title: MN_sample1_358_H1_R1


title: MN_sample1_358_G23_R1

status: Public on Sep 29 2023

type: SRA

city: Stockholm

first: Abdel

last: El Manira

address: Solnavagen 9

department: Neuroscience

country: Sweden

institute: Karolinaska Institutet

library_source: transcriptomic single cell

data_processing:
The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio_rerio, Ensembl, GRCz11” using STAR (version 2.5.3a).
The resulting bam files were filtered to keep only uniquely mapped reads.
Most of the following analysis was performed in R (version 4.0.5, R core team, 2022) using the Seurat package (version 4.0.2).
Assembly: GRCz11
Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis

molecule: polyA RNA

organism: Danio rerio

source_name: Spinal cord

extract_protocol:
Adult animals (7 weeks old) of either sex were deeply anesthetized in a slush of frozen extracellular solution containing (in mM): 134 NaCl, 2.9 KCl, 2.1 CaCl2, 1.2 MgCl2, 10 HEPES and 10 glucose, with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tg(islet1a:GFP) line, and two samples were prepared from the Tg(chx10:GFP) line. For each sample, 6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM-F12 medium (Thermo Fisher, #11039021, osmolarity adjusted to 280-280 mOsm) containing papain 10 U/ml (Worthington-biochem, #LK003178) on a heated shaker at 37°C for 15 min. DMEM/F-12 (1 ml, 280-290 mOsm) was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min, and then re-suspended in 0.5 ml of DMEM/F-12 (280-290 mOsm) after removal of the supernatant. Following mechanical trituration using fire-polished Pasteur pipettes, the cell suspension was filtered through a cell 16 strainer (40 μm). The sample was kept at room temperature for 20 min after the addition of 0,1 ml of the nuclear DNA stain DRAQ5 (Thermo Fisher, #65-0880-92). Using fluorescence activated cell sorting (FACs), cells positive for GFP and DRAQ5 in each sample were sorted into a 384-wells plate containing a mild hypotonic lysis buffer (0.2% Triton X-100, 2 U/ml RNase inhibitor) and immediately snap-frozen on ice, then stored at -80°C.
Smart-Seq2

tag: tissue

value: Spinal cord

tag: cell line

tag: cell type

value: motoneurons


title: MN_sample1_358_G20_R1


title: MN_sample1_358_G21_R1


title: MN_sample1_358_G17_R1


title: MN_sample1_358_G16_R1


title: MN_sample1_358_G13_R1


title: MN_sample1_358_G11_R1


title: MN_sample1_358_H23_R1


title: MN_sample1_358_G18_R1


title: MN_sample1_358_G12_R1


title: MN_sample1_358_G15_R1


title: MN_sample1_358_G19_R1


title: MN_sample1_358_G5_R1


title: MN_sample1_358_G6_R1


title: MN_sample1_358_G4_R1


title: MN_sample1_358_G3_R1


title: MN_sample1_358_F24_R1


title: MN_sample1_358_G7_R1


title: MN_sample1_358_G9_R1


title: MN_sample1_358_G10_R1


title: MN_sample1_358_G8_R1


title: MN_sample1_358_F21_R1


title: MN_sample1_358_G1_R1


title: MN_sample1_358_G22_R1


title: MN_sample1_358_G2_R1


title: MN_sample1_358_F20_R1


title: MN_sample1_358_F23_R1


title: MN_sample1_358_F22_R1


title: MN_sample1_358_F18_R1


title: MN_sample1_358_F19_R1


title: MN_sample1_358_F17_R1


title: MN_sample1_358_G14_R1


title: MN_sample1_358_F15_R1


title: MN_sample1_358_F14_R1


title: MN_sample1_358_F16_R1


title: MN_sample1_358_F13_R1


title: MN_sample1_358_F12_R1


title: MN_sample1_358_F6_R1


title: MN_sample1_358_F8_R1


title: MN_sample1_358_F7_R1


title: MN_sample1_358_F4_R1


title: MN_sample1_358_F11_R1


title: MN_sample1_358_F5_R1


title: MN_sample1_358_F10_R1


title: MN_sample1_358_F1_R1


title: MN_sample1_358_F2_R1


title: MN_sample1_358_F9_R1


title: MN_sample1_358_E24_R1


title: MN_sample1_358_E20_R1


title: MN_sample1_358_E22_R1


title: MN_sample1_358_F3_R1


title: MN_sample1_358_E21_R1


title: MN_sample1_358_E16_R1


title: MN_sample1_358_E17_R1


title: MN_sample1_358_E19_R1


title: MN_sample1_358_E18_R1


title: MN_sample1_358_E15_R1


title: MN_sample1_358_E14_R1


title: MN_sample1_358_E13_R1


title: MN_sample1_358_E12_R1


title: MN_sample1_358_E11_R1


title: MN_sample1_358_E9_R1


title: MN_sample1_358_E8_R1


title: MN_sample1_358_E10_R1


title: MN_sample1_358_E7_R1


title: MN_sample1_358_E6_R1


title: MN_sample1_358_E23_R1


title: MN_sample1_358_E4_R1


title: MN_sample1_358_E3_R1


title: MN_sample1_358_E5_R1


title: HSS-24h-rep3

type: RNA

city: Guangzhou

first: ziqi

last: chen

state: Guangdong

address: Zhongshan 2nd Road

country: China

institute: Sun Yat-sen University

description:
total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.
[HSS_3_1.10](normalized)

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array V2 (8x15K, Arraystar).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

molecule: total RNA

organism: Homo sapiens

source_name: HUVECs exposed to laminar flow with a shear stress of 15 dyne/cm2 for 24h.

label_protocol: Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.

treatment_protocol: Confluent HUVECs cultured on microscope slides were exposed to well-defined laminar flow with a shear stress of 15 dyne/cm2 or cultured under static conditions for 24h.

value: HUVECs

tag: shear stress

value: laminar  shear stress of 15 dyne/cm2


title: MN_sample1_358_E2_R1


title: MN_sample1_358_D24_R1


title: MN_sample1_358_D22_R1


title: MN_sample1_358_E1_R1


title: MA1

city: Guwahati

first: Narayana

middle: H

last: Mohan

state: Assam

address: Rani

department: ICAR-National Research Centre on Pig

country: India

institute: Indian Council of Agricultural Research

library_source: transcriptomic

data_processing:
Sequenced reads were removal of adaptor sequences, and phred scores abov 30, then mapped to Sus scrofa 11.1 reference genome using Hisat 2 and bowtie v0.12.2 and picard tools.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) and DEGs were calculated using CuffDiff data analysis pipeline.
Genome_build: Sus scrofa 11.1 reference genome
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample for RNA seq data

organism: Sus scrofa

source_name: Muscle

growth_protocol: Muscletranscriptome of two different breeds of pigs were compared.

extract_protocol:
RNA was isolated from muscle tissues using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Muscle tissues were removed using biopsy from pigs belonging to Hampshire and Mali breeds of pigs

tag: breed

value: Mali breed


title: Static-24h-rep2

description:
total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.
[S_2_1.10](normalized)

source_name: HUVECs cultured under static conditions

value: 0 dyne/cm2


title: MN_sample1_358_D20_R1


title: CSP-induced persisters, biol rep 3

city: Toronto

first: Delphine

last: Dufour

state: Ontario

address: 124 Edward Street

department: Oral Microbiology

country: Canada

institute: Faculty of Dentistry, University of Toronto

data_processing:
The Illumina bcl2fastq Conversion software was used for demultiplexing and to convert the base call files generated by the Illumina sequencing into FASTAQ files.
Quality of the raw data was assessed with FastQC (v0.11.9).
Removal of sequencing adapters and low-quality ends was performed using Trim Galore (v0.5.0) and the QC checks were repeated with FastQC to ensure that high-quality data was retained.
The reads were then aligned to S. Mutans UA159 complete genome (NC_004350.2) downloaded from NCBI using STAR aligner (v2.6.0c).
Assembly: NC_004350.2
Supplementary files format and content: htseq files include read counts for each sample

organism: Streptococcus mutans UA159

source_name: CSP-induced persisters

growth_protocol: S. mutans UA159 cells were grown in THYE broth at 37C with 5% CO2.

extract_protocol:
RNA  was harvested using the RiboPure-Bacteria purification kit. 0.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using an Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit following manufacturer's protocols.

treatment_protocol: For the CSP induction, the CSP pheromone was added at a final concentration of 0.05µg/ml. Peristers were isolated using the ofloxacin antibiotic at a concentration of 20µg/ml.

value: CSP-induced persisters

tag: genotype

value: WT


title: MN_sample1_358_D19_R1


title: HSS-24h-rep2

description:
total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.
[HSS_2_1.10](normalized)


title: CSP-induced persisters, biol rep 4


title: CSP-induced normal cells, biol rep 3

source_name: CSP-induced normal cells

value: CSP-induced normal cells


title: CSP-induced normal cells, biol rep 1


title: HSS-24h-rep1

description:
total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.
[HSS_1_1.10](normalized)


title: CSP-induced normal cells, biol rep 2


title: CSP-induced persisters, biol rep 1


title: Static-24h-rep1

description:
total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.
[S_1_1.10](normalized)


title: MA


title: Static-24h-rep3

description:
total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.
[S_3_1.10](normalized)


title: MN_sample1_358_D18_R1


title: MN_sample1_358_D17_R1


title: HA

value: Hampshire breed


title: MN_sample1_358_D15_R1


title: MN_sample1_358_D16_R1


title: MN_sample1_358_D14_R1


title: MN_sample1_358_D23_R1


title: MN_sample1_358_D13_R1


title: MN_sample1_358_D12_R1


title: MN_sample1_358_D21_R1


title: MN_sample1_358_D11_R1


title: MN_sample1_358_D10_R1


title: MN_sample1_358_D9_R1


title: MN_sample1_358_D8_R1


title: HA1


title: MN_sample1_358_D6_R1


title: MN_sample1_358_C20_R1


title: MN_sample1_358_C23_R1


title: MN_sample1_358_C17_R1


title: MN_sample1_358_D2_R1


title: MN_sample1_358_C16_R1


title: MN_sample1_358_D3_R1


title: MN_sample1_358_C21_R1


title: MN_sample1_358_D5_R1


title: MN_sample1_358_C24_R1


title: MN_sample1_358_C22_R1


title: MN_sample1_358_C19_R1


title: MN_sample1_358_C18_R1


title: MN_sample1_358_D4_R1


title: MN_sample1_358_C12_R1


title: MN_sample1_358_C15_R1


title: MN_sample1_358_C11_R1


title: MN_sample1_358_C10_R1


title: MN_sample1_358_C14_R1


title: MN_sample1_358_C13_R1


title: MN_sample1_358_C8_R1


title: MN_sample1_358_D7_R1


title: MN_sample1_358_C7_R1


title: MN_sample1_358_C6_R1


title: MN_sample1_358_C5_R1


title: MN_sample1_358_C4_R1


title: MN_sample1_358_D1_R1


title: MN_sample1_358_C3_R1


title: MN_sample1_358_B22_R1


title: MN_sample1_358_B19_R1


title: MN_sample1_358_C2_R1


title: MN_sample1_358_B17_R1


title: MN_sample1_358_B16_R1


title: MN_sample1_358_B18_R1


title: MN_sample1_358_C9_R1


title: MN_sample1_358_B21_R1


title: MN_sample1_358_B15_R1


title: MN_sample1_358_B13_R1


title: MN_sample1_358_B14_R1


title: MN_sample1_358_B20_R1


title: MN_sample1_358_B12_R1


title: MN_sample1_358_B11_R1


title: MN_sample1_358_B10_R1


title: MN_sample1_358_B8_R1


title: MN_sample1_358_B7_R1


title: MN_sample1_358_B6_R1


title: MN_sample1_358_B4_R1


title: MN_sample1_358_B3_R1


title: MN_sample1_358_B2_R1


title: MN_sample1_358_B1_R1


title: MN_sample1_358_A24_R1


title: MN_sample1_358_C1_R1


title: MN_sample1_358_B24_R1


title: MN_sample1_358_B23_R1


title: MN_sample1_358_A23_R1


title: MN_sample1_358_A22_R1


title: MN_sample1_358_A21_R1


title: MN_sample1_358_A20_R1


title: MN_sample1_358_A19_R1


title: MN_sample1_358_A17_R1


title: MN_sample1_358_A16_R1


title: MN_sample1_358_A13_R1


title: MN_sample1_358_A15_R1


title: MN_sample1_358_B9_R1


title: MN_sample1_358_B5_R1


title: MN_sample1_358_A12_R1


title: MN_sample1_358_A14_R1


title: MN_sample1_358_A11_R1


title: MN_sample1_358_A10_R1


title: MN_sample1_358_A9_R1


title: MN_sample1_358_A6_R1


title: MN_sample1_358_A5_R1


title: MN_sample1_358_A8_R1


title: MN_sample1_358_A7_R1


title: MN_sample1_358_A4_R1


title: MN_sample1_358_A3_R1


title: MN_sample1_358_A2_R1


title: Brain, BC, MPSIIIB, rep7 [22-01882_S42]

city: Adelaide

first: Lachlan

last: Baer

address: North Terrace

country: Australia

institute: The University of Adelaide

description:
22-01882_S42
counts_AC_BC_merged.out

data_processing:
Pre-processing was performed using a custom pipeline implemented in snakemake. Briefly, the raw fastq files were subjected to initial quality checks using fastQC version 0.11.9. Then, adaptors were trimmed and low-quality reads removed using fastp version 0.23.1. The remaining reads were aligned to the zebrafish genomes e (GRCz11, Ensembl release 101) using the splice-aware alignment software STAR version 2.7.0d. Aligned reads associated with the same unique molecular identifier (UMI) correspond to PCR duplicates generated using library preparation. These were deduplicated using the dedup function of umi_tools v1.0.1. A gene-level counts matrix was then generated using featureCounts version 2.0.1.
Assembly: GRCz11, Ensembl release 101
Supplementary files format and content: Both processed data files (counts_AB.out & counts_AC_BC.out) consist of count data in TSV format output by featureCounts software as described in the data processing section.

source_name: brain

growth_protocol: Each fish was raised until 3 months of age in a shared water circulation system. Fish were fed twice a day, with dry food in the morning and live food (Artermia salina) in the afternoon.

extract_protocol:
Each family of fish was raised until 3 months of age, at which time the entire family was humanely euthanised in an ice slurry. Entire heads were excised at the level of the gills and were each incubated in 600 µl of RNAlater™ Stabilization Solution (Invitrogen, Thermo Fisher Scientific, Waltham, USA) overnight at 4°C, before storage at -80°C until use. The tail of each fish was also removed for genomic DNA extraction and genotype determination by PCR. Total RNAs were isolated from RNAlater-preserved brains using the mirVana™ miRNA Isolation Kit (Ambion, Life Technologies, Thermo Fisher Scientific, Waltham, USA) following the manufacturer’s protocol. To remove any carried-over genomic DNA during RNA purification, we treated the total RNA samples with DNaseI using the DNA-free™ DNA Removal Kit (Invitrogen, Thermo Fisher Scientific, Waltham, USA) following the manufacturers protocol for routine DNase treatment.
500 ng of high-quality total RNA (with RINe generally ≥ 8) was delivered on dry ice to the South Australian Genomics Centre (SAGC, Adelaide, Australia) for preparation of stranded, polyA+ libraries using Nugen Universal Plus mRNA-seq (NuGEN, Ltd., UK). Cluster generation was performed using the Illumina to MGI Library Conversion (MGIEasy Universal Library Conversion Kit, Part No. MGI1000004155). Then, 2 x 98bp paired end sequencing was performed including 8 bp unique molecular identifiers (UMIs) using MGI DNBSEQ-G400 chemistry (MGI Tech, Shenzhen, China). Each of the libraries was sequenced over multiple lanes and the data from each library subsequently combined.

value: brain

tag: home tank

value: MPSIIIB

tag: Sex

value: male


title: Brain, BC, MPSIIIB, rep6 [22-01881_S41]

description:
22-01881_S41
counts_AC_BC_merged.out


title: Brain, BC, WT, rep9 [22-01879_S40]

description:
22-01879_S40
counts_AC_BC_merged.out


title: Brain, BC, WT, rep10 [22-01884_S44]

description:
22-01884_S44
counts_AC_BC_merged.out

value: female


title: Brain, BC, MPSIIIB, rep8 [22-01883_S43]

description:
22-01883_S43
counts_AC_BC_merged.out


title: MN_sample1_358_A18_R1


title: Brain, BC, MPSIIIB, rep5 [22-01876_S38]

description:
22-01876_S38
counts_AC_BC_merged.out


title: Brain, BC, MPSIIIC, rep5 [22-01872_S34]

description:
22-01872_S34
counts_AC_BC_merged.out

value: MPSIIIC


title: Brain, BC, MPSIIIC, rep6 [22-01873_S35]

description:
22-01873_S35
counts_AC_BC_merged.out


title: Brain, BC, WT, rep7 [22-01875_S37]

description:
22-01875_S37
counts_AC_BC_merged.out


title: Brain, BC, WT, rep6 [22-01874_S36]

description:
22-01874_S36
counts_AC_BC_merged.out


title: Brain, BC, WT, rep5 [22-01870_S32]

description:
22-01870_S32
counts_AC_BC_merged.out


title: Brain, BC, MPSIIIC, rep4 [22-01871_S33]

description:
22-01871_S33
counts_AC_BC_merged.out


title: Brain, BC, WT, rep4 [22-01869_S31]

description:
22-01869_S31
counts_AC_BC_merged.out


title: Brain, BC, WT, rep3 [22-01868_S30]

description:
22-01868_S30
counts_AC_BC_merged.out


title: Brain, BC, WT, rep1 [22-01864_S26]

description:
22-01864_S26
counts_AC_BC_merged.out


title: Brain, BC, MPSIIIC, rep2 [22-01865_S27]

description:
22-01865_S27
counts_AC_BC_merged.out


title: Brain, BC, MPSIIIB, rep4 [22-01863_S25]

description:
22-01863_S25
counts_AC_BC_merged.out


title: Brain, BC, MPSIIIB, rep3 [22-01862_S24]

description:
22-01862_S24
counts_AC_BC_merged.out


title: Brain, BC, MPSIIIC, rep3 [22-01866_S28]

description:
22-01866_S28
counts_AC_BC_merged.out


title: MN_sample1_358_A1_R1


title: Brain, BC, WT, rep11 [22-01885_S45]

description:
22-01885_S45
counts_AC_BC_merged.out


title: Brain, BC, MPSIIIB, rep2 [22-01860_S22]

description:
22-01860_S22
counts_AC_BC_merged.out


title: Brain, AC, MPSIIIC, rep5 [22-01857_S19]

description:
22-01857_S19
counts_AC_BC_merged.out


title: Brain, AC, WT, rep7 [22-01856_S18]

description:
22-01856_S18
counts_AC_BC_merged.out


title: Brain, BC, WT, rep8 [22-01877_S39]

description:
22-01877_S39
counts_AC_BC_merged.out


title: Brain, AC, MPSIIIA, rep7 [22-01855_S17]

description:
22-01855_S17
counts_AC_BC_merged.out

value: MPSIIIA


title: Brain, AC, MPSIIIA, rep5 [22-01851_S13]

description:
22-01851_S13
counts_AC_BC_merged.out


title: Brain, AC, WT, rep5 [22-01853_S15]

description:
22-01853_S15
counts_AC_BC_merged.out


title: Brain, AC, MPSIIIA, rep6 [22-01852_S14]

description:
22-01852_S14
counts_AC_BC_merged.out


title: Brain, AC, WT, rep6 [22-01854_S16]

description:
22-01854_S16
counts_AC_BC_merged.out


title: Brain, AC, WT, rep4 [22-01850_S12]

description:
22-01850_S12
counts_AC_BC_merged.out


title: Brain, AC, WT, rep3 [22-01849_S11]

description:
22-01849_S11
counts_AC_BC_merged.out


title: Brain, AC, MPSIIIC, rep4 [22-01848_S10]

description:
22-01848_S10
counts_AC_BC_merged.out


title: Brain, BC, WT, rep2 [22-01867_S29]

description:
22-01867_S29
counts_AC_BC_merged.out


title: Brain, AC, MPSIIIA, rep4 [22-01846_S8]

description:
22-01846_S8
counts_AC_BC_merged.out


title: Brain, AC, MPSIIIC, rep3 [22-01847_S9]

description:
22-01847_S9
counts_AC_BC_merged.out


title: Brain, AC, WT, rep2 [22-01844_S6]

description:
22-01844_S6
counts_AC_BC_merged.out


title: Brain, AC, MPSIIIC, rep2 [22-01845_S7]

description:
22-01845_S7
counts_AC_BC_merged.out


title: Brain, AC, MPSIIIC, rep6 [22-01858_S20]

description:
22-01858_S20
counts_AC_BC_merged.out


title: Brain, AC, MPSIIIC, rep1 [22-01840_S2]

description:
22-01840_S2
counts_AC_BC_merged.out


title: Brain, BC, MPSIIIB, rep1 [22-01859_S21]

description:
22-01859_S21
counts_AC_BC_merged.out


title: Brain, AC, MPSIIIA, rep1 [22-01839_S1]

description:
22-01839_S1
counts_AC_BC_merged.out


title: Brain, AC, WT, rep1 [22-01841_S3]

description:
22-01841_S3
counts_AC_BC_merged.out


title: Brain, AC, MPSIIIA, rep2 [22-01842_S4]

description:
22-01842_S4
counts_AC_BC_merged.out


title: Brain, AB, WT, rep4 [22-00160_S16]

description:
22-00160_S16
counts_AB.out


title: Brain, BC, MPSIIIC, rep1 [22-01861_S23]

description:
22-01861_S23
counts_AC_BC_merged.out


title: Brain, AB, MPSIIIB, rep4 [22-00159_S15]

description:
22-00159_S15
counts_AB.out


title: Brain, AB, MPSIIIA, rep3 [22-00156_S12]

description:
22-00156_S12
counts_AB.out


title: Brain, AB, MPSIIIA, rep4 [22-00157_S13]

description:
22-00157_S13
counts_AB.out


title: Brain, AB, MPSIIIB, rep3 [22-00155_S11]

description:
22-00155_S11
counts_AB.out


title: Brain, AB, sgsh_het, rep3 [22-00154_S10]

description:
22-00154_S10
counts_AB.out


title: Brain, AB, MPSIIIB, rep2 [22-00153_S9]

description:
22-00153_S9
counts_AB.out


title: Brain, AC, MPSIIIA, rep3 [22-01843_S5]

description:
22-01843_S5
counts_AC_BC_merged.out


title: Brain, AB, sgsh_het, rep2 [22-00152_S8]

description:
22-00152_S8
counts_AB.out


title: LPS_9h_Ana-1_rep4

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description:
Gene expression data from Ana-1 cells treated with Gene expression data from lPS for 9h, biological replicate 4
LPS_9h_Ana_4

hyb_protocol: According to the Thermo Fisher Scientific expression protocol (HWS kit)

scan_protocol: According to the Thermo Fisher Scientific expression protocol, Scanner 3000 7G

data_processing: SST-RMA gene-level probeset summary with standard settings of theTranscriptome Analysis Console (TAC; version 4.0.1.36; Thermo Fisher Scientific)

label: biotin

organism: Mus musculus

source_name: Ana-1 cells treated with LPS for 9h, biological replicate 4

label_protocol: Total RNA was amplified using the WT PLUS Reagent Kit (Thermo Fisher Scientific Inc., Waltham, USA).

growth_protocol: As described in the paper. Briefly, Ana-1 cell line (PMID: 2778838; 4079980) was cultured in RPMI 1640 medium (Gibco, Grand Island, NY, USA) supplemented with 15% fetal bovine serum (FBS, PAN Biotech, Aidenbach, Germany), 1% non-essential amino acids (NEAA; Gibco, Grand Island, NY, USA), 2 mM L-glutamine (Gibco, Grand Island, NY, USA), 100 U/ml Penicillin and 100 µg/ml Streptomycin (Gibco, Grand Island, NY, USA). Latently MHV-68 infected Ana-1 cells (Ana-1/MHV-68 cells) were cultured in RPMI 1640 medium supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml Penicillin, 100 µg/ml Streptomycin and 5 μg/ml Hygromycin (Merck KGaA, Darmstadt, Germany).

extract_protocol: Whole cell RNA was isolated with NucleoSpin RNA Plus kit (MACHEREY-NAGEL, Duren, Germany) following the instructions of the manufacturer.

treatment_protocol: As described in the paper. Briefly, carbonaceous spherical nanoparticles (CNP; Printex90, Degussa, Frankfurt, Germany) and double-walled carbon nanotubes (DWCNT; Nanocyl, SA, Belgium) were used in this study. 3 mg CNP or DWCNT were weighted and dispersed with 3 ml ultrapure H2O in a sterile glass tube to get a 1 mg/ml stock solution. Nanoparticles (NPs) dispersion was sonicated in an ice-cold water bath for 5 min followed by 30 seconds Bioruptor probe sonication (Diagenode, Liege, Belgium) at 30% power and continuous mode. For in vitro experiments, 50 µl stock NPs solution was diluted in 950 µl cell culture medium to reach a 50 µg/ml working concentration.

tag: strain

tag: infection

value: control

tag: treatment


title: Brain, AB, sgsh_het, rep4 [22-00158_S14]

description:
22-00158_S14
counts_AB.out


title: LPS_9h_Ana-1_rep3

description:
Gene expression data from Ana-1 cells treated with Gene expression data from lPS for 9h, biological replicate 3
LPS_9h_Ana_3

source_name: Ana-1 cells treated with LPS for 9h, biological replicate 3


title: LPS_9h_Ana-1_rep1

description:
Gene expression data from Ana-1 cells treated with Gene expression data from lPS for 9h, biological replicate 1
LPS_9h_Ana_1

source_name: Ana-1 cells treated with LPS for 9h, biological replicate 1


title: LPS_9h_Ana-1_rep2

description:
Gene expression data from Ana-1 cells treated with Gene expression data from lPS for 9h, biological replicate 2
LPS_9h_Ana_2

source_name: Ana-1 cells treated with LPS for 9h, biological replicate 2


title: LPS_9h_Ana-1_infected_with_MHV-68 _rep2

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with LPS for 9h, biological replicate 2
LPS_9h_AM_2

source_name: Latently MHV-68 infected Ana-1 cells treated with LPS for 9h, biological replicate 2


title: LPS_9h_Ana-1_infected_with_MHV-68 _rep4

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with LPS for 9h, biological replicate 4
LPS_9h_AM_4

source_name: Latently MHV-68 infected Ana-1 cells treated with LPS for 9h, biological replicate 4


title: LPS_9h_Ana-1_infected_with_MHV-68 _rep3

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with LPS for 9h, biological replicate 3
LPS_9h_AM_3

source_name: Latently MHV-68 infected Ana-1 cells treated with LPS for 9h, biological replicate 3


title: LPS_9h_Ana-1_infected_with_MHV-68 _rep1

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with LPS for 9h, biological replicate 1
LPS_9h_AM_1

source_name: Latently MHV-68 infected Ana-1 cells treated with LPS for 9h, biological replicate 1


title: Brain, AB, WT, rep3 [22-00151_S7]

description:
22-00151_S7
counts_AB.out


title: Brain, AB, WT, rep2 [22-00150_S6]

description:
22-00150_S6
counts_AB.out


title: Brain, AB, sgsh_het, rep1 [22-00148_S5]

description:
22-00148_S5
counts_AB.out


title: LPS_3h_Ana-1_rep3

description:
Gene expression data from Ana-1 cells treated with LPS for 3h, biological replicate 3
LPS_3h_Ana_3


title: Brain, AB, MPSIIIA, rep2 [22-00147_S4]

description:
22-00147_S4
counts_AB.out


title: Brain, AB, WT, rep1 [22-00145_S3]

description:
22-00145_S3
counts_AB.out


title: LPS_3h_Ana-1_infected_with_MHV-68 _rep3

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with LPS for 3h, biological replicate 3
LPS_3h_AM_3

source_name: Latently MHV-68 infected Ana-1 cells treated with LPS for 3h, biological replicate 3


title: LPS_3h_Ana-1_rep1

description:
Gene expression data from Ana-1 cells treated with LPS for 3h, biological replicate 1
LPS_3h_Ana_1


title: LPS_3h_Ana-1_infected_with_MHV-68 _rep4

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with LPS for 3h, biological replicate 4
LPS_3h_AM_4

source_name: Latently MHV-68 infected Ana-1 cells treated with LPS for 3h, biological replicate 4


title: Ctrl_9h_Ana-1_rep3

description:
Gene expression data from Ana-1 cells, 9h control, biological replicate 3
Ctrl_9h_Ana_3


title: Brain, AB, MPSIIIA, rep1 [22-00138_S2]

description:
22-00138_S2
counts_AB.out


title: Ctrl_9h_Ana-1_rep4

description:
Gene expression data from Ana-1 cells, 9h control, biological replicate 4
Ctrl_9h_Ana_4


title: LPS_3h_Ana-1_infected_with_MHV-68 _rep1

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with LPS for 3h, biological replicate 1
LPS_3h_AM_1

source_name: Latently MHV-68 infected Ana-1 cells treated with LPS for 3h, biological replicate 1


title: Ctrl_9h_Ana-1_rep2

description:
Gene expression data from Ana-1 cells, 9h control, biological replicate 2
Ctrl_9h_Ana_2


title: LPS_3h_Ana-1_rep2

description:
Gene expression data from Ana-1 cells treated with LPS for 3h, biological replicate 2
LPS_3h_Ana_2


title: Ctrl_9h_Ana-1_rep1

description:
Gene expression data from Ana-1 cells, 9h control, biological replicate 1
Ctrl_9h_Ana_1


title: LPS_3h_Ana-1_rep4

description:
Gene expression data from Ana-1 cells treated with LPS for 3h, biological replicate 4
LPS_3h_Ana_4


title: Brain, AB, MPSIIIB, rep1 [22-00136_S1]

description:
22-00136_S1
counts_AB.out


title: Tibpika-3

city: Beijing

first: wang

last: jiawen

address: 7 Science Park Road ZGC Life Science Park

institute: National institute of biological sciences

data_processing:
Basecalls performed using CASAVA version 1.9
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 (for mouse), Rnor6 (for rat), OryCun2 (for rabbit),OchPri3 (for pika) whole genome using STAR v2.6.1a with default parameters
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated using featureCounts function from Rsubread (v2.0.1) and rpkm function of edgeR (v3.28.1). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCm38, Rnor6, OryCun2, OchPri3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Ochotona curzoniae

source_name: Tibetan pika fibroblast

growth_protocol: Cells were cultured under 5% CO2, 37 ℃ with DMEM (10% FBS, 1% PS)

extract_protocol:
After growing to 90% confluency, cells were lysed with TRIZOL directly and total RNA was extracted with chloroform and  isopropanol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: epidermis


title: Tibpika-1


title: Ctrl_9h_Ana-1_infected_with_MHV-68 _rep4

description:
Gene expression data from latently MHV-68 infected Ana-1 cells, 9h control, biological replicate 4
Ctrl_9h_AM_4

source_name: Latently MHV-68 infected Ana-1 cells, 9h control, biological replicate 4


title: Ctrl_9h_Ana-1_infected_with_MHV-68 _rep1

description:
Gene expression data from latently MHV-68 infected Ana-1 cells, 9h control, biological replicate 1
Ctrl_9h_AM_1

source_name: Latently MHV-68 infected Ana-1 cells, 9h control, biological replicate 1


title: Ctrl_3h_Ana-1_rep4

description:
Gene expression data from Ana-1 cells, 3h control, biological replicate 4
Ctrl_3h_Ana_4


title: Ctrl_9h_Ana-1_infected_with_MHV-68 _rep2

description:
Gene expression data from latently MHV-68 infected Ana-1 cells, 9h control, biological replicate 2
Ctrl_9h_AM_2

source_name: Latently MHV-68 infected Ana-1 cells, 9h control, biological replicate 2


title: Human Neocortex, CONTROL-1, biol rep 1

city: Hannover

first: Maximilian

last: Lenz

address: Carl-Neuberg-Straße 1

department: Institute of Neuroanatomy and Cell Biology

institute: Hannover Medical School

data_processing:
Data analysis was performed at the Galaxy platform (usegalaxy.eu; (Galaxy, 2022)). All files contained more than 10 M high-quality reads (after mapping to the reference genomes) with a phred quality of at least 30 (>90% of total reads).
RNA sequencing data were uploaded to the galaxy web platform (public server: usegalaxy.eu; Afgan et al., 2018; Jalili et al., 2020; Afgan et al., 2016) and transcriptome analysis was performed using the Galaxy platform in accordance with the reference-based RNA-seq data analysis tutorial (Batut et al., 2021).
Adapter sequences, low quality, and short reads were removed via the CUTADAPT tool.
Reads were mapped using RNA STAR with the mm10 (Mus musculus) or the hg38 (Human) reference genome.
The evidence-based annotation of the mouse genome (GRCm38), version M25 (Ensembl 100) or the human genome (GRCh38), version 40 (Ensembl 106) served as gene model (GENCODE). For an initial assessment of gene expression, unstranded FEATURECOUNT analysis was performed from RNA STAR output.
Assembly: mm10
Supplementary files format and content: RNA STAR output (mapped BAM-files)
Supplementary files format and content: FEATURE COUNT output (tabular files)

source_name: Brain, adult, neocortex

extract_protocol:
For experiments in organotypic tissue cultures, 5-6 cultures of the same mouse were collected and used per sample. For in vivo experiments, the mPFC of treated and untreated adult mice was dissected and the mPFC of the left hemisphere was used as one sample. In experiments with human material, the tissue of each patient was seen as one biological sample. RNA was isolated using the Monarch® Total RNA Miniprep Kit (#T2010S; New England Biolabs) according to the manufacturer's instructions. RNA quantity and quality were assessed using an Agilent RNA 6000 Pico Kit (#5067-1513; Agilent) with a 2100 Bioanalyzer (#G2939BA; Agilent). After RNA isolation from TTX-treated tissue cultures, library preparation and RNA sequencing was performed using the genome sequencer Illumina HiSeq technology in NovaSeq 6000 S4 PE150 XP sequencing mode (service provided by Eurofins). After RNA isolation from the mPFC of mouse in vivo experiments and human neocortical samples, poly(A)- selection was performed using a poly(A)-selection mRNA magnetic isolation module (#E7490; New England Biolabs) according to the manufacturer’s instructions. For non-directional library preparation, NEBNext Ultra II RNA Library Preparation Kit for Illumina (#E7770; New England Biolabs) was used.
After fragmentation and adaptor ligation, dual index primers (New England Biolabs, #E7600S) were ligated in a library amplification step using 10 PCR cycles. Libraries were finally cleaned up with 0.8X SPRI beads following a standard bead purification protocol. Library purity and size distribution were assessed with a High Sensitivity DNA assay on a Bioanalyzer instrument (Agilent). We quantified the libraries using the NEBNext Library Quant Kit for Illumina (New England Biolabs, #E7630) based on the mean insert size provided by the Bioanalyzer. A 10 nM sequencing pool (120 µl in Tris-HCl, pH 8.5) was generated for sequencing on the NovaSeq6000 sequencing platform (Illumina; service provided by CeGaT GmbH, Tübingen, Germany). We performed a paired-end sequencing with 100 bp or 150 bp read length.

value: Brain, adult, neocortex

value: No AED (antiepileptic drug) treatment in medical record


title: Ctrl_3h_Ana-1_rep1

description:
Gene expression data from Ana-1 cells, 3h control, biological replicate 1
Ctrl_3h_Ana_1


title: Ctrl_3h_Ana-1_rep2

description:
Gene expression data from Ana-1 cells, 3h control, biological replicate 2
Ctrl_3h_Ana_2


title: Human Neocortex, AED-4, biol rep 4

value: AED (antiepileptic drug) treatment in medical record


title: LPS_3h_Ana-1_infected_with_MHV-68 _rep2

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with LPS for 3h, biological replicate 2
LPS_3h_AM_2

source_name: Latently MHV-68 infected Ana-1 cells treated with LPS for 3h, biological replicate 2


title: Ctrl_3h_Ana-1_infected_with_MHV-68 _rep3

description:
Gene expression data from latently MHV-68 infected Ana-1 cells, 3h control, biological replicate 3
Ctrl_3h_AM_3

source_name: Latently MHV-68 infected Ana-1 cells, 3h control, biological replicate 3


title: Ctrl_9h_Ana-1_infected_with_MHV-68 _rep3

description:
Gene expression data from latently MHV-68 infected Ana-1 cells, 9h control, biological replicate 3
Ctrl_9h_AM_3

source_name: Latently MHV-68 infected Ana-1 cells, 9h control, biological replicate 3


title: Ctrl_3h_Ana-1_infected_with_MHV-68 _rep4

description:
Gene expression data from latently MHV-68 infected Ana-1 cells, 3h control, biological replicate 4
Ctrl_3h_AM_4

source_name: Latently MHV-68 infected Ana-1 cells, 3h control, biological replicate 4


title: Ctrl_3h_Ana-1_infected_with_MHV-68 _rep2

description:
Gene expression data from latently MHV-68 infected Ana-1 cells, 3h control, biological replicate 2
Ctrl_3h_AM_2

source_name: Latently MHV-68 infected Ana-1 cells, 3h control, biological replicate 2


title: Human Neocortex, AED-3, biol rep 3


title: Ctrl_3h_Ana-1_infected_with_MHV-68 _rep1

description:
Gene expression data from latently MHV-68 infected Ana-1 cells, 3h control, biological replicate 1
Ctrl_3h_AM_1

source_name: Latently MHV-68 infected Ana-1 cells, 3h control, biological replicate 1


title: Human Neocortex, AED-2, biol rep 2


title: Ctrl_3h_Ana-1_rep3

description:
Gene expression data from Ana-1 cells, 3h control, biological replicate 3
Ctrl_3h_Ana_3


title: Human Neocortex, AED-1, biol rep 1


title: DWCNT_9h_Ana-1_rep2

description:
Gene expression data from Ana-1 cells treated with DWCNT for 9h, biological replicate 2
DWCNT_9h_Ana_2


title: DWCNT_9h_Ana-1_rep4

description:
Gene expression data from Ana-1 cells treated with DWCNT for 9h, biological replicate 4
DWCNT_9h_Ana_4


title: DWCNT_9h_Ana-1_rep1

description:
Gene expression data from Ana-1 cells treated with DWCNT for 9h, biological replicate 1
DWCNT_9h_Ana_1


title: DWCNT_9h_Ana-1_infected_with_MHV-68 _rep3

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with DWCNT for 9h, biological replicate 3
DWCNT_9h_AM_3

source_name: Latently MHV-68 infected Ana-1 cells treated with DWCNT for 9h, biological replicate 3


title: DWCNT_3h_Ana-1_rep4

description:
Gene expression data from Ana-1 cells treated with DWCNT for 3h, biological replicate 4
DWCNT_3h_Ana_4


title: DWCNT_9h_Ana-1_infected_with_MHV-68 _rep1

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with DWCNT for 9h, biological replicate 1
DWCNT_9h_AM_1

source_name: Latently MHV-68 infected Ana-1 cells treated with DWCNT for 9h, biological replicate 1


title: ATAC DPSC-day9_TSA_2

city: Okayama

first: Shigeki

last: Suzuki

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Operative Dentistry

country: Japan

institute: Okayama University

description: ss1625_day9_TSA_region_fragLength250.txt

library_source: genomic

data_processing:
Adapter trimming and quality check were conducted with Trim galore and then aligned to a reference genome (hg38) using Bowtie2 with `-seed` parameters to efficiently use multimap reads with assuring reproducibility. Tag directories were generated using `makeTagDirectory` command in HOMER and ATAC-seq peaks were identified using the `getDiffrentialPeaksReplicates.pl` command in HOMER, specifying `-style histone` to generate a high confidence set of peaks across duplicates. This HOMER command internally calls DESeq2 to calculate enrichment value for each peak using the individual raw counts and return only those peaks that pass 2-fold enrichment and a FDR-adjusted p-value of < 0.05. Input chromatin DNA was used as controls.
Assembly: hg38
Supplementary files format and content: bigwig files were generated by bamCoverage commond.

molecule: genomic DNA

source_name: dental pulp

extract_protocol: Cells used for ATAC-seq analysis were fixed with formaldehyde and ATAC-seq was performed using the ATAC-Seq Kit  (Active Motif) following the manufacturer’s protocol.

value: dental pulp

value: dental pulp stem cells

value: TSA stimulation for 9 days

value: normal culture

value: odontogenic induction with TSA  supplementation


title: DWCNT_9h_Ana-1_rep3

description:
Gene expression data from Ana-1 cells treated with DWCNT for 9h, biological replicate 3
DWCNT_9h_Ana_3


title: ATAC input_2

value: fragmented genomic DNA


title: ATAC DPSC-day9_TSA_1


title: ATAC input_1


title: DWCNT_3h_Ana-1_infected_with_MHV-68 _rep4

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with DWCNT for 3h, biological replicate 4
DWCNT_3h_AM_4

source_name: Latently MHV-68 infected Ana-1 cells treated with DWCNT for 3h, biological replicate 4


title: DWCNT_3h_Ana-1_rep3

description:
Gene expression data from Ana-1 cells treated with DWCNT for 3h, biological replicate 3
DWCNT_3h_Ana_3


title: DWCNT_3h_Ana-1_rep1

description:
Gene expression data from Ana-1 cells treated with DWCNT for 3h, biological replicate 1
DWCNT_3h_Ana_1


title: DWCNT_3h_Ana-1_rep2

description:
Gene expression data from Ana-1 cells treated with DWCNT for 3h, biological replicate 2
DWCNT_3h_Ana_2


title: DWCNT_9h_Ana-1_infected_with_MHV-68 _rep4

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with DWCNT for 9h, biological replicate 4
DWCNT_9h_AM_4

source_name: Latently MHV-68 infected Ana-1 cells treated with DWCNT for 9h, biological replicate 4


title: ATAC DPSC-day9_MS275_1

description: ss1625_day9_MS275_region_fragLength250.txt

value: MS275 stimulation for 9 days

value: odontogenic induction with MS275 supplementation


title: DWCNT_3h_Ana-1_infected_with_MHV-68 _rep3

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with DWCNT for 3h, biological replicate 3
DWCNT_3h_AM_3

source_name: Latently MHV-68 infected Ana-1 cells treated with DWCNT for 3h, biological replicate 3


title: ATAC DPSC-day9_RGFP966_2

description: ss1625_day9_RGFP966_region_fragLength250.txt

value: RGFP stimulation for 9 days

value: odontogenic induction with RGFP966 supplementation


title: Tibpika-2

source_name: Tibetan pika fibroblast


title: ATAC DPSC-day9_RGFP966_1


title: DWCNT_3h_Ana-1_infected_with_MHV-68 _rep1

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with DWCNT for 3h, biological replicate 1
DWCNT_3h_AM_1

source_name: Latently MHV-68 infected Ana-1 cells treated with DWCNT for 3h, biological replicate 1


title: ATAC DPSC-day9_MS275_2


title: CNP_9h_Ana-1_rep4

description:
Gene expression data from Ana-1 cells treated with CNP for 9h, biological replicate 4
CNP_9h_Ana_4


title: CNP_9h_Ana-1_rep3

description:
Gene expression data from Ana-1 cells treated with CNP for 9h, biological replicate 3
CNP_9h_Ana_3


title: CNP_9h_Ana-1_rep2

description:
Gene expression data from Ana-1 cells treated with CNP for 9h, biological replicate 2
CNP_9h_Ana_2


title: DWCNT_3h_Ana-1_infected_with_MHV-68 _rep2

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with DWCNT for 3h, biological replicate 2
DWCNT_3h_AM_2

source_name: Latently MHV-68 infected Ana-1 cells treated with DWCNT for 3h, biological replicate 2


title: CNP_9h_Ana-1_infected_with_MHV-68 _rep1

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with CNP for 9h, biological replicate 1
CNP_9h_AM_1

source_name: Latently MHV-68 infected Ana-1 cells treated with CNP for 9h, biological replicate 1


title: CNP_9h_Ana-1_infected_with_MHV-68 _rep3

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with CNP for 9h, biological replicate 3
CNP_9h_AM_3

source_name: Latently MHV-68 infected Ana-1 cells treated with CNP for 9h, biological replicate 3


title: CNP_9h_Ana-1_infected_with_MHV-68 _rep4

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with CNP for 9h, biological replicate 4
CNP_9h_AM_4

source_name: Latently MHV-68 infected Ana-1 cells treated with CNP for 9h, biological replicate 4


title: CNP_9h_Ana-1_infected_with_MHV-68 _rep2

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with CNP for 9h, biological replicate 2
CNP_9h_AM_2

source_name: Latently MHV-68 infected Ana-1 cells treated with CNP for 9h, biological replicate 2


title: CNP_3h_Ana-1_rep4

description:
Gene expression data from Ana-1 cells treated with CNP for 3h, biological replicate 4
CNP_3h_Ana_4


title: ATAC DPSC-day9_2

value: control at day 9

value: odontogenic induction


title: ATAC DPSC-day9_1


title: bre1d_day4_rep3

city: wuhan

first: yuchao

last: Mei

address: Bayi Road

department: Colleage of Life Science

institute: Wuhan University

description:
all_rawcount_matrix.xlsx, fpkm_matrix.xlsx
bre1d_day4.bw

data_processing:
FastQC (v0.11.8) was used to do quality control on raw sequence data.
The reads obtained from each sample were trimmed using Cutadapt (v2.6) using options -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -e 0.1 -O 5 -m 50 -pair-filter=both to remove any sequencing adapters.
After trimming, reads were mapped to the yeast genome SacCer3 (https://www.yeastgenome.org/) using STAR (v2.7.0b) with default parameter.
Read counts were concurrently calculated using HTSeq (v2.0.2). Combined raw count matrix were analyzed in R (v4.2.0). Differential expression analysis was done in DESeq2 (v1.36.0). Adjusted P‐value < 0.01 was used for term ranking and selection.
Assembly: SacCer3
Supplementary files format and content: gene expression matrix, bigWig files

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown overnight in YPD at 30 °C, diluted to an OD600 of 0.1 the next day and collected at day1 or day 4

extract_protocol:
Cells were harvested by spinning down with 3000 rpm for 5 min, then cell pellets were washed with 10 ml sterile water twice.The total sample RNA was extracted using Trizol reagent.
RNA Concentration was quantified using ultramicrospectrophotometer (NANO-ONE) and 1 μg RNA was put into the library building. RNA library was generated using PowerPrepTM Rapid mRNA-Seq Library Prep Kit. Libraries were sequenced on Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol:
none
none

value: bre1 deletion

tag: time


title: CNP_9h_Ana-1_rep1

description:
Gene expression data from Ana-1 cells treated with CNP for 9h, biological replicate 1
CNP_9h_Ana_1

value: control


title: bre1d_day4_rep1


title: CNP_3h_Ana-1_rep3

description:
Gene expression data from Ana-1 cells treated with CNP for 3h, biological replicate 3
CNP_3h_Ana_3


title: bre1d_day4_rep2


title: bre1d_day1_rep3

description:
all_rawcount_matrix.xlsx, fpkm_matrix.xlsx
bre1d_day1.bw


title: RNA DPSC-day9_TSA_2

data_processing:
Adapter trimming was conducted with Trimmomatic with default setting and then aligned to a reference genome (hg38) using HISAT2. The gene expression at exons was quantified using `analyzeRepeast.pl ` command in HOMER using `-strand both` and `-count exons` to identify expressed genes. Then, differentialy expressed genes were identified using `getDiffExpression.pl` command in HOMER.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for all 10 samples in ss1632_diffOutput_condenseGenes.txt

extract_protocol:
RNA was isolated from DPSC with RNAiso plus. Purified RNA was DNase-treated and further used for RNA-seq analyses.
Input RNA was converted to cDNA libraries using the NEBNExt poly(A) mRNA magnetic isolation module. Libraries were sequenced using 150-bp paired-end reads on an illumine Novaseq instruments.


title: CNP_3h_Ana-1_rep2

description:
Gene expression data from Ana-1 cells treated with CNP for 3h, biological replicate 2
CNP_3h_Ana_2


title: RNA DPSC-day9_TSA_1


title: bre1d_day1_rep2


title: bre1d_day1_rep1


title: CNP_3h_Ana-1_infected_with_MHV-68 _rep4

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with CNP for 3h, biological replicate 4
CNP_3h_AM_4

source_name: Latently MHV-68 infected Ana-1 cells treated with CNP for 3h, biological replicate 4


title: CNP_3h_Ana-1_infected_with_MHV-68 _rep3

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with CNP for 3h, biological replicate 3
CNP_3h_AM_3

source_name: Latently MHV-68 infected Ana-1 cells treated with CNP for 3h, biological replicate 3


title: RNA DPSC-day9_MS275_2


title: set2d_day4_rep3

description:
all_rawcount_matrix.xlsx, fpkm_matrix.xlsx
set2d_day4.bw

value: set2 deletion


title: CNP_3h_Ana-1_rep1

description:
Gene expression data from Ana-1 cells treated with CNP for 3h, biological replicate 1
CNP_3h_Ana_1


title: RNA DPSC-day9_MS275_1


title: Covid Sample Plate 1/2

city: Fremont

first: Xiao-Jun

last: Ma

state: California

address: 47071 Bayside Pkwy

country: USA

institute: Alamar Biosciences

data_processing:
Analyze raw data using NULISAseq analysis algorithm
Generate normalized read counts using NULISAseqR package
Assembly: N/A
Supplementary files format and content: Comma-separated value (csv) files include raw and normalized read counts for each protein included in NULISA 200-Plex V1 panel
Library strategy: NULISAseq

source_name: Plasma

extract_protocol:
For NULISAseq, immunocomplexes were formed by incubating plasma samples with capture and detection antibody cocktails in AD buffer. For Olink Explore, extraction was performed by a dedicated Olink service provider.
Sequencing libraries for NULISAseq were prepared by pooling the reporter molecules from each NULISAseq reaction and then amplifying the products by 16 cycles of PCR. Library construction and sequencing for Olink Explore was performed by a dedicated Olink service provider.

value: Plasma


title: Olink Explore Detectability Plate 1/2


title: NULISA 200Plex V1 Detectability Plate 1/2


title: CNP_3h_Ana-1_infected_with_MHV-68 _rep2

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with CNP for 3h, biological replicate 2
CNP_3h_AM_2

source_name: Latently MHV-68 infected Ana-1 cells treated with CNP for 3h, biological replicate 2


title: set2d_day4_rep1


title: set2d_day4_rep2


title: ATAC DPSC-day0_1

value: control at day 0


title: RNA DPSC-day9_RGFP966_2

value: dental pulp


title: ATAC DPSC-day0_2

value: dental pulp stem cells


title: RNA DPSC-day9_RGFP966_1


title: set2d_day1_rep3

description:
all_rawcount_matrix.xlsx, fpkm_matrix.xlsx
set2d_day1.bw


title: GFP stock, sample 3

city: Lund

first: Jessica

middle: K.

last: Abbott

state: Skåne

address: Sölvegatan 37

department: Biology

institute: Lund University

data_processing:
Reads were trimmed and remaining adaptors were removed using Trimmomatic (version 0.36)
A de novo transcriptome assembly using the three ancestral GFP line samples was then constructed using Trinity version 2.4.0
Bowtie2 (version 2.3.4.3) was used to map the raw reads back to the assembly, yielding a mapping rate of approximately 83%
To quantify transcript expression, Salmon (version 0.9.1) was used in quasi-mapping mode with 100 bootstrap replicates. A kmer length of 31 was used for indexing.
Differentially expressed transcripts between selection regimes (male-limited, female-limited, and control) were identified with EdgeR (version 3.24.3)
Assembly: De novo
Supplementary files format and content: Processed data files are in SF file format provided by Salmon and contain TPM (Transcripts Per Million) values for each Trinity transcript from our denovo transcriptome used for downward differential gene expression analyses.

organism: Macrostomum lignano

source_name: Whole organism

extract_protocol:
RNA was extracted from each sample using the RNA purification protocol for animal tissues with RNeasy Mini Kit spin column technology (Qiagen, Hilden, Germany) and DNase I treatment prior to elution in nuclease-free water.
Sequencing libraries were prepared from 200 ng total RNA using the TruSeq stranded total RNA library preparation kit with RiboZero Gold treatment (Illumina). The library preparation was performed according to the manufacturers’ protocol (#15031048).

value: Whole organism


title: RNA DPSC-day9_2

value: normal culture


title: RNA DPSC-day9_1


title: set2d_day1_rep2


title: GFP stock, sample 2


title: CNP_3h_Ana-1_infected_with_MHV-68 _rep1

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with CNP for 3h, biological replicate 1
CNP_3h_AM_1

source_name: Latently MHV-68 infected Ana-1 cells treated with CNP for 3h, biological replicate 1


title: GFP stock, sample 1


title: set2d_day1_rep1


title: RNA DPSC-day0_2

source_name: dental pulp


title: F2gen22

value: Female-selected


title: RNA DPSC-day0_1


title: WT_day4_rep2

description:
all_rawcount_matrix.xlsx, fpkm_matrix.xlsx
WT_day4.bw

value: wild type


title: WT_day4_rep3


title: WT_day1_rep3

description:
all_rawcount_matrix.xlsx, fpkm_matrix.xlsx
WT_day1.bw


title: M3gen21

value: Male-selected


title: C3gen22

value: Control


title: WT_day1_rep1


title: WT_day4_rep1


title: DM-8

city: West Hollywood

first: AGCT

last: Core

state: CA

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

library_source: other

data_processing:
The data were converted to FASTQ files from BCL using BCL2FASTQ
The demultiplexed raw reads were uploaded to GeneGlobe Data Analysis Center (Qi-agen) at https://www.qiagen.com/us/resources/geneglobe/ for quality control, alignment, and expression quantification. Briefly, 3’ adapter and low-quality bases are trimmed off from reads first using cutadapt (version 1.13) with default settings [50], then reads with less than 16bp insert sequences or with less than 10bp UMI sequences were discarded. The remaining reads were collapsed to UMI counts and aligned to miRBase (release v21) mature and hairpin databases sequentially using Bowtie v1.2 [51]. The UMI counts of each miRNA molecule were counted and the expressions of miRNAs were normalized based on total UMI counts for each sample. In addition, expression data were analyzed in conjunction with TargetScan to increase the likelihood of finding direct miRNA targets.
Assembly: miRBase (release v21)
Supplementary files format and content: xlsx file contain the read count for each sample and also QC metric for each sample

molecule: other

source_name: Cornea

extract_protocol:
Total Exos RNA was isolated by miRCURY RNA Isolation Kit–Cell & Plant (Exiqon, Woburn, MA) according to the manufacturer’s instructions.
RNA integrity was analyzed on the 2100 Bioanalyzer using the RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA) and RNA was quantified using the Qubit RNA HS Assay Kit (ThermoFisher Scientific). The QIASeqTM miRNA Library Kit (Qiagen, Hilden, Germany) was used to prepare miRNA sequencing libraries. Final library concentrations were measured using the Qubit 1X dsDNA HS Assay kit. Library fragment size was determined on the 4200 TapeStation (Agilent Technologies). Libraries were sequenced on a NovaSeq 6000 (Illumina, San Diego, CA) at an average sequencing depth of ~10M reads/sample and 1x75 bp sequencing.

value: Cornea

tag: disease state

value: diabetic

value: Primary limbal epithelial cells


title: DM-9


title: C4gen22


title: F4gen22


title: N-6

value: non-diabetic


title: C2gen21


title: M1gen22


title: WT_day1_rep2


title: DM-10


title: N-2


title: bre1d_day4_H3K36me3_rep2

data_processing:
FastQC (v0.11.8) was used to do quality control on raw sequence data.
The reads obtained from each sample were trimmed using Cutadapt (v2.6) using options -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -e 0.1 -O 5 -m 50 -pair-filter=both to remove any sequencing adapters.
As the ChIP experiments contained S. pombe spike-in, genomeGenerate tool in STAR (v2.7.0b) was used to generate a chimeric S. cerevisiae–S. pombe genome (sacCer3-ASM294v2). The chimeric genome allows all reads to align to their best overall fit between the two species at the same time. Then, reads were mapped to chimeric S. cerevisiae–S. pombe genome (sacCer3-ASM294v2) using STAR (v2.7.0b) with options --outFilterMismatchNmax 2 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --outFilterScoreMin 1 --outFilterMultimapNmax 1.
The aligned reads were subsequently filtered for quality and uniquely mapped reads were retained for further analysis using SAMtools (v1.14)and Sambamba (v0.8.1)
To account for S. pombe spike-in, each bigWig file was normalized with its own spike-in S. pombe reads, using the BEDTools (v2.27.1) genomecov –scale function. Spike-in normalized H3K36me3 signal was obtained by dividing H3K36me3 spike-in normalized signal by H3 spike-in normalized signal for each base pair for each replicate.
Assembly: SacCer3-ASM294v2
Supplementary files format and content: bigWig

extract_protocol:
Cells were cross-linked by 1% final concentration of formaldehyde with occasional shaking for 15 min and reactions were quenched by 0.375 M final concentration of glycine solution. Cells were washed and cell pellets were stored at -80 °C before used. Cells were lysed by bead beater with glass beads using 140 mM FA lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% deoxycholate) and the soluble fractions were removed. Resuspended chromatin fractions with 140 mM FA lysis buffer were sonicated on high intensity 3 times for 8 min each (cycles of 30 s “ON” and 30 s “OFF”) and clarified by centrifuging at full speed for 15 min. After determining protein concentration by Bradford reagent, S. cerevisiae chromatin were mixed with S. pombe chromatin that served as a spike-in control as followed as a 100: 15 ratio.. Immunoprecipitation was performed at 4°C overnight with incubation of appropriate chromatin fractions with 2 μL anti-H3K36me3 antibody or anti-H3 antibody, respectively. 10 μl Protein G beads were further added and incubated for additional 1 h. Enriched immunoprecipitateswere sequentially washed with 1 mL 140 mM FA lysis buffer for 10 min, 1 mL 500 mM FA lysis buffer (50 mM HEPES-KOH pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% deoxycholate) for 20 min,  and then 1 mL LiCl/NP40 buffer (10 mM Tris–HCl pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% Na Deoxycholate, 1 mM EDTA) for 10 min. DNA were eluted by 200 μL elution buffer (1% SDS, 0.1 M NaHCO3) twice. 16 μL of 5 M NaCl and proteinase K was added to the eluates and samples were incubated at 65 °C overnight to de-crosslink. DNA was purified using the Universal DNA Purification Kit. DNA Concentration was quantified using Equalbit dsDNA HS Assay Kit.
DNA library was generated using VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 and VAHTS® DNA Adapters set3 - set6 for Illumina as followed manufacturer protocols. Libraries were sequenced on the NovaSeq 6000 (Illumina).

value: bre1 deletion

tag: chip antibody

value: H3K36me3 (Abcam, Cat# ab9050)


title: M4gen22


title: N-1


title: C1gen21


title: bre1d_day4_H3_rep2

value: H3 (ABclonal, Cat# A2348)


title: CRC_153T

city: Wuhan

first: Bin

last: Li

address: Donghu Road 115

institute: Department of Epidemiology and Biostatistics, School of Public Health; Wuhan University

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low-quality reads from raw data.
Trimmed reads were aligned against human transcriptome using the Genome Reference Consortium human reference 38 assembly (GRCh38/hg38) with Hisat (v2.0.5) software using Ensemble release annotations,
Assembly: hg38
Supplementary files format and content: Gene and transcript expression were quantified using FPKM.

source_name: colorectal cancer

extract_protocol:
154 CRC tissues removed tumors or biopsy specimens, flash freozen by dry ice, and RNA was harvested using TRIzol (Invitrogen, USA)
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). For library preparation, the Illumina RNA Library Prep kit (NEBNext® UltraTM) was used. The libraries were tagged with unique adapter indexes. Final libraries were validated on the Agilent 2100 Bioanalyzer, quantified via qRT-PCR, pooled at equimolar ratios, diluted, denatured, and loaded onto an Illumina novaseq 6000.

value: colorectal cancer

tag: gender

value: Female

tag: age

tag: diagnosis

value: Rectal cancer

tag: tnm stage


title: CRC_154T

tag: tissue

value: Male


title: bre1d_day4_H3_rep1


title: CRC_152T

value: Colon cancer


title: F3gen21

value: Whole organism


title: bre1d_day1_H3K36me3_rep2


title: CRC_151T


title: C4gen21


title: CRC_147T


title: bre1d_day1_H3K36me3_rep1


title: M2gen22


title: bre1d_day1_H3_rep2


title: CRC_149T


title: F2gen21

value: Female-selected


title: M2gen21


title: CRC_150T


title: WT_day4_H3K36me3_rep1

value: wild type


title: WT_day4_H3K36me3_rep2


title: F1gen22


title: bre1d_day4_H3K36me3_rep1


title: CRC_148T


title: F4gen21


title: bre1d_day1_H3_rep1


title: M1gen21

value: Male-selected


title: CRC_145T


title: C3gen21

value: Control


title: WT_day4_H3_rep2


title: CRC_146T


title: WT_day4_H3_rep1


title: CRC_144T


title: WT_day1_H3K36me3_rep2


title: C2gen22


title: M4gen21


title: WT_day1_H3K36me3_rep1


title: CRC_142T


title: WT_day1_H3_rep1


title: CRC_139T


title: WT_day1_H3_rep2


title: CRC_140T


title: CRC_136T


title: CRC_141T


title: CRC_137T


title: Fs+Ar EMBR+ Rep2

city: Santa Barbara

first: Kellie

last: Heom

address: UC Santa Barbara

department: Chemical Engineering

institute: University of California Santa Barbara

description: EMBR-seq+

data_processing:
In the sequencing libraries, read 1 contains the sample barcode. Read 2 is mapped to the bacterial or fungal transcriptome. Prior to mapping, read 1 was trimmed to 25 bases, read 2 was trimmed to 51 bases, and only reads containing valid sample barcodes on read 1 were retained. Next, the reads were mapped to the appropriate reference transcriptome using Burrows-Wheeler Aligner (BWA) version 0.7.15 with default parameters.
Assembly: Escherichia coli K12 substr. MG1655 (ASM584v2); Geobacter metallireducens GS-15 (ASM1292v1); Fibrobacter succinogenes strain UWB7 (GCA_900142945.1); Anaeromyces robustus (Anaeromyces robustus v1.0); Caecomyces churrovis (Caecomyces churrovis A v1.0)
Supplementary files format and content: Text file where column 1 contains gene names or gene IDs and column 2 contains gene counts.

organism:
Fibrobacter succinogenes
Anaeromyces robustus

source_name: strain UWB7, A. robustus

extract_protocol:
For E. coli and G. metallireducens monocultures, total RNA extractions were performed using Trizol according to the manufacturer’s protocol. RNA was extracted from F. succinogenes strain UWB7 monoculture & co-culture pellets using the RNeasy Mini Kit following the protocol for purification of total RNA from plant cells and tissues and filamentous fungi, using liquid N2 method of cell lysis, QIAshredder homogenization, on-column DNase I digestion, and elution in 30 µL of RNAse-free water.
(1) Overview: EMBR-seq libraries were prepared according to the protocol described in Wangsanuwat et al. 100 ng of total RNA were used as input material for all libraries. For the libraries denoted “EMBR-seq” and “EMBR-seq+”, blocking primers were added during the polyadenylation step and reverse transcription step. For the libraries denoted “No depletion” and “RNase H”, water was added instead of blocking primers during these two steps. In the libraries denoted “RNase H” and “EMBR-seq+”, the RNase H treatment was performed as described below. In the libraries denoted “No depletion” and “EMBR-seq”, the RNase H treatment was skipped; the amplified RNA (aRNA) product of in vitro transcription (IVT) was used directly for the library reverse transcription step as described in Wangsanuwat et al. (2) Polyadenylation: 2 μL of total RNA (50 ng/μL) was mixed with 1 μL of 5x first strand buffer [250 mM Tris-HCl (pH 8.3), 375 mM KCl, 15 mM MgCl2, comes with Superscript II reverse transcriptase, Invitrogen Cat. # 18064014], 1 uL of blocking primer mix, 0.1 μL 10 mM ATP, and 0.1 μL E. coli poly-A polymerase (New England Biolabs, Cat. # M0276S). The samples were incubated at 37°C for 10 mins. In the “No depletion” and “RNase H” libraries, 1 μL of nuclease-free water was added instead of the blocking primer mix. (3) Reverse transcription: The polyadenylation product was mixed with 0.5 μL 10 mM dNTPs (New England Biolabs, Cat. # N0447L), 1 μL reverse transcription primers (25 ng/μL, Supplementary Table 2), and 1.3 μL blocking primer mix, and heated to 65°C for 5 mins, 58°C for 1 min, and then quenched on ice. In the “No depletion” and “RNase H” libraries, 1.3 μL of nuclease-free water was added instead of the blocking primer mix. This product was then mixed with 1.2 μL 5x first strand buffer, 1 μL 0.1 M DTT, 0.5 μL RNaseOUT (Thermo Fisher Scientific, Cat. #10777019), and 0.5 μL Superscript II reverse transcriptase, and then incubated at 42°C for 1 hr. Immediately afterwards, the samples were heat-inactivated at 70°C for 10 mins. (4) Second strand synthesis: The reverse transcription product was mixed with 33.5 μL nuclease-free water, 12 μL 5x second strand buffer [100 mM Tris-HCl (pH 6.9), 23 mM MgCl2, 450 mM KCl, 0.75 mM β-NAD, 50 mM (NH4)2SO4, Invitrogen, Cat. # 10812014], 1.2 μL 10 mM dNTPs, 0.4 μL E. coli ligase (Invitrogen, Cat. # 18052019), 1.5 μL DNA polymerase I (Invitrogen, Cat. # 18010025), and 0.4 μL RNase H (Invitrogen, Cat. # 18021071), and incubated at 16°C for 2 hrs. The cDNA was purified with 1x AMPure XP DNA beads (Beckman Coulter, Cat. # A63881) and eluted in 24 μL nuclease-free water that was subsequently concentrated to 6.4 μL. (5) In vitro transcription: The product from the previous step was mixed with 9.6 μL of in vitro transcription mix (1.6 μL of each ribonucleotide, 1.6 μL 10x T7 reaction buffer, 1.6 μL T7 enzyme mix, MEGAscript T7 Transcription Kit, Thermo Fisher Scientific, Cat. # AMB13345) and incubated at 37°C for 13 hrs. The IVT product was mixed with 6 μL ExoSAP-IT PCR Product Cleanup Reagent (Thermo Fisher Scientific, Cat. # 78200.200.UL) and incubated at 37°C for 15 mins. Next, it was treated with 5.5 μL fragmentation buffer (200 mM Tris-acetate (pH 8.1), 500 mM KOAc, 150 mM MgOAc) at 94°C for 3 mins and immediately quenched with 2.75 μL stop buffer (0.5 M EDTA) on ice. The fragmented aRNA was size-selected with 0.8x AMPure RNA beads (RNAClean XP Kit, Beckman Coulter, Cat. # A63987) and eluted in 18 μL nuclease-free water. In the libraries denoted “No depletion” and “EMBR-seq”, the fragmented and cleaned-up in vitro transcription product was used directly for Illumina library preparation by reverse transcription and PCR, as described previously (18, 30). In the “RNase H” and “EMBR-seq+” libraries, the RNase H treatment was performed before proceeding to Illumina library preparation. (6) RNase H treatment for monocultures: After ExoSAP treatment, RNA fragmentation, and bead-based size selection, the aRNA concentration was measured on a NanoDrop One spectrophotometer. 1000 ng of aRNA was mixed with 500 ng (3.2 μL) of RNase H probe mix, 3.2 μL of RNase H buffer mix, and nuclease-free water to reach a total volume of 15 μL for each reaction. This mixture was preheated at 65°C for 5 mins and quenched on ice. 1 μL of RNase H (Invitrogen, Cat. # 18021071) was added and the reaction was incubated at 16°C for 30 mins. Finally, the RNase H product was size-selected with 1x AMPure RNA beads and eluted in 15 μL nuclease-free water, and then concentrated to 5 μL volume for Illumina library preparation. (7) RNase H reaction for co-cultures: For co-culture samples, the RNase H probe mix was altered to include probes for depleting fungal rRNA along with bacterial rRNA. 1000 ng of aRNA derived from co-culture samples was mixed with 850 ng (5.5 μL) of co-culture RNase H probe mix, which consisted of: 100 ng each of the two fungal 28S probes with 50 ng each of the two fungal 18S, fungal 5.8S, and ten bacterial RNase H probes. The aRNA and probes were mixed with 3.2 μL RNase H buffer mix and nuclease-free water to reach a total volume of 15 μL for each reaction. The reactions were preheated at 65°C for 5 mins and quenched on ice. 1 μL of RNase H was added and the reaction was incubated at 16°C for 30 mins. The RNase H product was size-selected with 1x AMPure RNA beads and eluted in 15 μL nuclease-free water, and then concentrated to 5 μL volume for Illumina library preparation.
OTHER (EMBR-seq+). Method is detailed in Heom, Wangsanuwat et al.

tag: cell line

value: strain UWB7, A. robustus

tag: input material_for_library_preparation

value: total RNA (RNeasy), followed by poly-A depletion


title: Fs+Ar EMBR+ Rep3

description: EMBR-seq+

organism:
Fibrobacter succinogenes
Caecomyces churrovis

source_name: strain UWB7, C. churrovis

value: strain UWB7, C. churrovis


title: CRC_135T


title: P11 OPC_Ift88 control_1

city: San Francisco

first: Stephen

last: Fancy

address: 675 Nelson Rising Lane

institute: University of California, San Francisco

data_processing:
FastQC to assess quality
Aligned to mouse reference genome GRCm39 using STAR aligner
Normalization and differential expression analysis performed using DESeq2
Assembly: GRCm39
Supplementary files format and content: Delimited text files contain raw counts for each sample

source_name: oligodendrocyte precursor cell

extract_protocol:
Total RNA extracted using RNAeasy Mini Kit (Qiagen)
Libraries were prepared using the QuantSeq 3' mRNA-Seq Library Pre Kit FWD (Lexogen) following manufacturer's instructions.

tag: cell type

value: oligodendrocyte precursor cell

value: Pdgfra-Cre:Ift88 fl/wt; RosaEYFP


title: Fs+Cc EMBR+ Rep1

description: EMBR-seq+


title: Fs+Cc RNase H Rep3

description: RNase H


title: P11 OPC_Ift88 cKO_2

tag: genotype

value: Pdgfra-Cre:Ift88 fl/fl; RosaEYFP


title: P11 OPC_Ift88 control_3


title: Fs+Cc EMBR+ Rep2

description: EMBR-seq+


title: Fs+Cc RNase H Rep1

description: RNase H


title: CRC_143T


title: P11 OPC_Ift88 cKO_3


title: CRC_138T


title: P11 OPC_Ift88 cKO_1


title: CRC_134T


title: P11 OPC_Ift88 control_2


title: Fs+Ar EMBR+ Rep1

description: EMBR-seq+


title: P0_FB_M358_WTLM

city: Seattle

first: Christopher

last: Seward

state: WA

address: Stubbs Lab, Rm 404, 720 Broadway

institute: Pacific Northwest Research Institute

data_processing:
Raw reads were demultiplexed by Genewiz
STAR v2.7.5a was used to map paired end reads (mm10/GRCm38 genome and Ensembl v102 annotation) and quantify gene expression
Read counts were tabulated with STAR and differential expression was determined using EdgeR v3.12
Assembly: mm10/GRCm38 genome and Ensembl v102 annotation
Supplementary files format and content: STAR feature count tables containing the ensemble ID, total read count for each ID, forward read count for each ID, and reverse read count for each ID

source_name: Forebrain tissue

growth_protocol: The Auts2-ex7fl/fl allele (Auts2tm1.1Dare; Gao et al., 2014), was provided as a kind gift from the laboratory of Dr. Danny Weinberg (NYU). Nes-cre (B6.Cg-Tg(Nes-cre)1Kln/J), Calb1-cre (B6;129S-Calb1tm2.1(cre)Hze/J) and Cmv-cre (B6.C-Tg(CMV-cre)1Cgn/J) were purchased from the Jackson Laboratory. Cre-expressing strains were crossed to Auts2-ex7fl/fl animals to generate homozygotes, heterozygotes and wild-type littermates for tissue collection.

extract_protocol:
P0 Cmv-cre, Auts2-ex7-/- Forebrain and P14 Nes-cre, Auts2-ex7-/- Hippocampus, as well as littermate control samples were collected, and RNA was purified using Trizol followed by 45 min of RNase-free DNase I treatment (NEB) and RNA Clean & Concentrator Kit (Zymo Research). The quality of RNA was tested by Agilent BioAnalyzer and Qubit.
RNA-seq libraries were generated using Illumina TruSeq RNA Library Prep Kits. Samples were sequenced as 150 bp paired end reads (≥ 17 million read pairs per sample) on Illumina Hi-Seq 4000 sequencer through the GENEWIZ sequencing service

value: Forebrain tissue

value: BL6 WTLM


title: CRC_133T

value: colorectal cancer


title: Fs+Ar RNase H Rep3

description: RNase H


title: F3gen22


title: DWCNT_9h_Ana-1_infected_with_MHV-68 _rep2

description:
Gene expression data from latently MHV-68 infected Ana-1 cells treated with DWCNT for 9h, biological replicate 2
DWCNT_9h_AM_2

source_name: Latently MHV-68 infected Ana-1 cells treated with DWCNT for 9h, biological replicate 2


title: Fs+Cc EMBR+ Rep3

description: EMBR-seq+


title: CRC_132T


title: P0_FB_M356_cmv-cre_auts2-ex7koko


title: Fs+Ar RNase H Rep1

description: RNase H


title: Fs+Ar RNase H Rep2

description: RNase H


title: Fs+Ar total RNA EMBR

description: EMBR-seq

value: total RNA (RNeasy)


title: P0_FB_M354_WTLM

value: Male


title: CRC_131T

value: Rectal cancer


title: P0_FB_M373_cmv-cre_auts2-ex7koko


title: P0_FB_M375_cmv-cre_auts2-ex7koko


title: CRC_129T

value: Colon cancer


title: Fs+Ar Control Rep3

description: No depletion


title: P14_HC_M214_nes-cre_auts2-ex7koko

source_name: Hippocampus tissue of brain

value: Hippocampus tissue of brain


title: Fs+Ar EMBR Rep2

description: EMBR-seq


title: CRC_128T


title: CRC_127T

value: Female


title: P0_FB_M353_WTLM


title: Fs+Ar EMBR Rep3

description: EMBR-seq


title: Fs+Ar Control Rep2

description: No depletion


title: CRC_126T


title: CRC_125T


title: Fs+Ar EMBR Rep1

description: EMBR-seq


title: CRC_123T


title: P14_HC_M134_nes-cre_auts2-ex7koko


title: P14_HC_M212_auts2-ex7-fl-het


title: Fs EMBR+ Rep3

description: EMBR-seq+

organism: Fibrobacter succinogenes

source_name: strain UWB7

value: strain UWB7


title: CRC_130T


title: CRC_122T


title: P14_HC_M205_nes-cre_auts2-ex7koko


title: P14_HC_M213_auts2-ex7-fl-het


title: Fs EMBR+ Rep2

description: EMBR-seq+


title: CRC_121T


title: P14_HC_M215_auts2-ex7-fl-het


title: Fs RNase H Rep3

description: RNase H


title: Cebpa-KO Sample 21

city: philadelphia

first: Katherine

last: Quiroz-Figueroa

state: Pennsylvania

address: 11-135 Smilow Center for Translational Research, 3400 Civic Center Blvd

department: Division of Translational Medicine and Human Genetics, Department of Medicine

institute: University of Pennsylvania

description: Cebpa-KO

data_processing:
Raw sequence files (fastq) for 24 samples were mapped to the transcriptome using salmon against the mouse transcripts described in genecode.
Transcript counts were summarized to the gene level using tximport normalized and tested for differential expression using DESeq2.
Differential expression was determined using a False Discovery Rate cutoff of 10%.
Genome_build: mm22 built on the mouse genome GRCm38.p6
Supplementary_files_format_and_content: Matrix table with raw differential gene expression for every gene compared between all groups.

source_name: Liver

growth_protocol: Mice were 20-21 weeks of age at the time of injection. Mice were maintained on chow diet and fed ad libitum, and fasted for 4 hours prior to tissue harvest at midday (~1pm).

extract_protocol:
RNA was collected from approximately 100 mg flash-frozen liver tissue using the mirVana Kit (Invitrogen). Total RNA integrity was assessed using the Agilent RNA 600 Nano Kit.
Whole Transcriptome, High-throughput library was prepared using Illumina truSeq stranded mRNA kit. Molarity measurement of library using Kapa Biosystems Library quant kit. 3 technical replicates of 3 dilutions of sample. library quality check with Agilent.  library quality check with Agilent TapeStation bioAnalyzer.

treatment_protocol: Mice were intraperitoneally injected with AAV-Cre at a 1.5E 11 dose and sacrificed 4 weeks post-injection to collect the liver.

value: Cebpa Flox/Flox

value: 20-21 weeks old

value: AAV-CRE for 4 weeks

tag: cohort


title: Trib1; Cebpa KO (DKO) Sample 23

description: Trib1;Cebpa dLSKO

value: Trib1;Cebpa Flox/Flox

tag: Sex


title: Cebpa-KO Sample 22

description: Cebpa-KO

tag: strain


title: CRC_118T


title: CRC_119T


title: Trib1-KO Sample 19

value: Trib1 Flox/Flox


title: CRC_116T


title: WT Sample 18

description: WT

value: Wild Type


title: Fs EMBR Rep3

description: EMBR-seq


title: CRC_120T


title: Fs+Ar Control Rep1

description: No depletion

value: strain UWB7, A. robustus

value: total RNA (RNeasy), followed by poly-A depletion


title: Trib1; Cebpa KO (DKO) Sample 24

description: Trib1;Cebpa dLSKO


title: CRC_115T


title: WT Sample 17

description: WT


title: CRC_117T


title: CRC_114T


title: TKO_d7_hmedip

city: Toyonaka

first: Takamasa

last: Ito

state: Osaka

address: 1-1 Machikaneyama

department: Biological Science

institute: Osaka University

data_processing:
Raw sequence reads were trimmed using Trim Galore!, then mapped using Bowtie2 to mm10 genome.
The Sam file was converted to a bam file using the Samtools.
DIP-seq data were normalized and generated bigwig files using deepTools.

extract_protocol:
One μg of genomic DNA sheared to 200-500 bp using the LE220 Focused-ultrasonicator (Covaris) was end-repaired and A-tailed. The Illumina PE adapter-ligated DNA was heat-denatured and applied to MeDIP overnight with a monoclonal antibody for 5mC (AnaSpec, Inc.). hMeDIP was performed using a rat monoclonal antibody (Diagenode) for 5hmC. The IP material was recovered with a secondary antibody of rabbit and rat anti-mouse IgG, respectively (Jackson ImmunoResearch) along with protein A/G (Thermo Fisher Scientific), followed by digestion with 20 mg/ml Proteinase K (Invitrogen) for 2 hours.
IP DNA was purified using the MinElute PCR Purification Kit (Qiagen). Confirmation of concentration of 5mC and 5hmC DNA was evaluated by qPCR using positive and negative control primers. The final library amplification was performed using Phusion® hot start II DNA polymerase and 5× Phusion® GC Buffer (Thermo Fisher Scientific) with Illumina paired-end index primers. The PCR-amplified library was size-selected for 220–450-bp fragments on an 8% PAGE gel. The library was normalized based on molarity and pooled for sequencing using v4 ready-to-load reagents for HiSeq 2500 System (Illumina) at 75-bp paired-end reads.

value: DNMT TKO


title: TKO_d7_medip


title: TKO_d0_hmedip


title: Fs EMBR+ Rep1

description: EMBR-seq+


title: Trib1; Cebpa KO (DKO) Sample 16

description: Trib1;Cebpa dLSKO


title: Fs EMBR Rep1

description: EMBR-seq


title: Trib1-KO Sample 20


title: CRC_113T

value: colorectal cancer


title: Trib1; Cebpa KO (DKO) Sample 15

description: Trib1;Cebpa dLSKO


title: CRC_112T


title: Testis Ccer1 KO rep2

city: Nanjing

first: Jimiao

last: Gao

address: 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

institute: Nanjing Medical University

data_processing:
fastp(version 0.18.0)
Sequence reads were filtered by fastp (parameters:removing reads containing adapters;removing reads containing more than 10% of unknown nucleotides;removing low quality reads containing more than 50% of low quality(Q-value<=20)bases)
Bowtie2  (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database and the rRNA mapped reads then were removed.
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT2. 2.4.
Read count extraction and normalization were performed using StringTie v1.3.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: Testis

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA). Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and  buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen,  Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing  adapters.

value: Testis

value: untreated


title: CRC_111T

value: Male

value: Rectal cancer


title: Cebpa-KO Sample 13

description: Cebpa-KO


title: CRC_110T


title: Cebpa-KO Sample 14

description: Cebpa-KO


title: Testis Ccer1 WT rep3

value: WT


title: Trib1-KO Sample 12


title: TKO_d0_medip


title: Testis Ccer1 WT rep2


title: CRC_124T

value: Colon cancer


title: Trib1-KO Sample 11


title: CRC_108T


title: WT Sample 10

description: WT


title: CRC_107T


title: CRC_109T


title: WT Sample 9

description: WT


title: sample_33

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw reads were aligned to the mouse genome mm10 using HISAT2 for mouse vmPFC.
Counts of reads mapping to genes were obtained using featureCounts software of Subread package against Ensembl v90 annotation.
Normalization and differential expression analysis were performed using DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files

source_name: vmPFC

extract_protocol:
Brain microdissections were collected from mice that were euthanized by cervical dislocation. Brains were coronally sectioned using a brain matrix into 1 mm-thick slices. A 14G blunt needle was used for microdissection of the vmPFC. Viral expression and placement were confirmed using an epifluorescence microscope. Total RNA was purified from the tissue using the RNeasy micro kit (Qiagen, Germantown, MD) and TriZol. Samples were treated with DNase I and concentration and purity were tested using NanoDrop (Thermo Fisher Scientific, Waltham, MA).
Libraries were prepared from 7 individual mice per group using the TruSeq Stranded Total RNA Library Prep Gold (Illumina, San Diego, CA) from virally infected mPFC tissue from female mice at baseline or after 3 days of sCVS. Briefly, 1 µg ribosomal depleted RNA was converted to cDNA using random hexamers. Adapters were ligated and samples were size selected with AMPure XP beads (Beckman Coulter, Brea, CA). Barcode bases of 6 bp were introduced at one end of the adapters during PCR amplification steps. Quality and concentration of libraries were analyzed with a Bioanalyzer DNA 1000 chip (Agilent, Santa Clara, CA). 7 samples were pulled per lane for multiplexing and sequenced on an Illumina Hi-Seq machine with 260 bp paired-ends reads by Genewiz (South Plainfield, NJ) and gave rise to ~35 million reads per sample.

value: Ventromedial prefrontal cortex

value: Female

tag: virus

value: Slit1 (Slit1 KD group)

value: Stress


title: CRC_106T


title: Testis Ccer1 KO rep3

tag: treatment


title: Trib1; Cebpa KO (DKO) Sample 8

description: Trib1;Cebpa dLSKO

value: Trib1;Cebpa Flox/Flox

value: 20-21 weeks old

value: AAV-CRE for 4 weeks


title: sample_40

value: No Stress


title: CRC_105T


title: CRC_104T


title: Trib1; Cebpa KO (DKO) Sample 7

description: Trib1;Cebpa dLSKO


title: CRC_103T


title: Testis Ccer1 KO rep1


title: sample_28

value: Lac_Z (control group)


title: Trib1-KO Sample 4

value: Trib1 Flox/Flox


title: Cebpa-KO Sample 5

description: Cebpa-KO

value: Cebpa Flox/Flox


title: CRC_102T

value: colorectal cancer


title: sample_23


title: Testis Ccer1 WT rep1

value: Testis

value: untreated


title: sample_34


title: CRC_101T

value: Male


title: sample_27


title: WT Sample 2

description: WT

value: Wild Type


title: Trib1-KO Sample 3


title: sample_31


title: CRC_99T

value: Rectal cancer


title: WT Sample 1

description: WT


title: CRC_98T

value: Colon cancer


title: CRC_97T


title: sample_22

value: Ventromedial prefrontal cortex

value: Female


title: Cebpa-KO Sample 6

description: Cebpa-KO


title: rat-2

data_processing:
Basecalls performed using CASAVA version 1.9
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 (for mouse), Rnor6 (for rat), OryCun2 (for rabbit),OchPri3 (for pika) whole genome using STAR v2.6.1a with default parameters
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated using featureCounts function from Rsubread (v2.0.1) and rpkm function of edgeR (v3.28.1). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCm38, Rnor6, OryCun2, OchPri3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Rattus norvegicus

source_name: rat fibroblast

extract_protocol:
After growing to 90% confluency, cells were lysed with TRIZOL directly and total RNA was extracted with chloroform and  isopropanol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: SD

value: epidermis


title: sample_36

value: Slit1 (Slit1 KD group)


title: sample_5


title: sample_25

value: Stress


title: rat-1


title: CRC_95T


title: sample_20


title: CRC_94T


title: CRC_93T


title: CRC_100T


title: sample_35

value: No Stress


title: sample_10

value: Lac_Z (control group)


title: sample_37


title: sample_4


title: rat-3


title: sample_19


title: CRC_90T


title: CRC_91T


title: sample_9


title: CRC_96T


title: sample_14


title: sample_3


title: sample_18


title: Benign Breast Disease Biopsy FFPE [sample7]

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

description: Benign Breast Disease Biopsy

data_processing:
Paired-end sequencing reads were mapped to reference genome hg38 using STAR aligner
Gene and exon counts were generated using FeatureCounts using gene definition files from Ensembl v78
Quality control was carried out using RSeQC
Gene counts were normalized to counts per million (CPM) and transcript per million (TPM) using TMM method as implemented in edgeR.
Assembly: hg38
Supplementary files format and content: count_table.tsv : Gene count table

source_name: Breast

extract_protocol:
RNA was extracted from FFPE biopsy benign breast disease tissue
40–100ng of experimental FFPE RNA, FFPE control RNA, or 20ng fresh frozen control RNA was used for library preparation using the TruSeq RNA Library Prep for Enrichment and the Illumina Exome Panel-Enrichment Oligos kit. Additionally, 20–100 ng of FFPE RNA and paired fresh frozen RNA was used for library preparation using the NEBNext rRNA Depletion Kit

value: Breast

value: Biopsy

value: Benign Breast Disease


title: Benign Breast Disease Biopsy FFPE [sample8]

description: Benign Breast Disease Biopsy


title: Benign Breast Disease Biopsy FFPE [sample9]

description: Benign Breast Disease Biopsy


title: Benign Breast Disease Biopsy Fresh Frozen [sample69_FFzn_Exome]

description: Benign Breast Disease Biopsy


title: TA(d2/-)104_array

city: Yokosuka

first: Iyoko

last: Katoh

address: 82 Inaoka-cho

institute: Kanagawa Dental University

description: TAp63 genome editing

hyb_protocol: Cy3-labelled cRNA (0.6 μg) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: TAp63-knockout cell line TA(d2/-)104

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was extracted with NucleoSpin RNA Plus (MACHEREY-NAGEL) according to the protocol.

value: TAp63 knockout cell line derived from FaDu

value: TP63 exon 1 (2-base deletion/HDR)


title: Benign Breast Disease Biopsy FFPE [sample69_FFPE_Depletion]

description: Benign Breast Disease Biopsy


title: Benign Breast Disease Biopsy FFPE [sample69_FFPE_Exome]

description: Benign Breast Disease Biopsy


title: FaDu_array

description: Well-differentiated squamous cell carcinoma

source_name: FaDu, ATCC HTB-43

value: FaDu


title: TA(-/-)15_array

description: TAp63 genome editing

source_name: TAp63-knockout cell line TA(-/-)104

value: TP63 exon 1 (HDR/HDR)


title: CRC_86T

value: colorectal cancer


title: sample_8


title: CRC_87T

value: Colon cancer


title: CRC_89T


title: CRC_92T


title: Benign Breast Disease Biopsy Fresh Frozen [sample68_FFzn_Depletion]

description: Benign Breast Disease Biopsy


title: Benign Breast Disease Biopsy Fresh Frozen [sample68_FFzn_Exome]

description: Benign Breast Disease Biopsy


title: CRC_85T


title: CRC_84T

value: Male

value: Rectal cancer


title: Benign Breast Disease Biopsy FFPE [sample68_FFPE_Exome]

description: Benign Breast Disease Biopsy


title: CRC_83T


title: Benign Breast Disease Biopsy FFPE [sample68_FFPE_Depletion]

description: Benign Breast Disease Biopsy


title: CRC_88T


title: CRC_82T

value: Female


title: sample_12

value: Ventromedial prefrontal cortex


title: Benign Breast Disease Biopsy Fresh Frozen [sample67_FFzn_Exome]

description: Benign Breast Disease Biopsy


title: sample_7


title: CRC_81T


title: Benign Breast Disease Biopsy Fresh Frozen [sample67_FFzn_Depletion]

description: Benign Breast Disease Biopsy


title: sample_1


title: CRC_80T


title: sample_11

value: Slit1 (Slit1 KD group)


title: sample_38


title: P3_5_Flag

city: Beijing

first: wang

last: jiawen

address: 7 Science Park Road ZGC Life Science Park

institute: National institute of biological sciences

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie version 1.2.2 with parameters -p 30 -m 1 -S -q
peaks were called using MACS2 version 2.2.7.1 with parameters callpeak -g mm -B --SPMR
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were converted from bdg files generated by MACS2 version 2.2.7.1, reprsenting fold enrichment for each sites

source_name: MOUSE FIBROBLAST

growth_protocol: MAF was cultured under 5% CO2,20% O2,37 ℃ with DMEM (10% FBS, 1% PS)

extract_protocol:
Unsynchronized and confluent pika/rat Epas1 knock-in MAF cells in 15 cm dishes were treated with 1 mM DMOG for 16 h. After treatment, cells were cross-linked in DMEM containing 1 mM DMOG, PMSF, and 1% formaldehyde for 12 min at room temperature. The cross-link was stopped by adding glycine to a final concentration of 125 mM and incubated at room temperature for 5 min. ChIP assay and DNA sample preparation were performed strictly following the ChIP-IT High Sensitivity Kit instructions (Active Motif). Eluted DNA was analyzed with quantitative PCR and high-throughput sequencing.
Libraries were prepared according to Illumina's instructions

treatment_protocol: After growing to 60% confluency, cells were changed fresh culture medium with 1mM DMOG. After 12h, cells were harvested.

tag: chip-grade antibody

value: Sigma Aldrich (Cat #F3165)

tag: 2nd antibody

value: anti-rabbit IgG

value: 12h 1 mM DMOG treatment


title: P3_5_input


title: CRC_76T

source_name: colorectal cancer


title: CRC_79T


title: P1_5_Flag


title: CRC_77T


title: Benign Breast Disease Biopsy FFPE [sample67_FFPE_Depletion]

description: Benign Breast Disease Biopsy

value: Breast


title: Benign Breast Disease Biopsy Fresh Frozen [sample66_FFzn_Exome]

description: Benign Breast Disease Biopsy

value: Biopsy


title: sample_2

value: Lac_Z (control group)

value: No Stress


title: Benign Breast Disease Biopsy FFPE [sample67_FFPE_Exome]

description: Benign Breast Disease Biopsy

value: Benign Breast Disease


title: CRC_75T


title: P1_5_input


title: Benign Breast Disease Biopsy Fresh Frozen [sample66_FFzn_Depletion]

description: Benign Breast Disease Biopsy


title: CRC_78T


title: Benign Breast Disease Biopsy FFPE [sample66_FFPE_Exome]

description: Benign Breast Disease Biopsy


title: CRC_74T


title: P1_5_Bmal

value: Abcam (Cat #ab3350)


title: CRC_73T


title: RV-Failing_1

city: Bad Nauheim

first: Fatemeh

last: Khassafi

address: Parkstrasse

institute: Max Planck Institute

description:
processed-data-human.xlsx
count matrix column name: RV-Failing_1

data_processing:
Raw fastqs were assessed for quality, adapter content, and duplication rates using FastQC. Trimmomatic version 0.39 was employed to trim reads following a quality drop (below a mean of Q15) in a window of five nucleotides
STAR mapping-b1: --outFilterMismatchNoverLmax 0.1 --outFilterScoreMinOverLread 0.9 --outFilterMatchNminOverLread 0.9 --outFilterMatchNmin 20 --alignIntronMax 200000 --alignMatesGapMax 2000 --alignEndsProtrude 10 ConcordantPair --outFilterMultimapNmax 1 --genomeDir GRCh38/indices/star_GRCh38_gencode.v27
STAR mapping-b2: mode: single-end, keep duplicates: no, keep multi-mapping: no, keep ribosomal: no, keep mitochondria: no --outFilterMismatchNoverLmax 0.1 --outFilterScoreMinOverLread 0.9 --outFilterMatchNminOverLread 0.9 --outFilterMatchNmin 20 --alignIntronMax 200000 --alignMatesGapMax 2000 --alignEndsProtrude 10 ConcordantPair --outMultimapperOrder Random --limitOutSAMoneReadBytes 10000000 --outFilterMultimapNmax 1 --genomeDir GRCh38/indices/star_GRCh38_gencode.v27
The number of reads that aligned to genes was counted using featureCounts version 1.6.5 from the Subread package. Only reads mapping at least partially inside exons were aggregated and counted per gene. Reads aligning to multiple regions or genes were excluded. -t exon -g gene_id -s 2; multi-mapping: no; duplicates: no
Raw count values for each organism were normalized separately using DESeq2 version 1.30.0, then transformed into regularized logarithm values for further analysis. Because we had two different batches of human samples, we performed a batch effect correction on this data using the sva package. The normalized and batch-corrected data were the basis of downstream analysis.
Assembly: hg38; (GRCh38.27)
Supplementary files format and content: excel file containing sheet 1: sample labels and mapping parameters
Supplementary files format and content: excel file containing sheet 2: matrix of raw read counts for genes*samples

source_name: Right ventricle

extract_protocol:
Human RV tissues were manually dissected in cardiac biopsy or autopsy, according to the previously described protocol ( doi: 10.1161/CIRCULATIONAHA.120.047626 ), and Total RNA from each batch of RV samples were isolated separately using the RNeasy Mini Kit (Qiagen, Germantown, MA, USA) and snap-frozen. Purification of total RNA was performed as described in the RNeasy handbook, using DNase I digestion (RNase-Free DNase Set, Qiagen).
Following the RNA integrity measurement, approximately 10 ng of total RNA were used as starting material for library preparation using the SMARTer® Stranded Total RNA-seq Kit - Pico Input Mammalian, following manufacturers’ protocols

value: Right ventricle

value: F

tag: primary disease_characterization

value: Decompensated RV

tag: secondary group_characterization

value: Decompensated-1 RV


title: CRC_72T

value: colorectal cancer

tag: gender

tag: age

value: Colon cancer


title: Benign Breast Disease Biopsy FFPE [sample66_FFPE_Depletion]

description: Benign Breast Disease Biopsy


title: TKO_602_d0

data_processing:
Raw sequence reads were trimmed to remove low-quality reads and adapter sequences using Trim Galore! and then mapped to the mm10 genome using HISAT2 with default parameter.
The Sam file was converted to a bam file using the Samtools.
Expression data were obtained using the subread package Featurecounts, and then transcripts per million (TPM) was calculated. The bam file for WT ESCs was reanalysed from previous study (GSM5403455).
mm10
tab-delimited .txt files containing TPM value for each samples

extract_protocol:
All ESCs were cultured on mitomycin C-treated mouse embryonic fibroblasts (MEFs) in ESC medium [D-MEM/Ham’s F12 (Wako, Osaka, Japan), 10% fetal bovine serum (Corning, NY, USA), 1× penicillin-streptomycin and 2 mM L-glutamate (Gibco®, Thermo Fisher Scientific), 0.1 mM β-mercaptoethanol (Signa-Aldrich), and 10^3 U/ml ESGRO® LIF (Merck, Kenilworth, NJ, USA)] and grown under 5% CO2 at 37˚C. The medium was changed daily.
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
After the QC process, mRNA was enriched using oligo(dT) beads. First, mRNA was randomly fragmented by adding fragmentation buffer, cDNA was synthesized using mRNA template and random hexamer primer, and custom double-strand synthesis buffer (Illumina), dNTPs, RNase H, DNA polymerase Synthesis was performed. Next, end repair, A-ligation, sequencing adapter ligation, size selection, and PCR enrichment were performed to complete the double-stranded cDNA library.


title: RV-Failing_8

description:
processed-data-human.xlsx
count matrix column name: RV-Failing_8

value: M

value: Compensated-1 RV


title: Benign Breast Disease Biopsy FFPE [sample65_FFPE_Exome]

description: Benign Breast Disease Biopsy


title: CRC_71T

value: Male

tag: diagnosis

value: Rectal cancer

tag: tnm stage


title: RV-Failing_10

description:
processed-data-human.xlsx
count matrix column name: RV-Failing_10

tag: tissue


title: Benign Breast Disease Biopsy FFPE [sample65_FFPE_Depletion]

description: Benign Breast Disease Biopsy