title: A549 cells treated with BaP for 2w_rep6

city: Brno

first: Jirina

last: Prochazkova

address: Kralovopolska 135

department: Cytokinetics

country: Czech Republic

institute: Institute of Biophysics CAS

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: A549 cells were cultivated in plastic cell culture dishes (TPP, Transadigen, Switzerland) at 37 °C in an atmosphere of 5% CO2.

extract_protocol: Total RNA was isolated with NucleoSpin RNA II Purification Kit (Macherey Nagel, Düren, Germany) kit in accordance with the prescribed protocol provided with the kit. Quality control was performed.

treatment_protocol: A549 cells were treated with DMSO (0.01%), TCDD 10 nM, BaP (1 mM) for 2 weeks.

value: lung carcinoma


title: Hyp3_OX-At-tg/+

status: Public on Sep 01 2019

type: SRA

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

library_source: transcriptomic

data_processing:
Sequencing data was processed using the Illumina Pipeline Software version 1.82.
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.2.1, Martin 2011), and filtered for low complexity with Prinseq (v. 0.20.3, Schmieder and Edwards 2011).
Reads were aligned against Mus_musculus genome GRCm38 using TopHat2 (v. 2.0.9, Kim et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.5.4p3, Anders et al. 2014) using Ensembl annotation 75.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for each Sample.

molecule: total RNA

organism: Mus musculus

source_name: hypothalamus, Hcrt/Orexin-ataxin-3 transgenic, replicate 3

extract_protocol:
Total RNA from mice cortex, hypothalamus and brainstem was isolated with the RNeasy Lipid Tissue Midi kit (Quiagen).
RNA-seq libraries were prepared using 500 ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA) on a Caliper Sciclone liquid handling robot (PerkinElmer; Waltham, Massachusetts, USA) using a Caliper-developed automated script.

tag: strain

tag: tissue

value: hypothalamus

tag: genotype/variation

value: Hcrt/Orexin-ataxin-3 transgenic

tag: mouse model reference


title: Hog1_t15

city: Jerusalem

first: Nir

last: Friedman

address: Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
The original samples contained R2 to read inner barcodes and unique molelcular identifiers.
Base calling was performed with bcl2fastq (2.17).
Samples were demultiplexed using internal barcodes.
Reads were mapped to the yeast (sacCer3) genome using  bowtie2 default parameters.
Duplicated reads were filtered using UMI, to remove PCR bias.
To estimate the expression level of each gene we counted the number of reads that  mapped to the 3’ end of the gene (from 350bp upstream to 200bp downstream of  TTS).
Reads of HSP12 gene were counted separately after mapping of the raw data to the HSP12-GFP cassette.
The read counts in each sample were normalized to PPM.
Genome_build: sacCer3
Supplementary_files_format_and_content: A table containing the normalized read counts for each yeast gene in each one of the 144 samples.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Yeast strains were grown in SC media at 30°C with constant shaking to OD<1.

extract_protocol:
RNA was purified using a high-throughput RNA isolation protocol (Dye et al. 2005). Briefly, cells were washed in ddw and incubated with Proteinase K (Epicentre MPRK092) and 1% SDS at 70℃ to release the RNA. Cell debris were precipitated by centrifugation in the presence of KOAc precipitation solution. Finally the RNA was purified from the supernatant using nucleic acid binding plates (UNIFILTER plates, catalog #7700-2810) and was stored with RNAse-inhibitor (Murine #M0314L) at -80°C.
RNA-libraries were prepared as previously described (Klein-Brill et al. 2019). Briefly, RNA was reverse transcribed using  SmartScribe enzyme (TaKaRa) and in the presence of  oligo-dT RT primers with a 7bp barcode and a 8bp UMI (a gift from Ido Amit). Barcoded samples were then pooled and purified using SPRI beads X1.2 (AMPure XP). DNA-RNA molecules were tagmented using Tn5 transposase (loaded with oligo Tn5MEDS-A) and 0.2% SDS was used to strip off the Tn5 from the DNA (Picelli et al. 2014). followed by a SPRI X2 clean up. NGS sequences were added to the tagmented DNA by PCR (KAPA HiFi HotStart ReadyMix 2X - KAPA 33 Biosystems KM2605, 12 cycles). Finally, DNA was purified using double SPRI (X0.65  SPRI to clean large fragments followed by X0.8 SPRI beads).

treatment_protocol: Cells were  exposed to osmotic stress (final concentration of 0.4M KCL) and fixed in cold methanol (-80°C) at 0, 5, 10, 15, 20, 30, 45 and 60 minutes after stress addition.

tag: time-point


title: Hyp2_OX-KO

source_name: hypothalamus, Hcrt/Orexin knockout, replicate 2

value: Hcrt/Orexin knockout


title: 202075-positive_bisulfite

type: genomic

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

country: USA

institute: WRAIR

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Beachips were scanned using iScan software on a Hiscan

data_processing:
Raw intesities were imported into Champ R package to preprocess the data.We filtered 8877 probes with a detection p-value above 0.01 in one or more samples, 281 probes with beadcount <3 in at least 5% of samples, 26935 probes with overlapped SNPs, 8405 probes with multiple aligned locations, and 11066 probes on the X and Y chromosomes. Channel Quantile plus BMIQ normalization method was conducted
Raw data are available in the .idat files on the sample records and in the text file unmethylated_and_methylated_signal_intensities.txt on the series record.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from PAXgene DNA Blood tubes

value: Whole blood

tag: gender

value: Male

tag: ptsd diagnosis

value: positive


title: 201198-negative_bisulfite

value: negative


title: 201151-negative_bisulfite


title: A549 cells treated with BaP for 2w_rep4

type: RNA

label: biotin

tag: cell type


title: A549 cells treated with BaP for 2w_rep5


title: Hyp2_OX-At-tg/+

source_name: hypothalamus, Hcrt/Orexin-ataxin-3 transgenic, replicate 2


title: Hog1_t05


title: A549 cells treated with BaP for 2w_rep3


title: Hyp1_OX-KO

source_name: hypothalamus, Hcrt/Orexin knockout, replicate 1


title: Hog1_t10


title: Hog1_t00


title: 202143-positive_bisulfite


title: Hyp1_OX-At-tg/+

source_name: hypothalamus, Hcrt/Orexin-ataxin-3 transgenic, replicate 1


title: Hog1_2_t60


title: CX6_OX-+/+

source_name: cortex, Hcrt/Orexin wildtype, replicate 3

value: cortex

value: Hcrt/Orexin wildtype


title: Hog1_2_t45


title: 201018-negative_bisulfite


title: CX6_OX-At-+/+

source_name: cortex, Hcrt/Orexin-ataxin-3 wildtype, replicate 3

value: Hcrt/Orexin-ataxin-3 wildtype


title: Hog1_2_t30


title: Hog1_2_t20


title: Hog1_2_t15


title: CX5_OX-At-+/+

source_name: cortex, Hcrt/Orexin-ataxin-3 wildtype, replicate 2


title: 201017-positive_bisulfite


title: CX5_OX-+/+

source_name: cortex, Hcrt/Orexin wildtype, replicate 2


title: 201232-negative_bisulfite


title: A549 cells treated with BaP for 2w_rep2


title: A549 cells treated with TCDD for 2w_rep6


title: CX4_OX-+/+

source_name: cortex, Hcrt/Orexin wildtype, replicate 1


title: A549 cells treated with TCDD for 2w_rep4


title: Hog1_2_t10


title: A549 cells treated with TCDD for 2w_rep5


title: A549 cells treated with TCDD for 2w_rep1


title: A549 cells treated with TCDD for 2w_rep3


title: A549 cells treated with BaP for 2w_rep1


title: A549 cells treated with TCDD for 2w_rep2


title: 202002-negative_bisulfite


title: Hog1_2_t05


title: CX3_OX-KO

source_name: cortex, Hcrt/Orexin knockout, replicate 3


title: CX4_OX-At-+/+

source_name: cortex, Hcrt/Orexin-ataxin-3 wildtype, replicate 1


title: A549 cells treated with DMSO for 2w_rep5


title: A549 cells treated with DMSO for 2w_rep6


title: Hog1_2_t00


title: 202223-positive_bisulfite


title: 201178-negative_bisulfite


title: CX3_OX-At-tg/+

source_name: cortex, Hcrt/Orexin-ataxin-3 transgenic, replicate 3


title: 201009-negative_bisulfite


title: 202101-negative_bisulfite


title: Gal11_t60


title: A549 cells treated with DMSO for 2w_rep3


title: A549 cells treated with DMSO for 2w_rep4


title: Gal11_t45


title: CX2_OX-KO

source_name: cortex, Hcrt/Orexin knockout, replicate 2


title: CX2_OX-At-tg/+

source_name: cortex, Hcrt/Orexin-ataxin-3 transgenic, replicate 2


title: Gal11_t30


title: CX1_OX-KO

source_name: cortex, Hcrt/Orexin knockout, replicate 1


title: A549 cells treated with DMSO for 2w_rep2


title: Gal11_t20

source_name: Saccharomyces cerevisiae


title: CX1_OX-At-tg/+

source_name: cortex, Hcrt/Orexin-ataxin-3 transgenic, replicate 1


title: 201399-negative_bisulfite

source_name: Whole blood


title: 201287-negative_bisulfite


title: 201205-positive_bisulfite


title: 202085-positive_bisulfite


title: 201242-negative_bisulfite


title: Gal11_t15


title: BS6_OX-+/+

source_name: brainstem, Hcrt/Orexin wildtype, replicate 3

value: brainstem


title: Gal11_t10


title: 201042-negative_bisulfite


title: 202094-positive_bisulfite


title: A549 cells treated with DMSO for 2w_rep1


title: HepaRG cells treated with TCDD for 24h_rep4

source_name: HepaRG_TCDD for 24h

growth_protocol: HepaRG cells were cultivated in plastic cell culture dishes (TPP, Transadigen, Switzerland) at 37 °C in an atmosphere of 5% CO2.

treatment_protocol: HepaRG cells were treated with DMSO (0.01%), TCDD 10 nM for 24 h

tag: cell line

value: HepaRG

value: hepatic progenitors

tag: treatment

value: TCDD 10 nM for 24 h


title: 202073-positive_bisulfite


title: HepaRG cells treated with TCDD for 24h_rep3


title: 202112-positive_bisulfite


title: Gal11_t05


title: BS5_OX-+/+

source_name: brainstem, Hcrt/Orexin wildtype, replicate 2


title: BS6_OX-At-+/+

source_name: brainstem, Hcrt/Orexin-ataxin-3 wildtype, replicate 3


title: Gal11_t00


title: HepaRG cells treated with TCDD for 24h_rep2


title: BS5_OX-At-+/+

source_name: brainstem, Hcrt/Orexin-ataxin-3 wildtype, replicate 2


title: BS4_OX-+/+

source_name: brainstem, Hcrt/Orexin wildtype, replicate 1


title: Eaf7_t45


title: 201318-positive_bisulfite


title: BS4_OX-At-+/+

source_name: brainstem, Hcrt/Orexin-ataxin-3 wildtype, replicate 1


title: 201194-positive_bisulfite


title: HepaRG cells treated with DMSO for 24h_rep4

source_name: HepaRG_DMSO for 24h


title: HepaRG cells treated with TCDD for 24h_rep1


title: HepaRG cells treated with DMSO for 24h_rep3


title: 202052-negative_bisulfite


title: 201140-negative_bisulfite


title: Eaf7_t60


title: Eaf7_t20


title: BS3_OX-KO

source_name: brainstem, Hcrt/Orexin knockout, replicate 3


title: yaptaz-ccl4-3

city: Boston

first: Rory

last: Kirchner

state: MA

address: 677 Huntington Ave

department: Department of Biostatistics

institute: Harvard T.H. Chan School of Public Health

description:
note: replicates do not denote paired samples, they are just unique identifiers within a sample class
counts.csv

data_processing:
Samples were processed through the RNA-seq pipeline implemented in bcbio-nextgen version 1.0.0a0-8aa8f0c.
Quality control metrics were generated through alignment with STAR version 2.4.1d to mm10 augmented with Ensembl gene annotations. A combination of FastQC, qualimap and custom tools were used to generate a suite of quality control metrics to check for samples failing quality control and other non-biological possible confounders.
Transcript-level quantification was performed with Sailfish version 0.10.1 and transcript-level estimates were collapsed to gene-level counts using tximport.
Gene-level differential expression was performed with DESeq2. Both an interaction model (~genotype+treatment+genotype:treatment) and a pairwise model (~genotype_treatment) were fit to the data.
GO ontology and KEGG pathway analysis was performed with GSEA, ranking genes by signal to noise ratio for a given contrast.
Genome_build: mm10
Supplementary_files_format_and_content: counts.csv: table of counts per gene generated from tximport of sailfish quantitated transcripts, suitable for use with DESeq2/edgeR/limma/etc

source_name: hepatocytes, FACS sorted

extract_protocol:
FACS sorted hepatocytes were purified using a Qiagen MicroRNEasy kit
NEBNext Ultra II RNA Library Prep kit

treatment_protocol: male mice 2-3 months old were FACS sorted.  CCl4 injury was given at 1 ug/g, 7x every 3 days.  Hepatocytes were gathered 3 days after last dose of CCl4.

value: hepatocytes

tag: genotype

value: Yap/Taz KO

tag: Sex

value: male

tag: age

value: 2-3 months

tag: replicate


title: Eaf7_t15


title: 202004-positive_bisulfite


title: BS3_OX-At-tg/+

source_name: brainstem, Hcrt/Orexin-ataxin-3 transgenic, replicate 3

value: Hcrt/Orexin-ataxin-3 transgenic


title: yaptaz-ccl4-2


title: HepaRG cells treated with DMSO for 24h_rep2


title: yaptaz-ccl4-1


title: HepaRG cells treated with DMSO for 24h_rep1


title: BS2_OX-KO

source_name: brainstem, Hcrt/Orexin knockout, replicate 2

value: Hcrt/Orexin knockout


title: 202050-positive_bisulfite

value: Whole blood


title: BS2_OX-At-tg/+

source_name: brainstem, Hcrt/Orexin-ataxin-3 transgenic, replicate 2


title: yaptaz-untreated-4

value: untreated


title: yaptaz-untreated-3


title: Eaf7_t05


title: 201234-positive_bisulfite

value: Male

value: positive


title: BS1_OX-KO

source_name: brainstem, Hcrt/Orexin knockout, replicate 1


title: Eaf7_t10

source_name: Saccharomyces cerevisiae


title: yaptaz-untreated-1


title: Eaf7_t00


title: BS1_OX-At-tg/+

source_name: brainstem, Hcrt/Orexin-ataxin-3 transgenic, replicate 1


title: yaptaz-untreated-2


title: 202197-negative_bisulfite

source_name: Whole blood

value: negative


title: cGAMP high rep 1

city: Berkeley

first: David

last: Raulet

state: CA

address: 485 Life Sciences addition

department: Molecular and Cell Biology

institute: University of California Berkeley

description: Mageck_counts ML cGAMP.txt

library_source: genomic

data_processing:
Library strategy: CRISPR screen
Sequencing data was collected as part of the primary run processing using the innate HiSeq control software. Multiplexed sequencing data were demultiplexed using the BCL2Fastq program (version 2.17 and later).
The Python-based ScreenProcessing pipeline (https://github.com/mhorlbeck/ScreenProcessing) was used to analyze the CRISPRi sequencing results.
Illumina 50bp single end sequencing reads for pooled sublibraries one to four and five to seven were trimmed to 29bp and guides were quantified by counting exact matches to the CRISPRi v2 human library guides.
Counts from the ScreenProcessing pipeline were then used as input to the MAGeCK program (0.5.2.) to generate gRNA counts per gene
Genome_build: hg19
Supplementary_files_format_and_content: txt file generated by MaGeck showing CRISPRi v2 gRNA counts per gene

source_name: THP-1 monocyte

growth_protocol: THP-1 cells were cultured at 37°C in humidified atmosphere containing 5% CO2 with RPMI-1640 media supplemented with 100 U/ml penicillin, 100 μg/ml streptomycin, 0.2 mg/ml glutamine, 10 μg/ml gentamycin sulfate, 20 mM Hepes and 10% FCS. Cells were transduced with CDN reporter, dCas9-BFP-KRAB and single cell sorted. One clone was maintained in two separate cultures of THP-1 cells, and were transduced with the human genome-wide CRISPRi v2 library. Each culture was divided in two and screened separately after treatment with 2’3’-RR CDA or 2’3’-cGAMP, followed by selection and analysis. Hence, each screen was performed twice, with independent library transductions. For each transduction, the THP-1 clone was expanded to 3.2 x 10E8 cells and transduced with the human genome-wide CRISPRi v2 library, which contains approximately 100,000 gRNAs targeting around 20,000 genes. Sufficient cells were transduced and propagated to maintain at least 5 x 10E7 transduced (BFP+) cells, representing 500x coverage of the gRNA library. The transduction efficiency was around 20% to minimize the chance of multiple lentiviral integrations per cell. Two days after transduction, cells were cultured in the presence of puromycin for two days and one additional day without puromycin.

extract_protocol:
Genomic DNA was isolated from sorted cells using NucleoSpin Blood kits (Macherey-Nagel). PCR was used to amplify gRNA cassettes with Illumina sequencing adapters and indexes as described previously44. Genomic DNA samples were first digested for 18 hours with SbfI-HF (NEB) to liberate a ~500 bp fragment containing the gRNA cassette. The gRNA cassette was isolated by gel electrophoresis using NucleoSpin Gel and PCR Clean-up kits (Macherey-Nagel), and the DNA was then used for PCR.
Indexed samples were pooled and sequenced on an Illumina HiSeq-2500 for the 2’3’RR CDA screen and an Illumna HiSeq-4000 for the 2’3’-cGAMP screen using a 1:1 mix of two custom sequencing primers. Sequencing libraries were pooled proportional to the number of sorted cells in each sample. The target sequencing depth was at least 2,000 reads/gRNA in the library for unsorted “background” samples, and at least 10 reads/cell in sorted samples.

treatment_protocol: 4 x 10^8 cells were seeded to a density of 106 cells/ml and stimulated with 2’3’-RR CDA (2 µg/ml) or 2’3’-cGAMP (15 µg /ml). 20h later, cells were harvested, washed in PBS, and sorted based on BFP expression (presence of gRNAs), GFP expression (presence of reporter) and tdTomato expression using the BD Influx cell sorter and BD FACSaria Fusion cell sorter.

tag: facs sort

value: sorted for low CDN reporter expression

tag: stimulation

value: 2'3' cGAMP


title: 202171-positive_bisulfite


title: Eaf7_t30


title: wt-ccl4-5

value: wildtype


title: EGFP negative replicate 3

data_processing:
Sequencing data was processed using the Illumina Pipeline Software version 1.84.
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011). Reads matching to ribosomal RNA sequences were removed with fastq screen (v. 0.9.3). Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis 2013).
Reads were aligned against Mus musculus.GRCm38.86 genome using STAR (v. 2.5.2b, Dobin 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1, Anders et al. 2014) using Ensembl annotation 86.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for each Sample.

source_name: primary neuronal cultures from E18 hypothalamus

growth_protocol: For primary neuronal cultures and neurosphere formation for HCRT and MCH cell sorting, E18 embryonic hypothalami were dissected and cells were dissociated and suspended in neurosphere medium.

extract_protocol:
Sorted cells were collected in the medium or RLT lysis buffer of RNA extraction kit and total RNA was isolated using the RNeasy Micro kit (QIAGEN 74004) .
Double stranded cDNA for RNA-seq library preparation was generated using SMART-Seq v4 Ultra Low Input RNA reagents (Catalog Number 634888, Clontech, Mountain View, California, USA) according to the protocol provided with the reagents beginning with 2ng (Mch cells) or 0.8ng (for Hcrt cells) of total RNA and using 11 cycles of PCR amplification.  150 pg of the resulting cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (Catalog Number 15032354, Illumina, San Diego, California, USA) using the single cell RNA-seq library preparation protocol developed for the Fluidigm C1 (Fluidigm, South San Francisco, California, USA).

treatment_protocol: After addition of appropriate virus (lentivirus particles for MCH and AAV for HCRT cell sorting at MOI=10), cells were seeded in low adherent 96 wells in neurosphere medium. The same medium containing bFGF (10ng/ml) was added to the neurospheres 24h later. After one week in this medium the cells were dissociated for cell sorting.

tag: sorted cells

value: EGFP negative


title: wt-ccl4-4


title: EGFP negative replicate 1

tag: strain


title: cGAMP low rep 1

description: Mageck_counts ML cGAMP.txt


title: EGFP negative replicate 2


title: EGFP positive, replicate 3

value: EGFP positive


title: cGAMP background rep 2

description: Mageck_counts ML cGAMP.txt

value: unsorted control


title: cGAMP low rep 2

description: Mageck_counts ML cGAMP.txt

value: sorted for high CDN reporter expression


title: wt-ccl4-2

value: hepatocytes


title: wt-ccl4-3

value: male


title: EGFP positive, replicate 2


title: 202192-negative_bisulfite

tag: tissue


title: cGAMP background rep 1

description: Mageck_counts ML cGAMP.txt


title: wt-ccl4-1

value: 2-3 months


title: 201154-negative_bisulfite


title: 202123-positive_bisulfite


title: mCherry negative, replicate 3

value: mCherry negative


title: wt-untreated-1


title: mCherry positive, replicate 3

value: mCherry positive


title: wt-untreated-4


title: mCherry negative, replicate 2


title: wt-untreated-5


title: 202069-negative_bisulfite

value: Whole blood


title: 202088-positive_bisulfite


title: 201283-positive_bisulfite


title: wt-untreated-3

value: untreated


title: 202021-positive_bisulfite

value: Male


title: mCherry positive, replicate 2


title: wt-untreated-2


title: 202005-positive_bisulfite

value: positive


title: 201110-negative_bisulfite

value: negative


title: Exon 2 of tapasin gene in wild type Expi293F cells

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

data_processing:
Data was analyzed using Enrich: http://depts.washington.edu/sfields/software/enrich/
Fuser script (add 100 to index numbers for read2 when fastq files were generated with a 2x250nt instead of 2x150nt protocol): python Paired_read_fuser.py --path output/ --read1 TAPBPR_R2.fastq.bz2 --read2 TAPBPR_R1.fastq.bz2 --wtseq GGTGCGCACCGTGGAGCTCTCGCCAGCAGTGAGGAC --read1_overlap_start 22 --read1_overlap_end 58 --read2_overlap_start 34 --read2_overlap_end 70 --mode B --paired_mismatch_threshold 250
Aligner script:python Fused_read_aligner.py --path output/ --infile TAPBPR_R2.fast_B_qc1 --referenceDNA GGTGCGCACCGTGGAGCTCTCGCCAGCAGTGAGGAC --referenceAA GAHRGALASSED --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode B
MapCounts script: python mapCounts.py --path output/ --infile TAPBPR_R2.fast_B_qc1_PRO_qc2
MapRatios script: Example: python mapRatios.py --path ratios/ --templatepath /deepseq_scripts/r_deepseq_scripts/ --infile2 mapcounts_library --infile1 mapcounts_sorted
MapParts script: python mapParts.py --path ratios/ --infile mapratios_sorted_library --mode mutations:1
Unlink script:  python mapUnlink.py --path ratios/ --infile mapratios_sorted_library.m1 --type protein --mode ratios --size 12
In Excel, the log(base2) enrichment ratio of the wildtype sequence was subtracted from the log(2) enrichment ratios for all single mutations.
Genome_build: Not applicable
Supplementary_files_format_and_content: Excel spreadsheet of log(base2) enrichment ratios for each single amino acid substitution.  Also includes the frequency of each mutation in the naïve plasmid library.

source_name: Expi293F cell culture (wild type)

growth_protocol: For yeast surface display experiments to look at TAPBPR binding to HLA-A*02:01 tetramers, EBY100 yeast were electroporated with the TAPBPR scoop loop plasmid library, cultured in SDCAA medium at 30 deg C, and then protein expression was induced at a density of OD(600nm) = 0.5 in SGCAA for 3 days at 24 deg C. Induced yeast were incubated with HLA-A*02:01 tetramers (loaded with Goldie-Tax peptide) conjugated to APC, and with anti-myc-FITC to detect surface TAPBPR expression.  After washing, cells were FACS sorted based on expression (collected cells were positive in the FITC channel) and based on HLA-A*02:01 binding (highest 2.5% in the APC channel).

extract_protocol:
For yeast display, plasmid DNA was harvested from unsorted and sorted cells. For experiments in human Expi293F tapasin-KO cells, cDNA was synthesized from total RNA of the sorted cells and compared to the naive plasmid library.  In all cases, the scoop loop region was PCR amplified in 2 steps; in the first, primer overhangs added sequences for annealing to the Illumina sequencing primers, and in the second, primer overhangs added unique barcodes and Illumina adaptors.
Primer pair for 1st round of PCR to amplify TAPBPR scoop loop: Illumina_TAPBPR_111F (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAGACTGTTTCCTGGTGAAGG) and Illumina_TAPBPR_229R (TCTTTCCCTACACGACGCTCTTCCGATCTCCTTGGAAATCGGTGAAGTC).
Primer pair to amplify tapasin exon 2: Tapasin_Illumina_FOR (TCTTTCCCTACACGACGCTCTTCCGATCTGGCGACCGCCGTCTCAG) and Tapasin_Illumina_REV (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCAACAGCAGTGCACCGGGTC).
Primer pair for 2nd round of PCR (added I5 and I7 Illumina adaptors): MiSeq_Start_Adaptamer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and MiSeq_Index_Adaptamer (CAAGCAGAAGACGGCATACGAGAT-6nt-barcode-GTGACTGGAGTTCAGACGTGTGCTCTTC)
Amplicons were deep sequenced on a MiSeq using a 2x150nt PE v2 protocol (HLA-A2 processing experiments), Miseq using a 2x150nt PE NANO v2 protocol (validation of tapasin-kock out line), or HiSeq 2500 using a 2x250 nt paired end protocol.

treatment_protocol: For HLA-A2 processing experiments in human cells, tapasin-KO Expi293F cells were transfected with a plasmid library encoding variants of chimeric TAPBPR, where the TAPBPR C-terminus is replaced with the equivalent residues of tapasin.  Library DNA was diluted with a large excess of carrier DNA to ensure that cells typically acquired no more than one TAPBPR variant, maintaining a tight genotype-to-phenotype link.  24 h post-transfection, cells with the highest surface HLA-A2 (the top 0.5% of fluorescent cells after staining with PE-conjugated anti-HLA-A2) were collected by FACS.

tag: protein

value: Tapasin

tag: sort gate


title: mCherry positive, replicate 1


title: Chronic_Kif3a_KO_3

city: Cincinnati

first: John

middle: M.

last: Snowball

state: OH

address: 3333 Burnet Ave

department: Pulmonary Research

institute: Cincinnati Childrens Hospital

data_processing:
RNA-seq FASTQ files were aligned using Bowtie2 to mouse refernce genome mm10.
Normalized gene expressions were generated using Cufflinks.
Gene counts were obtained using Bioconductor’s GenomicAlignment.
DeSeq was used to analyze the raw gene counts and calculate differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: text file of RNA raw counts

source_name: EPCAM sorted Adult Mouse Lung

extract_protocol:
Qiagen RNeasy Micro Kit, 74004 (Valencia, CA).  RNA cleanup and on-column DNase digestion (Qiagen RNeasy Micro kit, Valencia, CA)
RNA sequencing was performed by CCHMC’s Gene Expression Core utilizing the Illumina HiSeq2500

treatment_protocol: Anesthetized 6-8-week-old mice were administered a dose of 10 µg Aspergillus fumigatus (Greer Laboratories, Lenoir, NC) diluted in 50 µl of saline by intratracheal (i.t.) instillation 3 times weekly for 3 weeks or as a single dose.

tag: genotype/variation

value: Kif3a deficient

value: Aspergillus Exposed

tag: level

value: Chronic


title: Chronic_Kif3a_KO_2


title: Exon 2 of tapasin gene in tapasin-knock out Expi293F cells

source_name: Expi293F cell culture (tapasin-knock out)


title: Tapasin-KO human cells expressing TAPBPR library sorted for high surface HLA-A2 (Replicate 2)

source_name: Synthetic coding sequences

value: TAPBPR

value: Highest 0.5 % of cells in the PE fluorescence channel after staining with PE-conjugated anti-HLA-A2


title: 202063-positive_bisulfite

tag: gender

tag: ptsd diagnosis


title: cGAMP high rep 2

description: Mageck_counts ML cGAMP.txt

value: sorted for high CDN reporter expression

value: 2'3' cGAMP

tag: cell line


title: mCherry negative, replicate 1


title: 201402-negative_bisulfite


title: 202127-negative_bisulfite


title: Tapasin-KO human cells expressing TAPBPR library sorted for high surface HLA-A2 (Replicate 1)


title: Chronic_Kif3a_KO_1

tag: treatment


title: Wild type TAPBPR-tapasin chimera: Control for sequencing errors

description: plasmid DNA


title: 201071-negative_bisulfite


title: Chronic_Control_3

value: wild type


title: EGFP positive, replicate 1

value: EGFP positive


title: Chronic_Control_1


title: TAPBPR-tapasin chimera naive library

description: plasmid DNA


title: WTclone2_iPSC

city: Utrecht

first: Onur

last: BASAK

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Reads were mapped to the latest human coding transcriptome, normalized and analyzed using the standard DESEQ2 package
The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. Unique molecular identifiers were omitted for the purpose of this study, however, can be used for unique transcript counting for mid- to low- expressed genes. The fastq files still contain the library barcode and the UMI. A list of the barcodes is included in cel-seq_barcodes.csv
Genome_build: hg19
Supplementary_files_format_and_content: *.csv: Tab separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples.  The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

extract_protocol:
RNA extraction was performed in 384-wells where cells were sorted using FACS. In brief, cells were sorted in a mixture of primers and dNTPs, heated to 60C for 5', followed by incubation 1' on ice (repeated twice) for lysis.
RNA was processed using the previously described SORT-seq technique, which is a combination of FACS and CEL-seq technique in a 384-well format. In brief, reverse transcription, second strand synthesis and in vitro transcription for RNA amplification were performed in 384-well format. Libraries were generate using Truseq small RNA primer (rpi) library primers, Libraries were sequenced on an Illumina HiSeq 4000 using 151bp paired end sequencing.

value: iPSC

tag: differentiation status

tag: genotype

value: WT


title: WTclone3_iPSC


title: PBS-1

city: Shanghai

first: Jian

last: Bing

address: Songhu Road, Yangpu District

department: School of Life Sciences

country: China

institute: Fudan University

data_processing:
Illumina OLB_1.9.4 were used for basecalling
Filter dirty raw reads by removing reads with adaptors and low quality, the obtained clean reads were mapped to reference sequences using SOAPaligner/soap2 according to Li et al., Bioinformatics, 2009. Mismatches no more than 2 bases were allowed in the alignment.
FPKM method is used in calculated expression level, the formula is shown as follows, and the formula is shown as follows: FPKM=106C/(NL/103). Given to be the expression of gene A , C to be number of fragments that are uniquely aligned to gene A , N to be total number of fragments that are uniquely aligned to all genes, and L to be number of bases on gene A.
Genome_build: Candida albicans SC5314 genome (ASM18296v1)
Supplementary_files_format_and_content: text file containing FPKM values for each Sample

organism: Candida albicans

source_name: candida albicans

extract_protocol:
Cells were lysed by Mini-beadbeater and total RNA was harvested using GeneJET RNA Purification Kit (Thermo Scientific #K0731, #K0732)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PBS


title: Acute_Kif3a_KO_3

value: Acute


title: 201229-negative_bisulfite

value: Whole blood

value: Male


title: 202018-positive_bisulfite

value: positive


title: Dk3clone3_iPSC

value: ASS1 mutant


title: SAA1-2


title: PBS-2


title: 201269-positive_bisulfite


title: 201208-negative_bisulfite

value: negative


title: Acute_Kif3a_KO_2

value: Kif3a deficient

value: Aspergillus Exposed


title: SAA1-1


title: Acute_Kif3a_KO_1


title: WTclone1_iPSC


title: DIC_5: BoneMarrow_dic(1;7)_5

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale Menghini n.9

department: Department of Medicine, Hematology and Bone Marrow Transplantation Unit

country: Italy

institute: University of Perugia

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
Protocol was supported by Affymetrix GeneChip Command Console (AGCC) software. Analysis was performed through Affymetrix Chromosome Analysis 3.1 (ChAS) software with filters set at 100 Kb dimension for Copy Number Alterations (CNAs) and 10 Mb dimensions for copy neutral loss of heterozygosity (cnLOH). Our data refer to NetAffx Build 32.3 (hg19) database.
Sample_primary_data_description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: Unsorted Bone Marrow Cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA were extracted from bone marrow cells of patients using All Prep DNA/RNA Mini Kit (Qiagen). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, Bioanalyzer and/or Tapestation visualization (Agilent 2100 Bioanalyzer) and agarose gel electrophoresis.

value: Unsorted Bone Marrow Cells

tag: cytogenetics

tag: mutations

tag: age


title: 201061-negative_bisulfite


title: 201418-positive_bisulfite


title: 201200-negative_bisulfite


title: 201143-negative_bisulfite


title: Acute_Control_3


title: 201327-positive_bisulfite


title: Acute_Control_2


title: Chronic_Control_2

value: Chronic


title: Dk1clone9_iPSC


title: 201058-negative_bisulfite


title: DIC_3: BoneMarrow_dic(1;7)_3

value: Not Available


title: WTclone3_Endoderm

value: Endoderm

value: Endoderm progenitor


title: DIC_2: BoneMarrow_dic(1;7)_2

value: GGPS1 (R74H); ANKS1B (T247I)


title: WTclone3_DM

value: endoderm derived hepatic organoids (eHEPOs)

value: eHEPO DM


title: Acute_Control_1

value: wild type


title: WTclone3_EM

value: eHEPO EM

value: WT


title: DIC_1: BoneMarrow_dic(1;7)_1


title: 202184-negative_bisulfite

value: Whole blood

value: Male


title: Adult cells biological replicate 1

city: San Diego

first: Chi-Yeh

last: Chung

address: 10770 Science Center Drive

institute: Pfizer Inc.

description:
Regions_promoter.ygi.gz
Regions_distal.ygi.gz
chromVar_TFscore_reads_cluster.csv.gz
Cicero_gene_accessibility_score.txt.gz
Cicero_all_connections_with_coaccess_score.txt.gz

data_processing:
Fastq files from the two sequencing run were merged. Pair-end sequencing reads were trimmed with sickle to remove low quality base pairs, and mapped to mm10 reference genome with bowtie2 with the following parameters: bowtie2 -p 16 -t -X 2000 --no-mixed --no-discordant. Data processing, which includes low quality reads filtering (MAPQ < 30), removal of duplicates and mitochondrial reads, adjusting for Tn5 insertion and separation of single cell reads, were performed with the snATAC-seq pipeline as previously described with the following parameters: snATAC pre -t 16 -m 30 -f 2000 -e 75. Open chromatin regions were determined by calling peaks for each replicates using macs2 with these parameters: macs2 callpeak --nolambda --nomodel --shift -100 --extsize 200 --keep-dup all --bdg --SPMR -q 5e-2. Peaks from each replicate were merged with bedtools into non-overlapping regions, resized to 1 kb and separated into promoter proximal (< ±1.5 kb TSS) and distal (>= ±1.5 kb TSS) regions. For cell selection, we filtered out cells that did not pass our quality threshold: reads per cell >= 2000 and reads in peak ratio >= 0.2. Data statistics for each biological replicate is shown in Table S1.
Genome_build: mm10
Supplementary_files_format_and_content: ".bed" files are mapped reads as bed format. ".xgi" files are cell indexes that passed our QC. ".ygi" files are open chromatin regions called from aggregate profile. "chromVar_TFscore" is TF z-score for all cells vs. TFs. "Cicero_gene_accessibility" is gene accessibility score for all cells vs. genes. "Cicero_connections" is all putative cis-regulatory interactions with co-access score.

source_name: WT mammary gland

extract_protocol:
The normal mammary epithelial cells were dissected and FACS isolated as EpCAM+ and Lin- from primary mammary tissue (see manuscript for details).
Cells were thawed and pelleted in a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf). Cell pellets were resuspended in 250 µl nuclei permeabilization buffer (10 mM Tris-HCl pH 7.4 (Sigma), 10 mM NaCl, 3 mM MgCl2, 0.1% GEPAL-CA630 (Sigma), 0.1% Tween-20, and 0.01% Digitonin (Promega, G9441), cOmplete (Roche) in water) (PMID: 28846090), incubated for 5 min at 4 °C with rotation and pelleted again (500 x g, 5 min, 4°C; 5920R, Eppendorf). Nuclei were resuspended in 500 µL high salt tagmentation buffer (36.3 mM Tris-acetate (pH = 7.8), 72.6 mM potassium-acetate, 11 mM Mg-acetate, 17.6% DMF) and counted using a hemocytometer. Concentration was adjusted to 2000 nuclei/9 µl, and 2,000 nuclei were dispensed into each well of a 96-well plate - 32 wells for each of the adult replicates and 16 wells for the fetal replicates, respectively. All downstream pipetting steps were performed on a Biomek i7 Automated Workstation (Beckman Coulter). For tagmentation, 1 µL barcoded Tn5 transposomes (PMID: 25079858) was added, mixed and incubated for 60 min at 37 °C with shaking (500 rpm). To inhibit the Tn5 reaction, 10 µL of 40-mM EDTA were added to each well and the plate was incubated at 37 °C for 15 min with shaking (500 rpm). Next, 5 µL 5 x sort buffer (5 % BSA, 5 mM EDTA in PBS) were added. All wells were combined and filtered using a 30-µm CellTric (Sysmex) into a FACS tube and stained with 3 µM Draq7 (Cell Signaling). Using a SH800 (Sony), 20 nuclei were sorted per well into eight 96-well plates (total of 768 wells) containing 10.5 µL EB (25 pmol primer i7, 25 pmol primer i5, 200 ng BSA (Sigma)). After addition of 1 µL 0.2% SDS, samples were incubated at 55 °C for 7 min with shaking (500 rpm). We added 1 µL 12.5% Triton-X to each well to quench the SDS and 12.5 µL NEBNext High-Fidelity 2× PCR Master Mix (NEB). Samples were PCR-amplified for 12 cycles (72 °C 5 min, 98 °C 30 s, (98 °C 10 s, 63 °C 30 s, 72 °C 60 s) × 11, held at 72 °C). After PCR, all wells were combined. Libraries were purified according to the MinElute PCR Purification Kit manual (Qiagen) and size selection was performed with SPRI Beads (Beckmann Coulter, 0.55x and 1.5x). Libraries were quantified using a Qubit fluorimeter (Life technologies) and the nucleosomal pattern was verified using a Tapestation (High Sensitivity D1000, Agilent).
snATAC-seq (PMID: 29434377, 25953818). Library for each sample was sequenced twice (v1 and v2) to obtain enpugh read depth.

tag: developmental stage

value: 8 weeks adult

value: Mammary gland


title: Dk1clone3_iPSC

value: iPSC

value: ASS1 mutant


title: Adult cells biological replicate 2


title: Fetal cells biological replicate 2


title: Azo-colonized vs. Non-colonized rice roots. Biological replicate 3, technical replicate 1 of 1 (Azo_4)

city: Bremen

first: Barbara

last: Reinhold-Hurek

state: Bremen

address: Leobener Str. 5

department: Microbe-Plant Interactions

country: Germany

institute: University of Bremen

description: Biological replicate 3 of 3, technical replicate 1 of 1

hyb_protocol: Hybridisation was performed according to Agilent protocol of Low Input Quick Amp Labeling acording to manufacture's instruction

scan_protocol: Agilent Technologies Scanner G2505B US45103132

data_processing:
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.
Normalized fold change calculated as signal_Azo-colonized(Ch1)/signal_Non-colonized(Ch2), value of SAMPLE "Azo_2" is an average fold change from two technical replicates

organism: Oryza sativa Japonica Group

source_name: 4-5 rice roots, colonized with Azoarcus olearius BH72

label_protocol: 200 ng of total RNA was subjected to the Agilent protocol of Low Input Quick Amp Labeling acording to manufacture's instruction

growth_protocol: Dehusked rice grains were surface sterilized, washed and germinated on agar plates, then after 3 days transferred to tubes containing quartz sand and 3 ml of plant medium (0.2 g of MgCl2 × 7H2O, 0.1 g of NaCl, 0.026 g of CaCl2 × 2H2O, 0.012 g of MnSO4 × H2O, 4 mg of Na2MoO4 × 2H2O, 3 mg of H3BO3, 0.2 mg of ZnSO4 × 7H2O, 0.1 mg of CuSO4 × 5H2O, 13 mg of Fe-citrate, 5 mg of DL-malic acid neutralized to pH 7.0 with KOH, 1.5 g each of K2HPO4 and KH2PO4, adjusted to pH 6.8)

extract_protocol:
RNA applied for microarray experiment were extracted per a hexadecyl trimethyl-ammonium bromide (CTAB)-based method: 0.5 g rice roots homogenized in liquid nitrogen were suspended in 18 ml extraction buffer (2% hexadecyl trimethyl-ammonium bromide (CTAB), 2% polyvinylpyrrolidone, 100 mM Tris-HCl, pH 8.0, 25 mM EDTA, 2 M NaCl, 0.5 g/L spermidine, and 2% β-mercaptoethanol
), incubated at 65 °C for 5 minutes; then 18 ml chloroform was added and mixed with root suspension; after centrifuging this mixture at 10000 xg for 5min, the supernatant was treated with chloroform again; the final supernatant was added of concentrated LiCl to make a final concentration of 2 M and kept overnight at 4°C for RNA precipitation; the final RNA was obtained in the pellet after centrifuging the mixture at 4°C at 10000 xg for 30 min and solved in RNase-free water.

treatment_protocol: Azoarcus olearius BH72 culture of OD 1, was added to tubes containing rice seedlings to final OD of 0.067 and incubated in gnotobiotic system for 14 days in phytotron (at 30°C, at 80% humidity and with a 14-h-day and 10-h-night cycle at approximately 170 μmol photons m–2 s–1).

tag: days post inoculation

value: 14 post inoculation with Azoarcus olearius BH72

value: total root

tag: cultivar

value: Nipponbare

source_name: 4-5 rice roots, sterile (non-colonized control)

value: 14 days of cultivation without Azoarcus olearius BH72 (control plants)


title: WTclone1_Endoderm

tag: tissue

value: Endoderm

value: Endoderm progenitor


title: 202091-positive_bisulfite

value: positive


title: 202160-positive_bisulfite


title: Fetal cells biological replicate 1

tag: strain


title: WTclone2_Endoderm


title: 201062-negative_bisulfite

value: negative


title: Azo-colonized vs. Non-colonized rice roots. Biological replicate 2, technical replicate 1 of 1 (Azo_3)

description: Biological replicate 2 of 3, technical replicate 1 of 1, dye swap


title: PATKO 71

city: La Jolla

first: Nasun

last: Hah

address: 10010 North Torrey Pines Rd

department: Next Generation Sequencing

institute: The Salk Institute

description: mRNA (oligo-dT selected)

data_processing:
Illumina HiSeq 2500 instrument software extracts intensities from images and performs quality-scored base calling on the instrument computer real time.
Genome_build: mm10
Supplementary_files_format_and_content: XLSX files contain gene expression information (RPKM) in each samples

source_name: Brown Adipose Tissue (BAT)

growth_protocol: 18 week old mice were housed at 30°C and fed ad libitum with chow diet

extract_protocol:
Total RNA was extracted using Direct-Zol RNA extraction kit (Zymo Research).
Libraries were prepared according to Illumina's instructions accompanying TruSeq Stranded mRNA Library Prep Kit. Briefly, total RNA (0.5µg) from each sample was used to isolate poly(A) mRNA. Steps involved in library preparation were mRNA fragmentation, first strand cDNA synthesis followed by second strand cDNA synthesis and adaptor ligation, cDNA fragments isolation and amplification.

value: PGRMC2 adipose tissue knockout

value: 18 wo


title: 201020-negative_bisulfite


title: WTclone2_DM

value: endoderm derived hepatic organoids (eHEPOs)

value: eHEPO DM

value: WT


title: 201210-negative_bisulfite

value: Whole blood

value: Male


title: Azo-colonized vs. Non-colonized rice roots. Biological replicate 1, technical replicate 2 of 2 (Azo_2)

description: Biological replicate 1 of 3, technical replicate 2 of 2, dye swap


title: PATKO 57

description: mRNA (oligo-dT selected)


title: Xan-infected vs. Non-infected rice roots. Biological replicate 3, technical replicate 1 of 1 (Xan-3)

description: Biological replicate 3 of 3, technical replicate 1 of 1, dye swap

data_processing:
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.
Normalized fold change calculated as signal_Xan-colonized(Ch1)/signal_Non-colonized(Ch2), value of SAMPLE "Xan-1" is an average fold change from two technical replicates

source_name: 4-5 rice roots, infected with Xanthomonas oryzae pv. oryzae strain PXO99

extract_protocol: RNA applied for microarray experiment were extracted per a hexadecyl trimethyl-ammonium bromide (CTAB)-based method: 0.5 g rice roots homogenized in liquid nitrogen were suspended in 18 ml extraction buffer (2% hexadecyl trimethyl-ammonium bromide (CTAB), 2% polyvinylpyrrolidone, 100 mM Tris-HCl, pH 8.0, 25 mM EDTA, 2 M NaCl, 0.5 g/L spermidine, and 2% β-mercaptoethanol), incubated at 65 °C for 5 minutes; then 18 ml chloroform was added and mixed with root suspension; after centrifuging this mixture at 10000 xg for 5min, the supernatant was treated with chloroform again; the final supernatant was added of concentrated LiCl to make a final concentration of 2 M and kept overnight at 4°C for RNA precipitation; the final RNA was obtained in the pellet after centrifuging the mixture at 4°C at 10000 xg for 30 min and solved in RNase-free water.

treatment_protocol: For infection of O. sativa with pathogen, Xan PXO99 was grown at 28°C on agar plate containing modified Wakimoto’s medium (Karnagilla and Natural. 1973). Roots of seedlings were dipped for 5 min into a bacterial suspension of 5 x 109 cells per mL. Later they were incubated in gnotobiotic system for 14 days in phytotron (at 30°C, at 80% humidity and with a 14-h-day and 10-h-night cycle at approximately 170 μmol photons m–2 s–1).

value: 14 post infection with Xanthomonas oryzae pv. oryzae strain PXO99

value: 14 days of cultivation without Xanthomonas oryzae pv. oryzae strain PXO99 (control plants)


title: PATKO 70

description: mRNA (oligo-dT selected)


title: WTclone1_EM

value: eHEPO EM


title: DIC_4: BoneMarrow_dic(1;7)_4

value: Unsorted Bone Marrow Cells

value: Not Available


title: 202082-negative_bisulfite


title: WTclone2_EM


title: PATKO 53

description: mRNA (oligo-dT selected)


title: Xan-infected vs. Non-infected rice roots. Biological replicate 2, technical replicate 1 of 1 (Xan-2)

description: Biological replicate 2 of 3, technical replicate 1 of 1

value: total root

value: Nipponbare


title: 202117-positive_bisulfite


title: 202031-positive_bisulfite


title: 201132-negative_bisulfite


title: 202020-positive_bisulfite


title: Dk3clone3_Endoderm

value: Endoderm

value: Endoderm progenitor

value: ASS1 mutant


title: WT 65

description: mRNA (oligo-dT selected)

value: wild type


title: Xan-infected vs. Non-infected rice roots. Biological replicate 1, technical replicate 2 of 2 (Xan-1)

description: Biological replicate 1 of 3, technical replicate 2 of 2


title: Dk3clone3_DM


title: WT 64

description: mRNA (oligo-dT selected)

value: 18 wo


title: Xan-infected vs. Non-infected rice roots. Biological replicate 1, technical replicate 1 of 2 (Xan-1)

description: Biological replicate 1 of 3, technical replicate 1 of 2


title: WTclone1_DM

value: endoderm derived hepatic organoids (eHEPOs)


title: Dk1clone3_DM

value: eHEPO DM


title: WT 62

description: mRNA (oligo-dT selected)


title: Dk1clone3_Endoderm


title: F8 [Liver-NP1-8]

city: Arcachon

first: Fanny

last: Perrier

address: place Peyneau

country: France

institute: Université de Bordeaux

data_processing:
Reads have been aligned to contigs with bwa (version 0.7.12) with standard parameters. Resulting sam files were sorted and indexed with samtools (version 1.1) with standard parameters. Expression counts were generated from the bam files with samtools.
Filtered reads were assembled using DRAP version 1.7 and the Trinity assembler (www.sigenae.org/drap)
Genome_build: Aanguilla_assembly.fasta
Supplementary_files_format_and_content: Aanguilla_raw counts : comma-separated csv file including count values for each sample
Supplementary_files_format_and_content: Aanguilla_assembly : fasta file listing the de novo assembled contigs

organism: Anguilla anguilla

source_name: Liver

extract_protocol:
SV Total RNA isolation system kit (Promega) according to manufacturer’s instructions
TruSeq RNA Library Prep Kit v2

value: Liver

tag: contamination level

tag: individual


title: F9 [Liver-NP1-9]


title: Azo-colonized vs. Non-colonized rice roots. Biological replicate 1, technical replicate 1 of 2 (Azo_2)

value: 14 post inoculation with Azoarcus olearius BH72

value: 14 days of cultivation without Azoarcus olearius BH72 (control plants)


title: WT 55

description: mRNA (oligo-dT selected)


title: LEDGF_LEDGFKO_ESC

city: Monterotondo

first: nicolas

last: descostes

address: via Ramarini 32

department: Bioinformatics

institute: EMBL

data_processing:
Quality of sequencing was assed with FastQC v0.11.4 & adapters were removed by the sequencing facility.
Human hg19 and mouse mm10 from Illumina igenomes UCSC collection were used as reference genomes. Chip-seq data were aligned with Bowtie v1.0.0 allowing 3 mismatches and keeping uniquely aligned reads.
Sam ouputs were converted to Bam with Samtools v1.0.6 and sorted with Picard tools v1.88
Data were further processed with Pasha to obtain wiggle files that were converted to bigwigs.
Some chip-seq tracks were further spike-in normalized using drosophila dna.
Genome_build: Hg19, mm10 and dm3
Supplementary_files_format_and_content: bigwig

growth_protocol: E14Tga2 (ATCC, CRL-1821) ESCs were grown in standard medium supplemented with LIF, 1 μM MEK1/2 inhibitor (PD0325901, Stemgent) and 3 μM GSK3 inhibitor (CHIR99021, Stemgent).  For embryoid body differentiation, 600K mESCs were plated in suspension plates with medium containing DMEM (Life Technologies), 20% FBS, 1% NEAA, 1% Pen/Strep, 2 mM L-Glutamine, 100 mM Ascorbic acid (Sigma).  After 5 days, EB colonies were collected for downstream applications. Human myoblasts are seeded on gelatinized plates and grown in Ham’s F-10 media (Gibco/Thermo Fisher) supplemented with 15% fetal bovine serum (Atlanta Biologicals), 1mM sodium pyruvate (Sigma), 100ug/ml penicillin/streptomycin (Gibco/Thermo Fisher), 2.5ng/ml basic human fibroblast growth factor (Promega), 1X GlutaMax (Thermo Fisher) and 1uM Dexamethasone.  Once 90% confluent the myoblasts are differentiated to myotubes by changing the media to DMEM (Gibco/Thermo Fisher) supplemented with 2% Horse Serum (Hyclone) and 100ug/ml penicillin/streptomycin (Gibco/Thermo Fisher).  Differentiation proceeds for 6 days and the efficiency can be monitored with microscopy as myotubes are easily visually detected.

extract_protocol:
For ChIP-seq, nuclei was isolated from cells fixed with 1% Formaldehyde. Next, chromatin was fragmented into ~250bp.  Chromatin immunoprecipitation was performed with the indicated antibodies. For RNA-seq, total RNA was isolated with RNAeasy (Qiagen) and reverse transcribed using Superscript III and random hexamers (Life Technologies) to synthesize the 1st strand. Second strand was synthesized with dUTP to generate strand asymmetry using DNA Pol I (NEB, M0209L) and the E. coli ligase (Enzymatics, L6090L).
For ChIP-seq and RNA-seq, libraries were prepared by standard protocol. First, fragments are repaired to generate  blunt 5' P ends  using 'EndIT DNA End Repair kit' (Epicentre). Second, 3' A overhang was generated using 'Klenow Fragment (3´→ 5´ exo-)' (NEB). Third,  Illumina barcodes were ligated using 'Rapid T4 DNA Ligase' (Enzymatics). Lastly, libraries were size selected using 'Ampure beads' (Beckman Coulter), then amplified, quantified and pooled.

value: LEDGF knockout

value: CRL-1821 cell line

tag: chip antibody

value: LEDGF, Proteintech, #25504-1-AP


title: 201367-positive_bisulfite

value: Whole blood

tag: gender

value: Male

value: positive


title: 202098-positive_bisulfite

tag: ptsd diagnosis


title: Dk1clone9_Endoderm


title: Dk3clone3_EM

value: eHEPO EM


title: F6 [Liver-NP0-6]


title: F7 [Liver-NP1-7]


title: 201190-negative_bisulfite

value: negative


title: Dk1clone3_EM


title: 202182-positive_bisulfite


title: Hdgf2_HDGF2KO

value: HDGF2 knockout

value: HDGF2, Proteintech, #15134-1-AP


title: F5 [Liver-NP0-5]


title: 201195-positive_bisulfite


title: Dk1clone9_DM

value: ASS1 mutant


title: F3 [Liver-NP0-3]


title: Dk1clone9_EM


title: Day5-mRNA-doubleKO-rep2

data_processing:
Reads having less than 80% of quality scores above 25 were removed with NGSQCToolkit v2.3.3
RNA-seq data were aligned with Tophat v2.0.9 allowing 3 mismatches.
Genome_build: Hg19, mm10 and dm3
Supplementary_files_format_and_content: bigwig

source_name: E14Tga2.mESC derived Embryoid bodies

value: LEDGF/HDGF2 double knockout


title: Day5-mRNA-doubleKO-rep1


title: F12 [Liver-NP1-12]


title: Day5-mRNA-LEDGFKO-rep2


title: LEDGF_WT_forLEDGFKO

value: Wild type


title: 201361-positive_bisulfite


title: Hdgf2_WT_forHDGF2KO


title: F11 [Liver-NP1-11]


title: F4 [Liver-NP0-4]


title: Fostamatinib_2

city: Columbus

first: Kelly

last: Regan

state: Ohio

address: 1800 Cannon Drive

department: Biomedical Informatics

institute: The Ohio State Univ

data_processing:
Illumina HCS 3.4.0 software was used for basecalling.
Fastq files containing sequenced reads were mapped to the human genome h19 using Hiearchical Indexing for Spliced Alignment of Transcripts (HISAT).
Raw read counts for each gene were quanitfied using featureCounts software and the GENCODE v.22 Gene Transfer Format (GTF) file as a transcript reference (GENCODE annotation).
Genes with read counts below 5 for at least 2 samples out of 3 within each group were filtered out.
Read counts were normalized using the TMM method.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files for each sample include normalized count values for ENSEMBL ENSG gene IDs.

source_name: Huh7 sorafenib-resistant HCC cell line (Huh7SR)

growth_protocol: Huh7SR cells were treated with either DMSO (2uM) or fostamatinib (2uM) 24 hr. Drug treatments were applied in triplicate per condition.

extract_protocol:
Cells were harvested with cold PSB and pellets were kept frozen at -80 deg. Total RNA was extracted using the Norgen Biotek total RNA purification plus kit (Cat #48300). RNA purity was assessed using Qubit RNA assay and BioAnalyzer RNA Nanochip tracings.
RNA libraries were prepared for sequencing using the New England Biolabs NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with the protocol for use with NEBNext Poly(A) mRNA magnetic isolation module.  We used 200ng of total RNA for the construction of sequencing libraries.

treatment_protocol: Drug solutions were prepared in cell culture media to reach a final concentraiton of 2uM.

tag: cell line

tag: parental cell line

tag: drug exposure

value: Fostamatinib

tag: treatment dose

value: 2 uM

tag: treatment length

value: 24 hr


title: 201199-negative_bisulfite

data_processing:
Raw intesities were imported into Champ R package to preprocess the data.We filtered 8877 probes with a detection p-value above 0.01 in one or more samples, 281 probes with beadcount <3 in at least 5% of samples, 26935 probes with overlapped SNPs, 8405 probes with multiple aligned locations, and 11066 probes on the X and Y chromosomes. Channel Quantile plus BMIQ normalization method was conducted
Raw data are available in the .idat files on the sample records and in the text file unmethylated_and_methylated_signal_intensities.txt on the series record.

source_name: Whole blood


title: 202064-positive_bisulfite


title: 201181-positive_bisulfite


title: DMSO_3

value: DMSO


title: Fostamatinib_1


title: Day5-mRNA-WT-rep2

tag: genotype


title: Fostamatinib_3


title: F1 [Liver-NP0-1]

value: Liver


title: Day5-mRNA-LEDGFKO-rep1

value: LEDGF knockout

value: CRL-1821 cell line


title: 201067-negative_bisulfite

value: Whole blood


title: F10 [Liver-NP1-10]


title: 201328-positive_bisulfite

value: Male


title: DMSO_1


title: DMSO_2


title: C24 [Brain-NP1-12]

source_name: Brain

value: Brain


title: Day0-mRNA-WT-rep2


title: 201035-negative_bisulfite


title: 202188-positive_bisulfite

value: positive


title: Day0-mRNA-WT-rep1


title: C22 [Brain-NP1-10]


title: C23 [Brain-NP1-11]


title: C21 [Brain-NP1-9]


title: Longissimus thoracis _Limited stress_cow331

city: Saint Genes Champanelle

first: Celine

last: BOBY

address: Centre INRA Auvergne-Rhône-Alpes

institute: INRA

hyb_protocol: For each hybridization, 600 ng of Cyanine 3 labeled cRNA were fragmented and hybridised at 65°C for 17 hours to an Agilent 8 x 15 K custom Oligo Microarray.

scan_protocol: After washing, microarrays were scanned using an Agilent DNA G2505B scanner.

data_processing: Feature extraction 9.1 software (Agilent Technologies) was used to assess fluorescent hybridization signals. Normalization was then calculated per probe from the median of the probe obtained from all arrays. This ensured to use the same scale for all probes. Then a log2 transformation was done. Differential analyses were conducted via linear modelling using the R/Limma package. (http://bioinf.wehi.edu.au/limma/) as described in [43]. The probabilities associated with stress effects were corrected using the Benjamini-Hochberg method (BH) [44]. The genes for which at least 80% of the probes were differential at the adjusted p-value 10% were retained.

organism: Bos taurus

source_name: Muscle Longissimus thoracis  Limited stress

label_protocol: The total RNA was amplified and labeled with Cyanine 3 using Agilent’s Low RNA Input Linear Amplification Kit, PLUS, One-Color (Agilent Technologies) following the detailed protocol described by Agilent. Briefly, 500 ng of total RNA was reverse transcribed to double-strand cDNA using a poly dT-T7 promoter primer. cDNA products were then used as templates for in vitro transcription to generate fluorescent cRNA. Labeled cRNAs were finally purified using QIAGEN’s RNeasy mini spin columns and eluted in 30 μl of nuclease-free water. After amplification and labeling, cRNA quantity and cyanine incorporation were determined using a Nanodrop ND.1000 spectrophotometer (Thermo Scientific).

growth_protocol: 32 Normand cows were fed as described by Gobert et al. (2010) : The cows were randomly assigned to one of two isoenergetic and isonitrogenous rations for a mean daily body weight gain of 1.6 kg for a 101 ± 3 d finishing period. The basic diet was straw (30%) and concentrate (70%) based supplemented with 40 g of lipids/kg DM obtained from extruded linseeds (60%) and rapeseeds (40%). Animals were given either the basic diet (lipid-rich) or the basic diet supplemented with vitamin E and the PERP mixture (Lipid VitE PERP). Water was provided ad libitum.

extract_protocol: Total RNA was extracted using TrizolTM as described by the manufacturer. Extraction was followed by a purification using RNeasy Mini kit (QIAgenTM). Total RNA was quantified with a Nanodrop ND.1000 spectrophotometer (Thermo Scientific, World Headquarters Location, Waltham, USA). RNA integrity was evaluated with the 2100 bioanalyzer (Agilent Technologies, Massy, France) and the RNA 6000 Lab Chip kit. RNA with RIN>0.8 were further analysed

treatment_protocol: Cows were finished and slaughtered under conditions of limited stress (n = 16) or physical and psychological stress (n = 16) as described by Bourguet et al. (2010). The latter was induced by the social isolation of animals during transport in a lorry and introduction during 30 minutes in a labyrinth built in an unfamiliar farm. Cows were slaughtered at the age of 4.5±0.1 years and at 768.7±11.4 kg live weight over a period of 16 weeks with one slaughter day per week. Stress status was evaluated through the plasma cortisol and heart rate [14]. All animals were slaughtered in the same conditions and without any electrical stimulation at the INRA experimental slaughterhouse in compliance with current INRA ethical guidelines for animal welfare (ref CE). Muscle samples from the Semitendinosus (ST) and Longissimus thoracis (LT) were excised within 15 minutes after slaughter. Muscle samples were immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction.

tag: race

value: Normand cows

value: Longissimus thoracis

tag: slaughtered conditions

value: Limited stress

tag: supplement diet

value: Lipid VitE PERP


title: Day0_input


title: Semitendinosus_Limited stress_cow331

source_name: Muscle Semitendinosus Limited stress

value: Semitendinosus


title: Semitendinosus_Moderated stress_cow330

source_name: Muscle Semitendinosus Moderated stress

value: Moderated stress


title: C20 [Brain-NP1-8]


title: F2 [Liver-NP0-2]


title: Day5_input

value: Wild type


title: H3K27me3_1

value: H3K27me3, Cell Signaling, #9733


title: C19 [Brain-NP1-7]


title: Longissimus thoracis _Moderated stress_cow330

source_name: Muscle Longissimus thoracis  Moderated stress


title: 202054-positive_bisulfite

extract_protocol: genomic DNA was extracted and purified from PAXgene DNA Blood tubes


title: Semitendinosus_Moderated stress_cow324


title: 201182-negative_bisulfite

value: negative


title: H3K36me3_1

value: H3K36me3, Abcam, #ab9050


title: 202067-positive_bisulfite


title: Day5-mRNA-WT-rep1


title: 201177-negative_bisulfite


title: 201008-negative_bisulfite


title: Day0_SPT16

value: SPT16, Cell Signaling, #12191


title: 202009-negative_bisulfite


title: 201415-positive_bisulfite


title: C17 [Brain-NP0-5]


title: Day5_SPT16


title: Longissimus thoracis _Moderated stress_cow324


title: Semitendinosus_Moderated stress_cow321

value: Lipid-rich


title: 202102-positive_bisulfite


title: C16 [Brain-NP0-4]


title: Day0_H3K36me2

value: CRL-1821 cell line

value: H3K36me2, Cell Signaling, #2901


title: C15 [Brain-NP0-3]


title: C14 [Brain-NP0-2]


title: Semitendinosus_Limited stress_cow320


title: 201044-negative_bisulfite

value: Whole blood

value: Male


title: Longissimus thoracis _Moderated stress_cow321


title: Day0_HDGF2

value: HDGF2, Proteintech, #15134-1-AP


title: Day5_HDGF2


title: C13 [Brain-NP0-1]

value: Brain


title: Day5_LEDGF

value: LEDGF, Proteintech, #25504-1-AP


title: Longissimus thoracis _Limited stress_cow320

value: Normand cows

value: Longissimus thoracis

value: Limited stress


title: 201345-positive_bisulfite

value: positive


title: 201324-negative_bisulfite


title: Day0_LEDGF

value: Wild type


title: AC1-M59 stimulated (rep3)

city: Jena

first: Diana

middle: Maria

last: Morales Prieto

address: Am Klinikum 1

department: Obstetrics

institute: Jena University Hospital

description: Test for AC1-M59

data_processing:
SDS software (Applied Biosystems) was used to collect data. Data were processed using DataAssist v3.0 (Applied Biosystems).
Normalized Ct values against RNU44 and RNU48. Fold Change was calculated against cells without stimuli

label: FAM

source_name: Cell line treated with LIF

label_protocol: 100 ng total RNA per sample was reverse-transcribed using Megaplex primers, sets A and B (Applied Biosystems). cDNA was pre-amplified for 12 cycles with Megaplex Pre-Amp primers. Sets A and B (Applied Biosystems) then diluted to 100 µl. Manufacturer´s protocol was followed throughout.

growth_protocol: Cells cultures were performed at 10^6 cells/175 cm2 flask, and maintained under standard conditions (37ºC, 5% CO2, humid atmosphere) in Ham’s F-12 Nutrient Mixture with L-glutamine (GIBCO, Paisley, UK) or RPMI Medium (GIBCO) (HTR-8 cells) supplemented with 10 % heat-inactivated fetal calf serum (FCS; GIBCO) and 1 % penicillin/streptomycin antibiotic solution (GIBCO).

extract_protocol: Total RNA was isolated by mirVana isolation kit (Life Technologies, Darmstadt, Germany), according to the manufacturer's protocol.

treatment_protocol: Cells were seeded in 12-well plates, allowed to attach overnight and serum deprived for two hours. Afterwards, cells were stimulated with LIF 10 ng/µl for 4h before RNA extraction

tag: type of cells

value: Hybridome


title: 201268-negative_bisulfite

tag: tissue

value: negative


title: Semitendinosus_Limited stress_cow316

value: Semitendinosus


title: Day5_Pol_II

value: RNAPII, Santa Cruz, #sc-899


title: Longissimus thoracis _Limited stress_cow316

value: Lipid-rich


title: Day0_Pol_II

value: CRL-1821 cell line


title: 202093-positive_bisulfite


title: 201086-negative_bisulfite


title: AC1-M59 stimulated (rep1)

description: Test for AC1-M59


title: AC1-M59 stimulated (rep2)

description: Test for AC1-M59


title: 201105-negative_bisulfite


title: Semitendinosus_Limited stress_cow314

value: Lipid VitE PERP


title: 202212-positive_bisulfite

value: Whole blood


title: Longissimus thoracis _Limited stress_cow314


title: Semitendinosus_Moderated stress_cow311

value: Moderated stress


title: SphK1-/-_RNASeq

city: 4-6-1, Komaba, Meguroku

first: Takahide

last: Kohro

state: Tokyo

country: Japan

institute: LSBM, RCAST

data_processing:
Basecall data was generated by Illumina's system software and then fastq file was generated with demultiplexation using CASAVA Ver.1.8.
RNAseq data  was aligned to genome mm10 using hisat2 with the parameter  '-q --dta-cufflinks'.
The SAM file was converted into BAM format and subsequently fpkm was calculated using cuffdiff and cummerBund.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file containing fpkm values

source_name: renal fibroblast

growth_protocol: The cells were maintained with 10 ml medium (DMEM, 10% FBS, 1% penicillin-streptomycin-amphotericin B) in 10 cm dish.

extract_protocol:
RNA was isolated from the renal fibroblasts using the RNeasy Micro Kit. Poly(A)-containing mRNA molecules were isolated from total RNA. Illumina TruSeq RNA Sample Prep Kit v2 was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: renal fibroblast

tag: passage

tag: strain


title: SphK2-/-_RNASeq


title: 201362-positive_bisulfite

city: Silver Spring

first: Aarti

last: Gautam

institute: WRAIR

value: Male


title: C18 [Brain-NP0-6]

value: Brain

tag: contamination level

tag: individual


title: 202130-positive_bisulfite

tag: gender

tag: ptsd diagnosis


title: WT_RNASeq


title: Longissimus thoracis _Moderated stress_cow311

value: Normand cows


title: AC1-M59 control (rep1)

description: Normalizer for AC1-M59

source_name: Cell line


title: AC1-M59 control (rep3)

description: Normalizer for AC1-M59


title: Semitendinosus_Limited stress_cow308


title: AC1-M59 control (rep2)

description: Normalizer for AC1-M59


title: 202106-positive_bisulfite


title: ACH-3P stimulated (rep3)

description: Test for ACH-3P


title: SphK2-/-_H3K27ac_ChIPSeq

data_processing:
Basecall data was generated by Illumina's system software and then fastq file was generated with demultiplexation using CASAVA Ver.1.8.
ChIPseq data was aligned to genome mm10 using bowtie with default paramaters.
Peak calling was performed by QuEST.
Genome_build: mm10

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
All of the protocols for Illumina/Solexa sequence preparation, sequencing and quality control were provided by Illumina.

tag: chip antibody

value: H3K27ac (Takara, MA309B)


title: ACH-3P stimulated (rep2)

description: Test for ACH-3P


title: SphK2-/-_H3K9ac_ChIPSeq

value: H3K9ac (Takara, MA305B)


title: Longissimus thoracis _Limited stress_cow308

value: Longissimus thoracis

value: Limited stress


title: 201063-positive_bisulfite

value: positive


title: SphK1-/-_input DNA


title: ACH-3P stimulated (rep1)

description: Test for ACH-3P

value: Hybridome


title: 202183-positive_bisulfite


title: Semitendinosus_Moderated stress_cow305

value: Semitendinosus


title: Longissimus thoracis _Moderated stress_cow305


title: ACH-3P control (rep3)

description: Normalizer for ACH-3P


title: SphK1-/-_H3K27ac_ChIPSeq


title: ACH-3P control (rep2)

description: Normalizer for ACH-3P


title: Semitendinosus_Limited stress_cow304


title: SphK2-/-_input DNA


title: Longissimus thoracis _Limited stress_cow304


title: SphK1-/-_H3K9ac_ChIPSeq


title: 202038-positive_bisulfite


title: 202147-negative_bisulfite

value: negative


title: ACH-3P control (rep1)

description: Normalizer for ACH-3P


title: Semitendinosus_Moderated stress_cow303


title: WT_input DNA

value: Wild type


title: HTR-8 stimulated (rep3)

description: Test for HTR-8

value: Immortalized cell line


title: WT_H3K27ac_ChIPSeq


title: 202047-negative_bisulfite


title: 202211-positive_bisulfite


title: HTR-8 stimulated (rep2)

description: Test for HTR-8


title: 202110-negative_bisulfite


title: Longissimus thoracis _Moderated stress_cow303

value: Lipid VitE PERP


title: Semitendinosus_Limited stress_cow302

value: Lipid-rich


title: WES_Kit_E302

city: Memphis

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
Library strategy: WES
Raw reads were mapped to mouse genome mm10 (GRCm38) using SpeedSeq version 0.1.0 with default parameters.
The variants were detected using SpeedSeq version 0.1.0 and VarScan version 2.3.9.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: VCF format
Supplementary_files_format_and_content: Tab-delimited SNP and Indel calls.

source_name: Mouse bone marrow cells

growth_protocol: Bone marrow cells were obtained by flushing femurs and tibias with a 25G needle or by crushing femurs, tibias, vertebrae and pelvic bones with a mortar in Ca2+ and Mg2+-free Hank’s buffered salt solution (HBSS; Gibco) supplemented with 2% heat-inactivated bovine serum (HIBS, Gibco). For flow cytometric analysis and isolation, cells were incubated with combinations of antibodies listed in the key resource table. Lineage markers for HSCs and progenitors were CD3, CD5, CD8, B220, Gr1 and Ter119. Antibody staining was performed at 4 °C for 30 min, or, when CD34 was included in the cocktail, on ice for 90 min. Biotinylated antibodies were visualized by incubation with PE/Cy7-conjugated streptavidin at 4°C for 30 min. DAPI (4′,6-diamidino-2-phenylindole; 2 μg/ml in PBS) or PI (propidium iodide; 1 μg/ml) were used to exclude dead cells during flow cytometry.

extract_protocol: Genome DNA were isolated from c-Kit+ leukemia cells from E2-KO moribund mice and processed for whole exome sequencing (WES) analysis using Agilent SureSelect XT Mouse All Exon Kit (cat# 1000001746) following manufacturer’s protocols.

tag: strain/background

tag: genotype/variation

value: Bone marrow

value: c-Kit+ leukemia cells


title: WT_H3K9ac_ChIPSeq

value: renal fibroblast


title: HTR-8 stimulated (rep1)

description: Test for HTR-8


title: HTR-8 control (rep3)

description: Normalizer for HTR-8


title: WT NB4 ATRA 2

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

data_processing:
standard Illumina HiSeq post-processing
alignment using TopHat
The aligned BAM files for biological replicates were uploaded to the galaxy server (usegalaxy.org) and expression levels calculated using the Galaxy implementation of Cufflinks and Cuffdiff.
Genome_build: HG19
Supplementary_files_format_and_content: fpkm

source_name: NB4 leukemic cells

growth_protocol: NB4 cells were maintained in at 37C, 5%CO2 in RPMI supplemented with 10% heat inactivated fetal calf serum.

extract_protocol:
RNA was extracted using RNeasy columns coupled with on-column DNase digestion (Qiagen)
Illumina TruSeq RNA sample preparation protocols

treatment_protocol: NB4 cells were treated with either ethanol (control) or all-trans retinoic acid (1microM) for 72 hours and differentiation monitored. RNA was isolated and sequenced.

tag: treatment

value: ATRA

tag: cell line


title: WT NB4 ATRA 1


title: 202105-positive_bisulfite

address: 503 Robert Grant Avenue

value: Whole blood

value: Male


title: Longissimus thoracis _Limited stress_cow302

tag: race

value: Normand cows


title: WT NB4 vehicle control 2

value: Vehicle control


title: Semitendinosus_Moderated stress_cow301

tag: slaughtered conditions

value: Moderated stress


title: 202062-positive_bisulfite

value: positive


title: WES_Kit_E258


title: WES_Kit_E251


title: HTR-8 control (rep1)

description: Normalizer for HTR-8


title: HTR-8 control (rep2)

description: Normalizer for HTR-8


title: WT NB4 vehicle control 1


title: BMSC TUMOR rep3

city: Changsha

first: Buqing

last: Sai

state: Hunan

address: 110 Xiangya Road

institute: Buqing Sai

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

Explanation for the generation of FPKM and the difference between FPKM and RPKM:
1.RPKM stands for Reads Per Kilobase of transcript per Million mapped reads. In RNA-Seq, the relative expression of a transcript is proportional to the number of cDNA fragments that originate from it. RPKM=(1000000*C)/(N*L/1000), C represents the amount of reads which mapped to the specific transcripts, N represents the amount of reads which mapped to any transcripts. L represents the base amount of the specific transcripts.
2.FPKM stands for Fragments Per Kilobase of transcript per Million mapped reads. FPKM=(1000000*C)/(N*L/1000), C represents the amount of fragment which mapped to the specific transcripts, N represents the amount of fragment which mapped to any transcripts. L represents the base amount of the specific transcripts.
3.In RNA-Seq, the relative expression of a transcript is proportional to the number of cDNA fragments that originate from it. Paired-end RNA-Seq experiments produce two reads per fragment, but that doesn't necessarily mean that both reads will be mappable. For example, the second read is of poor quality. If we were to count reads rather than fragments, we might double-count some fragments but not others, leading to a skewed expression value. Thus, FPKM is calculated by counting fragments, not reads.

Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: sorted bmsc

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

value: mouse bone marrow stem cells

tag: group

value: TUMOR (GFP-BMSCs collected from inoculation cancer site (co-injection of RFP-LLCs and GFP-BMSCs))

tag: genotype

value: wide type


title: JEG-3 stimulated (rep3)

description: Test for JEG3

tag: type of cells

value: Choriocarcinoma cell line


title: 202003-positive_bisulfite

tag: tissue


title: Longissimus thoracis _Moderated stress_cow299

value: Longissimus thoracis

tag: supplement diet


title: Semitendinosus_Moderated stress_cow299

value: Semitendinosus

value: Lipid VitE PERP


title: shTFEB NB4 ATRA 2

treatment_protocol: Standard lentiviral approaches were used to functionally deplete TFEB mRNA in the NB4 acute promyelocytic leukemia cell line. An scrambled sequence shRNA was used as a negative control. The parental wild type NB4 cell line was used as control. Biological replicates of wildtype NB4, scrambled shRNA control and TFEB knockdown NB4 cells were treated with either ethanol (control) or all-trans retinoic acid (1microM) for 72 hours and differentiation monitored. RNA was isolated and sequenced.

tag: knockdown

value: shTFEB


title: JEG-3 stimulated (rep2)

description: Test for JEG3


title: BMSC TUMOR rep2

tag: cell type

tag: strain


title: shTFEB NB4 ATRA 1


title: Semitendinosus_Moderated stress_cow297

value: Lipid-rich


title: BMSC HOMING rep3

value: HOMING (GFP-BMSCs collected from the bone marrow of mice (GFP-BMSCs injected subcutaneously))


title: BMSC TUMOR rep1


title: JEG-3 stimulated (rep1)

description: Test for JEG3


title: shTFEB NB4 vehicle control 2


title: Semitendinosus_Moderated stress_cow287


title: 201048-negative_bisulfite

tag: gender

value: negative


title: JEG-3 control (rep3)

description: Normalizer for JEG3


title: 202007-negative_bisulfite

value: Whole blood

tag: ptsd diagnosis


title: shTFEB NB4 vehicle control 1


title: JEG-3 control (rep2)

description: Normalizer for JEG3


title: Longissimus thoracis _Moderated stress_cow297


title: BMSC HOMING rep2


title: 201109-negative_bisulfite

value: Male


title: JEG-3 control (rep1)

description: Normalizer for JEG3


title: BMSC NC rep3

value: NC (primary cultured GFP-BMSCs)


title: shScr NB4 vehicle ATRA 1

value: ATRA

value: control


title: Longissimus thoracis _Moderated stress_cow287

value: Normand cows

value: Moderated stress


title: Longissimus thoracis _Moderated stress_cow301


title: 202144-negative_bisulfite


title: 201011-positive_bisulfite

value: positive


title: shScr NB4 vehicle control 2

value: Vehicle control


title: BMSC NC rep2

value: mouse bone marrow stem cells

value: wide type


title: Semitendinosus_Limited stress_cow286

value: Semitendinosus

value: Limited stress


title: 202014-positive_bisulfite


title: BMSC NC rep1


title: BMSC HOMING rep1


title: shScr NB4 vehicle control 1


title: BMSC BM rep3

value: BM (GFP-BMSCs collected from the bone marrow of tumor-bearing mice (co-injection of RFP-LLCs and GFP-BMSCs))


title: Longissimus thoracis _Limited stress_cow286

value: Longissimus thoracis

value: Lipid VitE PERP


title: BMSC BM rep2


title: Longissimus thoracis _Limited stress_cow282

value: Lipid-rich


title: BMSC BM rep1


title: shScr NB4 vehicleATRA 2


title: Semitendinosus_Limited stress_cow282


title: Longissimus thoracis _Limited stress_cow280


title: 201227-negative_bisulfite

value: Whole blood

value: negative


title: TBT24.2

city: Barcelona

first: Inmaculada

last: Fuertes

state: Barcelona

address: Calle Jordi Girona, 18-26

department: Department of Environmental Chemistry

country: Spain

institute: CSIC

description: SAMPLE 23

hyb_protocol: according to manufacturer protocols Low input Quick Amp lebelling

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1-v1_91 and Grid:066414_D_F_20140506)to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Daphnia magna

source_name: Daphnia TBT 24h

growth_protocol: daphnias were cultured and grown according to Barata and Baird, 200

extract_protocol: Total RNA was extracted using Trizol according to Soetaert et al. 2007

treatment_protocol: Experiments follow previous procedures (Jordão et al., 2015; Jordão et al., 2016b) with 1 mg/L for tributyltin and pyriproxyfen and 10 mg/L for bisphenol A

tag: Sex

value: female

tag: age

value: 5 days

value: Daphnia TBT 24h

value: all body


title: 3Jiyoye F1sh

city: Ulm

first: Alexey

last: Ushmorov

address: Albert-Einstein-Allee 11

department: Institute of Physiological Chemistry

institute: Ulm University

description: Jiyoyescr-VS-JiyoyeF1sh.DEseq2_Method.GeneDiffExp

data_processing:
SOAPnuke software was used for data filtering (version：v1.5.2, parameters: -l 15 -q 0.2 -n 0.05)
Bowtie2 was used to map clean reads to reference (Version: v2.2.5, Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200)
RSEM was used to calculate gene expression level (Version: v1.2.12, Parameters: default)
DEseq2 was used to detect DEGs (Parameters: Fold Change >= 2.00 and Adjusted P value <= 0.05)
Genome_build: hg38
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

source_name: BL cell line

growth_protocol: BL cells were grown in RPMI1640 medium with addition of 15 % FBS, glutamine and antibiotics at 37 ºC, 5% CO2.

extract_protocol:
Total RNA was isolated with RNeasy mini kit (QIAGEN) according to the manufacturers instruction.
RNA libraries were prepared for sequencing using standard BGI protocols (oligo dT mRNA enrichment)

treatment_protocol: BL cells were transduced with a lentiviral vector expressing scrambled shRNA of shRNA tageting human FOXO1 mRNA. The infected cells were sorted on day 4 after transduction.  The experiment was done in duplicates or triplicates.  Total RNA was isolated with RNeasy mini kit (QIAGEN).


title: 2Jiyoye F1sh


title: 201286-positive_bisulfite

value: Male


title: Semitendinosus_Limited stress_cow280

value: Normand cows


title: TBT24.4

description: SAMPLE 24

scan_protocol: according to manufacturer protocols Low input Quick Amp lebelling


title: Semitendinosus_Limited stress_cow277


title: TBT24.1

description: SAMPLE 22

label_protocol: according to manufacturer protocols Low input Quick Amp lebelling


title: Longissimus thoracis _Limited stress_cow277


title: M12

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

institute: Max Planck Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, 0.75µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 3µm resolution using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted single-color raw data txt files were further analyzed using R and the associated BioConductor package limma. Background was removed using method normexp with offset 15, followed by quantile normalization.

source_name: Mouse cervix Differentiated Organoids WNT-deficient media mc029

label_protocol: RNA was labeled with the single-color Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol: Mouse cervical cells were grown in Wnt-deficient or proficient media as described in the accompanying publication (materials and methods).

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier.

treatment_protocol: Cells were cultured in 3D Matrigel cultures in the described media. Differentiated organoids were harvested at 2 weeks after seeding while early organoids were harvested at 3 days post seeding into matrigel.

tag: tissue type

value: cervix

tag: medium

value: WNT-deficient media

tag: organoid type

value: Differentiated Organoids

tag: mouse id

tag: passage


title: 1Jiyoye F1sh


title: TBT8.4

description: SAMPLE 21

source_name: Daphnia TBT 8h

value: 4 days

tag: treatment

value: Daphnia TBT 8h


title: TBT8.2

description: SAMPLE 20


title: 2Jiyoye scr

tag: genotype

value: scrambled control


title: M11

source_name: Mouse cervix Differentiated Organoids WNT-deficient media mc028


title: Semitendinosus_Limited stress_cow275

tag: race

value: Semitendinosus

tag: slaughtered conditions

value: Limited stress


title: 1Jiyoye scr


title: PP24.5

description: SAMPLE 18

source_name: Daphnia PP 24h

value: Daphnia PP 24h

tag: tissue


title: Longissimus thoracis _Limited stress_cow275

value: Longissimus thoracis

tag: supplement diet

value: Lipid VitE PERP


title: Semitendinosus_Limited stress_cow270

value: Lipid-rich


title: 3Nam F1sh

description: Namscr-VS-NamF1sh.DEseq2_Method.GeneDiffExp


title: WES_Kit_E211

first: Jian

tag: strain/background

tag: genotype/variation

value: Bone marrow

tag: cell type

value: c-Kit+ leukemia cells


title: TBT8.1

description: SAMPLE 19

value: female

value: all body


title: M9

source_name: Mouse cervix Early Organoids WNT-deficient media mc028

value: Early Organoids


title: M10

source_name: Mouse cervix Early Organoids WNT-deficient media mc029

value: cervix


title: PP24.4

description: SAMPLE 17

value: 5 days


title: Longissimus thoracis _Limited stress_cow270

source_name: Muscle Longissimus thoracis  Limited stress

value: Normand cows


title: Semitendinosus_Moderated stress_cow269

source_name: Muscle Semitendinosus Moderated stress

value: Moderated stress


title: PP24.2

description: SAMPLE 16


title: 2Nam F1sh


title: Mpul_mutW8_repl3

city: Waedenswil

first: Christian

middle: H

last: Ahrens

state: Zurich

address: Mueller-Thurgau Strasse 29

institute: Agroscope

data_processing:
Quality control was performed using FastQC.
Reads were trimmed with TrimGalore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), with a quality cutoff of 20 and a minimal length cutoff of 20.
Alignment to genome was done with Bowtie2
Gene expression levels were estimated using Salmon (Patro et al 2017: https://www.nature.com/articles/nmeth.4197)
Normalization and differential expression analysis were performed using edgeR (edgeR, Bioconductor 3.5 package)
Genome_build: ASM421770v1; IMG genome ID 2721755843; https://genome.jgi.doe.gov/portal/IMG_2721755843/IMG_2721755843.info.html
Supplementary_files_format_and_content: tab-delimited text file includes CPM values for each sample

organism: Metschnikowia pulcherrima

source_name: M. pulcherrima mutant W8cells

growth_protocol: Wt and W8 mutant were grown in potato decxtrose broth ON, diluted to OD600 of 0.4 and grown for 5-6 hour at 23 degree before harvesting the pellet and freezing it.

extract_protocol:
Cells were mech. disrupted with a FastPrep FP120 (Thermo Electron Corp.), total RNA was extracted with Qiagen RNeasy mini kit, quantified and subjected to treatment with TruSeq Stranded mRNA sample kit (Illumina)
Illumina TruSeq Stranded mRNA Sample kit; selective enrichment by PCR, cluster generation with TruSeq SR and PE Cluster kits v4-cBot-HS

treatment_protocol: No additional treatments were carried out.

value: mutant W8


title: Mpul_mutW8_repl2


title: M8

source_name: Mouse cervix Early Organoids WNT-proficient media mC017

value: WNT-proficient media


title: M7

source_name: Mouse cervix Early Organoids WNT-proficient media mC012


title: Mpul_mutW8_repl1


title: 1Nam F1sh


title: PP8.5

description: SAMPLE 15

source_name: Daphnia PP 8h

value: 4 days

value: Daphnia PP 8h


title: Mpul_wt_repl2

source_name: M. pulcherrima wt cells

value: wt


title: 3Nam scr

value: scrambled control


title: Longissimus thoracis _Moderated stress_cow269

source_name: Muscle Longissimus thoracis  Moderated stress

value: Longissimus thoracis

value: Lipid VitE PERP


title: M2

source_name: Mouse cervix Differentiated Organoids WNT-proficient media mC012

value: Differentiated Organoids


title: Mpul_wt_repl1


title: PP8.4

description: SAMPLE 14


title: 2Nam scr


title: 1Nam scr


title: M1

source_name: Mouse cervix Differentiated Organoids WNT-proficient media mC017


title: Semitendinosus_Limited stress_cow267

source_name: Muscle Semitendinosus Limited stress

value: Semitendinosus

value: Limited stress


title: Longissimus thoracis _Moderated stress_cow268

value: Lipid-rich


title: M3125, 1.5 mM NO, rep 1

city: Athens

first: Anthony

middle: E.

last: Glenn

state: GA

address: 950 College Station Rd

department: Toxicology & Mycotoxin Research Unit

institute: USDA, ARS, USNPRC, R.B. Russell Research Center

description: Wild type NO-exposed, Rep1

data_processing:
FastQC
Removal of low quality reads (Phred score <20) and sequencing adapters using Trimmomatic 0.25
Bioconductor Rsubread align function for mapping filtered reads to the F. verticillioides genome
Read counting, normalization, and expression level (FPKM) calculations were executed using the featurecount function in Rsubread using the default settings.
Differential gene expression analysis was performed using edgeR and DESeq packages, by applying a false discovery rate threshold of < 0.05 for the adjusted p-value.
Genome_build: Fusarium verticillioides genome as downloaded from www.fungidb.org (Fusarium verticillioides_7600_3_supercontig)
Supplementary_files_format_and_content: FPKM values in tab delimited table format for all treatments and genes (.txt file)

organism: Fusarium verticillioides

source_name: PDB liquid culture

growth_protocol: Three milliliters of PDB (potato dextrose broth; Neogen Food Safety, Lansing, MI, USA) in sterile snap-cap tubes, with caps loose, were inoculated with 1x10^6 F. verticillioides conidia and grown at 27 °C, 250 rpm for 3 days. Cultures of both FRC M-3125 and ΔFVEG_10494-6.4 were prepared.

extract_protocol:
For each treatment, 1 ml of culture was transferred to lysing matrix S tubes (MP Biomedicals, LLC, Santa Ana, CA, USA), centrifuged at 10,000 x g for 5 min at 4°C, and the supernatant discarded. Lysis buffer (PureLink® RNA Mini Kit, Thermo Fisher Scientific) was immediately added to the fungal pellets, and the samples were homogenized using the FastPrep-24™ 5G Instrument (MP Biomedicals) at a speed of 6 m/sec with two segments of homogenization for 30 seconds with a 1 min rest in between. The total RNA was extracted following the manufacturer’s instructions (PureLink® RNA Mini Kit, Thermo Fisher Scientific). Isolated RNA samples were DNase treated (TURBO DNA-free™ Kit, Thermo Fisher Scientific), tested by conventional PCR for the complete removal of DNA, and checked for quality (RNA integrity number > 6.0) using an Agilent 2100 Bioanalyzer (Agilent Technology, Waldbronn, Germany).
Twelve libraries (wild type and mutant ΔFVEG_10494-6.4 treated with and without 1.5 mM DETA NONOate for 30 min, with three biological replicates each) were prepared and sequenced on an Illumina NextSeq (75 Cycles) High Output Flow Cell (paired end, 75 bp read length) by the Georgia Genomics Facility at the University of Georgia.

treatment_protocol: Prior to harvesting samples, half of the cultures of each strain received 22.5 ul of 200 mM DETA NONOate (1.5 mM DETA NONOate final concentration in the 3 ml cultures) and were incubated an additional 30 min.

tag: strain

value: Wild-type FRC M-3125

tag: hours growth

value: 3 days + 30 min NO exposure


title: M3125, 1.5 mM NO, rep 2

description: Wild type NO-exposed, Rep2


title: PP8.2

description: SAMPLE 13

tag: Sex

value: female

tag: age

value: all body


title: 3BL-41 F1sh

description: BL41scr-VS-BL41F1sh.DEseq2_Method.GeneDiffExp.xls

source_name: BL cell line


title: 2BL-41 F1sh


title: Longissimus thoracis _Limited stress_cow267

value: Normand cows


title: Semitendinosus_Moderated stress_cow268

value: Moderated stress


title: BPA24.2

description: SAMPLE 11

source_name: Daphnia BPA 24h

value: 5 days

value: Daphnia BPA 24h


title: Semitendinosus_Moderated stress_cow265


title: 3BL-41 scr


title: BPA24.1

description: SAMPLE 10


title: BPA8.4

description: SAMPLE 9

source_name: Daphnia BPA 8h

value: 4 days

value: Daphnia BPA 8h


title: BPA8.1

description: SAMPLE 7


title: BPA8.2

description: SAMPLE 8


title: Semitendinosus_Moderated stress_cow260


title: BPA24.4

description: SAMPLE 12


title: C24.4

description: SAMPLE 6

source_name: Daphnia control 24h

value: Daphnia control 24h


title: M3125, 0 mM NO, rep 2

description: Wild type unexposed control, Rep2

value: 3 days


title: Longissimus thoracis _Moderated stress_cow260

value: Longissimus thoracis


title: 1BL-41 scr

value: scrambled control


title: C24.3

description: SAMPLE 5


title: M3125, 0 mM NO, rep 3

description: Wild type unexposed control, Rep3


title: ΔFVEG_10494-6.4, 1.5 mM NO, rep 3

description: ΔFVEG_10494-6.4 NO-exposed, Rep3


title: control-3 [DuiA-3]

city: Ji Nan

first: Sai

last: Linlin

state: Shan Dong

address: 18877 Jingshi Road, Lixia District

institute: Shandong Academy of Occupational Health and Occupational Medicine, Jinan, Shandong, China

data_processing:
Basecalls performed using CASAVA version 1.8
circRNA-seq reads were aligned to the reference genome/transcriptome (NCBI xl_ref_Xenopus_laevis_v2) with bowtie2 software
circRNAs were detected and identified with find_circ software
lncRNA-seq and mRNA-seq reads were aligned to the reference genome/transcriptome (NCBI xl_ref_Xenopus_laevis_v2) with Hisat2 software
Genome_build: xl_ref_Xenopus_laevis_v2
Supplementary_files_format_and_content: *Expression_Profiling.xlsx containing FPKM and counts, or number of raw junction read data

organism: Xenopus laevis

extract_protocol:
Testes were removed, flash-frozen in liquid nitrogen,  stored at -80 C, and RNA was harvested using Trizol. The concentration and purity were measured using a NanoDrop® ND-2000 (Thermo, Waltham, MA, USA) spectrophotometer. The integrity of RNA was determined by denaturing gel electrophoresis  for the construction of sequencing libraries.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, USA).

tag: developmental stage

value: post natal day 193(13+180)

tag: exposed to

value: none (control)

value: testis


title: control-2 [DuiA-2]


title: M truncatula w TAP, IL, rep2

city: Norwich

first: Tamas

last: Dalmay

address: Earlham Road

department: School of Biological Sciences

institute: University of East Anglia

data_processing:
the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 3' adapters and HD signatures, for the HD samples, were trimmed and the files were converted from redundant to non-redundant format [Beckers et al 2017]
the reads were mapped to the reference genomes (host and virus), allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
the abundances of the reads were normalized using the RPM method [Mortazavi et al 2008]
the differential expression was called on offset fold change, offset = 20
Genome_build: Mt 4.0
Supplementary_files_format_and_content: csv, raw abundances

organism: Medicago truncatula

source_name: leaf

growth_protocol: the plants were grown in Panasonic Plant Growth Chambers set at 25 and 18°C ( day and night, respectively) with 16 hours of light

extract_protocol:
Leaf tissue was used for RNA extraction before small RNA library construction
Illumina compatible method using standard Illumina adapters

treatment_protocol: a TAP treatment was applied prior to library preparation

tag: adapters

value: standard


title: M3125, 0 mM NO, rep 1

description: Wild type unexposed control, Rep1

value: Wild-type FRC M-3125


title: ΔFVEG_10494-6.4, 0 mM NO, rep 3

description: ΔFVEG_10494-6.4 unexposed control, Rep3


title: ΔFVEG_10494-6.4, 1.5 mM NO, rep 1

description: ΔFVEG_10494-6.4 NO-exposed, Rep1

value: 3 days + 30 min NO exposure


title: control-1 [DuiA]


title: M truncatula w TAP, HD, rep2

value: HD


title: AZ-3 [A-3]

value: 100 µg/L atrazine (AZ)  for 180 days


title: Longissimus thoracis _Moderated stress_cow265

value: Normand cows

value: Moderated stress

value: Lipid-rich


title: ΔFVEG_10494-6.4, 1.5 mM NO, rep 2

description: ΔFVEG_10494-6.4 NO-exposed, Rep2


title: AZ-2 [A-2]


title: M truncatula w TAP, IL, rep1


title: Longissimus thoracis _Limited stress_cow259

source_name: Muscle Longissimus thoracis  Limited stress

value: Limited stress


title: Semitendinosus_Moderated stress_cow258

source_name: Muscle Semitendinosus Moderated stress

value: Semitendinosus

value: Lipid VitE PERP


title: Longissimus thoracis _Moderated stress_cow258


title: Semitendinosus_Limited stress_cow259


title: Longissimus thoracis _Limited stress_cow255


title: ΔFVEG_10494-6.4, 0 mM NO, rep 1

description: ΔFVEG_10494-6.4 unexposed control, Rep1

value: 3 days


title: ΔFVEG_10494-6.4, 0 mM NO, rep 2

description: ΔFVEG_10494-6.4 unexposed control, Rep2


title: C8.4

description: SAMPLE 3

source_name: Daphnia control 8h

value: female

value: 4 days

value: Daphnia control 8h

value: all body


title: C24.2

description: SAMPLE 4

value: 5 days

value: Daphnia control 24h


title: AZ-1 [A]

value: post natal day 193(13+180)

value: testis


title: C8.3

description: SAMPLE 2


title: Semitendinosus_Limited stress_cow255


title: C8.2

description: SAMPLE 1


title: Semitendinosus_Moderated stress_cow251