manufacturers instructions.
5 μg of total RNA was depleted of rRNA using a Ribo-Zero Gold kit (Epicentre) and first strand cDNA was made using 200 ng RNA, 3 ug random hexamers, 1 μg Superscript III, and standard dNTPs in the presence of Actinomycin D. First strand cDNA was purified by PCI extraction, ethanol precipitated, and resuspended in water. Second strand cDNA was synthesized with E. coli DNA polymerase, in the presence of E. coli DNA ligase and RNase H (all from NEB), using dNTPs in which dUTP was substituted for dTTP, at 16°C for 2 hrs. After purification on a Clean and Concentrate column (Zymo Research), cDNA was fragmented using Fragmentase (NEB), PCI extracted and precipitated as above. End repair, A-tailing, and barcoded adapter ligation were performed as described (Illumina), and the second strand cDNA was digested with USER enzyme (NEB). Libraries were amplified from the resulting adapter-ligated first-strand cDNA using Phusion (NEB) and 16 cycles of amplification. Libraries were size-selected on 1.5% agarose gels to a size range of ~180-250 bp.

treatment_protocol: The lyophilized peptide was dissolved in PBS (pH 7.4) containing 1% sucrose, resulting in a clear solution. The drinking water solution was replaced with fresh solution every other day. The mice were fed CHD or HFD with control (PBS with 1% sucrose) drinking water or peptide at a does of 180 μM (200 μg/mL) for two weeks.

value: Ileum

tag: genotype

value: LDLr -/-

tag: treatment

value: peptide

tag: diet

value: HFD


title: 27-VIII-13-3-014 [MS_096]


title: HFD_ileum_Treatment1


title: PR 238 [MS_095]


title: PR 149 [MS_094]


title: 1478_660_RNA

data_processing:
raw reads aligned to CanFam3.1 canine reference genome or GRCHM38 mouse reference genome using STAR
aligned transcripts were quantified using RSEM
Genome_build: GEMM and the mouse cell line were aligned to GRCHM38 mouse genome
Genome_build: Canine samples were aligned to CanFam3.1 canine genome
Supplementary_files_format_and_content: result files are in tabular format. These files have quantified TPM data with addional information.

source_name: tumor

extract_protocol:
RNA was isolated from preserved clinical tissue stored as cryopreserved tissue or FFPE tissue (except C2-C12, isolated from snap frozen cells folllowing harvesting from plateware). RNA isolation was performed at Beijing Genomics Institute
library construction was performed at Beijing Genomics Institute
Paired-End RNA sequencing of GEMM (mouse samples)
Single-End RNA sequencing (canine samples)

tag: tumor type

value: non-rhabdomyosarcoma soft tissue sarcoma

tag: sample type

value: primary tumor tissue; frozen tumor


title: R03-1

source_name: BPH6-transgenic line

value: BPH6-transgenic line

value: non-infested

value: Leaf sheath

value: Four-leaf stage


title: 27-VIII-13-3-008 [MS_092]


title: HFD_ileum_Control2

value: control


title: HFD_ileum_Control3


title: PR 159 [MS_090]


title: HFD_ileum_Treatment2


title: ARh2_0.1_3

city: Amsterdam

first: Anne-Catherine

last: Ahn

address: Science Park 904

department: IBED

country: Netherlands

institute: University of Amsterdam

data_processing:
The software program kallisto (Bray et al., 2016) (v0.44.0) was used to create index files for the quantification from those references (Tv. thiocyanoxidans ARh2T (NZ_ARQK00000000.1) and Tv. jannaschii ALM2T (NZ_ARLZ00000000.1)).
Pseudo-alignments were generated in kallisto by mapping the reads from the fastq RNA-Seq files against the indexed reference and reads were quantified using 100 bootstrap samples
Differential expression analysis was performed with the software program sleuth (Pimentel et al., 2017) (0.30.0) using the Wald test.
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample

organism: Thioalkalivibrio thiocyanoxidans ARh2

source_name: Bacterial cell

growth_protocol: Axenic cultures of Tv. jannaschii ALM2T and Tv. thiocyanoxidans ARh2T were grown in 200 ml batch cultures at 30°C on a shaker at 100 rpm. The medium was composed of 17.5 g/l Na2CO3, 13.9 g/l NaHCO3, 6.1 g/l NaCl, 1 g/l K2HPO4, 0.2 g/l MgCl2, 40 mM Na2S2O3, 5 mM NH4Cl and 1:1000 trace metals (Pfennig and Lippert, 1966). Sterile solutions of MgCl2, Na2S2O3 and trace elements were added from concentrated stock solutions after autoclaving. The final pH of the culture medium was adjusted to pH 9.8.

extract_protocol:
The frozen cell pellets were homogenized with a mortar and a pestle before being resuspended in QIAzol Lysis Reagent (Qiagen, Germany). Total RNA was extracted and purified with the RNeasy kit (Qiagen) following the manufacturer’s instructions. The purification step comprised a DNase treatment using the RNase-free DNase kit (Qiagen). The concentration was quantified with the NanoDrop ND2000 (Thermo Fisher Scientiﬁc, USA) and the integrity of the RNA was checked on the 2200 TapeStation with Agilent RNA ScreenTapes (Agilent Technologies, The Netherlands). Ribosomal RNA (rRNA) was removed by the Illumina Ribo-Zero rRNA Removal Kit (Bacteria) (Illumina, USA).
Bar-coded RNA libraries were prepared using the Ion Total RNA-Seq kit v2 and the Ion Xpress RNA-Seq barcoding kit according to the supplier’s instructions (Thermo Fisher Scientiﬁc). Ion Proton platform with an Ion PI Chip v3 (Thermo Fisher Scientiﬁc)

treatment_protocol: As(III) as sodium arsenite (NaAsO2) (Sigma Aldrich, USA) was added to the medium just before inoculation of the bacteria. Cultures were prepared at 0.1 mM As(III) for Tv. thiocyanoxidans ARh2 and Tv. jannaschii ALM2, and at 5 mM As(III) for Tv. jannaschii ALM2T.

tag: arsenite concentration (mm)


title: 29-VIII-13-1-003 [MS_091]


title: R_early3

value: before


title: R_early2-2


title: R_late1

value: late


title: S01-1

value: Nippnbare


title: R_early2-1


title: R_early1-2


title: R03-2


title: S02-2


title: S03-1


title: R_late3


title: R_early1-1


title: S01-2


title: S03-2


title: R_late2


title: S02-1


title: S_early1


title: ARh2_0.1_2


title: HFD_ileum_Control1


title: R01-2


title: PR 225 [MS_089]

value: PRTER

value: shallow


title: ARh2_0.1_1


title: CHD_ileum_Treatment3

value: CHD


title: CHD_ileum_Treatment2

value: Ileum


title: ARh2_Ref3


title: R02


title: R01-1


title: S-late-3

data_processing:
The clean reads were then aligned to rice genome (TIGR7) using the Hisat2.
HTseq was used to get gene counts and RPKM method was used to determine the gene expression.
Supplementary_files_format_and_content: Excel file with RPKM

source_name: Nipponbare

extract_protocol:
Total RNA was extracted from infested and mock the leaf sheathes using a RNAiso Plus kit (TaKaRa, code no. 9109) according to the manufacturer’s instructions.
The cDNA libraries were constructed for each sample using the NEBNext® Ultra™ directional RNA library prep kit (NEB, code no. E7420S) according to the manufacturer’s instructions.

value: Nipponbare

value: late feeding stage (48-72h)


title: S-late-2


title: anp1_UI

city: Tsukuba

first: Yoshikazu

last: Shimoda

state: Ibaraki

address: 3-1-1 Kannondai

country: Japan

institute: National Agriculture and Food Research Organization

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Obtained Fastq sequences were subjected to four steps of quality filtering and trimming by FastX-toolkit. Step1: select the reads with more than QV10 accounting for more than 10% (fastq_quality_filter). Step2: trim the sequence less than QV10 and select the reads of more than 30bp (fastq_quality_trimmer). Step3: remove the repetitive sequences (fastx_artifacts_filter). Step4: Remove the adaptor sequences if the read contains more than 5 characters of the adapter sequence from the 3’ end and select the reads of more than 30bp (fastx_clipper).
Selected reads were mapped to Lotus japonicus coding sequence (build 2.5) including 5' UTR and 3' UTR using Bowtie2 (ver. 2.0.2).
Normalization of mapped read counts was performed using DEseq with iDEGES/DESeq (Sun et al., BMC Bioinformatics, 2013).
Genome_build: build 2.5
Supplementary_files_format_and_content: tab-delimited text files include original mapped read count and DESeq normalized count.

organism: Lotus japonicus

source_name: root

growth_protocol: Lotus japonicus was planted in vermiculite soil supplemented with nitrogen-free B&D medium and was grown in a growth chamber under 16 h/8 h light/dark cycle at 25°C/23°C.

extract_protocol:
Nodule primordias and developing nodules were excised from roots. Total RNA was isolated using Cetyltrimethylammonium Bromide (CTAB) and LiCl. Total RNA was treated with DNase (Qiagen) and Ribo-Zero kit for plant seed/root and for gram-negative bacteria (Epicentre) to remove genomic and ribosomal DNA. 50 ng of RNA was used for library preparation.
RNA libraries were prepared using Scriptseq Ver2 library preparation kit (Epicentre) by following manufacture's instructions

treatment_protocol: Mesorhizobium loti was inoculated at 7 days after planting into vermiculite.

tag: plant genotype

value: Fix- mutant

tag: inoculation (rhizobial strain)

tag: time

value: root


title: WT(MG20)_UI

value: wild type


title: ARh2_Ref2


title: PR 168 [MS_087]

value: mesophotic


title: PR 167 [MS_086]


title: WT1_CTRL

value: Dendritic cells from bone marrow

tag: growth protocol

value: Bone marrow cells from the tibiae and femurs of 8-week-old male mouse were flushed with PBS with 0.5mM EDTA (Thermo Fisher Scientific, MA, USA), and depleted of red blood cells with ACK (Ammonium-Chloride-Potassium) lysing buffer (Thermo Fisher Scientific, MA, USA). Cells were plated in a 10 ml dish (1x106 cells/mL) in RPMI-1640 (Thermo Fisher Scientific, MA, USA) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Thermo Fisher Scientific, MA, USA), 2mM L-glutamine, 1mM sodium pyruvate, 1 mM nonessential amino acids, 25 mM HEPES, 100 U/mL penicillin (Thermo Fisher Scientific, MA, USA), 100 mg/mL streptomycin (Thermo Fisher Scientific, MA, USA), 25 μg/mL rmGM-CSF (Miltenyi Biotec, Bergisch Gladbach, Germany), and 25 μg/mL rmIL-4 (Miltenyi Biotec, Bergisch Gladbach, Germany) at 37°C in a humidified 5% CO2 atmosphere. On day 5 cells were harvested, restimulated with new growth factors and plated 1x106 cells/mL on 12-well culture plate.

tag: treatment protocol

value: no stimulation


title: S-early-3

value: Leaf sheath

tag: development stage

value: Four-leaf stage

tag: cultivar

tag: bph feeding status

value: early feeding stage (6-24h)


title: CHD_ileum_Control3

tag: tissue

value: LDLr -/-

value: control


title: CHD_ileum_Treatment1

value: peptide


title: PR 160 [MS_088]

tag: site

value: PRTER


title: PR 226 [MS_085]

tag: depth

value: shallow


title: S-late-1

value: Nipponbare


title: CHD_ileum_Control2

value: Ileum

tag: genotype

value: CHD


title: CHD_ileum_Control1

tag: treatment


title: 27-VIII-13-2-020 [MS_084]


title: S-early-2


title: HFD_liver_Treatment3

value: Liver

tag: diet

value: HFD


title: PR 227 [MS_083]


title: PR 169 [MS_082]

value: mesophotic


title: HFD_liver_Treatment2


title: HFD_liver_Control3


title: S-0-1

value: non-infested (0h)


title: S-0-2


title: S-0-3


title: 27-VIII-13-2-014 [MS_081]


title: S-early-1


title: ARh2_Ref1


title: PR 221 [MS_080]


title: HFD_liver_Control2


title: HFD_liver_Control1


title: R-late-3

value: BPH6-transgenic line

value: late feeding stage (48-72h)


title: R-late-2

value: Leaf sheath


title: CHD_liver_Treatment3


title: CHD_liver_Treatment2


title: 24-VIII-13-9-003 [MS_077]


title: R-early-2

value: Four-leaf stage


title: R-early-3

value: early feeding stage (6-24h)


title: R-late-1


title: CHD_liver_Treatment1

value: LDLr -/-


title: HFD_liver_Treatment1


title: R-early-1


title: CHD_liver_Control2

value: control


title: CHD_liver_Control3


title: PR 165 [MS_074]


title: R-0-3


title: CHD_liver_Control1


title: R-0-2


title: 29-VIII-13-1-005 [MS_071]


title: R-0-1


title: PR 219 [MS_070]


title: PR 164 [MS_078]


title: PR 220 [MS_079]


title: PR 251 [MS_072]


title: PR 161 [MS_076]


title: 27-VIII-13-3-010 [MS_066]


title: PR 250 [MS_067]


title: ALM2_5_3

organism: Thioalkalivibrio jannaschii


title: PR 143 [MS_075]


title: 6-III-16-2-86 [MS_064]

value: CBC


title: 6-III-16-1-90 [MS_065]


title: PR 237 [MS_069]

value: PRTER


title: 5-III-16-2-2 [MS_063]


title: ALM2_5_1


title: 5-III-16-1-139 [MS_062]

value: shallow


title: ALM2_5_2


title: 7-III-16-2-129 [MS_061]


title: 5-III-16-1-140 [MS_060]


title: 5-III-16-2-5 [MS_058]


title: ALM2_0.1_1


title: 27-VIII-13-2-008 [MS_073]


title: ALM2_Ref3


title: 7-III-16-2-132 [MS_057]


title: PR 218 [MS_068]


title: ALM2_Ref2


title: ALM2_Ref1


title: 6-III-16-2-2 [MS_054]


title: 5-III-16-1-143 [MS_050]


title: 4-III-16-2-68 [MS_051]


title: ALM2_0.1_3


title: ALM2_0.1_2


title: 5-III-16-3-4 [MS_049]


title: 5-III-16-2-4 [MS_053]


title: 8-III-16-3-135 [MS_052]


title: 7-III-16-2-1 [MS_040]


title: 6-III-16-1-91 [MS_039]


title: 6-III-16-1-5 [MS_046]


title: 5-III-16-2-142 [MS_045]


title: 5-III-16-1-4 [MS_043]


title: 5-III-16-2-145 [MS_044]


title: 7-III-16-2-126 [MS_037]


title: 8-III-16-1-137 [MS_042]


title: 5-III-16-3-5 [MS_036]


title: 5-III-16-3-2 [MS_035]


title: 6-III-16-2-98 [MS_034]


title: 7-III-16-2-100 [MS_048]


title: 6-III-16-3-3 [MS_056]