title: DG_6h_EE_rep1

description:
Library name: DG_6h_EE_rep1
bulk RNA-seq

value: hippocampus


title: M1_6h_C

status: Public on Jul 16 2025

type: SRA

city: Madison

first: Jing

last: Fan

state: WI

address: 330 N Orchard St., Fan Lab

department: Metabolism

country: USA

institute: Morgridge Institute for Research

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt

library_source: transcriptomic

data_processing:
RNA sequencing was performed by Novogene, utilizing Illumina’s Sequencing by Synthesis (SBS) technology.
Quality control was commenced with base recognition using CASAVA, followed by error rate assessment and GC content analysis.
The data were then subjected to stringent filtration, removing adapter contamination, reads with over 10% uncertain nucleotides, and reads where low-quality bases exceeded 50% of the sequence.
Assembly: Post-filtration, the data were aligned to the mm10 mouse genome using the STAR software.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Bone-marrow derived macrophage

growth_protocol: Murine bone marrow-derived macrophages (BMDMs) were isolated from wildtype C57BL/6J mice. Bone marrow cells were isolated and differentiated from 6–12-week-old males or females. BMDMs were cultured in RPMI 1640  with 10% dialyzed fetal bovine serum, 25mM HEPES, 2mM glutamine, 1% antibiotics (penicillin, streptomycin) and 20ng/mL M-CSF at 37°C and 5% CO2.

extract_protocol:
For RNA collection, cells were washed twice with DPBS and then lysed with RNA STAT 60. Chloroform was used for phase separation. RNA was precipitated with isopropanol, washed with 75% ethanol, and solubilized in DEPC H2O.
mRNA library preparation was performed by Novogene using poly A enrichment

treatment_protocol: To stimulate BMDMs, cells were incubated with 50ng/mL LPS and 30ng/mL recombinant mouse IFNγ  for 2h. Stimuli then were removed, cells were washed with DPBS, and cell culture was continued in fresh media without stimuli for the remaining timecourse.

tag: cell type

value: Bone-marrow derived macrophage

tag: genotype

value: Wild-type

tag: time stimulated_with_lps+ifny

value: 6h later


title: subject8_batch2_timeN_Homosapiens_RNAseq

city: Kingston

first: Amanda

middle: M

last: Zacharias

state: Ontario

address: 99 University Avenue

country: Canada

institute: Queen's University

description: Library name: 8_N_batch2

data_processing:
Raw-sequencing reads were cleaned by BGI using SOAPnuke v1.5.2 with the parameters “-l 15 -q 0.2 -n 0.05”.
Reads were aligned to GENCODE’s primary human reference genome vGRCh38.p13 with Hisat2 v2.2.1 using parameters "--dta --sensitive --no-discordant --no-mixed".
Samtools v1.10 was used to sort resulting BAM files, mark duplicates, index BAM files.
StringTie v2.1.5 assembled aligned reads into transcripts and quantified their abundance using GENCODE’s vGRCh38.p13 comprehensive gene annotation.
IsoformAnalyzeR v1.17.4 in R v4.2.1 assigned a known gene to “novel” transcripts based on their genomic coordinates when possible.
For network analysis, ComBat-seq from sva v3.36.0 adjusted raw and filtered transcript counts for batch effects. DESeq2 v1.26.0 applied the variance stabilizing transformation to these adjusted counts.
Assembly: Gencode GRCh38.p13
Supplementary files format and content: csv file includes raw transcript counts for each Sample
Supplementary files format and content: csv file includes batch-effect adjusted and variance stabilizing transformed transcript counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Whole peripheral blood

extract_protocol:
Two tubes of blood were collected twice 12 hours apart (7:00-9:00 and 19:00-21:00) by venipuncture in either arm. A 3mL TempusTM Blood RNA tube (Applied Biosystems, Foster City, CA) was used to collect stabilized whole blood RNA. RNA was extracted using Tempus Spin RNA Isolation kits, according to manufacturer’s protocol. RNA integrity (≥7.5) and concentration were assessed prior to library preparation, with globin clearance.
Library preparation was performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). RNA was taken to prepare the reaction system. The globin mRNA was removed by using GLOBINclear™ Whole Blood Globin Reduction Kit-Human (Ambion, USA). Then, the globin mRNA removed RNA samples were denatured at suitable temperature to open the secondary structure, and mRNA was enriched by oligo (dT) attached magnetic beads. After reacting at a suitable temperature for a fixed time period, the enriched mRNA was fragmented with fragmentation reaction. Then the first-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Related, the synthesized double strand cDNA was subject to end repairment reaction. After cDNA end repairment, a single ‘A’ nucleotide was added to the 3’ ends of the blunt fragments through a tailing reaction. Then the adaptors were connected to the double stranded cDNA with adaptor ligation reaction. Finally, the library products were amplified through PCR reaction and subjected to quality control. Next, the single-stranded library products were produced via denaturation. The reaction system for circularization was set up to get the single-stranded circularized DNA products. Any single stranded linear DNA molecules will be digested. The final single strand circularized library was amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs were loaded into the patterned nanoarray and sequencing reads of PE 150 bases length were generated on G400 platform (BGI-Shenzhen, China).

tag: tissue

value: Whole peripheral blood

tag: age

tag: Sex

value: male

tag: timepoint

value: N

tag: batch

tag: opioids


title: spoki, myo1a-EcRi,biorep1

city: Heidelberg

first: Yao

last: Zhang

address: Im Neuenheimer Feld 580

country: Germany

institute: Deutsches Krebsforschungszentrum (DKFZ)

description: Library name: EcRi1

data_processing:
CLC Genomics Workbench
Assembly: dm6
Supplementary files format and content: Feature counts for each sample

organism: Drosophila melanogaster

source_name: intestine

extract_protocol:
Total RNA were extracted using Qiagen RNeasy mini plus kit
SMARTER mRNA-seq library prep kit was used

value: intestine

value: EcRi


title: subject36_timeN_Homosapiens_RNAseq

description: Library name: 36_N


title: spoki, myo1a-con,biorep3

description: Library name: Con3

value: control


title: M1_6h_B

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt


title: DG_4h_EE_rep4

city: Boston

first: Erin

middle: Elizabeth

last: Duffy

state: MA

address: 200 Longwood Ave, Goldenson 405

department: Neurobiology

institute: Harvard Medical School

description:
Library name: DG_4h_EE_rep4
bulk RNA-seq

data_processing:
bulk RNA-seq: Illumina adapters were trimmed with Cutadapt (version 1.14) and aligned using Hisat252 (version 2.1.0) to the Mus musculus genome (GRCm39) and transcriptome (Ensembl). Aligned BAM files were sorted using Picard Tools (version 2.8.0). Reads were quantified over annotated exons using FeatureCounts (Subread version 2.0.6). Lowly expressed genes were filtered for counts per million >1 in at least five samples using edgeR (version 4.0.16).
snMultiome-seq: Raw sequencing data were processed using Cell Ranger ARC (v2.0.2, 10x Genomics) under default settings. Reads were mapped to mouse mm10 genome, with the GENCODE vm23 GTF file as used in the BICCN atlas.28 We performed unsupervised clustering with RNA UMI counts based on the SCANPY analysis pipeline61 and best practice steps.62,63 In brief, we first filtered for low-quality nuclei by requiring ≥1,000 ATAC fragments and ≥200 genes detected per nuclei and < 5% mitochondria RNA reads. We then performed a first-pass clustering for quality control. Top 3,000 highly variable genes were identified for principal component analysis (PCA). Top 30 PCs were used to perform K-nearest neighbor (k=25) graph-based Leiden clustering (resolution=1). Putative multiplets were predicted using Scrublet64 and Leiden clusters with mean doublets score > 0.2 were marked as doublets. 87-92% cells generated from Cell Ranger ARC for each replicate passed these filtering steps. We then integrated our high-quality cells with hippocampal formation (HPF) cells selected from the whole-mouse brain atlas dataset from BICCN.28 The integration was performed using Seurat's integration methods as previously described.65 We annotated 14 major cell types, and 33 sub-class level cell types based on the integration results as the cell type nomenclature used in this study.
Assembly: bulk RNA-seq: GRCm39; snMultiome-seq: GRCm38
Supplementary files format and content: bulk RNA-seq: one table of raw counts, with each column corresponding to a sample, pre-filtered for lowly expressed genes.
Supplementary files format and content: scMultiome: CellRanger count matrix after alignment, filtering, barcode counting, and UMI counting

source_name: hippocampus

growth_protocol: Mice were handled according to protocols approved by the Harvard University Standing Committee on Animal Care and were in accordance with federal guidelines. Wild-type C57/BL6 (JAX 000664) were housed in a 12 h light/dark cycle with ad libitum access to food. For all sequencing studies, male mice were used to avoid the confounding effects of estrogen cycles observed in females

extract_protocol:
Mice were deeply anesthetized with isoflurane, decapitated and brains were placed in a stainless-steel brain matrix on ice to cut 1mm sections of anterior to posterior hippocampus. Sections were transferred into ice-cold PBS and Cornu Ammonis (CA)1, CA3 and Dentate Gyrus (DG) separated under a dissection microscope. Tissue was frozen in liquid nitrogen and stored at -80° for further processing and RNA extraction. For bulk RNA-seq,tissue was resuspended in 500 µL TRIzol reagent (Life Technologies), followed by trituration with a 26G needle. RNA was chloroform extracted, an equal volume of 100% ethanol was added, and RNA was purified using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instruction, including the on-column DNase digest.  For single-nuclei multiomic-sequencing whole hippocampi were dissected on an ice-cold metal block and immediately processed for nuclei preparation.
For bulk RNA-seq, RNA concentration was assessed by Nanodrop and RNA-seq libraries were prepared from 10 ng of total RNA using the SMARTer Stranded Total RNA-seq Pico Input Mammalian V2 kit (Takara Bio) according to the manufacturer’s instructions. For snMultiom-seq, freshly dissected hippocampi were dissociated, nuclei were prepared then concentrated in 1X nucleus buffer from 10X Genomics.  1µl of nuclei was stained with Trypan Blue (Invitrogen, T10282) and manually counted. In total, 16,000–20,000 nuclei were used for the tagmentation reaction and 10x Chromium controller loading. The DNA and RNA libraries were generated according to the manufacturer’s recommended protocol (https://www.10xgenomics.com/support/single-cell-multiome-atac-plus-gene-expression).

treatment_protocol: Adult mice (8-10 weeks of age) were single housed and brought to the room in which behavior was conducted 2-3 nights prior to exposure to novel environment. During this time, mice were housed in a 12 h light/dark cycle with ad libitum access to food. For novel environment stimulation, mice were placed in a square arena (16”x16”) containing a running wheel, tunnel, falcon tubes, Lego pyramid, and a tube rack for 30 min, returned to their home cage, and brain tissue was harvested at indicated times after the start of novel environment (except for 15 and 30 min timepoints for which tissue was harvested without return to homecage). For 6 h continuous novel environment stimulation, mice were placed into the arena containing toys and hydro gel for 6 h. Arena and toys were cleaned prior to experimentation and in between animals with 70% EtOH.    Importantly, tissue was always collected before the animals entered the dark cycle, so the gene expression changes observed are likely not activated in response to changes in response to light state. We collected replicates from the same time point at different times of day to control for gene expression changes driven by circadian rhythms rather than NE exposure. Our initial dataset also included bulk RNA-seq following 12 h of NE exposure, but this time point was later excluded as all mice were harvested at the same time immediately before the dark cycle began and therefore gene expression changes due to NE exposure and circadian rhythms could not be deconvoluted.

tag: treatment

value: 30 min NE + 3.5 h HC


title: M1_6h_A

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt


title: DG_6h_EE_rep4

description:
Library name: DG_6h_EE_rep4
bulk RNA-seq

value: 30 min NE + 5.5 h HC


title: DG_4h_EE_rep3

description:
Library name: DG_4h_EE_rep3
bulk RNA-seq


title: DG_4h_EE_rep2

description:
Library name: DG_4h_EE_rep2
bulk RNA-seq


title: subject35_timeN_Homosapiens_RNAseq

description: Library name: 35_N

value: female


title: M1_2h_C

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt

value: 2h later


title: spoki, myo1a-con,biorep1

description: Library name: Con1


title: spoki, myo1a-con,biorep2

description: Library name: Con2


title: subject34_timeN_Homosapiens_RNAseq

description: Library name: 34_N


title: M1_2h_B

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt


title: DG_4h_EE_rep1

description:
Library name: DG_4h_EE_rep1
bulk RNA-seq


title: spoki, myo1a-EcRi,biorep2

description: Library name: EcRi2


title: subject33_timeN_Homosapiens_RNAseq

description: Library name: 33_N


title: Liver, female, LPD, rep 5

city: Lyon

first: Filipe

last: De Vadder

address: 32-34 Avenue Tony Garnier

country: France

institute: Institut de Génomique Fonctionnelle, ENS de Lyon, CNRS UMR5242, Université Claude Bernard Lyon 1

description: Library name: Sample 30

data_processing:
Reads were then analyzed using a local pipeline derived from the one supported by Lexogen.
Adapter sequences were first removed using the Cutadapt package (version 3.5) and quality control of reads was performed using FastQC.
Read mapping was achieved with STAR (Spliced Transcripts Alignment to a Reference, version 2.7.11a) using the Mus musculus GRCm39 genome reference (Ensembl, release 110).
Umi_tools dedup (version 1.1.2) was conducted to UMI deduplication.
The mapped reads were then quantified by htseq-count (version 2.0.3) [34] allowing to generate a count table by sample.
Assembly: GRCm39 (Ensembl, release 110)
Supplementary files format and content: One tsv file for each sample containig raw counts

source_name: liver

growth_protocol: Males and females were kept either on a control diet (20% in kcal) or on a low-protein diet (5% in kcal) for 5 weeks after weaning.

extract_protocol:
Total RNA was extracted from liver using Nucleospin RNA kit (Macherey-Nagel, 740955.250), following manufacturer's instructions.
For each sample, mRNA purification, based on oligo dT-based mRNA isolation, was conducted with a starting material of 1µg of total RNA using the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and following the manufacturer’s instructions. Then, single-indexed libraries were built using the CORALL Total RNA-Seq Library Prep Kit (Lexogen) and following the manufacturer’s instructions.

value: liver

tag: strain

value: WT

tag: diet

value: low-protein


title: DG_2h_EE_rep4

description:
Library name: DG_2h_EE_rep4
bulk RNA-seq

value: hippocampus

value: 30 min NE + 1.5 h HC


title: DG_2h_EE_rep3

description:
Library name: DG_2h_EE_rep3
bulk RNA-seq


title: Liver, female, LPD, rep 4

description: Library name: Sample 29


title: M0_24h_C

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt

value: Bone-marrow derived macrophage

value: Wild-type


title: subject58_timeD_Homosapiens_RNAseq

description: Library name: 58_D

value: Whole peripheral blood

value: D


title: subject57_timeD_Homosapiens_RNAseq

description: Library name: 57_D

value: male


title: M0_24h_B

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt


title: DG_2h_EE_rep2

description:
Library name: DG_2h_EE_rep2
bulk RNA-seq


title: subject56_timeD_Homosapiens_RNAseq

description: Library name: 56_D


title: Liver, female, LPD, rep 2

description: Library name: Sample 27


title: subject55_timeD_Homosapiens_RNAseq

description: Library name: 55_D


title: DG_2h_EE_rep1

description:
Library name: DG_2h_EE_rep1
bulk RNA-seq


title: M0_24h_A

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt


title: Liver, female, LPD, rep 1

description: Library name: Sample 26


title: M1_2h_A

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt


title: DG_1.5h_EE_rep4

description:
Library name: DG_1.5h_EE_rep4
bulk RNA-seq

value: 30 min NE + 1 h HC


title: subject53_timeD_Homosapiens_RNAseq

description: Library name: 53_D


title: DG_1.5h_EE_rep2

description:
Library name: DG_1.5h_EE_rep2
bulk RNA-seq


title: RRBS H3WT, rep2

first: Gracia

middle: M.

last: Bonilla

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital

library_source: genomic

data_processing:
Demultiplexed reads were trimmed using cutadapt and the Nugene diversity adapter trimming python script trimRRBSdiversityAdaptCustomers.py.
Reads were then aligned to the mouse mm10 genome using BSMAP with the parameters: -v 0.1 -s 12 -q 20 -w 100 -S 1 -u -R -D C-CGG. Duplicate reads were removed using the Nugen deduplication script nudup.py.
Methylation ratios were called using the MOABS mcall module
Assembly: mm10
Supplementary files format and content: Tab-separated files with methylation information for CpGs

molecule: genomic DNA

source_name: Bone marrow

growth_protocol: No in vitro culture was involved.

extract_protocol:
Genomic DNA was extracted using Invitrogen Purelink Genomic DNA Mini kit.
Genomic DNA was quantified using a Qubit 3.0 Fluorometer. RRBS was performed on 100 ng of each sample using the NuGen Ovation RRBS Methyl-seq System following the manufacturer’s recommendations. Bisulfite conversion of DNA was conducted using the Qiagen EpiTect Fast Bisulfite Conversion kit. Libraries were purified with Agencourt RNAclean XP beads and quality-assessed using an Agilent 4150 Tape-Station D1000 ScreenTape. Libraries were then sequenced on the Illumina NovaSeq6000, generating 100-bp single-end reads.

treatment_protocol: Mice harboring K-to-M mutation were induced with Doxycycline for 2 weeks and myeloid progenitor cells (Lineage-/cKit+/Sca1-) were sorted from bone marrow.

value: Bone marrow

value: Myeloid progenitors

value: Induce Dox for 2 weeks


title: RRBS H3WT, rep1


title: DG_1.5h_EE_rep3

description:
Library name: DG_1.5h_EE_rep3
bulk RNA-seq


title: Liver, female, CD, rep 4

description: Library name: Sample 24

value: control


title: RRBS H3K4M, rep2


title: Liver, female, CD, rep 5

description: Library name: Sample 25

value: female


title: subject52_timeD_Homosapiens_RNAseq

description: Library name: 52_D


title: DG_1.5h_EE_rep1

description:
Library name: DG_1.5h_EE_rep1
bulk RNA-seq


title: subject54_timeD_Homosapiens_RNAseq

description: Library name: 54_D


title: RRBS H3K4M, rep1


title: Liver, female, CD, rep 3

description: Library name: Sample 23


title: Liver, female, LPD, rep 3

description: Library name: Sample 28


title: subject51_timeD_Homosapiens_RNAseq

description: Library name: 51_D


title: DG_1h_EE_rep5

description:
Library name: DG_1h_EE_rep5
bulk RNA-seq

value: 30 min NE + 30 min HC


title: RRBS H3K27M, rep2


title: subject50_timeD_Homosapiens_RNAseq

description: Library name: 50_D


title: DG_1h_EE_rep4

description:
Library name: DG_1h_EE_rep4
bulk RNA-seq


title: Liver, female, CD, rep 1

description: Library name: Sample 21

value: liver


title: RRBS H3K27M, rep1


title: Liver, female, CD, rep 2

description: Library name: Sample 22

value: WT


title: Liver, male, LPD, rep 5

description: Library name: Sample 20

value: low-protein


title: DG_1h_EE_rep2

description:
Library name: DG_1h_EE_rep2
bulk RNA-seq

value: hippocampus


title: RRBS H3K4M/K27M, rep2


title: Liver, male, LPD, rep 4

description: Library name: Sample 19


title: subject48_timeD_Homosapiens_RNAseq

description: Library name: 48_D


title: DG_0.5h_EE_rep2

description:
Library name: DG_0.5h_EE_rep2
bulk RNA-seq

value: 30 min NE


title: Liver, male, CD, rep 5

description: Library name: Sample 15


title: Liver, male, LPD, rep 1

description: Library name: Sample 16


title: RRBS H3K4M/K27M, rep1


title: DPTIP, brain, 7 dpi, R12

city: Madrid

first: Miguel A.

last: Martín-Acebes

state: Madrid

address: Ctra. de La Coruña, km 7, 5

country: Spain

institute: INIA-CSIC

data_processing:
Average base quality was determined by Fastqc. Sequence reads were trimmed using trimmomatic to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Trimmed sequence reads were mapped to mm10 using HISAT2 version 2.1.0 and Bowtie2 2.3.4.1
Known genes and transcripts were assembled with StringTie based on reference genome model. After assembly, abundance of gene/transcript was calculated in the read count and normalized values as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million) for a sample.
Read count data was normalized with Relative Log Expression (RLE) method in DESeq2 R library. RLE normalized count was adopted for negative binomial Wald Test(nbinomWaldTest) in DESeq2.
Statistical analysis is performed using Fold Change, nbinomWaldTest using DESeq2 per comparison pair. Significant results are selected on conditions of |fc|>=2 & nbinomWaldTest raw p-value<0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including gene ID, gene symbol, log2 fold change (FC), raw pvalue, bh corrected pvalue (benjamini hochberg), expression level (normalized value), raw reads counts, FPKM and TMP values for each group comparison

source_name: Brain

growth_protocol: Experimental infections in mice were performed in the biosafety level 3 (BSL-3) facilities at Centro de Investigación en Sanidad Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (CISA, INIA-CSIC). Animals were kept with ad libitum access to food and water and were anesthetized under isoflurane and humanely sacrificed at 7 days post-infection (7 dpi)

extract_protocol:
Total brain RNA was extracted from tissue samples using Ribopure following manufacturer's protocols
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.

treatment_protocol: Mice were infected intraperitoneally (i.p.) with 10e4 plaque forming units (PFU) of WNV in 200 µL of Minimum Essential Medium Eagle (Corning) and mock-infected animals were also inoculated i.p. with 200 µL of culture media. DPTIP or vehicle (saline buffer-carboxymethylcellulose, 5% DMSO and 10% Tween-80) were orally administered at a dose of 15 mg/kg (DPTIP)

value: Brain

tag: cell line

value: DPTIP


title: DG_0.5h_EE_rep3

description:
Library name: DG_0.5h_EE_rep3
bulk RNA-seq


title: DG_1h_EE_rep1

description:
Library name: DG_1h_EE_rep1
bulk RNA-seq


title: subject44_timeD_Homosapiens_RNAseq

description: Library name: 44_D

value: Whole peripheral blood


title: JSH9_E14 replicate 1

city: Cambridge

first: Somdutta

last: Dhir

address: Robinson Way

department: CRUK-CI

country: United Kingdom

institute: University of Cambridge

data_processing:
*library strategy: Bisulfite-free profiling of methylation & hydroxymethylation
Initial filtering (Cutadapt v4.6)
Read pairing (SeqKit v2.7.0)
Trimming/insert sequence extraction (Cutadapt v4.6)
Discarding unmatched sequences (SeqKit v2.7.0)
Alignment (BSBolt v1.5.0)
Lane merging (SAMtools v2.5.2)
Deduplication (Picard v3.1.1)
Extracting methylation calls (custom Python script)
Reconstructing CpG states (pairwise combinations of C, mC and hmC at double-stranded CpG sites) (custom R script)
Filtering (blacklisted regions, errors, mininum double-stranded depth of 5x) (custom R & bash scripts)
Assembly: mm10
Supplementary files format and content: BED format file with following columns:
Supplementary files format and content: 1. Chromosome (Chr)
Supplementary files format and content: 2. Start
Supplementary files format and content: 3. End
Supplementary files format and content: 4. CpG ID (unique ID ascribed to each double-stranded CpG site
Supplementary files format and content: 5. CpG state: pairwise combination of cytosine (C), 5-methylcytosine (M) or 5-hydroxymethylcytosine (H) across the double-stranded CpG site.
Supplementary files format and content: The first letter of the pair corresponds to the plus strand, the second the minus
Supplementary files format and content: (e.g. ‘HC’ refers to a CpG site with 5-hydroxymethylcytosine on the plus strand and unmodified cytosine on the minus)
Supplementary files format and content: 6. CpG-state level (the level of a given CpG state at a given CpG site, expressed as %)
Supplementary files format and content: 7. Count (number of times a given CpG state is counted at a given site)
Supplementary files format and content: 8. Depth (double-stranded depth at given CpG site)
Supplementary files format and content: 9. Strand: Orientation of a given CpG state (order of priority: H > M > C, so HC denoted ‘+’ as H is on the plus strand,
Supplementary files format and content: CH denoted ‘–‘. Symmetric CpG states are arbitrarily assigned ‘+’)

source_name: Embryonic stem cells

growth_protocol: Basal medium for mESC cultures was DMEM high glucose (Sigma, D6546-500mL) containing 10% FBS (Gibco, 16141079), 2 mMGlutaMax-I (Gibco, 35050-038), 1× NEAA (Gibco, 11140-035) and 0.1 mM β-mercaptoethanol (Sigma, M3148 -25 mL diluted to 50 mM in 50 uM EDTA/PBS solution). mESCs were regularly maintained on gelatin (G9391-100G)-coated plates by supplementing basal medium with 1,000 U/mL LIF (PeproTech, murine LIF, 250-02-25UG). Cultures were routinely monitored for Mycoplasma contamination.

extract_protocol: Isolation of gDNA samples was performed as described in Pfaffeneder, T. et al., Nature Chemical Biology 10, 574–81 (2014) with the following modifications: Cultures were washed in PBS and lysed by adding RLT buffer (Qiagen) containing 1:100 β-mercaptoethanol. Isolation of genomic DNA was performed with Zymo-Spin IIC-XL columns according to the instruction of the ZR-Duet DNA/RNA MiniPrep Kit (Zymo Research). Lysates were applied onto spin columns and bound material was incubated for 10 min with Genomic Lysis Buffer (Zymo Research) supplemented with 0.2 mg/mL RNaseA (Qiagen). After washing genomic DNA was eluted in water.

value: Embryonic stem cells


title: subject47_timeD_Homosapiens_RNAseq

description: Library name: 47_D

value: D


title: Liver, male, LPD, rep 2

description: Library name: Sample 17

value: male


title: JSH11_E14 replicate 2


title: DG_0.5h_EE_rep1

description:
Library name: DG_0.5h_EE_rep1
bulk RNA-seq


title: subject46_timeD_Homosapiens_RNAseq

description: Library name: 46_D


title: DG_0.5h_EE_rep4

description:
Library name: DG_0.5h_EE_rep4
bulk RNA-seq


title: Liver, male, CD, rep 4

description: Library name: Sample 14


title: Liver, male, LPD, rep 3

description: Library name: Sample 18


title: DPTIP, brain, 7 dpi, R11


title: DG_0.25h_EE_rep3

description:
Library name: DG_0.25h_EE_rep3
bulk RNA-seq

value: 15 min NE


title: subject45_timeD_Homosapiens_RNAseq

description: Library name: 45_D


title: DPTIP, brain, 7 dpi, R10


title: Liver, male, CD, rep 3

description: Library name: Sample 13


title: DG_0.25h_EE_rep4

description:
Library name: DG_0.25h_EE_rep4
bulk RNA-seq


title: subject49_timeD_Homosapiens_RNAseq

description: Library name: 49_D


title: Liver, male, CD, rep 2

description: Library name: Sample 12


title: subject43_timeD_Homosapiens_RNAseq

description: Library name: 43_D


title: DPTIP, brain, 7 dpi, R9


title: subject16_batch2_timeD_Homosapiens_RNAseq

description: Library name: 16_D_batch2


title: DG_0.25h_EE_rep2

description:
Library name: DG_0.25h_EE_rep2
bulk RNA-seq


title: DPTIP, brain, 7 dpi, R6


title: Liver, male, CD, rep 1

description: Library name: Sample 11


title: DG_HC_rep4

description:
Library name: DG_HC_rep4
bulk RNA-seq

value: Home cage


title: subject38_timeD_Homosapiens_RNAseq

description: Library name: 38_D


title: DG_0.25h_EE_rep1

description:
Library name: DG_0.25h_EE_rep1
bulk RNA-seq


title: MEFs, Unstimulated, F33

first: Diego

last: Mañanes

address: C. de Melchor Fernández Almagro, 3

institute: Spanish National Center for Cardiovascular Research

description: Library name: F33_Directional_NEBNext_S33

data_processing:
Reads were preprocessed according to the type of library preparation using cutadapt to trim adapters and FastQC to assess read quality. In the case of directional RNA-seq reads (BMDM and MEFs) Illumina adaptor sequences were removed, and only reads longer than 30 bp were kept as valid. In addition to Illumina adaptor sequences, adaptors from the low input NEBNext protocol (MAECs) were detected and removed, and only reads longer than 30 bp were kept as valid.
Resulted reads were mapped to the reference transcriptome GRCm38.102 using STAR and gene expression levels were estimated using RSEM.
Further analyses were performed in R (v 4.3.2). In brief, counts per million (CPM) were calculated, and size factors for inter-sample normalization were determined using the trimmed mean of M values (TMM) method. Then, log-normalized data considering only genes with ≥ 20 counts in three samples were used for differential expression analysis, making all possible comparisons within the same cell type using the DESeq2 R package.
Assembly: mm10 (GRCm38.p6) mouse genome
Supplementary files format and content: raw-counts.tsv

source_name: MEFs

growth_protocol: Cultured BMDMs, MEFs  were plated in equal number (6e5 cells per well BMDM and MEF) in 6-well plates (2000-μl final volume, Corning) and 1e5 cells per well MAECs in p24 (1000-μl final volume, (Corning) nd rested overnight.

extract_protocol:
Total RNA was isolated from BMDMs, MEF (QIAamp DNA Mini Kit) and MAECs (miRNeasy Micro Kit).
For the BMDMs and MEFs samples, RNAseq libraries were prepared using the NEBNext Ultra II Directional RNA Library preparation kit (New England Biolabs) according to manufacturer’s instructions. For MAECs samples, libraries were prepared using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer’s instructions. All libraries were sequenced in a Nextseq 2000 (Illumina).

treatment_protocol: Cells were treated in vitro with or without ImP (10 μg/mL) for 1 or 2 hours. Total RNA was isolated from BMDMs, MEF (QIAamp DNA Mini Kit) and MAECs (miRNeasy Micro Kit).

value: MEFs

value: Unstimulated


title: MEFs, ImP for 2h, F35

description: Library name: F35_Directional_NEBNext_S35

value: ImP  for 2h


title: subject8_batch2_timeD_Homosapiens_RNAseq

description: Library name: 8_D_batch2


title: subject42_timeD_Homosapiens_RNAseq

description: Library name: 42_D


title: subject37_timeD_Homosapiens_RNAseq

description: Library name: 37_D

value: female


title: DPTIP, brain, 7 dpi, R8


title: DPTIP, brain, 7 dpi, R7


title: DG_HC_rep5

description:
Library name: DG_HC_rep5
bulk RNA-seq


title: DPTIP, brain, 7 dpi, R1


title: MEFs, ImP for 1h, F34

description: Library name: F34_Directional_NEBNext_S34

value: ImP  for 1h


title: subject41_timeD_Homosapiens_RNAseq

description: Library name: 41_D


title: subject40_timeD_Homosapiens_RNAseq

description: Library name: 40_D


title: MEFs, Unstimulated, F29

description: Library name: F29_Directional_NEBNext_S29


title: DPTIP, brain, 7 dpi, R4

value: WT


title: DPTIP, brain, 7 dpi, R5


title: subject36_timeD_Homosapiens_RNAseq

description: Library name: 36_D


title: DG_HC_rep1

description:
Library name: DG_HC_rep1
bulk RNA-seq


title: subject39_timeD_Homosapiens_RNAseq

description: Library name: 39_D


title: Mock, brain, 7 dpi, R4

value: Mock


title: DPTIP, brain, 7 dpi, R3


title: DG_HC_rep2

description:
Library name: DG_HC_rep2
bulk RNA-seq

value: hippocampus


title: MEFs, ImP for 2h, F31

description: Library name: F31_Directional_NEBNext_S31

value: ImP for 2h


title: CA3_24h_EE_rep4

description:
Library name: CA3_24h_EE_rep4
bulk RNA-seq

value: 30 min NE + 23.5 h HC


title: CA3_24h_EE_rep3

description:
Library name: CA3_24h_EE_rep3
bulk RNA-seq


title: subject35_timeD_Homosapiens_RNAseq

description: Library name: 35_D


title: MEFs, ImP for 1h, F30

description: Library name: F30_Directional_NEBNext_S30


title: Mock, brain, 7 dpi, R3

value: Brain


title: MEFs, ImP for 1h, F26

description: Library name: F26_Directional_NEBNext_S26


title: DG_HC_rep3

description:
Library name: DG_HC_rep3
bulk RNA-seq


title: BMDMs, ImP for 2h, M22

description: Library name: M22_Directional_NEBNext_S22

source_name: BMDMs

value: BMDMs


title: Mock, brain, 7 dpi, R1


title: CA3_18h_EE_rep4

description:
Library name: CA3_18h_EE_rep4
bulk RNA-seq

value: 30 min NE + 17.5 h HC


title: BMDMs, ImP for 1h, M23

description: Library name: M23_Directional_NEBNext_S23


title: subject33_timeD_Homosapiens_RNAseq

description: Library name: 33_D

value: Whole peripheral blood

value: D


title: CA3_18h_EE_rep3

description:
Library name: CA3_18h_EE_rep3
bulk RNA-seq


title: CA3_24h_EE_rep2

description:
Library name: CA3_24h_EE_rep2
bulk RNA-seq


title: Mock, brain, 7 dpi, R2


title: subject30_timeN_Homosapiens_RNAseq

description: Library name: 30_N

value: male

value: N


title: subject31_timeN_Homosapiens_RNAseq

description: Library name: 31_N


title: Vehicle, brain, 7 dpi, R12

value: Vehicle


title: CA3_18h_EE_rep2

description:
Library name: CA3_18h_EE_rep2
bulk RNA-seq


title: Vehicle, brain, 7 dpi, R10


title: BMDMs, ImP for 2h, M19

description: Library name: M19_Directional_NEBNext_S19


title: subject29_timeN_Homosapiens_RNAseq

description: Library name: 29_N


title: MEFs, ImP for 2h, F27

description: Library name: F27_Directional_NEBNext_S27

value: MEFs


title: subject34_timeD_Homosapiens_RNAseq

description: Library name: 34_D


title: Vehicle, brain, 7 dpi, R9


title: MEFs, Unstimulated, F25

description: Library name: F25_Directional_NEBNext_S25

value: Unstimulated


title: subject32_timeN_Homosapiens_RNAseq

description: Library name: 32_N


title: subject28_timeN_Homosapiens_RNAseq

description: Library name: 28_N


title: CA3_8h_EE_rep4

description:
Library name: CA3_8h_EE_rep4
bulk RNA-seq

value: 30 min NE + 7.5 h HC


title: Vehicle, brain, 7 dpi, R8

value: female


title: BMDMs, ImP for 1h, M18

description: Library name: M18_Directional_NEBNext_S18

value: ImP  for 1h


title: BMDMs, Unstimulated, M17

description: Library name: M17_Directional_NEBNext_S17


title: CA3_18h_EE_rep1

description:
Library name: CA3_18h_EE_rep1
bulk RNA-seq


title: BMDMs, Unstimulated, M21

description: Library name: M21_Directional_NEBNext_S21


title: Vehicle, brain, 7 dpi, R7

value: WT


title: Vehicle, brain, 7 dpi, R6


title: Vehicle, brain, 7 dpi, R11


title: BMDMs, ImP for 1h, M14

description: Library name: M14_Directional_NEBNext_S14


title: CA3_8h_EE_rep3

description:
Library name: CA3_8h_EE_rep3
bulk RNA-seq

value: hippocampus


title: subject27_timeN_Homosapiens_RNAseq

description: Library name: 27_N


title: CA3_8h_EE_rep1

description:
Library name: CA3_8h_EE_rep1
bulk RNA-seq


title: Vehicle, brain, 7 dpi, R5


title: CA3_8h_EE_rep2

description:
Library name: CA3_8h_EE_rep2
bulk RNA-seq


title: subject26_timeN_Homosapiens_RNAseq

description: Library name: 26_N


title: subject25_timeN_Homosapiens_RNAseq

description: Library name: 25_N


title: BMDMs, ImP for 2h, M15

description: Library name: M15_Directional_NEBNext_S15

value: ImP for 2h


title: subject24_timeN_Homosapiens_RNAseq

description: Library name: 24_N


title: BMDMs, Unstimulated, M13

description: Library name: M13_Directional_NEBNext_S13


title: Vehicle, brain, 7 dpi, R4


title: CA3_6h_EE_rep4

description:
Library name: CA3_6h_EE_rep4
bulk RNA-seq

value: 30 min NE + 5.5 h HC


title: subject23_timeN_Homosapiens_RNAseq

description: Library name: 23_N


title: Vehicle, brain, 7 dpi, R3

value: Brain


title: Vehicle, brain, 7 dpi, R2


title: subject22_timeN_Homosapiens_RNAseq

description: Library name: 22_N


title: CA3_6h_EE_rep3

description:
Library name: CA3_6h_EE_rep3
bulk RNA-seq


title: CA3_6h_EE_rep2

description:
Library name: CA3_6h_EE_rep2
bulk RNA-seq


title: subject21_timeN_Homosapiens_RNAseq

description: Library name: 21_N


title: MAECs, ImP  for 1h, E10

description: Library name: E10_LowInput_NEBNext_S10

source_name: MAECs

value: MAECs


title: subject20_timeN_Homosapiens_RNAseq

description: Library name: 20_N


title: CA3_24h_EE_rep1

description:
Library name: CA3_24h_EE_rep1
bulk RNA-seq

value: 30 min NE + 23.5 h HC


title: MAECs, Unstimulated, E9

description: Library name: E9_LowInput_NEBNext_S9


title: MAECs, ImP for 2h, E7

description: Library name: E7_LowInput_NEBNext_S7


title: CA3_4h_EE_rep4

description:
Library name: CA3_4h_EE_rep4
bulk RNA-seq

value: 30 min NE + 3.5 h HC


title: Vehicle, brain, 7 dpi, R1


title: subject19_timeN_Homosapiens_RNAseq

description: Library name: 19_N

value: Whole peripheral blood


title: 10x scRNAseq, Gene Expression

city: Hangzhou

first: Heping

last: Xu

state: Zhejiang

address: 18 Shilongshan Road

country: China

institute: Westlake University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
10x Genomics Cellranger v7.0.0 was used to process fastq files and generate matrix files. Downstream normalization, filtering and clustering were done using Seurat v4.1.1 in R v4.1.3/ Rstudio.
Assembly: mm 10
Supplementary files format and content: Cellranger output expression matrix files and feature barcode setting file packaged in tar.gz

source_name: subdural brain tissues

growth_protocol: primary cells

extract_protocol:
cDNA was extracted using gel beads from 10X Genomics
10x genomics scRNA-seq
HTO hashtags + Gene Expression

treatment_protocol: After the induction of EAE by transferring pathogenic 2D2 Th17 cells, the recipients were ICM-transferred with either WT or Th B cells

value: subdural brain tissues

value: CD45-CD31+ or PDPN+ cells

tag: strain name

value: 8 weeks

tag: gender

value: male

value: Th17 and B cell transfer


title: CA3_6h_EE_rep1

description:
Library name: CA3_6h_EE_rep1
bulk RNA-seq


title: MAECs, ImP for 1h, E6

description: Library name: E6_LowInput_NEBNext_S6


title: CA3_4h_EE_rep2

description:
Library name: CA3_4h_EE_rep2
bulk RNA-seq


title: MAECs, ImP for 2h, E3

description: Library name: E3_LowInput_NEBNext_S3

value: ImP  for 2h


title: subject17_timeN_Homosapiens_RNAseq

description: Library name: 17_N

value: N


title: LPS_8h_H3K4ac_rep2

city: Chuncheon-si, Gangwon-do

first: Jueun

last: Kim

address: 1 Kangwondaehak-gil

country: South Korea

institute: Kangwon National University

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with TruSeq adapter sequences.
Cleaned reads were mapped to reference genome using bowtie v2.4.2 with default parameter
BedGraph files were converted to BigWig files and the resulted bw files were averaged by WiggleTools 1.2 (https://github.com/Ensembl/WiggleTools).
Assembly: GRCm38
Supplementary files format and content: bigwig

source_name: Ascites

growth_protocol: 2×106 RAW264.7 cells were cultured in one well with 2 ml of DMEM containing 10% FBS and 1% penicillin-streptomycin. A total of 6 wells of cells were combined to form one sample.

extract_protocol:
To harvest the samples, 2 μl of DMEM was added to the cells, and formaldehyde was used to cross-link and fix the cells. After 10 minutes of incubation at room temperature, 2.5M glycine was added to quench the formaldehyde.
ChIP-seq libraries were prepared using the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina (NEB, E6240, following the manufacturer’s instructions. 10 ng of ChIPed DNA was used as starting material.

treatment_protocol: After 24 hours of incubation at 37°C in 5% CO2 incubator, 2 μl of LPS (100 μg/ml) was treated to the each well, followed by further incubation.

value: Ascites

value: macrophage

tag: chip antibody

value: acetyl H3K4


title: subject18_timeN_Homosapiens_RNAseq

description: Library name: 18_N


title: LPS_8h_H3K4ac_rep1


title: CA3_4h_EE_rep1

description:
Library name: CA3_4h_EE_rep1
bulk RNA-seq

value: hippocampus


title: MAECs, ImP for 1h, E2

description: Library name: E2_LowInput_NEBNext_S2

value: ImP  for 1h


title: subject16_batch1_timeN_Homosapiens_RNAseq

description: Library name: 16_N_batch1


title: LPS_1h_H3K4ac_rep2


title: subject15_timeN_Homosapiens_RNAseq

description: Library name: 15_N


title: LPS_1h_H3K4ac_rep1


title: CA3_2h_EE_rep3

description:
Library name: CA3_2h_EE_rep3
bulk RNA-seq

value: 30 min NE + 1.5 h HC


title: subject14_timeN_Homosapiens_RNAseq

description: Library name: 14_N


title: 10x scRNAseq, HTO Hashtags

description: 10x Genomics

library_source: other

molecule: other


title: CA3_2h_EE_rep2

description:
Library name: CA3_2h_EE_rep2
bulk RNA-seq


title: DW_H3K4ac_rep1

value: DW


title: CA3_2h_EE_rep1

description:
Library name: CA3_2h_EE_rep1
bulk RNA-seq


title: Mammary Gland, WT FVB, Mouse 49903

city: Detroit

first: Kay-Uwe

last: Wagner

state: MI

address: 421 East Canfield, EL01TM

department: Department of Oncology

institute: Barbara Ann Karmanos Cancer Institute Wayne State University School of Medicine

data_processing:
The 75 or 150 base pair paired-end reads were mapped to the mm10 mouse reference genome with Rsubread (v2.0.0).
Transcript abundance was determined using featureCounts from the Rsubread package. Transcript abundance was estimated in counts per million (cpm).
Assembly: mm10
Supplementary files format and content: csv file includes gene symbols and gene Entrez IDs and corresponding raw counts for each gene.

source_name: Mammary gland

extract_protocol:
Total RNA was extracted from flash-frozen mammary tumors and normal mammary gland tissues using the RNeasy Mini Kit (QIAGEN). The concentration of the RNA was determined on a NanoDrop spectrophotometer, and the integrity of the RNA was validated using gel electrophoresis.
The RNA expression library construction and next-generation sequencing were performed at the Genomics Core Facility at UNMC (NextSeq 500) and Novogene.

value: Mammary gland

value: Wildtype


title: subject13_timeN_Homosapiens_RNAseq

description: Library name: 13_N

value: Whole peripheral blood

value: female


title: Mammary tumor, MtTA Teto-TSG101wt, Mouse 51386, Mammary Gland#2

source_name: Mammary tumor

value: Mammary tumor

value: MtTA Teto-TSG101wt


title: DW_H3K4ac_rep2


title: subject11_timeN_Homosapiens_RNAseq

description: Library name: 11_N


title: subject12_timeN_Homosapiens_RNAseq

description: Library name: 12_N


title: CA3_4h_EE_rep3

description:
Library name: CA3_4h_EE_rep3
bulk RNA-seq

value: 30 min NE + 3.5 h HC


title: LPS_8h_H3K4me3_rep1


title: LPS_8h_H3K4me3_rep2


title: CA3_1.5h_EE_rep3

description:
Library name: CA3_1.5h_EE_rep3
bulk RNA-seq

value: 30 min NE + 1 h HC


title: CA3_1.5h_EE_rep4

description:
Library name: CA3_1.5h_EE_rep4
bulk RNA-seq


title: MAECs, ImP for 2h, E11

description: Library name: E11_LowInput_NEBNext_S11

value: MAECs

value: ImP  for 2h


title: subject10_timeN_Homosapiens_RNAseq

description: Library name: 10_N

value: male

value: N


title: Mammary tumor, MtTA Teto-TSG101wt, Mouse 51360


title: MAECs, Unstimulated, E1

description: Library name: E1_LowInput_NEBNext_S1

value: Unstimulated


title: LPS_1h_H3K4me3_rep2

value: Ascites

value: macrophage


title: CA3_2h_EE_rep4

description:
Library name: CA3_2h_EE_rep4
bulk RNA-seq

value: hippocampus

value: 30 min NE + 1.5 h HC


title: CA3_1.5h_EE_rep2

description:
Library name: CA3_1.5h_EE_rep2
bulk RNA-seq


title: subject9_timeN_Homosapiens_RNAseq

description: Library name: 9_N


title: Mammary tumor, MtTA Teto-TSG101wt, Mouse 51356, Mammary Gland#3


title: LPS_1h_H3K4me3_rep1


title: CA3_1.5h_EE_rep1

description:
Library name: CA3_1.5h_EE_rep1
bulk RNA-seq


title: Mammary tumor, MtTA Teto-TSG101wt, Mouse 51356, Mammary Gland#1


title: DW_H3K4me3_rep2

value: DW


title: MAECs, Unstimulated, E5

description: Library name: E5_LowInput_NEBNext_S5


title: subject7_timeN_Homosapiens_RNAseq

description: Library name: 7_N


title: Mammary tumor, MtTA Teto-TSG101wt, Mouse 51386, Mammary Gland#1


title: subject8_batch1_timeN_Homosapiens_RNAseq

description: Library name: 8_N_batch1


title: Mammary tumor, MtTA Teto-TSG101wt, Mouse 51071


title: DW_H3K4me3_rep1


title: subject6_timeN_Homosapiens_RNAseq

description: Library name: 6_N


title: CA3_1h_EE_rep4

description:
Library name: CA3_1h_EE_rep4
bulk RNA-seq

value: 30 min NE + 30 min HC


title: CA3_1h_EE_rep3

description:
Library name: CA3_1h_EE_rep3
bulk RNA-seq


title: CA3_1h_EE_rep5

description:
Library name: CA3_1h_EE_rep5
bulk RNA-seq


title: Mammary tumor, MtTA Teto-TSG101wt, Mouse 51067, Mammary Gland#3


title: Mammary tumor, MtTA Teto-TSG101wt, Mouse 51386, Mammary Gland#3


title: subject5_timeN_Homosapiens_RNAseq

description: Library name: 5_N

value: Whole peripheral blood


title: Mammary tumor, MtTA Teto-TSG101wt, Mouse 50074


title: subject4_timeN_Homosapiens_RNAseq

description: Library name: 4_N

value: female


title: CA3_1h_EE_rep1

description:
Library name: CA3_1h_EE_rep1
bulk RNA-seq


title: subject3_timeN_Homosapiens_RNAseq

description: Library name: 3_N


title: Mammary tumor, MtTA Teto-TSG101wt, Mouse 51067, Mammary Gland#1

value: Mammary tumor


title: CA3_0.5h_EE_rep4

description:
Library name: CA3_0.5h_EE_rep4
bulk RNA-seq

value: 30 min NE


title: subject2_timeN_Homosapiens_RNAseq

description: Library name: 2_N


title: TSC2-deficient 621-101 exposed to hydrocortisone (2.75uM) + 5% CS-FBS

city: L'Hospitalet del llobregat

first: Miquel Angel

last: Pujana

state: Barcelona

address: Gran via 199, Hospital Duran i Reynals

department: ProCURE

institute: Catalan Institute of Oncology IDIBELL

description:
Library name: 621-101_Hydro
10x Genomics

data_processing:
Data processed with CellRanger (10X Genomics) with
Assembly: GRCh38
Supplementary files format and content: Matrix Market Exchange format (.mtx) file containing the gene expression count matrix, accompanied by tab-separated values (.tsv) files listing gene identifiers/features and cell barcodes. These files are the standard output from the 10x Genomics Cell Ranger pipeline.

growth_protocol: DMEM + 5% charcoal-stripped FBS

extract_protocol:
Total RNA from tumor tissue lines was extracted using the RNeasy kit (Qiagen) and RNA quality was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies).
Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Gene Expression platform, following the manufacturer’s standard protocol.

treatment_protocol: DMEM + 5% charcoal-stripped FBS + hydrocortisone (2.75uM) for 72 hours

value: Hydrocortisone


title: subject1_timeN_Homosapiens_RNAseq

description: Library name: 1_N


title: CA3_0.5h_EE_rep3

description:
Library name: CA3_0.5h_EE_rep3
bulk RNA-seq


title: subject32_timeD_Homosapiens_RNAseq

description: Library name: 32_D

value: D


title: CA3_0.5h_EE_rep2

description:
Library name: CA3_0.5h_EE_rep2
bulk RNA-seq


title: CA3_1h_EE_rep2

description:
Library name: CA3_1h_EE_rep2
bulk RNA-seq


title: MV4-11, Palbociclib, Day 4, replicate 2

city: Marseille

first: Sophie

last: Lopez

address: 27 Bd Lei Roure

institute: INSERM

description: Library name: MV4-11_Palbo_2

data_processing:
Reads were aligned to the Homo sapiens reference genome (hg19) using Bowtie2 (v2.3.4.3) with default parameters.
PCR duplicates were marked and removed using Picard MarkDuplicates (v2.20.2).
Peaks representing high-confidence accessible chromatin regions were identified using MACS2 (sharp mode, -p 0.01).
Read counts within peak regions were quantified using featureCounts (v1.6.4).
BigWig files were generated using the deepTools suite (v3.2.1).
Differential accessibility analysis was performed using DESeq2 (v1.26.0) from the R/Bioconductor suite.
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: MV4-11 cells were maintained in RPMI 1640 medium (Thermo Fisher Scientific) supplemented with 10% heat-inactivated fetal bovine serum (FBS; Eurobio) and 2 mM L-glutamine (Thermo Fisher Scientific) at 37°C in a humidified incubator containing 5% CO2.

extract_protocol:
DNA tagmentation using the ATAC seq Kit (53150, Active Motif) following the manufacturer’s instructions.
Library preparation using the ATAC seq Kit (53150, Active Motif) following the manufacturer’s instructions.

treatment_protocol: MV4-11 cells were treated for 4 days with palbociclib at 0.5µM and/or TCP at 5µM.

value: AML cells

value: FLT3-ITD, MLL-AF4

value: Palbociclib


title: MV4-11, Palbociclib + TCP, Day 4, replicate 1

description: Library name: MV4-11_PalboTCP_1

value: Palbociclib + TCP


title: subject30_timeD_Homosapiens_RNAseq

description: Library name: 30_D

value: male


title: MV4-11, Palbociclib + TCP, Day 4, replicate 2

description: Library name: MV4-11_PalboTCP_2


title: CA3_0.25h_EE_rep3

description:
Library name: CA3_0.25h_EE_rep3
bulk RNA-seq

value: 15 min NE


title: MV4-11, Palbociclib, Day 4, replicate 1

description: Library name: MV4-11_Palbo_1


title: subject31_timeD_Homosapiens_RNAseq

description: Library name: 31_D


title: CA3_0.5h_EE_rep1

description:
Library name: CA3_0.5h_EE_rep1
bulk RNA-seq


title: subject29_timeD_Homosapiens_RNAseq

description: Library name: 29_D


title: CA3_0.25h_EE_rep2

description:
Library name: CA3_0.25h_EE_rep2
bulk RNA-seq


title: MV4-11, TCP, Day 4, replicate 2

description: Library name: MV4-11_TCP_2

value: TCP


title: TSC2-deficient 621-101 basal (5% CS-FBS)

description:
Library name: 621-101_Ctrl
10x Genomics

value: DMSO


title: Calcium-phosphate medium_5.5 mM_donor 2

type: RNA

city: Dresden

first: Claudia

last: Goettsch

state: SA

address: Fetsherstr. 74

institute: TU Dresden Faculty of Medicine Carl Gustav Carus

description: Gene expression data from CaP-calcified human coronary artery smooth muscle cells with 5.5 mM glucose at day 3.

hyb_protocol: Affymetrix GeneChip Hybridization, Wash & Stain Kit , according to the manufacturer's protocol;

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000 controlled by GeneChip Command Console (AGCC) version 4.0 to produce CEL intensity files.

data_processing: The raw data were analyzed by using the Transcriptome Analysis Console software (TAC4.0, ThermoFisher Scientific, USA) with default parameters for gene level expression analysis based on the annotation Hg38 clariom_D_Human.r1.na36.hg38.a1.transcript.csv. SST-RMA was applied for normalization and summarization.

label: biotin

label_protocol: Affymetrix GeneChip WT PLUS Reagent Kit, according to the manufacturer's protocol

growth_protocol: Human coronary artery smooth muscle cells from three independent donors were cultured in control media (DMEM, 10% FBS, 1% penicillin-streptomycin).

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

treatment_protocol: Calcification was induced for 3 days with CaP consisting of control medium supplemented with 1.8 mM CaCl2 and 0.9 mM Na2HPO4/NaH2PO4 to reach a final concentration of 3 mM calcium and 2 mM phosphate.

tag: treament

value: Calcium phosphate medium_5.5 mM glucose 2


title: Calcium-phosphate medium_25 mM_donor 3

description: Gene expression data from CaP-calcified human coronary artery smooth muscle cells with 25 mM glucose at day 3.

source_name: Human coronary artery smooth muscle cells

value: Calcium phosphate medium_25 mM glucose 3


title: subject28_timeD_Homosapiens_RNAseq

description: Library name: 28_D


title: MV4-11, TCP, Day 4, replicate 1

description: Library name: MV4-11_TCP_1

tag: cell type


title: Calcium-phosphate medium_25 mM_donor 1

value: Calcium phosphate medium_25 mM glucose 1


title: Calcium-phosphate medium_5.5 mM_donor 3

value: Calcium phosphate medium_5.5 mM glucose 3


title: Calcium-phosphate medium_5.5 mM_donor 1

value: Calcium phosphate medium_5.5 mM glucose 1


title: CA3_0.25h_EE_rep1

description:
Library name: CA3_0.25h_EE_rep1
bulk RNA-seq

value: hippocampus

tag: genotype


title: Control medium_donor 3

description: Gene expression data from non-calcified human coronary artery smooth muscle cells at day 3 (5.5 mM glucose).

value: Control 3


title: subject27_timeD_Homosapiens_RNAseq

description: Library name: 27_D

value: Whole peripheral blood

value: female


title: Calcium-phosphate medium_0 mM_donor 1

description: Gene expression data from CaP-calcified human coronary artery smooth muscle cells with 0 mM glucose at day 3.

value: Calcium phosphate medium_0 mM glucose 1


title: CA3_0.25h_EE_rep4

description:
Library name: CA3_0.25h_EE_rep4
bulk RNA-seq


title: Calcium-phosphate medium_25 mM_donor 2

value: Calcium phosphate medium_25 mM glucose 2


title: MV4-11, DMSO, Day 4, replicate 2

description: Library name: MV4-11_DMSO_2

value: AML cells

value: FLT3-ITD, MLL-AF4


title: Calcium-phosphate medium_0 mM_donor 3

value: Calcium phosphate medium_0 mM glucose 3


title: subject25_timeD_Homosapiens_RNAseq

description: Library name: 25_D

value: D


title: CA3_HC_rep4

description:
Library name: CA3_HC_rep4
bulk RNA-seq

value: Home cage


title: subject26_timeD_Homosapiens_RNAseq

description: Library name: 26_D


title: Calcium-phosphate medium_0 mM_donor 2

value: Calcium phosphate medium_0 mM glucose 2


title: U118 cells, siRIPK2_3, Day2

city: chongqing

first: Xue

address: 2 Chongwen Road, Nanan District, Chongqing

institute: Chongqing University of Posts and Telecommunications

description:
Library name: Sample 5
Column name in raw_counts_All_Samples.txt: siRIPK2_3

data_processing:
The original sequencing data was evaluated by FastQC and cut by Trimmomatic to obtain relatively accurate and effective data.
HISAT2 was used to compare the valid data of the sample to the reference genome for statistical Mapping information.
RSeQC was used to analyze the redundant sequence and insert fragment distribution according to the comparison results.
Qualimap was adopted to perform homogeneity distribution check and genome structure distribution analysis according to the comparison results.
BEDTools were used for statistical analysis of gene coverage and analysis of chromosome sequencing sequence distribution.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: U118 cells were maintained in DMEM supplemented with 10% fetal bovine serum(FBS) and Penicillin-streptomycin(P/S) in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was extracted using chloroform. 1ug of total RNA was used for the construction of  sequencing libraries.
According to the characteristics of the mRNA containing polyA tail structure, the mRNA in total RNA was first enriched with olig dT, and the purified mRNA was randomly interrupted with divalent cations. The segmented RNA was used as template and random oligonucleotides as primer to synthesize double-stranded cDNA. The purified double-stranded cDNA was added by end repair /dA tail and connected by sequencing splices. The linked products were purified and fragment size sorted to obtain the cDNA fragments of the required size. Then PCR amplification was performed and the PCR products were purified again, and finally a library was sequenced.

value: Human Brain Astroblastoma Cells

value: RIPK2 knockdown


title: MV4-11, DMSO, Day 4, replicate 1

description: Library name: MV4-11_DMSO_1

value: DMSO


title: subject24_timeD_Homosapiens_RNAseq

description: Library name: 24_D


title: CA3_HC_rep3

description:
Library name: CA3_HC_rep3
bulk RNA-seq


title: U118 cells, siRIPK2_4, Day2

description:
Library name: Sample 6
Column name in raw_counts_All_Samples.txt: siRIPK2_4


title: U118 cells, siRIPK2_2, Day2

description:
Library name: Sample 4
Column name in raw_counts_All_Samples.txt: siRIPK2_2


title: MV4-11, Palbociclib + TCP, Day 4 replicat2

description: Library name: MV4-11_PalboTCP_2

data_processing:
RNA-seq reads were aligned to the reference genome using Subread-align (v1.6.4) with default parameters.
Mapped reads were filtered using samtools (v1.9) with --exclude-flags 4.
Gene counts were obtained with featureCounts (v1.6.4).
Differential expression analysis was performed using DESeq2 (v1.26.0).
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes TPM counts for each sample

extract_protocol:
Total RNA was isolated using the RNAeasy kit (74104, Qiagen) following the manufacturer’s instructions.
RNA libraries were prepared using the Illumina Stranded mRNA Prep kit (20040532).

value: Palbociclib + TCP


title: CA3_HC_rep2

description:
Library name: CA3_HC_rep2
bulk RNA-seq


title: MV4-11, Palbociclib, Day 4 replicat2

description: Library name: MV4-11_Palbo_2

value: Palbociclib


title: subject23_timeD_Homosapiens_RNAseq

description: Library name: 23_D

value: male


title: MV4-11, Palbociclib + TCP, Day 4 replicat1

description: Library name: MV4-11_PalboTCP_1


title: subject22_timeD_Homosapiens_RNAseq

description: Library name: 22_D


title: CA3_HC_rep1

description:
Library name: CA3_HC_rep1
bulk RNA-seq

value: hippocampus


title: Control medium_donor 1

value: Control 1


title: U118 cells, siRIPK2_1, Day2

description:
Library name: Sample 3
Column name in raw_counts_All_Samples.txt: siRIPK2_1


title: MV4-11, Palbociclib, Day 4 replicat1

description: Library name: MV4-11_Palbo_1


title: Control medium_donor 2

value: Control 2


title: CA1_24h_EE_rep4

description:
Library name: CA1_24h_EE_rep4
bulk RNA-seq

value: 30 min NE + 23.5 h HC


title: U118 cells, siNC, Day2

description:
Library name: Sample 2
Column name in raw_counts_All_Samples.txt: siNC

value: NC


title: subject21_timeD_Homosapiens_RNAseq

description: Library name: 21_D

value: Whole peripheral blood

value: female


title: CA1_24h_EE_rep3

description:
Library name: CA1_24h_EE_rep3
bulk RNA-seq


title: MV4-11, TCP, Day 4 replicat2

description: Library name: MV4-11_TCP_2

value: AML cells

value: FLT3-ITD, MLL-AF4

value: TCP


title: CA1_24h_EE_rep2

description:
Library name: CA1_24h_EE_rep2
bulk RNA-seq


title: CA1_24h_EE_rep1

description:
Library name: CA1_24h_EE_rep1
bulk RNA-seq


title: MV4-11, TCP, Day 4 replicat1

description: Library name: MV4-11_TCP_1


title: subject19_timeD_Homosapiens_RNAseq

description: Library name: 19_D

value: D


title: CA1_18h_EE_rep3

description:
Library name: CA1_18h_EE_rep3
bulk RNA-seq

value: 30 min NE + 17.5 h HC


title: CA3_HC_rep5

description:
Library name: CA3_HC_rep5
bulk RNA-seq

value: Home cage


title: MV4-11, DMSO, Day 4 replicat2

description: Library name: MV4-11_DMSO_2

value: DMSO


title: subject17_timeD_Homosapiens_RNAseq

description: Library name: 17_D


title: subject20_timeD_Homosapiens_RNAseq

description: Library name: 20_D


title: Patient 6, Palbociclib + TCP, Day 4

description: Library name: Patient_PalboTCP_6

source_name: primary AML cells

growth_protocol: Primary AML cells were cultured in IMDM medium (Thermo Fisher Scientific), supplemented with 20% heat-inactivated FBS (Eurobio), 2 mM L-glutamine (Thermo Fisher Scientific), 100 U/mL Penicillin-Streptomycin (Thermo Fisher Scientific), 100 ng/mL human SCF (300-07, Peprotech), 100 ng/mL human FLT3-L (300-19, Peprotech), 5 ng/mL human IL-3 (200-03, Peprotech), and 10 ng/mL human GM-CSF (Leukine, Berlex) at 37°C in a humidified incubator containing 5% CO2, at a concentration of 0.5-1.106 cells/mL.

treatment_protocol: Primary AML cells were treated for 4 days with palbociclib at 0.5µM and/or TCP at 5µM.

value: primary AML cells

value: Palbociclib + TCP


title: 180-3

city: Yinchuan

first: Wei

last: Zhao

state: Ningxia Huizu Zizhiqu

address: 489 Ningxia University, Xixia district, Yinchuan , China

institute: Ningxia university

description:
Library name: B3_3
A sample of the breast muscle of the 3st chicken at 180 days of age

data_processing:
Reads from all samples were compared to the <study species> reference genome using the HISAT2 tool (https://daehwankimlab.github.Io /hisat2/, version:hisat2-2.2.1). And the mapped reads of each sample were assembled using the StringTie (http://ccb.jhu.edu/software/stringtie/, version: StringTie -2.1.6) tool, and the mapped reads of each sample were merged using the Gffcompare software (http://ccb.jhu.edu/ software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8) to merge all transcriptomes from all samples and reconstruct a comprehensive transcriptome. StringTie and ball package (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and by calculating FPKM (fragments per kilobase per million mapped reads of transcripts) values to calculate mRNA expression abundance.
Assembly: Reads from all samples were compared to the reference genome of Gallus gallus using the HISAT2 (https://daehwankimlab.github.io/hisat2/) package.Ballgown (htt:www.bioconductor.org/packages/ release/bioc/html/ballgown.html) calculates the expression abundance of mRNAs by calculating the expression per kilobase of transcription million mapped reads (FPKM) value.
Supplementary files format and content: FPKM_allsamples.txt

organism: Gallus gallus

source_name: Breast

extract_protocol:
RNA was isolated and purified from total samples using TRizol (thermofisher, USA) according to the manufacturer's protocol, followed by quality control of total RNA concentration and purity using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA) and RNA integrity testing using Bioanalyzer 2100 (Agilent, CA, USA).
Only qualified RNA samples were used for RNA sequencing. 2100 (Agilent, CA, USA) for RNA integrity Transcriptome libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep kit according to the instructions.

value: Breast

value: myoblast

value: primary cell

tag: group

value: slaughtered at 180 days (2.03 ± 0.09 kg)


title: MV4-11, DMSO, Day 4 replicat1

description: Library name: MV4-11_DMSO_1


title: 180-2

description:
Library name: B3_2
A sample of the breast muscle of the 2st chicken at 180 days of age

tag: tissue


title: subject18_timeD_Homosapiens_RNAseq

description: Library name: 18_D

data_processing:
Raw-sequencing reads were cleaned by BGI using SOAPnuke v1.5.2 with the parameters “-l 15 -q 0.2 -n 0.05”.
Reads were aligned to GENCODE’s primary human reference genome vGRCh38.p13 with Hisat2 v2.2.1 using parameters "--dta --sensitive --no-discordant --no-mixed".
Samtools v1.10 was used to sort resulting BAM files, mark duplicates, index BAM files.
StringTie v2.1.5 assembled aligned reads into transcripts and quantified their abundance using GENCODE’s vGRCh38.p13 comprehensive gene annotation.
IsoformAnalyzeR v1.17.4 in R v4.2.1 assigned a known gene to “novel” transcripts based on their genomic coordinates when possible.
For network analysis, ComBat-seq from sva v3.36.0 adjusted raw and filtered transcript counts for batch effects. DESeq2 v1.26.0 applied the variance stabilizing transformation to these adjusted counts.
Assembly: Gencode GRCh38.p13
Supplementary files format and content: csv file includes raw transcript counts for each Sample
Supplementary files format and content: csv file includes batch-effect adjusted and variance stabilizing transformed transcript counts for each Sample

source_name: Whole peripheral blood

extract_protocol:
Two tubes of blood were collected twice 12 hours apart (7:00-9:00 and 19:00-21:00) by venipuncture in either arm. A 3mL TempusTM Blood RNA tube (Applied Biosystems, Foster City, CA) was used to collect stabilized whole blood RNA. RNA was extracted using Tempus Spin RNA Isolation kits, according to manufacturer’s protocol. RNA integrity (≥7.5) and concentration were assessed prior to library preparation, with globin clearance.
Library preparation was performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). RNA was taken to prepare the reaction system. The globin mRNA was removed by using GLOBINclear™ Whole Blood Globin Reduction Kit-Human (Ambion, USA). Then, the globin mRNA removed RNA samples were denatured at suitable temperature to open the secondary structure, and mRNA was enriched by oligo (dT) attached magnetic beads. After reacting at a suitable temperature for a fixed time period, the enriched mRNA was fragmented with fragmentation reaction. Then the first-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Related, the synthesized double strand cDNA was subject to end repairment reaction. After cDNA end repairment, a single ‘A’ nucleotide was added to the 3’ ends of the blunt fragments through a tailing reaction. Then the adaptors were connected to the double stranded cDNA with adaptor ligation reaction. Finally, the library products were amplified through PCR reaction and subjected to quality control. Next, the single-stranded library products were produced via denaturation. The reaction system for circularization was set up to get the single-stranded circularized DNA products. Any single stranded linear DNA molecules will be digested. The final single strand circularized library was amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs were loaded into the patterned nanoarray and sequencing reads of PE 150 bases length were generated on G400 platform (BGI-Shenzhen, China).

tag: age

value: male


title: 180-5

description:
Library name: B3_5
A sample of the breast muscle of the 5st chicken at 180 days of age


title: 180-4

description:
Library name: B3_4
A sample of the breast muscle of the 4st chicken at 180 days of age


title: CA1_18h_EE_rep2

description:
Library name: CA1_18h_EE_rep2
bulk RNA-seq

value: hippocampus


title: Patient 6, Palbociclib, Day 4

description: Library name: Patient_Palbo_6

value: Palbociclib


title: 180-1

description:
Library name: B3_1
A sample of the breast muscle of the 1st chicken at 180 days of age


title: subject16_batch1_timeD_Homosapiens_RNAseq

description: Library name: 16_D_batch1

value: Whole peripheral blood

tag: Sex


title: CA1_18h_EE_rep1

description:
Library name: CA1_18h_EE_rep1
bulk RNA-seq


title: U118 cells, WT, Day2

description:
Library name: Sample 1
Column name in raw_counts_All_Samples.txt: WT

value: Human Brain Astroblastoma Cells

value: WT


title: subject14_timeD_Homosapiens_RNAseq

description: Library name: 14_D

tag: timepoint


title: CA1_8h_EE_rep4

description:
Library name: CA1_8h_EE_rep4
bulk RNA-seq

value: 30 min NE + 7.5 h HC


title: Patient 6, DMSO, Day 4

description: Library name: Patient_DMSO_6


title: CA1_8h_EE_rep3

description:
Library name: CA1_8h_EE_rep3
bulk RNA-seq


title: 126-4

description:
Library name: B2_4
A sample of the breast muscle of the 4st chicken at 126 days of age

tag: batch

value: slaughtered at 126 days (1.68 ± 0.14 kg)


title: subject13_timeD_Homosapiens_RNAseq

description: Library name: 13_D

value: female

value: D

tag: opioids


title: Patient 5, Palbociclib + TCP, Day 4

description: Library name: Patient_PalboTCP_5

tag: treatment


title: subject12_timeD_Homosapiens_RNAseq

description: Library name: 12_D


title: 126-2

description:
Library name: B2_2
A sample of the breast muscle of the 2st chicken at 126 days of age


title: Patient 5, Palbociclib, Day 4

description: Library name: Patient_Palbo_5


title: subject11_timeD_Homosapiens_RNAseq

description: Library name: 11_D


title: CA1_8h_EE_rep1

description:
Library name: CA1_8h_EE_rep1
bulk RNA-seq


title: 126-3

description:
Library name: B2_3
A sample of the breast muscle of the 3st chicken at 126 days of age


title: CA1_8h_EE_rep2

description:
Library name: CA1_8h_EE_rep2
bulk RNA-seq


title: Patient 5, TCP, Day 4

description: Library name: Patient_TCP_5

value: TCP


title: Patient 5, DMSO, Day 4

description: Library name: Patient_DMSO_5

value: primary AML cells

value: DMSO


title: subject9_timeD_Homosapiens_RNAseq

description: Library name: 9_D


title: CA1_6h_EE_rep4

description:
Library name: CA1_6h_EE_rep4
bulk RNA-seq

value: 30 min NE + 5.5 h HC


title: 126-1

description:
Library name: B2_1
A sample of the breast muscle of the 1st chicken at 126 days of age

value: Breast

value: myoblast


title: Patient 4, Palbociclib + TCP, Day 4

description: Library name: Patient_PalboTCP_4

value: Palbociclib + TCP


title: CA1_6h_EE_rep3

description:
Library name: CA1_6h_EE_rep3
bulk RNA-seq


title: 42-4

description:
Library name: B1_4
A sample of the breast muscle of the 4st chicken at 42 days of age

value: primary cell

value: slaughtered at 42 days of age (0.422 ± 0.03 kg)


title: subject15_timeD_Homosapiens_RNAseq

description: Library name: 15_D

value: male


title: Patient 6, TCP, Day 4

description: Library name: Patient_TCP_6


title: 126-5

description:
Library name: B2_5
A sample of the breast muscle of the 5st chicken at 126 days of age


title: Patient 4, Palbociclib, Day 4

description: Library name: Patient_Palbo_4

value: Palbociclib


title: CA1_6h_EE_rep2

description:
Library name: CA1_6h_EE_rep2
bulk RNA-seq

value: hippocampus


title: subject8_batch1_timeD_Homosapiens_RNAseq

description: Library name: 8_D_batch1

value: Whole peripheral blood


title: Patient 4, TCP, Day 4

description: Library name: Patient_TCP_4


title: subject7_timeD_Homosapiens_RNAseq

description: Library name: 7_D


title: CA1_6h_EE_rep1

description:
Library name: CA1_6h_EE_rep1
bulk RNA-seq


title: 42-3

description:
Library name: B1_3
A sample of the breast muscle of the 3st chicken at 42 days of age


title: CA1_4h_EE_rep4

description:
Library name: CA1_4h_EE_rep4
bulk RNA-seq

value: 30 min NE + 3.5 h HC


title: subject6_timeD_Homosapiens_RNAseq

description: Library name: 6_D


title: 42-2

description:
Library name: B1_2
A sample of the breast muscle of the 2st chicken at 42 days of age


title: 42-1

description:
Library name: B1_1
A sample of the breast muscle of the 1st chicken at 42 days of age


title: CA1_4h_EE_rep3

description:
Library name: CA1_4h_EE_rep3
bulk RNA-seq


title: Patient 4, DMSO, Day 4

description: Library name: Patient_DMSO_4


title: subject4_timeD_Homosapiens_RNAseq

description: Library name: 4_D


title: CA1_4h_EE_rep2

description:
Library name: CA1_4h_EE_rep2
bulk RNA-seq


title: Patient 3, Palbociclib + TCP, Day 4

description: Library name: Patient_PalboTCP_3


title: subject5_timeD_Homosapiens_RNAseq

description: Library name: 5_D


title: CA1_4h_EE_rep1

description:
Library name: CA1_4h_EE_rep1
bulk RNA-seq


title: 42-5

description:
Library name: B1_5
A sample of the breast muscle of the 5st chicken at 42 days of age


title: Patient 3, TCP, Day 4

description: Library name: Patient_TCP_3


title: Patient 3, DMSO, Day 4

description: Library name: Patient_DMSO_3


title: CA1_2h_EE_rep4

description:
Library name: CA1_2h_EE_rep4
bulk RNA-seq

value: 30 min NE + 1.5 h HC


title: subject2_timeD_Homosapiens_RNAseq

description: Library name: 2_D

value: female


title: subject10_timeD_Homosapiens_RNAseq

description: Library name: 10_D

value: D


title: subject3_timeD_Homosapiens_RNAseq

description: Library name: 3_D


title: CA1_2h_EE_rep3

description:
Library name: CA1_2h_EE_rep3
bulk RNA-seq


title: subject1_timeD_Homosapiens_RNAseq

description: Library name: 1_D


title: Patient 3, Palbociclib, Day 4

description: Library name: Patient_Palbo_3


title: Patient 2, Palbociclib + TCP, Day 4

description: Library name: Patient_PalboTCP_2


title: Patient 2, Palbociclib, Day 4

description: Library name: Patient_Palbo_2


title: CA1_2h_EE_rep2

description:
Library name: CA1_2h_EE_rep2
bulk RNA-seq


title: mutant, biol rep 3

city: Lund

first: Claes

last: von Wachenfeldt

state: State

address: Sölvegatan 35

department: Department of Biology

country: Sweden

institute: Lund University

data_processing:
CLC Genomics Workbench v 23.0.5
Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomics workbench (parameter - Quality limit: 0.05)
Trimmed sequence reads were mapped to CP020102.1 using CLC genomics workbench (parameters - mismatch cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomics workbench
Assembly: CP020102.1
Supplementary files format and content: tab-delimited text files include feature names, chromosome coordinates, and TPM values

organism: Bacillus subtilis

growth_protocol: RNA was isolated from Bacillus subtilis colony biofilms grown on LAGM plates for 24 hours at 30°C

extract_protocol:
RNA was isolated using RNeasy Mini Kit (QIAGEN)
SsTS RNA.NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. Library preparation (mRNA fragmentation, strand-specific cDNA synthesis) done by Eurofins Genomics (Germany)

value: {delta}dnaK {delta}tig


title: CA1_2h_EE_rep1

description:
Library name: CA1_2h_EE_rep1
bulk RNA-seq

data_processing:
bulk RNA-seq: Illumina adapters were trimmed with Cutadapt (version 1.14) and aligned using Hisat252 (version 2.1.0) to the Mus musculus genome (GRCm39) and transcriptome (Ensembl). Aligned BAM files were sorted using Picard Tools (version 2.8.0). Reads were quantified over annotated exons using FeatureCounts (Subread version 2.0.6). Lowly expressed genes were filtered for counts per million >1 in at least five samples using edgeR (version 4.0.16).
snMultiome-seq: Raw sequencing data were processed using Cell Ranger ARC (v2.0.2, 10x Genomics) under default settings. Reads were mapped to mouse mm10 genome, with the GENCODE vm23 GTF file as used in the BICCN atlas.28 We performed unsupervised clustering with RNA UMI counts based on the SCANPY analysis pipeline61 and best practice steps.62,63 In brief, we first filtered for low-quality nuclei by requiring ≥1,000 ATAC fragments and ≥200 genes detected per nuclei and < 5% mitochondria RNA reads. We then performed a first-pass clustering for quality control. Top 3,000 highly variable genes were identified for principal component analysis (PCA). Top 30 PCs were used to perform K-nearest neighbor (k=25) graph-based Leiden clustering (resolution=1). Putative multiplets were predicted using Scrublet64 and Leiden clusters with mean doublets score > 0.2 were marked as doublets. 87-92% cells generated from Cell Ranger ARC for each replicate passed these filtering steps. We then integrated our high-quality cells with hippocampal formation (HPF) cells selected from the whole-mouse brain atlas dataset from BICCN.28 The integration was performed using Seurat's integration methods as previously described.65 We annotated 14 major cell types, and 33 sub-class level cell types based on the integration results as the cell type nomenclature used in this study.
Assembly: bulk RNA-seq: GRCm39; snMultiome-seq: GRCm38
Supplementary files format and content: bulk RNA-seq: one table of raw counts, with each column corresponding to a sample, pre-filtered for lowly expressed genes.
Supplementary files format and content: scMultiome: CellRanger count matrix after alignment, filtering, barcode counting, and UMI counting

extract_protocol:
Mice were deeply anesthetized with isoflurane, decapitated and brains were placed in a stainless-steel brain matrix on ice to cut 1mm sections of anterior to posterior hippocampus. Sections were transferred into ice-cold PBS and Cornu Ammonis (CA)1, CA3 and Dentate Gyrus (DG) separated under a dissection microscope. Tissue was frozen in liquid nitrogen and stored at -80° for further processing and RNA extraction. For bulk RNA-seq,tissue was resuspended in 500 µL TRIzol reagent (Life Technologies), followed by trituration with a 26G needle. RNA was chloroform extracted, an equal volume of 100% ethanol was added, and RNA was purified using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instruction, including the on-column DNase digest.  For single-nuclei multiomic-sequencing whole hippocampi were dissected on an ice-cold metal block and immediately processed for nuclei preparation.
For bulk RNA-seq, RNA concentration was assessed by Nanodrop and RNA-seq libraries were prepared from 10 ng of total RNA using the SMARTer Stranded Total RNA-seq Pico Input Mammalian V2 kit (Takara Bio) according to the manufacturer’s instructions. For snMultiom-seq, freshly dissected hippocampi were dissociated, nuclei were prepared then concentrated in 1X nucleus buffer from 10X Genomics.  1µl of nuclei was stained with Trypan Blue (Invitrogen, T10282) and manually counted. In total, 16,000–20,000 nuclei were used for the tagmentation reaction and 10x Chromium controller loading. The DNA and RNA libraries were generated according to the manufacturer’s recommended protocol (https://www.10xgenomics.com/support/single-cell-multiome-atac-plus-gene-expression).


title: mutant, biol rep 2


title: Patient 2, TCP, Day 4

description: Library name: Patient_TCP_2

value: primary AML cells

value: TCP


title: CA1_1.5h_EE_rep4

description:
Library name: CA1_1.5h_EE_rep4
bulk RNA-seq

value: 30 min NE + 1 h HC


title: ZFA wildtype chimeras, IFN-gamma, biological rep5

city: Providence

first: Alexey

middle: V

last: Fedulov

state: Rhode Island

address: 593 Eddy St.

department: RIH / Surgical Research

institute: Alpert Medical School of Brown University

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: RMA extraction with background adjustment, quantile normalization and PLM summarization

label: Affymetrix Stain Cocktail

source_name: wildtype chimeras

label_protocol: Standard Affymetrix

extract_protocol: TRIzol

treatment_protocol: Intra-airway administration of ZFA-demethylases, followed by IFN-gamma.

value: lung epithelial cells

tag: sample group

value: wildtype constructs treated, IFN-stimulated mouse


title: ZFA wildtype chimeras, IFN-gamma, biological rep6


title: mutant, biol rep 1


title: ZFA wildtype chimeras, IFN-gamma, biological rep7


title: CA1_1.5h_EE_rep3

description:
Library name: CA1_1.5h_EE_rep3
bulk RNA-seq

source_name: hippocampus


title: wild-type, biol rep 3

value: wild-type


title: Patient 2, DMSO, Day 4

description: Library name: Patient_DMSO_2

value: DMSO


title: Patient 1, Palbociclib + TCP, Day 4

description: Library name: Patient_PalboTCP_1

value: Palbociclib + TCP


title: CA1_1.5h_EE_rep2

description:
Library name: CA1_1.5h_EE_rep2
bulk RNA-seq


title: CA1_1h_EE_rep5

description:
Library name: CA1_1h_EE_rep5
bulk RNA-seq

value: 30 min NE + 30 min HC


title: Patient 1, Palbociclib, Day 4

description: Library name: Patient_Palbo_1

value: Palbociclib


title: wild-type, biol rep 2


title: Patient 1, DMSO, Day 4

description: Library name: Patient_DMSO_1


title: CA1_1.5h_EE_rep1

description:
Library name: CA1_1.5h_EE_rep1
bulk RNA-seq

value: hippocampus


title: wild-type, biol rep 1


title: CA1_1h_EE_rep3

description:
Library name: CA1_1h_EE_rep3
bulk RNA-seq


title: BlaER1, STATKO, TAKdMRE, SIRE1

city: Paris

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

institute: Institut Pasteur

description: Library name: BlaER1_STATKO_TAKdMRE_SIRE1

data_processing:
Data were processed using c4ctus (https://github.com/NoordermeerLab/c4ctus) using the following primer file: >IFNB1|ttttcaaaccaaccagtcacagcccttttgatc|chr9:21078458-21078757|GATC|Exclude=chr9:21076458-21080757 ttttcaaaccaaccagtc >MRE|ctaagaaagataaaggcaaagagatc|chr9:20970181-20971214|GATC|Exclude=chr9:20968181-20973214 ctaagaaagataaaggca >ICE|TGAGAATAAAATCATACAACGCAGATAATAAGATC|chr9:21095837-21098117|GATC|Exclude=chr9:21093837-21100117 TGAGAATAAAATCATACA
Assembly: hg38
Supplementary files format and content: bedGraph
Library strategy: 4C-Seq

growth_protocol: PreB BlaER1 cells were transdifferentiated as described {Gaidt et.al DOI 10.1007/978-1-4939-7519-8_4}. Briefly, 0,5x106 cells per mL were seeded in 96 well plates in complete RPMI medium supplemented with 10ng/mL hrIL-3 (Peprotech), 10ng/mL hrM-CSF (Peprotech), and 100nM b-estradiol (Sigma).

extract_protocol:
10-15 million cells were collected, washed once with 1X PBS, and cross-linked using freshly prepared 2% formaldehyde solution by tumbling for 10 min at room temperature. The fixation was stopped by adding glycine and immediately transferring the tubes to ice. The cross-linked cells were collected at 300g for 5 min at 4℃ and washed once with 1X PBS. After removing the supernatant, the pellet was snap-freeze in liquid nitrogen and stored at -80°C. Chromatin fixation, cell lysis and 4C-seq procedure were done as described in Miranda et al, Methods in Molecular Biology 2022 using 10-15 million cells per cell experiment. MboI (New England Biolabs) was used as the primary restriction enzyme and NlaIII (New England Biolabs) as the secondary restriction enzyme.
4C-seq sequencing libraries were generated using a 2-step amplification approach with reduced amounts of input, as described in Haarhuis et al, Cell 2017 and Krijger et al, Methods 2020. In the first step, a total of 120ng of 4C material was amplified using the Expand Long Template PCR System (Roche Diagnostics) in 12 reactions in parallel for 12 cycles. All reactions were pooled, followed by clean-up of 1/6th of the material using Agencourt Ampure XP Beads (Beckman Coulter) to remove fragments smaller than 200 bp. In the second step, 20% of the purified PCR products were further amplified in 2 reactions using the Expand Long Template PCR System and universal index adapters for 20 cycles. Amplified 4C-seq libraries were again purified with Agencourt Ampure XP Beads to remove fragments smaller than 200 bp. Quality and size distribution of the PCR libraries was verified by Qubit ds DNA BR kit (Thermo Fisher Scientific) and Tapestation Genomic DNA reagents (Agilent).

treatment_protocol: When indicated, cells were treated with the SUMOi TAK-981 at a final concentration of 100nM, and with 100 ng/mL LPS.

value: STAT1-/- STAT2-/- MRE-/-


title: BlaER1, STATKO, TAKdMRE, MRE

description: Library name: BlaER1_STATKO_TAKdMRE_MRE


title: Patient 1, TCP, Day 4

description: Library name: Patient_TCP_1


title: ZFA wildtype chimeras, IFN-gamma, biological rep4


title: CA1_1h_EE_rep2

first: Erin

address: 200 Longwood Ave, Goldenson 405

institute: Harvard Medical School

description:
Library name: CA1_1h_EE_rep2
bulk RNA-seq


title: ZFA wildtype chimeras, IFN-gamma, biological rep2


title: CA1_1h_EE_rep4

description:
Library name: CA1_1h_EE_rep4
bulk RNA-seq


title: ZFA mutant control, IFN-gamma, biological rep6

source_name: mutant chimeras

value: mutant controls constructs treated, IFN-stimulated mouse


title: CA1_1h_EE_rep1

description:
Library name: CA1_1h_EE_rep1
bulk RNA-seq


title: ZFA wildtype chimeras, IFN-gamma, biological rep1


title: ZFA wildtype chimeras, IFN-gamma, biological rep3


title: ZFA mutant control, IFN-gamma, biological rep7


title: CA1_0.5h_EE_rep3

description:
Library name: CA1_0.5h_EE_rep3
bulk RNA-seq

value: 30 min NE


title: CA1_0.5h_EE_rep4

description:
Library name: CA1_0.5h_EE_rep4
bulk RNA-seq


title: ZFA mutant control, IFN-gamma, biological rep3


title: BlaER1, STATKO, TAK, MRE

description: Library name: BlaER1_STATKO_TAK_MRE

value: STAT1-/- STAT2-/-


title: BlaER1, STATKO, LPS, SIRE1

description: Library name: BlaER1_STATKO_LPS_SIRE1

value: LPS


title: CA1_0.5h_EE_rep2

description:
Library name: CA1_0.5h_EE_rep2
bulk RNA-seq


title: CA1_0.5h_EE_rep1

description:
Library name: CA1_0.5h_EE_rep1
bulk RNA-seq


title: BlaER1, STATKO, TAK, SIRE1

description: Library name: BlaER1_STATKO_TAK_SIRE1


title: BlaER1, STATKO, LPS, MRE

description: Library name: BlaER1_STATKO_LPS_MRE


title: ZFA mutant control, IFN-gamma, biological rep4


title: ZFA mutant control, IFN-gamma, biological rep5


title: CA1_0.25h_EE_rep4

description:
Library name: CA1_0.25h_EE_rep4
bulk RNA-seq

value: 15 min NE


title: ZFA mutant control, IFN-gamma, biological rep2


title: CA1_0.25h_EE_rep2

description:
Library name: CA1_0.25h_EE_rep2
bulk RNA-seq


title: CA1_0.25h_EE_rep3

description:
Library name: CA1_0.25h_EE_rep3
bulk RNA-seq


title: BlaER1, STATKO, DMSO, SIRE1

description: Library name: BlaER1_STATKO_DMSO_SIRE1


title: ZFA negative control, biological rep6

source_name: negative control

value: vehicle treated, unstimulated mouse


title: BlaER1, STATKO, TAK, IFNB1

description: Library name: BlaER1_STATKO_TAK_IFNB1


title: CA1_0.25h_EE_rep1

description:
Library name: CA1_0.25h_EE_rep1
bulk RNA-seq


title: ZFA negative control, biological rep4


title: ZFA mutant control, IFN-gamma, biological rep1


title: BlaER1, STATKO, DMSO, IFNB1

description: Library name: BlaER1_STATKO_DMSO_IFNB1


title: ZFA negative control, biological rep2


title: CA1_HC_rep5

description:
Library name: CA1_HC_rep5
bulk RNA-seq

value: Home cage


title: ZFA negative control, biological rep5


title: ZFA negative control, biological rep7


title: BlaER1, WT, TAK, MRE

description: Library name: BlaER1_WT_TAK_MRE

value: WT


title: BlaER1, STATKO, LPS, IFNB1

description: Library name: BlaER1_STATKO_LPS_IFNB1


title: CA1_HC_rep4

description:
Library name: CA1_HC_rep4
bulk RNA-seq


title: BlaER1, STATKO, DMSO, MRE

description: Library name: BlaER1_STATKO_DMSO_MRE


title: BlaER1, WT, TAK, IFNB1

description: Library name: BlaER1_WT_TAK_IFNB1


title: ZFA negative control, biological rep1

value: lung epithelial cells


title: CA1_HC_rep2

description:
Library name: CA1_HC_rep2
bulk RNA-seq


title: CA1_HC_rep1

description:
Library name: CA1_HC_rep1
bulk RNA-seq


title: BlaER1, WT, DMSO, MRE

description: Library name: BlaER1_WT_DMSO_MRE


title: BlaER1, WT, TAK, SIRE1

description: Library name: BlaER1_WT_TAK_SIRE1


title: CA1_HC_rep3

description:
Library name: CA1_HC_rep3
bulk RNA-seq


title: Heart, CCL4, rep6

city: Hefei

first: He

last: Sun

state: Anhui province

address: No. 678, Furong Road, Shushan District

department: Department of Cardiothoracic Surgery

institute: The Second Affiliated Hospital of Anhui Medical University

data_processing:
PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean data were mapped to the reference genome of mouse from NCBI using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Assembly: GRCm38
Supplementary files format and content: tab-delimited csv files include RPKM values for each Sample

source_name: Heart

extract_protocol:
Total RNAs were extracted from heart of mice using TRIzol Reagent (Invitrogen, cat. NO 15596026）.
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

value: Heart

value: carbon tetrachloride(CCL4)


title: BlaER1, WT, DMSO, IFNB1

description: Library name: BlaER1_WT_DMSO_IFNB1

value: DMSO


title: Heart, CCL4, rep5


title: treat-B-4

city: naning

first: Jingyao

last: Huang

state: Guangxi Autonomous

address: No. 6 Taoyuan Road, Qingxiu District, Nanning City, Guangxi Zhuang Autonomous Region

institute: People´s Hospital of Guangxi Autonomous Region

description: Library name: Sample 12

data_processing:
Quality control (QC) of the library was conducted using the Bioptic Qsep100 Analyzer to ensure the integrity and purity of the library.
Subsequently, the amplified flow cell was subjected to single-end 75-cycle (SE75) sequencing on an Illumina platform by Epibiotek (Guangzhou Epibiotek Co., Ltd., Guangzhou, China) to achieve deep sequencing coverage.
Assembly: hg38
Supplementary files format and content: Processed data files are in txt format, recording the raw count data of tsRNA sequences across different sample groups.

source_name: Ectopic Endometric Tisses (ECs)

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen, USA).
Small RNA library construction was initiated by resolving RNA segments through polyacrylamide gel electrophoresis (PAGE), followed by the precise isolation of a 15- to 45-nucleotide band. Adapters were procured from the QIAseq® miRNA Library Kit (QIAGEN; catalog number 331505) and sequentially ligated to the purified RNA fragments.

value: Ectopic Endometric Tisses (ECs)


title: ZFA negative control, biological rep3


title: Heart, CCL4, rep4


title: dCAS wildtype chimeras, IFN-gamma, biological rep5

treatment_protocol: Intra-airway administration of dCas9-demethylases, followed by IFN-gamma.

value: wildtype constructs treated, IFN-stimulated mouse


title: treat-B-3

description: Library name: Sample 11


title: BlaER1, WT, DMSO, SIRE1

description: Library name: BlaER1_WT_DMSO_SIRE1


title: dCAS wildtype chimeras, IFN-gamma, biological rep6


title: Heart, CCL4, rep3


title: dCAS wildtype chimeras, IFN-gamma, biological rep2


title: dCAS wildtype chimeras, IFN-gamma, biological rep1


title: treat-A-4

description: Library name: Sample 8

source_name: Eutopic Endometric Tisses (EUs)

value: Eutopic Endometric Tisses (EUs)


title: dCAS wildtype chimeras, IFN-gamma, biological rep4


title: dCAS wildtype chimeras, IFN-gamma, biological rep3


title: Heart, Control, rep6

value: control


title: treat-B-1

description: Library name: Sample 9


title: Heart, CCL4, rep1


title: treat-A-2

description: Library name: Sample 6


title: treat-A-3

description: Library name: Sample 7


title: Heart, Control, rep5


title: treat-A-1

description: Library name: Sample 5


title: dCAS mutant control, IFN-gamma, biological rep5


title: dCAS mutant control, IFN-gamma, biological rep4


title: Heart, CCL4, rep2


title: dCAS mutant control, IFN-gamma, biological rep6


title: Heart, Control, rep3


title: Heart, Control, rep4


title: treat-B-2

description: Library name: Sample 10


title: ctrl-4

description: Library name: Sample 4

source_name: Eutopic Endometric Tisses (ENs)

value: Eutopic Endometric Tisses (ENs)


title: dCAS IFN-gamma alone control, biological rep6

source_name: IFN alone control

value: vehicle treated, IFN-stimulated mouse


title: dCAS mutant control, IFN-gamma, biological rep1

value: mutant controls constructs treated, IFN-stimulated mouse


title: Heart, Control, rep1


title: Heart, Control, rep2


title: ctrl-2

description: Library name: Sample 2


title: MYCN_AKT_T_50d_4

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

description: Library name: Sample32

data_processing:
Raw reads were aligned to the mouse reference genome UCSC mm10 (GRCm38) or the human reference genome (GRCh38/hg38) using salmon for quasi-mapping-based transcript quantification. Transcript abundance was reported as transcripts per million (TPM)
Assembly: mm10, hg38
Supplementary files format and content: CSV file includes TPM values from mouse liver tissues
Supplementary files format and content: CSV file includes TPM values from huaman HCC cells

source_name: liver

extract_protocol:
Total RNA was extracted using a FastGene RNA Basic Kit (NIPPON Genetics) and quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific)
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol

value: liver

tag: time point

value: MYCN and myristoylated AKT overexpression


title: ctrl-3

description: Library name: Sample 3


title: ctrl-1

description: Library name: Sample 1


title: MYCN_AKT_early_50d_3

description: Library name: Sample30


title: RNA seq Mouse 10_Allo treated Hypoxia Ischemia whole brain

city: Hempstead

first: Anthony

last: Szema

state: New York

address: 500 Hofstra Blvd,

department: Department of Occupational Medicine, Epidemiology and Prevention,

institute: Donald and Barbara Zucker School of Medicine

description: Library name: 50515_RB_10

data_processing:
Partek Flow genomic suite is used for data processing steps genome assembly and differential gene expression are derived after alignment to mm10.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partekflow genomic suite (parameter- Quality limit: 0.05)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes Normalized gene counts for each Sample

source_name: Neonatoal whole brain

extract_protocol:
RNA was harvested using the RNeasy Mini Plus kit (Qiagen). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads following manufacturer's protocols.

value: Neonatoal whole brain

value: Allopregananolone


title: RNA seq Mouse 9_Allo treated Hypoxia Ischemia whole brain

description: Library name: 50515_RB_9


title: MYCN_AKT_T_50d_3

description: Library name: Sample29


title: RNA seq Mouse 8_Allo treated Hypoxia Ischemia whole brain

description: Library name: 50515_RB_8


title: dCAS mutant control, IFN-gamma, biological rep3


title: MYCN_AKT_early_50d_2

description: Library name: Sample28


title: dCAS IFN-gamma alone control, biological rep3


title: dCAS IFN-gamma alone control, biological rep5


title: dCAS IFN-gamma alone control, biological rep4


title: dCAS mutant control, IFN-gamma, biological rep2