title: invitro_Fp_PEB0191 [Fp-3]

status: Public on Nov 30 2021

city: Lausanne

first: Philipp

last: Engel

address: Biophore Building

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

data_processing:
Trimming for adapters and quality using trimmomatic
For the in vivo: separation of rRNA and non-rRNA reads using sortmerna
Mapping to reference with bowtie2
Generation of count files with HtSeq
Differential gene expression analysis with EdgeR
Genome_build: Reference genome used for read alignment
Supplementary_files_format_and_content: .count files containing counts per gene obtained with HtSeq

organism: Frischella perrara

source_name: in vitro culture

growth_protocol: Growth in mTYG for 16h; or bee gut colonization for 5 and 10 days

extract_protocol:
Trizol-based RNA extraction
RiboZero rRNA depletion followed by Illumina Truseq library preparation. In vivo samples were depleted of eukaryotic mRNA usig polyA-depletion

tag: strain

value: wild type growth in mTYG

tag: Stage

value: 16 hours of growth


title: invitro_Fp_PEB0191 [Fp-2]

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: treatment


title: invitro_Fp_PEB0191 [Fp-5]


title: CIC-KO2 (IDH1-R132H) WGBS rep 2

city: Vancouver

first: Marco

middle: A

last: Marra

state: BC

address: 675 W 10th Ave, 7th Floor

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

library_source: genomic

data_processing:
Sequencing reads were aligned to the human reference genome GRCh37-lite using NovoAlign
Fractional methylation values were obtained for each aligned CpG with a minimum coverage of 5 reads using NovoMethyl
Differentially methylated regions (DMRs) were identified using Defiant with default parameters
Genome_build: GRCh37-lite
Supplementary_files_format_and_content: Bed files with fractional methylation values for CpG that had at least 5 coverage

molecule: genomic DNA

organism: Homo sapiens

source_name: CIC-KO2 (IDH1-R132H) WGBS

growth_protocol: E6/E7 immortalized human astrocyte cell lines were cultured in Dulbecco's Modified Eagle's Medium supplemented with 10% (v/v) heat inactivated fetal bovine serum (Life Technologies)

extract_protocol: Whole genome bisulfite sequencing was performed on two replicates per each cell line. To track the efficiency of bisulphite conversion, 10 ng lambda DNA (Promega) was spiked into 1 µg genomic DNA, quantified using Qubit fluorometry, and arrayed in a 96-well microtitre plate. DNA was sheared to a target size of 300 bp using Covaris sonication (2 x 50 s at a “Duty cycle” of 30%, 450 Peak Incident Power [W] and 200 Cycles per Burst) and the fragments were subject to end-repair and phosphorylation in a single reaction, using an enzyme premix (NEB) containing T4 DNA polymerase, Klenow DNA Polymerase and T4 polynucleotide kinase, and incubated at 20 °C for 30 min. Repaired DNA was purified in 96- well format using PCR Clean DX beads (Aline Biosciences), and 3’-A-tailed (adenylation) using Klenow fragment (3’ to 5’ exo minus) at 37 °C for 30 min prior to enzyme heat inactivation. Cytosine methylated paired-end adapters: (5’- mCAmCTmCTTTmCmCmCTAmCAmCGAmCGmCTmCTTmCmCGATmCT-3’

tag: cell type

value: Immortalized Astrocyte Cells

tag: genotype

value: CIC-KO, IDH1-R132H


title: CIC-KO2 (IDH1-R132H) WGBS rep 1


title: Peripheral blood, Z180_3

status: Public on Dec 01 2021

city: Chengdu

first: Xuebin

last: Lv

state: SiChuan

address: Niusha Road

country: China

institute: Sichuan, Animal Science Academy

description: domestic pig

data_processing:
Illumina CASAVA ver.1.8.2 software was used for basecalling.
We removed low-quality reads including those with ≥ 10% unidentified nucleotides, > 10 nt aligned to the adapter, allowing ≤ 10% mismatches, and with > 50% of bases with phred quality < 5. Then, high-quality reads of ten strand-specific libraries were mapped to the pig reference genome (Suscrofa.11.1 from Ensemble) with Hisat2 (v.2.0.4)
Genome_build: Suscrofa.11.1 from Ensemble
Supplementary_files_format_and_content: miRNA_readcount_and_TPM.txt

molecule: polyA RNA

organism: Sus scrofa

source_name: blood tissue

extract_protocol:
Total RNA were extracted using mirVana miRNA isolation kit (Ambion, Austin, USA) according to the manufacture’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stage

value: day 180

tag: tissue

value: Peripheral blood


title: CIC-KO1 (IDH1-R132H) WGBS rep 1

source_name: CIC-KO1 (IDH1-R132H) WGBS


title: CIC-KO1 (IDH1-R132H) WGBS rep 2


title: CIC-WT (IDH1-R132H) WGBS rep 2

source_name: CIC-WT (IDH1-R132H) WGBS

value: CIC-WT, IDH1-R132H


title: CIC-KO2 (IDH1-WT) WGBS rep 2

source_name: CIC-KO2 (IDH1-WT) WGBS

value: CIC-KO, IDH1-WT


title: DS_20210824_KO_3

city: Philadelphia

first: Apoorva

last: Babu

state: PA

address: SCTR, 3400 Civic Center Blvd

department: Cardiovascular Institute

country: USA

institute: University of Pennsylvania

data_processing:
Fastq files were aligned to the mm39 reference genome using STAR and default parameters
Ensmebl (GRCm39) gene annotations were used for gene counts. Gene counts were obtained using STAR
Raw gene counts were transformed using 'LIMMA-Voom' method
Genome_build: mm39
Supplementary_files_format_and_content: Voom transformed abundance measurements

organism: Mus musculus

source_name: placenta

extract_protocol:
Deciduas were separated, flash frozen on dry ice, and RNA isolated using Direct-Zol RNA Kit (Zymo Research)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: Mix

value: Cyp19-Cre; Cdh5 fl/fl


title: CIC-WT (IDH1-WT) WGBS rep 1

source_name: CIC-WT (IDH1-WT) WGBS

value: CIC-WT, IDH1-WT


title: CIC-KO2 (IDH1-WT) WGBS rep 1


title: DS_20210824_KO_2


title: CIC-WT (IDH1-R132H) WGBS rep 1


title: CIC-KO1 (IDH1-WT) WGBS rep 1

source_name: CIC-KO1 (IDH1-WT) WGBS


title: CIC-KO1 (IDH1-WT) WGBS rep 2


title: DS_20210824_WT_2

value: Cdh5 fl/fl


title: DS_20210824_KO_1


title: DS_20210824_WT_1


title: DS_20210824_WT_3

value: Cdh5 fl/+


title: CIC-WT (IDH1-WT) WGBS rep 2


title: Spinal motor neurons, Wild-type, N272

city: Stockholm

first: Jorge

middle: C.

last: Correia

address: Biomedicum - Solnavägen 9

department: Dept. Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR 2.5.0a with parameters --outFilterMismatchNmax 33 --alignEndsType Local --alignSJoverhangMin 8 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --seedSearchStartLmax 12
Gene counts were obtained from bam files using htseq-count summarised at gene level
Differential gene expression at FDR level 0.1 was obtained using DESeq2 R package, genes with total raw counts less then 10 across all samples were excluded from analysis, DESeq2 model was fitted with sex as batch effect term
Normalized gene expression was calculated by DESeq2 R package using median of ratios
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: raw gene counts:  raw gene counts for each sample in tab delimited txt file
Supplementary_files_format_and_content: tg_wt_diffexp.txt :  tab-delimited file of differential expression between wild-type and transgenic mice
Supplementary_files_format_and_content: deseq2_sample_expression.csv:  comma-delimited file of deseq normalized gene expression

source_name: lumbar spinal cord motor neurons

extract_protocol:
Lumbar spinal cords were dissected and immediately snap-frozen in 2-methylbutane cooled in liquid nitrogen. Spinal cords were embedded in OCT, cryosectioned at −20°C (12 μm coronal sections) onto PEN membrane glass slides (Zeiss) and subsequently stored at −80°C until further processing. The sections were then used for laser capture microdissection of spinal motor neurons as described in Nichterwitz 2016. Briefly, the sections were thawed 30 seconds, subjected to quick histological staining (Histogene, Arcturus/LifeTechnologies) and cells were captured using the Leica LMD7000 system at 40x magnification. Only cells with a visible nucleus with nucleolus and with an area of more than 200 μm2 were captured. Cells were directly lysed with 5 μl lysis buffer (0.2% Triton X-100, with 2 U/μl recombinant RNase inhibitor, Clontech)
Libraries for RNA-seq were prepared using SMART-seq2 combined with Tn5 tagementation

value: lumbar spinal cord motor neurons

tag: Sex

value: F

value: wild-type (wt)


title: Spinal motor neurons, Wild-type, N271


title: Spinal motor neurons, HSA-NRTN transgenic, N269

value: nrtn transgenic (tg)


title: CIC-KO2 (IDH1-R132H) RNA-seq rep 2

data_processing:
Raw reads were aligned to the human reference genome GRCh37-lite using BWA v0.5.7
Raw read counts were mapped onto ensembl 75 gene annotations using Jaguar
DESeq2 v.1.8.2 was used to identify differentially expressed genes between each CIC-KO line and their CIC-WT counterpart as well as between CIC-WT (IDH1-R132H) and CIC-WT (IDH1-WT) cells. Differentially expressed genes were considered statistically significant if they met an Benjamini-Hochberg-adjusted p-value (q-value) of 0.05
Genome_build: GRCh37-lite
Supplementary_files_format_and_content: TSV file containing raw read counts mapped to ensembl 75 gene annotations

molecule: nuclear RNA

source_name: CIC-KO2 (IDH1-R132H) RNA-seq

extract_protocol:
To remove cytoplasmic and mitochondrial ribosomal RNA (rRNA) species from total RNA, the NEBNext rRNA Depletion Kit for Human/Mouse/Rat was used (NEB, E6310X). Enzymatic reactions were set-up in a 96-well plate (Thermo Fisher Scientific) on a Microlab NIMBUS liquid handler (Hamilton Robotics, Reno, Nevada, USA). 100ng of DNase I-treated total RNA in 6 µl was hybridized to rRNA probes in a 7.5 µl reaction. Heat-sealed plates were incubated at 95 °C for 2 min followed by incremental reduction in temperature by 0.1 °C per s to 22 °C (730 cycles). The 15 rRNA in DNA hybrids were digested using RNase H in a 10 µl reaction incubated in a thermocycler at 37 °C for 30 min. To remove excess rRNA probes (DNA) and residual genomic DNA contamination, DNase I was added in a total reaction volume of 25 µl and incubated at 37 °C for 30 min. RNA was purified using RNA MagClean DX beads (Aline Biosciences, Woburn, Massachusetts, USA) with 15 min of binding time, 7 min clearing on a magnet followed by two 70% ethanol washes, 5 minutes to air dry the RNA pellet and elution in 36 µl DEPC water. The plate containing RNA was stored at -80 °C prior to cDNA synthesis.
First-strand cDNA was synthesized from the purified RNA (minus rRNA) using the Maxima H Minus First Strand cDNA Synthesis kit (Thermo-Fisher, USA) and random hexamer primers at a concentration of 8 ng/µl along with a final concentration of 0.04 µg/µl Actinomycin D, followed by PCR Clean DX bead purification on a Microlab NIMBUS robot (Hamilton Robotics, USA). The second strand cDNA was synthesized following the NEBNext Ultra Directional Second Strand cDNA Synthesis protocol (NEB) that incorporates dUTP in the dNTP mix, allowing the second strand to be digested using USERTM enzyme (NEB) in the post-adapter ligation reaction and thus achieving strand specificity. cDNA was fragmented using Covaris LE220 sonication for 100 s (2 x 50 s) at a “Duty cycle” of 30%, 450 Peak Incident Power (W) and 200 Cycles per Burst in a microTUBE Strip (P/N: 520053) to achieve 200–250 bp average fragment lengths. The paired-end sequencing library was prepared following Canada’s Michael Smith Genome Sciences Centre’s strand-specific, plate-based library construction protocol on a Microlab NIMBUS robot (Hamilton Robotics, USA). In brief, the sheared cDNA was subject to end-repair and phosphorylation in a single reaction using an enzyme premix (NEB) containing T4 DNA polymerase, Klenow DNA Polymerase and T4 polynucleotide kinase, and incubated at 20 °C for 30 min. Repaired cDNA was purified in 96-well format using PCR Clean DX beads (Aline Biosciences, USA), and 3’-A-tailed (adenylated) using Klenow fragment (3’ to 5’ exo minus) and incubation at 37 °C for 30 min prior to enzyme heat inactivation. Illumina PE adapters were ligated at 20 °C for 15 min. The adapter-ligated products were purified using PCR Clean DX beads, then digested with USERTM enzyme (1 U/µl, NEB) at 37 °C for 15 min followed immediately by 13 cycles of indexed PCR using Phusion DNA Polymerase (Thermo Fisher Scientific Inc. USA) and Illumina’s PE primer set. PCR parameters were: 98 °C for 1 min followed by 13 cycles of 15 s at 98 °C, 30 s at 65 °C and 30 s at 65 °C, and then 72 °C for 5 min. The PCR products were twice purified and size-selected using a 1:1 PCR Clean DX beads-to- 16 sample ratio, and the eluted DNA quality was assessed using an Agilent DNA1000 Assay (Agilent, USA) and quantified using a Quant-iT dsDNA High Sensitivity Assay Kit on a Qubit fluorometer (Invitrogen). Libraries (3 replicates per cell line) were then pooled and size- corrected using a final molar concentration calculation for Illumina HiSeq2500 sequencing with paired-end 75 base reads.


title: Spinal motor neurons, HSA-NRTN transgenic, N270


title: Spinal motor neurons, HSA-NRTN transgenic, N259

value: M


title: CIC-KO2 (IDH1-R132H) RNA-seq rep 3


title: Spinal motor neurons, HSA-NRTN transgenic, N262


title: Spinal motor neurons, HSA-NRTN transgenic, N260


title: Spinal motor neurons, Wild-type, N261


title: invitro_Fp_PEB0191 [Fp-1]

value: wild type growth in mTYG

value: 16 hours of growth


title: CIC-KO2 (IDH1-R132H) RNA-seq rep 1

value: Immortalized Astrocyte Cells

value: CIC-KO, IDH1-R132H


title: CIC-KO1 (IDH1-R132H) RNA-seq rep 3

source_name: CIC-KO1 (IDH1-R132H) RNA-seq


title: CIC-KO1 (IDH1-R132H) RNA-seq rep 2


title: CIC-KO2 (IDH1-WT) RNA-seq rep 3

source_name: CIC-KO2 (IDH1-WT) RNA-seq


title: CIC-WT (IDH1-R132H) RNA-seq rep 3

source_name: CIC-WT (IDH1-R132H) RNA-seq


title: CIC-WT (IDH1-R132H) RNA-seq rep 1


title: CIC-WT (IDH1-R132H) RNA-seq rep 2


title: CIC-KO1 (IDH1-R132H) RNA-seq rep 1


title: Spinal motor neurons, Wild-type, N274


title: CIC-KO2 (IDH1-WT) RNA-seq rep 2


title: CIC-KO1 (IDH1-WT) RNA-seq rep 3

source_name: CIC-KO1 (IDH1-WT) RNA-seq


title: CIC-KO1 (IDH1-WT) RNA-seq rep 1


title: CIC-KO1 (IDH1-WT) RNA-seq rep 2


title: CIC-WT (IDH1-WT) RNA-seq rep 2

source_name: CIC-WT (IDH1-WT) RNA-seq


title: Spinal motor neurons, Wild-type, N268


title: CIC-WT (IDH1-WT) RNA-seq rep 1


title: CIC-WT (IDH1-WT) CIC ChIP-seq

data_processing:
Raw reads were aligned to the human reference genome GRCh37-lite using BWA v0.5.7
CIC peaks were identified using MACS2 v.2.1.1 with a q-value threshold of 0.05
Genome_build: GRCh37-lite
Supplementary_files_format_and_content: bed file containing CIC peaks identified using MACS2

source_name: Immortalized Astrocyte Cells

extract_protocol:
For each CIC-WT (IDH1-WT) cell line replicate, two ~70–80% confluent 15-cm plates were treated with 1% formaldehyde (Sigma, St. Louis, MO, USA) in PBS for 12 min with gentle rocking, followed by treatment with 0.125 M glycine (Sigma) for 5 min. Crosslinked cells were combined and pelleted using centrifugation at 1,200 rpm for 5 min at room temperature, resuspended in 450 μl ChIP lysis buffer (50 mM Tris-HCl pH 8.0, 1% SDS, 10 mM EDTA, 1X complete EDTA-free Protease Inhibitor cocktail [PIC, Roche]), and lysed on ice for 30 min. Cells were homogenized by 6 passages through a 20-gauge needle, and nuclei pellets were obtained by centrifugation at 5,000 rpm for 10 min at 4 °C. The pellet was resuspended in 900 μl shearing buffer (10 mM Tris-HCl pH 8.0, 0.1% SDS, 1 mM EDTA, 1X EDTA-free PIC) and transferred to a 1 ml milliTUBE with AFA fiber (D-Mark Biosciences) using a 30-gauge needle. Chromatin was sonicated using a Covaris S2 sonicator using the following settings: 10% duty cycle, 6 intensity, 500 burst, 16 cycles (20 s on, 40 s off) at 4–6 °C. Insoluble debris and unfragmented chromatin were removed by centrifugation at 14,000 rpm for 12 min at 4 °C. An aliquot of chromatin was de-crosslinked overnight at 68 °C (0.2 M NaCl, 0.05 mg/ml RNase), treated with proteinase K for 30 min at 42 °C, and purified using the MinElute PCR Purification Kit (28006, Qiagen). Concentration of the purified chromatin was determined using the Qubit dsDNA high sensitivity assay (Life Technologies) and the presence of DNA fragments in the 150–300 bp size range was confirmed by separation on a 2% agarose gel. Protein A Dynabeads (Life Technologies) blocked with bovine serum albumin and salmon sperm DNA for 3 h were used to pre-clear chromatin for 2 h. For immunoprecipitation, three volumes of IP buffer (10 mM Tris-HCl pH 8.0, 1% Triton X100, 0.1% deoxycholate, 0.1% SDS, 90 mM NaCl, 2mM EDTA, 1X EDTA-free PIC) were added to 22.5 μg of chromatin, which was then incubated with 5 μg of anti-CIC antibody (Sigma, HPA044341) for 1 h at 4 °C. Blocked Protein A Dynabeads (25 μl) were then added to the chromatin and antibody and incubated overnight at 4 °C. The samples were then washed twice in low salt buffer (20 mM Tris-HCl pH 8.0, 0.1% SDS, 1% Triton X100, 2 mM EDTA, 150 mM NaCl) and twice in high salt buffer (same as low salt buffer except 300 mM NaCl). DNA was eluted in 100 mM sodium bicarbonate with 1% SDS and 0.05 mg/ml RNase at 68 °C for 6 h or overnight, followed by treatment with proteinase K for 30 min at 42 °C. For each IP, 20 μl of chromatin was subjected to the same treatment to serve as input controls. Eluted DNA was purified using the MinElute PCR Purification Kit.
Sequencing libraries were prepared following a modified paired-end library protocol (Illumina Inc.). In brief, the DNA was subjected to end-repair and phosphorylation using T4 DNA polymerase with Klenow DNA Polymerase and T4 polynucleotide kinase, respectively, in a single reaction. 3’-A overhangs were generated using Klenow fragment (3’ to 5’ exo minus), and ligated to Illumina PE adapters containing 5’-T overhangs. The adapter-ligated products were purified using PCR Clean DX beads (ALINE Biosciences), then PCR-amplified with Phusion DNA Polymerase in 13 cycles using Illumina’s PE primer set (Illumina). PCR product was purified using PCR Clean DX beads (ALINE Biosciences), and the DNA quality was assessed and quantified using the Caliper LabChip GX DNA High Sensitivity assay (PerkinElmer) and the Quant-iT dsDNA high sensitivity assay (ThermoFisher Scientific). Libraries were normalized and pooled and the final concentration of the pooled library was determined using a Qubit dsDNA HS Assay Kit and a Qubit fluorometer (ThermoFisher Scientific). Clusters were generated on the Illumina cluster station and sequence data were generated using an Illumina HiSeq2500 platform following the manufacturer’s instructions.

value: Astrocyte

tag: chip antibody

value: anti-CIC antibody (Sigma, HPA044341)


title: CIC-KO2 (IDH1-R132H) H3K9me3 rep 2

data_processing:
Raw reads were aligned to the human reference genome GRCh37-lite using BWA v0.5.7
FindER (https://thisisepigenetics.ca/for-scientists/software) v1.0.1e was used with default parameters to identify peaks
The union of all peaks across all cell lines was first obtained using Bedtools for each mark. Raw read counts within these regions were obtained using Deeptools v3.0.1
DESeq2 was used to identify differentially enriched (DER) peaks between CIC-KO and CIC-WT cells (CIC-associated) or between cells expressing IDH1-R132H and cells expressing IDH1-WT cells (IDH1-associated), with a q-value threshold of 0.05 and a fold-change threshold of 2
Genome_build: GRCh37-lite
Supplementary_files_format_and_content: Bed files with coverage values for peaks indentified across all cell lines

source_name: CIC-KO2 (IDH1-R132H) H3K9me3

extract_protocol:
Samples for Native chromatin immunoprecipitation (N-ChIP) were prepared from ~100,000 cells per immunoprecipitation, two replicates per each cell line. In brief, cells were lysed using lysis buffer (0.1% Triton X-100, 0.1% deoxycholate) and protease inhibitor for 20 min on ice. The extracted chromatin was then digested using 90 U of MNase enzyme (NEB) for 6 min at 25 °C. Reactions were quenched by adding 5.5 µL of 250 µM EDTA. A mix of 1% Triton X- 100 and 1% deoxycholate was then added to the digested samples and the 96-well plate of samples was chilled on ice for 20 min. The digested chromatin was then pooled and 12 µl of chromatin was reserved for use as input control. The rest of the digested chromatin was pre- cleared using IP buffer (20 mM Tris-HCl [pH7.5], 2 mM EDTA, 150 mM NaCl, 0.1% Triton X-100, 0.1% deoxycholate) plus protease inhibitor with 20 µl of pre-washed Protein A/G Dynabeads (Invitrogen) at 4 °C for 1.5 h. Supernatants were removed from the beads and transferred to a 96-well plate containing the antibody-bead complex. The plate was sealed and incubated at 4 °C on a rotating platform overnight. The reaction plate containing the immunoprecipitation samples was placed on a magnetic plate and samples were washed twice with low salt buffer (20 mM Tris-HCl [pH 8.0], 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl) and twice with high salt buffer (20 mM Tris-HCl [pH 8.0], 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl). DNA-antibody complexes were eluted in 30 µl Elution Buffer (100 mM NaHCO3, 1% SDS), incubated at 65 °C for 1.5 h with mixing at 1,350 rpm on a thermomixer. Protein was digested by adding 1.75µl of Qiagen Protease to the eluted DNA samples at 50 °C for 30 min with mixing at 600 rpm on a thermomixer. ChIP DNA was then purified using Sera-Mag beads (ThermoFisher Scientific) with 30% PEG before library construction.
Library construction and sequencing were done identically to the CIC ChIP-seq samples with the only difference being that the adaptor-ligated products were amplified using 8 to 10 PCR cycles.


title: CIC-KO2 (IDH1-R132H) H3K9me3 rep 1


title: CIC-WT (IDH1-R132H) H3K9me3 rep 1

source_name: CIC-WT (IDH1-R132H) H3K9me3

value: CIC-WT, IDH1-R132H


title: CIC-KO1 (IDH1-R132H) H3K9me3 rep 2

source_name: CIC-KO1 (IDH1-R132H) H3K9me3


title: CIC-KO1 (IDH1-R132H) H3K9me3 rep 1


title: CIC-KO2 (IDH1-WT) H3K9me3 rep 1

source_name: CIC-KO2 (IDH1-WT) H3K9me3

value: CIC-KO, IDH1-WT


title: CIC-KO1 (IDH1-WT) H3K9me3 rep 1

source_name: CIC-KO1 (IDH1-WT) H3K9me3


title: CIC-WT (IDH1-R132H) H3K9me3 rep 2


title: CIC-KO2 (IDH1-WT) H3K9me3 rep 2


title: CIC-WT (IDH1-WT) H3K9me3 rep 2

source_name: CIC-WT (IDH1-WT) H3K9me3


title: CIC-KO2 (IDH1-R132H) H3K36me3 rep 1

source_name: CIC-KO2 (IDH1-R132H) H3K36me3


title: CIC-KO1 (IDH1-R132H) H3K36me3 rep 2

source_name: CIC-KO1 (IDH1-R132H) H3K36me3


title: CIC-KO1 (IDH1-WT) H3K9me3 rep 2


title: CIC-KO2 (IDH1-R132H) H3K36me3 rep 2


title: CIC-KO1 (IDH1-R132H) H3K36me3 rep 1


title: CIC-WT (IDH1-WT) H3K9me3 rep 1


title: CIC-KO2 (IDH1-WT) H3K36me3 rep 2

source_name: CIC-KO2 (IDH1-WT) H3K36me3


title: CIC-KO2 (IDH1-WT) H3K36me3 rep 1


title: CIC-KO2 (IDH1-WT) RNA-seq rep 1


title: CIC-WT (IDH1-R132H) H3K36me3 rep 1

source_name: CIC-WT (IDH1-R132H) H3K36me3


title: CIC-WT (IDH1-WT) RNA-seq rep 3


title: CIC-KO1 (IDH1-WT) H3K36me3 rep 1

source_name: CIC-KO1 (IDH1-WT) H3K36me3


title: CIC-WT (IDH1-WT) CIC ChIP-seq input DNA


title: CIC-WT (IDH1-WT) H3K36me3 rep 1

source_name: CIC-WT (IDH1-WT) H3K36me3


title: CIC-WT (IDH1-WT) H3K36me3 rep 2


title: CIC-KO1 (IDH1-WT) H3K36me3 rep 2


title: CIC-KO2 (IDH1-R132H) H3K27me3 rep 2

source_name: CIC-KO2 (IDH1-R132H) H3K27me3


title: CIC-WT (IDH1-R132H) H3K27me3 rep 2

source_name: CIC-WT (IDH1-R132H) H3K27me3


title: CIC-KO2 (IDH1-WT) H3K27me3 rep 2

source_name: CIC-KO2 (IDH1-WT) H3K27me3


title: CIC-WT (IDH1-R132H) H3K27me3 rep 1


title: CIC-KO2 (IDH1-R132H) H3K27me3 rep 1


title: CIC-WT (IDH1-WT) H3K27me3 rep 2

source_name: CIC-WT (IDH1-WT) H3K27me3


title: CIC-KO1 (IDH1-WT) H3K27me3 rep 1

source_name: CIC-KO1 (IDH1-WT) H3K27me3


title: CIC-KO2 (IDH1-R132H) H3K27ac rep 2

source_name: CIC-KO2 (IDH1-R132H) H3K27ac


title: CIC-KO1 (IDH1-R132H) H3K27ac rep 2

source_name: CIC-KO1 (IDH1-R132H) H3K27ac


title: CIC-KO2 (IDH1-R132H) H3K27ac rep 1


title: CIC-KO2 (IDH1-WT) H3K27me3 rep 1


title: WT4

city: Daejeon

first: Haemin

last: Chon

address: Daehak-ro 291

department: Graduate school of medical science and engineering

country: South Korea

institute: KAIST

description:
WT_GBM2_cancer_cell
tdTomato+
Column WT2 in 'modified_readcount.csv' file.

data_processing:
Trimming was done with > Average Q20 using BBDuk.
Mapping of reads were done using Bowtie2 to mm10 reference genome. Calculation of read counts were done using Bedtools.
Quality control of genes were done excluding of lowly expressed genes (< 10 counts).
Normalization of readcounts were done by log normalization.
Differentially expressed genes between WT and KO were extracted with DESeq2 (v1.32.0).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: modified_readcount.csv: Comma-separated text file.

source_name: cancer cell

extract_protocol:
FACS-sorted tumor cells were lysed with Qiazol Lysis Reagent (79306, Qiagen Sciences) and RNA was extracted and purified with RNeasy mini plus kit (74134, Qiagen Sciences). Protocols were followed from user guides of products.
Using Lexogen QuantSeq 3' mRNA-seq Library Prep Kit (Lexogen), cDNA libraries were constructed.

value: WT

tag: disease

value: Glioblastoma

value: FACS-sorted tumor cells

value: Adult


title: WT5

description:
WT_GBM3_cancer_cell
tdTomato+
Column WT3 in 'modified_readcount.csv' file.


title: CIC-WT (IDH1-R132H) H3K36me3 rep 2


title: CIC-KO1 (IDH1-R132H) H3K27ac rep 1


title: WT3

description:
WT_GBM1_cancer_cell
tdTomato+
Column WT1 in 'modified_readcount.csv' file.


title: CIC-WT (IDH1-R132H) H3K27ac rep 2

source_name: CIC-WT (IDH1-R132H) H3K27ac


title: CIC-WT (IDH1-R132H) H3K27ac rep 1


title: CIC-KO2 (IDH1-WT) H3K27ac rep 2

source_name: CIC-KO2 (IDH1-WT) H3K27ac


title: CIC-KO1 (IDH1-WT) H3K27ac rep 1

source_name: CIC-KO1 (IDH1-WT) H3K27ac


title: CIC-WT (IDH1-WT) H3K27ac rep 1

source_name: CIC-WT (IDH1-WT) H3K27ac

value: CIC-WT, IDH1-WT


title: CIC-KO1 (IDH1-R132H) H3K27me3 rep 2

source_name: CIC-KO1 (IDH1-R132H) H3K27me3


title: CIC-KO1 (IDH1-WT) H3K27ac rep 2


title: CIC-KO2 (IDH1-R132H) H3K4me3 rep 2

source_name: CIC-KO2 (IDH1-R132H) H3K4me3


title: CIC-WT (IDH1-WT) H3K27ac rep 2


title: CIC-KO2 (IDH1-R132H) H3K4me3 rep 1


title: CIC-KO2 (IDH1-WT) H3K27ac rep 1


title: CIC-KO1 (IDH1-WT) H3K27me3 rep 2


title: CIC-WT (IDH1-R132H) H3K4me3 rep 2

source_name: CIC-WT (IDH1-R132H) H3K4me3


title: CIC-KO1 (IDH1-R132H) H3K27me3 rep 1


title: CIC-KO1 (IDH1-R132H) H3K4me3 rep 1

source_name: CIC-KO1 (IDH1-R132H) H3K4me3


title: CIC-KO1 (IDH1-R132H) H3K4me3 rep 2


title: CIC-KO2 (IDH1-WT) H3K4me3 rep 2

source_name: CIC-KO2 (IDH1-WT) H3K4me3


title: CIC-WT (IDH1-R132H) H3K4me3 rep 1


title: CIC-WT (IDH1-WT) H3K4me3 rep 2

source_name: CIC-WT (IDH1-WT) H3K4me3


title: CIC-KO1 (IDH1-WT) H3K4me3 rep 1

source_name: CIC-KO1 (IDH1-WT) H3K4me3


title: CIC-WT (IDH1-WT) H3K4me3 rep 1


title: CIC-KO1 (IDH1-WT) H3K4me3 rep 2


title: LGDIT-INI1/ATRT-MYC_high-grade-tumor-area

type: genomic

city: Hamburg

first: Julia

middle: Elisabeth

last: Neumann

address: Martinistrasse 52

department: ZMNH

country: Germany

institute: University Hospital Hamburg Eppendorf

description: densely packed rhabdoid-like tumor cells with higher cellular atypia

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the iScan System and standard recommended Illumina scanner setting

data_processing:
Analysis was conducted using R version 3.6.0 with the packages minfi 1(version 1.32.0), IlluminaHumanMethylationEPICanno.ilm10b4.hg19 (v.0.6.0) and IlluminaHumanMethylationEPICmanifest (v.0.3.0). The data was read into an RGChannelSet. P-values for every individual probe were calculated using the detectionP()-function of minfi. Single-Sample-NOOB normalization was applied and the beta-values as well as the methylated and unmethylated intensities were directly extracted from the resulting MethylSet.
Unmethylated and methylated signal intensities of the Single-Sample-NOOB-normalized data.

label: Cy3, Cy5

source_name: brain(tumor)

label_protocol: Standard Illumina Protocol

extract_protocol: 10 x 10 µm sections were cut from FFPE tissue. DNA was isolated using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions. About 100-500 ng DNA was used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). Afterwards, the DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were employed to clean and restore the converted DNA. Finally, the Infinium MethylationEPIC BeadChip Kit  Illumina) was used to quantify the methylation status of 850,000 CpG sites on an iScan device (Illumina).

tag: cellularity, proliferation

value: high, high


title: CIC-KO2 (IDH1-R132H) H3K4me1 rep 1

source_name: CIC-KO2 (IDH1-R132H) H3K4me1


title: CIC-KO1 (IDH1-R132H) H3K4me1 rep 2

source_name: CIC-KO1 (IDH1-R132H) H3K4me1


title: CIC-KO1 (IDH1-R132H) H3K4me1 rep 1


title: CIC-WT (IDH1-R132H) H3K4me1 rep 1

source_name: CIC-WT (IDH1-R132H) H3K4me1


title: CIC-KO2 (IDH1-R132H) H3K4me1 rep 2


title: CIC-KO2 (IDH1-WT) H3K4me1 rep 2

source_name: CIC-KO2 (IDH1-WT) H3K4me1


title: CIC-KO1 (IDH1-WT) H3K4me1 rep 1

source_name: CIC-KO1 (IDH1-WT) H3K4me1


title: CIC-WT (IDH1-WT) H3K4me1 rep 2

source_name: CIC-WT (IDH1-WT) H3K4me1


title: CIC-KO2 (IDH1-WT) H3K4me1 rep 1


title: CIC-KO1 (IDH1-WT) H3K4me1 rep 2


title: LGDIT-INI1/ATRT-MYC_low-grade-tumor-area

description: diffusely infiltrating inconspicuous tumor cells

value: low, low


title: CIC-KO2 (IDH1-WT) H3K4me3 rep 1


title: CIC-KO2 (IDH1-R132H) Input DNA rep 2

source_name: CIC-KO2 (IDH1-R132H) Input DNA

value: Input DNA


title: CIC-WT (IDH1-WT) H3K4me1 rep 1


title: CIC-KO1 (IDH1-R132H) Input DNA rep 1

source_name: CIC-KO1 (IDH1-R132H) Input DNA


title: CIC-WT (IDH1-R132H) Input DNA rep 2

source_name: CIC-WT (IDH1-R132H) Input DNA


title: CIC-KO2 (IDH1-R132H) Input DNA rep 1


title: CIC-KO2 (IDH1-WT) Input DNA rep 1

source_name: CIC-KO2 (IDH1-WT) Input DNA


title: CIC-WT (IDH1-R132H) Input DNA rep 1


title: CIC-KO1 (IDH1-WT) Input DNA rep 2

source_name: CIC-KO1 (IDH1-WT) Input DNA


title: CIC-KO1 (IDH1-WT) Input DNA rep 1


title: CIC-WT (IDH1-WT) Input DNA rep 2

source_name: CIC-WT (IDH1-WT) Input DNA


title: CIC-WT (IDH1-WT) Input DNA rep 1


title: CIC-WT (IDH1-R132H) H3K4me1 rep 2


title: pMV306(1955)Comp (C)

type: RNA

city: New Delhi

first: Amita

last: Gupta

state: Delhi

address: University of Delhi south campus

department: Department of Biochemistry and CIIDRET

country: India

institute: University of Delhi

description: SAMPLE 8

hyb_protocol: The Gene Expression Hybridization Kit (Agilent Technologies, 5188-5279) and associated protocols were used (G4140-90040). To evaluate the effect of formamide on the specificity of annealing of the GC-rich targets, the purified cRNA (600ng) was fragmented with fragmentation blocking mix in the presence or absence of Formamide (7%) by incubating samples at 60°C for 30 minutes. Microarrays were prepared in Agilent Technologies Hybridization Chamber according to manufacturers instructions (G2534-90001). Once loaded into thehybridization chamber, samples were placed in thehybridization oven (Agilent Technologies, G2505-80085) and incubated for 17 hours at 65°C while rotating at setting 10. Following hybridization, samples were washed according to procedure described by Agilent Technologies.

scan_protocol: Microarray slides were scanned at the resolution of 5µmusing Agilent Microarray scanner (G2565CA) with scan control software as per manufacturer’s instructions (G2505-90020). Settings included Agilent HD_GX_1colour (61X21.6mm), TIFF 20 bit, and Photomultiplier tube (PMT) gain 100%. Scanned image displays were analyzed by quantifying the pixel density of each hybridization spot using the Agilent Feature Extraction software (v10.5). Local background signals were subtracted from the data automatically by this software and raw data was obtained.

data_processing: Normalization was done to 50th percentile of each sample and data transformation was done to median of all samples using GeneSpring Gx V 12.0 from Agilent Technologies

organism: Mycobacterium tuberculosis H37Rv

source_name: Mtb H37Rv HigB KO complemented strain early log phase cultures in 7H9-ADS medium+ Hygromycin+Kanamycin

label_protocol: The first priming method (PolyA-dT) involved initial polyadenylation of Mycobacterial RNA folllowed by oligo-dT based amplification and labelling to produce cRNA. Polyadenylation was carried out using Poly (A) polymerase tailing kit (Epicenter Biotechnologies, USA) as per the manufacturer’s instructions. 25 ng of Poly A tailed RNA was amplified and labeled using theoligo-dT based T7 promoter primers included in the Low Input Quick Amp labeling kit(Agilent Technologies, G4140-90040). The Agilent spike-in controls included in the One-Color RNA Spike-In Kit (Agilent Technologies, 5188-5282)were used as control.The second priming method (WT)involved random-priming based amplification and labelling of Mycobacterial RNA. For this, 25 ng of the native non-adenylated total RNA was amplified and labeled using random nucleotide-based T7 promoter primers included in the Low Input Quick Amp WT labeling kit(Agilent Technologies, G4140-90042)

growth_protocol: Mtb H37Rv wild type, Mtb H37Rv HigB KO and Mtb H37Rv HigB KO complemented strain were seeded at 0.05 OD600 in 7H9-ADS, 7H9-ADS+Hygromycin (50ug/ml) and 7H9-ADS +Hygromycin (50ug/ml) + Kanamycin (25ug/ml)  medium and grown till early log phase of ~1.0.

extract_protocol: The cells were harvested from 25 ml culture of M. tuberculosis grown under different conditions and RNA was isolated using published protocols. The RNA yield (absorbance at 260nm) and purity of the samples was measured by using the Nanodrop 2000c spectrophotometer (Thermo Scientific, USA). Yield of the RNA was calculated from the absorbance of the sample at 260 nm.

tag: strain/genotype

value: HigB KO complemented strain of Mtb H37Rv

tag: growth

value: early log phase cultures in 7H9-ADS medium+ Hygromycin (50ug/ml)+Kanamycin (25ug/ml)


title: HigB KO (C)

description: SAMPLE 5

source_name: Mtb H37Rv HigB KO mutant strain early log phase cultures in 7H9-ADS medium+ Hygromycin

value: HigB KO mutant strain of Mtb H37Rv

value: early log phase cultures in 7H9-ADS medium+ Hygromycin (50ug/ml)


title: pMV306(1955)Comp (B)

description: SAMPLE 7


title: HigB KO (B)

description: SAMPLE 4


title: pENTER_VEC

first: Ping

last: Lin

address: No.1, Keyuan 4th Road, Chengdu

institute: Sichuan University

data_processing:
All reads which pass Solexa CHASTITY quality filter in FASTQ format.
Genomic alignment result for the reads which pass Solexa CHASTITY quality filter.
ChIP-enriched regions (peaks) detected by MACS V1.4.2.
Genome_build: All the ChIP-seq signal densities in WIG format for visualizing the ChIP-seq profiles of each sample.

source_name: Breast

growth_protocol: MCF-7, ZR-75-30 were maintained in RPMI-1640 (Gibco), respectively. All the medium supplemented with 10% FBS (Gibco) with 100 units/mL  3  MCF-7 was maintained in RPMI-1640 with 10% FBS  in a 5% CO2-containing atmosphere at 37 ◦C.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with Flag-antibody.
DNA samples were end-repaired, A tailed, and adaptor ligated using TruSeq Nano DNA Sample Prep Kit (#FC-121-4002, Illumina), following the manufacturer’s instructions. ~200-1500 bp fragments were size selected using AMPure XP beads. The final size of the library was confirmed by Agilent 2100 Bioanalyzer. The samples were diluted to a final concentration of 8 pM and cluster generation was performed on the Illumina cBot using HiSeq 3000/4000 PE Cluster Kit (#PE-410-1001, Illumina), following manufacturer’s instructions. Sequencing was performed on Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit (300 cycles) (#FC-410-1003, Illumina), according to the manufacturer’s instructions.

treatment_protocol: The MCF-7 was transfected with the pENTER-ZNF32 or empty vector.

tag: cell line

tag: transfection

value: empty vector


title: TD7 scRNA-seq

city: Xi'an

first: Yue

last: Fan

address: Yanta West Road No.76

institute: Xi'an Jiaotong University

data_processing:
The cellranger software suite was used to perform sample de-multiplexing.
The final library pool was sequenced on the NovaSeq 6000 instrument using 150-base-pair paired-end reads.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

source_name: Lung adenocarcinoma

extract_protocol:
A human tumour dissociation kit enzyme solution (Miltenyi Biotec; 200 µl of H-enzyme, 100 µl of R-enzyme, 25 µl of A-enzyme, 4.7 ml of DMEM) was added for enzymatic digestion for 30 minutes at 37°C, and the sample was filtered through a Miltenyi 70-mm sieve. After centrifugation, the granular cells were suspended in erythrocyte lysis buffer. Finally, the cells were mixed with 1 ml of PBS, and the numbers of live cells and aggregated cells were measured with an automatic cell counter
For droplet-based scRNA-seq, GemCodeGel beads, chips and library kits (10x Genomics) were used to process single cells according to the gel beads in emulsion (GEMs) protocol (Genergy Inc., Shanghai, China). Based on the manufacturer's instructions, the Chromium Single Cell 3' V2/V3 Kit was used to construct the scRNA-seq reagent library. Then, the cell suspension generated from each sample was reacted with certain reagents to generate single-cell GEMs in the Chromium Controller for sample and cell barcoding, with a target output of 8,000 to 12,000 cells per sample. The amplified cDNA and final library were evaluated with an Agilent Bioanalyzer using a high-sensitivity DNA kit (2100, Agilent Technologies). Then, the libraries were assembled and sorted on a NovaSeq 6000; approximately 400 M readings were obtained for each sample.

tag: histolgical type

value: AIS

tag: radiological type

value: SSN

tag: gender

value: Female


title: TD9 scRNA-seq

value: IAC


title: H37Rv (A)

description: SAMPLE 1

source_name: Mtb H37Rv wild type early log phase cultures in 7H9-ADS medium

value: Wild type strain of Mtb H37Rv


title: TD8 scRNA-seq

value: pGGN

value: Male


title: TD5 scRNA-seq


title: TD3 scRNA-seq

value: MIA


title: TD4 scRNA-seq


title: TD2 scRNA-seq

value: SN


title: H37Rv (B)

description: SAMPLE 2

value: early log phase cultures in 7H9-ADS medium


title: CIC-KO2 (IDH1-WT) Input DNA rep 2

value: Immortalized Astrocyte Cells

value: CIC-KO, IDH1-WT


title: TD1 scRNA-seq


title: CIC-KO1 (IDH1-R132H) Input DNA rep 2

value: CIC-KO, IDH1-R132H

value: Input DNA


title: Group II - 7

city: Magdeburg

first: Ramiro

last: Vichez-Vargas

state: Saxony Anhalt

address: Leipzigerstr. 44

department: Gastroenterology, Hepatology and infectious diseases

institute: Otto-von-Guericke-Universität Magdeburg

data_processing:
Samples were sequenced using the 50 nt paired-end. Each sample produced 2 fastQ files and were screened for Illumina adapters and primers with the program fastq-mcf. Afterwards, filtered reads were aligned to the human genome GRCh38 using the program STAR.
The program Samtools was used to transform SAM files into BAM files and reads were sorted according the position of the alignments, based on their coordinates on each chromosome. The total number of reads per gene for each sample was generated. All samples were merged in a single table for downstream analysis using the packages uuid, stringr, parallel and data.table from R.
Genome_build: Homo_sapiens.GRCh38.97.gtf
Supplementary_files_format_and_content: count data

source_name: liver tissue

growth_protocol: life human lever tissue

extract_protocol:
Rneasy kit Qiagen for RNA extraction
Strand Specific RNA
2x 30 million reads per sample (2 x 50 nucleotides)

treatment_protocol: RNA extraction, DNA digestion, ribosomal RNA depletion and library construction

value: male

value: liver


title: Group II - 1

value: female


title: Group II - 6


title: Group II - 3


title: Group II - 5


title: Group II - 2


title: Group I - 9


title: Group I - 7


title: HigB KO (A)

description: SAMPLE 3

value: HigB KO mutant strain of Mtb H37Rv

value: early log phase cultures in 7H9-ADS medium+ Hygromycin (50ug/ml)


title: Group I - 8


title: pMV306(1955)Comp (A)

description: SAMPLE 6

value: HigB KO complemented strain of Mtb H37Rv

value: early log phase cultures in 7H9-ADS medium+ Hygromycin (50ug/ml)+Kanamycin (25ug/ml)


title: Group I - 6


title: Group I - 5


title: Group I - 2


title: Group I - 4


title: Group I - 3


title: TD6 scRNA-seq

value: SSN

value: Female


title: pENTER_ZNF32


title: Group II - 8


title: Group I - 1


title: Group II - 4


title: CIC-WT (IDH1-WT) H3K27me3 rep 1

source_name: CIC-WT (IDH1-WT) H3K27me3

value: CIC-WT, IDH1-WT


title: 20-27 (methylation)

city: Houston

first: James

middle: Cushing

last: Bayley

state: Texas

address: One Baylor Plaza

department: Neurosurgery

institute: Baylor College of Medicine

description:
20-01-027
DNA methylation profiling (EPIC 850K)

hyb_protocol: We quantified DNA with Picogreen and used 500ng for DNA bisulfite treatment. DNA was amplified for 20-24 hours at 37°C, then hybridized for 16-20 hours at 48ºC.

scan_protocol: Arrays were scanned using Illumina iScan with the Methylation NXT setting. We analyzed methylation data with Genomestudio v2011.1 and Methylation module 1.9.0

data_processing:
Raw data was imported, processed, and normalized using the ChAMP pipeline (ChAMP package, R 4.0.3) using default parameters.
Probes were filtered out if they failed to hybridize (detection p-value > 0.01), had <3 beads in 5% of samples, were not at CpG sites, were defined as multi-hit probes, were located on sex chromosomes, or were associated with single nucleotide polymorphisms (ChAMP package)
Beta values were calculated and normalized using the beta mixture quantile normalization (BMIQ, ChAMP package)
We performed SVD analysis to look for batch effects but found none that warranted correction (ChAMP package)

source_name: meningioma

label_protocol: Standard Illumina protocol.

extract_protocol: DNA was extracted from fresh-frozen blocks with an estimated purity of ≥95% using TRIzol (Thermo Fisher Scientific) according to the manufacturer’s protocol.

value: meningioma tumor


title: 17-20 (methylation)

description:
17-01-020
DNA methylation profiling (EPIC 850K)


title: 18-03 (methylation)

description:
18-01-003
DNA methylation profiling (EPIC 850K)


title: 17-24 (methylation)

description:
17-01-024
DNA methylation profiling (EPIC 850K)


title: 16-50 (methylation)

description:
16-01-050
DNA methylation profiling (EPIC 850K)


title: 18-30 (methylation)

description:
18-01-030
DNA methylation profiling (EPIC 850K)


title: DCC38 (methylation)

description:
DCC38
DNA methylation profiling (EPIC 850K)


title: DCC28 (methylation)

description:
DCC28
DNA methylation profiling (EPIC 850K)


title: 18-15 (methylation)

description:
18-01-015
DNA methylation profiling (EPIC 850K)


title: 17-10 (methylation)

description:
17-01-010
DNA methylation profiling (EPIC 850K)


title: 18-18 (methylation)

description:
18-01-018
DNA methylation profiling (EPIC 850K)


title: 18-20 (methylation)

description:
18-01-020
DNA methylation profiling (EPIC 850K)


title: 20-39 (methylation)

description:
20-01-039
DNA methylation profiling (EPIC 850K)


title: DCC23 (methylation)

description:
DCC23
DNA methylation profiling (EPIC 850K)


title: DCC29 (methylation)

description:
DCC29
DNA methylation profiling (EPIC 850K)


title: 17-03 (methylation)

description:
17-01-003
DNA methylation profiling (EPIC 850K)


title: 17-34 (methylation)

description:
17-01-034
DNA methylation profiling (EPIC 850K)


title: 18-40 (methylation)

description:
18-01-040
DNA methylation profiling (EPIC 850K)


title: DCC43 (methylation)

description:
DCC43
DNA methylation profiling (EPIC 850K)


title: DCC37 (methylation)

description:
DCC37
DNA methylation profiling (EPIC 850K)


title: 18-07 (methylation)

description:
18-01-007
DNA methylation profiling (EPIC 850K)


title: 18-29 (methylation)

description:
18-01-029
DNA methylation profiling (EPIC 850K)


title: 17-01 (methylation)

description:
17-01-001
DNA methylation profiling (EPIC 850K)


title: 18-39 (methylation)

description:
18-01-039
DNA methylation profiling (EPIC 850K)


title: 18-28 (methylation)

description:
18-01-028
DNA methylation profiling (EPIC 850K)


title: 18-45 (methylation)

description:
18-01-045
DNA methylation profiling (EPIC 850K)


title: 16-51 (methylation)

description:
16-01-051
DNA methylation profiling (EPIC 850K)


title: 18-49 (methylation)

description:
18-01-049
DNA methylation profiling (EPIC 850K)


title: ExVivoBlood-healthy control2

city: Nanchang

first: Junping

last: Yang

state: Jiangxi

address: 56 Yangming Road, Donghu District

department: Laboratory

institute: Jiangxi Chinese Medical University

description: Gene expression in peripheral blood mononuclear cells of healthy controls

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: The scanned images were analyzed with Agilent Feature Extraction software (version 11.0.1.1) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Peripheral blood mononuclear cell

label_protocol: total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA extraction from PBMCs specimens was carried out according to the manufacturer's instructions. the quality and integrity of RNA were measured by using the NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, USA) and agarose gel electrophoresis with 1% mass fraction.

treatment_protocol: 2.0-4.0ml fasting venous blood of study objects was collected in Ethylene Diamine Tetraacetic Acid (EDTA) anticoagulant tube in early morning and sent to the laboratory within 5 hours. The PBMCs were isolated using Lymphocyte Separation Medium (Human) (Solarbio, Beijing, China), TRIzol® reagent (Invitrogen; Thermo Fisher Scientific, USA) was added to the PBMCs and stored at ‑80˚C.

tag: disease state

value: healthy


title: ExVivoBlood-rheumatoid arthritis3

description: Gene expression in peripheral blood mononuclear cells of patients with rheumatoid arthritis

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

value: rheumatoid arthritis


title: ExVivoBlood-healthy control4


title: ExVivoBlood-healthy control3


title: ExVivoBlood-healthy control1


title: ExVivoBlood-rheumatoid arthritis1


title: ExVivoBlood-rheumatoid arthritis2


title: ExVivoBlood-rheumatoid arthritis4


title: DCC33 (methylation)

description:
DCC33
DNA methylation profiling (EPIC 850K)


title: 17-05 (methylation)

description:
17-01-005
DNA methylation profiling (EPIC 850K)


title: 18-08 (methylation)

description:
18-01-008
DNA methylation profiling (EPIC 850K)


title: DCC53 (methylation)

description:
DCC53
DNA methylation profiling (EPIC 850K)


title: 18-38 (methylation)

description:
18-01-038
DNA methylation profiling (EPIC 850K)


title: 15-13 (methylation)

description:
15-01-013
DNA methylation profiling (EPIC 850K)


title: 20-26 (methylation)

description:
20-01-026
DNA methylation profiling (EPIC 850K)


title: 20-28 (methylation)

description:
20-01-028
DNA methylation profiling (EPIC 850K)


title: DCC30 (methylation)

description:
DCC30
DNA methylation profiling (EPIC 850K)


title: DCC09 (methylation)

description:
DCC09
DNA methylation profiling (EPIC 850K)


title: 18-41 (methylation)

description:
18-01-041
DNA methylation profiling (EPIC 850K)


title: 17-22 (methylation)

description:
17-01-022
DNA methylation profiling (EPIC 850K)


title: 16-49 (methylation)

description:
16-01-049
DNA methylation profiling (EPIC 850K)


title: 18-26 (methylation)

description:
18-01-026
DNA methylation profiling (EPIC 850K)


title: 17-13 (methylation)

description:
17-01-013
DNA methylation profiling (EPIC 850K)


title: 20-18 (methylation)

description:
20-01-018
DNA methylation profiling (EPIC 850K)


title: 20-48 (methylation)

description:
20-01-048
DNA methylation profiling (EPIC 850K)


title: 20-22 (methylation)

description:
20-01-022
DNA methylation profiling (EPIC 850K)


title: DCC13 (methylation)

description:
DCC13
DNA methylation profiling (EPIC 850K)


title: 20-11 (methylation)

description:
20-01-011
DNA methylation profiling (EPIC 850K)


title: DCC42 (methylation)

description:
DCC42
DNA methylation profiling (EPIC 850K)


title: ATAC Ssrp1fl/+;CreERT2+/+ MCS treated with 4-OHT 2

city: Buffalo

first: Katerina

last: Gurova

state: NY

address: Elm and Carlton Str

institute: Roswell Park Cancer Institute

data_processing:
bowtie2 -p 8 --very-sensitive --no-mixed --no-unal --no-discordant -x /user/kgurova/MyProjects/Genomes/mm10_UCSC/mm10  -1 *R1*.fastq.gz  -2 *R2*.fastq.gz
picard FilterSamReads: noMulti
samtools filter on mapQ
Picard FilterSamReads: noDup
samtools filter mitochondrial reads
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: MSC

growth_protocol: DMEM 10% FBS for growth, 0.5% FBS for 48 hours before ATAC

extract_protocol:
cells were washed with PBS, lysed, and incubated with the transposition reaction mixture at 37⁰C for 30 min. The DNA was purified using the Qiagen MinElute PCR Purification Kit and amplified using PCR primer 1 and barcoded primer 2 (1 cycle of 72°C for 5 min, 98°C for 30 sec, 13 cycles of 98°C for 10 sec, 63°C for 30 sec, 72°C for 1 min). The primers were custom synthesized by Integrated DNA Technologies (IDT) using previously described sequences [Buenorstro etal].
The PCR products were purified using AmpureXP beads (Beckman Coulter). The resulting libraries were evaluated on High-Sensitivity D1000 ScreenTape using the TapeStation 4200 (Agilent Technologies). They were quantitated using the Kapa Biosystems qPCR quantitation kit for Illumina.  The libraries were pooled, denatured, and diluted to 350 pM, with a 1% PhiX control library added.  The resulting pool was loaded into a NovaSeq Reagent cartridge and sequenced using a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).

treatment_protocol: Cells were treated with 4-OHT for five days and then split. After attachment, the cells were cultured in medium containing 0.5% FBS for 48 hr. Cells (50,000) were prepared for ATAC-seq as previously described

value: primary cells

tag: cell type

tag: treatment


title: 16-41 (methylation)

description:
16-01-041
DNA methylation profiling (EPIC 850K)


title: 18-14 (methylation)

description:
18-01-014
DNA methylation profiling (EPIC 850K)


title: DCC32 (methylation)

description:
DCC32
DNA methylation profiling (EPIC 850K)


title: 16-28 (methylation)

description:
16-01-028
DNA methylation profiling (EPIC 850K)


title: 18-33 (methylation)

description:
18-01-033
DNA methylation profiling (EPIC 850K)


title: 20-50 (methylation)

description:
20-01-050
DNA methylation profiling (EPIC 850K)


title: ATAC Ssrp1fl/+;CreERT2+/+ MCS treated with 4-OHT 1


title: ATAC Ssrp1fl/+;CreERT2+/+ MCS control 2

value: control


title: 18-50 (methylation)

description:
18-01-050
DNA methylation profiling (EPIC 850K)


title: ATAC Ssrp1fl/+;CreERT2+/+ MCS control 1


title: ATAC Ssrp1fl/fl;CreERT2+/+ MCS treated with 4-OHT 2


title: ATAC Ssrp1fl/fl;CreERT2+/+ MCS treated with 4-OHT 1


title: ATAC Ssrp1fl/fl;CreERT2+/+ MCS control 2


title: ATAC Ssrp1fl/fl;CreERT2+/+ MCS control 1


title: insB 9-23_3

city: Jinan

first: Jin-Peng

last: Sun

address: 44 Wenhua Xi Rd

institute: Shandong University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data(raw reads) of fastq format were firstly processed through in-houseperl scripts.In this step,clean data(clean reads) were obtained by removing reads containing adapter,reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly.Index of the reference genome was built using Hisat 2v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat 2v2.0.5.
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.And then FPKM of each gene was calculated based on the length of the gene and readscount mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: tab_delimited text files include FPKM values for each Sample

source_name: Islets

extract_protocol:
The isolated islets are quickly put into liquid nitrogen and stored at low temperature. TRIzol (Invitrogen, Waltham, Massachusetts, USA) was used to isolate total RNA from islets according to the manufacturer's protocol. The amount of total RNA was measured with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA), and the quality was evaluated by 1% agarose gel electrophoresis, and stained with 4S Red Plus nucleic acid stain (Sango, Shanghai, China).
RNA-seq libraries were prepared using the KAPA Stranded RNA-Seq Library Preparation Kit.

value: Islets

tag: genotype

value: WT

tag: strain

value: ligand insB:9-23 stimulation


title: DCC35 (methylation)

description:
DCC35
DNA methylation profiling (EPIC 850K)

tag: tissue


title: insB 9-23_2


title: 17-04 (methylation)

description:
17-01-004
DNA methylation profiling (EPIC 850K)


title: 18-35 (methylation)

description:
18-01-035
DNA methylation profiling (EPIC 850K)


title: 18-17 (methylation)

description:
18-01-017
DNA methylation profiling (EPIC 850K)


title: 18-05 (methylation)

description:
18-01-005
DNA methylation profiling (EPIC 850K)


title: 17-35 (methylation)

description:
17-01-035
DNA methylation profiling (EPIC 850K)


title: DCC31 (methylation)

description:
DCC31
DNA methylation profiling (EPIC 850K)


title: 17-11 (methylation)

description:
17-01-011
DNA methylation profiling (EPIC 850K)


title: 17-33 (methylation)

description:
17-01-033
DNA methylation profiling (EPIC 850K)


title: 16-44 (methylation)

description:
16-01-044
DNA methylation profiling (EPIC 850K)


title: 16-14 (methylation)

description:
16-01-014
DNA methylation profiling (EPIC 850K)


title: 17-25 (methylation)

description:
17-01-025
DNA methylation profiling (EPIC 850K)


title: Vehicle_3

value: vehicle


title: DCC12 (methylation)

description:
DCC12
DNA methylation profiling (EPIC 850K)


title: Vehicle_1


title: 15-35 (methylation)

description:
15-01-035
DNA methylation profiling (EPIC 850K)


title: insB 9-23_1


title: DCC40 (methylation)

description:
DCC40
DNA methylation profiling (EPIC 850K)


title: 8096_5

first: Amruta

last: Naik

address: 3400 CIVIC CENTER BLVD

institute: Children's Hospital of Philadelphia

data_processing:
Sequencing for each library targeted 25,000 mean reads per cell.
Data was then processed using the Cell ranger pipeline (10x genomics, v.3.1.0) for demultiplexing and alignment of sequencing reads to the mouse mm10 transcriptome and creation of feature-barcode matrices
Individual single cell RNAseq libraries were aggregated using the cell ranger aggr pipeline
Data was analysed using Seurat
Genome_build: mm10

source_name: Lungs

extract_protocol:
Lungs were removed,Single cell suspension was sorted as DARQ7-CD31-CD45- lung cells . The sorted cells were loaded onto a Chromium Controller instrument (10× Genomics, Pleasanton, CA, USA) to generate single-cell barcoded droplets (GEMs) according to the manufacture’s protocol using the 10× Single Cell 3’ v1 chemistry
Resulting libraries were uniquely indexed using the Chromium i7 Sample Index Kit, pooled, and sequenced were sequenced on the Illumina NovaSeq 6000 sequencer using an SP 100 cycles flow cell in a paired-end, single indexing run

value: DARQ7-CD31-CD45- epithelial cells


title: 16-47 (methylation)

description:
16-01-047
DNA methylation profiling (EPIC 850K)


title: 18-34 (methylation)

description:
18-01-034
DNA methylation profiling (EPIC 850K)


title: 1899_3


title: DCC19 (methylation)

description:
DCC19
DNA methylation profiling (EPIC 850K)


title: 15-25 (methylation)

description:
15-01-025
DNA methylation profiling (EPIC 850K)


title: 17-15 (methylation)

description:
17-01-015
DNA methylation profiling (EPIC 850K)


title: 8096_2


title: 16-06 (methylation)

description:
16-01-006
DNA methylation profiling (EPIC 850K)


title: 15-18 (methylation)

description:
15-01-018
DNA methylation profiling (EPIC 850K)


title: 17-08 (methylation)

description:
17-01-008
DNA methylation profiling (EPIC 850K)


title: 16-02 (methylation)

description:
16-01-002
DNA methylation profiling (EPIC 850K)


title: 17-30 (methylation)

description:
17-01-030
DNA methylation profiling (EPIC 850K)


title: DCC21 (methylation)

description:
DCC21
DNA methylation profiling (EPIC 850K)


title: 14-04 (methylation)

description:
14-01-004
DNA methylation profiling (EPIC 850K)


title: Vehicle_2


title: TL-Om1 AZA-R

city: Saga

first: Tatsuro

last: Watanabe

state: Saga

address: 5-1-1 Nabeshima, Saga

country: Japan

institute: Saga University

hyb_protocol: According to the manufacturer’s instructions.

data_processing: Using GeneSpring GX (Agilent Technologies, Inc., CA). Normalized to expression of housekeeping gene controls using GeneSpring GX (Agilent Technologies, Inc., CA). Gene expression levels between samples were compared and expressed as -fold changes.

label: biotin

growth_protocol: Cells were maintained in RPMI-1640 medium (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 10% foetal bovine serum (FBS, Sigma-Aldrich, St. Louis, MO, USA).

extract_protocol: Total RNA was isolated using a Direct-zol RNA MiniPrep kit (Zymo Research, Orange, CA).

value: ATL

tag: sample type

value: azcitidine-resistant cells derived from TL-Om1 parent cells


title: 18-24 (methylation)

description:
18-01-024
DNA methylation profiling (EPIC 850K)


title: TL-Om1 DAC-R

scan_protocol: According to the manufacturer’s instructions.

value: decitabine-resistant cells derived from TL-Om1 parent cells


title: 1899_4


title: DCC27 (methylation)

description:
DCC27
DNA methylation profiling (EPIC 850K)


title: MT-2 AZA-R

label_protocol: According to the manufacturer’s instructions.

value: azacitidine-resistant cells derived from MT-2 parent cells


title: TL-Om1 parent

value: parent cells


title: 15-17 (methylation)

description:
15-01-017
DNA methylation profiling (EPIC 850K)


title: invivo_day10_Fp_PEB0191 [D10_10]

first: Philipp

last: Engel

address: Biophore Building

institute: University of Lausanne

data_processing:
Trimming for adapters and quality using trimmomatic
For the in vivo: separation of rRNA and non-rRNA reads using sortmerna
Mapping to reference with bowtie2
Generation of count files with HtSeq
Differential gene expression analysis with EdgeR
Genome_build: Reference genome used for read alignment
Supplementary_files_format_and_content: .count files containing counts per gene obtained with HtSeq

source_name: in vivo colonization

extract_protocol:
Trizol-based RNA extraction
RiboZero rRNA depletion followed by Illumina Truseq library preparation. In vivo samples were depleted of eukaryotic mRNA usig polyA-depletion

value: wild type colonization of microbiota-free bees, sampling at day 10 post inoculation

tag: Stage

value: 10 days of bee colonization


title: MT-2 DAC-R

value: decitabine-resistant cells derived from MT-2 parent cells


title: MT-2 parent


title: invivo_day10_Fp_PEB0191 [D10_7]


title: invivo_day10_Fp_PEB0191 [D10_2]


title: invivo_day10_Fp_PEB0191 [D10_1]


title: invivo_day5_Fp_PEB0194 [D5_10]

value: wild type colonization of microbiota-free bees, sampling at day 5 post inoculation

value: 5 days of bee colonization


title: invivo_day5_Fp_PEB0193 [D5_7]


title: DCC25 (methylation)

description:
DCC25
DNA methylation profiling (EPIC 850K)

value: meningioma tumor


title: TD8  [ST]

value: AIS

value: pGGN

value: Male


title: 17-19 (methylation)

description:
17-01-019
DNA methylation profiling (EPIC 850K)


title: 17-02 (methylation)

description:
17-01-002
DNA methylation profiling (EPIC 850K)


title: 18-42 (methylation)

description:
18-01-042
DNA methylation profiling (EPIC 850K)


title: invivo_day5_Fp_PEB0192 [D5_2]


title: 18-43 (methylation)

description:
18-01-043
DNA methylation profiling (EPIC 850K)


title: 17-28 (methylation)

description:
17-01-028
DNA methylation profiling (EPIC 850K)


title: 15-24 (methylation)

description:
15-01-024
DNA methylation profiling (EPIC 850K)


title: TD5  [ST]

value: SSN

value: Female


title: 18-13 (methylation)

description:
18-01-013
DNA methylation profiling (EPIC 850K)


title: invivo_day5_Fp_PEB0191 [D5_1]


title: 18-48 (methylation)

description:
18-01-048
DNA methylation profiling (EPIC 850K)


title: 17-12 (methylation)

description:
17-01-012
DNA methylation profiling (EPIC 850K)


title: DCC10 (methylation)

description:
DCC10
DNA methylation profiling (EPIC 850K)


title: 15-23 (methylation)

description:
15-01-023
DNA methylation profiling (EPIC 850K)


title: invitro_FpW3

source_name: in vitro culture

value: PEB0191 ihfA-1

value: ihfA-1 (Pro83-->Lys83) mutant growth in mTYG

value: 16 hours of growth


title: DCC07 (methylation)

description:
DCC07
DNA methylation profiling (EPIC 850K)


title: invitro_FpW2


title: TD3  [ST]

value: MIA


title: lung_room air_mouse 3_rep2

city: Braunschweig

first: Prof. Hamid

last: Hossain

state: Lower Saxony

address: Celler Str. 38

department: Microbiology

institute: Klinikum Braunschweig

hyb_protocol: Purified cRNA were fragmented in fragmentation buffer (40 mM Tris-acetate pH 7.9, 100 mM KOAc, 31.5 mM MgOAc) at 94gr.C for 20 minutes. For hybridization on CodeLink bioarrays, 10 ug of fragmented cRNA in 260 ul of hybridization solution was added to each bioarray via the Flex Chamber port and incubated for 18 hours in a Minitron shaker incubator (Infors AG, Germany) at 37gr.C, 300 rpm. cRNA of each group was hybridized in duplicate (technical replicates). Bioarrays were processed in parallel using the CodeLink Shaker Kit and CodeLink Parallel Processing Kit (Amersham Biosciences).

scan_protocol: Bioarrays were scanned using the GenePix 4000 B scanner and the GenePix Pro 4.0 Software (Axon Instruments, Arlington, USA).

data_processing: Spot signals of the CodeLink bioarrays were quantified using CodeLink System Software 5.0.0.31312 based on ImaGene 5.5 (BioDiscovery, Marina Del Ray, CA). The image segmentation and quantification process is outlined in the ImaGene 5.5 user's manual. CodeLink System Software 5.0.0.31312 generated background corrected raw as well as intra-slide normalized data. The intra-slide normalized data were used for further analysis.

source_name: lung

label_protocol: Total RNA were subjected to cDNA synthesis using a poly-A binding primer containing the T7-polymerase promoter (CodeLink Expression Assay Kit). Double-stranded DNA fragments were purified using the QIAquickTM PCR Purification Kit (Qiagen, Germany). For target labeling, the cDNA was in-vitro transcribed (IVT) by partially substituting UTP with bio-16-UTP in the reaction mixture. Labeled cRNA was purified using the RNeasy Mini Kit (Qiagen, Germany). The eluted cRNA was quantified with the NanoDrop (NanoDrop Technologies) and quality was assesed with the Agilent 2100 bioanalyser (Agilent Technologies GmbH).

growth_protocol: Animals were kept under controlled conditions of light, temperature and humidity receiving water and standard food ad libitum.

extract_protocol: Total RNA was extracted from frozen murine lung tissues using the miRNeasy Mini Kit (Qiagen, Germany). Quality and quantity of RNA were checked by Agilent 2100 Bioanalyzer and UV spectrophotometer.

treatment_protocol: All animals breathed spontaneously in room air and were investigated in two technical replicates.

tag: age

value: male

value: lung tissue

tag: body weight

value: wild type


title: 16-35 (methylation)

description:
16-01-035
DNA methylation profiling (EPIC 850K)


title: 15-32 (methylation)

description:
15-01-032
DNA methylation profiling (EPIC 850K)


title: TD2  [ST]

value: IAC

value: SN


title: lung_room air_mouse 3_rep1


title: DCC51 (methylation)

description:
DCC51
DNA methylation profiling (EPIC 850K)


title: TD1  [ST]


title: lung_room air_mouse 2_rep2


title: invitro_FpY3

value: PEB0191 wild type

value: wild type growth in mTYG


title: DCC06 (methylation)

description:
DCC06
DNA methylation profiling (EPIC 850K)

value: meningioma tumor


title: invitro_FpY2


title: DCC36 (methylation)

description:
DCC36
DNA methylation profiling (EPIC 850K)


title: 17-29 (methylation)

description:
17-01-029
DNA methylation profiling (EPIC 850K)


title: lung_room air_mouse 2_rep1


title: lung_room air_mouse 1_rep2


title: invitro_FpY1


title: WAT

status: Public on Nov 29 2021

city: Aurora

first: Makoto

last: Miyazaki

state: CO

address: 12700 E 22nd PL Denver CO

institute: University of Colorado

data_processing:
First the DEseq2 removes the abnormal readcounts including 0 or super high counts compared to others, then DEseq2 shall normalized the fpkm based on horizontal and vertical methods(gene across all samples and all genes within one sample.) The detailed information can be found in the DESeq2 manual script and within the fpkm function there are plenty of explanation of the calculation.
Supplementary_files_format_and_content: FPKMs

source_name: Epididymal fat

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with DirectZol kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: 8 week-old C57BL/6J males fed a chow diet.

value: Epididymal fat

tag: Sex


title: Thymus

source_name: Thymus

value: Thymus


title: Testis

source_name: Testis

value: Testis


title: 17-23 (methylation)

description:
17-01-023
DNA methylation profiling (EPIC 850K)


title: DCC22 (methylation)

description:
DCC22
DNA methylation profiling (EPIC 850K)


title: Skeletal Muscle

source_name: skeletal Muscle (Gastronemius)

value: skeletal Muscle (Gastronemius)


title: invitro_FpW1

city: Lausanne


title: Lung

source_name: Lung

value: Lung


title: 17-09 (methylation)

description:
17-01-009
DNA methylation profiling (EPIC 850K)


title: DCC18 (methylation)

description:
DCC18
DNA methylation profiling (EPIC 850K)


title: lung_room air_mouse 1_rep1


title: Spleen

source_name: Spleen

value: Spleen


title: Kidney

source_name: Kidney

value: Kidney


title: Stomach

source_name: Stomach

value: Stomach


title: Heart

source_name: Heart

value: Heart


title: Liver

source_name: Liver

value: Liver

value: male


title: Intestine

source_name: Intestine

value: Intestine


title: Eye

source_name: Eye

value: Eye


title: DCC34 (methylation)

description:
DCC34
DNA methylation profiling (EPIC 850K)

source_name: meningioma


title: TD6  [ST]

source_name: Lung adenocarcinoma

value: MIA

value: SSN

value: Female


title: Skin

source_name: Skin

value: Skin


title: Brain

source_name: Brain

value: Brain


title: Aorta

source_name: Aorta

value: Aorta


title: Parathyroid

source_name: Parathyroid

value: Parathyroid


title: Colon

source_name: Colon

value: Colon


title: BAT

source_name: Brown adipose tissue

value: Brown adipose tissue


title: ChIC_GM12878_IgG_Rep2

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

data_processing:
library strategy: ChIC-seq
Raw paired-end reads in FASTQ format were mapped to human reference genome hg38 by Bowtie2. Proper mapped unique paired-end reads with MAPQ >= 10 were used for following analysis. Peaks called by cLoops2 were performed with key parameters of cLoops2 callPeaks -eps 100,200 -minPts 5 -bdg IgG.
Genome_build: hg38
Supplementary_files_format_and_content: BEDPE files contain the high quality and unique processed paired-end  tags. BED files contain peaks called by cLoops2

growth_protocol: GM12878 cells were cultured in RPMI 1640 medium supplied with 15% fetal bovine serum and 2mM L-glutamine.

extract_protocol:
Small cell number ChIC-seq assays were performed similarly to our previous study (62). Briefly, GM12878 cells were fixed for 10 minutes in 1% formaldehyde in the DMEM medium. The reaction was stopped by adding 0.125 M glycine. Following permeabilization of 200,000 fixed GM12878 cells with 600 μl RIPA buffer with 0.1% SDS at room temperature for 5 minutes, the cells were rinsed with 600 μl binding buffer twice (10 mM Tris-Cl, 1 mM EDTA, 150 mM NaCl, 0.1% TX-100) and re-suspended in 250 μl binding buffer. Before mixing with the cells, antibodies ((CTCF (Millipore, 47-729), H3K4me3 (Millipore, CS200580), H3K27ac (Abcam, ab4729), IgG (Millipore, NI03)) and PA-MNase were pre-incubated with a molecular ratio of 1:2 at 4 °C for 30 minutes in 50 μl binding buffer for generating antibody+PA-MNase complexes. Then, the permeabilizated GM12878 cells in 50 μl binding buffer were mixed with each antibody+PA-MNase complex and incubated for 1 hour at 4 °C. Cells were washed using 600 μl RIPA buffer (10 mM Tris-Cl, 1 mM EDTA, 150 mM NaCl, 0.1% SDS, 0.1% NaDOC, 1% Triton X-100) four times and pelleted by centrifugation at 900g for 1 minute. Next, cells were rinsed using 200 μl rinsing buffer (10 mM Tris-Cl and 10 mM NaCl, 0.1% TX-100). MNase digestion reactions were activated by re-suspending cells in 40 μl reaction buffer (10 mM Tris-Cl, 10 mM NaCl, 0.1% TX-100, 2 mM CaCl2) and incubated at 37 °C for 3 minutes. Reactions were stopped by adding 80 μl stop buffer (20 mM Tris-Cl, 10 mM EGTA, 20 mM NaCl, 0.2% SDS). Reverse crosslinking was performed by adding 1 μl 20mg/ml proteinase K and incubating samples at 65 °C  overnight. DNA was purified using the MinElute reaction cleanup kit following the manufacturer's protocol.
The purified DNA was end-repaired using an End-It DNA-Repair kit (Epicenter, Cat#ER81050) and added an A base at the 3' end using the Klenow fragment (3’→5’ exo-) (NEB, Cat#M0212L). The DNA was then ligated with Y-shaped adaptors and amplified for 16 cycles using indexing primers with the PCR condition: 98 °C,10”; 67°C, 30”; 72°C, 30” as previously reported (63, 64). PCR products between 150-350 bp were isolated for sequencing on Illumina NovaSeq.

treatment_protocol: No treamtent.

tag: antibody

value: IgG


title: ChIC_GM12878_IgG_Rep1

tag: cell line


title: ChIC_GM12878_H3K27ac_Rep1


title: ChIC_GM12878_H3K4me3_Rep1


title: ChIC_GM12878_H3K27ac_Rep2


title: THP ko sham kidney

city: Indianapolis

first: Seth

last: Winfree

email: winfrees@iu.edu, swinfree@unmc.edu

state: Indiana

address: 950 W Walnut St

institute: Indiana University

description: generated from both kidneys from one mouse

data_processing:
Cellranger (10X Genomic v.3.0.2)  was used to process raw sequencing data including demultiplexing (bcl2fastq) and generate fastq files (as provided).
STAR was used to align the output fastq filesto the mm10 reference genome.
Expression levels for genes were tallied for each cell by UMIs from the aligned reads.
expression matrices, gene and cell UMI files generated (as provided in processed data .zip files).
Genome_build: mm10
Supplementary_files_format_and_content: tar.gz file contains barcode.tsv.gz, features.tsv.gz and matrix.mtx.gx for loading into analysis tool of choice

source_name: kidney

extract_protocol:
kidneys were removed and processed by a MACs cell isolation protocol which inlcuded mechanical and enzymatic dissolution and dead cell removal (Reference, PMID:33448928).
Cell suspension was loaded onto a Chromium Single Cell Instrument (10X Genomics)

value: 8-12 weeks

value: kidney

value: Umod/Tamm horsfall protein knock-out


title: ChIC_GM12878_CTCF_Rep2

value: CTCF


title: B6_ANAinduced

status: Public on Nov 27 2021

city: Perugia

first: Luigina

last: Romani

address: P.le Lucio Severi 1

country: Italy

institute: University of Perugia

data_processing:
By base calling, the original image data produced by the sequencer is transferred into sequences
Data filtering is carried out to obtain high quality reads as the clean reads (clean data). The procedure include following steps:  1. Remove reads with adaptor sequences. 2. Remove reads in which the percentage of unknown bases (N) is greater than 10%. 3. Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, we define this read as low quality.
Clean reads were mapped to reference sequences and/or reference gene set using SOAPaligner/SOAP2. No more than 2 mismatches were allowed in the alignment.
The expression level for each gene is determined by the numbers of reads uniquely mapped to the specific gene and the total number of uniquely mapped reads in the sample. The gene expression level is calculated by using RPKM method
Supplementary_files_format_and_content: Excel files including RPKM values for each Sample

source_name: alverolar macrophages

extract_protocol:
RNA was harvested using Trizol reagent.The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Macrophages were isolated from total lung cells after 2 h plastic adherence at 37 °C. Cells were stimulated with 10 ug/ml of anakinra for 5 h

value: Lung


title: B6_untreated


title: IL1R_ANAinduced


title: CSD 3

status: Public on Nov 24 2021

city: Beijing

first: Xiaoye

last: Duan

state: dongcheng

address: Beijing hospital

institute: beijing hospital

data_processing:
RNA-seq was performed on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data of FASTQ format were aligned to UCSC rn6 using hisat2 (v2.2.1) and the genes were quantified by HTSeq (v0.12.4).
Genome_build: rn6
Supplementary_files_format_and_content: raw counts

organism: Rattus norvegicus

source_name: bone tissue

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA)

value: Wistar

value: femur

value: 17 weeks

value: chronic sleep deprivation (CSD)


title: Coronal brain section, heme-albumin 10 nmol (10 µL of 1000 µmol/L)

status: Public on Nov 25 2021

city: Zürich

first: Raphael

middle: Matthias

last: Buzzi

address: Rämistrasse 100

department: Division of Internal Medicine

institute: Universitätsspital and University of Zurich

description: spatial transcriptome

data_processing:
The Space Ranger Software Suite (spaceranger-1.1.0) was used for cDNA oligopeptide alignment, barcode assignment and UMI counting from fastq data from the Illumina sequencing.
The resulting gene expression matrices were further analyzed with Python (version 3.8.8) using the Scanpy (version 1.6.0) library.
Ensembl GRCm38.p6 Release M23
Supplementary_files_format_and_content: heme_1000_tissue_positions_list.csv (A text file containing the table with rows that correspond to spots and columns specifiying the barcode, the tissue state, the row and column coordinate in the array, and the row and column pixel coordinate in the histological image.)
Supplementary_files_format_and_content: heme_1000_aligned_fiducials.jpg (Image with the overlay of the histological image and the fiducial spots found by the fiducial alignment algorithm.)
Supplementary_files_format_and_content: heme_1000_detected_tissue_image.jpg (Image with the overlay of the histological image and all features, where the features under tissue found by the  alignment algorithm are highted in red.)
Supplementary_files_format_and_content: heme_1000_scalefactors_json.json (Scale factors for the alignement of the feature spots and the image of the histological section calculagted by the alignment algorithm.)
Supplementary_files_format_and_content: heme_1000_tissue_hires_image.png (Image of the H&E stained histological section (high resolution))
Supplementary_files_format_and_content: heme_1000_tissue_lowres_image.png (Image of the H&E stained histological section (low resolution))
Supplementary_files_format_and_content: heme_1000_matrix.mtx.gz (Count expression matrix)
Supplementary_files_format_and_content: heme_1000_barcodes.tsv.gz (List of all unique 10 x barcode with sample origin)
Supplementary_files_format_and_content: heme_1000_features.tsv.gz (Identifier and name of all features)
Supplementary_files_format_and_content: heme_1000_filtered_feature_bc_matrix.h5 (Feature-barcode matrix filtered for barcodes from spots under tissue, where each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column).)
Supplementary_files_format_and_content: heme_1000_cloupe.cloupe (Proprietary file for visualization of the data in the Loupe browser from 10X genomics.)
Supplementary_files_format_and_content: heme_1000_metrics_summary.csv (Table with the summary of the experiment)

source_name: coronal brain section

extract_protocol:
Mice were transcardially perfused with 50 mL ice cold PBS. Then the brain was extracted, immediately flash frozen in cold Tissue-Tek OCT Compound (Sakura Finetek, Netherlands) using liquid nitrogen cooled isopentane and stored at -80 °C until sectioning. Time of brain extraction until freezing was kept below one minute. Then, using a Leica CM3050 S Cryostat (Leica, Germany) 10 µm coronal cryosections were prepared and placed within the etched frames of the capture areas on the active surface of the Visium Spatial Slide (10X Genomics, Pleasanton, CA, USA) and processed according to the manufacturer’s instructions (User Guide CG000239, Rev A). In brief, sections were fixed with cold methanol (-20°C), stained with haematoxylin and eosin. Brightfield images of stained sections in the fiducial frames were obtained with an AxioObserver (Zeiss, Germany) prior to permeabilization. Stained tissue sections were permeabilized for 6 minutes, as experimentally determined using the Visium Spatial Tissue Optimization Slide & Reagent kit (10X Genomics). After permeabilization the released mRNA bound to oligonucleotides on the capture areas, followed by reverse transcription, second strand synthesis, denaturation, cDNA amplification and SPRIselect cDNA cleanup.
The resulting barcoded cDNA was  and amplified for 15 cycles (as recommended by the 10x Genomics user guide based on the result of the RT-PCR). After amplification and clean up with SPRIselectc reagents, library was constructed as recommended by the 10x Genomics user guide. The quality and concentration of the cDNA were assessed using High-Sensitivity D5000 ScreenTape (Agilent) and then subjected to enzymatic fragmentation, end repair and A-tailing. Library quality and concentration were assessed using High-Sensitivity D5000 ScreenTape (Agilent). Then the  3ʹ Gene Expression libraries for each sample were pooled at an equimolar amount and sequenced using the Illumina NovaSeq 6000 system following the  recommendations of 10x Genomics.

treatment_protocol: Mice (C57BL/6J, male, 10-12 weeks) were anesthetized with isoflurane (4-5% for induction, 1-2% for maintenance; Baxter Healthcare Co. Deerfield, IL, USA) evaporated in 100% oxygen and placed in a motorized stereotaxic frame (Stoelting, Dublin, Ireland). Throughout the surgical procedure, body temperature was maintained constant. After a cranial midline skin incision, a small borehole was stereotactically localized and drilled, and a 33G needle was slowly advanced (0.1 mm/s) into the right striatum (bregma coordinates: 2 mm ML, 0.5 mm AP, 3.5 mm DV) followed by injection of 10 µl heme-albumin, heme-Hpx, or saline (sham) with an infusion rate of 1000 nL/min. The needle was left in place for 5 minutes, then removed slowly and the skin incision was closed with a suture. After the surgical procedure, the animals were placed in a heated wake-up box and monitored until they fully recovered and could be transferred back to their homecages.

value: male

value: 10-12 weeks

value: coronal brain section

value: 10 nmol heme-albumin in 10 µL (10 µL of 1000 µmol/L)


title: Coronal brain section, heme-albumin 5.0 nmol in 10 µL (10 µL of 500 µmol/L)

description: spatial transcriptome

data_processing:
The Space Ranger Software Suite (spaceranger-1.1.0) was used for cDNA oligopeptide alignment, barcode assignment and UMI counting from fastq data from the Illumina sequencing.
The resulting gene expression matrices were further analyzed with Python (version 3.8.8) using the Scanpy (version 1.6.0) library.
Genome_build: Ensembl GRCm38.p6 Release M23
Supplementary_files_format_and_content: heme_0500_tissue_positions_list.csv (A text file containing the table with rows that correspond to spots and columns specifiying the barcode, the tissue state, the row and column coordinate in the array, and the row and column pixel coordinate in the histological image.)
Supplementary_files_format_and_content: heme_0500_aligned_fiducials.jpg (Image with the overlay of the histological image and the fiducial spots found by the fiducial alignment algorithm.)
Supplementary_files_format_and_content: heme_0500_detected_tissue_image.jpg (Image with the overlay of the histological image and all features, where the features under tissue found by the  alignment algorithm are highted in red.)
Supplementary_files_format_and_content: heme_0500_scalefactors_json.json (Scale factors for the alignement of the feature spots and the image of the histological section calculagted by the alignment algorithm.)
Supplementary_files_format_and_content: heme_0500_tissue_hires_image.png (Image of the H&E stained histological section (high resolution))
Supplementary_files_format_and_content: heme_0500_tissue_lowres_image.png (Image of the H&E stained histological section (low resolution))
Supplementary_files_format_and_content: heme_0500_matrix.mtx.gz (Count expression matrix)
Supplementary_files_format_and_content: heme_0500_barcodes.tsv.gz (List of all unique 10 x barcode with sample origin)
Supplementary_files_format_and_content: heme_0500_features.tsv.gz (Identifier and name of all features)
Supplementary_files_format_and_content: heme_0500_filtered_feature_bc_matrix.h5 (Feature-barcode matrix filtered for barcodes from spots under tissue, where each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column).)
Supplementary_files_format_and_content: heme_0500_cloupe.cloupe (Proprietary file for visualization of the data in the Loupe browser from 10X genomics.)
Supplementary_files_format_and_content: heme_0500_metrics_summary.csv (Table with the summary of the experiment)

value: 5.0 nmol heme-albumin in 10 µL (10 µL of 500 µmol/L)


title: CSD 2

value: 16 weeks


title: Coronal brain section, heme-hemopexin 10 nmol (10 µL of 1000 µmol/L)

description: spatial transcriptome

data_processing:
The Space Ranger Software Suite (spaceranger-1.1.0) was used for cDNA oligopeptide alignment, barcode assignment and UMI counting from fastq data from the Illumina sequencing.
The resulting gene expression matrices were further analyzed with Python (version 3.8.8) using the Scanpy (version 1.6.0) library.
Genome_build: Ensembl GRCm38.p6 Release M23
Supplementary_files_format_and_content: hemeHpx_1000_tissue_positions_list.csv (A text file containing the table with rows that correspond to spots and columns specifiying the barcode, the tissue state, the row and column coordinate in the array, and the row and column pixel coordinate in the histological image.)
Supplementary_files_format_and_content: hemeHpx_1000_aligned_fiducials.jpg (Image with the overlay of the histological image and the fiducial spots found by the fiducial alignment algorithm.)
Supplementary_files_format_and_content: hemeHpx_1000_detected_tissue_image.jpg (Image with the overlay of the histological image and all features, where the features under tissue found by the  alignment algorithm are highted in red.)
Supplementary_files_format_and_content: hemeHpx_1000_scalefactors_json.json (Scale factors for the alignement of the feature spots and the image of the histological section calculagted by the alignment algorithm.)
Supplementary_files_format_and_content: hemeHpx_1000_tissue_hires_image.png (Image of the H&E stained histological section (high resolution))
Supplementary_files_format_and_content: hemeHpx_1000_tissue_lowres_image.png (Image of the H&E stained histological section (low resolution))
Supplementary_files_format_and_content: hemeHpx_1000_matrix.mtx.gz (Count expression matrix)
Supplementary_files_format_and_content: hemeHpx_1000_barcodes.tsv.gz (List of all unique 10 x barcode with sample origin)
Supplementary_files_format_and_content: hemeHpx_1000_features.tsv.gz (Identifier and name of all features)
Supplementary_files_format_and_content: hemeHpx_1000_filtered_feature_bc_matrix.h5 (Feature-barcode matrix filtered for barcodes from spots under tissue, where each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column).)
Supplementary_files_format_and_content: hemeHpx_1000_cloupe.cloupe (Proprietary file for visualization of the data in the Loupe browser from 10X genomics.)
Supplementary_files_format_and_content: hemeHpx_1000_metrics_summary.csv (Table with the summary of the experiment)

value: 10 nmol heme-hemopexin in 10 µL (10 µL of 1000 µmol/L)


title: Coronal brain section, heme-albumin 1.25 nmol in 10 µL (10 µL of 125 µmol/L)

description: spatial transcriptome

data_processing:
The Space Ranger Software Suite (spaceranger-1.1.0) was used for cDNA oligopeptide alignment, barcode assignment and UMI counting from fastq data from the Illumina sequencing.
The resulting gene expression matrices were further analyzed with Python (version 3.8.8) using the Scanpy (version 1.6.0) library.
Genome_build: Ensembl GRCm38.p6 Release M23
Supplementary_files_format_and_content: heme_0125_tissue_positions_list.csv (A text file containing the table with rows that correspond to spots and columns specifiying the barcode, the tissue state, the row and column coordinate in the array, and the row and column pixel coordinate in the histological image.)
Supplementary_files_format_and_content: heme_0125_aligned_fiducials.jpg (Image with the overlay of the histological image and the fiducial spots found by the fiducial alignment algorithm.)
Supplementary_files_format_and_content: heme_0125_detected_tissue_image.jpg (Image with the overlay of the histological image and all features, where the features under tissue found by the  alignment algorithm are highted in red.)
Supplementary_files_format_and_content: heme_0125_scalefactors_json.json (Scale factors for the alignement of the feature spots and the image of the histological section calculagted by the alignment algorithm.)
Supplementary_files_format_and_content: heme_0125_tissue_hires_image.png (Image of the H&E stained histological section (high resolution))
Supplementary_files_format_and_content: heme_0125_tissue_lowres_image.png (Image of the H&E stained histological section (low resolution))
Supplementary_files_format_and_content: heme_0125_matrix.mtx.gz (Count expression matrix)
Supplementary_files_format_and_content: heme_0125_barcodes.tsv.gz (List of all unique 10 x barcode with sample origin)
Supplementary_files_format_and_content: heme_0125_features.tsv.gz (Identifier and name of all features)
Supplementary_files_format_and_content: heme_0125_filtered_feature_bc_matrix.h5 (Feature-barcode matrix filtered for barcodes from spots under tissue, where each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column).)
Supplementary_files_format_and_content: heme_0125_cloupe.cloupe (Proprietary file for visualization of the data in the Loupe browser from 10X genomics.)
Supplementary_files_format_and_content: heme_0125_metrics_summary.csv (Table with the summary of the experiment)

value: 1.25 nmol heme-albumin in 10 µL (10 µL of 125 µmol/L)


title: CSD 1

value: 15 weeks


title: NC 3

value: 14 weeks

value: control


title: NC 2

value: 13 weeks


title: NC 1

value: 12 weeks


title: Coronal brain section, heme-albumin 0.30 nmol in 10 µL (10 µL of 30 µmol/L)

description: spatial transcriptome

data_processing:
The Space Ranger Software Suite (spaceranger-1.1.0) was used for cDNA oligopeptide alignment, barcode assignment and UMI counting from fastq data from the Illumina sequencing.
The resulting gene expression matrices were further analyzed with Python (version 3.8.8) using the Scanpy (version 1.6.0) library.
Genome_build: Ensembl GRCm38.p6 Release M23
Supplementary_files_format_and_content: heme_0030_tissue_positions_list.csv (A text file containing the table with rows that correspond to spots and columns specifiying the barcode, the tissue state, the row and column coordinate in the array, and the row and column pixel coordinate in the histological image.)
Supplementary_files_format_and_content: heme_0030_aligned_fiducials.jpg (Image with the overlay of the histological image and the fiducial spots found by the fiducial alignment algorithm.)
Supplementary_files_format_and_content: heme_0030_detected_tissue_image.jpg (Image with the overlay of the histological image and all features, where the features under tissue found by the  alignment algorithm are highted in red.)
Supplementary_files_format_and_content: heme_0030_scalefactors_json.json (Scale factors for the alignement of the feature spots and the image of the histological section calculagted by the alignment algorithm.)
Supplementary_files_format_and_content: heme_0030_tissue_hires_image.png (Image of the H&E stained histological section (high resolution))
Supplementary_files_format_and_content: heme_0030_tissue_lowres_image.png (Image of the H&E stained histological section (low resolution))
Supplementary_files_format_and_content: heme_0030_matrix.mtx.gz (Count expression matrix)
Supplementary_files_format_and_content: heme_0030_barcodes.tsv.gz (List of all unique 10 x barcode with sample origin)
Supplementary_files_format_and_content: heme_0030_features.tsv.gz (Identifier and name of all features)
Supplementary_files_format_and_content: heme_0030_filtered_feature_bc_matrix.h5 (Feature-barcode matrix filtered for barcodes from spots under tissue, where each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column).)
Supplementary_files_format_and_content: heme_0030_cloupe.cloupe (Proprietary file for visualization of the data in the Loupe browser from 10X genomics.)
Supplementary_files_format_and_content: heme_0030_metrics_summary.csv (Table with the summary of the experiment)

value: 0.30 nmol heme-albumin in 10 µL (10 µL of 30 µmol/L)


title: IL1R_untreated

value: Lung


title: 2-DCV+Enoxacin

status: Public on Nov 22 2021

city: Wuhan

first: Yang

last: Qiu

state: Hubei

address: No. 44 Xiaohongshan Central District, Wuchang District,

institute: Wuhan institue of virology, CAS

description: small RNA

data_processing:
Briefly, libraries of small RNAs from cells with different treatments were constructed using TruSeq Small RNA Library Preparation Kits (Illumina) according to manufacturer’s instructions. The libraries were sequenced by Illumina HiSeq 2000 at Bioacme (Wuhan, China). Quality control and adapter trimming were performed using Trim Galore (v0.6.4) with default parameter. Reads length between 17 and 70 were used for subsequent analysis. The sequencing reads were mapped to the Drosophila genome (release 6) by using Bowtie 2.2.5 and miRNA reads were determined on the basis of the number of reads, which were 100% identical to the annotated miRNA sequences in miRBase version 22. The vsRNA reads that cannot be mapped to the Drosophila genome were then mapped to the DCV genome allowing 2 nt mismatch. The subsequent analysis of distribution and length of these vsRNAs were calculated using in-house Perl scripts.
Bam files generated by Bowtie 2.2.5.
Genome_build: Drosophila genome (Release 6)
Supplementary_files_format_and_content: Tab-delimited text files include read counts.

organism:
Drosophila melanogaster
Drosophila C virus strain EB

source_name: Drosophila S2 cells

treatment_protocol: Infection with Drosophila C virus (DCV) (GenBank: NC_001834.1).

tag: infection

value: Drosophila C virus (DCV)

value: Enoxacin


title: 1-DCV

description: small RNA

extract_protocol: TruSeq Small RNA Library Preparation Kits (Illumina)

value: Control


title: 2-EV-A71 in shSTUB1 mice

description: small RNA

data_processing:
The deep sequencing and data analysis have been described previously. Briefly, libraries of small RNAs were constructed using TruSeq Small RNA Library Preparation Kits (Illumina) according to manufacturer’s protocols, and then sequenced by Illumina HiSeq 2000 at Bioacme (Wuhan, China). The sequenced reads were mapped to the mouse genome (release GRCm38) by using Bowite 2.2.5. The vsRNA reads were mapped to EV-A71 genome with 100% identity. The distribution and length of vsRNA reads were conducted by using in-house Perl scripts.
Bam files generated by Bowtie 2.2.5.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include read counts.

organism:
Mus musculus
Enterovirus A71

source_name: ICR mice

extract_protocol: TruSeq Small RNA Library Preparation Kits (Illumina).

treatment_protocol: EV-A71 VR1432 (GenBank: KC954664.1) infection.

value: ICR

tag: shRNA

value: Hind leg muscles

value: Human enterovirus A71


title: 1-EV-A71 in shScramble mice

description: small RNA

value: shScramble


title: Bone

source_name: Bone

value: Bone

value: male


title: FS12

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

data_processing:
The quality of the sequencing reads was evaluated using FastQC software (version 0.11.7). Read trimming was performed using Trim Galore software (version 0.4.4).
Reads were mapped to the mouse reference genome using Hisat2 sofware (version 2.1.0).
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty).
Genome_build: Mouse genome assembly (GRCm39)
Supplementary_files_format_and_content: Tab-delimited text files including ensembl gene id and number of mapped reads

source_name: mammary gland

extract_protocol:
RNA extraction was performed using Qiagen RNeasy Micro Kit (Qiagen Germantown, MD).
All the RNA-sequencing procedures were performed by Novogene Bioinformatics Technology Co., Ltd (Beijing, China). Sequencing libraries were prepared using a Poly-A tail capture method and sequenced with NovaSeq 6000.

value: mammary gland

tag: diet

value: folic acid supplemented diet

tag: drug

value: saline


title: ChIC_GM12878_H3K4me3_Rep2


title: FS5


title: FS4


title: ChIC_GM12878_CTCF_Rep1

value: CTCF


title: FF10

value: fluoxetine


title: FS3


title: FS1


title: FF12


title: FF6


title: FF4


title: FF5


title: FF3


title: FF1


title: FF2


title: BS10

value: breeder diet


title: BS12


title: BS6


title: BS3


title: BS2


title: BS1


title: BF13


title: BF9


title: BF6


title: BF7


title: BF5


title: BF2


title: FS10