title: HaCaT_Control3

city: Fuzhou

first: Pengjun

last: Zhou

state: Fujian

address: St 29Xianquan

institute: the Union Hospital, Fujian Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads 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: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: human immortalized keratinocyte

growth_protocol: The human immortalized keratinocyte line HaCaT was obtained from the American Type Culture Collection (Manassas, VA, USA) and was cultured in Dulbecco's modified Eagle's medium with high glucose containing 10% fetal calf serum. Transfection started when the density of HaCaT cells in 6-well plates reached 30% to 40%.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Life Technologies, Shanghai, China), and 1 µl of total RNA was taken and quantified using NanoDrop instrument (Thermo, Waltham, MA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HaCaT cells were divided into three groups: interference group transfected with 100 pmol siRNA targeting PSENEN (PSENEN-siRNA), negative control group transfected with a mismatch siRNA (m-siRNA), and blank control group transfected with the equal amounts of transfection reagent using Lipofectamine 2000 (Life Technologies, Shanghai, China). See Supplementary Table 1 for siRNA sequences. The mRNA was extracted at 48 h and 72 h after transfection and protein was extracted at 72 h after transfection.

value: HaCaT

value: human immortalized keratinocyte

value: treat with mismatch siRNA


title: Frontal-Cortex_Psilocybin_4-weeks-post-injection_6

status: Public on Aug 17 2022

type: SRA

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

library_source: transcriptomic

data_processing:
Fastq files were generated using bcl2fastq2 v. 2.20.0
Reads were aligned to the GRCm38 primary assembly using STAR v. 2.7.2b against a reference built using the GENCODE vM25 gene model
Aligned reads were counted against the same gene model using featureCounts v. 1.6.2 counting only reads where both ends mapped to the same strand
Counts from the two sequencing runs were added together
Assembly: mm10
Supplementary files format and content: csv file with read counts

molecule: total RNA

organism: Mus musculus

source_name: Frontal Cortex

extract_protocol:
Total RNA was isolated using an RNeasy mini kit (Qiagen, #74106) according to the manufacturer’s protocol
Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA protocol (Illumina). Poly-A containing mRNAs were purified by poly-T attached magnetic beads, fragmented, and cDNA was synthesized using SuperScript III Reverse Transcriptase (Thermo Fisher Scientific). cDNA was adenylated to prime for adapter ligation and after a clean-up using AMPure beads (Beckman coulter), DNA fragments were amplified using PCR followed by a final clean-up. Libraries were quality-controlled using a Fragment Analyzer instrument (Agilent Technologies) and subjected to 52-bp paired-end sequencing on a NovaSeq 6000 (Illumina). A total of 2.7 billion reads were generated.

treatment_protocol:
Ten-week-old chow-fed male C57BL/6J mice (group-housed) were randomized into one of four treatment groups (n=8 per group) as follows: Group 1: A single intraperitoneal injection of 3 mg/kg psilocybin, followed by tissue harvest 3 hours after treatment. Group 2: A single intraperitoneal injection of isotonic saline followed by tissue harvest 3 hours after treatment. Group 3: A single intraperitoneal injection of 3 mg/kg psilocybin followed by tissue harvest four weeks after treatment. Group 4: A single intraperitoneal injection of isotonic saline followed by tissue harvest 4 weeks after treatment.
Mice received a single intraperitoneal injection according to their grouping, and were sacrificed (decapitation) according to the above schedule. Prefrontal cortex and whole hypothalamus were immediately dissected out and flash frozen on dry ice. Mice were euthanized in the morning, four hours after the onset of the light phase, to ensure minimal diurnal variation in gene expression. Dissected brain regions were stored at -80⁰C until isolation of RNA was performed.

tag: tissue

value: Frontal Cortex

tag: treatment

value: Psilocybin

tag: timepoint

value: 4 weeks post-injection

tag: cage

tag: extraction pool

value: D


title: Frontal-Cortex_Psilocybin_3-hours-post-injection_6

value: 3 hours post-injection


title: RA-FLS, negative control

city: Shanghai

first: Yu

last: Du

address: 600 Yishan Road

department: Department of Rheumatology and Immunology

country: China

institute: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

data_processing:
Illumina Casavasoftware used for basecalling.
Remove adapter polluted reads (reads contain adapter more than 5bp), low-quality reads (reads in which more than 15% bases with base calling quality Q≤19), and reads which contain N higher than 5%.
The reference genomes and the annotation file were downloaded from ENSEMBL database. Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT v2.0.5.
Reads Count for each gene in each sample was counted by HISAT v2.0.5, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with nonbiological replicates.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample.

organism: Homo sapiens

source_name: rheumatoid arthritis fibroblast-like synoviocytes (RA-FLS)

growth_protocol: RA-FLS were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
After four days of transfection, total RNA was harvested using Trizol reagent.
NEBNext® Ultra™ RNA Library Prep Kit for Illumina was used with 2 ug of total RNA for the construction of sequencing libraries using standard Illumina protocols.

treatment_protocol: RA-FLS were transfected with negative control lentivirus or VGLL3-overexpressing lentivirus.

tag: disease state

value: rheumatoid arthritis (RA)

tag: cell type

tag: genotype

value: Negative control


title: Calu-3 +SARS-CoV-2, FG-4592 (C)

city: Oxford

first: Peter

last: Wing

address: Old Road Campus, Roosevelt Drive,

country: United Kingdom

institute: University of Oxford

data_processing:
Illumina adapters were removed and data transformed to sequencing reads by CASAVA base recognition
Reads were mapped against the reference human genome (hg38) using STAR aligner.
Non-human reads were aligned to the SARS-CoV-2 (Wuhan) reference; NC_045512.2
Read counts were transformed to FPKM to account for sequencing depth and gene length (Mortazavi et al. 2008)
Genome_build: Human hg38
Supplementary_files_format_and_content: FPKM and readcount values for every gene in n=6 samples

source_name: Lung adenocarcinoma cell line

growth_protocol: Calu-3 cells were seeded, and left overnight to adhere. Media was replaced and cells treated with 50µM FG-4592 for 24h. Cells were then infected with SARS-CoV-2 (MOI 0.01) and harvested 24h post infection.

extract_protocol:
Following treatment as described above, cells were lysed in RLT buffer and RNA extracted using Qiagen RNAeasy kit. RNAs were treated with on-column DNAse (Qiagen), and 2uG of material was used for the construction of sequencing libraries.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Drug treatment was applied 24 hours pre infection.

tag: cell line

value: Lung adenocarcinoma

tag: culture condition

tag: agent


title: HaCaT_Control2


title: Calu-3 +SARS-CoV-2, FG-4592 (B)


title: Frontal-Cortex_Saline_4-weeks-post-injection_5

value: Saline


title: Frontal-Cortex_Psilocybin_4-weeks-post-injection_5


title: CTH-57

type: RNA

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale Menghini n.9

department: Department of Medicine, Hematology and Bone Marrow Transplantation Unit

country: Italy

institute: University of Perugia

hyb_protocol: Hybridization of the microarrays was performed in a GeneChip® Hybridization Oven 645 (Affymetrix/Thermo Fisher Scientific). GeneChips were washed and stained

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 (Affymetrix Applied Biosystem Microarray, Thermo Fisher, Milan, Italy)

data_processing: Primary data analysis was performed with Transcriptome Analysis Console software version 4.0 (TAC 4.0.2.15). Differentially expressed RNA were estimated by fold-change filtering combined with Student’s t-test. Transcripts with fold change in expression ≥ ±2.0 and FDR<0.05 were considered significantly differentially expressed. Hierarchical clustering was performed to show the distinguishing genes expression pattern among samples

label: biotin

source_name: Unsorted Peripheral Blood Cells

label_protocol: GeneChip® WT PLUS Reagent Kit (Affymetrix Applied Biosystem Microarray, Thermo Fisher, Milan, Italy) was used to generates amplified and biotinylated sense-strand DNA targets from total RNA; it uses a reverse transcription priming method that primes the entire length of RNA. Amplified cDNA was quantified, fragmented, marked, and prepared for hybridization from the GeneChip® Clariom S Human Array (Thermo Fisher Scientific) for expression level measurement

extract_protocol: RNA was extracted from bone marrow or peripheral blood samples using a QIAamp RNA Blood Mini Kit (Qiagen) at a QIAcube automated station

value: T-ALL

value: Unsorted Peripheral Blood Cells

tag: chromothripsis status

value: negative

tag: phenotype

value: non-ETP


title: CTH-56

source_name: Unsorted Bone Marrow Cells

value: Unsorted Bone Marrow Cells

value: unknown


title: CTH-54


title: CTH-53


title: CTH-55


title: CTH-52


title: CTH-51


title: Calu-3 +SARS-CoV-2, FG-4592 (A)


title: Frontal-Cortex_Saline_3-hours-post-injection_5


title: HaCaT_SiRNA3

value: HaCaT

value: human immortalized keratinocyte

value: treat with PSENEN siRNA


title: HaCaT_SiRNA2


title: HaCaT_Control1

value: treat with mismatch siRNA


title: HaCaT_SiRNA1


title: Calu-3 +SARS-CoV-2, Control (B)

value: Untreated (Control)


title: S375E_09

city: Trieste

first: Maurizio

last: Romano

address: Via A. Valerio 28

department: Department of Life Sciences

institute: University of Trieste

description: Replicate TDP-43 S375E-09

data_processing:
1 Raw Data    The original raw data from Illumina are transformed to Sequenced Reads by base calling. Raw data are recorded in a FASTQ file, which contains sequence information (reads) and corresponding sequencing quality information.    Every read in FASTQ format is stored in four lines as follows:    @HWI-ST1276:71:C1162ACXX:1:1101:1208:2458 1:N:0:CGATGT     ANTTGTTAACAGGTCAAAATGCAGATCTTCGTGAAGACCCTGACCGGCAAGACCATCACCCTAGAGGTGGAGCCCAGTGACACCATCGAGAACGTGAAG  +  F#,FFFFFFFFFFFFF:FFFF::FFFFF:FFFFFFFFFFFFFFFFFF:F,FFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FF:FFFFFF:FFFFFFF    Line 1 begins with a '@' character and is followed by the Illumina Sequence Identifiers and an optional description.  Line 2 is the raw sequence read.  Line 3 begins with a '+' character and is optionally followed by the same sequence identifier and description.  Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of characters as there are bases in the sequence.
2 Data Filtering    Raw reads are filtered to remove reads with adapter contamination or reads with low quality. Only clean reads were used in the downstream analyses.    The filtering process is as follows:  (1) Discard reads with adaptor contamination.  (2) Discard reads when uncertain nucleotides constitute more than 10% of either read (N > 10%).  (3) Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50% of the read.
3 Mapping To Reference Genome    Mapping the clean reads to the reference genome or the transcriptome is the basis for the next following analysis. Novogene use STAR to accomplish the mapping. For the Human species, if only need the differential expression significant genes, can map reads to the transcriptome directly. In order to avoid losing a lot of effective junction reads, Novogene use STAR software to alignment for RNA-seq sequencing data analysis, the junction reads can be positioned precisely, as shown below.
4 Quantification  Gene expression level is measured by transcript abundance. The greater the abundance, the higher is the gene expression level. In our RNA-seq analysis, the gene expression level is estimated by counting the reads that map to genes or exons. Read count is not only proportional to the actual gene expression level, but is also proportional to the gene length and the sequencing depth. In order for the gene expression levels estimated from different genes and experiments to be comparable, the FPKM is used.    HTSeq software was used to analyze the gene expression levels in this experiment, using the union mode.    The result files present the number of genes with different expression levels and the expression level of single genes.  In general, an FPKM value of 0.1 or 1 is set as the threshold for determining whether the gene is expressed or not.    Comparison between Gene Expression Levels: To compare gene expression levels under different conditions, an FPKM distribution diagram and violin Plot are used. For biological replicates, the final FPKM would be the mean value.

Genome_build: Homo Sapiens (GRCh37/hg19)
Supplementary_files_format_and_content: fpkm_genename.xlsx: FPMK + Gene annotations (Excel format)
Supplementary_files_format_and_content: readcount_genenames.xlsx: Readcounts + Gene annotations (Excel format)

source_name: Hek293 Flp-In T-REx  monoclone expressing S375E TDP-43

growth_protocol: Hek293 Flp-In T-REx cells (ThermoFisher Scientific, Waltham, MA, USA)  were maintained in Dulbecco’s Modified Eagle Medium (DMEM)+Glutamax, supplemented with 10% tetracycline-free fetal bovine serum (FBS) and Blasticidin S HCL 15µg/ml (ThermoFisher Scientific, Waltham, MA, USA). For stable transfections, cells were co-transfected with a mixture of pOG44 plasmid and recombinant pcDNA5 FRT/TO vector carrying either the wild-type (WT) or mutant (S375G and S375E) version of the human flag-tagged TDP-43 (TARDBP, NM_007375) Open Reading Frame. Monoclonal colonies were selected and expanded under double selection (Blasticidine 15µg/ml and hygromicine 100µg/ml).

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA sequencing  (150PE, 60M read pair per sample) was performed by Novogene (https://en.novogene.com/).  RNA libraries were prepared for sequencing using standard Illumina protocols.  Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies).  Insert size was checked on an Agilent 2100 and quantified using quantitative PCR (Q-PCR).

treatment_protocol: All experiments using the stable clones were performed after 48 hours from the induction of TDP-43 expression with Tetracycline 1µg/ml (Sigma-Aldrich, St. Louis, MO, USA).

value: Hek293 Flp-In T-REx

value: 48hrs - Tetracycline induction


title: Frontal-Cortex_Psilocybin_3-hours-post-injection_4

value: Frontal Cortex

value: Psilocybin

value: 3 hours post-injection

value: C


title: Calu-3 +SARS-CoV-2, Control (A)

value: Lung adenocarcinoma


title: Frontal-Cortex_Psilocybin_3-hours-post-injection_5

value: D


title: Frontal-Cortex_Saline_4-weeks-post-injection_4

value: Saline

value: 4 weeks post-injection


title: Calu-3 +SARS-CoV-2, Control (C)


title: HK_1_EBV_eGFP_TPA_SB

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
Illumina bcl2fastq2.20.0 software was used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: NPC

growth_protocol: HK1-EBV-eGFP cells were cultured in RPMI-1640 containing penicillin-streptomycin, and G418 supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was collected using RNeasy Plus Mini (QIAGEN, Hulsterweg, Netherlands)
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: Before estradiol or TPA+SB treatment, cells were incubated in phenol red-free RPMI-1640 containing penicillin-streptomycin, supplemented with 5% dextran-coated charcoal-stripped FBS. Cells were treated with none (DMSO), estradiol (10nM) or TPA (10ng/mL) +SB (1mM) for 48h.

tag: cell type/genotype

value: TPA+SB.


title: SIRT3 K288R (KR)

first: JIAO

last: MA

address: No. 280 South Chongqing Road, west wing building #7 R408

department: Biochemistry and Molecular Cell Biology

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads 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: GRCh37
Supplementary_files_format_and_content: xlsx file for gene information and FPKM  for each gene in VEC, WT & KR groups
Supplementary_files_format_and_content: xlsx file for transcripts information and FPKM for each transcript in VEC, WT & KR groups

source_name: lentiviral encoding SIRT3 K288R transduced MV4-11 stable cells

growth_protocol: aformentiones stable cells  were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10-20% Fetal Bovine Serum (FBS) and 100 g/mL penicillin/streptomycin.

extract_protocol:
mRNA was isolated from total RNA using NEB Next poly (A) mRNA Magnetic Isolation Module (NEB, MA, USA) and rRNA was removed using RiboZero Magnetic Gold Kit (Epicentre NY, USA).
RNA library was prepared using KAPA Stranded RNA-SEQ Library Prep Kit (illumina, CA, USA) according to instruction manual prior to subject to sequencing using illumina NovaSeq 6000.

value: AML cells

tag: genotype/variation

value: SIRT3 K288R (KR)

value: untreated


title: WT SIRT3 (WT)

source_name: lentivrial encoding WT SIRT3 transduced MV4-11 stable cells

value: WT SIRT3 (WT)


title: Frontal-Cortex_Saline_3-hours-post-injection_4


title: CTH-48

value: T-ALL

value: Unsorted Peripheral Blood Cells

value: negative

value: non-ETP


title: CTH-47


title: CTH-49

value: Unsorted Bone Marrow Cells


title: CTH-46


title: Vector control (VEC)

source_name: lentiviral encoding vector control transduced MV4-11 stable cells

value: Vector control (VEC)


title: Frontal-Cortex_Psilocybin_4-weeks-post-injection_4

value: Frontal Cortex

value: Psilocybin


title: PC3-C5i2_IGO_10123_F_4_S26

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

country: USA

institute: Memorial SLoan-Kettering Cancer Center

description: CSN5i-3_10uM_ cell_2

data_processing:
Data processing were performed with Partek Flow according to Manufactures Instruction
Supplementary_files_format_and_content: Excel File contain the gene list

growth_protocol: Cell are cultured in standard condition according to ATCC

extract_protocol:
Total RNA was extracted using the Direct-Zol RNA kit  (Zymo Research, Irvine, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Prostate cancer Cell

tag: cell  type

value: drug treated  cell

tag: source

value: ATCC


title: Frontal-Cortex_Saline_3-hours-post-injection_3

tag: tissue

value: Saline

value: 3 hours post-injection

value: C


title: Tcf12-WT-2-cell-Rep 2

city: Hangzhou

first: Lan-Rui

last: Cao

state: Zhejiang

address: 866 Yu Hang Tang Rd

department: Life Sciences Institute

institute: Zhejiang University

data_processing:
RNA-Seq was performed with biological replicates for all samples.
Paired-end RNA-seq reads were trimmed and mapped to the mm9 genome by HISAT2 (version 2.1.0) .
Cufflinks v2.2.1 was used to calculate the FPKM per gene based on mm9 refFlat from UCSC genome annotation database.
Differential expression analysis was performed with R package edgeR. Genes with FDR of <0.01 and log2(fold change) >=2 were considered as differentially expressed.
Expression level  was further normalized with the ERCC spike-in.
Assembly: mm9
Supplementary files format and content: Tab-delimited text files include FPKM values of all RNA-seq samples

source_name: embryos

extract_protocol:
Oocytes and embryos were collected from indicated genotypes (10 oocytes per sample). Each sample was directly lysed with 4.2 ul lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 1:1000 ERCC spike-in) and immediately used for cDNA synthesis using the Smart-seq2 method as described previously (Picelli et al, 2014).
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina NovaSeq 6000 platform.

tag: strain

value: embryos

tag: developmental stage

value: Mouse 2-cell embryos

value: WT

tag: time


title: CTH-50

value: T-ALL


title: WM-266-4 HiChIP

city: Stanford

first: Margaret

last: Guo

state: CA

address: 269 Campus Dr. CCSR Room 2150

institute: Stanford University

library_source: genomic

data_processing:
Library strategy: HiChIP-Seq
Raw reads were mapped to hg19 and counts were obtained using STAR with the following settings (--runThreadN 16 --outSJfilterReads Unique --outFilterType BySJout --outSAMunmapped Within --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --alignIntronMin 20 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --outSAMtype BAM SortedByCoordinate --outBAMcompression 10 --limitBAMsortRAM 60000000000 --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBAMcompression 10 –outSAMstrandField intronMotif)37.
HiChIP paired-end reads were aligned to the hg19 genome using the HiC-Pro pipeline. Default settings were used to remove duplicate reads, assign reads to MboI restriction fragments, filter for valid interactions, and generate binned interaction matrices. HiC-Pro filtered reads were then processed using hichipper using the {EACH, ALL}  settings to call HiChIP peaks to MboI restriction fragments. HiC-Pro valid interaction pairs and hichipper HiChIP peaks were then processed using FitHiChIP to call significant chromatin contacts using the default settings except for the following: MappSize=500, IntType=3, BINSIZE=5000, QVALUE=0.01, UseP2PBackgrnd=0, Draw=1, TimeProf=1. We note that N-D28 samples were removed from subsequent analysis because of poor QC metrics.
Differential analysis was performed using diffloop and limma with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: looped regions outputed plus the count frequencies of the loop

molecule: genomic DNA

source_name: Human Melanoma Cell Line

growth_protocol: WM-266-4 human malignant melanoma cell line was obtained from ATCC (CRL-1676) and grown in DMEM (ThermoFisher, 11995-065) supplemented with 10% FBS.  Cells were grown in T-75 flasks.

extract_protocol:
The HiChIP protocol was performed for Astrocytes, ESC cells, N-D2, N-D4, N-D10, and N-D28 as previously described (Mumbach 2016) using antibody H3K27ac (Abcam, ab4729) with the following modifications. Samples were sheared using a Covaris E220 using the following parameters: Fill Level = 10, Duty Cycle = 5, PIP = 140, Cycles/Burst = 200, Time = 4 minutes and then clarified by centrifugation for 15 minutes at 16100 rcf at 4° C.  We used 4 ug of antibody to H3K27ac and captured the chromatin-antibody complex with 34 uL Protein A beads (Thermo Fisher). Qubit quantification following ChIP ranged from 125-150 ng. The amount of Tn5 used and number of PCR cycles performed were based on the post-ChIP Qubit amounts.
HiChIP samples were size selected by PAGE purification (300-700 bp) for effective paired-end tag mapping and where therefore removed of all primer contamination. All libraries were sequenced on the Illumina NovaSeq 6000 instrument to an average read depth of 300 million total reads.

tag: treatment

value: 6 uM DMSO

tag: time point

value: 24 hours


title: Frontal-Cortex_Psilocybin_3-hours-post-injection_3

tag: timepoint

tag: cage

tag: extraction pool


title: PC3-C5i1_IGO_10123_F_3_S25

description: CSN5i-3_10uM_ cell_1

tag: cell type

tag: cell line


title: COLO 829 HiChIP

growth_protocol: COLO 829 human melanoma cell line was obtained from ATCC (CRL-1974) and grown in RPMI 1640 Media (ThermoFisher, A1049101) supplemented with 10% FBS. Cells were grown in T-75 flasks.

value: 2 uM DMSO


title: PC3-NT1_IGO_10123_F_1_S23

description: DMSO treated cell_1


title: GM12878 Cells HiChIP

source_name: GM12878 Cell Line

growth_protocol: GM12878 were obtained from Coriel (Catalog # GM12878) and grown in RPMI-1640 supplemented with 2mM L-glutamine (Thermo Fisher 25030149), 15% FBS (XXX, non-heat-inactivated) and 1% pen/strep. Cells were grown in T-25 or T-75 flasks in accordance with ENCODE guidelines.

value: untreated


title: Frontal-Cortex_Psilocybin_4-weeks-post-injection_3

value: 4 weeks post-injection


title: PC3-NT2_IGO_10123_F_2_S24

description: DMSO treated cell_2


title: Uterine Epithelial Cells HiChIP

source_name: Endometrial Epithelial Cells

growth_protocol: Endometrial (Uterine) Epithelial Cells were obtained from Lifeline Cell Technology (FC-0078) and grown in ReproLife™ Reproductive Medium Complete Kit (Lifeline Cell Technology, LL-0068). Cells were grown in 15 cm dishes.


title: 22RV-C5ib_IGO_10123_K_4_S4

description: CSN5i-3_5uM_ cell_2


title: HK_1_EBV_eGFP_E2_10nM

value: estradiol 10nM


title: HK_1_EBV_eGFP_None

value: none (DMSO)


title: CTH-43

tag: disease state

value: Unsorted Bone Marrow Cells

tag: chromothripsis status

value: negative

value: unknown


title: CTH-45

tag: phenotype

value: non-ETP


title: CTH-42


title: 22RV-C5ia_IGO_10123_K_3_S3

description: CSN5i-3_5uM_ cell_1

value: Prostate cancer Cell

value: drug treated  cell

value: ATCC


title: Frontal-Cortex_Saline_3-hours-post-injection_2

value: Frontal Cortex

value: Saline

value: 3 hours post-injection

value: C


title: CTH-41

value: T-ALL


title: Frontal-Cortex_Psilocybin_3-hours-post-injection_2

value: Psilocybin


title: Frontal-Cortex_Saline_4-weeks-post-injection_2


title: Thyroid Epithelial Cells HiChIP

source_name: Human Primary Thyroid Epithelial Cells

growth_protocol: Human Primary Thyroid Epithelial Cells (Thyroid) were obtained from CellBiologics (H-6040) and grown in Complete Human Epithelial Cell Medium supplemented with Human Epithelial Cell Medium Supplement Kit (CellBiologics, H6621). Cells were grown in 15 cm dishes.

value: untreated


title: Frontal-Cortex_Saline_4-weeks-post-injection_3

value: 4 weeks post-injection


title: 22RV-NCb_IGO_10123_K_2_S2

description: DMSO treated cell_2


title: Renal Epithelial Cells HiChIP

growth_protocol: Human Primary Proximal Tubular Epithelial Cells (Renal) were obtained from CellBiologics (H-6015) and grown in Complete Human Epithelial Cell Medium supplemented with Human Epithelial Cell Medium Supplement Kit (CellBiologics, H6621). Cells were grown in 15 cm dishes.


title: CTH-44

value: Unsorted Peripheral Blood Cells


title: Prostate Epithelial Cells HiChIP

source_name: Human Prostate Epithelial Cells

growth_protocol: Human Prostate Epithelial Cells (Prostate) were obtained from Lonza (CC-2555) and grown in Prostate epithelial basal medium (Lonza, CC-3165) and supplemented with PrEGM Prostate Epithelial Cell Growth Medium SingleQuots Supplements and Growth Factors (Lonza, CC-4177)


title: CTH-39


title: C42-NT2c_IGO_10123_E_10_S9

description: CSN5i-3_1uM_ cell_2


title: Pancreas Epithelial Cells HiChIP

growth_protocol: Human Primary Pancreatic Epithelial Cells (Pancreas) were obtained from CellBiologics ( H-6037) and grown in Complete Human Epithelial Cell Medium supplemented with Human Epithelial Cell Medium Supplement Kit (CellBiologics, H6621). Cells were grown in 15 cm dishes.


title: Frontal-Cortex_Psilocybin_4-weeks-post-injection_2


title: Frontal-Cortex_Saline_3-hours-post-injection_1


title: Ovarian Epithelial Cells HiChIP

source_name: Human Primary Ovarian Epithelial Cells

growth_protocol: Human Primary Ovarian Epithelial Cells (Ovarian) were obtained from CellBiologics (H-6036) and grown in grown in Complete Human Epithelial Cell Medium supplemented with Human Epithelial Cell Medium Supplement Kit (CellBiologics, H6621). Cells were grown in 15 cm dishes.


title: C42-NT1c_IGO_10123_E_9_S16

description: CSN5i-3_1uM_ cell_1


title: Frontal-Cortex_Psilocybin_4-weeks-post-injection_1

source_name: Frontal Cortex


title: CTH-38


title: Human Mammary Epithelial Cells HiChIP

source_name: Human Mammary Epithelial Cells

growth_protocol: Human Mammary Epithelial Cells (HMECs) were obtained from Lonza (CC-2551) and grown in MEGM Mammary Epithelial Cell Growth Medium BulletKit (Lonza, CC-3150). Cells were grown in 15 cm dishes.


title: CTH-40


title: CTH-37


title: C42-C5i2_IGO_10123_E_8_S15

description: DMSO treated cell_2


title: Frontal-Cortex_Saline_4-weeks-post-injection_1


title: Lncap-C5i2_IGO_10123_E_4_S13

description: CSN5i-3_5uM_ cell_2

source_name: LNCaP

value: LNCaP


title: 22RV-NCa_IGO_10123_K_1_S1

description: DMSO treated cell_1


title: Frontal-Cortex_Psilocybin_3-hours-post-injection_1


title: Colon Epithelial Cells HiChIP

source_name: Human Primary Colonic Epithelial Cells

growth_protocol: Human Primary Colonic Epithelial Cells (Colon) were obtained from CellBiologics (H-6047) and grown in Complete Human Epithelial Cell Medium supplemented with Human Epithelial Cell Medium Supplement Kit (CellBiologics, H6621). Cells were grown in 15 cm dishes.


title: Bladder Epithelial Cells HiChIP

source_name: Primary Human Bladder Epithelial Cells

growth_protocol: Primary Human Bladder Epithelial Cells (A/T/N) (Bladder) were obtained from ATCC (PCS-420-010) and grown in Bladder Epithelial Cell Basal Medium ((ATCC PCS-420-032) supplemented with Bladder Epithelial Cell Growth Kit (ATCC PCS-420-042) . Cells were grown in 15 cm dishes.


title: CTH-36

source_name: Unsorted Bone Marrow Cells

value: Unsorted Bone Marrow Cells


title: C42-C5i1_IGO_10123_E_7_S14

description: DMSO treated cell_1


title: CTH-34

value: negative


title: Human Astrocytes HiChIP

source_name: Human Astrocyte Cells

growth_protocol: Human Astrocytes (Astrocytes) were obtained from Lonza (N7805-100) and grown in Gibco Astrocyte Medium (ThermoFisher, A1261301). Cells were grown in 15 cm dishes.


title: Lncap-NT2_IGO_10123_E_2_S11

description: DMSO treated cell_2


title: Hypothalamus_Saline_4-weeks-post-injection_7

source_name: Hypothalamus

value: Hypothalamus

value: B


title: Hypothalamus_Saline_4-weeks-post-injection_8


title: Airway Epithelial Cells HiChIP

source_name: Bronchial/Tracheal Epithelial Cells

growth_protocol: Bronchial/Tracheal Epithelial Cells (Airway) were obtained from ATCC (PCS-300-010) and grown in Airway Epithelial Cell Basal Medium (ATCC, PCS-300-030) supplemented with Bronchial Epithelial Cell Growth Kit (ATCC, PCS-300-040). Cells were grown in 15 cm dishes.


title: Lncap-C5i1_IGO_10123_E_3_S12

description: CSN5i-3_5uM_ cell_1

value: Prostate cancer Cell


title: Esophageal Epithelial Cells HiChIP

growth_protocol: Human Primary Esophageal Epithelial Cells (Esophageal) were obtained from CellBiologics (H-6046) and grown in Complete Human Epithelial Cell Medium supplemented with Human Epithelial Cell Medium Supplement Kit (CellBiologics H6621). Cells were grown in 15 cm dishes.


title: PC3-sh37b_IGO_10123_J_8_S21

description: shCSN5 treated cell_2

value: drug treated  cell


title: CTH-30

value: non-ETP


title: CTH-31


title: H_A_6_3_ATAC

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Demultiplexing was perfomed using bcl2fastq2 v2.20
Adapter trimming was performed using Trimmomatic v0.36 with following parameters ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:25 MINLEN:36 CROP:48
Alignment was performed using bowtie2 v2.3.5 against the human reference genome hg38.
Duplicated reads were removed using picard "dedup" function and the transposase-induced offset was removed using the deeptools v3.1.3 "alignmentSieve" function.
Sorting and indexing of bam files was done using samtools v1.9
Peak calling was performed using MACS2 v2.1.2.
Unification of peak regions from sample-specific peak calling results was performed in R 3.6.2 using the "reduce" function implemented in the GenomicRanges package v1.38.0.
Quantification of sequencing reads in unified peak regions was performed in R 3.6.2 using the "summarizeOverlaps" function implemented in the GenomicAlignments package v1.22.1.
Genome_build: hg38
Supplementary_files_format_and_content: comma separated files include raw count table

source_name: Colorectal cancer

growth_protocol: BxPC-3 and HCT-15 were cultured and treatred in RPMI medium (10% FCS + PS)

extract_protocol:
Cells were lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and tagmented with an in-house Tn5 in TAPS-DMF buffer
Barcoded Nextera i7 and i5 primers were used to amplify the tagmented gDNA and preapare it for Illumina sequencing
Paired End 50 on a NovaSeq6000 (SP and S2 v1 chemistry)

treatment_protocol: Cells were treated with T (CONC) or A (CONC) for 6 or 12 hours. Control cells were treated with equal percentage of DMSO

value: Colorectal cancer

value: A

tag: replicate


title: CTH-32


title: Hypothalamus_Saline_4-weeks-post-injection_4

value: Saline


title: Hypothalamus_Saline_4-weeks-post-injection_5


title: Lncap-NT1_IGO_10123_E_1_S10

description: DMSO treated cell_1

growth_protocol: Cell are cultured in standard condition according to ATCC

tag: cell  type

value: ATCC


title: CTH-35

value: T-ALL


title: H_A_6_2_ATAC


title: CTH-33

source_name: Unsorted Peripheral Blood Cells

value: unknown


title: CTH-28


title: Hypothalamus_Saline_4-weeks-post-injection_3


title: H_A_6_1_ATAC


title: PC3-sh37a_IGO_10123_J_7_S20

description: shCSN5 treated cell_1

value: shRNA infected cells

tag: source


title: CTH-29


title: PC3-nsb_IGO_10123_J_6_S19

description: scramble shRNA treated cell_2


title: Hypothalamus_Saline_4-weeks-post-injection_2

tag: tissue

value: 4 weeks post-injection


title: H_T_6_3_ATAC

value: T


title: PC3-nsa_IGO_10123_J_5_S18

description: scramble shRNA treated cell_1


title: Hypothalamus_Saline_4-weeks-post-injection_1


title: Hypothalamus_Psilocybin_4-weeks-post-injection_8

value: Psilocybin


title: CTH-27

value: Unsorted Bone Marrow Cells


title: LN-sh37a_IGO_10123_J_3_S16

description: shCSN5 treated cell_1

value: LNCaP


title: LN-nsb_IGO_10123_J_2_S15

description: scramble shRNA treated cell_2


title: Hypothalamus_Psilocybin_4-weeks-post-injection_7

value: Hypothalamus


title: CTH-26

value: negative


title: B_A_6_2_ATAC

source_name: Pancreatic cancer

value: Pancreatic cancer


title: H_T_6_1_ATAC


title: Hypothalamus_Psilocybin_4-weeks-post-injection_6

value: B


title: CTH-25

value: non-ETP


title: B_A_6_3_ATAC


title: CTH-24


title: CTH-23


title: Hypothalamus_Psilocybin_4-weeks-post-injection_5


title: LN-nsa_IGO_10123_J_1_S14

description: scramble shRNA treated cell_1

value: Prostate cancer Cell


title: C42-sh37b_IGO_10123_L_4_S19

description: shCSN5 treated cell_2


title: B_A_6_1_ATAC

value: A


title: Hypothalamus_Psilocybin_4-weeks-post-injection_4


title: CTH-21

value: immature


title: C42-sh37a_IGO_10123_L_3_S18

description: shCSN5 treated cell_1

value: ATCC


title: LN-sh37b_IGO_10123_J_4_S17

description: shCSN5 treated cell_2


title: CTH-22

value: T-ALL


title: B_T_6_3_ATAC


title: B_T_6_2_ATAC


title: Hypothalamus_Psilocybin_4-weeks-post-injection_3


title: H_T_6_2_ATAC

value: Colorectal cancer


title: C42-nsb_IGO_10123_L_2_S17

description: scramble shRNA treated cell_2

value: shRNA infected cells


title: Hypothalamus_Psilocybin_4-weeks-post-injection_2

value: 4 weeks post-injection


title: C42-nsa_IGO_10123_L_1_S16

description: scramble shRNA treated cell_1


title: B_T_6_1_ATAC

value: T


title: 22rv-sh37b_IGO_10123_L_8_S23

description: shCSN5 treated cell_2


title: CTH-19


title: Hypothalamus_Saline_3-hours-post-injection_8

value: Saline

value: 3 hours post-injection


title: CTH-20

value: Unsorted Bone Marrow Cells


title: CTH-18


title: Hypothalamus_Saline_3-hours-post-injection_7

value: Hypothalamus


title: H_C_3_ATAC

value: C

value: ctrl


title: H_C_2_ATAC


title: H_C_1_ATAC


title: 22rv-nsb_IGO_10123_L_6_S21

description: scramble shRNA treated cell_2


title: 22rv-sh37a_IGO_10123_L_7_S22

description: shCSN5 treated cell_1


title: 22rv-nsa_IGO_10123_L_5_S20

description: scramble shRNA treated cell_1


title: CTH-17

value: negative


title: B_C_3_ATAC

value: Pancreatic cancer


title: Hypothalamus_Saline_3-hours-post-injection_4


title: Hypothalamus_Psilocybin_4-weeks-post-injection_1

value: Psilocybin


title: Hypothalamus_Saline_3-hours-post-injection_5

value: B


title: B_C_1_ATAC


title: CTH-16

value: immature


title: B_C_2_ATAC


title: Hypothalamus_Saline_3-hours-post-injection_3

value: A


title: Hypothalamus_Saline_3-hours-post-injection_6


title: H_A_12_3_ATAC


title: CTH-15

value: T-ALL


title: Hypothalamus_Saline_3-hours-post-injection_2


title: Hypothalamus_Saline_3-hours-post-injection_1


title: H_A_12_2_ATAC

value: Colorectal cancer


title: H_A_12_1_ATAC


title: Hypothalamus_Psilocybin_3-hours-post-injection_8


title: CTH-11


title: H_T_12_3_ATAC


title: CTH-13


title: CTH-12

value: Unsorted Peripheral Blood Cells


title: H_T_12_2_ATAC


title: CTH-14


title: Hypothalamus_Psilocybin_3-hours-post-injection_7


title: CTH-10


title: Hypothalamus_Psilocybin_3-hours-post-injection_6


title: H_T_12_1_ATAC


title: CTH-9


title: SARS-CoV-2 Beta variant (B.1.351)-infected mouse (6 dpi), biological rep5

city: Daejeon

first: Dae-Gyun

last: Ahn

state: Daejeon

address: 141 Gajeong-ro, Yuseong-gu

department: Center for Convergent Research of Emerging Virus Infection (CEVI)

country: South Korea

institute: Korea Research Institute of Chemical Technology (KRICT)

description: Gene expression data from lungs of SARS-CoV-2-infected mice

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16 hours.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: The probe cell intensity data computation and a CEL file generation was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

source_name: Lungs of mouse infected with SARS-CoV-2 Beta variant (B.1.351) (6 dpi)

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: Mice were randomly divided into groups before infection. All experiments were conducted in a biosafety level 3 facility.

extract_protocol: Total RNA was isolated from homogenized tissues using a commercially available kit (Maxwell RSC simplyRNA Tissue Kit) (Promega).

treatment_protocol: Mice were intranasally infected with 2 × 10^3 pfu of SARS-CoV-2.

tag: mouse strain

value: Lungs

tag: infection status

value: SARS-CoV-2 Beta variant (B.1.351)


title: Hypothalamus_Psilocybin_3-hours-post-injection_5


title: B_A_12_3_ATAC


title: SARS-CoV-2 Beta variant (B.1.351)-infected mouse (6 dpi), biological rep4


title: CTH-8


title: SARS-CoV-2 Beta variant (B.1.351)-infected mouse (6 dpi), biological rep1


title: CTH-7


title: B_A_12_2_ATAC


title: Hypothalamus_Psilocybin_3-hours-post-injection_4


title: SARS-CoV-2 Beta variant (B.1.351)-infected mouse (6 dpi), biological rep2


title: SARS-CoV-2 Beta variant (B.1.351)-infected mouse (6 dpi), biological rep3


title: CTH-6


title: Hypothalamus_Psilocybin_3-hours-post-injection_3


title: SARS-CoV-2 Beta variant (B.1.351)-infected mouse (4 dpi), biological rep4

source_name: Lungs of mouse infected with SARS-CoV-2 Beta variant (B.1.351) (4 dpi)


title: SARS-CoV-2 Beta variant (B.1.351)-infected mouse (4 dpi), biological rep5


title: SARS-CoV-2 Beta variant (B.1.351)-infected mouse (4 dpi), biological rep3


title: B_A_12_1_ATAC


title: Hypothalamus_Psilocybin_3-hours-post-injection_2


title: CTH-4


title: SARS-CoV-2 Beta variant (B.1.351)-infected mouse (4 dpi), biological rep2


title: B_T_12_3_ATAC

value: T


title: CTH-5


title: CTH-2


title: CTH-3


title: Hypothalamus_Psilocybin_3-hours-post-injection_1

value: 3 hours post-injection


title: Hypothalamus_Saline_4-weeks-post-injection_6

value: Saline

value: 4 weeks post-injection


title: AG120 treated I1DN LSCs, scRNAseq

city: Melbourne

first: Emily

last: Gruber

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 against the mm10/GRCm38 genome (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
scRNA-seq quality control, normalization, data integration, dimensional reduction, k-nearest neighbor graph construction and clustering were performed using Seurat (v 4.0.4)
Low quality cells were removed by filtering out cells that had fewer than 1000 genes, fewer than 2000 unique molecular identifiers (UMIs), or greater than 15% mitochondrial RNA content
Seurat’s CellCycleScoring function was used to assign cell cycle phase using Seurat’s inbuilt list of cell cycle genes
Seurat’s SCTransform function was used for data normalization with percentage mitochondrial reads, and differences in cell cycle phase amongst proliferating cells (S and G2M cell cycle phase scores) included in the regression model as sources of technical variation to remove
Datasets were integrated using canonical correlation analysis (CCA) within Seurat using default parameters
The first 40 principal components were used to compute a non-linear dimensional reduction using the Uniform Manifold Approximation and Projection (UMAP) method, and clustering was performed at a resolution of 0.4
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (output from Cellranger)

source_name: I1DN cKit+ Cd11b- cells

extract_protocol:
I1DN progenitor cells (cKit+/Cd11b-) from mice were FACS sorted into PBS/2%FBS. Cells were washed once with RNase free PBS/1%BSA and resuspended in PBS/1%BSA+0.2U/ml RNase inhibitor (Protector RNAse inhibitor, Sigma) at a final concentration of 1000 cells/uL.
Cell suspensions were loaded onto separate channels of the 10XChromium Single Cell Chip and single cells were captured in droplet emulsions using the 10X Chromium Single-Cell Instrument. Reverse transcription, cDNA amplification and library preparation were performed using the Chromium Single Cell 5′ Library & Gel Bead Kit (10X Genomics).
Libraries were pooled and sequenced on the Illumina NovaSeq 6000 system with 150 bp paired end reads to a depth of ~50,000 reads per cell.

value: I1DN cKit+ Cd11b- cells


title: B_T_12_1_ATAC


title: SARS-CoV-2 Ancestral strain-infected mouse (6 dpi), biological rep5

source_name: Lungs of mouse infected with SARS-CoV-2 Ancestral strain (6 dpi)

value: SARS-CoV-2 Ancestral strain


title: H_A_12_3_RNA

data_processing:
Demultiplexing was perfomed using bcl2fastq2 v2.20
Alignment with STAR (2.5.2a) usign standard parameters
Reads were counted with STAR (--quantMode GeneCounts; implementation of htseq-count with default parameters)
reads mapped to each transcript against the RefSeq hs38
Normalization using DeSeq2
Genome_build: hs38
Supplementary_files_format_and_content: comma separated files include raw count table

extract_protocol:
Cells were lysed in Trizol. Total RNA was extracted using the miRNeasy kit (Qiagen) and checked the RNA integrity and quantity using the tapestation RNA assay on a tapestation4200 instrument (Agilent).
750ng total RNA were used to generate NGS libraries using the TruSeq stranded total RNA kit (Illumina) following manufacturer's instructions
Paired End 50 on a NovaSeq6000 (SP and S2 v1 chemistry)


title: Vehicle treated I1DN LSCs, scRNAseq

description: 10x Genomics


title: AG120_AZA.rep2

data_processing:
Sequencing reads were demultiplexed using bcl2fastq (v 2.17.1.14), low quality reads removed, and trimmed with TrimGalore (v 0.4.4) using --paired and --rrbs settings.
Bismark (v 0.22.3) was used to map the spike-in controls and samples using default parameters, and samtools (v 1.4.1) was used to sort and index bam files
Bismark was used to extract coverage files, and differential analysis was performed in R (v 4.0.2) using the standard edgeR (v 3.32) workflow for differential methylation analysis
Assembly: mm10
Supplementary files format and content: tab delimited methylated and unmethylated counts table generated by readBismark2DGE

source_name: I1DN leukemic progenitor cells (cKit+/Cd11b-)

extract_protocol:
DNA was extracted using the Quik-DNA Microprep Kit (Zymo Research) as per the manufacturer’s instructions.
Diagenode’s Premium RRBS kit was used according to the manufacturer’s instructions to generate the RRBS libraries from the purified DNA. Each sample contained methylated and unmethylated spike-in controls, as per the instructions in Diagenode’s Premium RRBS kit.

treatment_protocol: Mice transplanted with I1DN leukemic cells were treated for 5 vehicle, AG120, AZA or the combination

value: AG120 + AZA

tag: time

value: 5 Days


title: H_A_12_1_RNA

tag: treatment


title: H_A_12_2_RNA

tag: time point


title: AZA.rep2

value: I1DN leukemic progenitor cells (cKit+/Cd11b-)

value: AZA


title: SARS-CoV-2 Ancestral strain-infected mouse (6 dpi), biological rep3


title: B_T_12_2_ATAC

value: Pancreatic cancer


title: SARS-CoV-2 Ancestral strain-infected mouse (6 dpi), biological rep4


title: H_T_12_3_RNA


title: CTH+11

value: Unsorted Bone Marrow Cells

value: positive

value: immature


title: CTH+12

value: T-ALL


title: CTH+10

value: Unsorted Peripheral Blood Cells


title: AZA.rep1


title: SARS-CoV-2 Beta variant (B.1.351)-infected mouse (4 dpi), biological rep1

value: Lungs

value: SARS-CoV-2 Beta variant (B.1.351)


title: SARS-CoV-2 Ancestral strain-infected mouse (4 dpi), biological rep5

source_name: Lungs of mouse infected with SARS-CoV-2 Ancestral strain (4 dpi)


title: CTH-1

value: negative


title: SARS-CoV-2 Ancestral strain-infected mouse (6 dpi), biological rep2


title: AG120.rep2


title: SARS-CoV-2 Ancestral strain-infected mouse (6 dpi), biological rep1


title: SARS-CoV-2 Ancestral strain-infected mouse (4 dpi), biological rep4


title: H_T_12_2_RNA

value: Colorectal cancer

value: T


title: AG120_AZA.rep1


title: CTH+7


title: B_A_12_3_RNA

value: A


title: AG120.rep1


title: H_T_12_1_RNA


title: CTH+4


title: SARS-CoV-2 Ancestral strain-infected mouse (4 dpi), biological rep2

value: SARS-CoV-2 Ancestral strain


title: CTH+9


title: Vehicle.rep2

value: Vehicle


title: SARS-CoV-2 Ancestral strain-infected mouse (4 dpi), biological rep3


title: CTH+8


title: Vehicle.rep1

value: 5 Days


title: Uninfected mouse, biological rep5

description: Gene expression data from lungs of uninfected mice

source_name: Lungs of uninfected mouse

value: uninfected


title: CTH+6


title: Kidney_CON2

city: Shenzhen

first: Boyang

last: Liu

state: Guangdong

address: 628 Zhenyuan Street, Guangming District

institute: Department of Anesthesiology, The Seventh Affiliated Hospital of Sun Yat-sen University

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp(version 0.20.0) softeware with default parameters in pair end mode.
The clean data were obtained for downstream analyses by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
The clean reads were mapped to reference of mouse mRNAs and lncRNAs using bowtie2(version 2.3.1) with parameters -k30 -t -p 20.
FPKM value and read counts of each transcript were obtained by eXpress(version 1.5.1) with parameters --no-update-check --rf-stranded.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.
Supplementary_files_format_and_content: Tab-delimited text files include raw gene counts for each Sample.

source_name: Kidney

extract_protocol:
Total RNA of kidney samples was extracted respectively using the TRIzol (Thermo Scientific, USA) reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). A total amount of 1 µg RNA per sample was used as initial material for the RNA sample preparations. Ribosomal RNA was removed using Ribo-off™ rRNA Depletion Kit (Human/Mouse/Rat) (Vazyme, China).
The sequencing libraries were generated following manufacturer recommendations with varied index label by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, USA). The libraries were sequenced on an Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated.

tag: strain

value: Mus musculus

tag: age

value: 6-8 weeks old

value: Sham Operation


title: CTH+3

value: Unsorted Bone Marrow Cells

value: positive


title: SARS-CoV-2 Ancestral strain-infected mouse (4 dpi), biological rep1


title: B_A_12_1_RNA

value: Pancreatic cancer


title: B_T_12_3_RNA


title: B_A_12_2_RNA


title: Kidney_CON1


title: M-2

city: Huaibei

first: Deng

last: daogui

state: Anhui

address: 100 Dongshan Road

department: College of Life Sciences

institute: Huaibei Normal University

data_processing:
Illumina Casava1.8 software used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using   TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After   cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and   paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. Clean data (clean reads) for the JF, PF, SF and M samples were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. Simultaneously, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity with min_kmer_cov set to 2 by default, and all other parameters set default. The resulting sequences were named unigenes. The unigenes were annotated by BLASTx searching in NCBI non-redundant (Nr), Swiss-Prot, KEGG, PFAM and KOG and mapped to NCBI Nt database by BLASTn. Functional annotation by Gene Ontology (GO) terms was analyzed by using Blast2GO (http://www.balst2go.org/) software. GO functional classification for unigenes was analyzed using WEGO software. The similarity searches of unigenes were performed using the NCBI-BLAST network server (http://blast.ncbi.nlm.nih.gov/).
Differential expression analysis between two developmental stages (JF vs PF, PF vs SF and M vs PF) of D. similoides sinensis was performed using the DEGseq 2 package. P-value was adjusted using Q-value. Q-value<0.05 and |log2(fold change)|>1 were set as the threshold for significantly differential expression. GO enrichment analysis of DEGs was implemented by the GOseq packages based on Wallenius’ non-central hyper-geometric distribution.
Supplementary_files_format_and_content: Reads count

organism: Daphnia sinensis

source_name: male

growth_protocol: D. similoides sinensis employed in the experiment were collected from Lake Chaohu in Anhui Province, China. Parthenogenetic females were cultivated under a 12 h light /12 h dark photoperiod at 25±1℃ with a light intensity of 2500 lx, and fed with 40 mg L-1 of S. obliquus (wet weight). S. obliquus was obtained from the Freshwater Algae Culture Collection at Institute of Hydrobiology, Chinese Academy of Sciences, and cultured in BG-11 medium at 25±1℃ with a 12 h light/12 h dark photoperiod.

extract_protocol:
Total RNA was respectively extracted from samples at four developmental stages of D. similoides sinensis (juvenile females, parthenogenetic females, sexual females and males) using TRIzol reagent.
A total of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.

treatment_protocol: In one experiment, 20 D. similoides sinensis mothers were employed. Each mother was respectively cultured in a 50 ml beaker with 40 ml culture medium. The culture medium was freshed every two days. The culture medium was the filtered and aerated tap water. Offspring (brith time <12h) produced by D. similoides sinensis mother were collected as juvenile female samples (JF), and each juvenile female sample was about 500 individuals. These neonates produced by the mother were removed in time from beakers during the experiment.  In another experiment, 60 D. similoides sinensis mothers were employed. Each 10 mothers were placed in a 250 ml beaker with 200 ml culture medium, 6 replicates were conducted. The culture medium was freshed every two days. After 2-3 weeks, sexual females and males of D. similoides sinensis could be observed when population density became higher. The parthenogenetic females (PF), sexual females (SF) and males (M) were selected under the microscope. About 50 parthenogenetic females and 50 sexual females were respectively collected as PF sample and SF sample. Male juveniles were collected and cultured in a 100 mL beaker with 80 mL culture medium for two weeks. Each male sample (M) contained about 60 male individuals.  JF, PF, SF and M samples were put into EP tubes, respectively. These samples were immediately frozen in liquid nitrogen and stored at -80℃. In this study, two replicates of JF, PF, SF and M samples were collected for transcriptome sequencing, respectively.

value: 2-3 weeks

tag: developmental stage

value: adult

tag: Sex

value: male

tag: reproductive mode

value: sexual


title: M-1


title: CTH+2

tag: disease state

value: T-ALL

tag: cell type

value: immature


title: CTH+1

tag: chromothripsis status

tag: phenotype


title: Kidney_CLP1

value: CLP


title: B_T_12_1_RNA

tag: cell line

value: T

tag: replicate


title: SF-1

source_name: sexual female

value: female


title: Kidney_CLP2

tag: tissue


title: Kidney_CLP3


title: Uninfected mouse, biological rep4

tag: mouse strain

value: Lungs


title: H_A_6_3_RNA

value: Colorectal cancer

value: A


title: Uninfected mouse, biological rep3

tag: infection status

value: uninfected


title: PF-2

source_name: parthenogenetic female

value: parthenogenetic


title: H_A_6_2_RNA


title: B_T_12_2_RNA


title: PF-1


title: JF-2

source_name: juvenile female

value: birth time <12h

value: juvenile


title: Lung PS15 rep3

city: Chongqing China

first: Zhu

last: Qian

address: Chongqing China

institute: Chongqing Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two groups was performed using the DESeq2 R package (1.20.0). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung

extract_protocol:
Total RNA was extracted from frozen liver and lung tissues (~50 mg) using Trizol. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was used with 1 ug of total RNA for the construction of sequencing libraries.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Lung

tag: diet

value: phytosterols diet

tag: genotype

value: wild type


title: Lung PS09 rep2


title: Uninfected mouse, biological rep2


title: SF-2

value: 2-3 weeks

value: adult


title: Uninfected mouse, biological rep1


title: Lung PS04 rep1


title: Lung CS02 rep2

value: control diet


title: Lung CS04 rep3


title: IFNAR_MCAT3

city: Canberra

first: Daniel

last: Enosi Tuipulotu

address: Australian National University

institute: Australian National University

data_processing:
Read quality was assessed with FastQC
Sequencing reads were mapped to the mm10 (UCSC) reference genome using HISAT2. Transcripts were assembled and quantified with StringTie and differential expression analysis was performed using EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Raw gene counts (.txt)

source_name: Bone marrow

extract_protocol:
Total RNA was extracted from macrophages using TRIzol.
PolyA selection followed by library construction for the DNBSeq Platform (BGI)

treatment_protocol: Macrophages were left untreated (Med) or infected with M. catarrhalis (MOI 100) for 8 hr.

value: Macrophage

tag: treatment

value: Infected (M. catarrhalis)


title: Melanoma stereoseq

city: leuven

first: Panagiotis

middle: Cristophe

last: Karras

state: belgium

address: Herestraat 49

country: Belgium

institute: VIB Center for Cancer Biology

description: spatial transcriptomics in primary mouse melanoma tumors

data_processing:
CellRanger v.3.1.0
RSEM
SpaceRanger output  analyzed using the Seurat spatial vignett
Assembly: mm10 for mouse and hg19 for human

source_name: NRASQ61K/°;Ink4a-/- primary lesion

extract_protocol: Libraries for scRNA-seq were created using the 10X Genomics Chromium platform according to the manufacturer’s instructions. Library construction was performed with the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (n = 16; 10x Genomics, catalog number 1000092) or the Chromium Single Cell A Chip Kit and 5′ Library & Gel Bead Kit (10x Genomics, catalog number 1000014). We opted for high target recovery (median 5000, range 5000-10000), keeping within the range of optimal input concentration per target recovery, as recommended by the manufacturer. In brief, cells were partitioned into gel bead-in-emulsions (GEMs) at limiting dilutions, where lysis and reverse transcription occurred, yielding uniquely barcoded full-length cDNA from polyadenylated mRNA. GEMs were subsequently broken, and the pooled fraction was amplified and subjected to fragmentation, end repair and adaptor ligation of size-selected fractions.For bulk RNAseq about 500 pg of RNA per sample was reverse-transcribed and amplified using a modified SMARTseq2 protocol (Rambow et al. 2018). Prior to generating sequencing libraries using the NexteraXT kit (Illumina, cat. no. FC-131-10), cDNA profiles were monitored using the Bioanalyzer. Sequencing was performed on a Nextseq500 platform (Illumina, SE75bp). Differential analyses between siPRRX1 and siCtrl samples were executed using the DeSeq2 pipeline. Visium libraries were sequenced on the Illumina Novaseq 6000 instrument (parameters: SP flowcell 100 cycles single reads, lane 1 = 220pM + 1% PhiX / lane 2 = 215pM + 1% PhiX).  For stereo seq experiment, the cDNA library was loaded onto a G400 sequencer (MGI) for sequencing (pair-end, read 1 of 50 bp and read 2 of 100 bp).

value: engrafted tumor subcutaneously

tag: tumor

value: melanoma

tag: tumor stage


title: H_T_6_3_RNA

source_name: Colorectal cancer

value: T

tag: time point


title: H_T_6_1_RNA

value: Colorectal cancer


title: H_C_3_RNA

value: C

value: ctrl


title: H_T_6_2_RNA


title: JF-1

tag: age

tag: developmental stage

tag: Sex

value: female


title: Liver PS15 rep5

source_name: Liver

tag: strain

value: Liver


title: Lung CS01 rep1


title: H_C_2_RNA


title: IFNAR_MCAT1

tag: cell type


title: Liver PS11 rep4


title: H_C_1_RNA


title: H_A_6_1_RNA

value: A


title: IFNAR_MED3

value: Uninfected (Media)


title: B_A_6_3_RNA

source_name: Pancreatic cancer

value: Pancreatic cancer


title: Liver PS09 rep3

value: phytosterols diet

value: wild type


title: IFNAR_MED2


title: B_A_6_2_RNA


title: Liver PS05 rep2


title: IFNAR_MED1


title: B_A_6_1_RNA


title: Liver PS04 rep1


title: B_T_6_3_RNA


title: WT_MCAT3

value: WT


title: WT_MCAT2


title: Liver CS09 rep4

value: control diet


title: Liver CS04 rep3


title: WT_MCAT1

value: Macrophage


title: B_T_6_1_RNA


title: B_T_6_2_RNA


title: WT_MED2


title: Pro24

city: Guangzhou

first: Chen

last: Keyu

state: Guangdong Province

address: 58 Zhongshan Second Road

institute: Sun Yat-Sen University

description: One sample from NSPCs isolated from E14.5 C57/BL6 mice in L-Propofol group

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Assembly: GRCm38
Supplementary files format and content: TXT file contain counts for each sample

source_name: NSPCs

growth_protocol: NSPCs were cultured in plated with NSPCs growing medium

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NSPCs were administrated with low-dose Propofol (10µM)

value: NSPCs

value: L-Propofol


title: IFNAR_MCAT2

value: Infected (M. catarrhalis)


title: WT_MED3


title: Liver CS02 rep2


title: B_C_2_RNA


title: Liver CS01 rep1


title: Con24

description: One sample from NSPCs isolated from E14.5 C57/BL6 mice in Control group

value: Control


title: B_C_3_RNA


title: B_C_1_RNA


title: Jurkat cells, DMSO

status: Public on Aug 16 2022

first: Mengjun

last: Zhong

address: No.601, West Huangpu Avenue

institute: Jinan University

description: Jurkat-DMSO

data_processing:
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads.
Then Tophat v2.0.9 was used to map the cleaned reads to the GRCh38 reference genome with two mismatches.
After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM values for known gene models.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Jurkat

growth_protocol: Jurkat cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
After treating with DMSO and JQ1 in the absence or presence of PHA for 24 hours, the Jurkat cells were harvested and RNA was extracted with TRIzol reagent. Amplified cDNA was successively converted into short read sequencing libraries using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina®. Hisat2 (version:2.0.4).
Libraries were sequenced on an Illumina HiSeq2500.

treatment_protocol: The Jurkat cells were treated with DMSO and 0.5uM JQ1 in the absence or presence of PHA for 24 hours.

value: Jurkat

value: T lymphoblast

value: DMSO

tag: time

value: 24 hours


title: Jurkat cells, JQ1 and PHA

tag: cell line

value: 0.5uM JQ1 and 150ng/ml PHA


title: Jurkat cells, DMSO and PHA

description: Jurkat-DMSOjiaPHA

value: DMSO and 150ng/ml PHA


title: Jurkat cells, JQ1

value: 0.5uM JQ1


title: WT_MED1

value: Uninfected (Media)


title: HeLa WT cddp_1

city: Heidelberg

first: Prof. Dr. Felix

last: Hoppe-Seyler

address: Im Neuenheimer Feld 242

institute: German Cancer Research Center (DKFZ)

description: Gene expression data from CDDP-treated HeLa WT (parental)

hyb_protocol: (according to user manual Affymetrix WT PLUS Reagent Kit) 5,5 ug of fragmented and labeled ss-cDNA were hybridized for 17 hr at 45°C on Applied Biosystems™ human Clariom™ S Array.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays.

data_processing: The data were normalised using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore

source_name: HeLa cervical cancer cells (WT)

label_protocol: The Applied Biosystems™ WT PLUS Reagent Kit is used to generate labeled ss-cDNA from input amounts of 100ng total RNA

growth_protocol: HeLa WT and HeLa Dkk1 KO cells were seeded in 60mm cell culture dishes two days prior to treatment to be ~70% confluent when treatment was initiated.

extract_protocol: Total RNA was extracted using the PureLink RNA Mini Kit (Thermo Fisher Scientific) according to the manufacturer's instructions.

treatment_protocol: Medium was exchanged to 3mL of fresh medium supplemented either with or without 10µM CDDP and cells were cultivated for 16h under standard cell culture conditions (5% CO2, 21% O2, 37°C).

value: HeLa

value: CDDP


title: HeLa WT ctrl_1

description: Gene expression data from untreated HeLa WT (parental)

value: WT

value: control


title: Osteoblast-KO-Day28-1

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

hyb_protocol: Fragmented and Labeled ss-DNA (3.5 ug) was hybridized to Affymetrix Mouse Gene 2.0 ST GeneChips overnight at 45oC. Hybridized GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

scan_protocol: Microarrays were scanned using an Affymetrix 7G Scanner

data_processing: CEL files were imported into Affymetrix Expression Console software and data were anayzed by RMA (Gene Level Default RMA sketch) to obtain probe set expression values

source_name: osteoblast, calvarial

label_protocol: Total RNA (100 ng) was converted to fragmented and biotin-labeled ssDNA by WT Plus kit (Affymetrix)

growth_protocol: Dissected strips of calvaria from 7-10 day old Wild Type C57BL/6J and β-Arrestin 2 Knockout (C57BL/6J background) mice were incubated at 37oC with shaking for 20 min in a solution of 0.1% collagenase II (Worthington) and trypsin (0.05%, Invitrogen) in αMEM (Invitrogen). Supernatants were neutralized with 25% heat-inactivated fetal bovine serum (FBS, Invitrogen), and the digestion of calvarial strips was repeated twice. Supernatants from the three digestions were combined and centrifuged, and pellets were reconstituted in growth medium consisting of αMEM containing 10% heat-inactivated FBS and 0.1% Primocin (Invivogen). After 24 hours in culture, Primocin was reduced to 0.05%. Cells were sub-cultured at 90% confluency and at passage 2 differentiated post-confluence (Day 3).

extract_protocol: Total RNA was prepared with the RNeasy Plus Mini Kit (Qiagen).  RNA quality was assessed by Bioanalyzer 2100 (Agilent).

treatment_protocol: Cells were differentiated starting on Day 3 in αMEM containing 10% heat-inactivated FBS and 0.05% Primocin supplemented with 5 mM β-glycerophosphate (Millipore Sigma) and 50mg/L ascorbic acid (Millipore Sigma). Cells were harvested on Day 2, 5, 10 and 28

value: Osteoblast

value: Beta-Arrestin 2 Knockout

tag: differentiation day


title: HeLa Dkk1 KO ctrl_3

description: Gene expression data from untreated HeLa Dkk1 KO

source_name: HeLa cervical cancer cells (Dkk1 KO)

value: Dkk1 KO


title: Osteoblast-KO-Day10-3


title: HeLa Dkk1 KO cddp_3

description: Gene expression data from CDDP-treated HeLa Dkk1 KO


title: HeLa WT cddp_3


title: HeLa Dkk1 KO ctrl_2


title: HeLa WT ctrl_3


title: Osteoblast-KO-Day28-2


title: HeLa Dkk1 KO cddp_2


title: Osteoblast-KO-Day2-3


title: Osteoblast-KO-Day5-2


title: HeLa WT cddp_2


title: Osteoblast-WT-Day28-2

value: Wildtype


title: Osteoblast-KO-Day10-1


title: Osteoblast-KO-Day28-3


title: Osteoblast-KO-Day5-1


title: Osteoblast-KO-Day5-3


title: Osteoblast-KO-Day10-2


title: Osteoblast-WT-Day10-2


title: Osteoblast-KO-Day2-1


title: Osteoblast-WT-Day28-1


title: HeLa Dkk1 KO cddp_1


title: HeLa Dkk1 KO ctrl_1


title: HeLa WT ctrl_2


title: Osteoblast-WT-Day10-3


title: Osteoblast-KO-Day2-2


title: Osteoblast-WT-Day10-1


title: Osteoblast-WT-Day28-3


title: Osteoblast-WT-Day5-2


title: Osteoblast-WT-Day5-1


title: Osteoblast-WT-Day2-2


title: Osteoblast-WT-Day2-3


title: injured, 8 weeks, rep4

city: Valencia

first: Victoria

last: Moreno Manzano

state: Valencia

address: No. 3 Eduardo Primo Yúfera street

country: Spain

institute: Centro de Investigación Príncipe Felipe

description:
SCI_week8_rep4
t8v4

hyb_protocol: Cyanine 3-labeled cRNA targets were hybridized to Whole Rat Genome Oligo Microarray at 65°C for 17 h following the procedures recommended by the manufacturer (Agilent Technologies). After hybridization, the microarray slide was washed and dried according to the protocol provided by the manufacturer.

scan_protocol: Arrays were scanned in an Agilent Microarray Scanner (Agilent G2565BA) according to the manufacturer’s protocol and data extracted using Agilent Feature Extraction Software 10.7.1

data_processing: Agilent raw data files where background corrected using Agilent methodology as recomended in 'Agilent Feature Extraction Software Reference Guide'.Intensity signal was standardized across arrays via quantile normalizaton algorithm.

organism: Rattus norvegicus

source_name: spinal cord, injury epicentre T6-T10 (~1.5 cm) excluding dura mater, sacrificed 8 week post-injury

label_protocol: 500 ng of total RNA were used to produce Cyanine 3-CTP-labeled cRNA using the Quick Amp Labeling Kit (Agilent p/n 5190-0442) according to the manufacturer’s instructions.

growth_protocol: NPCs generation protocol to be used for transplantation (only aplicable to u1t1 and u2t2 animals): 'injury-activated' NPCs were harvested from adult rat spinal cords subjected to traumatic SCI and sacrificed one week after. Once the overlying meninges and blood vessels were removed, the dissected tissue was cut into 1 mm pieces and gently pipetted for mechanical disaggregation. NPCs were cultured in ultralow attachment plates in neurospere-like culture. Proliferation culture was comprised of NeuroCult™ Proliferation Medium (Stemcell Technologies, Grenoble, France) supplemented with NeuroCult™ Proliferation Supplement (Stemcell Technologies), 0.7 U/mL heparin (Sigma), P/S at 10 ml/L (Sigma) and enriched with 20 ng/mL of epidermal growth factor (EGF; Thermo Fisher, Horsham, UK), and 20 ng/mL of basic fibroblast growth factor (bFGF; Invitrogen). NPCs transplantation was carried out right after contusion (u1t1 ; acute model) or 1 week later (u2t2; subacute model). One million NPCs were delivered intramedullary into two injection points (2 mm caudally and rostrally from the lesion epicentre), using a 26 G Hamilton pipette coupled to a siliconized glass pipette containing the cell suspension.  NPCs were infused at a rate of 2µl/min at a total volume of 5 µl/injection waiting 2 min before removing the syringe to allow cell deposition into the tissue, as previously described. Transplanted animals were sacrificed one week after transplantation.

extract_protocol: For tissue extraction animals were overdosed with sodium pentobarbital (100 mg/kg) and transcardially perfused with 0.9% saline solution. The spinal cord tissue was carefully removed and dissected into 1.5-cm length containing the injury epicentre.Total RNA was extracted using RNeasy Mini Kit (QIAGEN) following manufacturer’s instructions

treatment_protocol: For the surgical interventions, rats were medicated with morphine (2.5 mg/kg) and 2% isoflurane in a continuous oxygen flow of 1 L/min. Laminectomy was performed at the level of T7-T9, to expose the spinal cord at T8 to and induce the severe SCI by contusion applying 250 kdyn force using Infinite Horizon Impactor. Post-surgery care consisted on 5 mg/kg of Alsir for 7 days, 0.1 mg /kg of Buprenorphine 2 times/day for 4 days and 1mg/kg of FK-506 starting from one day before NPCs transplantation until the end point.

tag: gender

value: Female

value: Adult

value: SCI

tag: tissue

value: spinal cord, injury epicentre (1.5 cm)


title: injured, 8 weeks, rep3

description:
SCI_week8_rep3
t8v3


title: transplant t1, sacrifice 2 weeks, rep4

description:
SCI_week2_NPCs_T1_rep4
u2t2v4

source_name: spinal cord + NPCs transplantation 1 week after injury, injury epicentre T7-T10 (1.5 cm) , sacrificed 2 week post-injury

value: SCI, NPCs transplantation 1 week after


title: transplant t1, sacrifice 2 weeks, rep1

description:
SCI_week2_NPCs_T1_rep1
u2t2v1


title: transplant t1, sacrifice 2 weeks, rep3

description:
SCI_week2_NPCs_T1_rep3
u2t2v3


title: transplant t0, sacrifice 1 week, rep1

description:
SCI_week1_NPCs_T0_rep1
u1t1v1

source_name: spinal cord + NPCs transplantation at time 0, injury epicentre T6-T10 (~1.5 cm) excluding dura mater, sacrificed 1 week post-injury

value: SCI, NPCs transplantation right after


title: injured, 1 week, rep4

description:
SCI_week1_rep4
t1v4

source_name: spinal cord, injury epicentre T6-T10 (~1.5 cm) excluding dura mater, sacrificed 1 week post-injury


title: transplant t0, sacrifice 1 week, rep3

description:
SCI_week1_NPCs_T0_rep3
u1t1v3


title: transplant t0, sacrifice 1 week, rep4

description:
SCI_week1_NPCs_T0_rep4
u1t1v4


title: injured, 2 weeks, rep4

description:
SCI_week2_rep4
t2v4

source_name: spinal cord, injury epicentre T6-T10 (~1.5 cm) excluding dura mater, sacrificed 2 week post-injury


title: injured, 8 weeks, rep2

description:
SCI_week8_rep2
t8v2


title: injured, 2 weeks, rep2

description:
SCI_week2_rep2
t2v2


title: injured, 4 weeks, rep4

description:
SCI_week4_rep4
t4v4

source_name: spinal cord, injury epicentre T6-T10 (~1.5 cm) excluding dura mater,sacrificed  4 week post-injury


title: injured, 4 weeks, rep2

description:
SCI_week4_rep2
t4v2


title: injured, 4 weeks, rep1

description:
SCI_week4_rep1
t4v1


title: injured, 1 week, rep2

description:
SCI_week1_rep2
t1v2


title: transplant t0, sacrifice 1 week, rep2

description:
SCI_week1_NPCs_T0_rep2
u1t1v2


title: injured, 8 weeks, rep1

description:
SCI_week8_rep1
t8v1


title: transplant t1, sacrifice 2 weeks, rep2

description:
SCI_week2_NPCs_T1_rep2
u2t2v2


title: injured, 2 weeks, rep1

description:
SCI_week2_rep1
t2v1


title: injured, 1 week, rep3

description:
SCI_week1_rep3
t1v3


title: K16/2935

city: Ghent

first: Jolien

last: Vanhooren

address: Corneel Heymanslaan 10

institute: Ghent University

data_processing:
Sequencing reads were filtered based on stringent read quality control
After adapter trimming, reads were collapsed and mapped to the reference genome using Bowtie
Genome_build: UCSC
Genome_build: Ensembl release 84
Genome_build: miRBase v21
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Mononuclear cells were isolated by Ficoll density gradient (Axis-shield), complemented by CD34 isolation if CD34 expression was <50% (CD34 MicroBead Kit, Milteny). Cell sorting was performed to isolate CD34+/CD38- and CD34+/CD38+ cells from patients and controls, defined as LSC and HSC, and L-blasts and C-blasts, respectively. Sorted cells were spun down (10 min, 3000 rpm, 4°C) and resuspended in 700µl TRIzol for RNA extraction. RNA was extracted using the miRNeasy Mini or Micro Kit (Qiagen) in combination with on-column Dnase I digestion (RNAse-Free DNase set, Qiagen) according to the manufacturer's instructions. RNA concentrations were measured by Nanodrop (ThermoFisher Scientific) or Qubit RNA HS Assay (Invitrogen).
Libraries for RNA sequencing were prepared by Biogazelle using a TruSeq small RNA library kit (Illumina) according to the manufacturer's instructions. The resulting small RNA libraries were concentrated via ethanol precipitation and quantified using the Qubit 2.0 Fluorometer before sequencing with a read length of 75 bp on a NextSeq 500 sequencer (Illumina).

tag: cellular subpopulation

value: Lymphocyt

tag: disease state

value: Leukemic


title: Osteoblast-WT-Day2-1

tag: genotype


title: K16/2928

value: Myeloblast


title: K16/2930

value: Leukemic stem cell


title: injured, 2 weeks, rep3

description:
SCI_week2_rep3
t2v3

tag: treatment


title: K16/2902

source_name: Cord blood

value: Healthy control


title: K16/2886


title: K16/2883

value: Hematopoeitic stem cell


title: K16/2936

source_name: Bone marrow


title: K16/2929


title: K16/2932


title: sham, rep2

description:
Sham_rep2
t0v2

source_name: spinal cord,thoracic segment T6-T10 (~1.5 cm) excluding dura mater

value: Sham

value: control


title: K16/2923


title: sham, rep3

description:
Sham_rep3
t0v3


title: sham, rep4

description:
Sham_rep4
t0v4


title: K16/2899


title: K16/2224


title: injured, 1 week, rep1

description:
SCI_week1_rep1
t1v1


title: K16/2924


title: sham, rep1

description:
Sham_rep1
t0v1


title: K16/2933


title: K16/2216


title: K21/2884


title: K16/2183


title: K16/1322


title: NC_CRY1KO3

city: Seoul

first: Jae Bum

last: Kim

address: Bldg 105-Rm. 333, Seoul National University, San 56-1, Sillim Dong, Kwanak-Gu

department: Biological Sciences

institute: Seoul National University

data_processing:
Raw sequence reads were trimmed and quality-controlled using TrimGalore (version 0.6.7)
Trimmed reads were mapped to the mouse reference genome GRCm39/mm39 using HISAT2 (version 2.2.1)
Mapped reads were assembled and quantified using StringTie (version 2.1.7)
Differential expression analysis was conducted using Limma (version 3.42.2)
Genome_build: mm39
Supplementary_files_format_and_content: tsv file includes read counts for each sample

growth_protocol: Noone

extract_protocol:
RNA was isolated using phenol-chloroform extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols. TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E

value: Liver

value: hepatocyte


title: NC_CRY1KO2


title: NC_CRY1KO1


title: PE25T

city: Vejle

first: Silvia

middle: Regina

last: Rogatto

address: Beriderbakken 4

department: Clinical Genetics

institute: University Hospital of Southern Denmark – Vejle

description: Gene expression data from penile usual carcinoma

hyb_protocol: Hybridization of 200 μl of the hybridization cocktail was performed onto the GeneChip® Human Transcriptome Array 2.0 (Affymetrix, Santa Clara, CA, USA) at 45°C, 60 rpm for 18 hours in a hybridization oven.

scan_protocol: The scanning was performed using Affymetrix GeneChip Scanner 7000 (Affymetrix/ThermoFisher, USA).

data_processing: The data normalization was performed with Transcriptome Analysis Console (TAC, ThermoFisher, USA, v.4.0) using RMA.

source_name: Penile cancer

label_protocol: Following the manufacturer protocol, we reverse-transcribed and amplified 2 ug of total RNA to cDNA using the GeneChip® Whole Transcript Labeling Assay(Affymetrix, Santa Clara, CA, USA).

extract_protocol: RNA was isolated from fresh-frozen samples using the RNeasy mini kit (Qiagen, Valencia, USA), according to the manufacturers’ instructions

value: penis

value: Penile cancer


title: NC_WT3

source_name: Liver


title: PE23T


title: NC_WT1


title: NC_WT2


title: PA7T


title: PA9T


title: PE2T


title: N1.2

description: Gene expression data from penile normal tissues

source_name: Normal penile glans

value: Normal


title: PA40T.1


title: PA26T


title: PA27T


title: PA29T


title: PA23T


title: PA17T


title: PA41T.1


title: N5.1


title: N10.2


title: PA42T.1


title: N10.1


title: N1.1


title: N5.2


title: PA13T


title: PE17T


title: PA6T


title: Zscan4 OE2 ATAC-Seq

city: Tian jin

first: Jiao

last: Yang

address: 94 Weijin Road

institute: Nankai University

description:
Zscan4 OE2
Zscan4 OE ATAC rpkm

data_processing:
The ATAC-seq reads were aligned to the mouse reference genomemm10 using bowtie2
Sequenced reads were trimmed for adaptor sequence using Trimmomatic
the read counts were adjusted for each sequenced library by featureCounts R package through one scaling normalized factor
Genome_build: mm10
Supplementary_files_format_and_content: csv file include rpkm values for Embryonic stem cells

source_name: Embryonic stem cells

growth_protocol: J1 cultured without feeder at traditional culture conditions

extract_protocol: Sequencing libraries were generated  by using TruePrep DNA Library Prep Kit V2 for Illumina® (TD503-02, Vazyme Biotech)

value: J1 mouse embryonic cells

tag: passages

value: Zscan4 OE2


title: Zscan4 OE1 ATAC-Seq

description:
Zscan4 OE1
Zscan4 OE ATAC rpkm

value: Zscan4 OE1


title: control2 ATAC-Seq

description:
control2
Zscan4 OE ATAC rpkm

value: wild type2


title: control1 ATAC-Seq

description:
control1
Zscan4 OE ATAC rpkm

value: wild type1


title: Dermal_EC_rep2_plateA

city: Uppsala

first: Sofia

last: Nordling

address: Dag Hammarskölds väg 20

country: Sweden

institute: Uppsala University

data_processing:
Alignment to the GRCm38 reference genome was done with tophat (v.2.1.1).
Duplicated reads were filtered out with samtools (v.0.1.18).
Gene counts were generated with Subread (v.1.4.6-p5).
Assembly: mm10 (GRCm38)
Supplementary files format and content: csv files containing the read counts for each cell in the sample.

source_name: Ear dermis

growth_protocol: Mice were maintained until adulthood (12-26 weeks).

extract_protocol:
Ears were mechanically disrupted before enzymatic dissociation (10 mg/ml Collagenase IV, 0.2% FBS and 0.2 mg/ml DNase I in PBS) at 37 ˚C for 20 minutes. Cells were incubated with an anti-CD16/32 antibody (ThermoFischer Scientific, 14-0161-85), followed by staining with CD31-FITC (BD Biosciences, 553372), CD45-APC (BioLegend, 103112), Lyve1-eFluor 660 (ThermoFischer Scientific, 50-0443-82) and Live/Dead near IR cell stain (ThermoFischer Scientific, L10119). CD31+/CD45-/Lyve1- cells were sorted using a BD FACSAria III (100 μm nozzle size, 20 psi sheet pressure).
Single-cell libraries were prepared using SMART-seq2 methodology as described previously (Picelli et al., 2014). The libraries were sequenced on a HiSeq2500 with single 50-bp reads (dual indexing reads).

value: Female

value: Adult

value: Ear dermis

value: Blood vascular endothelial cells


title: Zscan4 RNAi6 RNA-Seq

description:
Zscan4 RNAi6
zscan4 KD in 2-cell

data_processing:
The RNA-seq reads were aligned to the mouse reference genome mm10 using Hisat2
Sequenced reads were trimmed for adaptor sequence using Trimmomatic
the read counts were adjusted for each sequenced library by featureCounts R package through one scaling normalized factor
Genome_build: mm10
Supplementary_files_format_and_content: csv file include CPM values for ESCs, TPM values for 2-cell embryos …

source_name: 2-cell embryo

extract_protocol: Sequencing libraries were generated  by using TruePrep DNA Library Prep Kit V2 for Illumina® (TD503, Vazyme Biotech)

value: embryo

value: Zscan4 RNAi


title: Zscan4 RNAi5 RNA-Seq

description:
Zscan4 RNAi5
zscan4 KD in 2-cell


title: Dermal_EC_rep1_plateB


title: Zscan4 RNAi3 RNA-Seq

description:
Zscan4 RNAi3
zscan4 KD in 2-cell


title: Dermal_EC_rep1_plateA


title: Zscan4 RNAi2 RNA-Seq

description:
Zscan4 RNAi2
zscan4 KD in 2-cell


title: DRIP-seq input

city: San Francisco

first: Bjoern

last: Schwer

institute: University of California, San Francisco

data_processing:
Library strategy: DRIP-seq
DRIP-seq read files in fastq format were adapter trimmed before mapping (TrimGalore 0.6.6 with default settings).
DRIP-seq analysis was performed as in Sanz et al., 2016 using a Hidden Markov Model-based peak calling algorithm for identification of DRIP-seq peaks.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: NSPC_DRIP.bw: Reads per kb per million (RPKM)-normalized bigWig tracks generated from BAM files containing uniquely mapped reads.
Supplementary_files_format_and_content: NSPC_input.bw: Reads per kb per million (RPKM)-normalized bigWig tracks generated from BAM files containing uniquely mapped reads.
Supplementary_files_format_and_content: NSPC_DRIP_peaks.bed: DRIP-seq peaks identified by Hidden Markov Model-based peak calling algorithm in BED format.

source_name: Neural stem/progenitor cells

growth_protocol: NSPCs were isolated from frontal brains of postnatal day seven mice and cultured as in Wei et al., 2016. All experiments were authorized by the Institutional Animal Care and Use Committee and Institutional Biosafety Committee at the University of California, San Francisco and performed in accordance with relevant guidelines and regulations.

extract_protocol:
Genomic DNA for DRIP was isolated and digested as in Stork et al., 2016 and Ginno et al., 2012. RNase A treatment prior to DRIP was performed as in Stork et al., 2016. Digested DNA was phenol/chloroform-extracted, precipitated, washed and resuspended. For each DRIP reaction, 4.4 ug DNA were incubated with 10 ug S9.6 antibody for 16 h at 4 C, followed by incubation with magnetic protein G beads for 2 h at 4 C. Samples were washed for 3 x 10 min with 140 mM NaCl, 0.05% (w/v) Triton X-100, 10 mM NaPO4, pH 7.0, at room temperature and eluted in 10 mM EDTA, 0.5% (w/v) SDS, 50 mM Tris-Cl, pH 8.0 containing Proteinase K for 45 min at 55 C. DNA was phenol/chloroform-extracted and precipitated as described above.
Per biological replicate, three repeat DRIP reactions were first analyzed separately by DRIP-qPCR to verify the DRIP procedure as in Sanz et al., 2019. Three DRIP reactions per biological replicate were then pooled for preparation of each DRIP-seq library. Input and DRIP DNA was sonicated to a size of ~300–700 bp and DRIP-seq library preparation was performed using NEB E6050 for end repair, NEB M0212 for A-tailing, and NEB E7335 for adapter ligation. 12 cycles of PCR were performed for library amplification and libraries were cleaned and size selected (Ampure XP beads).

value: Primary neural stem/progenitor cells

value: postnatal day 7

tag: drip antibody


title: Control7 RNA-Seq

description:
Control7
zscan4 KD in 2-cell

value: wild type


title: Zscan4 RNAi1 RNA-Seq

description:
Zscan4 RNAi1
zscan4 KD in 2-cell


title: Zscan4 RNAi4 RNA-Seq

description:
Zscan4 RNAi4
zscan4 KD in 2-cell


title: Control6 RNA-Seq

description:
Control6
zscan4 KD in 2-cell


title: C57BL/6N_Rep_4 [175111]

city: Erlangen

first: Christian

last: Büttner

address: Schwabachanlage 10

department: Institut of Human Genetics

institute: University Hospital Erlangen

description: Transcriptome Sequencing

data_processing:
Basecalling with Illumina RTA 1.18.61
Adapter trimming and quality trimming of reads of poly-N-ends and bases with quality lower 20.
Alignment to strain pseudogenomes generated wth GRCm38 Reference using Tophat2 (version 2.1.1) in very high sensitivity mode, the reference being alterted with modtools (version 1.0.2) to include SNPs and short InDels from the Sanger Mouse Genomes Variant call sets (Release 0515).
Conversion of the Tophat2 generated BAM alignments files using Lapels (version 1.1.1) to conform to the standard GRCm38 Reference coordinates again.
Counting of exonic alignments relative to Ensembl Mouse genes model (Release 94) to quantify gene level expression with HTSeq (version 0.7.1) in union mode.
Genome_build: GRCm38.
Supplementary_files_format_and_content: Expression normalized and regularized log-transformed with DESeq2 (version 1.30) function rlog.

source_name: Naive cornea_C57BL/6N

extract_protocol:
Total RNA was extracted from mouse cornea using the Qiagen RNeasy Micro Kit with DNA digestion.
Nugen Ovation RNA-seq system for model organisms (mouse)

value: Naive cornea


title: Control5 RNA-Seq

description:
Control5
zscan4 KD in 2-cell


title: Control3 RNA-Seq

description:
Control3
zscan4 KD in 2-cell


title: Control4 RNA-Seq

description:
Control4
zscan4 KD in 2-cell


title: C57BL/6N_Rep_2 [175109]

description: Transcriptome Sequencing


title: C57BL/6N_Rep_1 [175108]

description: Transcriptome Sequencing


title: Control1 RNA-Seq

description:
Control1
yj RNAseqZscan4 OE


title: Control2 RNA-Seq

description:
Control2
yj RNAseqZscan4 OE


title: Zscan4 OE2 RNA-Seq

description:
Zscan4 OE2
yj RNAseqZscan4 OE

value: Zscan4 OE


title: Zscan4 OE1 RNA-Seq

description:
Zscan4 OE1
yj RNAseqZscan4 OE


title: CD4 T cells, pooled input, 24 hr iTreg differentation

city: Bryan

first: Preston

last: Arnold

state: TX

address: Health Professions Education Building 8447 Riverside Pkwy

institute: Texas A&M School of Medicine

data_processing:
Reads mapped to mm10 using BWA with default settings. Duplicate reads removed
75-nt reads extended in silico at 3' ends to length of 200 bp. Fragment density determined with 32-nt bins and the number of fragments in each bin determined.
Peaks called using MACS peak algorithim.
Assembly: mm10
Supplementary files format and content: bigWig files show fragment density for 32-nt bins along the genome

source_name: CD4 T cells

extract_protocol:
Cells were sorted for virus+ cells, flash frozen, and then fixed in 1% formaldehyde for 15 min at room temp. After quenching, cells were lysed and the genomic DNA sonicated to 200-1500bp fragments. ChIP was performed for IRF4.
75-nt single-end generated by Illumina sequencing (NextSeq 500)

value: CD4 T cells

value: Batf-/- Batf3-/-

value: Pooled input BATF3 WT and BATF3 Mut overexpression


title: CD4 T cells, overexpress BATF3 WT, 24 hr iTreg diffrentiation, IRF4 CHIP

value: Batf3 WT retroviral overexpression, followed by IRF4 ChIP-seq


title: CD4 T cells, overexpress BATF3 Mut, 24 hr iTreg diffrentiation, IRF4 CHIP

value: Batf3 Mut retroviral overexpression, followed by IRF4 ChIP-seq


title: TP53_R172_12weeksold [SampleID.1145.3]

city: Melbourne

first: Sue

last: Haupt

address: 305 Grattan St

institute: Peter MacCallum Cancer Centre

data_processing:
Reads were aligned to GRCm38 using hisat2 (2.0.4) in unpaired mode with -qc-filter 2. Gene level counts were quantified ht-seq (v0.9.1). Raw counts were converted to counts per million (CPM) and lowly expressed genes <5 CPM were removed. CPM counts were normalized using the RUVIII method (k=10) within the ruv (v0.9.7.1) R package
Assembly: GRCm38
Supplementary files format and content: Log normalized CPM using the RUVIII method (k=10).

source_name: anterior prostate lobes

growth_protocol: No growth protocol was used. Samples came from anterior prostates of mice.

extract_protocol: RNA was purified from 50μm Formalin-Fixed Paraffin-Embedded (FFPE) tissue sections  (Catalog No. 73504, Qiagen) according to the manufacturer’s instructions. RNA was then eluted from the columns in 20 μL of DEPC-Treated Water (Catalog No. AM9906, Thermo Fisher Scientific). RNA quality was tested using a High Sensitivity RNA TapeStation assay (Agilent) with a DV200 cutoff of >50%. 150ng of total RNA from each sample were used for genome-wide transcriptomic analyses

value: anterior prostate lobes

value: Prostate cancer cells


title: TP53_R172_12weeksold [SampleID.1145.2]


title: TP53_R172_12weeksold [SampleID.1145.1]


title: TP53_R245_12weeksold [SampleID.1152.1]


title: Osteoblast-WT-Day5-3

source_name: osteoblast, calvarial

value: Osteoblast

value: Wildtype


title: TP53null_12weeksold [SampleID.1149.2]

value: PTEN (fl/fl); TP53 (fl/fl)


title: Control_12weeksold [SampleID.1140.2]

value: PTEN (fl/fl); TP53 (wt/wt)


title: Control_12weeksold [SampleID.1140.3]


title: TP53null_12weeksold [SampleID.1149.1]


title: C57BL/6N_Rep_3 [175110]

description: Transcriptome Sequencing


title: Control_12weeksold [SampleID.1140.1]


title: TP53_R245_ENDPOINT [SampleID.1115]


title: TP53_R245_ENDPOINT [SampleID.1114]


title: TP53_R172_ENDPOINT [SampleID.1102]


title: TP53_R172_ENDPOINT [SampleID.1100]


title: TP53_R245_12weeksold [SampleID.1152.3]


title: TP53null_ENDPOINT [SampleID.1062]


title: TP53null_ENDPOINT [SampleID.346]


title: Control_ENDPOINT [SampleID.1054]


title: TP53_R245_12weeksold [SampleID.1152.2]


title: Control_ENDPOINT [SampleID.1055]


title: TP53_R172_ENDPOINT [SampleID.1101]


title: TP53null_ENDPOINT [SampleID.60]


title: injured, 4 weeks, rep3

description:
SCI_week4_rep3
t4v3

value: Female

value: Adult

value: SCI

value: spinal cord, injury epicentre (1.5 cm)


title: Control_ENDPOINT [SampleID.847]


title: Control_ENDPOINT [SampleID.848]


title: small RNase H1-/- rep4

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

institute: The Kids Research Institute Australia

data_processing:
Single-end reads were aligned to the mouse genome (mm10) with bowtie2 v2.3.4.1 using default parameters.
Gene counts were produced with featureCounts v1.6.3 (-s 1) using the Ensembl GRCm38 v94 annotation combined with an in-house mitochondrial annotation.
Differential expression was analyzed with DESeq2 v1.18.1 in R v3.5.1.
Strand-specific coverage profiles were generated with samtools and bedtools genomecov, normalised to total reads mapped to mitochondria.
Assembly: mm10
Supplementary files format and content: wig files of per-strand normalised mitochondrial coverage

source_name: Heart tissue

growth_protocol: The tissue-specific conditional knockout of RNase H1 in heart and skeletal muscle was obtained by crossing Rnaseh1+/loxP with transgenic mice expressing Cre recombinase under the control of the muscle creatinine kinase promoter (Ckmm-cre). Animals were housed in a 12-hour light/dark cycle at 21°C and fed with a normal chow diet ad libitum.

extract_protocol:
Small RNA was extracted form 24-week-old mouse heart tissues with Qiagen miRNeasy kit according to the kit instructions for transcriptome analysis.
An Illumina small RNA library was constructed according to manufacturers instructions.

value: 24 weeks

tag: genotype/variation


title: TP53null_12weeksold [SampleID.1149.3]


title: small RNase H1+/+ rep4

tag: age

value: wild type


title: small RNase H1-/- rep3


title: small RNase H1+/+ rep3


title: TP53_R245_ENDPOINT [SampleID.1116]


title: small RNase H1+/+ rep2


title: small RNase H1+/+ rep1


title: small RNase H1-/- rep1