title: ChIP_gw_Smc3_G2_salt_rep1

city: Moscow

first: Arkadiy

last: Golov

address: Vavilova, 34/5

country: Russia

institute: Institute of Gene Biology, RAS

data_processing:
Standard Illumina Sequencing Pipeline
C-TALE Processing: Reads were mapped to the 4 Mb fragment of the genome (hg19, chr21:27,922,688-32,028,897), in which the region of interest was embedded, using Bowtie2 v2.3.5. The data were processed using the hiclib pipeline (https://github.com/mirnylab/hiclib-legacy). Statistics for the C-TALE data processing can be found in the table. 10kb-binned HDF5 files were converted to cool format matrices using cooler v0.8.7. Data from three biological replicates for each experimental condition (control and high salt treated chromatin) were merged in two matrices which were then iteratively normalized using publicly available script (https://github.com/Phlya/C-TALE-Normalization) (“--mult_factor 2” option). Weights in a few poorly covered bins were reduced to NA during the normalization procedure; rhdf5 R package was used to manually replace these NA weights with the values of the highest weight found in each matrix.
ChIP-seq processing: Reads were mapped to the 4 Mb fragment of the genome (hg19, chr21:27,922,688-32,028,897), in which the region of interest (hg19, chr21: 28,981,189-30,260,402) was embedded, using Bowtie2 v2.3.5. Illumina TruSeq adapters were trimmed with cutadapt. Read pairs with at least one non-uniquely mapped read as well as PCR and optical duplicates were filtered using samtools v1.7. Bedtools v2.25.0 and bedGraphToBigWig utility (from UCSC) were used to generate bigwig coverage files. All bigwig files were scaled to 1 mln uniquely mapped read pairs with deeptools v3.4.3. Corresponding input bigwig files were subtracted from each immunoprecipitation bigwig file and then mean profiles were calculated from pairs of biological replicates. Both operations were performed with deeptools v3.4.3.
Genome-wide ChIP-seq processing: Reads were mapped to the hg19 reference human genome using Bowtie2 v2.3.5. Illumina TruSeq adapters were trimmed with cutadapt v1.15. Non-uniquely mapped reads as well as PCR and optical duplicates were filtered using samtools v1.7. RPKM-normalized bigwig files were generated with deeptools v3.4.3.
Genome_build: hg19 (chr21:27,922,688-32,028,897 region)
Supplementary_files_format_and_content: .cool files contain C-TALE contact matrices in an easy to visualize and access format (see https://cooler.readthedocs.io/en/latest/schema.html)
Supplementary_files_format_and_content: bigwig files are binary files containing ChIP-seq profiles in an easy to visualize and access format

source_name: HeLa cells

growth_protocol: Human HeLa cells were cultured in a DMEM medium supplemented with 10% FBS, 100 U/ml penicillin and 100 U/ml streptomycin at 37°C in 5% CO2 in a humidified atmosphere. For G1 synchronization, cells were treated with 2 mM thymidine for 20 hours, washed twice with DPBS, and released into a complete medium. After 6 h, nocodazole (Sigma) was added (100 ng/ml) for 8 h. Mitotic cells were collected by shake-off and centrifugation. Cells were washed twice with DPBS and released into a fresh complete medium.Mitotic cells were seeded in poly-L-lysine-coated dishes. For coating, dish bottoms were covered with 0.1 mg/mL solution of poly-L-lysine (Sigma, P6282) in DPBS and incubated for 1 h at room temperature; after the solution was discarded dishes were rinsed twice with DPBS and dried for 45 min under the hood. G1 cells were harvested for experiments after 5 h of release from mitotic arrest.

extract_protocol:
C-TALE was performed as described previously (Golov AK, Ulianov SV, Luzhin AV, Kalabusheva EP, Kantidze OL, Flyamer IM, Razin SV, Gavrilov AA. C-TALE, a new cost-effective method for targeted enrichment of Hi-C/3C-seq libraries. Methods. 2020 Jan). For ChIP-seq experiments, fixed chromatin pellets were resuspended in 600 uL of ice cold RIPA buffer supplemented with protease inhibitors. Chromatin was sheared on ice with a VirSonic 100 cell disrupter with 10 30-sec pulses on “15” power setting, separated with 3 min periods of recovery. Input DNA was isolated from 1/10 aliquots of sonicated samples. Sheared chromatin from approximately 1 mln of cells and 1 ug of antibodies (against either CTCF, Smc3, or Rad21) were used in each immunoprecipitation reaction. Chromatin immunoprecipitation was performed as described in Abcam X-ChIP manual (https://www.abcam.com/protocols/cross-linking-chromatin-immunoprecipitation-x-chip-protocol) with minor modifications. 25 ul of protein A/G magnetic beads (Thermo Scientific, 26162) was used per reaction instead of agarose beads, thus a magnet was used instead of a centrifuge to reclaim beads. Beads were blocked with 1% BSA solution in RIPA overnight, while chromatin was incubated with antibodies. BSA-blocked beads were mixed with antibody-bound chromatin for 6 h. Immunoprecipitated DNA was separated from beads by overnight treatment with proteinase K (Thermo Scientific, EO0491) in PBS supplemented with 1% SDS at 65C. Solution was then cleared from beads with a magnet and DNA was isolated with standard phenol-chloroform extraction and ethanol precipitation.
Sequencing libraries from 3C-seq material, immunoprecipitated DNA and ChIP inputs were generated as described previously (Golov AK, Ulianov SV, Luzhin AV, Kalabusheva EP, Kantidze OL, Flyamer IM, Razin SV, Gavrilov AA. C-TALE, a new cost-effective method for targeted enrichment of Hi-C/3C-seq libraries. Methods. 2020 Jan).

treatment_protocol: G1 synchronized HeLa cells in 10-cm dishes were washed once with PBS and dishes were cooled on ice for several minutes. 5 mL of ice cold isotonic lysis buffer (10 mM Hepes pH 8.0, 145 mM NaCl, 1.5 mM MgCl2, 1% NP-40, 1x protease inhibitors) were added to each dish, cells were permeabilized for 10 min on ice, then the buffer was removed. 5 mL of either ice cold isotonic buffer (10 mM Hepes pH 8.0, 145 mM NaCl, 1.5 mM MgCl2, 0.5% NP-40, 1x protease inhibitors) or high salt buffer (10 mM Hepes pH 8.0, 500 mM NaCl, 1.5 mM MgCl2, 0.5% NP-40, 1x protease inhibitors) was added to permeabilized cells. Dishes were incubated at 4°C for 30 min. In one series of ChIP-seq experiments incubation time was shortened to 1 min. After the incubation, permeabilized cells  were rinsed three times with 5 mL of ice cold wash buffer (10 mM Hepes pH 8.0, 145 mM NaCl, 1.5 mM MgCl2). Each washing was performed on ice and lasted for 10 min. After the final portion of wash buffer was discarded, chromatin was fixed for 10 min at room temperature with 9 ml of 2% formaldehyde solution in the wash buffer. Fixation was quenched by adding 1 ml of 2 M glycine for 10 min. Fixed chromatin was washed once with PBS and scraped in 7 mL of ice cold Farnham lysis buffer (5 mM Hepes pH 8.0, 85 mM KCl, 0.5% NP-40 ) supplemented with protease inhibitors. Chromatin was collected with centrifugation at 1,000 g for 5 min at 4°C.

value: HeLa

value: cervical carcinoma cells

tag: chip antibody

value: Smc3 (Abcam, ab9263)

value: high salt buffer


title: ChIP_gw_Smc3_G1_salt_rep1

status: Public on Jul 20 2021

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment


title: ChIP_gw_Smc3_G2_control_rep1

value: isotonic buffer


title: ChIP_gw_Smc3_G1_control_rep2


title: ChIP_gw_Smc3_G2_salt_rep2


title: ChIP_gw_Smc3_G2_control_rep2


title: ChIP_gw_Smc3_G1_salt_rep2


title: Nasal associated lymphoid tissue, XCR1+ dendritic cells, replicate 3

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

library_source: transcriptomic

data_processing:
Base calling and quality scoring was performed by Illumina Real-Time Analysis (v2) software. FASTQ file generation and de-multiplexing was performed by bcl2fastq conversion software (v2.15.0.4).
Reads were aligned to the mouse genome by Rsubread version 1.28.0
Read counts were summarized by Entrez Gene ID using the Rsubread's featureCounts function and Rsubread's built-in NCBI annotation.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files (tsv). Columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

molecule: polyA RNA

organism: Mus musculus

source_name: Nasal mucosa

growth_protocol: Dendritic cell populations were recovered from either the nasal associated lymphoid tissue or the cervical lymph node of naïve C57BL/6 mice

extract_protocol:
RNA from sorted NALT and cLN DC subsets was isolated using the microRNeasy Micro Kit (Qiagen) with on column DNase digestion according to manufacturer’s instructions.
First strand cDNA synthesis and cDNA amplification were performed using the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Clontech Laboratories) according to manufacturer’s instructions. Complementary DNA libraries were prepared and indexed separately using the Nextera® XT DNA Library Preparation Kit (Illumina) following manufacturer’s instructions.

treatment_protocol: Cells were FACs sort purified from the cervical lymph node or NALTs  of naïve C57BL/6 mice

tag: tissue

value: Nasal associated lymphoid tissue (NALT)

tag: dendritic cell subset

tag: gender

value: Female


title: Nasal associated lymphoid tissue, CD11b+ dendritic cells, replicate 3


title: Nasal associated lymphoid tissue, XCR1+ dendritic cells, replicate 2


title: Nasal associated lymphoid tissue, XCR1+ dendritic cells, replicate 1


title: ChIP_gw_CTCF_control_rep2

value: CTCF (Active Motif, 61311)


title: ChIP_gw_CTCF_salt_rep2


title: ChIP_gw_CTCF_control_rep1


title: TIG-3 siControl

city: Hiroshima

first: Kimiyoshi

last: Yano

address: Kasumi 1-2-3, Minami-ku

country: Japan

institute: Hiroshima University

data_processing:
Raw sequence reads were trimmed and quality-filtered with Trim Galore! (ver. 0.4.4), Trimmomatic (ver. 0.36), and cutadapt (ver. 1.16) software.
Trimmed reads were mapped to the human reference genome (GRCh38.p10) using STAR (ver. 2.6.1a).
Genome_build: GRCh38
Supplementary_files_format_and_content: BigWig files for each sample

molecule: total RNA

growth_protocol: Cells were cultured in DMEM containing 10% FBS at 37°C 5% CO2.

extract_protocol:
Total RNA was purified using miRNeasy Mini Kit with RNase-free DNase.
RNA sequencing library was prepared using SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian following the manufacturer’s instruction by DNAFORM

treatment_protocol: Cells were reverse-transfected with siControl or siPRPF19 using Lipofectamine RNAiMAX Transfection Reagent (Thermo Fisher Scientific).

value: Normal human diploid fibroblasts

value: siControl


title: Nasal associated lymphoid tissue, CD11b+ dendritic cells, replicate 1


title: TIG-3 siPRPF19


title: Nat_ATAC_13

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

institute: SAHMRI

data_processing:
Reads were aligned to the mm10 mouse genome using Bowtie2.
Peaks were called using Genrich v0.6.
Counts per peak were generated using FeatureCounts v1.53p.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.featureCounts_mm10.txt: FeatureCounts output; Tab-delimited text files with raw peak counts for every peak for each sample.

source_name: Murine Dendritic Cells

extract_protocol:
50,000 cells per sample were lysed in 50µl ATAC-seq lysis buffer containing 0.1% NP-40, 0.1% Tween-20 and 0.001% digitonin (Promega) in 0.5mL tubes and nuclei pelleted via centrifugation. Nuclei were transposed using 2µl Tn5 transposase (Illumina) in 50µl 1x TD buffer for 30 minutes at 37°C.
Transposed DNA samples were purified using DNA Clean and Concentrator 5 columns (Zymo Research) prior to PCR amplification with adaptor-specific primers containing Illumina index sequences. Amplified libraries were cleaned up with DNA Clean and Concentrator 5 columns and libraries were quantified using a 4150 TapeStation system (Agilent) with High Sensitivity D1000 reagents. Following QC, libraries were sequenced on a NextSeq 500 Sequencer (Illumina) using a High-Output Flow Cell. 2x75bp.

value: Dendritic cells

value: DTPw vaccinated


title: Cervical lymph node, XCR1+ dendritic cells, replicate 3

source_name: Upper airway

value: Cervical lymph node (cLN)


title: Cervical lymph node, XCR1+ dendritic cells, replicate 2


title: Cervical lymph node, XCR1+ dendritic cells, replicate 1


title: Cervical lymph node, CD11b+ dendritic cells, replicate 3


title: ChIP_gw_Smc3_G1_control_rep1


title: H3K4me3_ChIP_seq_6

city: Ste Anne-de-Bellevue

first: Romain

last: Lambrot

state: QC

address: 21111 Lakeshore road

department: Animal Science

country: Canada

institute: McGill University

data_processing:
ChIP-seq processing: Raw reads were trimmed from the 3' end to have a phred score of at least 30. Illumina sequencing adapters were removed from the reads. Trimming and clipping were performed using Trimmomatic version 0.36 (Bolger et al., 2014).
Each read was mapped against the Feb. 2009 assembly of the human genome (hg19, GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1) downloaded from UCSC genome browser (Haeussler et al., 2019) using Bowtie 2 version 2.3.4.1 (Langmead and Salzberg, 2012).
We excluded reads that exhibited more than 3 mismatches. SAMtools version 1.9 (Li et al., 2009) was then used to sort and convert SAM files.
Targeted sperm panel MCC-Seq HiSeq reads were aligned using the Genpipes pipeline (Bourgey et al. 2019). Specifically, the MCC-Seq paired-end fastq reads were first trimmed for quality (phred33 >= 30), length (n>50bp) and Illumina adapters using Trimmomatic (version 0.36) (Bolger et al. 2014).
Trimmed reads were aligned, per sequencing lane, to the bisulfite-converted hg19/GRCh37 reference genome using Bismark (version 0.18.1) (Krueger and Andrews 2011) with Bowtie 2 (version 318 2.3.1)(Langmead and Salzberg 2012) in pair-end mode using the non-directional protocol setting and other default parameters. Methylation calls were obtained using Bismark  to record counts of methylated and unmethylated cytosines at each cytosine position in the  genome. A methylation level  of each  CpG was calculated by the number of methylated reads over the total number of sequenced reads. CpG sites with less than 20x read coverage were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-seq, coverage tracks were generated from aligned reads using deepTools2 (Ramirez et al., 2016). The coverage was calculated as the number of reads extended to 150bp fragment size per 25 bp bin and normalized using Reads Per Kilobase per Million mapped reads (RPKM) not located in chromosome X. MCC-seq track files were prepared by converting methylation call files returned by Bismarck into bigwig files.

source_name: human sperm individual 6

extract_protocol:
Semen samples were collected by masturbation after at least 3 days of abstinence. Following semen liquefaction (20-30min at room temperature), an aliquot was used for sperm count and the remaining sample was immediately frozen.
ChIP-seq libraries were prepared using the Kapa HTP Library Preparation Kit (Roche) as per the manufacturer's recommendations except that the size selection was performed after the PCR step. For MCC-seq, bisulfite DNA was quantified with OliGreen® (Life Technology) and amplified with 9–12 PCR cycles using the KAPA® HiFi HotStart Uracil+ DNA Polymerase kit. SeqCap® Epi Enrichment System protocol (Roche NimbleGen®) was used to capture the regions of interest. Equal amounts of multiplexed libraries were combined to obtain 1μg of total input library, which was hybridized to the capture panel at 47°C for 72 h. Washing, recovery, and PCR amplification of the captured libraries, as well as final purification were conducted as recommended by the manufacturer (Roche/KAPA® Biosystems) according to suggested protocols.

value: sperm

value: spermatozoa

value: H3K4me3 (Cell Signaling Technology 9751S)


title: H3K4me3_ChIP_seq_7

source_name: human sperm individual 7


title: ChIP_gw_CTCF_salt_rep1


title: H3K4me3_ChIP_seq_4

source_name: human sperm individual 4


title: H3K4me3_ChIP_seq_2

source_name: human sperm individual 2


title: H3K4me3_ChIP_seq_5

source_name: human sperm individual 5


title: H3K4me3_ChIP_seq_3

source_name: human sperm individual 3


title: Fibroblast_Control5

city: Irvine

first: Timothy

middle: Lamont

last: Downing

state: CA

address: 4151 Engineering Hall

department: Biomedical Engineering

country: USA

institute: University of California Irvine

data_processing:
Raw fastq files were trimmed by 11bp on both 5’ and 3’ ends of both reads 1 and 2 using Trim Galore (Version 0.4.4).
Trimmed reads were aligned to hg19/GRCh37 using Bowtie2 as part of Bismark (Version 0.20.1).
Bismark was used to make methylation calls, which were then merged for neighboring CpGs on opposite sides of the strand.
Methylation ratios generated were filtered to keep only CpGs with a minimum read coverage of >= 5x.
Genome_build: hg19
Supplementary_files_format_and_content: BED file containing CpG methylation levels

source_name: Fibroblast

growth_protocol: Dermal fibroblasts from skin biopsies were cultured in DMEM with 10% FBS as previously described (Zaragoza et al. (2016) PLoS ONE). To generate matched iPSC lines, dermal fibroblasts were reprogrammed using the CytoTune-iPS 2.0 Sendai Reprogramming Kit (Life Technologies, Carlsbad, CA). Once reprogrammed, iPSCs were maintained on Matrigel-coated plates with mTESR1.

extract_protocol:
Genomic DNA was extracted from fibroblasts using the Blood and Cell Culture DNA Mini Kit (Qiagen, Valencia, CA) as previously described (Zaragoza et al. (2016) PLoS ONE). For iPSCs, cells were harvested using ReLeSR, and gDNA was isolated using the MasterPure Complete DNA Purification Kit (Lucigen, Middleton, WI).
RRBS libraries were prepared for sequencing from MspI-digested gDNA using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, Ann Arbor, MI).

tag: disease state

value: Control

value: Fibroblast

tag: Sex

value: Male

tag: age

tag: group

value: Family C


title: Nasal associated lymphoid tissue, CD11b+ dendritic cells, replicate 2


title: Fibroblast_Control4


title: 381_KO_VtB6_pos_Hip

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description:
Raw_Counts.txt
RPKM.txt

data_processing:
Bulk RNA-seq reads were aligned with STAR v2.7.1a to the reference sequence (mm10 from UCSC). Mouse reference was used for gene annotation and counting (gencode M11). Uniquely mapped reads were quantified using HTSeq v0.9.1 suite using protein coding genes by gene.
Genome_build: Mouse mm10
Supplementary_files_format_and_content: Raw_Counts.txt, RPKM.txt

extract_protocol:
mRNA was extracted from the analyzed tissues using a miRNeasy Kit (Qiagen) according to the manufacturer’s instructions. All mRNA samples were examined for quantity and quality by a Bioanalyzer (Agilent).
Total RNAs with an average RIN value of 8.52 ± 0.05 were used for RNA-seq library preparation. mRNA was purified from 2 μg of total RNA by NEXTflex poly(A) beads (Bioo Scientific, 512981), subjected to fragmentation and first and second strand syntheses, and cleaned up by EpiNext beads (EpiGentek, P1063). The second strand DNA was adenylated, ligated, and cleaned up twice by EpiNext beads. cDNA libraries were amplified by PCR and cleaned up twice by EpiNext beads. cDNA library quality was quantified by a 2100 Bioanalyzer using an Agilent high-sensitivity DNA kit (Agilent, 5067-4626). Libraries were sequenced separately as 75-bp single ends on an Illumina NextSeq 500. The sequencing was performed at the McDermott Sequencing Core at UTSW.

tag: experiment

tag: genotype

value: KO

value: Hip

tag: diet

value: VtB6_normal diet

tag: vtb6 (ng/ul)

tag: rin

tag: batch

tag: protocol

value: Protocol 1


title: 339_KO_VtB6_neg_Hip

description:
Raw_Counts.txt
RPKM.txt

value: VtB6_lacking diet


title: Fibroblast_Control3

value: Female

value: Family A


title: Cervical lymph node, CD11b+ dendritic cells, replicate 2


title: 390_KO_VtB6_pos_Hip

description:
Raw_Counts.txt
RPKM.txt


title: 452_KO_VtB6_neg_Hip

description:
Raw_Counts.txt
RPKM.txt


title: H3K4me3_ChIP_seq_1

source_name: human sperm individual 1

tag: chip antibody


title: Fibroblast_Control2

tag: cell type

value: Donor


title: Cervical lymph node, CD11b+ dendritic cells, replicate 1


title: 317_WT_VtB6_pos_Hip

description:
Raw_Counts.txt
RPKM.txt

value: WT


title: Fibroblast_Patient5

value: dilated cardiomyopathy (DCM)


title: 325_KO_VtB6_neg_Hip

description:
Raw_Counts.txt
RPKM.txt


title: 286_WT_VtB6_pos_Hip

description:
Raw_Counts.txt
RPKM.txt


title: Fibroblast_Patient4


title: Fibroblast_Control1


title: 283_WT_VtB6_pos_Hip

description:
Raw_Counts.txt
RPKM.txt


title: 273_WT_VtB6_pos_Hip

description:
Raw_Counts.txt
RPKM.txt


title: 272_WT_VtB6_pos_Hip

description:
Raw_Counts.txt
RPKM.txt


title: Fibroblast_Patient3


title: Fibroblast_Patient2


title: Fibroblast_Patient1


title: 268_KO_VtB6_pos_Hip

description:
Raw_Counts.txt
RPKM.txt


title: iPSC_Patient5

source_name: iPSC

value: iPSC


title: 368_KO_VtB6_pos_Hip

description:
Raw_Counts.txt
RPKM.txt


title: 259_WT_VtB6_neg_Hip

description:
Raw_Counts.txt
RPKM.txt


title: iPSC_Control5


title: 267_KO_VtB6_pos_Hip

description:
Raw_Counts.txt
RPKM.txt


title: 246_WT_VtB6_neg_Hip

description:
Raw_Counts.txt
RPKM.txt


title: iPSC_Control4


title: 244_KO_VtB6_neg_Hip

description:
Raw_Counts.txt
RPKM.txt


title: 242_KO_VtB6_neg_Hip

description:
Raw_Counts.txt
RPKM.txt


title: iPSC_Control3


title: iPSC_Patient4


title: 452_KO_VtB6_neg_Str

description:
Raw_Counts.txt
RPKM.txt

value: Str


title: iPSC_Patient3


title: 390_KO_VtB6_pos_Str

description:
Raw_Counts.txt
RPKM.txt


title: 226_WT_VtB6_neg_Hip

description:
Raw_Counts.txt
RPKM.txt


title: iPSC_Control1


title: iPSC_Patient2


title: 241_WT_VtB6_neg_Hip

description:
Raw_Counts.txt
RPKM.txt


title: iPSC_Patient1


title: Swi6LH_2

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

country: China

institute: Zhejiang University

description: Replicate 2 of library Swi6LH

data_processing:
Illumina Hiseq X Ten used for sequencing
The sequenced tags were filtered to remove low-quality tags, empty tags and tags with a copy number of <2. All the clean tags vectoring the CATG and 49 bp tag fragments were mapped to the sequenced genome of Beauveria bassiana ARSEF2860 with the precision of no more than two nucleotide mismatch.
All mapped genes were quantified in terms of the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) with Cufflinks software.
Genome_build: Beauveria bassiana ARSEF 2860
Supplementary_files_format_and_content: Excel files, including Gene ID, Gene length, FPKM value and gene discription  for each gene.

organism: Beauveria bassiana

growth_protocol: Mycelia of ΔBbSwi6 of Beauveria bassiana were inoculated on the SDA plates (Glucose 4%, Peptone 1%, and Yeast extract 1% plus 1.5% Agar) and in SDB broth (SDA without agar), respectively, and incubated at 25 °C for 3 day.

extract_protocol:
Resultant mycelia of each strain were ground into powder in liquid nitrogen. Total RNA was isolated from mycelial powder using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA).
The double-stranded cDNA were prepared with the Illumina gene expression sample prep kit for Illumina arrays.

treatment_protocol: Resultant mycelia of each strain were harvested from the culture plates.

tag: strain

tag: incubation duration

value: 3 days

value: mycelia


title: 381_KO_VtB6_pos_Str

description:
Raw_Counts.txt
RPKM.txt

tag: tissue


title: 325_KO_VtB6_neg_Str

description:
Raw_Counts.txt
RPKM.txt


title: 368_KO_VtB6_pos_Str

description:
Raw_Counts.txt
RPKM.txt


title: Swi6AH_2

description: Replicate 2 of library Swi6AH


title: Swi6AH_1

description: Replicate 1 of library Swi6AH


title: 286_WT_VtB6_pos_Str

description:
Raw_Counts.txt
RPKM.txt


title: 339_KO_VtB6_neg_Str

description:
Raw_Counts.txt
RPKM.txt


title: Swi6LH_1

description: Replicate 1 of library Swi6LH


title: 317_WT_VtB6_pos_Str

description:
Raw_Counts.txt
RPKM.txt


title: 225_WT_VtB6_neg_Hip

description:
Raw_Counts.txt
RPKM.txt


title: 283_WT_VtB6_pos_Str

description:
Raw_Counts.txt
RPKM.txt


title: iPSC_Control2

value: Control


title: RNA1NonInjCD27 posCD11bneg

city: Marseille

first: Ghislain

last: BIDAUT

address: 27 Bd Leï Roure

department: Bioinformatics

country: France

institute: Centre de Recherche en Cancérologie de Marseille

data_processing:
RNA-seq reads were aligned on reference genome with SubRead 1.6 with removal of multiple-aligned reads.
Gene Counts were computed with featureCount from Subread 1.6 package.
CPM count matrix was calculated with EdgeR under R/Bioconductor.
Genome_build: mm10
Supplementary_files_format_and_content: Count matrix txt file contained TMM EdgeR normalised count provided with EdgeR for every gene and every sample.

source_name: NK Cells

growth_protocol: FLB1 cells are a primary AML cell line syngeneic to C57BL/6 mice. Freshly thawed 50 000 FLB1 cells (CD45.1) were resuspended in PBS and injected intravenously in congenic CD45.2 mice. In all cases, AML development was monitored by flow cytometry analysis of the percentage of CD45.2 or CD45.1 positive cells in the blood. Control (named as not injected) mice consisted of PBS injected mice.

extract_protocol:
BM cells from five mice per group (control or FLB1 injected) were pooled per experiment prior to NK cell sorting, and three independent experiments were performed. NK cells were first sorted using EasySep™ Mouse NK Cell Isolation Kit (STEMCELL Technologies), then with Aria II on the basis of live/CD3-CD19-NK1.1+CD27+CD11b± gating. RNA was isolated from sorted cells using the RNeasy micro plus kit (Qiagen) and mRNA quality was evaluated using an Agilent 2100 (Pico Chip).
Full length cDNA were generated from 4ng of total RNA using Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 10 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, CA) followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris. The libraries were sequenced on Illumina Hiseq 4000 sequencer as Single-Read 50 base reads following Illumina’s instructions. Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14. Adapter dimer reads were removed using DimerRemover

treatment_protocol: FLB1 cells were injected in mice and the percentage of leukemia cells in the blood was monitored by flow cytometry as previously described. Control mice were injected with PBS. Experiment was stopped when the percentage of FLB1 cells in leukemic mice reached 10-20% of total CD45+ cells in the blood. Mice were then sacrificed 24h later.

tag: treatment

value: untreated

value: Rapamycin


title: RNA2InjCD27pos CD11bneg

value: FLB1 Injected


title: RNA1InjCD27pos CD11bneg


title: RNA3NonInjCD27 posCD11bneg


title: RNA3InjCD27pos CD11bneg


title: RNA2NonInjCD27 posCD11bneg


title: 268_KO_VtB6_pos_Str

description:
Raw_Counts.txt
RPKM.txt

value: KO


title: 272_WT_VtB6_pos_Str

description:
Raw_Counts.txt
RPKM.txt

value: VtB6_normal diet


title: 273_WT_VtB6_pos_Str

description:
Raw_Counts.txt
RPKM.txt

value: Protocol 1


title: 246_WT_VtB6_neg_Str

description:
Raw_Counts.txt
RPKM.txt

value: VtB6_lacking diet


title: Ascl1-neuron-17 [MUC9903]

city: Neuherberg

first: Pawel

last: Smialowski

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Zentrum Muenchen

data_processing:
Sequencing reads were mapped to the GRCm38 reference genome using STAR software version 2.6.0a.
TPM expression values based on ENSEMBL annotation version GRCm38.92 were calculated with RSEM (1.3.0).
Supplementary_files_format_and_content: TPM

source_name: spinal cord astrocytes

growth_protocol: Reprogrammed cells were maintained for 3-to-4 weeks in differentiation medium (DMEM/F12, 2% B27, P/S)

extract_protocol:
Single cells were sucked with an electrophysiological tip after being analyzed by ephys
SmartSeq2 + illumina protocols

treatment_protocol: Cells were treated every 3rd day with BDNF, GDNF, cAMP, N2, NT-3

tag: transcription factor

value: neuron


title: Ascl1-neuron-14 [MUC9900]


title: Ascl1-neuron-18 [MUC9904]


title: Ascl1-neuron-15 [MUC9901]


title: Ascl1-neuron-16 [MUC9902]


title: 244_KO_VtB6_neg_Str

description:
Raw_Counts.txt
RPKM.txt


title: 242_KO_VtB6_neg_Str

description:
Raw_Counts.txt
RPKM.txt


title: 259_WT_VtB6_neg_Str

description:
Raw_Counts.txt
RPKM.txt


title: 241_WT_VtB6_neg_Str

description:
Raw_Counts.txt
RPKM.txt


title: Ascl1-neuron-13 [MUC9899]


title: Ascl1-neuron-12 [MUC9898]


title: 226_WT_VtB6_neg_Str

description:
Raw_Counts.txt
RPKM.txt


title: Ascl1-neuron-11 [MUC9891]


title: 225_WT_VtB6_neg_Str

description:
Raw_Counts.txt
RPKM.txt


title: Ascl1-neuron-10 [MUC9890]


title: Ascl1-neuron-9 [MUC9889]


title: 390_KO_VtB6_pos_Pfc

description:
Raw_Counts.txt
RPKM.txt

value: Pfc


title: Ascl1-neuron-8 [MUC9888]


title: 452_KO_VtB6_neg_Pfc

description:
Raw_Counts.txt
RPKM.txt


title: Ascl1-neuron-7 [MUC9887]


title: Ascl1-neuron-5 [MUC9885]


title: 267_KO_VtB6_pos_Str

description:
Raw_Counts.txt
RPKM.txt


title: Ascl1-neuron-6 [MUC9886]


title: 339_KO_VtB6_neg_Pfc

description:
Raw_Counts.txt
RPKM.txt


title: 381_KO_VtB6_pos_Pfc

description:
Raw_Counts.txt
RPKM.txt


title: 325_KO_VtB6_neg_Pfc

description:
Raw_Counts.txt
RPKM.txt


title: Ascl1-neuron-4 [MUC9884]


title: 317_WT_VtB6_pos_Pfc

description:
Raw_Counts.txt
RPKM.txt


title: 368_KO_VtB6_pos_Pfc

description:
Raw_Counts.txt
RPKM.txt


title: Ascl1-neuron-3 [MUC9883]


title: 286_WT_VtB6_pos_Pfc

description:
Raw_Counts.txt
RPKM.txt


title: 283_WT_VtB6_pos_Pfc

description:
Raw_Counts.txt
RPKM.txt


title: Ngn2-neuron-15 [MUC9880]


title: Ascl1-neuron-2 [MUC9882]


title: 272_WT_VtB6_pos_Pfc

description:
Raw_Counts.txt
RPKM.txt


title: Ascl1-neuron-1 [MUC9881]


title: 268_KO_VtB6_pos_Pfc

description:
Raw_Counts.txt
RPKM.txt


title: 273_WT_VtB6_pos_Pfc

description:
Raw_Counts.txt
RPKM.txt


title: 267_KO_VtB6_pos_Pfc

description:
Raw_Counts.txt
RPKM.txt


title: 259_WT_VtB6_neg_Pfc

description:
Raw_Counts.txt
RPKM.txt


title: Ngn2-neuron-13 [MUC9878]


title: 246_WT_VtB6_neg_Pfc

description:
Raw_Counts.txt
RPKM.txt


title: Ngn2-neuron-14 [MUC9879]


title: 244_KO_VtB6_neg_Pfc

description:
Raw_Counts.txt
RPKM.txt


title: Ngn2-neuron-11 [MUC9876]


title: Ngn2-neuron-10 [MUC9875]


title: Ngn2-neuron-9 [MUC9874]


title: Ngn2-neuron-12 [MUC9877]


title: 242_KO_VtB6_neg_Pfc

description:
Raw_Counts.txt
RPKM.txt


title: Ngn2-neuron-8 [MUC9873]


title: 241_WT_VtB6_neg_Pfc

description:
Raw_Counts.txt
RPKM.txt


title: Ngn2-neuron-6 [MUC9871]


title: 226_WT_VtB6_neg_Pfc

description:
Raw_Counts.txt
RPKM.txt


title: Ngn2-neuron-5 [MUC9870]


title: Ngn2-neuron-7 [MUC9872]


title: Ngn2-neuron-4 [MUC9869]


title: Ngn2-neuron-3 [MUC9868]


title: Ngn2-neuron-2 [MUC9867]


title: RNAseq D-OSKM kidney DoxONd14 mCherryplus -1

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

description: 4.TPM (in vivo).xlsx

data_processing:
For RNA-seq analysis, after trimming of adaptor sequences and low-quality bases with cutadapt-1.18, sequenced reads were mapped to the mouse reference genome (mm10) and expression levels were calculated as TPM using RSEM 1.3.1 with STAR (v. 2.6.0c) aligner and the GENCODE version M23 annotation gtf file.
For WGBS and MethylC-seq analyses, bases with low-quality scores and the adapters in all sequenced reads were trimmed with cutadapt-1.18. Trimmed reads were mapped to mouse reference genomes (mm10) using the Bismark software-v0.20.1 with bowtie2 (version 2.3.5). Methylated cytosines were extracted from reads using the Bismark methylation extractor with the following options: --ignore 10 --ignore_r2 10 --ignore_3prime 5 --ignore_3prime_r2 5.
Genome_build: mm10

source_name: Kidney cells

extract_protocol:
RNAeasy plus Mini or Micro Kit (QIAGEN) for RNA and PureLink Genomic DNA mini kit (invitrogen) for genomic DNA.
For RNA-seq library, RNA (in vitro and in vivo samples; 200 ng, FACS-sorted mCherry-positive tumor cells; 50 ng) was prepared for library construction. RNA-seq libraries were generated using the TruSeq Stranded mRNA LT sample prep kit (Illumina) or NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB). The libraries were sequenced on a NextSeq500 (Illumina) as 86 bp single reads. For whole genome bisulfite sequencing library, 500ng of DNA was fragmented by sonication (Covaris) and ligated with methylated adapters using TruSeq™ Nano DNA Library Prep Kit and TruSeq™ ChIP Libary Preparation Kit (Illumina). Subsequently, DNA was bisulfite-treated using EZ DNA Methylation-Gold Kit™ (ZYMO RESEARCH). Final library amplification was performed using Pfu Turbo Cx (Agilent Technologies). For methyl-seq library, 1μg of DNA was fragmented by sonication. Subsequently, library preparation was performed using the SureSelectXT Mouse Methyl-Seq Reagent Kit (Agilent Technologies). DNA was bisulfite-treated using the EZ DNA Methylation-Gold Kit™. The libraries were then sequenced on a Hiseq 2500 (Illumina) in a rapid mode as paired-end reads (Read1:109 bp, Read2:108bp). For ATAC-seq library, cells were lysed with a lysis buffer (10mM Tris-HCl pH7.4, 3mM MgCl2, 10mM NaCl and 0.1% IGEPAL CA-630). Yielded nuclei were suspended in the transposase reaction mix (25 µl of 2X TD Buffer (Illumina), 2.5 µl of TD Enzyme 1 (Illumina), and 22.5 µl of nuclease-free water), and incubated for 30 minutes at 37 ℃. Fragmented DNA was then purified using MinElute PCR purification kit (QIAGEN). After that, fragmented DNA was amplified by PCR to obtain ATAC-seq libraries. The libraries were paired-end sequenced with a length of 50 bp on Hiseq 1500 (Illumina).

value: kidney cells

tag: experimental type

value: in vivo

value: Dox treatment for 14days


title: Ngn2-neuron-1 [MUC9866]


title: Ascl1-astrocyte-5 [MUC9865]

value: astrocyte


title: RNAseq S-OSKM kidney DoxONd14 mCherryplus -1

description: 4.TPM (in vivo).xlsx


title: Ascl1-astrocyte-4 [MUC9863]


title: Ascl1-astrocyte-5 [MUC9864]


title: RNAseq D-OSKM MEF DoxON14d mCherryplus -3

description: 3.TPM (in vitro).xlsx

source_name: MEFs

value: MEFs

value: in vitro


title: RNAseq S-OSKM kidney DoxONd14 mCherryplus -2

description: 4.TPM (in vivo).xlsx


title: Ascl1-astrocyte-3 [MUC9862]


title: RNAseq D-OSKM MEF DoxON14d mCherryplus -2

description: 3.TPM (in vitro).xlsx


title: RNAseq LacZ kidney DoxONd14 mCherryplus

description: 4.TPM (in vivo).xlsx


title: 225_WT_VtB6_neg_Pfc

description:
Raw_Counts.txt
RPKM.txt

value: WT


title: RNAseq D-OSKM MEF DoxON7d mCherryplus -3

description: 3.TPM (in vitro).xlsx

value: Dox treatment for 7days


title: RNAseq D-OSKM kidney DoxONd14 mCherryplus -3

description: 4.TPM (in vivo).xlsx


title: RNAseq D-OSKM MEF DoxON14d mCherryplus -1

description: 3.TPM (in vitro).xlsx


title: E12.5 inv2 posterior proximal forelimb, replicate 2 scRNA-seq

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

description: 10x 3.1 scRNA-seq

data_processing:
Sequencing reads were processed with Cell Ranger 3.1.0 for demultiplexing, barcode processing, and 3' gene counting using a modified gene annotation file (10.5281/zenodo.4456702).
Genome_build: mm10
Supplementary_files_format_and_content: archive containing the output of Cell Ranger (features.tsv.gz, barcodes.tsv.gz, matrix.mtx.gz)

source_name: posterior proximal forelimb

growth_protocol: Crosses were made between heterozygous adults. Animals were checked for vaginal plugs on the next morning, establishing the timepoint 0.5 embryonic days. Embryos were collected 12 days later.

extract_protocol:
Embryos were collected and stored in 1X PBS treated with DEPC and held on ice while genotyping was performed. Embryos with the desired genotype were selected and the posterior portion of each of the forelimbs was isolated for each replicate (1 replicate is the pool of left and right forearm cells). The cells were digested in collagenase and stored in 1X PBS containing 10% FCS and 0.2mM EDTA to prevent cellular aggregation. The cells samples were transferred to the EPFL Gene Expression Core Facility for preparation into 10X GEMs and reverse transcription according to the 10X Chromium 3.1 protocol.
Libraries were constructed with the 10X Chromium 3.1 protocol.

treatment_protocol: No treatment

tag: age

value: posterior proximal forelimb


title: E12.5 inv2 posterior proximal forelimb, replicate 1 scRNA-seq

description: 10x 3.1 scRNA-seq


title: RNAseq D-OSKM kidney DoxONd14 mCherryplus -2

description: 4.TPM (in vivo).xlsx


title: Ascl1-astrocyte-1 [MUC9860]


title: E12.5 wild type distal forelimb, replicate 2 CR_HOXD13

description: CUT&RUN

data_processing:
Library strategy: CUT&RUN
CUT and RUN reads processing was done on the Duboule local Galaxy server (Afgan et al., 2016). Adapters and bad-quality bases were removed with Cutadapt version 1.16 (Martin, 2011). Reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.3.4.1) (Langmead and Salzberg, 2012), (-I 0 -X 1000 –fr –dovetail –very-sensitive).
Reads with mapping quality below 30 or not properly paired were removed from the analysis. PCR duplicates were removed.
The output BAM file was converted to BED using bamtobed bedtools v2.18.2 (Quinlan, 2014).
The coverage was obtained as the output of MACS2 (v2.1.1.20160309) (Zhang et al., 2008) (--format BED --keep-dup all --bdg --nomodel --extsize 200 --shift 100).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig: coverage from macs2
narrowPeak: narrowPeak from macs2

source_name: distal forelimb

extract_protocol:
The forelimbs of embryos were dissected and placed into PBS with 10% FCS and 8ul collagenase at 50mg/ml (Sigma C9697) at 37º for approximately 5min.
DNA isolated from the CUT&RUN protocol were prepared with KAPA HyperPrep reagents (07962347001) with 2.5ul of adaptors at 0.3uM and ligated for 1 hour at 20ºC. The DNA was amplified for fourteen cycles. Post-amplified DNA was cleaned and size selected using 1:1 ration of DNA:Ampure SPRI beads (A63881) followed by an additional 1:1 wash and size selection with HXB. HXB is equal parts 40% PEG8000 (Fisher FIBBP233) and 5M NaCl. The anti-CTCF  antibody is Active Motif 61311, and the anti-HOXD13 antibody is Abcam Ab19866.

value: wild-type

tag: antibody

value: anti-HOXD13 (Abcam Ab19866)

value: distal forelimb


title: RNAseq D-OSKM MEF DoxON7d mCherryplus -1

description: 3.TPM (in vitro).xlsx


title: RNAseq D-OSKM MEF DoxON3d mCherryplus -3

description: 3.TPM (in vitro).xlsx

value: Dox treatment for 3days


title: E12.5 wild type posterior proximal forelimb scRNA-seq

description: 10x 3.1 scRNA-seq

value: wild type


title: RNAseq S-OSKM kidney DoxONd14 mCherryplus -3

description: 4.TPM (in vivo).xlsx


title: RNAseq D-OSKM MEF DoxON3d mCherryplus -2

description: 3.TPM (in vitro).xlsx


title: RNAseq D-OSKM MEF NoDox

description: 3.TPM (in vitro).xlsx

value: Not applicable


title: RNAseq S-OSKM MEF DoxON14d mCherryplus -3

description: 3.TPM (in vitro).xlsx


title: idAG-4-2: dTag13_R2

city: South San Francisco

first: Samuel

last: Pollock

address: 1 DNA way

department: MPL

institute: Genentech

data_processing:
The sequencing libraries were pooled and clustered on 1 lane of a flowcell. After clustering, the  flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to  manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE)  configuration. Image analysis and base calling were conducted by the HiSeq Control Software  (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq  files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for  index sequence identification.
Sequenced reads were mapped to mm10 whole genome with Rsubread v2.4.2 using the 'buildindex' function with parameters 'basename="mm10",reference="./genomes/mm10.fa.gz",gappedIndex=T', followed by the 'align' function with parameters 'index="mm10",readfile1=ff[i],readfile2=rf[i],nthreads = 4'. Following alignment, a .bam file was generated for each paired end run.
Meta-features/genes were counted using the .bam files generated above using the 'featureCounts' function with parameters 'files = bam.files,  annot.inbuilt="mm10", isPairedEnd = T, nthreads = 4, useMetaFeatures = T'.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw counts for every gene (Entrez ID) and sample.

source_name: Colon

growth_protocol: The murine colon adenocarcinoma cell line MC38 stably transfected with an inducible, degradable, Adpgk(R304M) over-expression construct fused to turboGFP (MC38-idAdpgkG) was obtained from the Genentech cell line bank. MC38-idAdpgkG cells were grown in RPMI-1640 supplemented with 10% FBS, 2 mM glutamine, and 25 mM HEPES. Cells were passaged with an 18 h doubling time, at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted from fresh frozen cell pellets using Qiagen RNeasy Plus Universal mini  kit following manufacturer’s instructions (Qiagen, Hilden, Germany). Extracted RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies,  Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent  Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for  Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first  enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First  strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end  repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments,  followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries  were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and  quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative  PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: idAdpgkG MC38 cells were treated with 20 ng/mL mouse IFNg (mIFNg, R&D Systems, Inc.) alone for 51 h prior to harvest (“Control” condition), mIFNg for 48 h followed by 1 µM dTAG-13 addition for 3 h (“dTag” condition), mIFNg and 1 µg/mL doxycycline for 51 h (“Doxycycline” condition), or mIFNg and doxycycline for 48 h followed by dTAG-13 addition for 3 h (“doxycycline+dTag” condition).

value: Colon carcinoma

tag: cell line

value: mouse IFNg + dTag13


title: idAG-4-1: dTag13_R1


title: RNAseq S-OSKM MEF DoxON14d mCherryplus -2

description: 3.TPM (in vitro).xlsx


title: RNAseq D-OSKM MEF DoxON7d mCherryplus -2

description: 3.TPM (in vitro).xlsx


title: Ascl1-astrocyte-2 [MUC9861]


title: idAG-2-3: Doxycycline_R3

value: mouse IFNg + doxycycline


title: idAG-3-1: Doxycycline+dTag13_R1

value: mouse IFNg + doxycycline + dTag13


title: RNAseq S-OSKM MEF DoxON3d mCherryplus -3

description: 3.TPM (in vitro).xlsx


title: RNAseq S-OSKM MEF DoxON7d mCherryplus -3

description: 3.TPM (in vitro).xlsx


title: RNAseq S-OSKM MEF DoxON7d mCherryplus -2

description: 3.TPM (in vitro).xlsx


title: idAG-2-2: Doxycycline_R2


title: RNAseq S-OSKM MEF DoxON7d mCherryplus -1

description: 3.TPM (in vitro).xlsx


title: idAG-2-1: Doxycycline_R1


title: RNAseq S-OSKM MEF DoxON3d mCherryplus -2

description: 3.TPM (in vitro).xlsx


title: idAG-1-2: Control_R2

value: mouse IFNg


title: RNAseq S-OSKM MEF NoDox

description: 3.TPM (in vitro).xlsx


title: idAG-1-3: Control_R3


title: RNAseq D-OSKM MEF DoxON3d mCherryplus -1

description: 3.TPM (in vitro).xlsx


title: idAG-4-3: dTag13_R3


title: RNAseq S-OSKM MEF DoxON3d mCherryplus -1

description: 3.TPM (in vitro).xlsx


title: RNAseq d4c7PGCLCs -2

description: 2.TPM (Kidney tumor).xlsx

source_name: d4c7 PGCLCs (Primordial germ cell-like cells)

value: PGCLC induction for 4 days, followed by in vitro expansion with Forskolin and Rolipram for 7days


title: RNAseq d4c7PGCLCs -1

description: 2.TPM (Kidney tumor).xlsx

value: PGCLCs (Primordial germ cell-like cells)


title: idAG-3-2: Doxycycline+dTag13_R2


title: RNAseq d6PGCLCs -2

description: 2.TPM (Kidney tumor).xlsx

source_name: d6 PGCLCs (Primordial germ cell-like cells)

value: in vitro

value: PGCLC induction for 6 days


title: RNAseq d6PGCLCs -1

description: 2.TPM (Kidney tumor).xlsx


title: RNAseq S-OSKM MEF DoxON14d mCherryplus -1

description: 3.TPM (in vitro).xlsx

value: MEFs

value: Dox treatment for 14days


title: idAG-3-3: Doxycycline+dTag13_R3


title: RNAseq v6.5 ESCs -2

description: 2.TPM (Kidney tumor).xlsx

source_name: ES cells

value: ES cells


title: RNAseq v6.5 ESCs -1

description: 2.TPM (Kidney tumor).xlsx


title: RNAseq D-OSKM kideny tumor DoxON14dplusOFF7d -6

description: 2.TPM (Kidney tumor).xlsx

source_name: Kidney tumors

value: Kidney tumors

value: in vivo

value: Dox treatement for 14days, followed by withdrawal for 7days


title: Negative control 1

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

institute: Burnet Institute

data_processing:
Basecalling was conducted with the Illumina bcl2fastq 2.18.0.12 pipeline
Cleaned sequence reads were mapped to the Homo sapiens genome (Build version HG38) with the Tophat aligner (v2.0.14)
The transcripts were assembled with the Stringtie tool v1.2.4 (http://ccb.jhu.edu/software/stringtie/) utilising the reads alignment with hg38 and reference annotation based assembly option (RABT).
Genome_build: HG38
Supplementary_files_format_and_content: CAGRF13809_cnt.tsv  count matrix

growth_protocol: 143BTK- osteosarcoma cells (ATCC CRL-8303) were cultured in glucose free DMEM media supplemented with 10 mM galactose, 5% (v/v) dialyzed fetal calf serum (dFCS), 50 units/mL penicillin, 50 μg/mL streptomycin, 50 μg/mL uridine and 1x GlutaMAXTM (ThermoFisher Scientific, Waltham, MA, USA) (GAL media) at 37°C/5% CO2. 143BTK- cells were used in accordance with Deakin University Human Research Ethics Committee approval (2019-087).

extract_protocol:
Total RNA was extracted using a mirVana miRNA Isolation Kit (Thermofisher Scientific) according to manufacturer’s instructions.
Transcriptome-wide mRNA sequencing was performed by the Australian Genome Research Facility (Melbourne, Australia) from four independent miRNA transfection experiments (n=4). RNA purity and integrity were confirmed by BioAnalyser (Agilent, CA). Libraries were prepared using the Ribo-zero Gold protocol (Illumina) and assessed by Bioanalyser DNA 1000 chip (Agilent).

treatment_protocol: For miRNA transfections, 80 pmol of the mirVana miRNA mimic Negative Control #1 (miR-NEG, 4464058, ThermoFisher Scientific) or the mirVana miRNA mimic hsa-miR-101-3p (miR-101, 4464066, ID MC11414, ThermoFisher Scientific) were diluted in 150 μL of glucose free DMEM and incubated for 5 min at room temperature. 16 μL of Lipofectamine RNAiMAX Transfection Reagent (ThermoFisher Scientific) was diluted in 150 μL of glucose free DMEM, then combined with the miRNA mix and incubated for 30 min at room temperature. This transfection mix was then combined with 6 mL of GAL media (without pen/strep), added to 1.7 x 106 143BTK- cells in a 10 cm dish (approximately 60% confluent) and incubated at 37°C/5% CO2 (t=0 h). After 24 h the transfection mix was removed and replaced with GAL media for 24 h. At t=48 h, the GAL media was removed and a second transfection (using the same protocol) was performed, although this time the transfection mix was left on the cells for 48 h. At t=96 h, the second transfection mix was removed and replaced with GAL media for 24 h. At t=120 h the cells were harvested for analysis.

tag: miRNA transfection

value: scrambled negative control


title: idAG-1-1: Control_R1


title: RNAseq D-OSKM kideny tumor DoxON14dplusOFF7d -5

description: 2.TPM (Kidney tumor).xlsx


title: Negative control 3

source_name: 143BTK- osteosarcoma cells (ATCC CRL-8303)


title: Negative control 2


title: RNAseq D-OSKM kideny tumor DoxON14dplusOFF7d -4

description: 2.TPM (Kidney tumor).xlsx


title: MiRNA-101 overexpression 4


title: MiRNA-101 overexpression 3


title: MiRNA-101 overexpression 2


title: RNAseq D-OSKM kideny tumor DoxON14dplusOFF7d -2

description: 2.TPM (Kidney tumor).xlsx


title: Negative control 4


title: RNAseq D-OSKM kideny tumor DoxON14dplusOFF7d -3

description: 2.TPM (Kidney tumor).xlsx


title: RNAseq D-OSKM kideny tumor DoxON14dplusOFF7d -1

description: 2.TPM (Kidney tumor).xlsx


title: RNAseq S-OSKM kideny tumor DoxON14dplusOFF7d -3

description: 2.TPM (Kidney tumor).xlsx


title: MiRNA-101 overexpression 1


title: RNAseq S-OSKM kideny tumor DoxON14dplusOFF7d -2

description: 2.TPM (Kidney tumor).xlsx


title: RNAseq S-OSKM kideny tumor DoxON14dplusOFF7d -1

description: 2.TPM (Kidney tumor).xlsx


title: Senescent TIG-3

type: RNA

hyb_protocol: RNA samples were hybridized onto 3D-Gene human oligo chip 25k V2.1.

scan_protocol: Oligo chips were scanned by a 3D-Gene scanner.

data_processing: The raw signal intensity was subtracted with the background mean and normalized to the value in which the median intensity was 25.

source_name: TIG-3 77 PDL

label_protocol: RNA samples were labelled with Cy5 using Amersham Cy5 Mono-Reactive Dye.

extract_protocol: Total RNAs were purified using ISOGEN II.

value: Normal human diploid fibroblasts

value: Senescent


title: RNAseq S-OSKM kideny tumor DoxON7dplusOFF7d -3

description: 2.TPM (Kidney tumor).xlsx

value: Dox treatement for 7days, followed by withdrawal for 7days


title: Young TIG-3

source_name: TIG-3 41 PDL

value: Young


title: RNAseq S-OSKM kideny tumor DoxON7dplusOFF7d -2

description: 2.TPM (Kidney tumor).xlsx


title: RNAseq S-OSKM kideny tumor DoxON7dplusOFF7d -1

description: 2.TPM (Kidney tumor).xlsx


title: IPF_S2_ATAC-seq

city: Houston

first: Lisha

last: Zhu

address: 7000 fannin st

institute: UT Health Science Center at Houston

description: IPF sample 2

data_processing:
ATAC-Seq reads were aligned to the human genome hg38 using bowtie2 with default parameters. All mapped reads were offset by +4 bp for the + strand and -5 bp for the – strand.
peaks were called using MACS2 with following parameters “-q 0.05 -B --nomodel --shift 37 --extsize 73 --broad --keep-dup all”
Genome_build: Homo sapiens hg38
Supplementary_files_format_and_content: BROADPEAK file reports peaks with FDR q <0.05

source_name: ID no: 121

growth_protocol: Fibroblasts were cultured in DMEM containing 10% FBS (Sigma-Aldrich), penicillin/streptomycin (Sigma-Aldrich), plasmocin (Invivogen) and amphotericin B (Sigma-Aldrich). Passage 3 and 4 were used for all subsequent analysis.

extract_protocol: genomic DNA extraction

treatment_protocol: Primary human lung fibroblasts were isolated directly from the upper half of the upper lobe close to apical regions from human lungs

value: fibroblasts

tag: disease state

value: Idiopathic Pulmonary Fibrosis (IPF)


title: Healthy_S1_ATAC-seq

description: Healthy sample 1

value: Healthy


title: Healthy_S2_ATAC-seq

description: Healthy sample 2


title: Healthy_S4_ATAC-seq

description: Healthy sample 4


title: IPF_S3_ATAC-seq

description: IPF sample 3

source_name: ID no. 127


title: IPF_S1_ATAC-seq

description: IPF sample 1

source_name: ID no: 120


title: Organoid, AMC-17CT-147

city: Seoul

first: Chang Ohk

last: Sung

address: Song-Pa gu,Pung-nap dong

department: Pathology

country: South Korea

institute: Asan Medical Center

description: gene expression

data_processing:
Sequenced reads were removed low quality and adapter sequence before analysis. Then th raw RNA-seq data were analyzed using TCGA RNAseq RSEMv2 pipeline.
Mapping by MapSplice v2.2.1 and gene expression estimation after filtering by RSEM v1.3.0, and fixed upper quartile normaliztion for gene expression.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file include column head with sample name, and row name with gene symbol, and upper quartile normalized log2 values for each sample.

source_name: colorectal cancer

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen).
cDNA library was constructed using the TruSeq RNA Access Library Prep Kit (Illumina)

treatment_protocol: Fresh tissue

tag: cancer site

value: Large intestine

value: Colorectal cancer organoids (CCOs)


title: Organoid, AMC-17CT-051

description: gene expression


title: Organoid, AMC-17CT-093

description: gene expression


title: Organoid, AMC-17CT-146

description: gene expression


title: RNAseq Normal kindey -1

description: 2.TPM (Kidney tumor).xlsx

source_name: Kidney tissues

value: Kidney tissues

value: Not applicable


title: RNAseq D-iPSCs-2-1 Passage25

description: 1.TPM (D-OSKM iPSCs).xlsx

source_name: iPS cells (Passage25)

value: iPS cells

value: in vitro


title: Organoid, AMC-17CT-065

description: gene expression


title: Organoid, AMC-17CT-063

description: gene expression


title: RNAseq D-iPSCs-3-1 Passage4

description: 1.TPM (D-OSKM iPSCs).xlsx

source_name: iPS cells (Passage4)


title: RNAseq D-iPSCs-3-3 Passage4

description: 1.TPM (D-OSKM iPSCs).xlsx


title: Organoid, AMC-17CT-039

description: gene expression


title: RNAseq S-iPSCs-3-1 Passage4

description: 1.TPM (D-OSKM iPSCs).xlsx


title: RNAseq D-iPSCs-2-1 Passage4

description: 1.TPM (D-OSKM iPSCs).xlsx


title: RNAseq S-iPSCs-2-1 Passage4

description: 1.TPM (D-OSKM iPSCs).xlsx


title: Organoid, AMC-17CT-078

description: gene expression


title: RNAseq S-iPSCs-1-1 Passage4

description: 1.TPM (D-OSKM iPSCs).xlsx


title: Organoid, AMC-17CT-031

description: gene expression


title: Organoid, AMC-17CT-044

description: gene expression


title: RNAseq KH2 LacZ ESCs

description: 1.TPM (D-OSKM iPSCs).xlsx

value: ES cells


title: Organoid, AMC-17CT-043

description: gene expression


title: Organoid, AMC-17CT-091

description: gene expression


title: Organoid, AMC-17CT-125

description: gene expression


title: Organoid, AMC-17CT-033

description: gene expression


title: RNAseq Normal kindey -3

description: 2.TPM (Kidney tumor).xlsx

value: in vivo


title: RNAseq Normal kindey -2

description: 2.TPM (Kidney tumor).xlsx


title: Organoid, AMC-17CT-049

description: gene expression


title: Organoid, AMC-17CT-059

description: gene expression


title: Organoid, AMC-17CT-058

description: gene expression


title: PON2-KO-R3

city: Mainz

first: Piyush

last: More

address: Langenbeckstrasse 1

department: Department of Pharmacology

institute: University Medical Center, Johannes Gutenberg University of Mainz

description: processed data file: PON2_KO_vs_CTR_DEG_DESeq2.xls

data_processing:
Quality of raw sequencing reads was checked using FastQC version 0.11.5 (Babraham Bioinformatics, Cambridge, UK).
Adaptors were trimmed using Trimmomatic version 0.36 (Bolger AM et al., Bioinformatics, 2014, 30(15):2114-2120).
RNA-Seq reads were aligned to the GRCm38 genome (gencode release M12 GRCm38.p5) using STAR aligner version 2.5.3a (Dobin A et al., Bioinformatics, 2013, 29(1):15-21) with the option "--quantMode GeneCounts".
Differential gene expression analysis was performed using DESeq2 version 1.18.1 (Love MI et al., Genome Biology, 2014, 15(12):550).
Genome_build: GRCm38
Supplementary_files_format_and_content: *ReadsPerGene.out.txt: Tab-delimited text files include mapped gene counts for each sample; STAR gene counts output.
Supplementary_files_format_and_content: PON2_KO_vs_CTR_DEG_DESeq2.xls: Excel file includes DESeq2 differential gene expression analysis (Pon2-/- vs. WT mice) using edgeR.

source_name: Bone marrow

growth_protocol: Wildtype (WT) C57BL/6J (obtained from Charles River) as well as Pon2-/- mice were housed in the translational animal research center of the JGU Mainz. All strains had access to water and standard chow diet at libitum. Experimental mice were 10-14 weeks old. The animals were sacrificed by i.p. injection of 2% pentobarbital (0.4 ml/25 g body weight). Studies were approved by the Ethical Committee and Landesuntersuchungsamt Rheinland-Pfalz (# 23177-07/G13-1-055).

extract_protocol:
LT-HSCs (Lin-, Sca1+, ckit+, CD135-, CD150+) were isolated from BM of young WT- or Pon2-/--mice (n=6 each) by FACS. 10 LT-HSCs per well and a total of 8 wells per mouse were FACS sorted into a 96 well plate (8 RNA-Seq per mouse and 48 RNA-Seq per genotype) containing lysis buffer.
The library was prepared using Smart-seq2-protocol and NextSeq® 500/550 High Output Kit v2 was used for sequencing.

treatment_protocol: Pon2-/- mice were originally generated by insertion of a loxP-site flanked, β-geo-containing gene trap vector into Pon2 intron-2.

tag: strain/background

tag: genotype/variation

value: young (10-14 weeks)

value: LT-HSCs


title: PON2-KO-R4


title: PON2-KO-R5


title: PON2-KO-R6


title: PON2-KO-R2


title: Organoid, AMC-17CT-012

description: gene expression


title: PON2-KO-R1


title: Organoid, AMC-17CT-106

description: gene expression


title: Organoid, AMC-17CT-062

description: gene expression


title: PON2-CTR-R3

value: wild type


title: Organoid, AMC-17CT-083

description: gene expression


title: Organoid, AMC-17CT-018

description: gene expression


title: PON2-CTR-R5


title: Organoid, AMC-17CT-113

description: gene expression


title: PON2-CTR-R4


title: Organoid, AMC-17CT-072

description: gene expression


title: PON2-CTR-R2


title: Organoid, AMC-17CT-086

description: gene expression


title: Organoid, AMC-17CT-131

description: gene expression


title: Organoid, AMC-17CT-085

description: gene expression


title: PON2-CTR-R1


title: Organoid, AMC-17CT-046

description: gene expression


title: Organoid, AMC-17CT-055

description: gene expression


title: PON2-CTR-R6


title: Organoid, AMC-17CT-009

description: gene expression


title: Organoid, AMC-17CT-080

description: gene expression


title: LELab_ChIP_seq_TLS3080_anti_GFP_replicate2

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

data_processing:
For analysis of ChIP-seq data, Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command:bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. For analysis of E. coli ChIP-seq data, reference genomes were first reconstructed in silico by inserting the nucleotide sequence of C. crescentus parS 3 and 4 and apramycin antibiotic resistance cassette acc(3)IV to the ygcE locus of E. coli MG1655 genome. Afterwards, Hiseq 2500 Illumina short reads were mapped back to these reconstructed reference genomes using Bowtie 1. Sequence coverage at each nucleotide position was also computed using BEDTools. Finally, ChIP-seq profiles were plotted with the x-axis representing genomic positions and the y-axis is the number of reads per base pair per million mapped reads (RPBPM) using custom R scripts.
Genome_build: NC_011916.1
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Files ending with _coverage.txt: tab-delimited text file of nucleotide-resolution coverage from ChIP-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

organism: Escherichia coli

source_name: Escherichia coli AB1157

growth_protocol: Cultures of Caulobacter (TLS3050 and TLS3059) were grown at 30oC in PYE and supplemented with antibiotics, as necessary, at appropriate concentrations. To deplete wild-type non-tagged ParB, exponential-phase cells were washed off xylose and re-introduced to PYE+0.2% glucose for an additional 5 hours. After 4 hours, vanillate was added to induce the expression of flag-parB (WT) or flag-parB (E102A) for an hour. After an hour, formadehyde (1% final concentration) were added to fix cells for ChIP-seq.  Cultures of Escherichia coli (TLS3079-3080) were grown at 30oC in LB and supplemented with antibiotics, as necessary, at appropriate concentrations. No IPTG was added. CFP-ParB (WT/E102A) were expressed via the leaky Plac promoter on a medium-copy-number plasmid. When the cultures reached mid-exponential phase, formadehyde (1% final concentration) were added to fix cells for ChIP-seq.

extract_protocol:
DNA was isolated using the Qiagen Cell Lysis and Protein Precipitation solutions. Detailed protocols are listed in the Supplementary Materials
Standard library construction for Illumina Hiseq2500 sequencing platform

treatment_protocol: CFP-ParB (E102A) were produced via the leaky expression of Plac (no IPTG was included). When the culture reached exponential phase, formadehyde were added to 1% (final concentraation) to fix cells for ChIP-seq.

tag: developmental stage

value: mixed population, exponential phase

tag: genotype

value: AB1157 ygcE::parS3+4 acc(3)IV pKTN25::cfp-parB(E102A)

value: anti-GFP


title: LELab_ChIP_seq_TLS3080_anti_GFP_replicate1


title: LELab_ChIP_seq_TLS3079_anti_GFP_replicate2

treatment_protocol: CFP-ParB (WT) were produced via the leaky expression of Plac (no IPTG was included). When the culture reached exponential phase, formadehyde were added to 1% (final concentraation) to fix cells for ChIP-seq.

value: AB1157 ygcE::parS3+4 acc(3)IV pKTN25::cfp-parB(WT)


title: Organoid, AMC-17CT-109

description: gene expression


title: Organoid, AMC-17CT-108

description: gene expression


title: MBP1LH_R1

description: Replicate 1 of library MBP1LH

data_processing:
Illumina Hiseq X Ten used for sequencing
The sequenced tags were filtered to remove low-quality tags, empty tags and tags with a copy number of <2. All the clean tags vectoring the CATG and 49 bp tag fragments were mapped to the sequenced genome of Beauveria bassiana ARSEF2860 with the precision of no more than two nucleotide mismatch.
All mapped genes were quantified in terms of the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) with Cufflinks software.
Screening of differentially expressed genes in paired library of WT/∆BbMbp1. FDR (False Discovery Rate) is a method to determine the threshold of P-value in multiple tests (Benjamini, Y. and Yekutieli D. The Annals of Statistics. 2001, 29: 1165-1188).
Genome_build: Beauveria bassiana ARSEF 2860
Supplementary_files_format_and_content: Excel files, including Gene ID, mean FPKM values, log2(fold change), FDR-value and gene discription  for the paired sample.

organism: Beauveria bassiana ARSEF 2860

growth_protocol: Conidia suspension (100 ul,5X10^6 conidia ml-1) of WT and ΔBbMbp1 of Beauveria bassiana were inoculated on the SDA plates (Glucose 4%, Peptone 1%, and Yeast extract 1% plus 1.5% Agar) and in SDB broth (SDA without agar), respectively, and incubated at 25 °C for 3 day.

tag: strain background

tag: culture condition

value: SDB broth (SDA without agar); incubated at 25 °C for 3 day.

value: mycelia


title: Organoid, AMC-17CT-068

description: gene expression

value: Large intestine


title: LELab_ChIP_seq_TLS3079_anti_GFP_replicate1


title: Organoid, AMC-17CT-082

description: gene expression

value: Colorectal cancer organoids (CCOs)


title: WTLH_R2

description: Replicate 2 of library WTLH

value: WT


title: TBI_24h _Rep3_Lib2

city: Philadelphia

first: Nancy

middle: M

last: Bonini

address: 433 South University Ave

institute: University of Pennsylvania

description: Severe TBI injured males, 24 h post-injury, biological replicate 3

data_processing:
demultiplexed fastq files were obtained from Illumina's BaseSpace and quality checked with fastqc/multiqc
sequenced reads were were mapped to the fly genome (FlyBase d. mel build 6.17) using HISAT2 with parameter --rna-strandness R; index reference was created using hisat2-build
aligned reads were converted to  bam files sorted by aligned position
sample bam files were merged across sequencing runs using Picard
Htseq-count was used to generate unnormalized read count table (with parameters: htseq-count --format bam --order pos --mode union --stranded reverse --minaqual 1 --type exon --idattr gene_id --nonunique=none) for differential expression analysis with DESeq2
Genome_build: Flybase dmel r6.17
Supplementary_files_format_and_content: matrix table (.csv) with raw gene counts for every gene (FlyBase gene ID) and every sample

organism: Drosophila melanogaster

source_name: whole heads

growth_protocol: reared at 25C; 12 hour light-dark cycle; standard medium

extract_protocol:
whole flies were flash frozen in liquod nitrogen; heads (n=20/sample) were dissociated by vortexing then collected. Total RNA was extracted by TRIzol/chloroform.
sample libraries were prepared in two batches (separate days) using the same Illumina TruSeq Stranderd Sample Kit (Cat# RS-122-2103)
RNA-seq; sequenced on Illumina NextSeq using NextSeq® 500/550 High Output Kit v2 (75 cycles; FC-404-2005)

treatment_protocol: 3d old male flies were subjected to sham or severe dTBI injury. control animals are 3d old males.

tag: strain

value: w[1118]; Bloomington stock 5905

tag: post-injury timepoint

tag: condition

value: TBI

tag: library

value: library 2

value: whole heads


title: Lung adenocarcinoma patients-6's adjacent non-tumor tissues (Sup)

city: Shanghai

first: Ping

last: Ji

address: 389 Xincun Road

department: Laboratory Medicine

institute: Shanghai Tongji Hospital, Tongji University School of Medicine

description:
6-B.txt
Lung adenocarcinoma patients-6's adjacent non-tumor tissues

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystar Human m6A-mRNA & lncRNA Epitranscriptomic microarray(8×60K,Arraystar) at 65℃ for 17 hours in an Aglient Hybridization Oven.

scan_protocol: The arrays were scanned in two-color channels by an Agilent Scanner G2505C.

data_processing:
Data was extracted using Agilent Feature Extraction software. The probe signals passing P or M QC flags in at least 6 samples were retained for futher analysis.
“m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. “expression level” was calculated based on the total of IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities of RNA.

source_name: Sup_The m6A unmodified RNAs were recovered from the supernatant

label_protocol: IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.

growth_protocol: A total of six pairs of LUAD tissuesand paired adjacent non-tumor tissues were collected from the Department of Otorhinolaryngology at the Shanghai Tongji Hospital.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

tag: gender

value: male


title: MBP1LH_R2

description: Replicate 2 of library MBP1LH

tag: tissue


title: WTLH_R1

description: Replicate 1 of library WTLH


title: TBI_24h _Rep2_Lib2

description: Severe TBI injured males, 24 h post-injury, biological replicate 2


title: Lung adenocarcinoma patients-2's adjacent non-tumor tissues (Sup)

description:
2-B.txt
Lung adenocarcinoma patients-2's adjacent non-tumor tissues

tag: age


title: Peripheral Blood #4

city: Fukuoka

first: Hikaru

last: Kanemasa

state: Fukuoka

address: Maidashi, 3-1-1

department: Department of pediatric

institute: Kyushu university

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay human array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The raw data were normalized with SST-RMA algorithm (gene level) using Affymetrix Expression Console 1.4.1 software.

label: biotin

source_name: CD71 + erythroid cell derived from peripheral blood

label_protocol: The cRNA was amplified, labeled using GeneChip WT Pico Reagent Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

tag: diagnosis

value: systemic-onset juvenile idiopathic arthritis

value: peripheral blood

tag: cell type

value: erythroid cell

tag: cell marker


title: Lung adenocarcinoma patient-4's tumor tissues (Sup)

description:
4-A.txt
Lung adenocarcinoma patient-4's tumor tissues


title: Lung adenocarcinoma patients-5's adjacent non-tumor tissues (Sup)

description:
5-B.txt
Lung adenocarcinoma patients-5's adjacent non-tumor tissues


title: Cord Blood #2

source_name: CD71 +  erythroid cell derived from cord blood

value: healthy

value: cord blood


title: Cord Blood #1


title: Organoid, AMC-17CT-036

description: gene expression

tag: cancer site


title: Lung adenocarcinoma patients-4's adjacent non-tumor tissues (Sup)

description:
4-B.txt
Lung adenocarcinoma patients-4's adjacent non-tumor tissues


title: Lung adenocarcinoma patients-1's adjacent non-tumor tissues (Sup)

description:
1-B.txt
Lung adenocarcinoma patients-1's adjacent non-tumor tissues

value: female


title: TBI_24h _Rep1_Lib2

description: Severe TBI injured males, 24 h post-injury, biological replicate 1


title: Peripheral Blood #3


title: Lung adenocarcinoma patients-3's adjacent non-tumor tissues (Sup)

description:
3-B.txt
Lung adenocarcinoma patients-3's adjacent non-tumor tissues


title: sham_24h _Rep3_Lib2

description: Sham injured males, 24 h post-injury, biological replicate 3

value: sham


title: Organoid, AMC-17CT-069

description: gene expression


title: Organoid, AMC-17CT-088

description: gene expression


title: WTAH_R2

description: Replicate 2 of library WTAH

value: SDA plates; incubated at 25 °C for 3 day.


title: Lung adenocarcinoma patient-6's tumor tissues (Sup)

description:
6-A.txt
Lung adenocarcinoma patient-6's tumor tissues


title: Lung adenocarcinoma patient-3's tumor tissues (Sup)

description:
3-A.txt
Lung adenocarcinoma patient-3's tumor tissues


title: Lung adenocarcinoma patient-5's tumor tissues (Sup)

description:
5-A.txt
Lung adenocarcinoma patient-5's tumor tissues


title: Peripheral Blood #1


title: Organoid, AMC-17CT-096

description: gene expression


title: Peripheral Blood #2


title: MBP1AH_R1

description: Replicate 1 of library MBP1AH

value: mycelia


title: MBP1AH_R2

description: Replicate 2 of library MBP1AH


title: WTAH_R1

description: Replicate 1 of library WTAH


title: Organoid, AMC-17CT-054

description: gene expression

value: Large intestine


title: Lung adenocarcinoma patients-5's adjacent non-tumor tissues (IP)

source_name: IP_The modified RNAs were eluted from the m6A immunoprecipitated magnetic beads


title: Lung adenocarcinoma patients-6's adjacent non-tumor tissues (IP)


title: sham_24h _Rep2_Lib2

description: Sham injured males, 24 h post-injury, biological replicate 2


title: Organoid, AMC-17CT-004

description: gene expression

value: Colorectal cancer organoids (CCOs)


title: Lung adenocarcinoma patient-1's tumor tissues (Sup)

description:
1-A.txt
Lung adenocarcinoma patient-1's tumor tissues


title: siccna1_rep3

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

institute: INSERM-UGA

data_processing:
The sequenced reads were aligned from raw sequence fastq data using STAR v2.5.2b software on UCSC hg38 reference genome.
The aligned reads were normalized using the R bioconductor package DEseq2 (http://bioconductor.org/packages/3.12/bioc/html/DESeq2.html) and then pseudo log2 tranformed using the following formula: log2(norm_count + 1).
Genome_build: hg38
Supplementary_files_format_and_content: counts

source_name: FaDu cells (OSCC cell line ATCC)

growth_protocol: FaDu cell line (ATCC- HTB-43) were subcultured in EMEM complete medium.

extract_protocol:
RNA extractions were performed from control and CCNA1 knock down FaDu cells in independent triplicates for each condition. RNA was extracted from each sample directly after cell harvesting with TRIZOL, following the manufacturer’s protocol (AMBION). RNA pellets were dissolved in RNAse-free water, and then cleaned up on QIAGEN columns using the RNA Clean Up protocol of RNeasy Mini Kit (QIAGEN), which includes an on column-DNase treatment of 15 minutes. RNA was eluted with 40 µl of RNAse-free water and its concentration measured with Nanodrop.
RNAseq was subcontracted to BGI Tech Solution (Hong Kong). For each sample, 1 µg RNA was used for libraries preparation with LncRNA library(H/M/R) according to the manufacturer’s instructions and sequenced on a DNBSEQ PE100 Eukaryotic Long Non-Coding RNA platform.

treatment_protocol: CCNA1 Knock Down was performed using the Lipofectamin RNAiMax transfection reagent (INVITROGEN) according to the manufacturer’s protocol. The siRNA sequence targeting CCNA1 was GAACCUGGCUAAGUACGUA, and the RNA sequence used as Control was the siRNA pGL3 luciferase control (Eurogentec reference SR-CL011-005).

tag: experimental condition

tag: cell line

value: FaDu


title: sham_12h_Rep2_Lib2

description: Sham injured males, 12 h post-injury, biological replicate 2

value: w[1118]; Bloomington stock 5905


title: sham_12h_Rep3_Lib2

description: Sham injured males, 12 h post-injury, biological replicate 3


title: siccna1_rep2


title: Organoid, AMC-17CT-139

description: gene expression


title: Organoid, AMC-17CT-120

description: gene expression


title: sicntrl_rep3


title: TBI_12h_Rep3_Lib2

description: Severe TBI injured males, 12 h post-injury, biological replicate 3

value: TBI


title: sham_12h_Rep1_Lib2

description: Sham injured males, 12 h post-injury, biological replicate 1

value: library 2


title: siccna1_rep1


title: sham_24h _Rep1_Lib2

description: Sham injured males, 24 h post-injury, biological replicate 1

value: whole heads


title: sicntrl_rep2


title: Organoid, AMC-17CT-075

description: gene expression


title: Organoid, AMC-17CT-048

description: gene expression


title: sicntrl_rep1


title: Organoid, AMC-17CT-112

description: gene expression


title: TBI_12h_Rep1_Lib2

description: Severe TBI injured males, 12 h post-injury, biological replicate 1


title: sham_6h_Rep3_Lib2

description: Sham injured males, 6 h post-injury, biological replicate 3


title: Organoid, AMC-17CT-114

description: gene expression


title: TBI_12h_Rep2_Lib2

description: Severe TBI injured males, 12 h post-injury, biological replicate 2


title: Lung adenocarcinoma patient-2's tumor tissues (Sup)

description:
2-A.txt
Lung adenocarcinoma patient-2's tumor tissues

value: male


title: sham_6h_Rep2_Lib2

description: Sham injured males, 6 h post-injury, biological replicate 2


title: Organoid, AMC-17CT-028

description: gene expression


title: TBI_6h_Rep3_Lib2

description: Severe TBI injured males, 6 h post-injury, biological replicate 3


title: sham_6h_Rep1_Lib2

description: Sham injured males, 6 h post-injury, biological replicate 1


title: TBI_6h_Rep2_Lib2

description: Severe TBI injured males, 6 h post-injury, biological replicate 2


title: Control, non cancer subject (CTRL 1093)

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

department: Biology

country: Italy

institute: University of Padova

description: Circulating miRNA expression profiling of non cancer subject (control 1093)

hyb_protocol: Probes were hybridized at 55°C for 22 hours using the Agilent's hybridization oven that is suited for bubble-mixing and microarray hybridization processes.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) at 100% and 10% sensitivity settings. Agilent Feature Extraction software version 12.0.0.7 was used for image analysis.

data_processing: Inter-array normalization of miRNA expression levels was performed with cyclic Lowess for miR [Risso et al., 2009] and the average of replicates was used. Feature Extraction software (Agilent Technologies) was used to obtain spot quality measures in order to evaluate the quality and the reliability of the hybridization. In particular, the flag “glsFound” (set to 1 if the spot has an intensity value significantly different from the local background, 0 otherwise) was used to filter out unreliable probes: flag equal to 0 will be noted as “not available” (NA). So, in order to perform a more robust and unbiased statistical analysis, probes with a high proportion of NA values were removed from the dataset. NA (47%) was used as threshold in the filtering process, obtaining a total of 142 available human miRNAs.

source_name: serum

label_protocol: Total RNA (4.000 pg) was labeled with pCp Cy3, according to the Agilent’s protocol and unincorporated dyes were removed with MicroBioSpin6 columns (BioRad, Hercules, CA, USA).

extract_protocol: Total RNA, including miRNA, was extracted from archival sera (600 ul) of 15 PDAC patients and from 4 non cancer subjects (controls) by miRNeasy Serum/Plasma Advanced Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. miRNAs were quantified by Qubit microRNA assay kit (Thermo Fisher Scientific, Waltham, Massachusetts, United States). RNA integrity and the content of microRNAs (%) in each sample were assessed by capillary electrophoresis with the RNA 6000 Nano LabChip and the Small RNA Nano LabChip, respectively, using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Only samples with RNA Integrity Number (R.I.N.) values higher than 6 and and quantity ≥4000 pg were used for microarray. analysis.

tag: disease

value: Control, non cancer subject


title: Organoid, AMC-17CT-097

description: gene expression


title: Control, non cancer subject (CTRL 1078)

description: Circulating miRNA expression profiling of non cancer subject (control 1078)


title: Organoid, AMC-17CT-089

description: gene expression


title: Organoid, AMC-17CT-052

description: gene expression


title: TBI_6h_Rep1_Lib2

description: Severe TBI injured males, 6 h post-injury, biological replicate 1


title: Organoid, AMC-17CT-057

description: gene expression


title: Control, non cancer subject (CTRL 321)

description: Circulating miRNA expression profiling of non cancer subject (control 321)


title: Lung adenocarcinoma patients-4's adjacent non-tumor tissues (IP)

description:
4-B.txt
Lung adenocarcinoma patients-4's adjacent non-tumor tissues


title: Lung adenocarcinoma patients-2's adjacent non-tumor tissues (IP)

description:
2-B.txt
Lung adenocarcinoma patients-2's adjacent non-tumor tissues


title: Control, non cancer subject (CTRL 287)

description: Circulating miRNA expression profiling of non cancer subject (control 287)


title: Lung adenocarcinoma patient-4's tumor tissues (IP)

description:
4-A.txt
Lung adenocarcinoma patient-4's tumor tissues


title: Lung adenocarcinoma patients-3's adjacent non-tumor tissues (IP)

description:
3-B.txt
Lung adenocarcinoma patients-3's adjacent non-tumor tissues


title: Organoid, AMC-17CT-116

description: gene expression


title: Lung adenocarcinoma patient-6's tumor tissues (IP)

description:
6-A.txt
Lung adenocarcinoma patient-6's tumor tissues


title: Lung adenocarcinoma patients-1's adjacent non-tumor tissues (IP)

description:
1-B.txt
Lung adenocarcinoma patients-1's adjacent non-tumor tissues


title: Lung adenocarcinoma patient-2's tumor tissues (IP)


title: Lung adenocarcinoma patient-5's tumor tissues (IP)

description:
5-A.txt
Lung adenocarcinoma patient-5's tumor tissues


title: sham_3h_Rep3_Lib2

description: Sham injured males, 3 h post-injury, biological replicate 3


title: Lung adenocarcinoma patient-3's tumor tissues (IP)

description:
3-A.txt
Lung adenocarcinoma patient-3's tumor tissues


title: Lung adenocarcinoma patient-1's tumor tissues (IP)

description:
1-A.txt
Lung adenocarcinoma patient-1's tumor tissues


title: Organoid, AMC-17CT-053

description: gene expression


title: CSU-070 tumor pre-treatment replicate C

city: Fort Collins

first: Sunetra

last: Das

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

description: Gene expression data from osteosarcoma sample CSU-070C

hyb_protocol: Fragmented and labeled cRNA were frozen at -20°C and overnight shipped on dry ice to the University of Colorado Cancer Center Genomics and Miroarray Shared Resource (University of Colorado, Anschutz Medical Campus, Aurora, CO) where Hybridized chips were washed, stained and scanned using an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The Affymetrix GeneChip scanner 3000 7G was used to acquire images

data_processing: The data were analyzed  in R using RMA and COMBAT normalization methods for batch correction.

organism: Canis lupus familiaris

source_name: Osteosarcoma

label_protocol: Reverse transcription of cRNA as well as cRNA in vitro transcription, amplification, purification, biotin-labeling, and fragmentation were performed using a GeneChip 3’ IVT PLUS Reagent Kit (Affymetrix, Cat. 902416) following manufacturer instructions.

growth_protocol: Following diagnosis and amputation of the affected limb, biopsy material was collected using a Michele Trephine bone biopsy instrument and collected biopsies reviewed by a veterinary pathologist for assessment of the percent of viable tumor present within each sample.  Two samples from each tumor with the highest percent viable tumor were selected for mRNA isolation and subsequent Affymetrix Canine 2.0 microarray analysis

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, total RNA was further purified using Qiagen RNeasy Purification Kits.

treatment_protocol: Tumor samples were frozen in liquid N2, pulverized to a powder by freeze-fracture using a manual Bio-Pulverizer

tag: breed

value: Golden Retriever

tag: Sex

value: Male

tag: neutered status

value: Yes

tag: age (years)

tag: time to progression (days)

tag: overall survival (days)

tag: body weight (kgs)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)

tag: number of doxorubicin treatments

tag: number of carboplatin treatments


title: CSU-067 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-067A

value: German Shep

value: Female


title: CSU-068 tumor pre-treatment replicate D

description: Gene expression data from osteosarcoma sample CSU-068D

value: Mix breed


title: PDAC patient with long (> 2 years) survival (pz 713

description: Circulating miRNA expression profiling of PDAC patient with long survival (pz 713)


title: CSU-068 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-068A


title: CSU-070 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-070B


title: CSU-067 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-067B


title: Organoid, AMC-17CT-101

description: gene expression

tag: age

tag: tissue


title: Organoid, AMC-17CT-011

description: gene expression

tag: cancer site


title: Organoid, AMC-17CT-040

description: gene expression


title: TBI_3h_Rep3_Lib2

description: Severe TBI injured males, 3 h post-injury, biological replicate 3

tag: strain

tag: post-injury timepoint

tag: condition

tag: library


title: PDAC patient with long (> 2 years) survival (pz 585)

description: Circulating miRNA expression profiling of PDAC patient with long survival (pz 585)

tag: disease


title: sham_3h_Rep1_Lib2

description: Sham injured males, 3 h post-injury, biological replicate 1

value: sham


title: TBI_3h_Rep2_Lib2

description: Severe TBI injured males, 3 h post-injury, biological replicate 2


title: sham_3h_Rep2_Lib2

description: Sham injured males, 3 h post-injury, biological replicate 2


title: Organoid, AMC-17CT-073

description: gene expression


title: TBI_3h_Rep1_Lib2

description: Severe TBI injured males, 3 h post-injury, biological replicate 1


title: Organoid, AMC-17CT-074

description: gene expression


title: PDAC patient with long (> 2 years) survival (pz 386)

description: Circulating miRNA expression profiling of PDAC patient with long survival (pz 386)


title: PDAC patient with long (> 2 years) survival (pz 310)

description: Circulating miRNA expression profiling of PDAC patient with long survival (pz 310)


title: PDAC patient with long (> 2 years) survival (pz 703)

description: Circulating miRNA expression profiling of PDAC patient with long survival (pz 703)


title: sham_1h_Rep3_Lib2

description: Sham injured males, 1 h post-injury, biological replicate 3


title: PDAC patient with long (> 2 years) survival (pz 708)

description: Circulating miRNA expression profiling of PDAC patient with long survival (pz 708)


title: Organoid, AMC-17CT-121

description: gene expression


title: Organoid, AMC-17CT-103

description: gene expression


title: sham_1h_Rep1_Lib2

description: Sham injured males, 1 h post-injury, biological replicate 1


title: sham_1h_Rep2_Lib2

description: Sham injured males, 1 h post-injury, biological replicate 2


title: PDAC patient with long (> 2 years) survival (pz 664)

description: Circulating miRNA expression profiling of PDAC patient with long survival (pz 664)


title: PDAC patient with long (> 2 years) survival (pz 642)

description: Circulating miRNA expression profiling of PDAC patient with long survival (pz 642)


title: Organoid, AMC-17CT-084

description: gene expression


title: CSU-062 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-062A

tag: breed

tag: Sex

tag: neutered status


title: CSU-063 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-063C

value: St. Bernard

value: No

tag: age (years)

tag: time to progression (days)

tag: overall survival (days)


title: CSU-063 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-063B

tag: body weight (kgs)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)


title: CSU-061 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-061C

tag: number of doxorubicin treatments

tag: number of carboplatin treatments


title: CSU-059 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-059C


title: CSU-059 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-059A


title: Organoid, AMC-17CT-111

description: gene expression

tag: cancer site

value: Large intestine

tag: age

tag: tissue

value: Colorectal cancer organoids (CCOs)


title: CSU-062 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-062C


title: TBI_1h_Rep3_Lib2

description: Severe TBI injured males, 1 h post-injury, biological replicate 3

tag: strain

value: w[1118]; Bloomington stock 5905

tag: post-injury timepoint

tag: condition


title: PDAC patient with short (< 1 year) survival (pz 517)

description: Circulating miRNA expression profiling of PDAC patient with short survival (pz 517)

tag: disease


title: Organoid, AMC-17CT-060

description: gene expression


title: TBI_1h_Rep2_Lib2

description: Severe TBI injured males, 1 h post-injury, biological replicate 2

value: TBI

tag: library


title: TBI_1h_Rep1_Lib2

description: Severe TBI injured males, 1 h post-injury, biological replicate 1

value: library 2


title: control_0_Rep3_Lib2

description: Uninjured 3d old males, biological replicate 3

value: control

value: whole heads


title: Organoid, AMC-17CT-010

description: gene expression


title: PDAC patient with short (< 1 year) survival (pz 354)

description: Circulating miRNA expression profiling of PDAC patient with short survival (pz 354)


title: control_0_Rep2_Lib2

description: Uninjured 3d old males, biological replicate 2


title: PDAC patient with short (< 1 year) survival (pz 607)

description: Circulating miRNA expression profiling of PDAC patient with short survival (pz 607)


title: PDAC patient with short (< 1 year) survival (pz 550)

description: Circulating miRNA expression profiling of PDAC patient with short survival (pz 550)


title: Organoid, AMC-17CT-066

description: gene expression


title: CSU-057 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-057A

tag: breed

tag: Sex

tag: neutered status


title: PDAC patient with short (< 1 year) survival (pz 584)

description: Circulating miRNA expression profiling of PDAC patient with short survival (pz 584)


title: PDAC patient with short (< 1 year) survival (pz 699)

description: Circulating miRNA expression profiling of PDAC patient with short survival (pz 699)


title: CSU-057 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-057C

tag: age (years)

tag: time to progression (days)

tag: overall survival (days)


title: CSU-056 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-056B

value: Greyhound

tag: body weight (kgs)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)


title: CSU-055 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-055C

value: Belgian Tervuren

tag: number of doxorubicin treatments

tag: number of carboplatin treatments


title: Organoid, AMC-17CT-081

description: gene expression

tag: cancer site

tag: age

tag: tissue


title: TBI_15d_Rep2_Lib1

description: Severe TBI injured males, 15 d post-injury, biological replicate 2

tag: strain

tag: post-injury timepoint

tag: condition

value: library 1


title: Organoid, AMC-17CT-050

description: gene expression


title: control_0_Rep1_Lib2

description: Uninjured 3d old males, biological replicate 1

tag: library


title: sham_15d_Rep2_Lib1

description: Sham injured males, 15 d post-injury, biological replicate 2


title: PDAC patient with short (< 1 year) survival (pz 301)

description: Circulating miRNA expression profiling of PDAC patient with short survival (pz 301)

tag: disease


title: CSU-055 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-055A

tag: breed

tag: Sex

tag: neutered status

value: Yes


title: Organoid, AMC-17CT-117

description: gene expression


title: CSU-054 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-054B

value: Akita

tag: age (years)

tag: time to progression (days)

tag: overall survival (days)


title: Organoid, AMC-17CT-138

description: gene expression


title: Organoid, AMC-17CT-045

description: gene expression


title: sham_15d_Rep1_Lib1

description: Sham injured males, 15 d post-injury, biological replicate 1


title: Organoid, AMC-17CT-019

description: gene expression


title: TBI_15d_Rep1_Lib1

description: Severe TBI injured males, 15 d post-injury, biological replicate 1


title: TBI_10d_Rep2_Lib1

description: Severe TBI injured males, 10 d post-injury, biological replicate 2


title: TBI_10d_Rep1_Lib1

description: Severe TBI injured males, 10 d post-injury, biological replicate 1


title: Organoid, AMC-17CT-037

description: gene expression


title: CSU-051 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-051A

value: Irish Wolfhound

value: Male

tag: body weight (kgs)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)


title: Organoid, AMC-17CT-115

description: gene expression

tag: cancer site


title: CSU-052 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-052C

value: Golden Ret

tag: number of doxorubicin treatments

tag: number of carboplatin treatments


title: CSU-052 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-052A


title: CSU-051 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-051C


title: CSU-056 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-056C

value: Female


title: CSU-053 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-053B

value: Mix breed


title: ΔoxyR grown to post-exponential phase exposed to 10mM H2O2, biological replicate 3

type: mixed

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

address: 21,111 Lakeshore

department: Natural Resource Sciences

institute: McGill University

description: Exposed to 10 mM H2O2

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

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

data_processing: Data were processed with the mapix software. Values from each channel were background substracted and the % contribution of each sopts to the total fluorsecence in each channel was calculated. Then the ratio Ch2/Ch1 was calculated. We used gDNA for data normalization accross slides, as described in Talaat, 2002, NAR.

label: Alexa Fluor 546

organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

source_name: genomic DNA, reference channel

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

growth_protocol: Aces-buffered yeast extract (AYE) broth at 37°C shaking.

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

treatment_protocol: Grown to post-exponential phase, treated or not (control) with 10 mM H2O2

tag: growth

value: AYE broth, 37°C shaking

label: Alexa Fluor 647


title: ΔoxyR grown to post-exponential phase not exposed to H2O2, biological replicate 1


title: ΔoxyR grown to post-exponential phase not exposed to H2O2, biological replicate 2


title: Organoid, AMC-17CT-042

description: gene expression

value: Large intestine

tag: age

tag: tissue

value: Colorectal cancer organoids (CCOs)


title: sham_10d_Rep2_Lib1

description: Sham injured males, 10 d post-injury, biological replicate 2

tag: strain

value: w[1118]; Bloomington stock 5905

tag: post-injury timepoint

tag: condition

value: sham

tag: library


title: TBI_10d_Rep3_Lib1

description: Severe TBI injured males, 10 d post-injury, biological replicate 3

value: TBI


title: ΔoxyR grown to post-exponential phase exposed to 10mM H2O2, biological replicate 1

description: Exposed to 10 mM H2O2


title: ΔoxyR grown to post-exponential phase exposed to 10mM H2O2, biological replicate 2

description: Exposed to 10 mM H2O2


title: ΔoxyR grown to post-exponential phase not exposed to H2O2, biological replicate 3


title: Organoid, AMC-17CT-135

description: gene expression


title: Organoid, AMC-17CT-035

description: gene expression


title: sham_10d_Rep3_Lib1

description: Sham injured males, 10 d post-injury, biological replicate 3

value: whole heads


title: sham_10d_Rep1_Lib1

description: Sham injured males, 10 d post-injury, biological replicate 1


title: CSU-050 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-050C

tag: breed

value: Malamute

tag: Sex

tag: neutered status


title: KS79 grown to post-exponential phase exposed to 10mM H2O2, biological replicate 2

description: Exposed to 10 mM H2O2


title: KS79 grown to post-exponential phase exposed to 10mM H2O2, biological replicate 1

description: Exposed to 10 mM H2O2


title: KS79 grown to post-exponential phase exposed to 10mM H2O2, biological replicate 3

description: Exposed to 10 mM H2O2


title: Organoid, AMC-17CT-090

description: gene expression


title: CSU-049 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-049B

tag: age (years)

tag: time to progression (days)

tag: overall survival (days)


title: TBI_7d_Rep3_Lib1

description: Severe TBI injured males, 7 d post-injury, biological replicate 3


title: CSU-047 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-047B

value: Labrador Ret

tag: body weight (kgs)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)


title: KS79 grown to post-exponential phase not exposed to H2O2, biological replicate 3


title: Organoid, AMC-17CT-032

description: gene expression

tag: cancer site


title: CSU-047 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-047A

tag: number of doxorubicin treatments

tag: number of carboplatin treatments


title: TBI_7d_Rep1_Lib1

description: Severe TBI injured males, 7 d post-injury, biological replicate 1

value: library 1

tag: tissue