title: RIC-seq_fly_S2_HeLa_rep2

city: Beijing

first: Yuanchao

last: Xue

address: Datun Road #15

department: Institute of Biophysics

institute: Chinese Academy of Sciences

description:
HeLa cells and Drosophila S2 cells are mixed at a 1:5 ratio.
The processed data file for this sample includes both fly and human RNA interactions. The sequencing data was used to assess the cell-to-cell random ligation rate of RIC-seq approach.

data_processing:
Library strategy: RIC-seq
Illumina bcl2fastq conversion software (v.2.16) was used for base calling.
After the sequencing of RIC libraries, adapters and PCR duplicates were trimmed off using the Trimmomatic program (v.0.36) (Bolger et al., 2014) and homemade scripts, respectively. The poly(N) tails at the 3’ end were further clipped using the Cutadapt program (v.1.15) (Martin, 2011).
After filtering, the paired reads were first aligned to 45S pre-rRNA, and the unmapped reads were further aligned to the human reference genome (assembly version: hg19) using the STAR software (v.020201) (Dobin et al., 2013). The parameters used were as follows: STAR --runMode alignReads --genomeDir index --readFilesIn read.fq --outFileNamePrefix outprefix --outFilterMultimapNmax 100 --outSAMattributes All --alignIntronMin 1 --scoreGapNoncan -4 --scoreGapATAC -4 --chimSegmentMin 15 --chimJunctionOverhangMin 15. Three additional parameters were further applied (--alignSJoverhangMin 15 --alignSJDBoverhangMin 10 --alignSJstitchMismatchNmax 5 -1 5 5) to improve the mapping quality.
The low-quality and secondary mapping results were filtered using the SAMtools package (v.0.1.19).
Genome_build: hg19 and dm6
Supplementary_files_format_and_content: genome-wide RNA-RNA interaction in hic format produced by Juicebox

organism:
Drosophila melanogaster
Homo sapiens

source_name: Mixture of fly S2 and human HeLa cells

growth_protocol: HeLa and 293T cells were grown in DMEM containing 10% fetal bovine serum plus 100 U/ml penicillin/streptomycin (Life Technologies; 15140) at 37 °C in 5% CO2. HT29 and HCT116 cells were cultured in modified McCoy’s 5A supplemented with 10% fetal bovine serum and 100 U/ml penicillin/streptomycin. GM12878 cells were grown in RPMI 1640 supplemented with 10% fetal bovine serum and 100 U/ml penicillin/streptomycin. MCF-7 cells were maintained in MEM containing 10% fetal bovine serum and 100 U/ml penicillin/streptomycin. IMR-90 cells were grown in DMEM/F12 + Glutamax (Life Technologies; 10565) supplemented with 5 ng/ml fibroblast growth factor-basic (R&D), 1 μg/ml hydrocortisone hemisuccinate, 50 μg/ml ascorbic acid, 5 μg/ml rh Insulin, 2% fetal bovine serum and 100 U/ml penicillin/streptomycin. S2 cells were maintained in Schneider’s drosophila medium supplemented with 10% heat-inactivated fetal bovine serum and 100 U/ml penicillin/streptomycin.

extract_protocol:
After pCp-biotin labeling and proximity ligation, 200 μl of proteinase K buffer (10 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.5% SDS) and 50 μl of proteinase K were applied to cell pellets and sequentially incubated at 37 °C for 60 min and 56 °C for 15 min. The RNA was extracted with 750 μl of TRIzol LS and 220 μl of chloroform following the manufacture’s instruction.
To remove the potential RNA-DNA ligation byproducts mediated by T4 RNA ligase, 20 μg of total RNA was treated with a mixture containing 10 μl of 10 × RQ1 DNase I buffer, 3 μl of RNAsin and 5 μl of DNase I at 37 °C for 20 min. RNA was then purified by acid Phenol: chloroform extraction and ethanol precipitation. The rRNA can be optionally removed using the Ribo-off rRNA Depletion Kit (Vazyme, N406-01) or one can directly proceed to the next step (to probe the rRNA structure and interactions). For fragmentation, 16 μl of total RNA was mixed with 4 μl of 5 × first-strand buffer (250 mM Tris-HCl pH 8.3, 375 mM KCl, 15 mM MgCl2) and incubated at 94 °C for 5 min, and then quickly put on ice. To enrich pCp-biotin marked chimeric RNAs, 20 μl of pre-blocked MyOne Streptavidin C1 beads, 30 μl of NF-H2O and 50 μl of 2 × TWB buffer were applied to each RNA sample and incubated at room temperature for 30 min by rotating. After washing four times with 1× TWB buffer, the beads were resuspended in 100 μl of PK buffer (100 mM NaCl, 10 mM Tris-HCl pH 7.0, 1 mM EDTA, 0.5% SDS) and incubated in Thermomixer at 95 °C for 10 min (1000 rpm). The tube was quickly placed on a magnet stand for 1 min and the supernatant was transferred to a new EP tube. This elution process was repeated two more times. Finally, the enriched RNAs were extracted with acid Phenol: chloroform and precipitated at the final concentration of 300 mM NaCl, with 3 volumes of -20°C ethanol and 1 μl of glycoblue. RNA was pelleted at 13,000 rpm and washed twice with 75% ETOH before resuspending in 10 μl of nuclease-free water. To synthesis first-strand cDNA, 0.5 μl of N6 primer (0.1 μg/μl) was added to the mixture and incubated at 65 °C for 5 min, followed by rapid placement on ice for at least 2 min. Reverse transcription was performed by further addition of 5.5 μl of reverse transcription mix (3 μl of 5 × first-strand buffer, 1 μl of 10 mM dNTPs, 0.5 μl of 100 mM DTT, 0.5 μl of RNase inhibitor, 0.5 μl of Superscript II reverse transcriptase) to the mixture and incubation at 25 °C for 10 min, 42 °C for 40 min and then 70 °C for 15 min. We next created dUTP second strand cDNA by adding the following reaction mixture (10 μl of 5 × second-strand buffer, 0.8 μl of 25 mM dNTPs with 80% of the dTTP replaced by dUTP, 20.5 μl of RNase-free water, 0.2 μl of 5 U/μl RNase H and 2.5 μl of E. coli DNA polymerase I) to the first-strand cDNA mixture, and incubated at 16 °C for 2 h. The double-stranded (ds)DNA products were purified using 1.8 × AMPure beads following the manufacturer’s protocol and end-repaired with a mixture of T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase. The end-repaired DNA was then treated with Klenow exo- to add an adenine to the 3’ ends. For paired-end library construction, adaptors were ligated to dsDNA using quick T4 DNA ligase and incubated at 20 °C for 15 min. Subsequently, the ligated DNA product was purified twice with AMPure beads. The adaptor-ligated cDNA was mixed with 1 μl of 10 μM Illumina PE1.0, 1 μl of 10 μM index primer, 1 μl of 50 mM MgSO4, 2.5 μl of 10 × Pfx buffer, 0.4 μl of 25 mM dNTPs, 0.4 μl of 2.5 U/μl Platinum Pfx DNA polymerase (Thermo Fisher, 11708-013) and 3 μl of USER enzyme (NEB, M5505S). The mixture was incubated at 37 °C for 15 min to allow the USER enzyme to digest the dUTP strand, then at 94 °C for 2 min. PCR was performed with the following programme: 11 to 13 cycles of 94 °C for 15 s, 62 °C for 30 s and 72 °C for 30 s. The 200 to 450 bp of PCR products were purified from agarose gel by Qiaqucik mini Elute Kit. The DNA concentration was measured by Qubit and sequenced by Illumina paired-end sequencing.

treatment_protocol: Cells were fixed in 10 ml of PBS containing 1% formaldehyde at room temperature for 10 min and then quenched by addition of 1/20 volume of 2.5 M glycine. After washing three times with ice-cold PBS, cells were scraped into 15 ml tubes and collected by centrifugation at 2,500 rpm for 10 min at 4 °C. The cell pellet was resuspended in 1 ml of permeabilization buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.5% NP-40, 0.3% Triton X-100, 0.1% Tween 20, 1× protease inhibitors, 2 U/ml SUPERase In RNase inhibitor), mixed briefly and incubated on ice for 15 min. The integrity of the cells was examined at this step under a microscope. Cells were spun down at 3,500 rpm for 5 min at 4 °C. After washing three times with 1 × PNK buffer (50 mM Tris-HCl pH7.4, 10 mM MgCl2, 0.2% NP-40), the cell pellet was briefly incubated with 200 μl of 1 × MN mixture (50 mM Tris-HCl pH 8.0, 5 mM CaCl2, 0.03 U/μl micrococcal nuclease) for 10 min at 37 °C. The reaction was stopped by washing twice with 1 × PNK + EGTA buffer (50 mM Tris- HCl pH7.4, 20 mM EGTA 0.5% NP-40) and twice with 1 × PNK buffer (50 mM Tris-HCl pH7.4, 10 mM MgCl2, 0.2% NP-40).

value: mixture of HeLa and fly S2


title: Invasive mycelium below bark layer [ARCE], replicate 1

status: Public on May 04 2020

type: SRA

city: Szeged

first: Laszlo

middle: G.

last: Nagy

state: Csongrad

address: Temesvari krt 62

department: Institute of Biochemistry, Synthetic and Systems Biology Unit

country: Hungary

institute: Biological Research Centre, Hungarian Academy of Sciences

library_source: transcriptomic

data_processing:
Reads were quality trimmed using CLC Genomics Workbench Tool (v 11.0.2). Ambiguous base limit=0, Error probability cutoff value=0.05.
Reads were mapped using RNA-Seq analysis package 2.16 of CLC Genomics Workbench Tool (v. 11.0.2). Parameters: min. read length fraction = 0.8, min. read similarity fraction = 0.8. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=10, Count paired reads as two=no, Expression value= Total counts.
Genes were filtered based on their expression levels in R (v. 3.0.2) keeping only those features that were detected by at least 5 mapped reads in at least 25% of the samples included in the study.
Trimmed mean of M values (TMM) scale normalization was used. Function: calcNormFactors, Package: edgeR, Version 3.4.2
Voom log2 transformation together with quantile normalization was applied. Function: voom normalize=quantile, Package: limma, Version: 3.18.13
Genome_build: JGI Mycocosm: Armillaria cepistipes B5 (Armcep1)
Supplementary_files_format_and_content: Comma separated files containing RNA-Seq count data, exported from CLC Genomics Workbench Tool

molecule: total RNA

organism: Armillaria cepistipes

source_name: mycelium

growth_protocol: Cultures of Armillaria cepistipes B2 were inoculated on Malt extract agar (MEA) and incubated at 25oC in dark for a week. 4-5 cm long, autoclaved sterilized spruce roots were introduced to the week-old cultures of A. cepistipes and were again kept at 25oC in the dark for 2-3 weeks until they were colonized by the fungi

extract_protocol:
Total RNA was extracted from the four tissue types in three biological replicates, using the Quick-RNA Miniprep kit (Zymo Research, Irvine, CA, USA), following the manufacturer’s protocol.
Ribo-Zero rRNA removal Kit (Yeast) was used to deplete rRNA from total RNA. Subsequently, samples were processed with Illumina TruSeq V2 library preparation protocol. (cDNA synthesis with random hexa primers resulting in a non-strand specific library)

treatment_protocol: After colonization, roots were dissected to collect mycelium from below the outer bark layer and rhizomorphs emerging out of the colonized wood. Cultures of Armillaria without the addition of sterilized spruce roots were used as non-invasive controls. Tissues were flash frozen in liquid nitrogen and kept at -80oC until futher extraction.

tag: strain

tag: group


title: Invasive mycelium below bark layer [AROC18], replicate 1

data_processing:
Reads were quality trimmed using CLC Genomics Workbench Tool (v 11.0.2). Ambiguous base limit=0, Error probability cutoff value=0.05.
Reads were mapped using RNA-Seq analysis package 2.16 of CLC Genomics Workbench Tool (v. 11.0.2). Parameters: min. read length fraction = 0.8, min. read similarity fraction = 0.8. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=10, Count paired reads as two=no, Expression value= Total counts.
Genes were filtered based on their expression levels in R (v. 3.0.2) keeping only those features that were detected by at least 5 mapped reads in at least 25% of the samples included in the study.
Trimmed mean of M values (TMM) scale normalization was used. Function: calcNormFactors, Package: edgeR, Version 3.4.2
Voom log2 transformation together with quantile normalization was applied. Function: voom normalize=quantile, Package: limma, Version: 3.18.13
Genome_build: FUEG00000000.1
Supplementary_files_format_and_content: Comma separated files containing RNA-Seq count data, exported from CLC Genomics Workbench Tool

organism: Armillaria ostoyae

growth_protocol: Cultures of Armillaria ostoyae C18 were inoculated on Malt extract agar (MEA) and incubated at 25oC in dark for a week. 4-5 cm long, autoclaved sterilized spruce roots were introduced to the week-old cultures of A. ostoyae and were again kept at 25oC in the dark for 2-3 weeks until they were colonized by the fungi


title: WT1_P63

city: Seoul

first: Jonghyo

last: Lim

address: Yonsei-ro 50

department: Biochemistry

country: South Korea

institute: Yonsei university

data_processing:
bcl2fastq v1.8.4 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Mus musculus using HISAT2 2.1.0, which is capable of reporting split-read alignments across splice junctions and determined using StringTie 1.3.4d software in default options.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: mm10

organism: Mus musculus

source_name: skin

extract_protocol:
Skins were removed and dispase treated 30mins in 37℃, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared for multiplex sequencing using Illumina TruSeq RNA Sample Prep Kit , according to the manufacturer’s protocol.

tag: tag

tag: tissue

value: Back skin

tag: age

value: post natal day 63

tag: genotype/variation

value: wild type


title: RIC-seq_fly_S2_HeLa_rep1

country: China

tag: cell line


title: 202073220008/202073220008_R05C01

status: Public on May 03 2020

type: genomic

city: London

first: Sarah

last: Marzi

address: Du Cane Road

country: United Kingdom

institute: Imperial College London

description:
replication_obese_sperm_17
motile portion of sperm sample

hyb_protocol: DNA methylation was measured using the Illumina Infinium MethylationEPIC BeadChip according to the manufacturer's protocol.

scan_protocol: DNA methylation quantification was run on an Illumina iScan System according to the manufacturer's protocol. The Illumina Genome Studio software was used to extract the raw signal intensities of each probe.

data_processing: DNA methylation data was processed using the wateRmelon package in R. An outlier analysis was performed using the outlyx() function. The 59 non-CpG SNP probes on the array were used to confirm matched samples. 9,779 probes were removed from the discovery data because more than 5% samples displayed a detection P value > 0.05. 3,337 probes were removed because of having a bead count < 3. Probes containing SNPs in close proximity to the CpG site as well as  cross-reactive probes were filtered using annotated lists. The final discovery data set comprised 704,356 CpG sites. Data was normalized using the dasen() function. The lean and obese replication cohorts were processed together experimentally and therefore jointly pre-processed and normalized using the same parameters as for the discovery dataset. A total of 697,442 probes survived quality control and filtering in the replication data. DNA methylation was analysed and reported as beta values.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: sperm

label_protocol: DNA was sodium bisulphite-treated using the Zymo EZ 96 DNA methylation kit.

extract_protocol: DNA from 200 µL buffy coat derived from whole blood was extracted using Qiagen QIAamp DNA Blood Mini Kit. DNA from the pellet of motile spermatozoa was extracted phenol-chloroform extraction. DNA extracted from whole blood and sperm was quality controlled using a Qubit 3.0 Fluorometer. DNA was stored in -80°C prior to bisulphite conversion.

treatment_protocol: Semen samples were processed within one hour of sample production and analysed for sperm concentration, motility and average progressive velocity. All semen samples were within normal parameters according to World Health Organization criteria. Samples underwent gradient centrifugation to select for motile spermatozoa. The processed samples were microscopically assessed for cell purity.

tag: participant id

tag: Sex

value: male

value: Sperm

tag: bmi

tag: bmi group

value: obese

tag: cohort

value: replication - obese


title: 202093120051/202093120051_R02C01

description:
replication_obese_sperm_15
motile portion of sperm sample


title: 202073220008/202073220008_R06C01

description:
replication_obese_sperm_21
motile portion of sperm sample


title: 202093120080/202093120080_R06C01

description:
replication_obese_sperm_19
motile portion of sperm sample


title: 202073210092/202073210092_R02C01

description:
replication_obese_sperm_18
motile portion of sperm sample


title: 202073210095/202073210095_R05C01

description:
replication_obese_sperm_14
motile portion of sperm sample


title: 202093120005/202093120005_R08C01

description:
replication_obese_sperm_12
motile portion of sperm sample


title: 202073220007/202073220007_R01C01

description:
replication_obese_sperm_16
motile portion of sperm sample


title: 202073210092/202073210092_R08C01

description:
replication_obese_sperm_9
motile portion of sperm sample


title: 202073210095/202073210095_R07C01

description:
replication_obese_sperm_10
motile portion of sperm sample


title: 202073220026/202073220026_R04C01

description:
replication_obese_sperm_7
motile portion of sperm sample


title: 202093120051/202093120051_R07C01

description:
replication_obese_sperm_6
motile portion of sperm sample


title: 202073220025/202073220025_R08C01

description:
replication_obese_sperm_8
motile portion of sperm sample


title: 202073210101/202073210101_R02C01

description:
replication_obese_sperm_5
motile portion of sperm sample


title: 202093120080/202093120080_R08C01

description:
replication_obese_blood_21
whole blood sample

source_name: whole blood

value: Blood


title: 202073220007/202073220007_R07C01

description:
replication_obese_sperm_2
motile portion of sperm sample


title: 202073210092/202073210092_R07C01

description:
replication_obese_sperm_1
motile portion of sperm sample


title: 202093120080/202093120080_R05C01

description:
replication_obese_blood_20
whole blood sample


title: 202073210092/202073210092_R04C01

description:
replication_obese_sperm_3
motile portion of sperm sample


title: 202073220026/202073220026_R06C01

description:
replication_obese_sperm_4
motile portion of sperm sample


title: 202093120051/202093120051_R04C01

description:
replication_obese_blood_16
whole blood sample


title: 202093120051/202093120051_R08C01

description:
replication_obese_blood_17
whole blood sample


title: 202093120080/202093120080_R04C01

description:
replication_obese_blood_19
whole blood sample


title: 202073220007/202073220007_R06C01

description:
replication_obese_sperm_20
motile portion of sperm sample


title: 202093120080/202093120080_R01C01

description:
replication_obese_blood_18
whole blood sample


title: 202093120006/202093120006_R05C01

description:
replication_obese_sperm_11
motile portion of sperm sample


title: 202093120006/202093120006_R07C01

description:
replication_obese_blood_15
whole blood sample


title: 202093120005/202093120005_R05C01

description:
replication_obese_blood_13
whole blood sample


title: 202073220026/202073220026_R02C01

description:
replication_obese_blood_12
whole blood sample


title: 202073210090/202073210090_R01C01

description:
replication_obese_sperm_13
motile portion of sperm sample


title: 202093120005/202093120005_R06C01

description:
replication_obese_blood_14
whole blood sample


title: 202073220025/202073220025_R02C01

description:
replication_obese_blood_9
whole blood sample


title: 202073210101/202073210101_R06C01

description:
replication_obese_blood_7
whole blood sample


title: 202073220025/202073220025_R03C01

description:
replication_obese_blood_10
whole blood sample


title: 202073220025/202073220025_R06C01

description:
replication_obese_blood_11
whole blood sample


title: 202073210101/202073210101_R05C01

description:
replication_obese_blood_6
whole blood sample


title: 202073220008/202073220008_R04C01

description:
replication_obese_blood_8
whole blood sample


title: 202073210090/202073210090_R07C01

description:
replication_obese_blood_3
whole blood sample


title: 202073210090/202073210090_R04C01

description:
replication_obese_blood_2
whole blood sample


title: 202073210090/202073210090_R03C01

description:
replication_obese_blood_1
whole blood sample


title: 202073210101/202073210101_R01C01

description:
replication_obese_blood_5
whole blood sample


title: 202073210095/202073210095_R01C01

description:
replication_obese_blood_4
whole blood sample


title: 202073210090/202073210090_R06C01

description:
replication_lean_sperm_22
motile portion of sperm sample

value: lean

value: replication - lean


title: 202073220008/202073220008_R03C01

description:
replication_lean_sperm_20
motile portion of sperm sample


title: 202073210101/202073210101_R03C01

description:
replication_lean_sperm_21
motile portion of sperm sample


title: 202093120005/202093120005_R04C01

description:
replication_lean_sperm_19
motile portion of sperm sample


title: 202093120005/202093120005_R01C01

description:
replication_lean_sperm_18
motile portion of sperm sample


title: 202073210095/202073210095_R08C01

description:
replication_lean_sperm_16
motile portion of sperm sample


title: 202093120005/202093120005_R07C01

description:
replication_lean_sperm_15
motile portion of sperm sample


title: 202073220026/202073220026_R05C01

description:
replication_lean_sperm_14
motile portion of sperm sample


title: 202093120006/202093120006_R04C01

description:
replication_lean_sperm_13
motile portion of sperm sample


title: 202093120006/202093120006_R02C01

description:
replication_lean_sperm_12
motile portion of sperm sample


title: 202073210101/202073210101_R07C01

description:
replication_lean_sperm_10
motile portion of sperm sample


title: 202073210095/202073210095_R04C01

description:
replication_lean_sperm_8
motile portion of sperm sample


title: 202073210095/202073210095_R03C01

description:
replication_lean_sperm_7
motile portion of sperm sample


title: 202073210092/202073210092_R03C01

description:
replication_lean_sperm_11
motile portion of sperm sample


title: 202073220007/202073220007_R02C01

description:
replication_lean_sperm_6
motile portion of sperm sample


title: 202073220025/202073220025_R05C01

description:
replication_lean_sperm_5
motile portion of sperm sample


title: 202093120006/202093120006_R01C01

description:
replication_lean_sperm_17
motile portion of sperm sample


title: Invasive rhizomorphs emerging out of bark [ARCE], replicate 2


title: 202073220008/202073220008_R08C01

description:
replication_lean_sperm_4
motile portion of sperm sample


title: 202073220026/202073220026_R01C01

description:
replication_lean_sperm_3
motile portion of sperm sample


title: CTL_29

type: RNA

city: Kyoto

first: Ryo

last: Kimura

address: Yoshida-Konoe-cho

department: Anatomy and Developmental Biology

country: Japan

institute: Kyoto University Graduate School of Medicine

hyb_protocol: Following manufacturer's instructions, labelled RNA was hybridized to the SurePrint G3 Human miRNA 8x60K Microarray (G4870C) (Agilent Technologies) using the miRNA Complete Hyb Kit (Agilent Technologies). Hybridization step was performed for 20 hours at 55°C at a constant speed rotation of 20rpm. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 5 minute with 37°C GE Wash buffer 2 (Agilent Technologies), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on Agilent Microarray Scanner(p/n G2565BA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent Technologies) using default parameters (protocol: miRNA_1100_Jul11 and Grid: 070156_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Peripheral blood from control subject

label_protocol: Following manufacturer's instructions, total RNA (100ng) was labeled with Cy3 using the miRNA Complete Labeling Kit (Agilent Technologies, Tokyo, Japan).

extract_protocol: miRNA was extracted from peripheral blood of participants by using the PAXgene Blood miRNA System (QIAGEN, Tokyo, Japan) following the manufacturer's protocol with DNase treatment step. RNA was quantified using a NanoDrop-2000 spectrophotometer (Thermo Fisher Scientific, Yokohama, Japan), and quality was determined by the Agilent 2100 Bioanalyzer (Agilent Technologies, Tokyo, Japan).

tag: diagnosis

value: control

value: whole blood

tag: gender


title: CTL_23

value: female


title: CTL_22


title: CTL_24


title: CTL_27


title: CTL_28


title: 202073210101/202073210101_R08C01

description:
replication_lean_sperm_9
motile portion of sperm sample


title: CTL_19


title: CTL_30


title: CTL_25


title: 202073210092/202073210092_R06C01

description:
replication_lean_sperm_1
motile portion of sperm sample


title: CTL_21


title: CTL_26


title: CTL_20


title: 202073220007/202073220007_R04C01

description:
replication_lean_sperm_2
motile portion of sperm sample


title: 202093120080/202093120080_R07C01

description:
replication_lean_blood_22
whole blood sample


title: 202093120051/202093120051_R01C01

description:
replication_lean_blood_18
whole blood sample


title: 202093120051/202093120051_R06C01

description:
replication_lean_blood_20
whole blood sample


title: 202093120006/202093120006_R03C01

description:
replication_lean_blood_16
whole blood sample


title: 202093120051/202093120051_R05C01

description:
replication_lean_blood_19
whole blood sample


title: 202093120006/202093120006_R06C01

description:
replication_lean_blood_17
whole blood sample


title: 202073220026/202073220026_R08C01

description:
replication_lean_blood_14
whole blood sample


title: CTL_17


title: 202093120005/202093120005_R02C01

description:
replication_lean_blood_15
whole blood sample


title: 202093120080/202093120080_R02C01

description:
replication_lean_blood_21
whole blood sample


title: CTL_14


title: 202073220008/202073220008_R01C01

description:
replication_lean_blood_9
whole blood sample


title: 202073220008/202073220008_R07C01

description:
replication_lean_blood_11
whole blood sample


title: 202073220008/202073220008_R02C01

description:
replication_lean_blood_10
whole blood sample


title: 202073220007/202073220007_R08C01

description:
replication_lean_blood_8
whole blood sample


title: 202073220007/202073220007_R03C01

description:
replication_lean_blood_7
whole blood sample


title: 202073220025/202073220025_R07C01

description:
replication_lean_blood_12
whole blood sample


title: 202073220026/202073220026_R03C01

description:
replication_lean_blood_13
whole blood sample


title: CTL_12


title: CTL_15


title: 202073210095/202073210095_R06C01

description:
replication_lean_blood_5
whole blood sample


title: CTL_05


title: 202073210092/202073210092_R01C01

description:
replication_lean_blood_3
whole blood sample


title: CTL_01


title: CTL_18


title: CTL_16


title: CTL_03


title: CTL_08


title: 202073210090/202073210090_R08C01

description:
replication_lean_blood_2
whole blood sample


title: CTL_04


title: CTL_09


title: 202073210095/202073210095_R02C01

description:
replication_lean_blood_4
whole blood sample


title: CTL_10


title: CTL_13


title: CTL_06


title: KO1_P63


title: CTL_11


title: CTL_02


title: 202073210090/202073210090_R02C01

description:
replication_lean_blood_1
whole blood sample


title: ASD_27

source_name: Peripheral blood from ASD patient

value: autism spectrum disorder (ASD)


title: 203259060046/203259060046_R05C01

description:
discovery_sperm_47
motile portion of sperm sample

value: discovery


title: 202073210101/202073210101_R04C01

description:
replication_lean_blood_6
whole blood sample


title: CTL_07


title: 203259060165/203259060165_R03C01

description:
discovery_sperm_45
motile portion of sperm sample


title: 203259060140/203259060140_R07C01

description:
discovery_sperm_46
motile portion of sperm sample


title: ASD_24


title: 203259060046/203259060046_R08C01

description:
discovery_sperm_43
motile portion of sperm sample


title: 203259060046/203259060046_R03C01

description:
discovery_sperm_42
motile portion of sperm sample


title: 203259060165/203259060165_R04C01

description:
discovery_sperm_41
motile portion of sperm sample


title: ASD_29


title: ASD_23


title: ASD_28


title: ASD_22


title: ASD_25


title: 203259060004/203259060004_R02C01

description:
discovery_sperm_39
motile portion of sperm sample


title: 203259060054/203259060054_R08C01

description:
discovery_sperm_38
motile portion of sperm sample


title: 203259060104/203259060104_R08C01

description:
discovery_sperm_36
motile portion of sperm sample


title: ASD_17


title: 203259060054/203259060054_R01C01

description:
discovery_sperm_35
motile portion of sperm sample


title: 203259060040/203259060040_R01C01

description:
discovery_sperm_40
motile portion of sperm sample


title: ASD_21


title: 203259060031/203259060031_R08C01

description:
discovery_sperm_34
motile portion of sperm sample


title: 203259060031/203259060031_R06C01

description:
discovery_sperm_37
motile portion of sperm sample


title: 203259060137/203259060137_R04C01

description:
discovery_sperm_33
motile portion of sperm sample


title: ASD_15


title: ASD_11


title: ASD_16


title: ASD_14


title: ASD_19


title: ASD_18


title: ASD_13


title: ASD_30


title: ASD_08


title: ASD_10


title: 203259060104/203259060104_R02C01

description:
discovery_sperm_31
motile portion of sperm sample


title: 203259060040/203259060040_R05C01

description:
discovery_sperm_30
motile portion of sperm sample


title: 203259060040/203259060040_R07C01

description:
discovery_sperm_44
motile portion of sperm sample


title: ASD_06


title: ASD_05


title: 203259060165/203259060165_R05C01

description:
discovery_sperm_29
motile portion of sperm sample


title: 203259060148/203259060148_R06C01

description:
discovery_sperm_28
motile portion of sperm sample


title: 203259060004/203259060004_R08C01

description:
discovery_sperm_32
motile portion of sperm sample


title: 203259060104/203259060104_R01C01

description:
discovery_sperm_27
motile portion of sperm sample


title: ASD_04


title: ASD_20


title: 203259060137/203259060137_R03C01

description:
discovery_sperm_26
motile portion of sperm sample


title: NS_16

first: xiaoqun

last: wang

state: Beijing

address: 15 Datun Road, Chaoyang District

data_processing:
Lower quality sequences and adapters were trimmed using python script AfterQC
Sequenced reads were aligned to reference genome GRCm38 primary assembly downloaded from ensemble using STAR version 2.5.3a
Reads were counted using featureCounts
Gene expression were normalized to the number of fragments per kilobase million (FPKM value)
Non-protein-coding genes and genes that didn't have expression value of at least 1 FPKM across all samples were excluded from further analysis
Genome_build: GRCm38 dna primary assembly
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: brain

extract_protocol:
The autoclaved RNase-free pipette tip was sufficiently close to a targeted cell, we suddenly sucked the soma into the pipette and collected the sample immediately via breaking the pipette tip in the lysis-buffer filled tube.
RNA libraries were prepared for sequencing using standard protocol of Smart-seq2

value: brain

value: 70 days

tag: genotype

tag: phenotype

value: non-light sensitive


title: NS_15


title: ASD_09


title: NS_12


title: NS_13


title: 203259060046/203259060046_R07C01

description:
discovery_sperm_22
motile portion of sperm sample


title: 203259060148/203259060148_R08C01

description:
discovery_sperm_24
motile portion of sperm sample


title: 203259060046/203259060046_R06C01

description:
discovery_sperm_23
motile portion of sperm sample


title: NS_14


title: 203259060127/203259060127_R01C01

description:
discovery_sperm_25
motile portion of sperm sample


title: ASD_03


title: NS_11


title: ASD_02


title: NS_10


title: 203259060181/203259060181_R03C01

description:
discovery_sperm_19
motile portion of sperm sample


title: NS_9


title: 203259060040/203259060040_R06C01

description:
discovery_sperm_21
motile portion of sperm sample


title: NS_17


title: NS_8


title: 203259060004/203259060004_R07C01

description:
discovery_sperm_18
motile portion of sperm sample


title: 203259060040/203259060040_R04C01

description:
discovery_sperm_17
motile portion of sperm sample


title: NS_6


title: 203259060031/203259060031_R02C01

description:
discovery_sperm_20
motile portion of sperm sample


title: 203259060148/203259060148_R03C01

description:
discovery_sperm_16
motile portion of sperm sample


title: NS_5


title: NS_7


title: 203259060127/203259060127_R06C01

description:
discovery_sperm_14
motile portion of sperm sample


title: 203259060004/203259060004_R04C01

description:
discovery_sperm_13
motile portion of sperm sample


title: 203259060046/203259060046_R01C01

description:
discovery_sperm_12
motile portion of sperm sample


title: NS_3


title: NS_1


title: NS_4


title: 203259060140/203259060140_R03C01

description:
discovery_sperm_11
motile portion of sperm sample


title: 203259060104/203259060104_R05C01

description:
discovery_sperm_10
motile portion of sperm sample


title: 203259060104/203259060104_R03C01

description:
discovery_sperm_9
motile portion of sperm sample


title: LS_45

value: light sensitive


title: LS_44

value: wild type


title: LS_46


title: 203259060004/203259060004_R01C01

description:
discovery_sperm_7
motile portion of sperm sample

value: male


title: 203259060181/203259060181_R06C01

description:
discovery_sperm_6
motile portion of sperm sample

value: Sperm


title: LS_43


title: LS_42


title: 203259060004/203259060004_R05C01

description:
discovery_sperm_15
motile portion of sperm sample


title: LS_41


title: 203259060127/203259060127_R08C01

description:
discovery_sperm_5
motile portion of sperm sample


title: LS_40


title: 203259060165/203259060165_R01C01

description:
discovery_sperm_8
motile portion of sperm sample


title: LS_39


title: 203259060031/203259060031_R03C01

description:
discovery_sperm_3
motile portion of sperm sample


title: ASD_07


title: NS_2


title: 203259060148/203259060148_R02C01

description:
discovery_sperm_2
motile portion of sperm sample


title: 203259060054/203259060054_R03C01

description:
discovery_sperm_1
motile portion of sperm sample


title: LS_37


title: ASD_26


title: 203259060181/203259060181_R08C01

description:
discovery_blood_47
whole blood sample


title: 40A

city: Stockholm

first: Konstantinos

last: Meletis

address: Solnavägen 9

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

data_processing:
Quality trimming
Mapping to reference genome
Spatial demultiplexing
Gene annotation & UMI filtering
Registration with the wholebrain package to align sections to the Allen Brain Atlas: extracting stereotaxic coordinates and region label of every spot according to a reference atlas.
Genome_build: GRCm38_86v2
Supplementary_files_format_and_content: For each section we provide:
Supplementary_files_format_and_content: The bright field microscopy image of the coronal section cropped around the Spatial Transcriptomics array in .jpg format (HE_ID.jpg)
Supplementary_files_format_and_content: The matrix of UMI raw counts in .tsv format (expr_raw_counts_table_ID.tsv.gz). Each row corresponds to one spot and is indexed by a unique spot identifier. Each column corresponds to the gene indicated in the header.
Supplementary_files_format_and_content: A meta table in .tsv format with spots as rows (meta_table_ID.tsv.gz). Rows are indexed by a unique spot identifier. Columns represent respectively the section ID (section_index); the stereotaxic coordinates in mm: Medial-Lateral (stereo_ML), Dorsal-Ventral (stereo_DV) and Antero-Posterior (stereo_AP) based on registration in the Allen Brain Atlas; the X (HE_X) and Y (HE_Y) coordinates of the spots on the HE image based on alignment; the acronym (ABA_acronym) and name (ABA_name) of the region in which the spot was registered according to the Allen Brain Atlas; the name of the region in which the spot was registered according to the Allen Brain Atlas using a coarse scale (ABA_parent); the number of nuclei segmented in the spot (nuclei_segmented); the estimated radius of the spot in pixels (spot_radius); a boolean indicating whether the spot successfully passed the quality control (passed_QC); the id (cluster_id) and name (cluster_name) of the cluster to which the spot was assigned.

molecule: polyA RNA

source_name: Brain, coronal section

extract_protocol:
Mice were killed with an overdose of isoflurane. The brains were rapidly extracted from the skull and immediately submerged in ice-cold ACSF. The brains were then blotted to remove excess liquid and the hemispheres separated along the sagittal midline. The left hemisphere was subsequently embedded in OCT and frozen in isopentane on dry ice. The hemisphere was cut into 10 μm sections on a cryostat.
mRNA captured by the surface probes was reverse-transcribed using Superscript III. Next, 2nd strand synthesis, cDNA purification, in vitro transcription, aRNA purification, adapter ligation, post-ligation purification, a second 2nd strand synthesis and purification were carried out using an automated MBS 8000 system as described previously (Jemt et al). cDNA was amplified by PCR using Illumina Indexing primers and purified using carboxylic acid beads.

tag: animal id

value: 9 weeks

value: Male


title: 40B

tag: strain


title: 203259060181/203259060181_R05C01

description:
discovery_blood_45
whole blood sample

value: Blood


title: LS_33


title: 39B


title: ASD_12


title: 39A


title: 203259060054/203259060054_R05C01

description:
discovery_sperm_4
motile portion of sperm sample

value: lean


title: LS_32


title: LS_36


title: 38A


title: 203259060181/203259060181_R02C01

description:
discovery_blood_43
whole blood sample


title: LS_38


title: 203259060181/203259060181_R01C01

description:
discovery_blood_42
whole blood sample


title: 37A


title: 203259060181/203259060181_R07C01

description:
discovery_blood_46
whole blood sample


title: LS_30


title: LS_35


title: 36A


title: 203259060165/203259060165_R08C01

description:
discovery_blood_41
whole blood sample


title: LS_34


title: 38B


title: 35A


title: 203259060165/203259060165_R07C01

description:
discovery_blood_40
whole blood sample


title: LS_29


title: LS_28


title: 203259060181/203259060181_R04C01

description:
discovery_blood_44
whole blood sample


title: 203259060165/203259060165_R06C01

description:
discovery_blood_39
whole blood sample


title: 34A


title: 34B


title: 35B


title: LS_31


title: LS_27


title: 36B


title: 33A


title: 37B


title: 203259060148/203259060148_R07C01

description:
discovery_blood_37
whole blood sample


title: 30A


title: LS_25


title: 31A


title: LS_24


title: 29B


title: 203259060148/203259060148_R01C01

description:
discovery_blood_35
whole blood sample


title: 203259060148/203259060148_R04C01

description:
discovery_blood_36
whole blood sample


title: LS_23


title: LS_26


title: 28A


title: 203259060165/203259060165_R02C01

description:
discovery_blood_38
whole blood sample


title: 33B


title: 28B


title: 32A


title: LS_22


title: 29A


title: 203259060140/203259060140_R08C01

description:
discovery_blood_34
whole blood sample


title: 203259060140/203259060140_R06C01

description:
discovery_blood_33
whole blood sample


title: 26B


title: LS_21


title: 25A


title: 27A


title: 27B


title: 26A


title: LS_20


title: 24A


title: 24B


title: 203259060140/203259060140_R02C01

description:
discovery_blood_31
whole blood sample


title: 23B


title: 23A


title: 203259060140/203259060140_R01C01

description:
discovery_blood_30
whole blood sample


title: LS_19


title: LS_18


title: 203259060137/203259060137_R08C01

description:
discovery_blood_29
whole blood sample


title: 22B


title: 22A


title: 203259060137/203259060137_R07C01

description:
discovery_blood_28
whole blood sample


title: 21B


title: 203259060137/203259060137_R06C01

description:
discovery_blood_27
whole blood sample


title: ASD_01


title: 203259060140/203259060140_R05C01

description:
discovery_blood_32
whole blood sample


title: LS_16


title: 19B


title: 21A


title: LS_17


title: 20A


title: 203259060137/203259060137_R05C01

description:
discovery_blood_26
whole blood sample


title: 19A


title: 20B


title: 18B


title: 203259060137/203259060137_R02C01

description:
discovery_blood_25
whole blood sample


title: 18A


title: 203259060137/203259060137_R01C01

description:
discovery_blood_24
whole blood sample


title: LS_14


title: LS_13


title: 17B


title: 17A


title: 203259060127/203259060127_R07C01

description:
discovery_blood_23
whole blood sample


title: LS_12


title: 16B


title: 15B


title: 16A


title: 203259060127/203259060127_R05C01

description:
discovery_blood_22
whole blood sample


title: 15A


title: 14B


title: 203259060127/203259060127_R04C01

description:
discovery_blood_21
whole blood sample


title: 14A


title: LS_15


title: LS_10


title: 203259060127/203259060127_R03C01

description:
discovery_blood_20
whole blood sample


title: 13B


title: 13A


title: LS_9


title: 12B


title: LS_8


title: 12A


title: 203259060127/203259060127_R02C01

description:
discovery_blood_19
whole blood sample


title: 11A


title: 10B


title: LS_7


title: LS_6


title: 10A


title: 203259060104/203259060104_R06C01

description:
discovery_blood_17
whole blood sample


title: 09B


title: 09A


title: LS_5


title: 08B


title: LS_11


title: 203259060104/203259060104_R04C01

description:
discovery_blood_16
whole blood sample


title: LS_4


title: 07B


title: 08A


title: 203259060054/203259060054_R07C01

description:
discovery_blood_15
whole blood sample


title: 203259060054/203259060054_R06C01

description:
discovery_blood_14
whole blood sample


title: LS_3


title: 07A


title: 203259060054/203259060054_R04C01

description:
discovery_blood_13
whole blood sample


title: LS_2


title: 06B


title: 203259060104/203259060104_R07C01

description:
discovery_blood_18
whole blood sample


title: 203259060054/203259060054_R02C01

description:
discovery_blood_12
whole blood sample


title: LS_1


title: 05B


title: 04B


title: S0WT_S_C_RNA-Seq

city: Bern

first: Nadia

last: Mercader

address: Baltzerstrasse 2

country: Switzerland

institute: University of Bern

data_processing:
Illumina HiSeq 2500
FASTQ files were checked for quality control metrics using FastQC (version 0.11.8)
Raw reads were pseudo-mapped to the index created by Kallisto  using Danio rerio cDNA. Next, we used standard values for single-end reads  with 100 bootstraps, fragment length 200bp and sd of fragments lengt was 30 bp.
Genome_build: Ensembl cDNA (build 11, release 94)
Supplementary_files_format_and_content: H5 and Tab-delimited files containing the Ensembl transcript ID version (Ensembl) and the  length, eff_length, est_counts and tpm of  the “counts”. To be imported using  tximport or sleuth.

organism: Danio rerio

source_name: WT_Standard Diet_Muscle

growth_protocol: Zebrafish were grown at same density 13 fish in 2 l tanks

extract_protocol:
Adult zebrafish skeletal muscle were dissected and stored at -80°C. RNA was isolated using Trizol and purified (Zymo RNA Clean & Concentrator kit).
RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation.
Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System

treatment_protocol: Zebrafish were fed during 6 weeks in two different diets: standard diet (S), gemma-300 3 times/day, double diet (DD) gemma-300 5 times/day

value: WT

tag: treatment

value: Standard Diet

value: Muscle


title: 203259060046/203259060046_R04C01

description:
discovery_blood_11
whole blood sample


title: 05A


title: 04A


title: 203259060046/203259060046_R02C01

description:
discovery_blood_10
whole blood sample


title: 02A


title: 02B


title: S0WT_S_7_RNA-Seq

value: female


title: 01B


title: S0WT_S_B_RNA-Seq


title: 203259060040/203259060040_R08C01

description:
discovery_blood_9
whole blood sample


title: 203259060040/203259060040_R03C01

description:
discovery_blood_8
whole blood sample


title: 06A


title: 01A


title: S0WT_DD_4_RNA-Seq

source_name: WT_Double Diet_Muscle

value: Double Diet


title: rrm_2_Pep

city: La Jolla

first: Keini

last: Dressano

state: California

address: 9500 Gilman Drive #0116

department: Biology

country: USA

institute: UC San Diego

data_processing:
Illumina HiSeq platform PE150 sequencing and bioinformatic data analysis were performed at the Novogene Corporation Inc.
Mapping Reads to Reference Genome (Arabidopsis thaliana v.10)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated according to Novogene pipeline. The exons of transcripts were counted and normalized by the size of the meta-transcript and by the size of the library. Data Quality Control: filtering reads containing adapter or with low quality.
Genome_build: Arabidopsis thaliana v.10
Supplementary_files_format_and_content: Tab-delimited text and excel files include RPKM values and alternatice splicing analysis for samples

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Sterile seeds were sown on half-strength MS media for 7-10 days.

extract_protocol:
Total RNA was isolated with the Spectrum Plant Total RNA kit (Sigma) and treated with Turbo DNA-free kit (Ambion). RNA quality was checked using the Agilent2100 Bioanalyzer (Agilent Technologies)
Total RNA was isolated with the Spectrum Plant Total RNA kit (Sigma) and treated with Turbo DNA-free kit (Ambion).
The preparation of RNA-Seq 250-300 bp insert cDNA library was performed at the Novogene Corporation Inc.
Illumina HiSeq platform PE150 sequencing was performed at the Novogene Corporation Inc. (20 M raw reads/sample)

treatment_protocol: 7-10 days-old seedlings were transferred to 24 well plates containing liquid half-strength MS. Approximately 15 plants were transferred to individual wells. Three hours after the transference, plants were treated with either water or 1 μM peptide for 24 hours (unless indicated otherwise) at room temperature and constant light. The plant tissue was harvested in liquid nitrogen.

tag: cultivar

value: Columbia 0

value: rrm/irr

value: 1 µM AtPep1 for 24 hours


title: rrm_3_Pep


title: S0WT_S_6_RNA-Seq

tag: tissue


title: 203259060040/203259060040_R02C01

description:
discovery_blood_7
whole blood sample

tag: age

value: discovery


title: S0WT_DD_3_RNA-Seq

tag: genotype/variation


title: rrm_2

value: untreated


title: rrm_1_Pep


title: 03B


title: 203259060031/203259060031_R07C01

description:
discovery_blood_6
whole blood sample


title: 203259060031/203259060031_R05C01

description:
discovery_blood_5
whole blood sample


title: 03A


title: S0WT_DD_2_RNA-Seq


title: S0KO_S_C_RNA-Seq

source_name: KO_Standard Diet_Muscle

value: KO


title: rrm_1


title: rrm_3


title: WT_3_Pep


title: WT_1_Pep


title: S0KO_S_B_RNA-Seq


title: WT_3


title: WT_2


title: 203259060031/203259060031_R04C01

description:
discovery_blood_4
whole blood sample

value: male


title: S0KO_S_A_RNA-Seq


title: stage III CRC patient_favorable_IonXpress_024

city: Firenze

first: Stefania

last: Nobili

address: viale Pieraccini 6

department: Health Sciences

country: Italy

institute: University of Florence

data_processing:
Sequence reads were aligned to the Ion AmpliSeq Transcriptome reference file (hg19_AmpliSeq_Transcriptome_ERCC_v1.fasta) containing 20,802 using the Ion Torrent Mapping Alignment Program (TMAP)
Following alignment, the AmpliSeqRNA plug-in was used to count the number of reads mapping to the expected amplicon ranges as defined in the BED file hg19_ AmpliSeq_Transcriptome_21K_v1.bed.
Genome_build: hg19_AmpliSeq_Transcriptome_ERCC_v1.fasta
Supplementary_files_format_and_content: Tab separated files with raw reads count.

source_name: stage III CRC patient_favorable

extract_protocol:
Total RNA was isolated from frozen CRC specimens. Tissues samples were homogenized with an Ultraturrax in 1ml of TRI Reagent® (Invitrogen). RNA was purified by RiboPureTM Kit according to the manufacturer’s protocol (Invitrogen) and treated with RNase-free DNase. RNA was quantified by Qubit™ 3.0 Fluorometer (Invitrogen). After quantification total RNA was analyzed to determine the quality of samples by the Agilent RNA 6000 Nano LabChip® kit with the Agilent 2100 Bioanalyzer (Agilent Technologies). The accepted values of RNA integrity were between 5 and 8.
Libraries for sequencing were prepared according to Ion Proton System’s instructions

treatment_protocol: standard adjuvant chemotherapy

tag: subject status

value: colorectal cancer (CRC) patient

value: M

tag: stage ajcc

value: IIIB

tag: outcome

value: favorable; no evidence of disease recurrence within 5 yrs from chemotherapy


title: 203259060004/203259060004_R06C01

description:
discovery_blood_2
whole blood sample

tag: participant id

tag: Sex

value: Blood

tag: bmi

value: lean


title: stage III CRC patient_unfavorable_IonXpress_023

source_name: stage III CRC patient_unfavorable

value: F

value: unfavorable; evidence of disease recurrence within 3 yrs from chemotherapy


title: stage III CRC patient_unfavorable_IonXpress_022


title: stage III CRC patient_favorable_IonXpress_021


title: 203259060004/203259060004_R03C01

description:
discovery_blood_1
whole blood sample

tag: bmi group

tag: cohort


title: S0KO_DD_7_RNA-Seq

source_name: KO_Double Diet_Muscle

value: female

value: Muscle


title: stage III CRC patient_unfavorable_IonXpress_020

tag: gender


title: WT_2_Pep

value: Columbia 0

tag: genotype

value: WT


title: S0KO_DD_6_RNA-Seq

value: Double Diet


title: stage III CRC patient_favorable_IonXpress_018


title: stage III CRC patient_unfavorable_IonXpress_019


title: control_30min rep2

city: Davis

first: Ilias

last: Tagkopoulos

state: CA

address: 451 Health Science Dr.

institute: UC Davis

description:
Bacteria grown in M9 for 12h.
processed data file: processed_data_file_ecoli_biocides.xlsx

data_processing:
Adapters and low-quality reads were removed from the raw reads by Trimmomatic.
Alignment to the reference files for E. coli MG 1655 by Bowtie2.
Bam files generated by Bowtie2 were fed into FeatureCounts.
Differentially expressed genes (DEGs) were identified using edgeR and Deseq-2 with a false discovery rate of 0.05 as the threshold for calling differential expression.
Gene ontology terms (GO: biological process) were captured from Ecocyc for all DEGs.
Genome_build: E. coli MG1655 (GenBank U00096.3)
Supplementary_files_format_and_content: *_raw.csv: Comma-separated text files include raw counts.
Supplementary_files_format_and_content: *_norm.csv: Comma-separated text files include normalized counts.
Supplementary_files_format_and_content: processed_data_file_ecoli_biocides.xlsx: Excel file containing DEGs and GO biological process terms.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: whole cells

growth_protocol: Escherichia coli MG1655 was grown in minimal media (M9 with 0.4% w/v glucose) for 12h (mid to late exponential growth) at 37°C (pre-inoculum).

extract_protocol:
Cold 5% (v/v) phenol:ethanol was added (1.5 mL per 3 mL sample) to each tube. The cells were pelleted by centrifugation at 4000 RPM at 4°C for 10 min and stored at -80°C for up to two weeks.
Total RNA was recovered from pelleted cells with the RNeasy mini kit (Qiagen) and on-column DNase digestion (Qiagen). Ribosomal RNA was removed with capture oligonucleotide mix (MICROBExpress, Ambition). RNA clean-up was performed with NucleoSpin RNA Clean-up (Macherey-Nagel).
For the library preparation, the KAPA Stranded RNA-Seq Library Preparation kit for Illumina platforms (Kapa Biosystems) was used according to the manufacturer’s instructions. An extra step of size selection was performed using Agencourt AMPure XP magnetic beads (Beckman Coulter).

treatment_protocol: One of 10 biocides (disinfectants and antiseptics).

tag: time


title: control_30min rep3


title: 203259060031/203259060031_R01C01

description:
discovery_blood_3
whole blood sample

value: discovery


title: stage III CRC patient_unfavorable_IonXpress_017


title: control_30min rep1


title: stage III CRC patient_favorable_IonXpress_016


title: WT_1

value: untreated


title: stage III CRC patient_unfavorable_IonXpress_015

value: IIIA


title: S0KO_DD_2_RNA-Seq

value: KO


title: S0KO_DD_3_RNA-Seq


title: stage III CRC patient_unfavorable_IonXpress_014

value: colorectal cancer (CRC) patient


title: stage III CRC patient_unfavorable_IonXpress_013

value: M


title: stage III CRC patient_unfavorable_IonXpress_012

value: IIIB


title: stage III CRC patient_favorable_IonXpress_010

value: favorable; no evidence of disease recurrence within 5 yrs from chemotherapy


title: S0KO_S_6_RNA-Seq

value: Standard Diet


title: HLB-affected (T) D3-Rep4

city: Lake Alfred

first: Faisal

last: Shahzad

state: FL

address: 700 Experiment Station Road, CREC

department: Horticultural Sciences

institute: University of Florida

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Csinensis_154_v1.1 using STAR 2.5.1b
Gene expression was calculated using RSEM 1.2.28
Differential expressed genes were called using edgeR
Genome_build: Citrus sinensis_154_v1.1, annotation: https://phytozome.jgi.doe.gov/pz/portal.html
Supplementary_files_format_and_content: tab-delimited text files include Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values for each Sample

organism: Citrus sinensis

source_name: Citrus feeder roots

growth_protocol: Two-year-old sweet orange Healthy and HLB-affected trees were witheld from fertilizer solution for six months. Then, both Healthy and HLB-affecetd plants were grown in the presence of Hogalnd solution treatment. All the trees were grown in a greenhouse at Citrus Research and Education Center, Lake Alfred, University of Florida, USA.

extract_protocol:
Total RNA was extracted using TRIzol method. The quality and quantity of RNA was evaluated using a spectrophotometer and with denaturing formaldehyde 1.2% agarose gels.
RNA libraries were prepared for sequencing using the Illumina TruSeq mRNA protocol.

treatment_protocol: Experiment was executed in the month of January, 2017 and four trees of both healthy and HLB-affected trees, representing four biological replicates, were given the Hoagland solution treatment. The comparison were made at three different timepoints: D1 (befor the Hoagland solution treatment), D2(After three days of giving Hoagland solution), D3 (After nine days of Hoagland solution treatment). The feeder roots of both Healthy and HLB-affected feeder roots were collected for  comparisons.

value: feeder roots

value: Hoagland treatment

tag: day after treatment

value: After 9 days of Hoagland treatment

tag: biological replicate

value: Biological replicate 4


title: HLB-affected (T) D3-Rep3

tag: treatment

value: Biological replicate 3


title: stage III CRC patient_favorable_IonXpress_011

value: F


title: control_12h rep3

description:
Bacteria grown in M9 for 12h, followed by 1:100 dilution in M9 and growth to mid-exponential.
processed data file: processed_data_file_ecoli_biocides.xlsx


title: stage III CRC patient_unfavorable_IonXpress_009

value: unfavorable; evidence of disease recurrence within 3 yrs from chemotherapy


title: control_12h rep1


title: stage III CRC patient_favorable_IonXpress_008


title: pov_30min rep3

description:
Bacteria grown in M9 for 12h, followed by exposure to povidone-iodine (12.5 ug/mL) for 30min.
processed data file: processed_data_file_ecoli_biocides.xlsx

value: povidone-iodine


title: HLB-affected (T) D3-Rep2

tag: tissue

value: Biological replicate 2


title: stage III CRC patient_favorable_IonXpress_007

tag: age


title: HLB-affected (T) D3-Rep1

value: Biological replicate 1


title: stage III CRC patient_unfavorable_IonXpress_006


title: Healthy (C) D3-Rep4


title: stage III CRC patient_favorable_IonXpress_005


title: stage III CRC patient_unfavorable_IonXpress_004


title: pov_30min rep1


title: control_12h rep2


title: pov_30min rep2


title: Healthy (C) D3-Rep3


title: stage III CRC patient_favorable_IonXpress_003


title: Healthy (C) D3-Rep2


title: phe_30min rep3

description:
Bacteria grown in M9 for 12h, followed by exposure to chlorophene (0.25 mM) for 30min.
processed data file: processed_data_file_ecoli_biocides.xlsx

value: chlorophene


title: stage III CRC patient_favorable_IonXpress_002


title: Healthy (C) D3-Rep1


title: phe_30min rep2


title: DKO nonTfh_rep4 (KLH)

first: Jinyong

last: Choi

address: 9420 Athena Circle

department: Center for Infectious Disease and Vaccine Research

institute: La Jolla Institute for Immunology

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr).
The reads were aligned with the mm10 reference genome using using Tophat v1.4.1. DUST scores were calculated with PRINSEQ Lite (v 0.20.3) and low-complexity reads (DUST > 4) were removed.
The alignment results were parsed via the SAMtools to generate SAM files.
Read counts to each genomic feature were obtained with the HTSeq-count program (v 0.7.1) using the “union” option.
After removing absent features (zero counts in all samples), the raw counts were imported to R/Bioconductor package DESeq2 (v3.1).
Genome_build: mm10
Supplementary_files_format_and_content: Read count matrix with rows as genes and columns as cells

source_name: SMARTA CD4 T cells

extract_protocol:
Total RNA was extracted in Trizol LS reagent.
This assay was adapted from the SmartSeq2 protocol (Seumois et al. 2016). Cells were directly sorted into 1.7 mL microtubes containing 500 μL Trizol LS buffer. RNA extraction was performed using miRNeasy micro kits for downstream RNA-SmartSeq2 input requirements (Rosales et al. 2013). cDNA was purified using AMPure XP beads. One nanogram cDNA was used to prepare a standard Nextera XT sequencing library (Illumina Nextera XT DNA sample preparation kit and index kit). Samples were sequenced using a HiSeq2500 (Illumina) with single-end sequencing.
RNA-seq based on SmartSeq2

value: Lymph node

tag: cell type


title: Naive_rep1 (KLH)


title: Naive_rep2 (KLH)


title: Naive_rep4 (KLH)


title: HLB-affected (T) D2-Rep4

value: After 3 days of Hoagland treatment


title: DKO nonTfh_rep3 (KLH)


title: benz_30min rep3

description:
Bacteria grown in M9 for 12h, followed by exposure to benzalkonium chloride (3.63 mg/L) for 30min.
processed data file: processed_data_file_ecoli_biocides.xlsx

value: benzalkonium chloride


title: phe_30min rep1


title: HLB-affected (T) D2-Rep3


title: DKO nonTfh_rep1 (KLH)


title: DKO nonTfh_rep2 (KLH)


title: Prdm1KO Tfh_rep4 (KLH)


title: HLB-affected (T) D2-Rep2


title: benz_30min rep1


title: stage III CRC patient_favorable_IonXpress_001

tag: subject status

value: colorectal cancer (CRC) patient

value: M

value: IIIB


title: HLB-affected (T) D2-Rep1

value: feeder roots


title: Prdm1KO Tfh_rep2 (KLH)


title: Healthy (C) D2-Rep4

value: Hoagland treatment


title: Prdm1KO Tfh_rep3 (KLH)


title: Prdm1KO Tfh_rep1 (KLH)


title: Prdm1KO nonTfh_rep4 (KLH)


title: Naive_rep3 (KLH)


title: xid_12h rep3

description:
Bacteria grown in M9 for 12h, followed by 1:100 dilution in M9 + chlorhexidine (1.48 uM) and growth to mid-exponential.
processed data file: processed_data_file_ecoli_biocides.xlsx

value: chlorhexidine


title: Prdm1KO nonTfh_rep3 (KLH)


title: Prdm1KO nonTfh_rep2 (KLH)


title: Healthy (C) D2-Rep3


title: Prdm1KO nonTfh_rep1 (KLH)


title: Bcl6KO nonTfh_rep3 (KLH)


title: xid_12h rep2


title: Healthy (C) D2-Rep1


title: Bcl6KO nonTfh_rep4 (KLH)


title: Healthy (C) D2-Rep2


title: Bcl6KO nonTfh_rep2 (KLH)


title: Bcl6KO nonTfh_rep1 (KLH)


title: sod_12h rep3

description:
Bacteria grown in M9 for 12h, followed by 1:100 dilution in M9 + sodium hypochlorite (3.64 uM) and growth to mid-exponential.
processed data file: processed_data_file_ecoli_biocides.xlsx

value: sodium hypochlorite


title: HLB-affected (T) D1-Rep3

value: No Hoagland treatment

value: At the start of experiment

value: Biological replicate 3


title: benz_30min rep2


title: sod_12h rep2


title: WT Tfh_rep3 (KLH)


title: WT Tfh_rep4 (KLH)


title: HLB-affected (T) D1-Rep2


title: sod_12h rep1


title: WT Tfh_rep2 (KLH)


title: WT Tfh_rep1 (KLH)


title: pov_12h rep3

description:
Bacteria grown in M9 for 12h, followed by 1:100 dilution in M9 + povidone-iodine (12.5 ug/mL) and growth to mid-exponential.
processed data file: processed_data_file_ecoli_biocides.xlsx

value: povidone-iodine


title: WT nonTfh_rep4 (KLH)


title: xid_12h rep1


title: pov_12h rep2


title: WT nonTfh_rep2 (KLH)


title: Healthy (C) D1-Rep4

value: Biological replicate 4


title: pov_12h rep1


title: Naïve_rep3 (LCMV)

value: Spleen


title: WT nonTfh_rep3 (KLH)


title: HLB-affected (T) D1-Rep1

value: Biological replicate 1


title: Healthy (C) D1-Rep2

value: Biological replicate 2


title: Naïve_rep2 (LCMV)


title: phe_12h rep3

description:
Bacteria grown in M9 for 12h, followed by 1:100 dilution in M9 + chlorophene (0.25 mM) and growth to mid-exponential.
processed data file: processed_data_file_ecoli_biocides.xlsx

value: chlorophene


title: Naïve_rep1 (LCMV)


title: phe_12h rep2


title: Naïve_rep2

library_source: genomic

data_processing:
Fastq reads were aligned with the mm10 reference genome with Bowtie2.
PCR duplicates were removed by samtools.
Peaks were called with MACS2.
Bigwig files for ATAC seq signal visualization on UCSC genome browser was generated by converting MACS2 output read pileup file into bigwig files with bedgraphtobigwig from UCSC tools.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Naïve

extract_protocol:
The nuclear pellet was resuspended into transposition reaction mixture containing Tn5 transposase from Illumina Nextera DNA Sample Prep Kit and incubated at 37 °C for 30 min. Then the transposase-associated DNA was purified using Qiagen MinElute Purification kit.
The DNA was amplified for twelve cycles using KAPA Real-Time Library amplification kit (KAPAbiosystems) with Nextera indexing primers as per Buenrostro et al, 2015. The total amplified DNA was purified using AmPureXP beads.

tag: genotype/variation

value: Naive

value: SMARTA CD4 T cells

tag: molecule subtype

value: Tn5 transposase treated nuclei DNA


title: Naïve_rep3


title: phe_12h rep1


title: Naïve_rep1


title: DKO Tfh-like_rep3 (LCMV)


title: Healthy (C) D1-Rep1


title: pera_12h rep3

description:
Bacteria grown in M9 for 12h, followed by 1:100 dilution in M9 + peracetic acid (9 uM) and growth to mid-exponential.
processed data file: processed_data_file_ecoli_biocides.xlsx

value: peracetic acid


title: DKO Tfh-like_rep2 (LCMV)


title: DKO Tfh-like_rep2

source_name: DKO Tfh-like

value: DKO

tag: cell subtype

value: Tfh-like


title: YCG1 in CDC5-AID 2: YCG1 localization in CDC5-depleted strain replicate 2

city: Berkeley

first: lorenzo

last: costantino

address: 16 Barker Hall # 3202

department: MCB

institute: university of california, berkeley

organism: Saccharomyces cerevisiae

source_name: yeast culture

growth_protocol: cells were grown to early-log phase (OD600 0.1-0.2) at 23°C overnight and arrested in G1 using the pheromone alpha factor at a concentration of 10-8M (Sigma-Aldrich T6901-5MG).  Cells were released from G1 by washing with YPD containing auxin (if indicated) and 0.15mg/mL pronase E (Sigma Aldrich) three times, and once with YPD plus auxin.  After the last wash Cells were resuspended in YPD medium containing auxin and 15 µg/mL nocodazole (Sigma Aldrich). Cultures were then once again incubated at 23°C for 3h.

extract_protocol:
60OD of mid-M cells were collected, fixed for one hour with 1% formaldehyde, quenched with 5mM glycine and processed for ChIP as previously described (Robison and Koshland 2017, with the following modifications). Frozen cell pellets were disrupted 3 times using a FastPrep-24 5G instrument (40 seconds, 6.0m/sec each) (MP Bio, Santa Ana, CA).  Chromatin was sheared 10 x 30s ON/30s OFF with a Bioruptor Pico (Diagenode, Denville, NJ). For ChIP-qPCR, 1/20 of sheared and cleared lysate was reserved as input. Chromatin extracts were incubated with 4uL of the following antibodies monoclonal mouse anti-MYC (Roche), monoclonal mouse anti-FLAG (Sigma Aldrich), polyclonal rabbit anti-Pds5p (Covance Biosciences, Princeton, NJ), or polyclonal rabbit anti-Mcd1p (Covance Biosciences, Princeton, NJ) overnight at 4C. Antibody-bound lysates were incubated with 120uL Protein A dynabeads (Invitrogen, Cat#: 10001D) for 1h.
Following ChIP, the library was prepared using the Accel-NGS 1S Plus DNA Library Kit (Swift Bioscience) following the manufacturer protocol. Libraries were sequenced using Illumina Hiseq 4000. The sequencing files were aligned to the SacCer3 yeast genome using Bowtie2 tool.

treatment_protocol: If indicated, auxin was added to a final concentration of 500µM to deplete AID-tagged proteins after a 2:30h arrest.

value: yeast culture

tag: strain

tag: chip antibody


title: Healthy (C) D1-Rep3

value: feeder roots


title: YCG1 in CDC5-AID 1: YCG1 localization in CDC5-depleted strain replicate 1

data_processing: The sequencing files were aligned to the SacCer3 yeast genome using Bowtie2 tool


title: WT nonTfh_rep1 (KLH)

value: Lymph node


title: DKO Th1-like_rep3 (LCMV)


title: DKO Tfh-like_rep1 (LCMV)


title: YCG1 in MCD1-AID 1: YCG1 localization in MCD1-depleted strain replicate 1


title: YCG1 in MCD1-AID 2: YCG1 localization in MCD1-depleted strain replicate 2


title: DKO Th1-like_rep3

source_name: DKO Th1-like


title: pera_12h rep1


title: DKO Tfh-like_rep1


title: isop_12h rep3

description:
Bacteria grown in M9 for 12h, followed by 1:100 dilution in M9 + isopropanol (2.7% v/v) and growth to mid-exponential.
processed data file: processed_data_file_ecoli_biocides.xlsx

value: isopropanol


title: YCG1 in WT 2: YCG1 localization in Wild Type strain replicate 2


title: DKO Th1-like_rep2 (LCMV)


title: DKO Th1-like_rep2


title: isop_12h rep2


title: CDC5 in MCD1-AID in G2 1: CDC5 localization in MCD1-depleted after G2 arrest strain replicate 1

value: Flag (Sigma Cat#F3165)


title: DKO Tfh-like_rep3


title: isop_12h rep1


title: YCG1 in WT 1: YCG1 localization in Wild Type strain replicate 1


title: Prdm1KO Tfh_rep3

source_name: Prdm1KO Tfh

value: Tfh


title: DKO Th1-like_rep1 (LCMV)


title: h2o2_12h rep3

description:
Bacteria grown in M9 for 12h, followed by 1:100 dilution in M9 + hydrogen peroxide (272 uM) and growth to mid-exponential.
processed data file: processed_data_file_ecoli_biocides.xlsx

value: hydrogen peroxide


title: Prdm1KO Tfh_rep2 (LCMV)

value: Spleen


title: Prdm1KO Tfh_rep1 (LCMV)


title: CDC5 in BRN1-AID 2: CDC5 localization in BRN1-depleted strain replicate 2


title: CDC5 in BRN1-AID 1: CDC5 localization in BRN1-depleted strain replicate 1


title: h2o2_12h rep1


title: Prdm1KO Tfh_rep1


title: Prdm1KO Tfh_rep3 (LCMV)


title: Bcl6KO Th1_rep3 (LCMV)


title: Bcl6KO Th1_rep3

source_name: Bcl6KO Th1


title: DKO Th1-like_rep1


title: Bcl6KO Th1_rep2 (LCMV)


title: gluta_12h rep3

description:
Bacteria grown in M9 for 12h, followed by 1:100 dilution in M9 + glutaraldehyde (29 uM) and growth to mid-exponential.
processed data file: processed_data_file_ecoli_biocides.xlsx

value: glutaraldehyde


title: CDC5 in MCD1-AID 1: CDC5 localization in MCD1-depleted strain replicate 1


title: CDC5 in WT 2: CDC5 localization in Wild Type strain replicate 2


title: pera_12h rep2


title: Bcl6KO Th1_rep1 (LCMV)


title: gluta_12h rep2


title: Bcl6KO Th1_rep2


title: Prdm1KO Tfh_rep2


title: h2o2_12h rep2


title: CDC5 in WT 1: CDC5 localization in Wild Type strain replicate 1


title: gluta_12h rep1


title: WT Tfh_rep3 (LCMV)


title: WT Tfh_rep3

source_name: WT Tfh

value: WT


title: CDC5 in MCD1-AID 2: CDC5 localization in MCD1-depleted strain replicate 2


title: WT Tfh_rep2 (LCMV)


title: WT Tfh_rep2


title: etoh_12h rep2

description:
Bacteria grown in M9 for 12h, followed by 1:100 dilution in M9 + ethanol (2.8% v/v) and growth to mid-exponential.
processed data file: processed_data_file_ecoli_biocides.xlsx

value: ethanol


title: MCD1 in BRN1-AID 1: MCD1 localization in BRN1-depleted strain replicate 1

value: Rabbit polyclonal Anti-Mcd1p V. Guacci (via Covance)


title: WT Tfh_rep1 (LCMV)


title: etoh_12h rep1


title: MCD1 in CDC5-AID 2: MCD1 localization in CDC5-depleted strain replicate 2


title: WT Th1_rep3

source_name: WT Th1

value: SMARTA CD4 T cells


title: benz_12h rep3

description:
Bacteria grown in M9 for 12h, followed by 1:100 dilution in M9 + benzalkonium chloride (3.63 mg/L) and growth to mid-exponential.
processed data file: processed_data_file_ecoli_biocides.xlsx

value: benzalkonium chloride


title: WT Th1_rep3 (LCMV)


title: MCD1 in CDC5-AID 1: MCD1 localization in CDC5-depleted strain replicate 1


title: MCD1 in WT 2: MCD1 localization in Wild Type strain replicate 2


title: Bcl6KO Th1_rep1

value: Tn5 transposase treated nuclei DNA


title: WT Th1_rep1 (LCMV)


title: WT Th1_rep1


title: WT Th1_rep2 (LCMV)


title: benz_12h rep2


title: WT Th1_rep2


title: etoh_12h rep3


title: MCD1 in WT 1: MCD1 localization in Wild Type strain replicate 1


title: Input_PS_Scml2KO_rep2 [5916]

status: Public on May 02 2020

city: Cincinnati

first: Satoshi

last: Namekawa

state: Ohio

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description:
5916
F7494B7A-BE22-7B51-E144-D1CD73534BAB

data_processing:
Data analysis was performed using the BioWardrobe (PMID: 26248465 )
Briefly, reads were mapped using Bowtie and peaks were identified using MACS2
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes identified peaks for each sample

extract_protocol:
Germ  cells were isolated from mouse testis by STA-PUT method or MACS. Cells were fixed in 1% formaldehyde for 10 min at RT. Nuclei were isolated by lysis buffer. Chromatin was sonicated by Covaris sonicater and used for ChIP experiments.
see ChIPmentation (PMID: 26280331)

tag: strain background

value: adult

value: testis

value: Pachyten spermatocytes


title: Input_RS_Scml2KO_rep2 [5920]

description:
5920
h7F0A25F-07F2-9E21-7E17-87A4EB4D494D

value: Round spermatides


title: Input_RS_Scml2KO_rep1 [5919]

description:
5919
BF81221C-DA78-2907-5B6A-6C94455EEA65


title: MCD1 in BRN1-AID 2: MCD1 localization in BRN1-depleted strain replicate 2

value: yeast culture


title: Input_KIT_Scml2KO_rep2 [5912]

description:
5912
HAE35BC9-29B3-4399-CCBB-C041237C08CE

value: c-Kit+ spermatogonia


title: Input_PS_Scml2KO_rep1 [5915]

description:
5915
U7A2D9A3-90DA-AC39-69C0-5900752749F1


title: Input_KIT_Scml2KO_rep1 [5911]

description:
5911
d04A054A-1D8A-2A54-3DFB-D50F635C8799


title: Input_Thy1_Scml2KO_rep2 [5908]

description:
5908
m336ACAA-5598-78BA-1AE6-ED6591808FD0

value: Thy1+ spermatogonia


title: Input_Thy1_Scml2KO_rep1 [5907]

description:
5907
X32CFEB6-B347-9A4B-B190-9F8E35DB61D8


title: Input_RS_WT_rep2 [5918]

description:
5918
l97E4D66-1AB1-20B4-E63F-BFB7EFAFCBF8

value: wild type


title: Input_PS_WT_rep2 [5914]

description:
5914
l9A98DD1-B90B-4F92-DA41-8759A1622BCA


title: Input_RS_WT_rep1 [5917]

description:
5917
S1AC6472-6A55-5BAF-5486-B603FB289A39


title: Input_PS_WT_rep1 [5913]

description:
5913
z205A1B9-C41F-6E54-955F-5F34C34BED82


title: Input_KIT_WT_rep2 [5910]

description:
5910
C4E9C30E-6A1D-68A9-F092-3B437C457DA6


title: Input_KIT_WT_rep1 [5909]

description:
5909
XE1EA657-BD8F-A470-F88B-EB009DF3DCA2


title: Input_Thy1_WT_rep1 [5905]

description:
5905
s1562A72-5D00-FACE-CE67-90E5234080E5


title: Input_Thy1_WT_rep2 [5906]

description:
5906
sEA209DB-DFF3-CE51-64EB-3828C82EAB5C


title: H3K27ac_RS_Scml2KO_rep2 [4319]

description:
4319
CFC327F3-E3F1-FF84-9533-F859DBC721E9


title: H3K27ac_RS_Scml2KO_rep1 [4311]

description:
4311
pDEA0900-8B78-7C71-2301-194598ECE38A


title: H3K27ac_PS_Scml2KO_rep1 [4310]

description:
4310
I05D4274-531F-FB32-0863-468C360E760B


title: H3K27ac_Thy1_WT_rep2 [4312]

description:
4312
wB226859-9DFA-B475-AAA3-FA589E56B126


title: H3K27ac_Thy1_Scml2KO_rep2 [4313]

description:
4313
i235E790-9889-7732-E909-FA9FD5893E8D


title: WT Tfh_rep1

value: Tfh


title: H3K27ac_KIT_WT_rep1 [4299]

description:
4299
pC51D06F-A408-D5B6-EAD8-EDE9308D7E27


title: H3K27ac_PS_Scml2KO_rep2 [4317]

description:
4317
g8ABDFD1-8DC0-8BED-8AEC-4052A9E4211C


title: H3K27ac_KIT_WT_rep2 [4314]

description:
4314
L2E0F294-2F68-DF3D-22DA-2B921C525467


title: H3K27ac_Thy1_WT_rep1 [4298]

description:
4298
sE10070A-B0D3-1A96-709D-41818164737C


title: WT_4

city: Toronto

first: Amy

middle: J

last: Ramsey

state: ON

address: 1 King's College Circle, Room 4302 MSB

department: Pharmacology & Toxicology

country: Canada

institute: University of Toronto

description:
[processed data file:]
Galaxy1171-[Cuffdiff_on_data_492,_data_486,_and_others__gene_differential_expression_testing].tabular
Galaxy1381-[Cuffdiff_on_data_657,_data_525,_and_others__gene_differential_expression_testing].tabular

data_processing:
FASTQ files were checked for quality with FastQC (V 0.65)
FASTQ files were prepared for use on main public Galaxy server (https://usegalaxy.org/) with FASTQ Groomer (V 1.0.4)
Reads were aligned with TopHat (V 2.1.0), using mm10 reference genome and supplied read group (genotype groups) data
Transcripts were assembled with Cufflinks (V 2.2.1.0) for each sample and then combined with Cuffmerge (V 2.2.1.0), using mm10 reference genome and RefSeq reference annotation
Gene expression was quantified and compared with Cuffdiff (V 2.2.1.3), using mm10 reference genome and output from TopHat and Cuffmerge
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tabular files denoting normalized gene expression values were generated for each pair of groups between WT, GluN1, and GluN1Cre mice (due to computational resource constraints); p and q values testing for significance in these comparisons are also in the processed data files. Galaxy1171*txt contains WT vs GluN1 data. Galaxy1250*txt contains GluN1 vs GluN1Cre data. Galaxy1381*txt contains WT vs GluN1Cre data.

source_name: Cortex

extract_protocol:
Mouse brains were flash frozen in isopentane, frontal cortex was isolated and homogenized, followed by total RNA isolation via Tri Reagent. RNA was sent to the Centre for Applied Genomics in Toronto, Canada for poly-A isolation, library generation, amplification, and sequencing.
Protocol according to The Centre for Applied Genomics (TCAG, Toronto, ON, CAN)

treatment_protocol: 6mg oral gavage tamoxifen + ~14mg tamoxifen (chow ad libitum) for two weeks starting at 10 weeks of age

value: C57Bl/6 and 129/SvlmJ F1 Hybrids

value: Cortex

value: 14 Weeks

tag: Sex

value: Male


title: H3K27ac_KIT_Scml2KO_rep1 [4309]

description:
4309
l8971B55-193B-AD84-EB4E-C764BD4875D4


title: H3K27ac_Thy1_Scml2KO_rep1 [4308]

description:
4308
S80A8538-DC9D-3478-0490-683037139273


title: WT_3

value: WT


title: GluN1Cre_2

description:
[processed data file:]
Galaxy1250-[Cuffdiff_on_data_657,_data_525,_and_others__gene_differential_expression_testing].tabular
Galaxy1381-[Cuffdiff_on_data_657,_data_525,_and_others__gene_differential_expression_testing].tabular


title: GluN1Cre_1


title: GluN1Cre_4


title: OVCAR5R3

city: Bethesda

first: Jayakumar

middle: R

last: Nair

state: MD

address: 10 center drive

department: Women malignancies Branch

institute: National Cancer Institute

data_processing:
Samples were pooled and sequenced on HiSeq4000 using Illumina TruSeq Stranded Total RNA Library Prep and paired-end sequencing
CPM-TMM values are presented as a soft text file.
Genome_build: HG38
Supplementary_files_format_and_content: Soft text files were generated using excel.

growth_protocol: Cell lines were routinely cultured in RPMI1640 media with L-glutamine (Life Technologies) containing 10% FBS, 1000 U/ml penicillin/streptomycin, 1 mM sodium pyruvate and 5 µg/ml of insulin from bovine pancreas (Sigma-Aldrich). CHK1i Prex-resistant (PrexR) cell lines OVCAR5R and OVCAR8R were developed from their parental OVCAR5 and OVCAR8 [2] by culturing them in progressively increasing concentrations of Prex up to 3 µM over 3-4 months.  .

extract_protocol: Qiagen total RNA isolation kit

treatment_protocol: PrexR cells were routinely maintained at 2 µM of Prex. Cells were cultured without Prex for at least 4 days until use

value: ovarian cancer cell line

tag: cell line

tag: resistance

value: resistant

tag: replicate


title: OVCAR5R2


title: GluN1_4

description:
[processed data file:]
Galaxy1250-[Cuffdiff_on_data_657,_data_525,_and_others__gene_differential_expression_testing].tabular
Galaxy1171-[Cuffdiff_on_data_492,_data_486,_and_others__gene_differential_expression_testing].tabular

tag: genotype


title: WT_1


title: GluN1_3


title: OVCAR5_WT3

value: Parent


title: GluN1_2


title: GluN1_1


title: OVCAR5_WT2


title: OVCAR5_WT1


title: H3K27ac_KIT_Scml2KO_rep2 [4315]

description:
4315
v4E609BB-B772-E4D1-AA7E-3B49CAC82034


title: Shiv-iOPC-Rd3

city: Cleveland

first: Paul

last: Tesar

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

data_processing:
Output FASTQ files were aligned to the mm9 genome using Tophat (Version 2.0.8) with default settings.
Data was normalized and fragments per kilobase per million reads (FPKM) were calculated for known RefSeq genes using Cufflinks (Version 2.0.2).
Genome_build: mm9
Supplementary_files_format_and_content: Standard cufflinks output (genes.fpkm_tracking)

source_name: Mouse induced Oligodendrocyte Progenitor Cell

extract_protocol:
500,000 cells were pelleted, resuspended in TRIzol, and frozen at -80 degrees Celsius. Total RNA was isolated using the Qiagen Rneasy Mini Kit (ThermoFisher #15596026), beginning with chloroform extraction and separation by PhaseLock gel tubes (5 Prime #2302830).
1ug of each sample was rRNA depleted (Ribo-Zero Gold, Illumina #MRZG12324), fragmented, and indexed using the TruSeq Stranded mRNA Library Preparation Kit (Illumina #RS-122-2103) per the manufacturer’s protocol.

value: Mouse Embryonic Fibroblasts directly repgrogrammed to induced Oligodendrocyte Progenitor Cells (induced with doxycycline)


title: WT_2


title: P37-PostPR13.5

source_name: Tumor biopsies

growth_protocol: Tumor needle biopsies were frozen in OCT compound at -80 Celsius.  Sections were used for total RNA isolation

extract_protocol: Qiagen micro RNA isolation kit

tag: disease status

value: high grade serous ovarian cancer (HGSOC)

tag: day of treatment

tag: response

value: Partial response

tag: response period (months)


title: Shiv-iOPC-Rd2-Dox

source_name: Mouse induced Oligodendrocyte Progenitor Cell (not induced with doxycycline)

tag: cell type

value: Mouse Embryonic Fibroblasts directly repgrogrammed to induced Oligodendrocyte Progenitor Cells (not induced with doxycycline)


title: P35-PostSD8.5

value: Stable disease


title: Shiv-iOPC-Rd1-Dox


title: Shiv-iOPC-Rd2


title: P42-PostSD9.5


title: Shiv-iOPC-Rd1


title: GluN1Cre_3

tag: tissue

tag: age


title: P48-PostPD2

value: Progressive disease


title: P38-PostSD3


title: P23-PostSD4


title: OVCAR5R1


title: Shiv-iOPC-MBP

description: Shiv-iOPC-MBP


title: Shiv-MEF

description: Shiv-MEF

source_name: Mouse Embryonic Fibroblasts

value: Mouse Embryone Fibroblasts derived from Shiverer embryos and depleted with A2B5 microbeads


title: P17-PostPR13


title: P10-PostPD2


title: HEK293T cells, LARP4 siRNA C3

city: Irvine

first: Lei

last: Li

address: University of California, Irvine

institute: University of California, Irvine

data_processing:
Reads were filtered, trimmed, aligned, clustered, and differential expression was analyzed using the exon centric method from the DPAC version 1.4 protocol from Routh, G3, 2019.
Briefly reads were trimmed and quality filtered using fastp, aligned using hisat2, 3 prime ends were clustered using a 20nt window to get PASs, DeSeq2 was used to determine DE of gene expression, exon usage, and PASs usage all using the DPAC pipeline
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph files were generated using bedtools

source_name: HEK 293T cells

growth_protocol: Cells were grown on treated 10cm plates with DMEM 10% FBS

extract_protocol:
Trizol extraction
Libraries were perpared accoring to the poly(A)-ClickSeq protocol by Routh et al., NAR, 2017 which uses an oligo dT primer and azido nucleotides to determine the 3 prime end of the UTR before the poly-A tail is added

treatment_protocol: siRNA was performed using RNAiMax with 60 picomoles of siRNA 12 well plate in triplicate

value: HEK 293T

tag: sirna

value: LARP4 siRNA

tag: sirna sigma number


title: HEK293T cells, LARP4 siRNA C2


title: P7-PostPD2


title: P6-PostSD8


title: HEK293T cells, LARP4 siRNA C1


title: P4-PostPR9


title: HEK293T cells, Control siRNA C2

value: Control siRNA


title: HEK293T cells, Control siRNA C3


title: P1-PostPR9


title: P46-PrePD2


title: HEK293T cells, Control siRNA C1


title: P42-PreSD9.5


title: P41-PreuPR13.5


title: P40-PrePR12.5


title: P37-PrePR13.5


title: P35-PreSD8.5


title: WM115NEG3

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

description:
VC3AI-ve/DAPI-ve/AnnexinV-ve
Replicate 3

data_processing:
Illumina basecalling.
Standard Illumina bioinformatics analysis were used to generate fastq files, followed by quality assessment [MultiQC v1.7 https://multiqc.info/], trimming and demultiplexing.
Rsubread v1.34.6 was used for mapping to the hg38 genome and creating a matrix of RNA-Seq counts
Next, a DGElist object was created with the edgeR package v3.26.7.
After filtering (min.count = 10, min.total.count = 15) and normalization for composition bias, genewise exact tests were computed for differences in the means between groups.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file with normalized rpkm values for each sample

source_name: Melanoma cell line

growth_protocol: Cells were grown in Dulbecco’s Modified Eagle’s Medium supplemented with 10% FCS, 2 mM glutamine , non-essential amino acids , 1 mM sodium pyruvate and penicillin/streptomycin/ampicillin.

extract_protocol:
Total RNA was extracted using the Nucleospin RNA extraction kit (Macherey Nagel, 740955) according to the manufacturer’s instruction. Libraries were prepared from 600 ng total RNA per sample with TruSeq Stranded mRNA kit (Illumina) following the manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols.
RNA sequencing was performed using the NextSeq500 Illumina sequencer in 75 bp paired-end.

treatment_protocol: Cells were treated with doxycycline, ranging in concentration from 1 μg/mL to 10 ng/mL and the expression of tBID was validated by both western blot and immunofluorescence analyses.

tag: strain

value: caspase reporter + inducible tBID


title: WM115NEG1

description:
VC3AI-ve/DAPI-ve/AnnexinV-ve
Replicate 1


title: WM115NEG2

description:
VC3AI-ve/DAPI-ve/AnnexinV-ve
Replicate 2


title: P36-PrePD2


title: EpiSC5-OPC

source_name: Oligodendrocyte Progenitor Cells

value: Epiblast Stem Cell derived Oligodendrocyte Progenitor Cells


title: WM115POS3

description:
VC3AI+ve/DAPI-ve/AnnexinV-ve
Replicate 3


title: P33-PreSD16


title: WM852NEG3


title: WM115POS1

description:
VC3AI+ve/DAPI-ve/AnnexinV-ve
Replicate 1


title: P23-PreSD4


title: WM852NEG2


title: P47-PreSD7.5


title: benz_12h rep1

description:
Bacteria grown in M9 for 12h, followed by 1:100 dilution in M9 + benzalkonium chloride (3.63 mg/L) and growth to mid-exponential.
processed data file: processed_data_file_ecoli_biocides.xlsx

source_name: whole cells

tag: treatment

value: benzalkonium chloride

tag: time


title: WM852NEG1


title: WM852POS2

description:
VC3AI+ve/DAPI-ve/AnnexinV-ve
Replicate 2


title: P17-PrePR13


title: P10-PrePD2


title: P6-PreSD8


title: WM852POS1


title: RNA_Dmoj_brain

city: Leuven

first: Stein

last: Aerts

address: Herestraat 49

department: Center for Human Genetics

country: Belgium

institute: KULeuven

data_processing:
Reads with residual adapter sequences were discarded (FastX cliper version 0.012 option -M15)
Reads were mapped against their own-species genome by  TOPHAT v2.0 (default parameters)
Gene expression counts were computed by HTSeq (str=no) with the following genome annotations (D.melanogaster 5.46, D.simulans 1.4, D.yakuba 1.3, D.ananassae 1.3, D.pseudoobscura 2.30, D.willistoni 1.3, D.mojavensis 1.3 and D.virilis 1.2)
Genome_build: Drosophila melanogaster FB5, D.pseudoobscura FB2 and the rest of species, D.simulans, D.yakuba, D.ananassae, D.willistoni, D.mojavensis and D.virilis FB1
Supplementary_files_format_and_content: RNAseq samples:Gene counts in original species annotation and normalized data across species and tissues in D.melanogaster gene annotation.

organism: Drosophila mojavensis

source_name: brain

growth_protocol: All flies were raised at 25 degrees Celsius on standard fly food

extract_protocol:
RNA was extracted with the RNAqueous micro kit (Ambion)
RNA libraries were generated for sequencing using standard Illumina TruSeq protocols

treatment_protocol: Wandering 3rd instar larvae were dissected in PBS to extract the tissues of interest

tag: developmental time point

value: third instar wandering larvae

value: brain

value: Dmow\wild-type

tag: stock


title: WM115POS2


title: P4-PrePR9


title: P5-PrePD2


title: RNA_Dmoj_wing

source_name: wing imaginal disc

value: wing imaginal disc


title: RNA_Dmoj_EA

source_name: eye-antennal imaginal disc

value: eye-antennal imaginal disc


title: P1-PrePR9

value: high grade serous ovarian cancer (HGSOC)


title: RNA_Dpse_brain

organism: Drosophila pseudoobscura

value: Dpse\wild-type


title: RNA_Dana_brain

organism: Drosophila ananassae


title: RNA_Dpse_wing


title: RNA_Dana_wing


title: S25697_S7

city: Chicago

first: Erica

last: Davis

state: IL

address: 225 E Chicago Avenue

department: Advanced Center for Translational and Genetic Medicine (ACT-GeM)

institute: Ann & Robert H Lurie Children's Hospital of Chicago

data_processing:
The quality of reads, in FASTQ format, was evaluated using FastQC.  Reads were trimmed to remove Illumina adapters from the 3’ ends using cutadapt. Trimmed reads were then aligned to the human genome (hg19) using STAR. Read counts for each gene were calculated using htseq-count in conjunction with a gene annotation file for hg19 obtained from Ensembl (http://useast.ensembl.org/index.html).
Normalization and differential expression were calculated using DESeq2 that employs the Wald test.  The cutoff for determining significantly differentially expressed genes was an FDR-adjusted p-value less than 0.05 using the Benjamini-Hochberg method.
Gene set enrichment analysis was performed to identify gene ontology terms associated with altered gene expression for each comparison.
Isoform expression and analysis was performed using rMATS.
DAVID pathway analysis was run on significant genes (FDR <= 5%) on each of the five alternative splicing event categories as well as the union set of all five lists.
Genome_build: human genome (hg19)
Supplementary_files_format_and_content: The processesd files are in Excel sheet format. The differential expression file includes differential expression values (Log2Fold change) along with statistical significance. The rMATs file contain alternative splicing events analysis across control and FAM50A patients

source_name: Transformed lymphocyte cell line

growth_protocol: We established transformed lymphocyte cell lines (LCLs) derived from cases harboring mutations in FAM50A (K9648, p.Trp206Gly and K9656, p.Glu254Gly) and unaffected male control following standard cell culture protocol. Briefly the cells were grown in RPMI 1640 medium (ThermoFisher Scientific Cat # 11875119), supplemented with 10% heat inactivated fetal bovine serum (ThermoFisher Scientific, Cat # 10082147) and 1% Penicillin-Streptomycin (CCF GIBCO INVITROGEN, Cat # 15140-122).

extract_protocol:
We isolated total RNA from lymphoblast derived from cases harboring mutations in FAM50A (K9648, p.Trp206Gly and K9656, p.Glu254Gly) and unaffected male control following  TRIzol (ThermoFisher) RNA extraction method . Prior to RNAseq all the samples were treated with DNA-free™ DNA Removal Kit (ThermoFisher Scientific) following manufacturer’s guidelines.
The stranded mRNA-seq was conducted in the Northwestern University NUSeq Core Facility. Total RNA samples were checked for quality using Agilent Bioanalyzer 2100, with high RINs in the range of 9.8-10. RNA quantity was determined with Qubit fluorometer. The Illumina TruSeq Stranded mRNA Library Preparation Kit was used to prepare sequencing libraries from 1 ug RNA. The Kit procedure was performed without modifications. This procedure includes mRNA purification and fragmentation, cDNA synthesis, 3’ end adenylation, Illumina adapter ligation, library PCR amplification and validation. lllumina HiSeq 4000 Sequencer was used to sequence the libraries with the production of single-end, 50 bp reads.

tag: sample type

value: Biological replicate 1

tag: clinical presentation

value: Armfield XLID syndrome patient


title: S25697_S9

tag: genotype

value: Biological replicate 3


title: S25697_S8

value: Biological replicate 2


title: RNA_Dpse_EA


title: P31-PrePR7.5

tag: disease status

value: Partial response


title: WM852POS3


title: P14-PrePD2

tag: day of treatment

value: Progressive disease


title: S25595_S4

value: FAM50A p.W206G


title: THF IFNAR-/- SeV-UV rep3

city: Hamilton

first: Karen

last: Mossman

state: Ontario

address: 1280 Main St. West

department: Department of Pathology

institute: McMaster University

data_processing:
Raw sequence data were exported to FASTQ format and were filtered based on quality scores.
Next the reads were mapped to the GRCh38/hg38 reference version using HISAT.
The counts were obtained by using ht-seq count with the “intersection-strict” option.
Counts were transformed with TMM transformation and then normalized with VOOM.
For the preprocessed CSV file - we have used the filterByExpr function in the edgeR package (all default parameters).
Genome_build: hg38
Supplementary_files_format_and_content: Processed data file contains a matrix containing normalized data from all samples.

source_name: fibroblast

growth_protocol: THF cells were cultured in DMEM containing 10% fetal bovine serum in 150cm flasks at 37C 5% CO2 and re-plated every 3-4 days

extract_protocol:
THF cells were pelleted and RNA harvested and purified using an Invitrogen PureLink RNA Mini Kit.
Libraries were generated using an Illumina TruSeq Stranded RNA kit

treatment_protocol: THF cells were seeded to 6-well plates 24 hours before infection for 1 hour in minimal serum-free DMEM containing 0.02 pfu/cell HCMV, 8e-5 HAU/cell SeV, or media alone inactivated with 800uJ/cm^2. Infection media was replaced with complete media and THF cells incubated at 37C for 6 hours.

value: IFNAR-/-

tag: infection

value: Sendai virus

value: fibroblast


title: S25595_S5


title: THF IFNAR-/- SeV-UV rep2


title: S25595_S6


title: DM007_S3

value: FAM50A wild type

value: Healthy control subject


title: THF IFNAR-/- HCMV-UV rep3

value: human cytomegalovirus


title: THF IFNAR-/- HCMV-UV rep2


title: THF IFNAR-/- SeV-UV rep1


title: RNA_Dana_EA

value: third instar wandering larvae


title: DM007_S2


title: THF IFNAR-/- HCMV-UV rep1


title: THF IFNAR-/- mock rep3


title: DM007_S1


title: RNA_Dsim_brain

organism: Drosophila simulans

value: brain


title: THF IFNAR-/- mock rep2


title: THF SeV-UV rep2

value: wildtype


title: RNA_Dsim_wing

value: wing imaginal disc


title: THF SeV-UV rep1


title: THF HCMV-UV rep3


title: THF SeV-UV rep3


title: RNA_Dsim_EA

value: eye-antennal imaginal disc


title: THF HCMV-UV rep2


title: THF HCMV-UV rep1


title: RNA_Dvir_brain

organism: Drosophila virilis

value: Dvir\wild-type


title: Liver_Fast food diet_5 months

city: Pittsburgh

first: George

middle: K

last: Michalopoulos

state: Pennsylvania

address: 411 SBST, 200 Lothrop Street

institute: University of Pittsburgh

description:
C57BL6/J male mice
Gene expression data at 5 months in fast food diet-fed mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Fast food diet-fed mice liver tissue at 5 months

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: For the two months study, 6-8 weeks old male C57BL6/J mice were fed ad libitum (i) chow diet, (ii) fast-food diet [western diet - high saturated fats (21% by weight; 42% kcal from fat), high cholesterol (0.2%) and high carbohydrates (sucrose: 34% by weight)  in diet  (TD.88137, Teklad) - along with high-fructose-glucose solution (d-glucose: 18.9g/L  and d-fructose: 23.1g/L) in drinking water] or (iii) Canertinib (a highly potent and selective EGFR inhibitor/ EGFRi) added in the same fast-food diet for 2-months. Canertinib was administered to mice in diet for estimated dose of 80 mg/kg/day. For the five months study, 6-8 weeks old male C57BL6/J mice were fed ad libitum (i) chow diet, (ii) and (iii) fast-food diet for 5-months. Group (ii) and (iii) were administered vehicle (PBS) and Canertinib (80mg/kg; i.p.), respectively, 5 days/week for the last 5-weeks of 5-months period.

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

treatment_protocol: For the two months study, Canertinib (a highly potent and selective EGFR inhibitor/ EGFRi) was added in the fast-food diet for entire 2-months period. For the five months study, Canertinib (80mg/kg; i.p.) was administered 5 days/week for the last 5-weeks of 5-months period.

tag: gender

value: male


title: THF mock rep2

tag: cell type


title: THF mock rep1


title: THF mock rep3


title: RNA_Dvir_wing

tag: tissue


title: Liver_Chow_5 months

description:
C57BL6/J male mice
Gene expression data at 5 months in Chow-fed mice

source_name: Chow diet-fed mice liver tissue at 5 months