title: d22-3-30-2

description:
d22-infected HeP2 cells at 3 hpi with 30 min of run on rep 2
labeled RNA was extracted and prepared for sequencing with sequential, specific 3' and 5' RNA adapters.  Libraries were reverse transcribed and sequenced with Illumina Next Seq550 75bp single end sequencing, the spiked in drosophila s2 cells were used for normalization after BigWig creation

source_name: HeP-2 cells, S2 Cells, HSV-2


title: d22-3-30-1

status: Public on Jan 05 2022

type: SRA

city: Ithaca

first: Joel

middle: D

last: Baines

state: NY

address: 235 Hungerfordhill Rd

country: USA

institute: Cornell University

description:
d22-infected HeP2 cells at 3 hpi with 30 min of run on rep 1
labeled RNA was extracted and prepared for sequencing with sequential, specific 3' and 5' RNA adapters.  Libraries were reverse transcribed and sequenced with Illumina Next Seq550 75bp single end sequencing, the spiked in drosophila s2 cells were used for normalization after BigWig creation

library_source: transcriptomic

data_processing:
Library strategy: PRO-seq
Adapter trimming and processing using Cut Adapt
Raw genome algnments usign BWA
Conversion of BAM files to strand specific BigWigs using kentsource
https://github.com/Danko-Lab/tutorials/blob/master/PRO-seq.md
Genome_build: hg38 human genome build, Dm3 Drosophila genome build, HSV-1 (F) strain in-house genome build
Supplementary_files_format_and_content: read count data in BigWig files

molecule: total RNA

organism:
Drosophila melanogaster
Homo sapiens
Human alphaherpesvirus 1

source_name: HeP-2 cells, S2 Cells, HSV-1

growth_protocol: Hep-2 cells were grown and maintained with DMEM 10% fetal bovine serum and the Drosophila S2 cells were grown in Schneider's medium supplemented with 10% NBS

extract_protocol:
Nuclei were extracted as previoulsy described (Birkenheuer and Baines 2020, Journal of Virology).  Global run-on reactions were performed as described by Lopes et al 2017, GRO-seq, A Tool for Identification of Transcripts Regulating Gene Expression. Methods Mol Biol 1543:45-55, and were allowed to proceed for 5 or 30 mins of run-on.  Reactions were stopped by the addition of Trizol.
Libraries were constructed similar to the construction of PRO-seq libraries with adapter ligations for the 3' end being performed first and cap removal and 5' phosphate repair and 5' adapter ligation being performed after the 3' end of the RNA was ligated to the sequencing adapter.  However, instead of using magnetic beads for this process, anti Br-dUTP conjugated agarose beads were used for this process with the blocking, washing, and elution conditions described by (Lopes et al, 2017, GRO-seq, A Tool for Identification of Transcripts Regulating Gene Expression. Methods Mol Biol 1543:45-55.).
Libraries were created using Illumina Index primers for sequencing on the NextSeq550 75 base pair single end sequencing.

treatment_protocol: Hep-2 cells were infected with the mutant viruses at a MOI of 5 and allowed to progress to 3 or 6 hours post infection.

tag: cell line (human)

value: HeP-2 cells

tag: cell line (drosophila)

value: S2 cells

tag: cell type (human)

value: lung epithelial carcinoma cells

tag: viral infection

value: infected with HSV-1 bearing full US1/US1.5 gene deletion

tag: infection timepoint

value: 3 hours post infection

tag: run-on time

value: 30 min of run on with Br-UTP


title: SK-MEL-239.ms023_1uM.B

city: Seattle

first: James

middle: Douglas

last: Thomas

state: WA

address: 1100 Fairview Ave. N., B3-111

department: Computational Biology

institute: Fred Hutchinson Cancer Research Center

description: RNA-seq of cell line treated with the indicated compound

data_processing:
Illumina Casava software was used for base calling.
For RNA-seq, reads were aligned to the mouse or human transcriptome using RSEM followed by mapping to the mouse genome (mm10) or human (hg19) using Bowtie and TopHat.
RNA splicing was quantified using MISO.
Genome_build: mm10 for mouse data; hg19 for human data
Supplementary_files_format_and_content: The final processed data is found in the file "d.isoforms.txt"

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
RNA was extracted from cells of interest using an RNeasy kit (Qiagen, Frederick, MD) and quantified using a NanoDrop 8000 (ThermoFisher Scientific); a minimum of 500 ng of high quality RNA (as determined by Agilent Bioanalyzer) per sample or replicate was used for library preparation.
Poly(A)-selected, stranded Illumina libraries were prepared with a modified TruSeq protocol and sequenced on the Illumina HiSeq 2000

treatment_protocol: Cell lines were treated with splicing inhibitors at the indicated concentrations for 96 hours in vitro, harvested and washed three times with PBS in excess to remove all drug, and then used for downstream analyses, continued growth in vitro or tumor challenge in vivo into syngeneic animals.

tag: cell line

tag: agent


title: SK-MEL-239.ms023_1uM.C


title: RPAA_6hr_1

source_name: HSV-1 infected HeP2 cells and Drosophila S2 cells

extract_protocol:
Nuclei were extracted as previously described (Birkenheuer and Baines 2020, Journal of Virology)
nascent RNA was labelled with biotinylated nuclotides during a nuclear run-on.  The biotinylated transcripts were isolated and used to prepare sequencing libraries from the reverse transcribed products.
Libraries were constructed as previously described (Mahat and others, 2016,  Base-Pair Resolution Genome-Wide Mapping Of Active RNA polymerases using Precision Nuclear Run-On (PRO-seq), Nature Protocols).
Libraries were created using Illumina Index primers for sequencing on the NextSeq550 75 base pair single end sequencing.

treatment_protocol: Hep-2 cells were infected with the mutant viruses at a MOI of 5 and allowed to progress to 3 or 6 hours post infection.  PAA treatment occurred at the time of infection and PAA was maintained in the medium over the course of infection

tag: developmental stage (drosophila)

value: late stage embryo

value: HSV-1 (F) strain BAC mutant with repaired US1 open reading frame

tag: time

tag: drug treatment

value: Phosphonoacetic Acid (PAA)


title: SAMPLE 243 [Genotype 243]

type: genomic

city: Brandon

middle: Raymond

last: Tucker

state: MB

address: 2701 Grand Valley Rd.

country: Canada

institute: Agriculture and Agri-Food Canada

hyb_protocol: not provided

scan_protocol: Illuina iScan instrument

data_processing: Illumina Genome Studio software was used for clustering

label: Cy3, Cy5

molecule: genomic DNA

organism: Hordeum vulgare

source_name: leaf tissue

label_protocol: not provided

growth_protocol: Seeds of barley were surface sterilized with dilute bleach solution (6% per vol) then germinated on cotton balls.

extract_protocol: Qiagen, 96 well DNeasy protocol as per manufacturers instructions

treatment_protocol: leaves were cut and placed in liquid nitorgen then freeze dried.

tag: tissue

value: leaf

tag: genotype

value: barley genotype 243


title: SK-MEL-239.ms023_1uM.A


title: SAMPLE 240 [Genotype 240]

value: barley genotype 240


title: B10406-T4c

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description:
Bisulfite-treated DNA
CpG_quantification.txt

library_source: genomic

data_processing:
Read pairs were merged with PEAR. Assembled reads were mapped to the reference fasta file using Bismark with the --non_directional flag. Methylation status per CpG per read was extracted using bismark_methylation_extractor, and then summarized to a total count, methylated count, and % methylation per CpG for all reads in the sample.
Genome_build: Custom amplicon reference is a combination of HBV genomic sequence derived from subtype ayw (ACCESSION No: V01460 J02203) (sequence "virus_ref" in amplicon_reference.fa) and promoter sequences for 3 genes from mm10 (sequences "IGFBP1", "APOB", and "CYP2E1")
Supplementary_files_format_and_content: CpG Tab-delimited text (contains total read counts, methylated read counts, and % methylation for each CpG in each sample)
Supplementary_files_format_and_content: FASTA (reference genomic sequences for HBV and mouse sequences)

organism: Mus musculus

source_name: Liver

growth_protocol: 12-15 month old mice

extract_protocol:
Protein-free mouse genomic DNA was isolated from liver tissue as described (McFadden, V.C., Shalaby, R.E., Iram, S., Oropeza, C.E., Landolfi, J.A., Lyubimov, A.V., Maienschein-Cline, M., Green, S.J., Kaestner, K.H., and McLachlan, A. (2017). PLOS Pathogens 13, e1006239).
Genomic DNA for methylation analysis was performed using the EZ DNA Methylation-Lightning™ Kit (D5030; Zymo Research, Inc., Irvine, CA, USA). The CpG sequences in the HBV DNA genome were targeted using PCR amplification of the bisulfite- treated DNA, followed by sequencing of the amplicons on an Illumina MiSeq instrument.  Preparation of DNA for high-throughput amplicon sequencing was performed in two PCR steps as described previously (McFadden et al. 2017).  Twelve HBV primer pairs targeting 94 of the 99 CpG sites were used.   The primer pairs targeting the bisulfite converted HBV DNA were (i) 5’-ACACTGACGACATGGTTCTACACAATACCTAAACCTTTACCC-3’ (oligo CS1FP1; HBV nucleotide coordinates 1131-1150) and 5’-TACGGTAGCAGAGACTTGGTCTGTTTTAGTTAGTGGGGGT-3’ (oligo CS2RP1; HBV coordinates 1214-1197), (ii) 5’-ACACTGACGACATGGTTCTACACAAACTTTCACTTTCTC-3’ (oligo CS1FP1a; HBV coordinates 1086-1102) and 5’-TACGGTAGCAGAGACTTGGTCTGTTGATGGTTTATGATTAA (oligo CS2RP1a; HBV coordinates 1233-1215), (iii) 5’-ACACTGACGACATGGTTCTACACCCCCACTAACTAAAAC-3’ (oligo CS1FP2; HBV nucleotide coordinates 1198-1214) and 5’-TACGGTAGCAGAGACTTGGTCTGGGTAATATTTGGTGG-3’ (oligo CS2RP2; HBV nucleotide coordinates 1645-1630), (iv) 5’-ACACTGACGACATGGTTCTACATTAAACTCTCAACAATATCA-3’ (oligo CS1FP3; HBV nucleotide coordinates 1668-1687) and 5’-TACGGTAGCAGAGACTTGGTCTAAGTTATTTAAGGTATAGTTTG-3’ (oligoCS2RP3; HBV nucleotide coordinates 1896-1875), (v) 5’-ACACTGACGACATGGTTCTACAGTGGTTTTGGGGTATGG-3’ (oligo CS1FP4; HBV nucleotide coordinates 1890-1906) and 5’-TACGGTAGCAGAGACTTGGTCTCAAATTAACACCCACCC-3’ (oligo CS2RP4; HBV nucleotide coordinates 2130-2114), (vi) 5’-ACACTGACGACATGGTTCTACAAGTTATAGAGTATTTGGTGT-3’ (oligo CS1FP5a; HBV nucleotide coordinates 2244-2263) and 5’-TACGGTAGCAGAGACTTGGTCTCCCAATAAAATTCCCCA-3’ (oligo CS2RP5a; HBV nucleotide coordinates 2491-2475), (vii) 5’- ACACTGACGACATGGTTCTACAGATTGTAATTGATTATGTTTG -3’ (oligo CS1FP6; HBV nucleotide coordinates 2625-2645) and 5’- TACGGTAGCAGAGACTTGGTCTCCATACTATAAATCTTATTCCC-3’ (oligo CS2RP6; HBV nucleotide coordinates 2832-2853), (viii) 5’-ACACTGACGACATGGTTCTACAGGGAATAAGATTTATAGTATGG (oligo CS1FP7; HBV  nucleotide coordinates 2832-2853) and 5’-TACGGTAGCAGAGACTTGGTCTTAAACCTAAAAACTCCACC-3’ (oligo CS2RP7; HBV nucleotide coordinates 3061-3043, (ix) 5’-ACACTGACGACATGGTTCTACAAATCAAAAAAACAACCTACC-3’ (oligo CS1FP8; HBV  nucleotide coordinates 3115-3134) and 5’-TACGGTAGCAGAGACTTGGTCTGTGAGTGATTGGAGGT-3’ (oligo CS2RP8; HBV  nucleotide coordinates 340-325), (x) 5’-ACACTGACGACATGGTTCTACAACCTCCAATCACTCAC-3’ (oligo CS1FP9; HBV  nucleotide coordinates 325-340) and 5’-TACGGTAGCAGAGACTTGGTCTGTTAAATAGTGGGGGAAAG-3’ (oligo CS2RP9; HBV nucleotide coordinates 730-712), (xi) 5’-ACACTGACGACATGGTTCTACAGGATGATGTGGTATTGG-3’ (oligo CS1FP10; HBV nucleotide coordinates 743-759) and 5’-TACGGTAGCAGAGACTTGGTCTCAAAACCCAAAAAACCCAC-3’ (oligo CS2RP10; HBV nucleotide coordinates 1020-1002), and (xii) 5’-  ACACTGACGACATGGTTCTACATTGATGTTTTTGTATGTA-3’ (oligo CS1FP11;  HBV nucleotide coordinates 1053-1070) and 5’-TACGGTAGCAGAGACTTGGTCTATAACCAAACCCCAACC-3’ (oligo CS2RP11; HBV nucleotide coordinates 1222-1206).  These primers contained linker sequences (underlined) at the 5’ ends of the oligonucleotides, termed common sequences (CS1 and CS2). These PCR reactions were performed using ZymoTaq PreMix according to the manufacturer’s instructions (Zymo Research).  PCR amplification involved 10 minutes denaturation at 95°C, followed by 40 cycles of 95°C for 30 s, 50°C for 40 s (ramp rate 95-50 was set to 0.3C/s), 72°C for 60 s.  Finally, a 7 minute incubation at 72°C was performed.  The HBV amplicons were subsequently subjected to a second stage PCR reaction (MyTaq HS Mix, 2X, Bioline USA Inc., Taunton, MA, USA), used to incorporate unique barcodes and sequencing adapters. The PCR primers used were 5’-  AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA-3’ (oligo PE1CS1) and 5’-CAAGCAGAAGACGGCATACGAGATNNNNNNNNNNTACGGTAGCAGAGACTTGGTCT-3’ (oligo PE2BCCS2).  The 10-base sample-specific barcodes are indicated with bold Ns and represent barcode sequences from a set of 384 unique primer pairs (Fluidigm Access Array Barcode Library for Illumina Sequencers).  PCR amplification involved 5 minutes denaturation at 95°C, followed by 8 cycles of 95°C for 30 s, 60°C for 30 s, 72°C for 30 s.  Finally, a 7 minute incubation at 72°C was performed.  The resulting final PCR products (libraries) contain Illumina sequencing adapters and a sample-specific barcode. Pooled libraries were sequenced using an Illumina MiSeq instrument and data were analyzed using the Casava1.8 pipeline. Sequencing was performed using MiSeq V3 chemistry, with paired-end 2x300 base reads, employing Access Array custom sequencing primers.

value: HBV(+/-)Pten(fl/fl)Cre(+/-)

tag: disease state

value: HCC

value: liver


title: d22-6-30-2

description:
d22-infected HeP2 cells at 6 hpi with 30 min of run on rep 2
labeled RNA was extracted and prepared for sequencing with sequential, specific 3' and 5' RNA adapters.  Libraries were reverse transcribed and sequenced with Illumina Next Seq550 75bp single end sequencing, the spiked in drosophila s2 cells were used for normalization after BigWig creation

source_name: HeP-2 cells, S2 Cells, HSV-6

value: 6 hours post infection


title: RPAA_6hr_2


title: RPAA_3hr_2


title: SAMPLE 241 [Genotype 241]

value: barley genotype 241


title: RPAA_3hr_1

value: HeP-2 cells


title: SK-MEL-239.indisulam.C

value: indisulam


title: R_3hr_2

value: S2 cells

value: lung epithelial carcinoma cells

value: No treatment


title: R_6hr_2


title: SAMPLE 236 [Genotype 236]

value: barley genotype 236


title: SAMPLE 237 [Genotype 237]

value: barley genotype 237


title: SAMPLE 235 [Genotype 235]

value: barley genotype 235


title: SK-MEL-239.indisulam.B


title: SK-MEL-239.indisulam.A


title: US1_6hr_1

value: late stage embryo

value: HSV-1 (F) strain BAC mutant with deleted US1 open reading frame


title: SAMPLE 238 [Genotype 238]

value: leaf

value: barley genotype 238


title: R_3hr_1

value: HSV-1 (F) strain BAC mutant with repaired US1 open reading frame


title: R_6hr_1


title: SAMPLE 239 [Genotype 239]

value: barley genotype 239


title: SK-MEL-239.dmso.C

value: dmso


title: Repair_6hr_2


title: US1_3hr_1


title: SK-MEL-239.dmso.A


title: Repair_6hr_1


title: US1_6hr_2


title: Repair_3hr_2


title: Repair_3hr_1


title: A375.ms023_1uM.C


title: SAMPLE 233 [Genotype 233]

value: barley genotype 233


title: Cocci Mycelia csRNA-seq rep2

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: cocci.tsr-mycelia.txt

data_processing:
For csRNA-seq, sequencing reads were trimmed for 3’ adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20”) and aligned to the appropriate genome using STAR with default parameters[PMID: 23104886]. Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. Furthermore, reads with spliced or soft clipped alignments were discarded. Transcription Start Regions (TSRs), representing loci with significant transcription initiation activity (i.e. ‘peaks’ in csRNA-seq), were defined using HOMER’s findcsRNATSS.pl tool, which uses short input RNA-seq, traditional total RNA-seq, and annotated gene locations to eliminate loci with csRNA-seq signal arising from non-initiating, high abundance RNAs that nonetheless are captured and sequenced by the method (Duttke et al. for more details[PMID:31649059]). Replicate experiments were first pooled to form meta-experiments for each condition prior to identifying TSRs. Annotation information, including gene assignments, promoter distal, stable transcript, and bidirectional annotations are provided by findcsRNATSS.pl.
For RNA-seq, reads from accession GSE171286 were downloaded and aligned to the C. immitis genome (ASM14933v2)  using STAR with default parameters. Reference-guided transcranscript assembly was performed using StringTie2 (Kovaka et al. 2019) with the Ensembl gene annotation (GTF file) and additional parameters “-m 100 --rf”. Assembled transcripts were compared to the existing C. immitis annotation using cuffcompare.
Genome_build: C. immitis (ASM14933v2), S. cerevisiae (R64-1-1/sacCer3), S. pombe (ASM294v2), A. bisporus (gca_000300555/Agabi_varbur_1)
Supplementary_files_format_and_content: Tab-delimited Text file describing TSR positions and annotations, GTF formated transcript definition files

organism: Coccidioides immitis

source_name: Coccidioides immitis mycleia

growth_protocol: C. immitis R.S. strain was grown as mycelia or spherules as previously described (Viriyakosol et al. 2013). To grow mycelia, 2×10^6 arthroconidia/ml were incubated in 250 ml flat-bottom Erlenmeyer flasks (Corning) in 50 ml GYE media. Flasks were cultured in a 30°C incubator without shaking for 5 days. To grow spherules, arthroconidia were washed 2 times in modified Converse media (Converse 1956). The spores were inoculated at 4×106 arthroconidia/ml into a 250 ml baffled Erlenmeyer flask containing 50 ml of modified Converse media. Flasks were set up and grown on a shaker at 160 rpm, in 14% CO2 at 42°C. Four flasks were harvested 2 days after inoculation and the remaining four flasks after 8 days. Fresh Converse media was not added.  The spherules did not rupture and release endospores within that time in this culture system. Saccharomyces cerevisiae (strain RYH2863) was grown as described previously (Neal et al. 2018). Schizosaccharomyces pombe (strain TH972) was generously provided by Tony Hunter (SALK Institute for Biological Sciences) and grown in Yeast Extract with Supplements (YES)(Leverson et al. 2002). White and brown ecotypes of Agaricus bisporus, better known as ‘Champignon’ or ‘crimini mushroom’ were kindly provided by Monterey Mushroom farms.

extract_protocol:
Trizol extraction after tissue homogenisation
For RNA-Seq, strand-specific, paired-end libraries were prepared from total RNA by ribosomal depletion using the Yeast Ribo-Zero rRNA Removal Kit (Illumina) and then using the TruSeq Stranded total RNA-Seq kit (Illumina) according to manufacturer's instructions. Then 100 bases were sequenced from both ends using a HiSeq 4000 according to the manufacturer's instructions (Illumina).    csRNA-seq was performed as described in (Duttke et al. 2019). Small RNAs of ~20-60 nt were size selected from 0.4-2 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen) and RNAs were 5’dephosporylation by quickCIP (NEB). Input (sRNA) and csRNA-seq libraries were prepared as described in (Hetzel et al. 2016) using RppH (NEB) and the NEBNext Small RNA Library Prep kit, amplified for 14 cycles and sequenced SE75 on the Illumina NextSeq 500.
csRNA-seq, sRNA-seq, total RNA-seq

treatment_protocol: untreated

tag: strain

value: RS strain

tag: tagtreatment

value: untreated

tag: method

value: csRNA-seq


title: Cocci Mycelia csRNA-input rep2

description: cocci.tsr-mycelia.txt

value: sRNA-seq (csRNA-seq input)


title: US1_3hr_2

tag: cell line (human)

value: HeP-2 cells

value: S2 cells

value: lung epithelial carcinoma cells


title: SAMPLE 232 [Genotype 232]

value: barley genotype 232


title: SAMPLE 231 [Genotype 231]

value: barley genotype 231


title: SAMPLE 229 [Genotype 229]

value: barley genotype 229


title: Cocci Mycelia csRNA-input rep1

description: cocci.tsr-mycelia.txt


title: SAMPLE 230 [Genotype 230]

value: barley genotype 230


title: A375.ms023_1uM.A


title: B10423-T3c

value: HBV(+/-)Pten(fl/fl)Cre(+/-)

value: HCC

value: liver


title: SK-MEL-239.dmso.B


title: Cocci Mycelia csRNA-seq rep1

description: cocci.tsr-mycelia.txt


title: Cocci Spherule 8d csRNA-input rep2

source_name: Coccidioides immitis 8d spherule


title: SAMPLE 228 [Genotype 228]

value: leaf

value: barley genotype 228


title: A375.indisulam.C

value: indisulam


title: Cocci Spherule 8d csRNA-input rep1

value: RS strain


title: Cocci Spherule 48h csRNA-input rep2

source_name: Coccidioides immitis 48h spherule

value: untreated


title: Cocci Spherule 8d csRNA-seq rep1

value: csRNA-seq


title: A375.ms023_1uM.B


title: A375.indisulam.B


title: SAMPLE 234 [Genotype 234]

value: barley genotype 234


title: Cocci Spherule 8d csRNA-seq rep2


title: Cocci Spherule 48h csRNA-seq rep1


title: Cocci Spherule 48h csRNA-seq rep2


title: Cocci Spherule 48h csRNA-input rep1

value: sRNA-seq (csRNA-seq input)


title: A375.dmso.C

value: dmso


title: catfish_liver_BxB_rep2

city: Auburn University

first: Xu

last: Wang

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

description: Illumina mRNA-seq

data_processing:
FastQC (version 0.11.5) software was used for quality check.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic (version 0.39), and masked for low-complexity or low-quality sequence.
The ramaining high-quality clean reads were mapped to the channel catfish reference genome using TopHat (version 2.1.1)
Bedtools (version 2.29.0) was conducted to calculate the number of aligned reads of each gene overlapping its exons.
edgeR was used to calculate log2-fold change (log2FC), |log2FC| >1.5 and FDR < 0.05 was used as cutoff for generating DEGs.
Genome_build: Ictalurus punctatus genome (GenBank assembly accession GCA_001660625.1 IpCoco_1.2)
Supplementary_files_format_and_content: Gzipped, tab-delimiited text file inlcuding raw gene counts for every gene and every sample

organism: Ictalurus furcatus

extract_protocol:
AllPrep DNA/RNA Mini Kit (Qiagen, CA, USA)
The RNA integrity was evaluated with the LabChip GX Touch HT (PerkinElmer, MA, USA). The RNA library preparation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, MA, USA). Enriched RNAs were fragmented for 10 minutes at 94 °C. The first strand cDNA synthesis, second strand cDNA synthesis, end repair and adaptor ligation according to the manufacturer’s protocol. The library PCR amplification were performed with 16 cycle PCR. The average size of the RNA libraries was approximately 350 bp (including the adapters). The RNA sequencing libraries were checked using the LabChip GX Touch HT (PerkinElmer, MA, USA) and quantified by using Qubit 3.0 Fluorometer (Invitrogen, CA, USA).

value: Blue catfish


title: A375.indisulam.A


title: catfish_liver_BxB_rep1

description: Illumina mRNA-seq


title: A375.dmso.B


title: SAMPLE 225 [Genotype 225]

value: barley genotype 225


title: A375.dmso.A


title: catfish_liver_CxC_rep2

description: Illumina mRNA-seq

organism: Ictalurus punctatus

value: Channel catfish


title: 501-MEL.ms023_1uM.C


title: SAMPLE 226 [Genotype 226]

value: barley genotype 226


title: SAMPLE 227 [Genotype 227]

value: barley genotype 227


title: SAMPLE 224 [Genotype 224]

value: barley genotype 224


title: B6839T

description:
polyA RNA
GeneExpMatrix.txt

data_processing:
Raw reads were trimmed using Trimmomatic v0.32 with parameters LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20  MINLEN:20. Trimmed reads were mapped to mouse rRNA sequences using bowtie2, and unmapped reads were mapped to mm10 using Tophat2 with parameters -i 70 -I 50000 --segment-length 25 --no-novel-juncs --no-coverage-search. Normalized expression was quantified using Cuffnorm v2.2.1 against UCSC gene annotations.
Genome_build: mm10
Supplementary_files_format_and_content:  FPKM normalized gene expression levels per sample.

extract_protocol:
RNA was isolated following the protocol of Chomczynski and Sacci (Chomczynski, P., and N. Sacchi. 1987. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162:156–159.).
Poly-A capture was performed on the samples to purify the mRNA, and directional mRNA libraries were made using the PrepX mRNA Library Kit.

value: HBV(+/-)Pten(fl/fl)Cre(+/-)

value: HCC


title: SAMPLE 223 [Genotype 223]

value: leaf

value: barley genotype 223


title: SAMPLE 222 [Genotype 222]

value: barley genotype 222


title: 501-MEL.ms023_1uM.B


title: catfish_liver_CxC_rep1

description: Illumina mRNA-seq

value: liver


title: 501-MEL.ms023_1uM.A


title: B6591

description:
polyA RNA
GeneExpMatrix.txt

value: HBV(+/-)Pten(fl/fl)Cre(-/-)

value: Control wildtype liver


title: SAMPLE 221 [Genotype 221]

value: barley genotype 221


title: B6839

description:
polyA RNA
GeneExpMatrix.txt

value: Pten-null non-tumor liver


title: TOL l

type: RNA

city: Rotterdam

first: Aafke

last: Duizendstra

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

description:
test
StepOnePlus Real-Time PCR System

data_processing: Gene expression was considered positive when <35 cycles were needed to detect a signal. After each measurement the meltcurve was examined to confirm exclusive amplification of the intended target gene. Expression of twenty selected genes was normalized with mean expression of three housekeeping genes (GAPDH, GUSB, and HPRT1) using the comparative Ct method.

label: SYBR green

source_name: PBMCs

label_protocol: cDNA was generated in 50μl (36ng/μl) using 5x PrimeScript™ RT Master Mix Perfect Real Time (Takara, Shiga, Japan) and SimpliAmp Thermal Cycler (Thermo Scientific). Concentration of cDNA was set to 2.5 ng/μl and stored at 4°C until short-term further use.

growth_protocol: not applicable

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll density gradient centrifugation (GE Healthcare, Little Chalfont, England), and were stored in RA1 lysis buffer (MACHEREY-NAGEL, Dueren, Germany) and β-Mercaptoethanol (Merck) at a concentration of 3x106 cells at -80°C until further use. RNA was isolated with NucleoSpin RNA Mini (MACHEREY-NAGEL) according to standard protocol that includes a DNase step.

treatment_protocol: not applicable

tag: group

value: TOL


title: TOL m

description:
test
StepOnePlus Real-Time PCR System


title: HC g

description:
test
StepOnePlus Real-Time PCR System

value: HC


title: HC e

description:
test
StepOnePlus Real-Time PCR System


title: HC f

description:
test
StepOnePlus Real-Time PCR System


title: 501-MEL.indisulam.C

value: indisulam


title: SAMPLE 218 [Genotype 218]

value: barley genotype 218


title: SAMPLE 219 [Genotype 219]

value: barley genotype 219


title: B6585

description:
polyA RNA
GeneExpMatrix.txt


title: HC d

description:
test
StepOnePlus Real-Time PCR System


title: B6500

description:
polyA RNA
GeneExpMatrix.txt


title: TOL k

description:
test
StepOnePlus Real-Time PCR System


title: B6312

description:
polyA RNA
GeneExpMatrix.txt


title: B6312T

description:
polyA RNA
GeneExpMatrix.txt


title: 501-MEL.dmso.A

value: dmso


title: 501-MEL.dmso.B


title: 501-MEL.dmso.C


title: TOL i

description:
test
StepOnePlus Real-Time PCR System


title: SAMPLE 220 [Genotype 220]

value: barley genotype 220


title: B6585T

description:
polyA RNA
GeneExpMatrix.txt

value: HBV(+/-)Pten(fl/fl)Cre(+/-)


title: TOL h

description:
test
StepOnePlus Real-Time PCR System


title: SNU449_TI3

city: Montreal

first: Sylvain

last: Meloche

state: Quebec

address: 2950, Chemin de Polytechnique

institute: Institute of Research in Immunology and Cancer

description: Stable cell line expressing Yes T348I

data_processing:
Sequencing was performed with the Illumina HiSeq 2000 and basecalls analyzed using Illumina RTA 1.17.21.3.
Samples demultiplexed using Illumina Casava 1.8.2 using adapter masking.
Sequenced reads were trimmed for masked adapters and low quality extremities using Trimmomatic 0.35 and then mapped to the reference genome using STAR version 2.5.1b, guided by transcript annotations from Gencode version 26.
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode 26
Genome_build: GRCh38
Supplementary_files_format_and_content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned

extract_protocol:
Trizol extraction and Qiagen Rneasy column purification
KAPA RNA Stranded PolyA

value: Liver

tag: tumor stage

value: grade II-III/IV, hepatocellular carcinoma

tag: condition

value: Yes T348I

tag: compound

value: Dasatinib (100 nM)


title: SAMPLE 217 [Genotype 217]

value: leaf

value: barley genotype 217


title: SAMPLE 215 [Genotype 215]

value: barley genotype 215


title: SAMPLE 213 [Genotype 213]

value: barley genotype 213


title: SAMPLE 212 [Genotype 212]

value: barley genotype 212


title: SAMPLE 216 [Genotype 216]

value: barley genotype 216


title: 501-MEL.indisulam.A


title: SAMPLE 214 [Genotype 214]

value: barley genotype 214


title: SNU449_TI2

description: Stable cell line expressing Yes T348I


title: SNU449_TI1

description: Stable cell line expressing Yes T348I


title: HC c

description:
test
StepOnePlus Real-Time PCR System

value: HC


title: SNU449_WT3

description: Stable cell line expressing Yes WT

value: Yes WT


title: HC b

description:
test
StepOnePlus Real-Time PCR System


title: TOL j

description:
test
StepOnePlus Real-Time PCR System

value: TOL


title: SAMPLE 211 [Genotype 211]

value: barley genotype 211


title: TOL g

description:
test
StepOnePlus Real-Time PCR System


title: SAMPLE 210 [Genotype 210]

value: barley genotype 210


title: SNU449_WT2

description: Stable cell line expressing Yes WT


title: TOL f

description:
test
StepOnePlus Real-Time PCR System


title: MIN h

description:
test
StepOnePlus Real-Time PCR System

value: MIN


title: 501-MEL.indisulam.B

value: indisulam


title: TOL e

description:
test
StepOnePlus Real-Time PCR System


title: SNU449_WT1

description: Stable cell line expressing Yes WT

value: Liver

value: grade II-III/IV, hepatocellular carcinoma


title: SNU387_shYes3

description: Stable cell line expressing YES1 shRNA

value: grade IV/V, pleomorphic hepatocellular carcinoma

value: sh YES1


title: CTRL x

description:
test
StepOnePlus Real-Time PCR System

value: CTRL


title: SAMPLE 209 [Genotype 209]

value: leaf

value: barley genotype 209


title: TOL d

description:
test
StepOnePlus Real-Time PCR System


title: SAMPLE 208 [Genotype 208]

value: barley genotype 208


title: HC a

description:
test
StepOnePlus Real-Time PCR System


title: SNU387_shYes2

description: Stable cell line expressing YES1 shRNA


title: SNU387_shNT3

description: Stable cell line expressing non-target shRNA

value: sh non-target


title: SAMPLE 206 [Genotype 206]

value: barley genotype 206


title: SNU387_shNT2


title: SAMPLE 207 [Genotype 207]

value: barley genotype 207


title: SNU387_shYes1

description: Stable cell line expressing YES1 shRNA


title: TOL c

description:
test
StepOnePlus Real-Time PCR System


title: SAMPLE 204 [Genotype 204]

value: barley genotype 204


title: TOL a

description:
test
StepOnePlus Real-Time PCR System

value: TOL


title: SAMPLE 203 [Genotype 203]

value: barley genotype 203


title: SAMPLE 205 [Genotype 205]

value: barley genotype 205


title: CTRL v

description:
test
StepOnePlus Real-Time PCR System


title: CTRL w

description:
test
StepOnePlus Real-Time PCR System


title: TOL b

description:
test
StepOnePlus Real-Time PCR System


title: SAMPLE 202 [Genotype 202]

value: barley genotype 202


title: SAMPLE 200 [Genotype 200]

value: barley genotype 200


title: SAMPLE 201 [Genotype 201]

value: barley genotype 201


title: SNU387_shNT1

value: Liver


title: SAMPLE 199 [Genotype 199]

value: barley genotype 199


title: genomic DNA from sample 67-pp [204391650166_R08C01]

city: Taipei City

first: Shin-yu

last: Lin

state: Taipei

address: Zhongzheng Dist.

country: Taiwan

institute: National Taiwan University Hospital

hyb_protocol: bisulfite converted DNA (ThermoFisher) was amplified, fragmented and hybridised to Illumina Infinium MethylaionEPIC BeadChip using standard Illumina protocol

scan_protocol: Beadchip images were scanned on the HiScan system

data_processing:
Infinium MethylationEPIC BeadChip images were scanned on the HiScan system. Raw data were read by GenomeStudio from IDAT files and converted to beta values, which is the ratio of methylated (M) intensity to the
The 'Matrix_signal_intensities.csv' contains unmethylated and methylated signal intensities

label: Cy3 and Cy5

source_name: genomic DNA from sample 67

label_protocol: Experiments were following by Infinium® HD Assay MethylationEPIC Protocol Guide

extract_protocol: Genomic DNA extraction was performed using the QIAamp DNA Micro Kit

tag: subject id

tag: gender

value: Female

tag: trimester

value: Post-Partum

value: whole blood


title: SNU-387_TI_dasatinib_3

description: Stable cell line expressing Yes T348I

tag: tag

value: grade IV/V, pleomorphic hepatocellular carcinoma

tag: cell line

value: Yes T348I

value: Dasatinib (100 nM)


title: 387_TI_Dasa1

description: Stable cell line expressing Yes T348I


title: SNU-387_TI_dasatinib_2

description: Stable cell line expressing Yes T348I


title: CTRL u

description:
test
StepOnePlus Real-Time PCR System

value: CTRL


title: genomic DNA from sample 67-1 [204391650166_R05C01]


title: SAMPLE 196 [Genotype 196]

value: leaf

value: barley genotype 196


title: MIN g

description:
test
StepOnePlus Real-Time PCR System

value: MIN


title: genomic DNA from sample 151-pp [204391650166_R04C01]

source_name: genomic DNA from sample 151


title: SAMPLE 197 [Genotype 197]

value: barley genotype 197


title: SNU-387_TI_dasatinib_1

description: Stable cell line expressing Yes T348I


title: 387_TI_Dasa2

description: Stable cell line expressing Yes T348I


title: CTRL t

description:
test
StepOnePlus Real-Time PCR System


title: genomic DNA from sample 67-7 [204391650166_R07C01]


title: 387_WT_Dasa2

description: Stable cell line expressing Yes WT

value: Yes WT


title: CTRL s

description:
test
StepOnePlus Real-Time PCR System


title: genomic DNA from sample 67-4 [204391650166_R06C01]


title: genomic DNA from sample 151-4 [204391650166_R02C01]


title: SAMPLE 194 [Genotype 194]

value: barley genotype 194


title: SAMPLE 195 [Genotype 195]

value: barley genotype 195


title: 387_WT_Dasa1

description: Stable cell line expressing Yes WT


title: CTRL q

description:
test
StepOnePlus Real-Time PCR System


title: genomic DNA from sample 97-7 [204391650142_R07C01]

source_name: genomic DNA from sample 97


title: genomic DNA from sample 151-7 [204391650166_R03C01]


title: genomic DNA from sample 151-1 [204391650166_R01C01]


title: CTRL r

description:
test
StepOnePlus Real-Time PCR System


title: genomic DNA from sample 97-pp [204391650142_R08C01]


title: SAMPLE 193 [Genotype 193]

value: barley genotype 193


title: MIN f

description:
test
StepOnePlus Real-Time PCR System


title: CTRL p

description:
test
StepOnePlus Real-Time PCR System


title: SAMPLE 198 [Genotype 198]

value: barley genotype 198


title: SNU-387_WT_dasatinib_3

description: Stable cell line expressing Yes WT

value: Liver


title: genomic DNA from sample 97-4 [204391650142_R06C01]

value: Female


title: genomic DNA from sample 75-7 [204391650142_R03C01]

source_name: genomic DNA from sample 75


title: genomic DNA from sample 75-1 [204391650142_R01C01]


title: SAMPLE 192 [Genotype 192]

value: barley genotype 192


title: SNU-387_WT_dasatinib_2

description: Stable cell line expressing Yes WT


title: SAMPLE 189 [Genotype 189]

value: barley genotype 189


title: SAMPLE 191 [Genotype 191]

value: barley genotype 191


title: SNU-387_WT_dasatinib_1

description: Stable cell line expressing Yes WT

value: grade IV/V, pleomorphic hepatocellular carcinoma


title: PLC_TI_Dasa1

description: Stable cell line expressing Yes T348I

value: hepatoma

value: Yes T348I

value: Dasatinib (100 nM)


title: MIN e

description:
test
StepOnePlus Real-Time PCR System


title: genomic DNA from sample 97-1 [204391650142_R05C01]

value: whole blood


title: PLC_TI_Dasa2

description: Stable cell line expressing Yes T348I


title: genomic DNA from sample 75-pp [204391650142_R04C01]

value: Post-Partum


title: CTRL o

description:
test
StepOnePlus Real-Time PCR System

value: CTRL


title: PLC_TI_dasatinib_3

description: Stable cell line expressing Yes T348I


title: CTRL n

description:
test
StepOnePlus Real-Time PCR System


title: PLC_TI_dasatinib_2

description: Stable cell line expressing Yes T348I


title: SAMPLE 190 [Genotype 190]

value: leaf

value: barley genotype 190


title: SAMPLE 188 [Genotype 188]

value: barley genotype 188


title: genomic DNA from sample 75-4 [204391650142_R02C01]


title: CTRL l

description:
test
StepOnePlus Real-Time PCR System


title: PLC_TI_dasatinib_1

description: Stable cell line expressing Yes T348I


title: SAMPLE 186 [Genotype 186]

value: barley genotype 186


title: PLC_WT_Dasa1

description: Stable cell line expressing Yes WT

value: Yes WT


title: SAMPLE 185 [Genotype 185]

value: barley genotype 185


title: PLC_WT_dasatinib_3

description: Stable cell line expressing Yes WT

value: Liver


title: MIN d

description:
test
StepOnePlus Real-Time PCR System

value: MIN


title: CTRL k

description:
test
StepOnePlus Real-Time PCR System


title: genomic DNA from sample 74-7 [204391650104_R07C01]

source_name: genomic DNA from sample 74

value: Female


title: SAMPLE 184 [Genotype 184]

value: barley genotype 184


title: genomic DNA from sample 36-pp [204391650104_R04C01]

source_name: genomic DNA from sample 36


title: CTRL j

description:
test
StepOnePlus Real-Time PCR System


title: SAMPLE 183 [Genotype 183]

value: barley genotype 183


title: PLC_WT_dasatinib_2

description: Stable cell line expressing Yes WT

value: hepatoma


title: CTRL m

description:
test
StepOnePlus Real-Time PCR System


title: genomic DNA from sample 74-pp [204391650104_R08C01]


title: SAMPLE 182 [Genotype 182]

value: barley genotype 182


title: CTRL i

description:
test
StepOnePlus Real-Time PCR System


title: SAMPLE 181 [Genotype 181]

value: barley genotype 181


title: MIN c

description:
test
StepOnePlus Real-Time PCR System


title: genomic DNA from sample 36-4 [204391650104_R02C01]

value: whole blood


title: SAMPLE 180 [Genotype 180]

value: barley genotype 180


title: PLC_WT_dasatinib_1

description: Stable cell line expressing Yes WT

value: Dasatinib (100 nM)


title: genomic DNA from sample 74-4 [204391650104_R06C01]


title: genomic DNA from sample 36-1 [204391650104_R01C01]


title: CTRL h

description:
test
StepOnePlus Real-Time PCR System

value: CTRL


title: genomic DNA from sample 141-7 [203723060026_R07C01]

source_name: genomic DNA from sample 141


title: genomic DNA from sample 74-1 [204391650104_R05C01]


title: SAMPLE 187 [Genotype 187]

value: leaf

value: barley genotype 187


title: W2

city: Guangzhou

first: Jun

last: Xiao

state: Guangdong

address: Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, No.1838 Guangzhou North Avenue, Baiyun District, Guangzhou, Guangdong Province, P.R.C

department: Department of Orthopaedic Surgery

country: China

data_processing:
Qubit 3.0 fluorometer (Invitrogen, CA, USA) and the Agilent 2100 bioanalyzer (Applied Biosystems, CA, USA) were used for quality control.
PE150 mode of HiSeq X10 (Illumina Inc., CA, USA) was used for sequencing.
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 [1]and the gene expression level was estimated using RSEM v1.2.15.
TMM (trimmed mean of M-values) was used to normalize the gene expression.
For circRNA expression analysis, the reads were to mapped genome using the STAR and DCCwas used to identify the cirRNA and to estimate the circRNA expression.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: peripheral blood mononuclear cells

extract_protocol:
PBMCs from three recruited AS patients and three health control were separated, total RNA was extracted and purified using Magen Hipure Total RNA Mini Kit (Magen, Guangzhou, China).
RNA sequencing libraries were constructed using KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems, Inc., MA, USA).
circRNA-seq

value: peripheral blood mononuclear cells

tag: age

value: Healthy Control (HC)


title: S

institute: Nanfang Hospital, Southern Medical University

tag: tissue


title: 99

value: Ankylosing Spondylitis (AS)


title: CTRL f

description:
test
StepOnePlus Real-Time PCR System


title: CTRL g

description:
test
StepOnePlus Real-Time PCR System


title: SAMPLE 179 [Genotype 179]

tag: genotype

value: barley genotype 179


title: SAMPLE 178 [Genotype 178]

value: barley genotype 178


title: Y2


title: 94


title: MIN b

description:
test
StepOnePlus Real-Time PCR System

value: MIN


title: 91


title: SAMPLE 177 [Genotype 177]

value: barley genotype 177


title: CTRL e

description:
test
StepOnePlus Real-Time PCR System


title: genomic DNA from sample 80-pp [203723060026_R04C01]

source_name: genomic DNA from sample 80

value: Female

value: Post-Partum


title: genomic DNA from sample 36-7 [204391650104_R03C01]


title: RL4, liver, whole egg-based diet

city: Birmingham

first: Melissa

last: Harris

address: 1300 University Blvd, CH464

department: Biology

institute: University of Alabama at Birmingham

data_processing:
Basecalling was performed using Illumina’s bcl2fastq software
Quality of the sequencing reads was assessed using FastQC (ver. 0.11.8) and showed that on average, the Phred quality score across all samples was greater than 35. rRNA reads were filtered out using trimmomatic (ver. 0.36).
Sequences were aligned to the Ensembl zebrafish reference genome (GRCz11) using the full annotated (49K genes) gtf file.
Individual gene counts were obtained for each sample using the quantMode feature of the STAR aligner (ver. 2.5.2b) with an average 76.5% of the total reads per sample uniquely mapping.
The final read depth across all samples was approximately 20-23 million reads per sample and the gene counts from these reads were used for differential gene expression analysis using DESeq2 (ver. 1.22.2)
Genome_build: GRCz11
Supplementary_files_format_and_content: raw counts after alignment using STAR -genecounts feature

organism: Danio rerio

source_name: whole liver

growth_protocol: Zebrafish were reared in standard conditions and euthanized at 36 weeks for tissue harvest.

extract_protocol:
Whole livers were dissected out, frozen in liquid nitrogen, and transferred to a -80C freezer for long-term storage. RNA was isolated from tissue using RNeasy™ Lipid Tissue Mini Kit (Qiagen, Hilden, Germany) per the manufacturer’s instructions.
RNA with an RNA Integrity Number (RIN) of 7.0 or above was used for sequencing library preparation. The Agilent SureSelect Strand Specific mRNA library kit as per the manufacturer’s instructions (Agilent, Santa Clara, CA).  Library construction began with ribosome reduction using the NEBNext rRNA depletion kit for human/mouse/rat as described by the manufacturer (New England Biolabs, Ipswich MA).  The resulting RNA was randomly fragmented with cations and heat, which was followed by first strand synthesis using random primers with inclusion of Actinomycin D (2.4ng/µL final concentration).  Second strand cDNA production was done with standard techniques, the ends of the resulting cDNA were made blunt, A-tailed and adaptors ligated for amplification and indexing to allow for multiplexing during sequencing.  The cDNA libraries were quantitated using RT-PCR in a Roche LightCycler 480 with the Kapa Biosystems kit for Illumina library quantitation (Kapa Biosystems, Woburn, MA) prior to cluster generation.  Cluster generation was performed according to the manufacturers recommendations for onboard clustering (Illumina). Samples were sequenced to achieve a minimum of 30 million, single-end, 75bp reads per sample.

treatment_protocol: At day 21, individuals were fed (twice daily at 08:00 and 16:00) experimental diets . All formulated diets were fed at ca. 6% body weight per day, a ration level shown to promote a high growth rate. Diets included a control diet, a multi-source protein diet shown previously to provide lifelong health and growth,  and a diet with whole egg product substituted for ca. 50% of the total protein.

value: whole liver

tag: treatment

value: fed whole egg-based diet

value: female


title: RL3, liver, whole egg-based diet


title: SAMPLE 175 [Genotype 175]

source_name: leaf tissue

value: barley genotype 175


title: genomic DNA from sample 141-1 [203723060026_R05C01]

value: whole blood


title: genomic DNA from sample 80-7 [203723060026_R03C01]


title: RL2, liver, whole egg-based diet


title: SAMPLE 174 [Genotype 174]

value: barley genotype 174


title: CTRL b

description:
test
StepOnePlus Real-Time PCR System

value: CTRL


title: SAMPLE 173 [Genotype 173]

value: leaf

value: barley genotype 173


title: SAMPLE 172 [Genotype 172]

value: barley genotype 172


title: CTRL c

description:
test
StepOnePlus Real-Time PCR System


title: MIN a

description:
test
StepOnePlus Real-Time PCR System


title: SAMPLE 176 [Genotype 176]

value: barley genotype 176


title: Spombe csRNA-input rep2

description: spombe-tsr.txt

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe

tag: strain

value: strain TH972

value: untreated

value: sRNA-seq (csRNA-seq input)


title: Spombe csRNA-seq rep2

description: spombe-tsr.txt

tag: tagtreatment

value: csRNA-seq


title: genomic DNA from sample 141-4 [203723060026_R06C01]

value: Female


title: RL1, liver, whole egg-based diet


title: Spombe csRNA-input rep1

description: spombe-tsr.txt

tag: method


title: GL4, liver, control diet

value: fed control diet


title: GL3, liver, control diet

value: whole liver


title: Spombe csRNA-seq rep1

description: spombe-tsr.txt


title: GL2, liver, control diet


title: genomic DNA from sample 141-pp [203723060026_R08C01]

value: Post-Partum


title: genomic DNA from sample 38-7 [203723050004_R07C01]

source_name: genomic DNA from sample 38


title: CTRL d

description:
test
StepOnePlus Real-Time PCR System


title: SAMPLE 171 [Genotype 171]

value: barley genotype 171


title: S4b_SW

city: Shanghai

first: 丽华

last: 王

state: 上海

address: 300 Fenglin Road

institute: Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS)

description:
WT-SD-sp rep2
Gene expression data from  arabidopsis rosette leaves

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) following the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Affymetrix packages in R. Probe sets with signal values lower than the detectable range were adjusted to 75 and probe sets with the values of 75 for all conditions were removed from subsequent analysis. The averages of normalized ratios are calculated by dividing the average of normalized signal channel intensity by the average of the normalized control channel intensity. The standard deviation of the ground control (two biological replicates) was employed to identify genes of significant changes relative to the ground controls (P value<0.05). Only genes that showed transcript level changes in at least two folds in comparison with its ground control and with the same tendency in both biological replicates were considered as relevant for microgravity.

label: biotin

organism: Arabidopsis thaliana

source_name: rosette leaves of Arabidopsis thaliana Columbia (Col-0) ecotype grown on space, under short-day condition  rep2

label_protocol: RNA amplified, labeled and purified by using GeneChip 3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US) following the manufacturer’s instructions to obtain biotin labeled cRNA

growth_protocol: Arabidopsis thaliana Columbia (Col-0) ecotype was used as the wild-type. Plants were germinated and grown in plastic cups under long-day (16h light /8h dark) at 120 mol. m-2.s-1 conditions for 5 days, then set in the root modules (240×120×65 mm3) containing a commercially available vermiculite immersed by a medium containing MS macronutrients (Murashige and Skoog, 1962 ) and cultived in greenhouse for 20 days prior to flight.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Two set of plants were prepared and placed in the plant growth units (PGUs) for spaceflight experiment (Fig.1a, b and c) and the ground control, respectively. The flight PGU was positioned in the capsual of satellite about 8 h prior to launch. The SJ-10 satellite was in orbit for about 12 days and 15h (lauch: 1:38, April 6, 2016; landing: 16:30, April 18, 2016). Illumination was provided by light banks made up of 200 solid state light emitting diode (LED) lamps (400-700 nm white light and red light, 2:1) on a long-day (LD, 16h light/8h dark) or a short-day (SD, 8h light/16h dark) photoperiod. Inside the chambers, temperatures were 22±2C, relateve humidity was between 90% and 100%. The photosynthetically active photon flux density produced by LED lamps was 120 μmol.m-2.s-1 for Arabidopsis at surface of the first leaf of the experimental plants. Temperature and humidity were recorded every 1min during flight. These data were used to set the ground control in a control growth chamber.

value: rosette leaves

tag: genotype/variation

value: WT

value: short-day


title: S4b_SG

description:
FG-SD-sp rep2
Gene expression data from  arabidopsis rosette leaves

source_name: rosette leaves of  transgenic Arabidopsis in which pHSP::FT, pHSP:GFP (FG) gene were co-expression by genetic crossing grown on space, under short-day condition  rep2


title: eye disc fuss overexpression rep2

city: Regensburg

first: Mathias

last: Rass

address: Universitätsstraße 31

department: Developmental Biology

country: Germany

institute: University of Regensburg

description:
GMR_fuss_9_GATCAG_L006
processed data file: eyes_rnaseq_table.xlsx

data_processing:
fastq files have been quantified with Salmon v1.1.0
TXIMETA v1.8.0 has been used to summarize transcript-level quantifications to gene-level and for further import into DESeq2
Differential expression analysis has been conducted with DESeq2 v1.30.0
Genome_build: BDGP6.22 (Ensembl release 98)
Supplementary_files_format_and_content: xlsx and differential gene expression analysis

organism: Drosophila melanogaster

source_name: eye disc rna from nub-gal4 driverline crossed to uas-fuss

extract_protocol:
Per replicate and genotype 40 eye antennal discs or 30 wing discs from third instar larvae were dissected. RNA was extracted via peqGold MicroSpin Total RNA Kit.
Library preparation and RNA-Seq were carried out according to the NEBNext Ultra RNA Library Prep protocol, the Illumina HiSeq 1000 System User Guide, and the KAPA Library Quantification Kit - Illumina/ABI Prism User Guide

value: GMR-Gal4 > UAS-fuss

tag: developmental stage

value: third instar larvae

tag: tissue/cell type

value: eye disc cells


title: eye disc fuss overexpression rep3

description:
GMR_fuss_10_TAGCTT_L006
processed data file: eyes_rnaseq_table.xlsx


title: genomic DNA from sample 38-1 [203723050004_R05C01]

value: whole blood


title: SAMPLE 170 [Genotype 170]

value: leaf

value: barley genotype 170


title: genomic DNA from sample 80-1 [203723060026_R01C01]


title: genomic DNA from sample 38-pp [203723050004_R08C01]


title: GL1, liver, control diet

value: female


title: eye disc fuss overexpression rep1

description:
GMR_fuss_3_TTAGGC_L005
processed data file: eyes_rnaseq_table.xlsx


title: SAMPLE 167 [Genotype 167]

value: barley genotype 167


title: SAMPLE 168 [Genotype 168]

value: barley genotype 168


title: S4b_LW

description:
WT-LD-sp rep2
Gene expression data from  arabidopsis rosette leaves

source_name: rosette leaves of Arabidopsis thaliana Columbia (Col-0) ecotype grown on space, under long-day condition  rep2

value: long-day


title: eye disc control rep3

description:
GMR_white_12_CTTGTA_L006
processed data file: eyes_rnaseq_table.xlsx

source_name: eye disc rna from nub-gal4 driverline crossed to w1118

value: GMR-Gal4 > w1118


title: SAMPLE 169 [Genotype 169]

value: barley genotype 169


title: S4b_LG

description:
FG-LD-sp rep2
Gene expression data from  arabidopsis rosette leaves

source_name: rosette leaves of  transgenic Arabidopsis in which pHSP::FT, pHSP:GFP (FG) gene were co-expression by genetic crossing grown on space, under long-day condition  rep2


title: S4a_SW

description:
WT-SD-sp rep1
Gene expression data from  arabidopsis rosette leaves

source_name: rosette leaves of Arabidopsis thaliana Columbia (Col-0) ecotype grown on space, under short-day condition  rep1


title: eye disc control rep2

description:
GMR_white_11_GGCTAC_L006
processed data file: eyes_rnaseq_table.xlsx


title: eye disc control rep1

description:
GMR_white_4_TGACCA_L005
processed data file: eyes_rnaseq_table.xlsx


title: genomic DNA from sample 10-4 [203723050004_R02C01]

source_name: genomic DNA from sample 10

value: Female


title: SAMPLE 166 [Genotype 166]

value: barley genotype 166


title: Sinonasal inverted papilloma tissue sample 4

city: Hangzhou

first: Yaoshu

last: Teng

state: China

address: No. 261, Huansha Road

institute: Hangzhou First People' Hospital

description:
Endoscopic assisted resection
SNIP 4

hyb_protocol: Each slide was hybridized with 1.65 μg Cy3-labeled cRNA using a   Gene Expression Hybridization Kit (Agilent Technologies, Santa Clara, CA,   US). After 17 hours of hybridization, the slides were washed with the Gene   Expression Wash Buffer Kit (Agilent Technologies, Santa Clara, CA, US).

scan_protocol: These slides were scanned by an Agilent Microarray Scanner (Agilent  Technologies, Santa Clara, CA, US).

data_processing: Data were extracted with Feature   Extraction software10.7 (Agilent Technologies, Santa Clara, CA, US). Raw   data were normalized by the quantile algorithm, Gene Spring Software 11.0   (Agilent Technologies, Santa Clara, CA, US). Differentially expressed lncRNAs   and mRNAs with statistical significance between two groups were identified   through volcano plot filtering (fold change ≥2.0 and P<0.05). The Gene Cluster   (v 3.0) and Java TreeView software programs were used to perform   hierarchical cluster analysis of these differentially expressed lncRNAs and   mRNAs.

source_name: Nasal tissue

label_protocol: Total RNA was amplified and labeled by the   Low Input Quick Amp WT Labeling Kit (Agilent Technologies, Santa Clara, CA,   US). Labeled cRNA was purified with the RNeasy mini kit (QIAGEN, GmBH,   Germany).

extract_protocol: Total RNA was isolated from nasal mucosal tissues using TRIzol Reagent (Life   Technologies, Carlsbad, CA, US) following the manufacturer’s instructions and   then quantified using a NanoDrop ND-1000 spectrophotometer (Thermo   Fisher Scientific, Waltham, MA).RNA integrity was inspected by an Agilent   Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US), and RNA   samples with an RNA integrity number (RIN) values ≥6.0 and 28S/18S   values >0.7 were deemed acceptable for microarray and reverse transcription   (RT) experiments.

value: Nasal tissue

tag: disease state

value: Sinonasal inverted papilloma

value: Male


title: S4a_SG

description:
FG-SD-sp rep1
Gene expression data from  arabidopsis rosette leaves

source_name: rosette leaves of  transgenic Arabidopsis in which pHSP::FT, pHSP:GFP (FG) gene were co-expression by genetic crossing grown on space, under short-day condition  rep1

value: rosette leaves

value: short-day


title: wing disc fuss overexpression rep3

description:
numb_fuss_6_GCCAAT_L005
processed data file: wings_rnaseq_table.xlsx

source_name: wing disc rna from nub-gal4 driverline crossed to uas-fuss

value: nub-Gal4 > UAS-fuss

value: third instar larvae

value: wing disc cells


title: SAMPLE 165 [Genotype 165]

value: leaf

value: barley genotype 165


title: genomic DNA from sample 38-4 [203723050004_R06C01]

value: whole blood


title: SAMPLE 164 [Genotype 164]

value: barley genotype 164


title: wing disc fuss overexpression rep2

description:
numb_fuss_5_ACAGTG_L005
processed data file: wings_rnaseq_table.xlsx


title: wing disc fuss overexpression rep1

description:
numb_fuss_1_ATCACG_L005
processed data file: wings_rnaseq_table.xlsx


title: S4a_LW

description:
WT-LD-sp rep1
Gene expression data from  arabidopsis rosette leaves

source_name: rosette leaves of Arabidopsis thaliana Columbia (Col-0) ecotype grown on space, under long-day condition  rep1

value: WT

value: long-day


title: CTRL a

description:
test
StepOnePlus Real-Time PCR System

source_name: PBMCs

tag: group

value: CTRL


title: genomic DNA from sample 10-7 [203723050004_R03C01]

tag: subject id

value: Female


title: SAMPLE 163 [Genotype 163]

value: barley genotype 163


title: genomic DNA from sample 10-pp [203723050004_R04C01]

tag: gender

value: Post-Partum


title: wing disc control rep3

description:
numb_white_8_ACTTGA_L006
processed data file: wings_rnaseq_table.xlsx

source_name: wing disc rna from nub-gal4 driverline crossed to w1118

value: nub-Gal4 > w1118


title: SAMPLE 162 [Genotype 162]

source_name: leaf tissue

value: barley genotype 162


title: S4a_LG

description:
FG-LD-sp rep1
Gene expression data from  arabidopsis rosette leaves

source_name: rosette leaves of  transgenic Arabidopsis in which pHSP::FT, pHSP:GFP (FG) gene were co-expression by genetic crossing grown on space, under long-day condition  rep1

value: rosette leaves


title: Sinonasal inverted papilloma tissue sample 2

description:
Endoscopic assisted resection
SNIP 2

value: Nasal tissue

value: Sinonasal inverted papilloma


title: C4b_SG

description:
FG-SD-g r rep2
Gene expression data from  arabidopsis rosette leaves

source_name: rosette leaves of  transgenic Arabidopsis in which pHSP::FT, pHSP:GFP (FG) gene were co-expression by genetic crossing grown on ground, under short-day condition  rep2

value: short-day


title: C4b_SW

description:
WT-SD-g r rep2
Gene expression data from  arabidopsis rosette leaves

source_name: rosette leaves of Arabidopsis thaliana Columbia (Col-0) ecotype grown on ground, under short-day condition  rep2


title: Sinonasal inverted papilloma tissue sample 1

description:
Endoscopic assisted resection
SNIP 1


title: C4b_LW

description:
WT-LD-g r rep2
Gene expression data from  arabidopsis rosette leaves

source_name: rosette leaves of Arabidopsis thaliana Columbia (Col-0) ecotype grown on ground, under long-day condition  rep2


title: XL21 Frog eye, Optic nerve crush, Unoperated eye, Replicate 3

city: Albany

first: Ben

middle: Gregory

last: Szaro

address: 1400 Washington Avenue

department: Biological Sciences

institute: University at Albany, SUNY

data_processing:
For Bisulfite-SEQ: Sequencing reads were aligned to the Xenopus laevis genome (v 9.1: xenbase RRID:SCR_003280) using Bismark (v 0.18.2). Alignments were performed using default parameters for pairwise alignments, except for the more relaxed scoring parameters needed to align bisulfite sequences (--score_min L,0,-0.6) in Bowtie2 (v2.2.9)). Bismark methylation extractor script (with  --paired-end and –comprehensive options) was then run on each of the alignments to produce the methylation coverage files in CpG, CHH, and CHG contexts. The external module “bismark2bedGraph” was then used to convert these files into the bedGraph format, which in turn were transformed into bigWig files using the script BedGraphToBigWig  (v.4) with default parameters  (http://hgdownload.cse.ucsc.edu/admin/exe/). The bigWig score files were used for direct observation in IntegrativeGenomics Viewer (IGV) v2.3.88 [94; 108]
Supplementary_files_format_and_content: All processed files are in the bigWig (bw) format. Bisulfite-seq files represent methylation in CpG context and are combined for the three biological replicates for each condition. ChIP-Seq and 5hmC DIP-seq files represent alignments for each read and are provided separately for each biological replicate.

organism: Xenopus laevis

source_name: 6 unoperated frog eyes, 11 days after contralateral orbital optic nerve crush

growth_protocol: All animals used in this study were purchased from Xenopus Express, Inc (Brooksville, FL). Prior to surgery, they were acclimated to the lab for at least one week, under a 12L:12D photoperiod, in tanks of condition water at 22C, and fed every other day.

extract_protocol:
Bisulfite-Seq: Eyes for optic nerve crush studies were rapidly dissected and then homogenized immediately, pooling six eyes for each biological replicate. Because dissections of hindbrain required more time, each hindbrain was placed in 1 mL of RNAlater at room temperature over-night. RNAlater was then aspirated and five pooled hindbrains homogenized for each biological replicate. Total DNA, along with RNA, was isolated using the RNA/DNA/Protein Purification kit from Norgen Biotek Corp. with DNase I treatment, following manufactuer's protocols.
For Bisulfite-Seq: 300 ng of intact genomic DNA quantified by Qubit assay (Thermo Fisher, Waltham, MA) was sheared by Covaris S2 focused-ultrasonicator (Covaris, Woburn, MA) to a peak size of 150-200 bp, and validated by 2100 Bioanalyzer High Sensitivity DNA assay (Agilent, Santa Clara, CA). Next, using the NEBNext Ultra DNA Library Prep Kit (New England BioLabs, Ipswich, MA), DNA fragments were end-repaired, 3’ end adenylated, and ligated to NEBNext Methylated Adaptors. The ligated DNA was then bisulfite-modified using an EZ DNA Methylation-Gold kit (Zymo, Irvine, CA), enriched and indexed by 8 cycles of PCR using Platinum Taq DNA Polymerase (Thermo Fisher) and NEBNext Index and Universal PCR primers. After AMPure XP bead purification (Beckman Coulter, Indianapolis, IN) and size selection of the indexed libraries, the quality of the libraries was assessed by Bioanalyzer.  Finally, the library concentration was qPCR-quantified using an NEBNext Library Quant Kit (New England BioLabs) and QuantStudio 5 Real-Time PCR System (Thermo Fisher). To generate sequencing data, the uniquely indexed, imbalanced WGBS libraries were pooled with well-balanced libraries to fill each lane of a flow cell for clustering in a cBot system (Illumina, San Diego, CA). The pooled libraries at the final concentration of 15 pM were clustered onto a flow cell using Illumina TruSeq PE Cluster kit v3 and sequenced under paired-end conditions at 2X101 bp, using a TruSeq SBS kit v3 on an Illumina HiSeq system, according to the Illumina recommended protocol.

treatment_protocol: Unilateral orbital optic nerve crushes (Zhao and Szaro 1994, doi: 10.1002/cne.903430112) and complete spinal cord transections (Gibbs and Szaro 2018, doi: 10.1101/pdb.prot101030) were performed on fully anesthetized animals (MS222).

value: albino, Xenopus Express

value: 1-3 mos. postmetamorphic juvenile frog

tag: surgery

value: optic nerve crush, unoperated eye

value: Whole eye

tag: Sex

value: not determined


title: wing disc control rep1

description:
numb_white_2_CGATGT_L005
processed data file: wings_rnaseq_table.xlsx

value: third instar larvae

value: wing disc cells


title: SAMPLE 160 [Genotype 160]

value: leaf

value: barley genotype 160


title: Normal nasal mucosal tissue sample 3

description:
Endoscopic assisted resection
Control 3

value: normal

value: Male


title: Sinonasal inverted papilloma tissue sample 3

description:
Endoscopic assisted resection
SNIP 3


title: Normal nasal mucosal tissue sample 2

description:
Endoscopic assisted resection
Control 2

value: Female


title: SAMPLE 161 [Genotype 161]

value: barley genotype 161


title: genomic DNA from sample 10-1 [203723050004_R01C01]

tag: trimester

value: whole blood


title: XL20 Frog eye, Optic nerve crush, Unoperated eye, Replicate 2

tag: age


title: C4b_LG

description:
FG-LD-g r rep2
Gene expression data from  arabidopsis rosette leaves

source_name: rosette leaves of  transgenic Arabidopsis in which pHSP::FT, pHSP:GFP (FG) gene were co-expression by genetic crossing grown on ground, under long-day condition  rep2

tag: tissue

value: rosette leaves

value: long-day


title: genomic DNA from sample 80-4 [203723060026_R02C01]

source_name: genomic DNA from sample 80


title: Normal nasal mucosal tissue sample 1

description:
Endoscopic assisted resection
Control 1

value: Nasal tissue


title: Normal nasal mucosal tissue sample 4

description:
Endoscopic assisted resection
Control 4


title: XL19 Frog eye, Optic nerve crush, Unoperated eye, Replicate 1

value: albino, Xenopus Express


title: wing disc control rep2

description:
numb_white_7_CAGATC_L006
processed data file: wings_rnaseq_table.xlsx

value: nub-Gal4 > w1118


title: SAMPLE 157 [Genotype 157]

tag: genotype

value: barley genotype 157


title: SAMPLE 158 [Genotype 158]

value: barley genotype 158


title: XL18 Frog eye, Optic nerve crush, Operated eye, Replicate 3

source_name: 6 operated frog eyes, 11 days after orbital optic nerve crush

value: 1-3 mos. postmetamorphic juvenile frog

value: optic nerve crush, operated eye

value: Whole eye

value: not determined


title: XL17 Frog eye, Optic nerve crush, Operated eye, Replicate 2


title: C4a_SG

description:
FG-SD-g r rep1
Gene expression data from  arabidopsis rosette leaves

source_name: rosette leaves of  transgenic Arabidopsis in which pHSP::FT, pHSP:GFP (FG) gene were co-expression by genetic crossing grown on ground, under short-day condition  rep1

tag: treatment

value: short-day


title: C4a_SW

description:
WT-SD-g r rep1
Gene expression data from  arabidopsis rosette leaves

source_name: rosette leaves of Arabidopsis thaliana Columbia (Col-0) ecotype grown on ground, under short-day condition  rep1

value: WT


title: C4a_LG

description:
FG-LD-g r rep1
Gene expression data from  arabidopsis rosette leaves

source_name: rosette leaves of  transgenic Arabidopsis in which pHSP::FT, pHSP:GFP (FG) gene were co-expression by genetic crossing grown on ground, under long-day condition  rep1


title: XL15 Frog eye, Unoperated animal, Replicate 3

source_name: 6 frog eyes from unoperated animals

tag: strain

value: unoperated


title: C4a_LW

description:
WT-LD-g r rep1
Gene expression data from  arabidopsis rosette leaves

source_name: rosette leaves of Arabidopsis thaliana Columbia (Col-0) ecotype grown on ground, under long-day condition  rep1


title: connective tissue disease without associated interstitial lung disease patient peripheral blood mononuclear cells_rep1

city: Nanchong City

first: daifei

last: dai

state: Sichuan Province

address: No. 234, Fujiang Road, Shunqing District

institute: North Sichuan Medical College

description: Randomly select qualified 1case systemic sclerosis without associated interstitial lung diseases (SSc-NILD), 1case rheumatoid arthritis without associated interstitial lung diseases (RA-NILD), 1case systemic lupus erythematosus without associated interstitial lung diseases (SLE-NILD), 1case Sjogren’s syndrome without associated interstitial lung diseases (SS-NILD) patients with peripheral blood mononuclear cells and mix them equally into 1 connective tissue disease without associated interstitial lung diseases  (CTD-NILD) specimen

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed and  fixed.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

label_protocol: MRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: RNA purification was prepared using TRIzol reagent (Invitrogen, Gran Island, NY, USA) according to the manufacturer’s instructions followed by the application of PBMCs to RNeasy spin columns (Qiagen, Venlo, Limburg, Netherlands). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis or Agilent 2100 Bioanalyzer.

treatment_protocol: Peripheral blood anticoagulated with ethelene diamine tetraccetic (EDTA) was obtained from all subjects. Human peripheral blood mononuclear cells (PBMCs) were isolated with Ficoll-Hypaque gradients.

tag: subject status

value: not collected


title: XL14 Frog eye, Unoperated animal, Replicate 2


title: SAMPLE 156 [Genotype 156]

value: leaf

value: barley genotype 156


title: connective tissue disease without associated interstitial lung disease patient peripheral blood mononuclear cells_rep2

value: peripheral blood mononuclear cells (PBMCs)


title: connective tissue disease without associated interstitial lung disease patient peripheral blood mononuclear cells_rep3


title: BRB_48h_DoxPlus_4 (BRB-seq)

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

data_processing:
Library strategy: BRB-seq
For CEL-Seq2 and BRB-seq, extraction of sample barcodes and unique-molecular-identifiers (UMIs) was performed using UMI-tools (T. S. Smith et al., 2017) (version 1.0.1) with the following commands: umi_tools extract -I r1.fastq --read2-in=r2.fastq --bc-pattern=NNNNNNCCCCCC --read2-stdout for CEL-Seq2, and umi_tools extract -I r1.fastq --read2-in=r2.fastq --bc-pattern= NNNNNNCCCCCCCCC --read2-stdout for BRB-seq.
The reads were trimmed using Cutadapt (M. Martin, 2011)  (version 2.6) wapper, Trim Galore! (version 0.6.6), with the option:  -a GATCGTCGGACT.
The reads were mapped by the aligning software HISAT2 (D. Kim et al., 2015, M. Pertea et al., 2016, D. Kim et al., 2019) (version 2.1.0) to the reference genome (GRCm38, pre-built HISAT2 index, genome_snp_tran).
Read counts per gene were obtained using featureCounts (Liao Y et al., 2014) (version 2.0.1). Note that UMIs were not used and mitochondrial chromosome genes are excluded in the analysis.
DESeq2 software (M. I. Love et al., 2014) (1.28.1) was used to calculate normalized counts.
*.csv files include comma-delimited read count matrices and normalized count matrices.
Genome_build: GRCm38/mm10

source_name: NIH3T3 cell line (Dox inducible H3mm18)

growth_protocol: NIH3T3 cells were grown in DMEM supplemented with 10% calf serum.

extract_protocol:
Total RNA was extracted from cells using Sepasol-RNA I Super G (Nacalai Tesque) and reverse-transcribed with PrimeScript II Reverse Transcriptase (Takara) and either oligo-dT primer or random 6-mer according to the manufacturer’s protocols.
BRB-seq was carried out as described previously (Alpern et al. 2019 Genome Biol) except that cDNA was synthesized with RT primers for CEL-Seq2 instead of those described in the original BRB-seq protocol.. Sequencing was performed using HiSeq PE Rapid Cluster Kit v2 (Illumina) in an Illumina HiSeq 1500 system with 15 cycles for read 1 and 40 cycles for read 2 in BRB-seq for NIH3T3 samples.

treatment_protocol: Introduction of MyoD into NIH3T3 cells was carried out using the retroviral vector MyoD-T2A-3xNLS-mKO2.

value: NIH3T3 cell line (Dox inducible H3mm18)

tag: cell type

value: Differentiated for 48 hours

tag: sample barcode

value: TGTGTCCTA


title: SAMPLE 155 [Genotype 155]

value: barley genotype 155


title: XL16 Frog eye, Optic nerve crush, Operated eye, Replicate 1

value: albino, Xenopus Express


title: XL13 Frog eye, Unoperated animal, Replicate 1


title: SAMPLE 153 [Genotype 153]

value: barley genotype 153


title: CRC organoid 34

city: Tokyo

first: Kohta

last: Toshimitsu

address: 35, Shinanomachi, Shinjuku-ku

institute: Keio University

description: Gene expression data of CRC organoid 34

hyb_protocol: Standard Affymetrix procedures

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing: Raw expression data were normalized by RMA together with normal colon and colorectal tumor organoid data from GSE74843 and GSE137336. A batch effect was compensated by ComBat algorithm.

source_name: CRC organoid 34

label_protocol: Standard Affymetrix procedures

growth_protocol: Organoids were cultured from single cells for 5 days in the optimized culture condition for each organoid line.

extract_protocol: Total RNA was extracted using the Rneasy Plus Mini Kit according to the manufacturer's instructions.

value: Colon

value: colorectal cancer organoid


title: SAMPLE 154 [Genotype 154]

data_processing: Illumina Genome Studio software was used for clustering

extract_protocol: Qiagen, 96 well DNeasy protocol as per manufacturers instructions

value: barley genotype 154


title: BRB_48h_DoxPlus_3 (BRB-seq)

value: TCAGGAGAT


title: connective tissue disease-associated interstitial lung diseases patient peripheral blood mononuclear cells_rep4

description: Randomly select qualified 1case systemic sclerosis-associated interstitial lung diseases (SSc-ILD), 1case rheumatoid arthritis-associated interstitial lung diseases (RA-ILD), 1case systemic lupus erythematosus-associated interstitial lung diseases (SLE-ILD), 1case Sjogren’s syndrome-associated interstitial lung diseases (SS-ILD) patients with peripheral blood mononuclear cells and mix them equally into 1 connective tissue disease-associated interstitial lung diseases  (CTD-ILD) specimen


title: XL10 Frog hindbrain, Spinal cord transected, Replicate 3

source_name: 5 frogs, 1 week after spinal cord transection

value: 1-3 mos. postmetamorphic juvenile frog

value: spinal cord transection

value: Hindbrain

value: not determined


title: CRC organoid 32

description: Gene expression data of CRC organoid 32

source_name: CRC organoid 32


title: connective tissue disease-associated interstitial lung diseases patient peripheral blood mononuclear cells_rep3

value: not collected


title: BRB_48h_DoxPlus_2 (BRB-seq)

value: GTACCTCTA


title: CRC organoid 33

description: Gene expression data of CRC organoid 33

source_name: CRC organoid 33


title: H10B1_6-gut-CL

city: Lausanne

first: Joanito

last: Liberti

address: Biophore

country: Switzerland

institute: University of Lausanne

data_processing:
Trimmomatic was used to remove adapters and low-quality bases with the following parameters: LEADING: 10 (trim the leading nucleotides until quality > 10), TRAILING: 10 (trim the trailing nucleotides until quality > 10), SLIDINGWINDOW: 4:20 (trim the window of size four for reads with local quality below a score of 20), and MINLEN: 80 (discard reads shorter than 80 bases).
Reads were aligned with STAR v.2.5.4b to the honeybee genome (Apis mellifera assembly HAv3.1).
Mapped reads were converted into raw read counts with the htseq-count script (http://www.huber.embl.de/users/anders/HTSeq/doc/count.html).
Genome_build: Amel_HAv3.1
Supplementary_files_format_and_content: Separate .txt file for each sample contaning counts of reads mapped to individual genes

organism: Apis mellifera

growth_protocol: We collected pupae from each of 10 hives and kept them in an incubator at 70% RH and 34.5 °C in the dark for two days. We transferred newly emerged adult bees in sterile cages built with a 100 mm petri dish and an inverted sterile plastic cup of 3 dl.

extract_protocol:
Guts were thawed on ice and homogenized in a FastPrep-24 5G homogenizer (MP Biomedicals) at 6 m/s for 45 s in 1 ml 1X PBS containing ca. 100 µl of 0.1 mm Zirconia/Silica beads (Carl Roth). Half of the volume of these homogenates was used for RNA extraction. RNA was extracted with a hot phenol protocols as described in Kešnerová et al. (2017), doi:10.1371/journal.pbio.2003467
RNA-sequencing libraries were prepared with the KAPA stranded mRNA kit (Roche) following the manufacturer’s protocol, except that we appended TruSeq unique dual indexes (UDIs, Illumina) instead of the adapters provided by the kit to better control for index hopping during sequencing.

treatment_protocol: Four cages from each of the ten hives were randomly assigned to one of four treatments. Bees were either (i) kept microbiota-depleted (MD) or colonized with (ii) the gut homogenate (CL) inoculum (iii) the community of 13 strains (CL_13) inoculum, or (iv) the two strains of Bifidobacterium asteroides (CL_Bifi) inoculum. Colonizations were performed three days after pupae extraction.

value: gut

value: Colonized with a gut homogenate (CL)

tag: hive


title: XL10 Frog hindbrain, Spinal cord transected, Replicate 2


title: connective tissue disease-associated interstitial lung diseases patient peripheral blood mononuclear cells_rep1

value: peripheral blood mononuclear cells (PBMCs)


title: connective tissue disease-associated interstitial lung diseases patient peripheral blood mononuclear cells_rep2


title: H10B6_3-gut-CL_13

value: Colonized with a community of 13 different gut microbiota strains (CL_13)


title: SAMPLE 150 [Genotype 150]

city: Brandon

first: James

last: Tucker

address: 2701 Grand Valley Rd.

institute: Agriculture and Agri-Food Canada

source_name: leaf tissue

value: leaf

value: barley genotype 150


title: SAMPLE 151 [Genotype 151]

value: barley genotype 151


title: SAMPLE 149 [Genotype 149]

value: barley genotype 149


title: H10B5_5-gut-CL_Bifi

value: Colonized with two strains of Bifidobacterium asteroides (CL_Bifi)


title: BRB_48h_DoxMinus_4 (BRB-seq)

value: NIH3T3 cell line (Dox inducible H3mm18)

value: Differentiated for 48 hours

value: GTCATTAAT


title: SAMPLE 148 [Genotype 148]

value: barley genotype 148


title: H9B3_5-gut-CL


title: BRB_48h_DoxMinus_3 (BRB-seq)

value: GGTTACACG


title: XL9 Frog hindbrain, Unoperated , Replicate 3

source_name: 5 unoperated frogs

value: albino, Xenopus Express

value: 1-3 mos. postmetamorphic juvenile frog

value: unoperated

value: Hindbrain

value: not determined


title: SAMPLE 152 [Genotype 152]

value: barley genotype 152


title: XL8 Frog hindbrain, Unoperated , Replicate 2


title: BRB_48h_DoxPlus_1 (BRB-seq)

value: GGAACACAC


title: H9B1_3-gut-CL_13

value: gut

value: Colonized with a community of 13 different gut microbiota strains (CL_13)


title: XL10 Frog hindbrain, Spinal cord transected, Replicate 1

value: spinal cord transection


title: SAMPLE 159 [Genotype 159]

value: leaf

value: barley genotype 159


title: BRB_48h_DoxMinus_2 (BRB-seq)

value: NIH3T3 cell line (Dox inducible H3mm18)

value: GCGCACACC


title: H9B4_7-gut-CL_Bifi

value: Colonized with two strains of Bifidobacterium asteroides (CL_Bifi)


title: BRB_48h_DoxMinus_1 (BRB-seq)

value: Differentiated for 48 hours

value: GACTGCGCA


title: SAMPLE 147 [Genotype 147]

value: barley genotype 147


title: XL6 Tadpole hindbrain, Unoperated, Replicate 3

source_name: 5 unoperated tadpoles, age-matched with 1 week, spinal cord transected tadpoles

value: albino, Xenopus Express

value: stage 53 tadpole


title: BRB_24h_DoxPlus_3 (BRB-seq)

value: Differentiated for 24 hours

value: GAGACACAG


title: BRB_24h_DoxPlus_4 (BRB-seq)

value: GGTTCACAG


title: XL4 Tadpole hindbrain, Unoperated, Replicate 1

value: unoperated

value: Hindbrain

value: not determined


title: XL5 Tadpole hindbrain, Unoperated, Replicate 2


title: H8B3_3-gut-CL_13

value: gut

value: Colonized with a community of 13 different gut microbiota strains (CL_13)


title: H8B1_3-gut-CL_Bifi


title: SAMPLE 146 [Genotype 146]

value: leaf

value: barley genotype 146


title: XL7 Frog hindbrain, Unoperated , Replicate 1

value: 1-3 mos. postmetamorphic juvenile frog


title: BRB_24h_DoxPlus_1 (BRB-seq)

value: NIH3T3 cell line (Dox inducible H3mm18)

value: GATCTCCTT


title: XL2 Tadpole hindbrain, Spinal Cord Transected, Replicate 2

source_name: 5 tadpoles, 1 week after spinal cord transection

value: spinal cord transection


title: SAMPLE 145 [Genotype 145]

value: barley genotype 145


title: XL3 Tadpole hindbrain, Spinal Cord Transected, Replicate 3

value: albino, Xenopus Express


title: BRB_24h_DoxMinus_4 (BRB-seq)

value: GTGTAGAGG


title: H8B2_3-gut-CL

value: Colonized with a gut homogenate (CL)


title: SAMPLE 143 [Genotype 143]

value: barley genotype 143


title: XL1 Tadpole hindbrain, Spinal Cord Transected, Replicate 1

value: stage 53 tadpole


title: H7B2_3-gut-CL


title: SAMPLE 144 [Genotype 144]

value: barley genotype 144


title: SAMPLE 142 [Genotype 142]

value: barley genotype 142


title: BRB_24h_DoxMinus_3 (BRB-seq)

value: Differentiated for 24 hours

value: GGCCTCTCG


title: SAMPLE 141 [Genotype 141]

value: barley genotype 141


title: SAMPLE 140 [Genotype 140]

value: leaf

value: barley genotype 140


title: SAMPLE 138 [Genotype 138]

value: barley genotype 138


title: Delta smc Delta mksB-rep2

city: NORMAN

first: Valentin

last: Rybenkov

state: OK

address: 101 Stephenson Parkway

institute: University of Oklahoma

data_processing:
The FastQ files were generated and trimmed using MiSeq Reporter. Raw data were analyzed and mapped to the P. aeruginosa PAO1 genome (AE004091) using CLC Genomics Workbench version 11.0.1 software from Qiagen with the auto-detection of paired distances, mismatch cost of 2, insertion and deletion costs of 3, length fraction of 0.5 and similarity fraction of 0.8.
The read counts for each sample were scaled through normalization of median log expression values. Genes with an average count of less than one read per sample were removed from further analysis. The normalized read counts for the remaining 5548 genes were modeled as negative binomial distributions using a constant link between the variance and the mean and statistical significance of expression changes evaluated from pairwise comparisons of each mutant to the wild type strain. The resulting p-values were then adjusted using the Benjamini-Hochberg correction to yield false discovery rates.

organism: Pseudomonas aeruginosa

source_name: exponential phase cells

growth_protocol: Cells were grown in LB at 37°C until late exponential (OD600 of 0.6)

extract_protocol:
Total RNA was isolated by hot phenol method, followed by DNase I treatment and rRNA removal using Ribo-Zero rRNA depletion kit
RNAseq libraries were constructed using the Illumina TruSeq RNA LT v2 kit and established protocols.

value: PAO1 ATCC 47085

value: PAO1 {delta}mksB {delta}smc


title: BRB_24h_DoxPlus_2 (BRB-seq)

value: NIH3T3 cell line (Dox inducible H3mm18)

value: GACTCATGT


title: BRB_24h_DoxMinus_2 (BRB-seq)

value: CCTTACACC


title: Delta smc Delta mksB-rep1


title: H7B4_9-gut-CL_Bifi

value: gut

value: Colonized with two strains of Bifidobacterium asteroides (CL_Bifi)


title: BRB_24h_DoxMinus_1 (BRB-seq)

value: CTTCGTGTA


title: Delta mksB-rep2

value: PAO1 {delta}mksB


title: H6B6_2-gut-MD

value: Microbiota-depleted (MD)


title: BRB_0h_DoxPlus_4 (BRB-seq)

value: Differentiated for 0 hours

value: CGGCGATCC


title: Delta mksB-rep1


title: SAMPLE 137 [Genotype 137]

value: barley genotype 137


title: SAMPLE 139 [Genotype 139]

value: barley genotype 139


title: SAMPLE 136 [Genotype 136]

value: leaf

value: barley genotype 136


title: H6B4_3-gut-CL

value: Colonized with a gut homogenate (CL)


title: SAMPLE 135 [Genotype 135]

value: barley genotype 135


title: BRB_0h_DoxPlus_2 (BRB-seq)

value: CGATCAGTT


title: SAMPLE 134 [Genotype 134]

value: barley genotype 134


title: Delta smc-rep2

value: PAO1 ATCC 47085

value: PAO1 {delta}smc


title: BRB_0h_DoxPlus_3 (BRB-seq)

value: NIH3T3 cell line (Dox inducible H3mm18)

value: CAACTGGTA


title: H6B2_5-gut-CL_13

value: gut

value: Colonized with a community of 13 different gut microbiota strains (CL_13)


title: Delta smc-rep1


title: H6B5_4-gut-CL_Bifi

value: Colonized with two strains of Bifidobacterium asteroides (CL_Bifi)


title: BRB_0h_DoxMinus_4 (BRB-seq)

value: Differentiated for 0 hours

value: CCAAGTACA


title: BRB_0h_DoxPlus_1 (BRB-seq)

value: CGTATGCAC


title: H8B5_3-gut-MD

value: Microbiota-depleted (MD)


title: WT PAO1-rep2

value: PAO1 ATCC 47085 wild type


title: H5B5_6-gut-MD


title: SAMPLE 133 [Genotype 133]

value: leaf

value: barley genotype 133


title: BRB_0h_DoxMinus_3 (BRB-seq)

value: CTAGGCATA


title: H5B4_4-gut-CL

value: Colonized with a gut homogenate (CL)


title: SAMPLE 132 [Genotype 132]

value: barley genotype 132


title: H5B1_3-gut-CL_13


title: ab-99547

city: Wuhan

first: qiwen

last: man

state: Hubei

address: Luyu road

institute: wuhan university

data_processing:
Basecalls performed using bcl2fastq V2.19.
equenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Quantify gene expression using read2 by featureCounts software
Genome_build: GRCh38
Supplementary_files_format_and_content: .txt file was mitochondrial content statistics

source_name: odontogenic keratocyst tissue

extract_protocol:
Single-cell suspensions were then loaded onto microfluidic devices and scRNA-seq libraries were constructed according to Singleron GEXSCOPE® protocol by GEXSCOPE® Single-Cell RNA Library Kit
Single cell suspension was loaded onto a microfluidic chip and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron GEXSCOPE Single Cell RNAseq Library Kit, Singleron Biotechnologies).

treatment_protocol: The tissue pieces were digested with 2 ml GEXSCOPE® Tissue Dissociation Solution at 37℃ for 15 min

value: odontogenic keratocyst tissue

value: Untreated

value: Female


title: SAMPLE 130 [Genotype 130]

value: barley genotype 130


title: SAMPLE 131 [Genotype 131]

value: barley genotype 131


title: BRB_0h_DoxMinus_2 (BRB-seq)

value: NIH3T3 cell line (Dox inducible H3mm18)

value: CTGATGACG


title: SAMPLE 129 [Genotype 129]

value: barley genotype 129


title: WT PAO1-rep1

value: PAO1 ATCC 47085


title: B-98618

value: 6 y


title: A-98763

value: Male


title: H4B4_7-gut-MD

value: gut

value: Microbiota-depleted (MD)


title: Control IP, Frog eye, Optic nerve crush, Unoperated eye

description: MeDIP-Seq (5hmC)

data_processing:
For histone ChIP-Seq and 5hmC DIP-Seq: Adapter sequences and barcodes were removed using Trimmomatic and FastX Tookit, and low-quality reads (quality score Q < 30) were filtered from the data using Trim Galore! (v0.3.7) with Cutadapt (v1.9). Read alignments were performed against the Xenopus laevis genome (v.9.1) using Bowtie2 (v2.2.9), with the --very-sensitive preset option. BAM alignment files were converted into the bigWig files using bam2bigwig.
Supplementary_files_format_and_content: All processed files are in the bigWig (bw) format. Bisulfite-seq files represent methylation in CpG context and are combined for the three biological replicates for each condition. ChIP-Seq and 5hmC DIP-seq files represent alignments for each read and are provided separately for each biological replicate.

source_name: contralateral unoperated frog eyes, 11 days after orbital nerve crush

extract_protocol:
5hmC MeDIP-Seq: Eyes for optic nerve crush studies were rapidly dissected and then homogenized immediately, pooling six eyes for each biological replicate.Total DNA, along with RNA, was isolated using the RNA/DNA/Protein Purification kit from Norgen Biotek Corp. with DNase I treatment, following manufactuer's protocols. For histone ChIP-Seq: Eyes and hindbrain were frozen on dry ice immediately upon dissection. Dissected tissues were frozen immediately on dry ice and stored at  80°C for later processing. Tissues were thawed while homogenizing them in PBS containing protease inhibitor cocktail, in 2-ml Pyrex glass homogenizers. After low-speed centrifugation (1,300 rpm for 5 min at 4°C), pellets were resuspended and cross-linked in PBS with 1% formaldehyde for 10 min at room temperature. Cross-linking reactions were quenched with glycine. Samples were subsequently prepared for lysis and sonication in a Diagenode Standard Bioruptor (Chromatin Shearing and Optimization kit, Diagenode #C01020010). Sonication was performed at the high-power setting for 30 cycles of 30 seconds on and 30 seconds off. This was repeated until the sheared chromatin was 150-350 bp in size, as verified by gel electrophoresis. Immunoprecipitation was done using 5 μg of antibody and 50 μl of DiaMag protein A-coated magnetic beads.
For histone ChIP-seq: Samples for ChIP-seq were prepared using the Manual iDEAL ChIP-seq kit for histones (Diagenode #C1010051) according to the manufacturer’s protocols, and the following antibodies: H3K4me3 (Abcam ab8580; lot GR3201240-1), H3K27ac (Abcam ab4729; lot GR3205523-1), H3K27me3 (Abcam MsMAb ab6002; lot GR275911-8), H3K9me3 (Abcam RbPAb ab8898; lots GR3176466-4/GR250850-1). Samples were subsequently prepared for lysis and sonication in a Diagenode Standard Bioruptor (Chromatin Shearing and Optimization kit, Diagenode #C01020010). Sonication was performed at the high-power setting for 30 cycles of 30 seconds on and 30 seconds off. This was repeated until the sheared chromatin was 150-350 bp in size, as verified by gel electrophoresis. Immunoprecipitation was done using 5 μg of antibody and 50 μl of DiaMag protein A-coated magnetic beads. Barcoded DNA libraries were prepared from the immunoprecipitated DNA, as well as from equal amounts of pre-IP DNA from sheared chromatin, using the NEBNext Ultra II DNA Library Prep kit for Illumina sequencing. Sequencing (Illumina NextSeq500) was performed at the University at Albany Center for Functional Genomics core facility (75 bp, single end reads). 5hmC MeDIP: Genomic DNA (1 μg each) was sonicated for 14 cycles of 15 seconds on and 90 seconds off, using a Diagenode Standard Bioruptor to produce fragments of 200--600 bp in length, which was verified by gel electrophoresis. The sheared DNA was then subjected to 5hmC-IP using the kit’s 5hmC antibody and its non-specific IgG control antibody, overnight at 4°C, according to the manufacturer's instructions (hMeDIP Kit, Diagenode #C02010031, mouse monoclonal mAb). The immunoprecipitated DNA was washed and released from the antibody complex by proteinase-K digestion and resuspended in 100 μl of DNA-IP buffer (DIB) provided by the kit. Library preparation and sequencing was then performed as for histone ChIP-Seq.

value: albino, Xenopus Express

value: Post metamorphic frog

value: unilateral optic nerve crush, unoperated eye

value: not determined

tag: antibody

value: IgG Control


title: H4B3_4-gut-CL_13

value: Colonized with a community of 13 different gut microbiota strains (CL_13)


title: BRB_0h_DoxMinus_1 (BRB-seq)

value: Differentiated for 0 hours

value: CTCTATTAA


title: H7B1_3-gut-CL_13


title: BRB_UI_DoxPlus_4 (BRB-seq)

value: Before retroviral infection (UnInfected, UI)

value: CAACGAGAT


title: H4B6_2-gut-CL

value: Colonized with a gut homogenate (CL)


title: Control IP, Frog eye, Optic nerve crush, Operated eye

description: MeDIP-Seq (5hmC)

source_name: operated frog eyes, 11 days after orbital nerve crush

value: unilateral optic nerve crush, operated eye


title: H5B2_3-gut-CL_Bifi

value: Colonized with two strains of Bifidobacterium asteroides (CL_Bifi)


title: H4B5_2-gut-CL_Bifi


title: BRB_UI_DoxPlus_1 (BRB-seq)

value: NIH3T3 cell line (Dox inducible H3mm18)

value: AAGGAGAGT


title: H7B3_4-gut-MD

value: gut


title: SAMPLE 128 [Genotype 128]

value: leaf

value: barley genotype 128


title: BRB_UI_DoxMinus_4 (BRB-seq)

value: ACTGCGCGG


title: SAMPLE 127 [Genotype 127]

value: barley genotype 127


title: SAMPLE 126 [Genotype 126]

value: barley genotype 126


title: SAMPLE 125 [Genotype 125]

value: barley genotype 125


title: BRB_UI_DoxMinus_3 (BRB-seq)

value: ATCGGTTGC


title: BRB_UI_DoxPlus_2 (BRB-seq)

value: AGGAGAGAG


title: BRB_UI_DoxPlus_3 (BRB-seq)

value: CAGTCTAGA


title: Control IP, Frog eye, Unoperated animal

description: MeDIP-Seq (5hmC)

source_name: unoperated frog eyes

value: albino, Xenopus Express

value: Post metamorphic frog

value: unoperated

value: not determined

value: IgG Control


title: 5hmC IP, Frog eye, Optic nerve crush, Unoperated eye

description: MeDIP-Seq (5hmC)

value: unilateral optic nerve crush, unoperated eye


title: H3B6_2-gut-MD

value: Microbiota-depleted (MD)


title: SAMPLE 124 [Genotype 124]

value: barley genotype 124


title: 5hmC IP, Frog eye, Optic nerve crush, Operated eye

description: MeDIP-Seq (5hmC)

value: unilateral optic nerve crush, operated eye


title: SAMPLE 123 [Genotype 123]

value: leaf

value: barley genotype 123


title: H3B1_3-gut-CL

value: gut

value: Colonized with a gut homogenate (CL)


title: Input DNA, Frog eye, Optic nerve crush, Unoperated eye, Replicate 1

source_name: 6 unoperated frog eyes, 11 days after contralateral orbital optic nerve crush

value: 1-3 mos. postmetamorphic juvenile frog

value: optic nerve crush, unoperated eye


title: BRB_UI_DoxMinus_2 (BRB-seq)

value: NIH3T3 cell line (Dox inducible H3mm18)

value: Before retroviral infection (UnInfected, UI)

value: ATTATGCAA


title: H3B3_4-gut-CL_Bifi

value: Colonized with two strains of Bifidobacterium asteroides (CL_Bifi)


title: Wildtype_2

city: Ulm

first: Sabine

last: Vettorazzi

address: Helmholtzstr. 8/1

institute: University Ulm

data_processing:
Quality control
Filtering of low quality reads
Alignment and mapping to mus musculus reference genome for read count analysis
Read count normalization
DEG analysis with DESeq2
Treshold for sig. DEG with p-adjusted value 0.05
Genome_build: mm10
Supplementary_files_format_and_content: Readcounts

source_name: RNA from lung tissue

extract_protocol:
RNA was isolated using Trizol and purified by alcoholic nucleinacid precipitation
PolyA capture and reverse transcription

value: 129/SvEv x C57BL/6

tag: genotype/variation

value: wild type


title: 5hmC IP, Frog eye, Unoperated animal

description: MeDIP-Seq (5hmC)

value: albino, Xenopus Express

value: Post metamorphic frog

value: unoperated

value: not determined


title: H2B5_1-gut-MD

value: Microbiota-depleted (MD)


title: SAMPLE 121 [Genotype 121]

value: leaf

value: barley genotype 121


title: H3B5_2-gut-CL_13

value: gut

value: Colonized with a community of 13 different gut microbiota strains (CL_13)


title: H2B3_3-gut-CL

value: Colonized with a gut homogenate (CL)


title: BRB_UI_DoxMinus_1 (BRB-seq)

value: ATGCATATG


title: Input DNA, Frog eye, Optic nerve crush, Unoperated eye, Replicate 2

value: 1-3 mos. postmetamorphic juvenile frog

value: optic nerve crush, unoperated eye


title: Wildtype_3


title: SAMPLE 122 [Genotype 122]

value: barley genotype 122


title: GRdim/dim_3

value: impaired GR (GRdim/dim)


title: Input DNA, Frog eye, Optic nerve crush, Operated eye, Replicate 2

source_name: 6 operated frog eyes, 11 days after orbital optic nerve crush

value: optic nerve crush, operated eye


title: SAMPLE 119 [Genotype 119]

value: barley genotype 119


title: H1B1_6-gut-MD


title: SAMPLE 120 [Genotype 120]

value: barley genotype 120


title: Input DNA, Frog eye, Optic nerve crush, Operated eye, Replicate 1

value: albino, Xenopus Express


title: SAMPLE 118 [Genotype 118]

value: barley genotype 118


title: GRdim/dim_2

value: 129/SvEv x C57BL/6


title: H2B4_3-gut-CL_13


title: GRdim/dim_1


title: Input DNA, Frog hindbrain, Unoperated, Replicate 2

value: unoperated

value: not determined


title: Input DNA, Frog hindbrain, Spinal cord transected, Replicate 2

value: spinal cord transection


title: Input DNA, Frog hindbrain, Unoperated, Replicate 1


title: H1B5_3-gut-CL_13

value: gut


title: H1B6_4-gut-CL


title: H2B1_4-gut-CL_Bifi

value: Colonized with two strains of Bifidobacterium asteroides (CL_Bifi)


title: H1B3_5-gut-CL_Bifi


title: Wildtype_1

value: wild type