title: NPM1 patient 10, diagnosis sample

description:
Library name: NPM1_10_DX_bulk_RNA_Seq
Counts are in column "P10_DX" in the processed data file


title: NPM1 patient 08, relapse sample

status: Public on May 01 2026

type: SRA

city: Napels

first: Wout

last: Megchelenbrink

address: Vico de Crecchio 7

department: Precision Medicine

country: Italy

institute: University of Campania "Luigi Vanvitelli”

description:
Library name: NPM1_08_RL_bulk_RNA_Seq
Counts are in column "P08_RL" in the processed data file

library_source: transcriptomic

data_processing:
RNA-seq data were quantified using STAR-Fusion, using the Gencode GRCh38 (v37) reference genome, with parameters “--quantMode GeneCounts” and “--twopassMode Basic”. Gene counts were processed in R using DESeq2.
Assembly: GRCh38 (v37)
Supplementary files format and content: BulkRNAseq_STAR_CountTable.tsv contains the STAR-Fusion raw read counts (unnormalized) per gene per sample.

molecule: total RNA

organism: Homo sapiens

source_name: bone marrow mononuclear cells

extract_protocol:
Total RNA was extracted using a RNeasy RNA extraction kit (QIAGEN). A 300 ng/sample of total RNA was used as input for library preparation.
Libraries were prepared using a KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche), following the manufacturer’s instructions.

tag: cell type

value: bone marrow mononuclear cells


title: YN 02m Cor Exp1 33898 20 Cx20

city: South San Francisco

first: Oliver

last: Hahn

state: CA

address: 1170 Veterans Blvd

country: USA

institute: Calico Life Sciences, LLC

description: Unstranded mRNA-seq

data_processing:
Raw sequence reads were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore! (v0.3.7, parameters: --paired --length 25). Trimmed sequences were aligned using STAR (v2.5.3a). Multi-mapped reads were filtered. Data visualization and analysis were performed using SeqMonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), custom RStudio (https://www.rstudio.com/) scripts and the following Bioconductor packages: DESeq2 (Love et al., 2014), topGO (Alexa and Rahnenfuhrer, 2010) and org.Mm.eg.db.
Genome_build: GRCm38
Supplementary_files_format_and_content: OPLCB_counttable.txt: Tab-delimited text file including raw counts for each sample.

organism: Mus musculus

source_name: cortex

extract_protocol:
RNeasy Qiagen RNA isolation from homogenized tissue.
Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT. Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2.

tag: strain

tag: tissue

value: cortex

tag: Sex

value: Male

tag: age

tag: treatment

value: Naive


title: Foxp3-GFP+ Treg, Nfkbid KO, rep4

city: Bar Harbor

first: Dave

last: Serreze

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: Library name: NFKBID_KO_GFP_NA962-NFKBID_KO_GFP_NA950_pool

data_processing:
bowtie2
edgeR
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include expected counts for each sample

molecule: polyA RNA

source_name: Spleen

extract_protocol:
RNeasy Mini Kit
KAPA mRNA HyperPrep Kit

value: Spleen

value: Foxp3-GFP+ Treg

tag: genotype

value: NOD- Nfkbid-KO

tag: batch


title: Foxp3-GFP+ Treg, Nfkbid KO, rep1

description: Library name: NFKBID_KO_GFP_NA941-NFKBID_KO_GFP_NA970_pool


title: YN 02m Cor Exp1 33898 17 Cx17

description: Unstranded mRNA-seq


title: YN 02m Cor Exp1 33898 14 Cx14

description: Unstranded mRNA-seq


title: Foxp3-GFP+ Treg, Nfkbid transgenic, rep6

description: Library name: NFKBID_60A_GFP_NA952

value: NOD-60A Tg+


title: NPM1 patient 09, diagnosis sample

description:
Library name: NPM1_09_DX_bulk_RNA_Seq
Counts are in column "P09_DX" in the processed data file


title: Sfp1, +rapa, H3K9ac, rep2

city: Quebec city

first: Jacques

last: Cote

address: 9 McMahon Street

department: CHU de Québec-Université Laval Research Center

country: Canada

institute: Laval University

library_source: genomic

data_processing:
Raw reads were trimmed using fastp v0.20.1. Trimmed reads were aligned on the Saccharomyces cerevisiae genome (R64-1-1 - sacCer3) using bwa mem v0.7.17 and samtools v1.13. The macs2 v2.2.1 software was used to perform the peak calling and regions were annotated using the ChIPseeker package v1.30.3 in R v4.1.2. Raw signal tracks and normalized tracks (in reads per million, RPM) were produced from mapped reads using deepTool's bamCoverage tool v3.3.0 and bedtools genomecov tool v2.17.0, respectively. Tracks were converted to the bigwig format using bedGraphToBigWig v2.8 and signal tracks were visualized with IGV. For transcription factors, IgG negative control tracks were subtracted from normalized RPM tracks using deepTools 'bigwigCompare'. For histone marks, signal tracks were normalized to histone H3 levels. Cut&Run reads mapping were then divided into promoter groups of genes (RIBI, RIBI-like, RP genes and subcategories) for the generation of heat maps using ComplexHeatmap v2.10.0 and EnrichedHeatmap v1.24.0 packages. Box plots and associated Wilcoxon tests were computed using means of bins per gene and were produced using the ggboxplot and stat_compare_means functions, respectively, with the default settings of the ggpubr v0.5.0 package. Publicly available Htz1 ChIP-seq data in wild-type yeast were obtained from Gene Expression Omnibus (GEO) under accession code GSE54105. Following alignment and peak calling as previously described, intersection of Htz1 genomic regions with Sfp1 peaks was completed using Intervene v0.6.5.
Assembly: sacCer3
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Saccharomyces cerevisiae

extract_protocol:
Cells were fixed with 1% formaldehyde for 20 minutes and quenched by the addition of 125mM glycine for 5 minutes. Sonication was performed to obtain 200-500bp chromatin frangments
KAPA hyperprep kit

tag: cell line

value: SFP1-FRB::KanMX fpr1-delta::HphMX tor1-1::URA3 RPL13A-2-asterisk-FKBP12::TRP1


title: NPM1 patient 09, relapse sample

description:
Library name: NPM1_09_RL_bulk_RNA_Seq
Counts are in column "P09_RL" in the processed data file


title: NPM1 patient 07, relapse sample

description:
Library name: NPM1_07_RL_bulk_RNA_Seq
Counts are in column "P07_RL" in the processed data file


title: Sfp1, -rapa, H3K9ac, rep2


title: Sfp1, +rapa, H3K9ac, rep1


title: YN 02m Cor Exp1 33898 12 Cx12

description: Unstranded mRNA-seq


title: NPM1 patient 08, diagnosis sample

description:
Library name: NPM1_08_DX_bulk_RNA_Seq
Counts are in column "P08_DX" in the processed data file


title: Sfp1, -rapa, H3K9ac, rep1


title: Foxp3-GFP+ Treg, Nfkbid transgenic, rep4

description: Library name: NFKBID_60A_GFP_NA939


title: YN 02m Ceb Exp1 33898 20 Ce20

description: Unstranded mRNA-seq

source_name: cerebellum

value: cerebellum


title: YN 02m Ceb Exp1 33898 17 Ce17

description: Unstranded mRNA-seq


title: Sfp1, +rapa, Htz1, rep2


title: NPM1 patient 07, diagnosis sample

description:
Library name: NPM1_07_DX_bulk_RNA_Seq
Counts are in column "P07_DX" in the processed data file


title: Foxp3-GFP+ Treg, Nfkbid transgenic, rep5

description: Library name: NFKBID_60A_GFP_NA945


title: Foxp3-GFP+ Treg, Nfkbid transgenic, rep3

description: Library name: NFKBID_60A_GFP_NA938


title: NPM1 patient 06, relapse sample

description:
Library name: NPM1_06_RL_bulk_RNA_Seq
Counts are in column "P06_RL" in the processed data file


title: NPM1 patient 06, diagnosis sample

description:
Library name: NPM1_06_DX_bulk_RNA_Seq
Counts are in column "P06_DX" in the processed data file


title: Foxp3-GFP+ Treg, Nfkbid transgenic, rep2

description: Library name: NFKBID_60A_GFP_NA923


title: NPM1 patient 05, relapse sample

description:
Library name: NPM1_05_RL_bulk_RNA_Seq
Counts are in column "P05_RL" in the processed data file


title: Sfp1, -rapa, Htz1, rep2


title: YN 02m Ceb Exp1 33898 14 Ce14

description: Unstranded mRNA-seq


title: Foxp3-GFP+ Treg, Nfkbid transgenic, rep1

description: Library name: NFKBID_60A_GFP_NA922


title: Sfp1, +rapa, Htz1, rep1


title: YN 02m Ceb Exp1 33898 12 Ce12

description: Unstranded mRNA-seq


title: NPM1 patient 05, diagnosis sample

description:
Library name: NPM1_05_DX_bulk_RNA_Seq
Counts are in column "P05_DX" in the processed data file


title: Sfp1, -rapa, Htz1, rep1


title: PBS 22m Hip Exp1 32556 18 Hi18

description: Unstranded mRNA-seq

source_name: hippocampus

value: hippocampus

value: PBS


title: NPM1 patient 04, relapse sample

description:
Library name: NPM1_04_RL_bulk_RNA_Seq
Counts are in column "P04_RL" in the processed data file


title: Sfp1, -rapa, H4K8ac, rep2


title: Aa9_Myc_young

city: La Jolla

first: Kathryn

last: Lande

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute

description:
Library name: Aa-9_S9
Column name in batch1_raw_counts.txt: Aa9_Myc_young (23170772.0 total)

data_processing:
Alignment to GrCM38/mm10 using STAR aligner, tag counting using HOMER.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: whole liver

extract_protocol:
RNA extracted using Trizol-chloroform methodology.
NEB polyA mRNA library prep kits.

value: whole liver

value: young

tag: date of_birth

tag: date of_cull

value: Myc-AAV

value: male


title: Aa8_CyclinD1_old

description:
Library name: Aa-8_S8
Column name in batch1_raw_counts.txt: Aa8_CyclinD1_old (25749247.0 total)

value: old


title: Sfp1, +rapa, H4K8ac, rep2


title: PBS 22m Hip Exp1 32556 15 Hi15

description: Unstranded mRNA-seq


title: NPM1 patient 04, diagnosis sample

description:
Library name: NPM1_04_DX_bulk_RNA_Seq
Counts are in column "P04_DX" in the processed data file

value: bone marrow mononuclear cells


title: PBS 22m Hip Exp1 32381 21 Hi21

description: Unstranded mRNA-seq


title: NPM1 patient 03, relapse sample

description:
Library name: NPM1_03_RL_bulk_RNA_Seq
Counts are in column "P03_RL" in the processed data file


title: Aa6_CyclinD1_young

description:
Library name: Aa-6_S6
Column name in batch1_raw_counts.txt: Aa6_CyclinD1_young (26902584.0 total)


title: Sfp1, +rapa, H4K8ac, rep1


title: Aa5_CyclinD1_young

description:
Library name: Aa-5_S5
Column name in batch1_raw_counts.txt: Aa5_CyclinD1_young (25987286.0 total)


title: PBS 22m Cor Exp1 32556 15 Cx15

description: Unstranded mRNA-seq

value: cortex


title: Aa7_CyclinD1_old

description:
Library name: Aa-7_S7
Column name in batch1_raw_counts.txt: Aa7_CyclinD1_old (27018721.0 total)


title: NPM1 patient 02, relapse sample

description:
Library name: NPM1_02_RL_bulk_RNA_Seq
Counts are in column "P02_RL" in the processed data file


title: PBS 22m Cor Exp1 32381 21 Cx21

description: Unstranded mRNA-seq

value: Male


title: NPM1 patient 03, diagnosis sample

description:
Library name: NPM1_03_DX_bulk_RNA_Seq
Counts are in column "P03_DX" in the processed data file


title: Sfp1, -rapa, H4K8ac, rep1


title: Aa4_mApple_old

description:
Library name: Aa-4_S4
Column name in batch1_raw_counts.txt: Aa4_mApple_old (24817504.0 total)

value: mApple-AAV


title: PBS 22m Ceb Exp1 32556 18 Ce18

description: Unstranded mRNA-seq


title: Sfp1, -rapa, H3, rep2


title: PBS 22m Cor Exp1 32556 18 Cx18

description: Unstranded mRNA-seq


title: Sfp1, +rapa, H3, rep1


title: Aa3_mApple_old

description:
Library name: Aa-3_S3
Column name in batch1_raw_counts.txt: Aa3_mApple_old (25816143.0 total)


title: Aa2_mApple_young

description:
Library name: Aa-2_S2
Column name in batch1_raw_counts.txt: Aa2_mApple_young (21631128.0 total)


title: Sfp1, +rapa, H3, rep2


title: NPM1 patient 02, diagnosis sample

description:
Library name: NPM1_02_DX_bulk_RNA_Seq
Counts are in column "P02_DX" in the processed data file


title: NPM1 patient 01, relapse sample

description:
Library name: NPM1_01_RL_bulk_RNA_Seq
Counts are in column "P01_RL" in the processed data file


title: Aa26_mApple_old

description:
Library name: Aa-26_S26
Column name in batch1_raw_counts.txt: Aa26_mApple_old (21428743.0 total)


title: PBS 22m Ceb Exp1 32381 21 Ce21

description: Unstranded mRNA-seq


title: PBS 18m Hip Exp2 111 71 H71

description: Unstranded mRNA-seq


title: PBS 18m Hip Exp2 111 69 H69

description: Unstranded mRNA-seq


title: Aa24_mApple_young

description:
Library name: Aa-24_S24
Column name in batch1_raw_counts.txt: Aa24_mApple_young (20797749.0 total)


title: NPM1 patient 01, diagnosis sample

description:
Library name: NPM1_01_DX_bulk_RNA_Seq
Counts are in column "P01_DX" in the processed data file


title: Input for HA TOPmentation in SEM cells with MYB endogenously tagged with FKBP12(F36V)

city: Oxford

first: I-Jun

last: Lau

address: Old Rd

department: Botnar Research Centre

country: United Kingdom

institute: University of Oxford

description: Library name: SEM-DMSO-24hr_INPUT

data_processing:
FASTQ fils were quality checked using FastQC version v0.12.1.
Adapter sequences were removed and low quality reads were trimmed using trim_galore version 0.6.10 using the following parameters: --2colour 20.
Reads were aligned to the reference genome hg38 using bowtie2 vbowtie2-align-s version 2.5.1 with with default parameters.
Duplicate reads were removed using Picard MarkDuplicates v3.1.1 with with default parameters
BigWig files were generated using deepTools bamCoverage 3.5.5 with the following parameters: --extendReads -bs 1 --normalizeUsing RPKM --minMappingQuality 10.
Assembly: hg38
Supplementary files format and content: BigWig files were generated using deepTools bamCoverage 3.5.5 with the following parameters: --extendReads -bs 1 --normalizeUsing RPKM --minMappingQuality 10.
Supplementary files format and content: Peak calling and annotation using Homer v4.11

source_name: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation

extract_protocol:
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones and HT-CM) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (TFs). Cells were sonicated to give fragments of 100-300bp followed by IP.
IPed chromatin was tagmented by incubating in 29 µl Tagmentation Buffer (10 mM Tris-HCl pH 8.0, 5 mM MgCl2, 10% dimethylformamide) and adding 1 µl of transposase (Illumina) at 37 ˚C for 10 min. Tagmented DNA was amplified and indexed with NEBNext Ultra II Q5 Master Mix (NEB).

value: DMSO


title: Sfp1, +rapa, Input, rep2


title: Sfp1, -rapa, H3, rep1


title: HA TOPmentation in SEM cells with MYB endogenously tagged with FKBP12(F36V)

description: Library name: SEM-DMSO-24hr_HA

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation

tag: chip antibody

value: CST 3724S


title: MCC in SEM cells with MYB endogenously tagged with FKBP12(F36V) following 24 h dTAG-13 treatment, replicate 3

description: Library name: SEM-MYB-FKBP-dTAG13-24hr_3

data_processing:
MCC analysis was performed using the MCC pipeline (https://github.com/jojdavies/Micro-Capture-C).
Assembly: hg38
Supplementary files format and content: Bigwigs generated as part of MCC pipeline (https://github.com/jojdavies/Micro-Capture-C).

extract_protocol:
Cells were fixed with 2% formaldehyde for 10 min, then quenched with glycine and PBS-washed. After permeabilized with 0.005% digitonin for 15 min, cells were snap frozen. Thawed cells were pelleted and resuspended in reduced-calcium MNase buffer (10 mM Tris-HCl pH7.5, 1 mM CaCl2), then divided into three aliquots. Cells were titrated with different micrococcal nuclease (NEB) concentrations (typically 10-30 Kunitz U in 800 µl) for 1h at 37 ˚C with shaking at 550 rpm. The reaction was stopped by addition of EGTA to 5 mM, with 200 µl removed to assess the digestion. Remaining cells were pelleted and washed with PBS/EGTA, then cell pellets were resuspended in DNA ligase buffer, supplemented with 400 µM dNTPs and 5 mM EDTA, before addition of DNA Polymerase I large (Klenow) fragment (NEB) to 100 U/µl, T4 polynucleotide kinase (NEB) to 200 U/µl and T4 DNA ligase (Thermo Scientific) to 300 U/µl. The reaction was incubated for 2h at 37 ˚C, then for 8h at 20 ˚C, at 550 rpm, then cooled to 4 ˚C overnight. The digested and ligated chromatin was decrosslinked at 65 ˚C in the presence of proteinase K, then DNA was purified using a DNeasy Blood and Tissue Kit (Qiagen). Digestion and ligation was assessed by D1000 TapeStation (Agilent).
The protocol used for the generation of the 3C libraries was similar to other 3C-based methods. Briefly, cells were crosslinked with 2% formaldehyde, quenched with cold glycine, washed in phosphate buffered saline, resuspended in cold lysis buffer and snap frozen to -80. Cells were thawed on ice, pelleted and resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37 °C for 1h at 1400 rpm on a Thermomixer, followed by a further incubation of 1h after the addition of Triton X-100 (final concentration 1.67%). An overnight digestion was performed using DpnII (final concentration 500U/ml; 37 °C / 1400 rpm). The digested chromatin was ligated overnight using T4 DNA HC ligase (final concentration 10U/ml; 16 °C / 1400 rpm). The samples were de-crosslinked overnight with Proteinase K at 65 °C, followed by a 30 min incubation at 37 °C with RNase. A Phenol/Chloroform extraction was performed, followed by an ethanol precipitation and wash. Digestion efficiencies were assessed by gel electrophoresis and RT-PCR, which showed digestion efficiencies higher than 80%. The DNA contents of the DpnII 3C libraries were quantitated using a Qubit fluorometer. 2 ug DNA was adapter ligated using a strategy based on sonication combined with the NEBNext Ultra II DNA Library Prep kit. The quality of the libraries was assessed using the Agilent ScreenTape system. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. 700 ng of the adapter ligated libraries was hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resulting captured library was assessed using the Agilent ScreenTape system. The libraries were sequenced using the Illumina NextSeq (150bp paired end reads) platform.

value: 0.5µM dTAG13 for 24hr


title: MCC in SEM cells with MYB endogenously tagged with FKBP12(F36V) following 24 h dTAG-13 treatment, replicate 2

description: Library name: SEM-MYB-FKBP-dTAG13-24hr_2


title: PBS 18m Hip Exp1 33810 11 Hi11

description: Unstranded mRNA-seq


title: PBS 18m Hip Exp2 111 70 H70

description: Unstranded mRNA-seq


title: MCC in SEM cells with MYB endogenously tagged with FKBP12(F36V), replicate 3

description: Library name: SEM-MYB-FKBP-DMSO-24hr_3


title: Sfp1, -rapa, Input, rep2

value: SFP1-FRB::KanMX fpr1-delta::HphMX tor1-1::URA3 RPL13A-2-asterisk-FKBP12::TRP1


title: PBS 18m Hip Exp2 111 68 H68

description: Unstranded mRNA-seq


title: Sfp1, +rapa, Input, rep1


title: Aa23_Myc_old

description:
Library name: Aa-23_S23
Column name in batch1_raw_counts.txt: Aa23_Myc_old (22959805.0 total)


title: PBS 18m Hip Exp1 33645 5 Hi05

description: Unstranded mRNA-seq


title: Aa20_Myc_young

description:
Library name: Aa-20_S20
Column name in batch1_raw_counts.txt: Aa20_Myc_young (22134586.0 total)


title: Aa21_Myc_young

description:
Library name: Aa-21_S21
Column name in batch1_raw_counts.txt: Aa21_Myc_young (28179705.0 total)


title: MCC in SEM cells with MYB endogenously tagged with FKBP12(F36V), replicate 2

description: Library name: SEM-MYB-FKBP-DMSO-24hr_2


title: PBS 18m Hip Exp1 33645 8 Hi08

description: Unstranded mRNA-seq


title: PBS 18m Hip Exp1 33645 2 Hi02

description: Unstranded mRNA-seq


title: MCC in SEM cells with MYB endogenously tagged with FKBP12(F36V), replicate 1

description: Library name: SEM-MYB-FKBP-DMSO-24hr_1


title: P55-siNTC

city: EDINBURGH

first: Andrew

last: Baker

state: Not applicable

address: 47 Little France Crescent

institute: University of Edinburgh

description: Library name: P55-siNTC

data_processing:
Gene quantification (read count and FPKM) was obtained using RSEM (options: -bowtie2 -paired-end) (36), based on GENCODE annotation (Release 38). For both RNA-sequencing experiments the differential expression was performed utilizing DESeq2 (37)
Assembly: hg38
Supplementary files format and content: GENCODEv38 annotation per gene, Sample FPKM via RSEM, mean/se FPKM per condition, DESeq2 log fold changes and adjusted p values

source_name: Saphenous vein-derived smooth muscle cells

extract_protocol:
RNA sequencing was performed on RNA extracted and DNAse-treated samples using the miRNeasy mini kit (Qiagen) obtained from five biological replicates of either quiescent, non-transfected (0.2% NT), mock-transfected, IL-PDGF-treated, siNTC-transfected, IL1-PDGF-treated, or BHF7-transfected, IL1-PDGF-treated vSMCs
Ribosomal-depleted unstranded libraries were prepared by GENEWIZ, Inc. (South 79 Plainfield, New Jersey, USA) and were sequenced with Illumina HiSeq (paired-end 2x150bp).

treatment_protocol: Transient transfection was performed with Lipofectamine RNAiMax (Invitrogen 13778150, Thermo Fisher Scientific, Massachusetts, USA) following the manufacturers guidelines. 1x105 cells were transfected with siRNA to a final dose of 25nM in 6-well plates in Opti-MEM (Thermo Fisher Scientific, Massachusetts, USA). Six hours post-transfection, cells were quiesced for 48 hours in Dulbecco’s Modified Eagle’s Medium (DMEM) (Gibco, Thermo Fisher Scientific, Massachusetts, USA) supplemented with 50 μg/mL penicillin (Invitrogen, Thermo Fisher Scientific, Massachusetts, USA), 50 μg/mL streptomycin (Invitrogen, Thermo Fisher Scientific, Massachusetts, USA) and 0.2% [v/v] foetal bovine serum (FBS) (Gibco, Thermo Fisher Scientific, Massachusetts, USA)  and then stimulated for a further 48 hours with fresh 0.2% FBS DMEM media containing 10 ng/mL IL1α (R&D Systems 200-LA-010, Minnesota, USA)  and 20 ng/mL PDGF-ββ (R&D Systems 220-BB-010, Minnesota, USA). After 48 hours, cells were washed once with 1xPBS, and cells removed from culture plates by trypsinisation (Gibco, Thermo Fisher Scientific, Massachusetts, USA).

value: siNTC

tag: patient id


title: Aa1_mApple_young

description:
Library name: Aa-1_S1
Column name in batch1_raw_counts.txt: Aa1_mApple_young (21115698.0 total)


title: Sfp1, -rapa, Input, rep1


title: P55-NT

description: Library name: P55-NT

value: Saphenous vein-derived smooth muscle cells

value: NT


title: Aa19_CyclinD1_old

description:
Library name: Aa-19_S19
Column name in batch1_raw_counts.txt: Aa19_CyclinD1_old (25248150.0 total)

value: whole liver


title: IBD patient 4

type: RNA

city: Erlangen

first: Weber

last: Simone

state: Bavaria

address: Ulmenweg 18

department: Medicine

country: Germany

hyb_protocol: following fragmentation, 1.65 µg of Cy3-labeled cRNA were hybridisied for 17h at 65°C on 4x44K Agilent human GE V2 design 26652 arrays . Arrays were washed according to the protocol (One-Color Microarray-based gene expression analysis v.5.5)

scan_protocol: Microarrays were scanned using Agilent G2505C Microarray Scanner. Data were extracted using Feature Extraction Version: FE Version 11.5.1.1 (Agilent Technologies Germany). Data extraction using protocol GE1_1105_Oct12

data_processing: txt. Files derived from feature extraction were imported into Genespring GX 12.5 (Silicon Genetics). Data were log2 transformed followed by normalization to the 75th percentile and adjusted to the median of all samples. Subsequently entities present in all replicates in at least one conditions were selected by filtering and subjected to an One-Way-ANOVA test (p-value </= 0.05) corrected by Bejamini-Hochberg-FDR). Entities differentially expressed mean an at least 2-fold change in expression level in all transgenic lines compared to wild-type Col-0 plants were further analysed.

source_name: Laminar propria mononuclear cell

label_protocol: Cy3-labeled cRNA were prepared according to the agilent protocol from 100ng total RNA using the low Input Quick Amp Labeling Kit, (One-Color Microarray-based gene expression analysis v.5.5)  according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Laminar propria mononuclear cell were isolated from resected gut specimens of IBD or control patients using the lamina propria dissociation kit (Miltenyi Biotec). CD14-positve cells were isolated magnetic bead-based cell separation (Miltenyi Biotec)

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer's protocol

value: Laminar propria mononuclear cell


title: MCC in SEM cells with MYB endogenously tagged with FKBP12(F36V) following 24 h dTAG-13 treatment, replicate 1

description: Library name: SEM-MYB-FKBP-dTAG13-24hr_1


title: Aa18_CyclinD1_young

description:
Library name: Aa-18_S18
Column name in batch1_raw_counts.txt: Aa18_CyclinD1_young (28577494.0 total)

value: young


title: PBS 22m Ceb Exp1 32556 15 Ce15

description: Unstranded mRNA-seq

value: cerebellum

value: PBS


title: IBD patient 3


title: IBD patient 2


title: IBD patient 1


title: Aa22_Myc_old

description:
Library name: Aa-22_S22
Column name in batch1_raw_counts.txt: Aa22_Myc_old (26150521.0 total)

value: old

value: Myc-AAV

value: male


title: PBS 18m Cor Exp1 33645 8 Cx08

description: Unstranded mRNA-seq

value: cortex

value: Male


title: Aa17_CyclinD1_young

description:
Library name: Aa-17_S17
Column name in batch1_raw_counts.txt: Aa17_CyclinD1_young (26723161.0 total)


title: control 4


title: P55-Mock

description: Library name: P55-Mock

value: Mock


title: P55-BHF7

description: Library name: P55-BHF7


title: PBS 18m Cor Exp1 33645 5 Cx05

description: Unstranded mRNA-seq


title: Aa27_Myc_old

description:
Library name: Aa-27_S27
Column name in batch1_raw_counts.txt: Aa27_Myc_old (24140973.0 total)


title: PBS 18m Cor Exp1 33645 2 Cx02

description: Unstranded mRNA-seq


title: control 3


title: Aa16_mApple_old

description:
Library name: Aa-16_S16
Column name in batch1_raw_counts.txt: Aa16_mApple_old (21600695.0 total)

value: mApple-AAV


title: PBS 18m Ceb Exp1 33810 11 Ce11

description: Unstranded mRNA-seq


title: P248-siNTC

description: Library name: P248-siNTC


title: P248-NT

description: Library name: P248-NT


title: Aa15_mApple_old

description:
Library name: Aa-15_S15
Column name in batch1_raw_counts.txt: Aa15_mApple_old (22493858.0 total)


title: control 1


title: PBS 18m Ceb Exp1 33645 8 Ce08

description: Unstranded mRNA-seq


title: Aa13_mApple_young

description:
Library name: Aa-13_S13
Column name in batch1_raw_counts.txt: Aa13_mApple_young (23992372.0 total)


title: Aa14_mApple_young

description:
Library name: Aa-14_S14
Column name in batch1_raw_counts.txt: Aa14_mApple_young (19252504.0 total)


title: IL-1b/IL-36g stimulated, plus inhibitor, patient 4

source_name: resected gut

growth_protocol: Primary human intestinal fibroblasts were isolated from resected gut specimen of IDB patients. Intestinal tissue was washed in Hanks' Balanced Salt Solution (Gibco) supplemented with 0.5 M EDTA (Invitrogen), 0,1 M EGTA (Carl Roth) and 10 % fetal calf serum (Sigma Aldrich) and then digested with DNase I (1,000 U/mL), collagenase D (0.1 U/mL), and Dispase II (1.5 U/mL). Enzymes were obtained from Roche. Adherent cells were cultivated in Dulbecco’s modified Eagle medium F-12 (Sigma-Aldrich) containing 10 % fetal calf serum (Sigma-Aldrich), 2.5 % HEPES (Gibco), and 1 % penicillin/streptomycin (Gibco).

treatment_protocol: Fibroblast were seeded for 24 h in 10 % FCS containing medium. Afterwards cells were stimulated with IL-1β (10 ng/ml R&D System) and IL-36γ (100 ng/ml R&D System) and left untreated or treated with NLRP3 inhibitor (10 µM) for 9 days in serum free medium.

value: plus inhibitor

value: fibroblasts


title: PBS 18m Ceb Exp1 33645 2 Ce02

description: Unstranded mRNA-seq


title: P248-BHF7

description: Library name: P248-BHF7


title: Aa12_Myc_old

description:
Library name: Aa-12_S12
Column name in batch1_raw_counts.txt: Aa12_Myc_old (26713119.0 total)


title: PBS 18m Ceb Exp1 33645 5 Ce05

description: Unstranded mRNA-seq


title: OPL 22m Hip Exp1 32381 22 Hi22

description: Unstranded mRNA-seq

value: hippocampus

value: OPL


title: P235-siNTC

description: Library name: P235-siNTC

value: Saphenous vein-derived smooth muscle cells

value: siNTC


title: Aa11_Myc_old

description:
Library name: Aa-11_S11
Column name in batch1_raw_counts.txt: Aa11_Myc_old (18117029.0 total)

value: whole liver


title: P248-Mock

description: Library name: P248-Mock


title: Aa10_Myc_young

description:
Library name: Aa-10_S10
Column name in batch1_raw_counts.txt: Aa10_Myc_young (25601292.0 total)

value: young


title: P235-NT

description: Library name: P235-NT

value: NT


title: IL-1b/IL-36g stimulated, plus inhibitor, patient 3


title: IL-1b/IL-36g stimulated, no inhibitor, patient 4

value: no inhibitor


title: OPL 22m Hip Exp1 32381 19 Hi19

description: Unstranded mRNA-seq


title: P235-Mock

description: Library name: P235-Mock


title: Calvarium, LMO

city: Melbourne

first: Lucas

last: Tobar

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Library name: Calvarium_Barcoding
Lipid-modified oligonucleotide (LMO)
calvarium_GEX_LMO_raw_feature_bc_matrix.h5

library_source: other

data_processing:
Demultiplexed data was processed using the Celranger count pipeline
Assembly: mm10
Supplementary files format and content: CellRanger output files: raw_feature_bc_matrix.h5
Supplementary files format and content: feature_reference.csv

molecule: other

source_name: Calvarium

extract_protocol:
CD45+ and CD45- cells sorted from brain, dura, and calvarium. Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10X Controller with a Chromium Single Cell 5' GEM Library and Gel Bead kit (Peter MacCallum Cancer Centre - Molecular Genomics Core).
The hashing protocol described by Stockius et al was used to generate a hashtag/lipid-modified oligo (HTO/LMO) library and a 5' gene expression library.

value: Calvarium


title: control 2

value: Laminar propria mononuclear cell


title: Dura stromal, LMO

description:
Library name: Dura_CD45-_Barcoding
Lipid-modified oligonucleotide (LMO)
dura_cd45_neg_GEX_LMO_raw_feature_bc_matrix.h5

source_name: Dura

value: Dura


title: IL-1b/IL-36g stimulated, no inhibitor, patient 3


title: P235-BHF7

description: Library name: P235-BHF7


title: OPL 22m Hip Exp1 32381 16 Hi16

description: Unstranded mRNA-seq


title: IL-1b/IL-36g stimulated, no inhibitor, patient 2


title: IL-1b/IL-36g stimulated, plus inhibitor, patient 2


title: P219-NT

description: Library name: P219-NT


title: OPL 22m Cor Exp1 32381 22 Cx22

description: Unstranded mRNA-seq

value: cortex


title: Brain stromal, LMO [Multi-seq]

description:
Library name: Brain_CD45-_Barcoding_LMO
Hashtag-derived oligonucleotide (HTO) and Lipid-modified oligonucleotide (LMO)
brain_cd45_neg_LMO_raw_feature_bc_matrix.h5

source_name: Brain

value: Brain


title: OPL 22m Cor Exp1 32381 19 Cx19

description: Unstranded mRNA-seq

value: Male


title: MOR-sired_VTA_BIO REPLICATE 5

city: Philadelphia

first: Dana

last: Zeid

state: PA

address: 1701 North 13th St

institute: Temple University

description: Library name: 37

data_processing:
Adaptors were trimmed from raw sequencing reads using TrimGalore software
Trimmed reads were mapped to the GRCr8 rat genome using Kallisto
Kallisto abundance estimates were imported into R software using the tximport package and analyzed using the DESeq2 package.
Assembly: GRCr8
Supplementary files format and content: tab delimited text files contain scaledTPM kallisto count matrix that includes all samples ("NAC_kallisto_scaledTPM_counts.txt" contains NAC counts; "VTA_kallisto_scaledTPM_counts.txt" contains VTA counts)

organism: Rattus norvegicus

source_name: Brain tissue

extract_protocol:
Brain tissue was dissected from adult (postnatal day 60+) rats: Immediately after euthanasia via decapitation, whole brains were removed and sectioned on a 1mM brain block. Bilateral NAc and VTA punches were quickly micro dissected & flash frozen on dry ice. Total RNA was isolated using a Qiazol/chloroform procedure and purified using the Qiagen RNeasy Micro kit.
Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit per manufacturer instructions

value: Brain tissue

tag: experimental group_(sire_treatment)

value: MOR-sired

tag: brain region

value: ventral tegmental area


title: IL-1b/IL-36g stimulated, plus inhibitor, patient 1

value: plus inhibitor

value: fibroblasts


title: MOR-sired_VTA_BIO REPLICATE 4

description: Library name: 36


title: IL-1b/IL-36g stimulated, no inhibitor, patient 1


title: P219-Mock

description: Library name: P219-Mock

value: Saphenous vein-derived smooth muscle cells

value: Mock


title: P219-siNTC

description: Library name: P219-siNTC

value: siNTC


title: OPL 22m Ceb Exp1 32381 22 Ce22

description: Unstranded mRNA-seq

value: cerebellum

value: OPL


title: SAL-sired_VTA_BIO REPLICATE 5

description: Library name: 34

value: SAL-sired


title: Dura immune, LMO

description:
Library name: Dura_CD45+_Barcoding
Lipid-modified oligonucleotide (LMO)
dura_cd45_pos_GEX_LMO_raw_feature_bc_matrix.h5


title: Brain stromal, HTO [totalseq]

description:
Library name: Brain_CD45-_Barcoding_HTO
Hashtag-derived oligonucleotide (HTO) and Lipid-modified oligonucleotide (LMO)
brain_cd45_neg_HTO_raw_feature_bc_matrix.h5


title: OPL 22m Cor Exp1 32381 16 Cx16

description: Unstranded mRNA-seq


title: PBS 18m Cor Exp1 33810 11 Cx11

description: Unstranded mRNA-seq

value: PBS


title: SAL-sired_VTA_BIO REPLICATE 4

description: Library name: 33


title: Aa25_CyclinD1_young

description:
Library name: Aa-25_S25
Column name in batch1_raw_counts.txt: Aa25_CyclinD1_young (18802075.0 total)

value: whole liver

value: young

value: male


title: P219-BHF7

description: Library name: P219-BHF7


title: Brain immune, LMO [Multi-seq]

description:
Library name: Brain_CD45+_Barcoding_LMO
Hashtag-derived oligonucleotide (HTO) and Lipid-modified oligonucleotide (LMO)
brain_cd45_pos_LMO_raw_feature_bc_matrix.h5

value: Brain


title: SAL-sired_VTA_BIO REPLICATE 3

description: Library name: 29


title: OPL 22m Ceb Exp1 32381 19 Ce19

description: Unstranded mRNA-seq

value: Male


title: P217-siNTC

description: Library name: P217-siNTC


title: Brain immune, HTO [totalseq]

description:
Library name: Brain_CD45+_Barcoding_HTO
Hashtag-derived oligonucleotide (HTO) and Lipid-modified oligonucleotide (LMO)
brain_cd45_pos_HTO_raw_feature_bc_matrix.h5


title: OPL 22m Ceb Exp1 32381 16 Ce16

description: Unstranded mRNA-seq


title: MOR-sired_VTA_BIO REPLICATE 2

description: Library name: 28

value: Brain tissue


title: MOR-sired_VTA_BIO REPLICATE 3

description: Library name: 32

value: MOR-sired


title: Input for H3K27ac ChIP-seq in E14 (TOT2N variant) cells containing stable integration of TetR-MYBTA constuct (control)

description: Library name: TetR-MYB-TA-nodox_Input

data_processing:
FASTQ fils were quality checked using FastQC version v0.12.1.
Adapter sequences were removed and low quality reads were trimmed using trim_galore version 0.6.10 using the following parameters: --2colour 20.
Reads were aligned to the reference genome hg38 using bowtie2 vbowtie2-align-s version 2.5.1 with with default parameters.
Duplicate reads were removed using Picard MarkDuplicates v3.1.1 with with default parameters
BigWig files were generated using deepTools bamCoverage 3.5.5 with the following parameters: --extendReads -bs 1 --normalizeUsing RPKM --minMappingQuality 10.
Assembly: mm10
Supplementary files format and content: BigWig files were generated using deepTools bamCoverage 3.5.5 with the following parameters: --extendReads -bs 1 --normalizeUsing RPKM --minMappingQuality 10.
Supplementary files format and content: Peak calling and annotation using Homer v4.11

source_name: E14 (TOT2N variant) containing stable integration of TetR-MybTA constuct

extract_protocol:
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (TFs). Cells were sonicated to give fragments of 100-300bp followed by IP.
DNA libraries were made using the NEBnext Ultra DNA II library preparation kit for Illumina (Cat no. E7645).


title: P217-Mock

description: Library name: P217-Mock


title: P217-NT

description: Library name: P217-NT

value: NT


title: Input for H3K27ac ChIP-seq in E14 (TOT2N variant) cells with integration of TetR-MYBTA constuct +doxycycline

description: Library name: TetR-MYB-TA-dox_Input

value: E14 (TOT2N variant) containing stable integration of TetR-MybTA constuct

value: Doxycycline 1 µg/ml


title: OPL 18m Hip Exp2 111 76 H76

description: Unstranded mRNA-seq

value: hippocampus


title: Input for H3K27ac ChIP-seq in E14 (TOT2N variant) cells containing stable integration of TetR constuct

description: Library name: TetR_SFX-Input

source_name: E14 (TOT2N variant) containing stable integration of TetR constuct


title: OPL 18m Hip Exp2 111 74 H74

description: Unstranded mRNA-seq


title: SAL-sired_VTA_BIO REPLICATE 1

description: Library name: 25

value: ventral tegmental area


title: Input for FS2 ChIP-seq in E14 (TOT2N variant) cells containing stable integration of TetR-MYBTA constuct

description: Library name: TetR-MYB-TA_DFX-Input


title: MOR-sired_NAC_BIO REPLICATE 7

description: Library name: 14

value: nucleus accumbens


title: Double-Positive4

city: London

first: Rahel

last: Feleke

address: Ducane Road

institute: Imperial College

description: Library name: P88

library_source: transcriptomic single cell

data_processing:
The analysis of FASTQ files commenced with the utilization of Cell Ranger software (version 3.1.0). Reads were mapped against the human reference genome GRCh38, encompassing intronic and exonic regions. Gene annotation was performed using Ensembl (version 93), culminating in generating raw and filtered cell matrices.
Assembly: Genome Reference Consortium Human Build 38
Supplementary files format and content: Cell-Ranger output matrix

molecule: nuclear RNA

source_name: Brain Tissue

extract_protocol:
Nuclei were isolated as previously described (refer to "Method section" for a detailed protocol). Briefly, frozen tissue was homogenized in 500 µl of lysis buffer (Nuclei Pure prep; NUC201-1KT, Sigma) using a disposable Eppendorf tube and incubated on ice for 12 min. The lysate was filtered through a 70 µm filter to remove debris and centrifuged at 500 g for 5 min at 4°C to pellet nuclei. The supernatant was discarded, and nuclei were resuspended in nuclei wash buffer, then filtered through a 40 µm filter. After another centrifugation at 500 g for 5 min, the pelleted nuclei were resuspended in 250 µl of nuclei wash buffer mixed with 250 µl of 50% iodixanol. This mixture was layered onto 500 µl of 29% iodixanol and centrifuged at 5000 g for 20 min at 4°C. For cell counting, 2 µl of acridine orange was added to 18 µl of the sample, analyzed using a Luna Countess to count nuclei, and the suspension was adjusted to the desired concentration for further experiments.
Libraries were prepared using the Chromium Single Cell 3′ Library and Gel Bead v3 kit according to manufacturer’s instructions. cDNA libraries were sequenced using the Illumina NovaSeq 6000 system at a minimum sequencing depth of 30,000 paired-end reads per nucleus.

value: Brain Tissue

value: Excitatory neurons,Astrocytes, Inhibitory neurons,Oligodendrocytes,Oligodendrocyte precursor cells,Microglia, Vascular

value: tauPLA+/ AT8+

value: Batch 1


title: OPL 18m Hip Exp2 111 72 H72

description: Unstranded mRNA-seq

value: OPL


title: Double-Positive3

description: Library name: P68


title: OPL 18m Hip Exp1 33810 10 Hi10

description: Unstranded mRNA-seq


title: Input for FS2 ChIP-seq in E14 (TOT2N variant) cells containing stable integration of TetR constuct

description: Library name: TetR_DFX-Input

value: E14 (TOT2N variant) containing stable integration of TetR constuct


title: OPL 18m Hip Exp1 33810 13 Hi13

description: Unstranded mRNA-seq


title: Double-Positive1

description: Library name: C83


title: Double-Positive2

description: Library name: P110


title: MOR-sired_NAC_BIO REPLICATE 6

description: Library name: 13


title: H3K27ac ChIP-seq in E14 (TOT2N variant) cells containing stable integration of TetR-MYBTA constuct (control)

description: Library name: TetR-MYB-TA-nodox_H3K27ac

value: Diagenode C15410196


title: H3K27ac ChIP-seq in E14 (TOT2N variant) cells containing stable integration of TetR-MYBTA constuct

description: Library name: TetR-MYB-TA2_H3K27ac


title: SAL-sired_NAC_BIO REPLICATE 7

description: Library name: 11

value: SAL-sired


title: OPL 18m Hip Exp2 111 75 H75

description: Unstranded mRNA-seq

value: Male


title: Intermediate5

description: Library name: P7

value: tauPLA+/ AT8-


title: OPL 18m Hip Exp1 33646 7 Hi07

description: Unstranded mRNA-seq


title: H3K27ac ChIP-seq in E14 (TOT2N variant) cells containing stable integration of TetR-MYBTA constuct +doxycycline

description: Library name: TetR-MYB-TA-dox_H3K27ac


title: OPL 18m Hip Exp1 33646 4 Hi04

description: Unstranded mRNA-seq


title: MOR-sired_VTA_BIO REPLICATE 1

description: Library name: 26

value: Brain tissue

value: MOR-sired


title: MOR-sired_NAC_BIO REPLICATE 5

description: Library name: 12


title: P217-BHF7

description: Library name: P217-BHF7

value: Saphenous vein-derived smooth muscle cells


title: Input for H3K27ac ChIP-seq in E14 (TOT2N variant) cells containing stable integration of TetR-MYBTA constuct

description: Library name: TetR-MYB-TA2_SFX-Input

value: E14 (TOT2N variant) containing stable integration of TetR-MybTA constuct


title: H3K27ac ChIP-seq in E14 (TOT2N variant) cells containing stable integration of TetR constuct

description: Library name: TetR_H3K27ac


title: SAL-sired_NAC_BIO REPLICATE 6

description: Library name: 10


title: MOR-sired_NAC_BIO REPLICATE 4

description: Library name: 9


title: Intermediate4

description: Library name: P85


title: SAL-sired_VTA_BIO REPLICATE 2

description: Library name: 27


title: FS2 ChIP-seq in E14 (TOT2N variant) cells containing stable integration of TetR-MYBTA constuct

description: Library name: TetR-MYB-TA_FS2

value: FS2 (TetR), gift of Prof Rob Klose (University of Oxford)


title: OPL 18m Hip Exp1 33646 1 Hi01

description: Unstranded mRNA-seq

value: hippocampus


title: OPL 18m Hip Exp2 111 73 H73

description: Unstranded mRNA-seq


title: Intermediate3

description: Library name: P84


title: FS2 ChIP-seq in E14 (TOT2N variant) cells containing stable integration of TetR constuct

description: Library name: TetR_FS2


title: SAL-sired_NAC_BIO REPLICATE 5

description: Library name: 8

value: nucleus accumbens


title: OPL 18m Cor Exp1 33810 13 Cx13

description: Unstranded mRNA-seq

value: cortex


title: OPL 18m Cor Exp1 33646 4 Cx04

description: Unstranded mRNA-seq


title: Double-Negative6

description: Library name: C46

value: Brain Tissue

value: Excitatory neurons,Astrocytes, Inhibitory neurons,Oligodendrocytes,Oligodendrocyte precursor cells,Microglia, Vascular

value: tauPLA-/ AT8-


title: Intermediate2

description: Library name: P107

value: Batch 1


title: PolyA minus RNA-seq in wild type E14 (TOT2N variant) cells, replicate 3

description: Library name: WT-6

data_processing:
FASTQ fils were quality checked using FastQC version v0.12.1.
Adapter sequences were removed and low quality reads were trimmed using trim_galore version 0.6.10 using the following parameters: --2colour 20.
Reads were aligned to the reference genome hg38 using STAR v2.7.11a with the following parameters: --quantMode TranscriptomeSAM GeneCounts --outSAMunmapped Within --outSAMattributes Standard.
BigWig files were generated using deepTools bamCoverage 3.5.5 with the following parameters: -bs 1 --normalizeUsing CPM.
Strands were separated using the --filterRNAstrand option. Alignments were quantified using featureCounts v2.0.6 with the following parameters: -s 0 -p --countReadPairs -t exon -g gene_id
Assembly: mm10
Supplementary files format and content: Read counts were determined using featureCounts (Subread package)
Supplementary files format and content: Differential gene expression analysis was conducted using edgeR

source_name: E14 (TOT2N variant)

extract_protocol:
RNA was extracted from cells using the RNeasy Mini Kit (Qiagen). PolyA-minus RNA was isolated using the NEBNext Poly(A) mRNA magnetic isolation module (retaining the unbound fraction).
DNA libraries were prepared using the NEB Next Ultra II Directional RNA library preparation kit for Illumina (E7760).

treatment_protocol: see sample table

value: E14 (TOT2N variant)


title: Intermediate1

description: Library name: C87


title: MOR-sired_NAC_BIO REPLICATE 3

description: Library name: 6


title: OPL 18m Cor Exp1 33646 7 Cx07

description: Unstranded mRNA-seq

source_name: cortex

value: OPL


title: SAL-sired_NAC_BIO REPLICATE 4

description: Library name: 7

value: SAL-sired


title: PolyA minus RNA-seq in wild type E14 (TOT2N variant) cells, replicate 1

description: Library name: WT-1


title: Double-Negative5

description: Library name: P5


title: PolyA minus RNA-seq in wild type E14 (TOT2N variant) cells, replicate 2

description: Library name: WT-5


title: MOR-sired_NAC_BIO REPLICATE 1

description: Library name: 4


title: OPL 18m Cor Exp1 33646 1 Cx01

description: Unstranded mRNA-seq

value: Male


title: SAL-sired_NAC_BIO REPLICATE 3

description: Library name: 3


title: PolyA minus RNA-seq in E14 (TOT2N variant) cells containing stable integration of TetR-MYBTA constuct, replicate 3

description: Library name: TetR-MYB-TA-5


title: OPL 18m Ceb Exp1 33810 10 Ce10

description: Unstranded mRNA-seq

value: cerebellum


title: OPL 18m Cor Exp1 33810 10 Cx10

description: Unstranded mRNA-seq


title: Double-Negative3

description: Library name: P1


title: MOR-sired_NAC_BIO REPLICATE 2

description: Library name: 5

value: Brain tissue


title: SAL-sired_NAC_BIO REPLICATE 2

description: Library name: 2


title: OPL 18m Ceb Exp1 33810 13 Ce13

description: Unstranded mRNA-seq


title: Double-Negative4

description: Library name: P39


title: PolyA minus RNA-seq in E14 (TOT2N variant) cells containing stable integration of TetR-MYBTA constuct, replicate 2

description: Library name: TetR-MYB-TA-4


title: PolyA minus RNA-seq in E14 (TOT2N variant) cells containing stable integration of TetR-MYBTA constuct, replicate 1

description: Library name: TetR-MYB-TA-1


title: Double-Positive5

description: Library name: P59

value: tauPLA+/ AT8+


title: OPL 18m Ceb Exp1 33646 7 Ce07

description: Unstranded mRNA-seq


title: SAL-sired_NAC_BIO REPLICATE 1

description: Library name: 1


title: Double-Negative2

description: Library name: C79


title: OPL 18m Ceb Exp1 33646 4 Ce04

description: Unstranded mRNA-seq


title: PolyA minus RNA-seq in E14 (TOT2N variant) cells containing stable integration of TetR constuct, replicate 2

description: Library name: TetR-3

value: E14 (TOT2N variant) containing stable integration of TetR constuct


title: PolyA minus RNA-seq in E14 (TOT2N variant) cells containing stable integration of TetR constuct, replicate 3

description: Library name: TetR-4


title: Double-Negative1

description: Library name: C41


title: OPL 18m Ceb Exp1 33646 1 Ce01

description: Unstranded mRNA-seq


title: primary cortical neurons, NMDA 10min stim 20min recovery, after 4rounds of ETP treatment, rep2, Npas4

city: Dallas

first: Ram

last: Madabhushi

state: TX

address: 5323 Harry Hines Blvd

department: Psychiatry

institute: UT Southwestern Medical Center

description: Library name: Npas4_ETPx4NMDA_2

data_processing:
4Cker mapping was performed using Bowtie2 to a reduced genome consisting of all unique x-nt (nucleotide count differs depending on sequencing run and viewpoint specific primers) regions surrounding DpnII sites from the hg38 or mm10 reference genome allowing for zero mismatches.
To define regions with significant interaction with the viewpoint we used either cisAnalysis (cis) or nearBaitAnalysis (nb) of 4Cker inputting three replicates per sample
Mapping with pipe4C was done with the following parameters: normalization to 1 million reads in cis, non-blind fragments only, window size 21, top 2 read counts removed.
Assembly: mm10 and hg38
Supplementary files format and content: Bigwig files
Library strategy: 4C-Seq

source_name: primary cortical neurons

growth_protocol: Dissociated primary cortical neurons from E16 Swiss-Webster mice were plated at a density of 0.25 million cells/cm2 in 10 cm culture dishes, 6 well plates, or 24 well plates coated beforehand with poly-D-lysine (0.5 mg/ml) overnight at 37°C, followed by washing twice with dH2O. Neurons were maintained for 13 days in neurobasal media (GIBCO) and supplemented with L-glutamine, penicillin/streptomycin (final of 1%), and B27. Human embryonic kidney cells, HEK293, were maintained in Dulbecco’s modified Eagle’s medium (DMEM, high glucocse) supplemented with 10% fetal bovine serum and 5% penicillin/streptomycin.

extract_protocol:
Approximately 10 million primary cortical neurons (DIV13) or Hek 293T cells were cross-linked in 2% formaldehyde for 10 min at room temperature and quenched with glycine (0.13M final concentration). Cells were incubated for 20 min on ice in lysis buffer (50mM Tris-HCl pH 75, 150mM NaCl, 5mM EDTA, 0.5% NP-40, 1% TX-100, and protease inhibitors).
Nuclei were resuspended in 450uL 1.2x CutSmart buffer and permeabilized with 15uL 10% SDS for 1hr and 75uL 20% Triton X-100. A sample of undigested chromatin was collected to assess chromatin integrity. DNA was digested with 100U NlaIII at 37°C for 3hrs while shaking at 750rpm and then an additional 100U of NlaIII was added and incubated overnight. The extent of chromatin digestion was assessed via gel electrophoresis. NlaIII was deactivated for 20 min at 65°C. Chromatin was diluted to 7mL, supplemented with 10X ligation buffer, and 4000U NEB T4 DNA Ligase for overnight ligation at 16°C while shaking. Ligation efficiency was checked by gel electrophoresis. Crosslinks were reversed and proteins digested with proteinase K (30uL of 10mg/ml) overnight at 65°C. DNA was extracted via phenol:chloroform and precipitated with ethanol. DNA was then digested overnight at 37°C with 50U DpnII supplemented with 10X DpnII Buffer while shaking. Second digestion efficiency was determined via gel electrophoresis. DpnII was deactivated at 65°C for 20 min. DNA circularized in a 7mL reaction, supplemented with 10X ligation buffer, and 4000U NEB T4 DNA Ligase overnight at 16°C with shaking. Indexed Illumina sequencing adapters were introduced to ligation fragments of interest with a two-step PCR strategy using Expand Long Template Polymerase starting with 200ng of 4C library template. Viewpoint-specific primers were used to amplify circular templates with the bait of interest. The first round of amplification with the following thermocycler conditions 94°C  for 2 min; 94°C for 10sec, 58° C for 1 min, 68°C for 3 min, for 16 cycles; and 68°C for 5 min. Five different PCR reactions per sample were pooled and 50uL of the pool was used to perform 0.8 x AMPure XP bead purification. 5uL of purified round 1 PCR product was then used for the second round of amplification conducted with the following cycling conditions 94°C for 2 min; 94°C for 10 sec, 60°C for 1 min, 68°C for 3 min for 20 cycles; and 68°C for 5 min. PCR clean up was doing using Qiagen PCR Purification.  DNA fragment size of final, clean PCR products was assessed via Tapestation (Agilent). Library concentrations for each sample was assessed using fluormetry (dsDNA high sensitivity Qubit assay, Thermo) and RT-qPCR (KAPA Biosystems) library quantification.

treatment_protocol: All ETP treatments were conducted with 10mM final concentration, for at most 1hr. NMDA treatments were with 50mM and lasted for 10 min followed by a recovery in conditional neuron media. Serum starvation of the Hek293 cells was done in 0.5% fetal bovine serum for ~16.5hrs and then serum stimulated in 18% fetal bovine serum.

value: primary cortical neurons

tag: bait

value: Npas4 promoter

value: WT Swiss Webster Mice


title: OPLTPBS 19m Hip Exp1 33643 28 Hi28

description: Unstranded mRNA-seq

value: hippocampus

value: OPLTPBS


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct +24h doxycycline, replicate 3, sequencing run 3

description: Library name: 24HR_3-run-3

data_processing:
Capture-C analysis was performed using CapCruncher v0.2.0 (https://doi.org/10.5281/zenodo.6326102).
Assembly: mm10
Supplementary files format and content: Bigwigs generated as part of CapCruncher v0.2.0 (63) (https://doi.org/10.5281/zenodo.6326102).
Library strategy: Capture-C

extract_protocol:
Cells fixed with 2% formaldehyde and lysed on ice
The Capture-C technologies combine 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. Detailed description follows. The protocol used for the generation of the 3C libraries was similar to other 3C-based methods. Briefly, cells were crosslinked with 2% formaldehyde, quenched with cold glycine, washed in phosphate buffered saline, resuspended in cold lysis buffer and snap frozen to -80. Cells were thawed on ice, pelleted and resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37 °C for 1h at 1400 rpm on a Thermomixer, followed by a further incubation of 1h after the addition of Triton X-100 (final concentration 1.67%). An overnight digestion was performed using DpnII (final concentration 500U/ml; 37 °C / 1400 rpm). The digested chromatin was ligated overnight using T4 DNA HC ligase (final concentration 10U/ml; 16 °C / 1400 rpm). The samples were de-crosslinked overnight with Proteinase K at 65 °C, followed by a 30 min incubation at 37 °C with RNase. A Phenol/Chloroform extraction was performed, followed by an ethanol precipitation and wash. Digestion efficiencies were assessed by gel electrophoresis and RT-PCR, which showed digestion efficiencies higher than 80%. The DNA contents of the DpnII 3C libraries were quantitated using a Qubit fluorometer. 2 ug DNA was adapter ligated using a strategy based on sonication combined with the NEBNext Ultra II DNA Library Prep kit. The quality of the libraries was assessed using the Agilent ScreenTape system. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. 700 ng of the adapter ligated libraries was hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resulting captured library was assessed using the Agilent ScreenTape system. The libraries were sequenced using the Illumina NextSeq (150bp paired end reads) platform.

value: E14 (TOT2N variant) containing stable integration of TetR-MybTA constuct

value: Doxycycline 1 µg/ml


title: PolyA minus RNA-seq in E14 (TOT2N variant) cells containing stable integration of TetR constuct, replicate 1

description: Library name: TetR-1


title: primary cortical neurons, NMDA 10min stim 20min recovery, after 4rounds of ETP treatment, rep3, Npas4

description: Library name: Npas4_ETPx4NMDA_3


title: OPLTPBS 19m Hip Exp1 33643 29 Hi29

description: Unstranded mRNA-seq


title: Brown adipose tissue_lunar_2

city: Tokyo

first: Taro

last: Kasai

address: Bunkyoku Hongo7-3-1

country: Japan

institute: The University of Tokyo

description:
Library name: Sample 14
Column name in read_counts.csv: Brown adipose tissue_lunar_2

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 System using 2 × 150 bp paired-end reads. The sequenced reads were aligned to the mouse reference genome (GRCm39/mm39), and gene expression counts along with transcripts per million values were calculated using DRAGEN version 4.3.
Assembly: GRCm39/mm39
Supplementary files format and content: csv files include read counts for each Smaple

source_name: Brown adipose tissue

extract_protocol:
Total RNA was extracted from the Achilles tendons, quadriceps femoris muscles, and brown adipose tissue. These tissues were homogenized using zirconia beads in TRI Reagent (Cosmo Bio, Tokyo, Japan). Total RNA was then extracted using the Direct-zol RNA Kit (Zymo Research, CA, USA) according to the manufacturer’s protocol.
Sequence libraries were prepared using the SMART-Seq mRNA (Takara Bio, Japan) and Nextera XT DNA Library Preparation Kit (Illumina, USA) according to the manufacturer’s protocol.

value: Brown adipose tissue

value: WT


title: Brown adipose tissue_lunar_3

description:
Library name: Sample 15
Column name in read_counts.csv: Brown adipose tissue_lunar_3


title: Brown adipose tissue_earth_3

description:
Library name: Sample 18
Column name in read_counts.csv: Brown adipose tissue_earth_3


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct +24h doxycycline, replicate 1, sequencing run 3

description: Library name: 24HR_1-run-3


title: OPLTPBS 19m Hip Exp1 33643 26 Hi26

description: Unstranded mRNA-seq

source_name: hippocampus


title: OPLTPBS 19m Hip Exp1 33643 24 Hi24

description: Unstranded mRNA-seq


title: Brown adipose tissue_earth_1

description:
Library name: Sample 16
Column name in read_counts.csv: Brown adipose tissue_earth_1


title: primary cortical neurons, 30min after a 5th round of ETP treatment, rep3, Npas4

description: Library name: Npas4_ETPx5_3


title: primary cortical neurons, 30min after a 5th round of ETP treatment, rep2, Npas4

description: Library name: Npas4_ETPx5_2


title: Brown adipose tissue_earth_2

description:
Library name: Sample 17
Column name in read_counts.csv: Brown adipose tissue_earth_2


title: Brown adipose tissue_lunar_1

description:
Library name: Sample 13
Column name in read_counts.csv: Brown adipose tissue_lunar_1


title: primary cortical neurons, 30min after a 5th round of ETP treatment, rep1, Npas4

description: Library name: Npas4_ETPx5_1


title: primary cortical neurons, NMDA 10min stim 20min recovery, after 4rounds of ETP treatment, rep1, Npas4

description: Library name: Npas4_ETPx4NMDA_1


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct +1h doxycycline, replicate 3, sequencing run 3

description: Library name: 1HR_3-run-3


title: primary cortical neurons, 24hrs post 4 rounds of 1hr ETP treatment, rep3, Npas4

description: Library name: Npas4_ETPx4rec_3


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct +24h doxycycline, replicate 2, sequencing run 3

description: Library name: 24HR_2-run-3


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct +1h doxycycline, replicate 2, sequencing run 3

description: Library name: 1HR_2-run-3


title: Quadriceps muscle_earth_3

description:
Library name: Sample 12
Column name in read_counts.csv: Quadriceps muscle_earth_3

source_name: Quadriceps muscle

value: Quadriceps muscle


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct +1h doxycycline, replicate 1, sequencing run 3

description: Library name: 1HR_1-run-3


title: OPLTPBS 19m Cor Exp1 33643 26 Cx26

description: Unstranded mRNA-seq

value: cortex


title: OPLTPBS 19m Cor Exp1 33643 28 Cx28

description: Unstranded mRNA-seq


title: primary cortical neurons, 24hrs post 4 rounds of 1hr ETP treatment, rep2, Npas4

description: Library name: Npas4_ETPx4rec_2


title: Quadriceps muscle_earth_1

description:
Library name: Sample 10
Column name in read_counts.csv: Quadriceps muscle_earth_1


title: primary cortical neurons, 24hrs post 4 rounds of 1hr ETP treatment, rep1 , Npas4

description: Library name: Npas4_ETPx4rec_1


title: Quadriceps muscle_earth_2

description:
Library name: Sample 11
Column name in read_counts.csv: Quadriceps muscle_earth_2


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct, replicate 3, sequencing run 3

description: Library name: TA_3-run-3


title: OPLTPBS 19m Cor Exp1 33643 24 Cx24

description: Unstranded mRNA-seq


title: primary cortical neurons, control, Exp2, rep3, Npas4

description: Library name: Npas4_Control_Exp2_3


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct, replicate 2, sequencing run 3

description: Library name: TA_2-run-3


title: Quadriceps muscle_lunar_3

description:
Library name: Sample 9
Column name in read_counts.csv: Quadriceps muscle_lunar_3


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct, replicate 1, sequencing run 3

description: Library name: TA_1-run-3

source_name: E14 (TOT2N variant) containing stable integration of rTetR-MybTA constuct


title: Quadriceps muscle_lunar_2

description:
Library name: Sample 8
Column name in read_counts.csv: Quadriceps muscle_lunar_2


title: primary cortical neurons, control, Exp2, rep2, Npas4

description: Library name: Npas4_Control_Exp2_2


title: OPLTPBS 19m Ceb Exp1 33643 28 Ce28

description: Unstranded mRNA-seq

source_name: cerebellum


title: primary cortical neurons, control, Exp2, rep1, Npas4

description: Library name: Npas4_Control_Exp2_1


title: OPLTPBS 19m Ceb Exp1 33643 29 Ce29

description: Unstranded mRNA-seq


title: Quadriceps muscle_lunar_1

description:
Library name: Sample 7
Column name in read_counts.csv: Quadriceps muscle_lunar_1


title: Capture-C in E14 (TOT2N variant) cells with rTetR-MybTA construct +30min doxcycline, replicate 3

description: Library name: r30_3

value: E14 (TOT2N variant) containing stable integration of rTetR-MybTA constuct


title: Achilles tendon_earth_2

description:
Library name: Sample 5
Column name in read_counts.csv: Achilles tendon_earth_2

source_name: Achilles tendon

value: Achilles tendon


title: Capture-C in E14 (TOT2N variant) cells  with rTetR-MybTA construct +30min doxcycline, replicate 1

description: Library name: r30_1


title: primary cortical neurons, NMDA 10min stim 20min recovery, after a 24hr rec. period, rep2, Npas4

description: Library name: Npas4_ETPNMDA_2


title: OPLTPBS 19m Cor Exp1 33643 29 Cx29

description: Unstranded mRNA-seq

value: Male


title: primary cortical neurons, NMDA 10min stim 20min recovery, after a 24hr rec. period, rep1, Npas4

description: Library name: Npas4_ETPNMDA_1


title: OPLTOPL 19m Hip Exp1 33642 27 Hi27

description: Unstranded mRNA-seq

value: OPLTOPL


title: OPLTPBS 19m Ceb Exp1 33643 24 Ce24

description: Unstranded mRNA-seq

value: cerebellum


title: Capture-C in E14 (TOT2N variant) cells with rTetR-MybTA construct, replicate 2

description: Library name: rNO_2


title: Achilles tendon_lunar_3

description:
Library name: Sample 3
Column name in read_counts.csv: Achilles tendon_lunar_3


title: OPLTOPL 19m Hip Exp1 33642 25 Hi25

description: Unstranded mRNA-seq


title: OPLTOPL 19m Hip Exp1 33642 23 Hi23

description: Unstranded mRNA-seq


title: Capture-C in E14 (TOT2N variant) cells with rTetR-MybTA construct, replicate 1

description: Library name: rNO_1


title: Achilles tendon_lunar_2

description:
Library name: Sample 2
Column name in read_counts.csv: Achilles tendon_lunar_2


title: OPLTOPL 19m Cor Exp1 33642 27 Cx27

description: Unstranded mRNA-seq


title: primary cortical neurons, 24hrs post 1hr ETP treatment, rep2, Npas4

description: Library name: Npas4_ETP_rec_2


title: Capture-C in E14 (TOT2N variant) cells with rTetR-MybTA construct, replicate 3

description: Library name: rNO_3


title: OPLTOPL 19m Cor Exp1 33642 25 Cx25

description: Unstranded mRNA-seq


title: primary cortical neurons, 24hrs post 1hr ETP treatment, rep1, Npas4

description: Library name: Npas4_ETP_rec_1


title: Achilles tendon_earth_1

description:
Library name: Sample 4
Column name in read_counts.csv: Achilles tendon_earth_1


title: primary cortical neurons, NMDA 10min stim 20min recovery, rep3, Npas4

description: Library name: Npas4_NMDA_3


title: primary cortical neurons, NMDA 10min stim 20min recovery, rep2, Npas4

description: Library name: Npas4_NMDA_2


title: OPLTOPL 19m Cor Exp1 33642 23 Cx23

description: Unstranded mRNA-seq


title: Achilles tendon_lunar_1

description:
Library name: Sample 1
Column name in read_counts.csv: Achilles tendon_lunar_1


title: OPLTOPL 19m Ceb Exp1 33642 27 Ce27

description: Unstranded mRNA-seq


title: Ovary tissue, EMS 4

city: Seoul

first: YunSoo

last: Chung

address: Yonseiro 50-1, Yonsei University College of Medicine

department: OBGY

country: South Korea

institute: Severance Hospital

description: Library name: Sample 18

data_processing:
FastQCvv011.7 and Trimmomatic 0.38 Preprocessed data were mapped to reference genomes by hierarchical indexing for spliced alignment of transcript 2 (HISAT2) version 2.1.0 (Johns Hopkins University, Baltimore, MD, USA), to produce aligned reads.
Assembly: Transcript assembly was carried out using StringTie version 2.1.3b (National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA). The pre-filtered data were then analyzed using DESeq2 (R package, v. 1.36.0).
Supplementary files format and content: Processed data saved as excel file

source_name: Ovary tissue

extract_protocol:
RNA was purified after removal of DNA contamination using DNase and a Ribo-Zero rRNA Removal Kit (Illumina, San Diego, CA, USA).
SureSelectXT RNA Direct For Preparation of Strand-Specific Sequencing for the Illumina Platform Version A0, July 2017

value: Ovary tissue


title: Ovary tissue, EMS 3

description: Library name: Sample 17


title: ATAC-seq in E14 (TOT2N variant) cells containing stable integration of TetR-MYBTA constuct, replicate 3

description: Library name: TetR-MYB-TA-3

data_processing:
FASTQ fils were quality checked using FastQC version v0.12.1.
Adapter sequences were removed and low quality reads were trimmed using trim_galore version 0.6.10 using the following parameters: --2colour 20.
Reads were aligned to the reference genome mm10 using bowtie2 vbowtie2-align-s version 2.5.1 with with default parameters.
Duplicate reads were removed using Picard MarkDuplicates v3.1.1 with with default parameters
BigWig files were generated using deepTools bamCoverage 3.5.5 with the following parameters: --extendReads -bs 1 --normalizeUsing RPKM --minMappingQuality 10.
Assembly: mm10
Supplementary files format and content: BigWig files were generated using deepTools bamCoverage 3.5.5 with the following parameters: --extendReads -bs 1 --normalizeUsing RPKM --minMappingQuality 10.
Supplementary files format and content: Peak calling and annotation using Homer v4.11

extract_protocol:
Cells were washed with cold PBS and lysed in mild lysis buffer as described in Buenrostro el al., 2023(https://doi.org/10.1038/nmeth.2688).
DNA libraries were made using Nextera Tn5 transposase (Illumina) as described in Buenrostro el al., 2023(https://doi.org/10.1038/nmeth.2688).


title: primary cortical neurons, NMDA 10min stim 20min recovery, rep1, Npas4

description: Library name: Npas4_NMDA_1

value: primary cortical neurons


title: OPLTOPL 19m Ceb Exp1 33642 25 Ce25

description: Unstranded mRNA-seq

data_processing:
Raw sequence reads were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore! (v0.3.7, parameters: --paired --length 25). Trimmed sequences were aligned using STAR (v2.5.3a). Multi-mapped reads were filtered. Data visualization and analysis were performed using SeqMonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), custom RStudio (https://www.rstudio.com/) scripts and the following Bioconductor packages: DESeq2 (Love et al., 2014), topGO (Alexa and Rahnenfuhrer, 2010) and org.Mm.eg.db.
Genome_build: GRCm38
Supplementary_files_format_and_content: OPLCB_counttable.txt: Tab-delimited text file including raw counts for each sample.

extract_protocol:
RNeasy Qiagen RNA isolation from homogenized tissue.
Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT. Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2.


title: primary cortical neurons, ETP 30min, rep3, Npas4

description: Library name: Npas4_ETP_3

value: Npas4 promoter


title: OPLTOPL 19m Ceb Exp1 33642 23 Ce23

description: Unstranded mRNA-seq


title: Ovary tissue, EMS 2

description: Library name: Sample 16


title: ATAC-seq in wild type E14 (TOT2N variant) cells, replicate 2

description: Library name: WT-2

value: E14 (TOT2N variant)


title: ATAC-seq in wild type E14 (TOT2N variant) cells, replicate 1

description: Library name: WT-1


title: ON 18m Hip Exp1 33644 9 Hi09

description: Unstranded mRNA-seq

value: hippocampus

value: Naive


title: ATAC-seq in wild type E14 (TOT2N variant) cells, replicate 3

description: Library name: WT-3


title: primary cortical neurons, 24hrs post 1hr ETP treatment, rep3, Npas4

description: Library name: Npas4_ETP_rec_3

value: WT Swiss Webster Mice


title: ATAC-seq in E14 (TOT2N variant) cells containing stable integration of TetR-MYBTA constuct, replicate 2

description: Library name: TetR-MYB-TA-2

value: E14 (TOT2N variant) containing stable integration of TetR-MybTA constuct


title: ATAC-seq in E14 (TOT2N variant) cells containing stable integration of TetR-MYBTA constuct, replicate 1

description: Library name: TetR-MYB-TA-1


title: primary cortical neurons, ETP 30min, rep2, Npas4

description: Library name: Npas4_ETP_2


title: primary cortical neurons, ETP 30min, rep1, Npas4

description: Library name: Npas4_ETP_1


title: Ovary tissue, EMS 1

description: Library name: Sample 15


title: Ovary tissue, OCCC 5

description: Library name: Sample 14


title: ON 18m Hip Exp1 33644 6 Hi06

description: Unstranded mRNA-seq


title: ATAC-seq in E14 (TOT2N variant) cells containing stable integration of TetR constuct, replicate 3

description: Library name: TetR-3

value: E14 (TOT2N variant) containing stable integration of TetR constuct


title: OPLTPBS 19m Ceb Exp1 33643 26 Ce26

description: Unstranded mRNA-seq

value: OPLTPBS


title: Ovary tissue, OCCC 4

description: Library name: Sample 13


title: primary cortical neurons, control, Exp1, rep3, Npas4

description: Library name: Npas4_Control_Exp1_3


title: Ovary tissue, OCCC 3

description: Library name: Sample 12


title: ON 18m Hip Exp1 33644 3 Hi03

description: Unstranded mRNA-seq


title: ATAC-seq in E14 (TOT2N variant) cells containing stable integration of TetR constuct, replicate 2

description: Library name: TetR-2


title: ON 18m Cor Exp1 33644 9 Cx09

description: Unstranded mRNA-seq


title: Ovary tissue, OCCC 2

description: Library name: Sample 11


title: ON 18m Cor Exp1 33644 6 Cx06

description: Unstranded mRNA-seq


title: primary cortical neurons, control, Exp1, rep2, Npas4

description: Library name: Npas4_Control_Exp1_2


title: primary cortical neurons, control, Exp1, rep1, Npas4

description: Library name: Npas4_Control_Exp1_1


title: ON 18m Cor Exp1 33644 3 Cx03

description: Unstranded mRNA-seq


title: primary cortical neurons, NMDA 10min stim 20min recovery, after 4rounds of ETP treatment, rep3, Fos

description: Library name: Fos_ETPx4NMDA_3

value: Fos promoter


title: Ovary tissue, OCCC 1

description: Library name: Sample 10


title: ATAC-seq in E14 (TOT2N variant) cells containing stable integration of TetR constuct, replicate 1

description: Library name: TetR-1


title: Ovary tissue, OCCC_EMS EMS 5

description: Library name: Sample 9


title: ON 18m Ceb Exp1 33644 9 Ce09

description: Unstranded mRNA-seq


title: Ovary tissue, OCCC_EMS OCCC 4

description: Library name: Sample 8


title: primary cortical neurons, NMDA 10min stim 20min recovery, after 4rounds of ETP treatment, rep1, Fos

description: Library name: Fos_ETPx4NMDA_1


title: Female_3_PFF_Non-injected_W_3

city: Grand Rapids

first: Gerry

last: Coetzee

state: MI

address: 333 Bostwick Ave NE

department: CNS

institute: Van Andel Research Institute

data_processing:
RNA-seq: Trimmed fastq files were aligned to MM10/GRCm38 using STAR v2.7 (Dobin and Gingeras, 2015).
RNA-seq: The resulting gene_id map counts were normalized using edgeR (TMM) and tested for significant differential expression with Limma and Voom, in R (v3.3.1) (Law et al., 2014; Ritchie et al., 2015; Robinson and Oshlack, 2010).
Assembly: GRCm38/MM10
Supplementary files format and content: .xlsx, counts in log2cpm for each gene, statistical significance for muliple comparison tests using LIMMA

extract_protocol:
Neuronal nuclei were isolated from mouse cortex using flow cytometry and filtering for an anti-NeuN antibody.
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboseErase. RNA was sheared to an average of 300 bp . Individually indexed libraries were pooled, and 75-bp single-end sequencing was performed on an Illumina NextSeq 500 sequencer. Base calling was done by Illumina NextSeq Control Software (NCS; v2.0), and the output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq (v1.9.0)
bulk RNA-seq on neuronal nuclei.

value: cortex

value: Female

tag: timepoint (month_post_injection)

tag: injection

value: PFF

tag: hemisphere

value: Non-injected

tag: cage

value: W

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: rna date_isolated

tag: case id

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: notes

value: slightly less than 20 in thawed aliquot

tag: volume to_genomics


title: Female_3_PFF_Injected_W_10

tag: tissue

tag: cell line

tag: Sex

tag: timepoint (month_post_injection)

tag: injection

tag: hemisphere

value: Injected


title: primary cortical neurons, NMDA 10min stim 20min recovery, after 4rounds of ETP treatment, rep2, Fos

description: Library name: Fos_ETPx4NMDA_2

value: primary cortical neurons

tag: bait

tag: genotype


title: primary cortical neurons, 30min after a 5th round of ETP treatment, rep3, Fos

description: Library name: Fos_ETPx5_3


title: Female_3_PFF_Injected_W_3

tag: cage

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: rna date_isolated

tag: case id


title: ON 18m Ceb Exp1 33644 3 Ce03

description: Unstranded mRNA-seq

tag: strain

value: cerebellum

value: Male

tag: age

tag: treatment


title: ON 18m Ceb Exp1 33644 6 Ce06

description: Unstranded mRNA-seq

tag: tissue

tag: Sex


title: Female_3_PFF_Non-injected_W_1

tag: cell line

tag: timepoint (month_post_injection)

tag: injection

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: volume to_genomics


title: Ovary tissue, OCCC_EMS EMS 4

description: Library name: Sample 6

value: Ovary tissue


title: primary cortical neurons, 30min after a 5th round of ETP treatment, rep1, Fos

description: Library name: Fos_ETPx5_1

tag: bait

tag: genotype


title: Omentum, OCCC_EMS OCCC3

description: Library name: Sample 7

source_name: Omentum tissue

value: Omentum tissue


title: primary cortical neurons, 30min after a 5th round of ETP treatment, rep2, Fos

description: Library name: Fos_ETPx5_2

value: WT Swiss Webster Mice


title: Female_3_PFF_Non-injected_W_0

tag: hemisphere

tag: cage

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: rna date_isolated

tag: case id


title: D30-3

city: Shanghai

first: Jiawen

last: Qian

address: 130 Dong'an Road

department: Immunology

country: China

institute: Fudan University

description: orthotopic glioma model, day 30 after tumor innoculation

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
* MT% < 20%;
* Cell Gene Number < 10000;
* Cell Gene Number > 200.
PCA and tSNE/UMAP analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: tumor-bearing brain hemisphere

extract_protocol:
Tumor-bearing hemisphere were harvested, percoll gradient isolation of immune cells were conducted, CD45hi/loCD11b+ cells were sorted by FACS analysis, and RNA was harvested. Chromium Single Cell 3’V3.1 Reagent Kits (10X Genomics, Pleasanton, CA) was used for the construction of sequencing libraries.
RNA libraries were generated by 10xGenomics Single Cell 3' Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: tumor-bearing brain hemisphere

tag: cell type

value: CD45hi/loCD11b+ cells

value: wild type

tag: disease state

value: GL261 glioma

tag: time

value: GL261 glioma day 30


title: primary cortical neurons, 24hrs post 4 rounds of 1hr ETP treatment, rep3, Fos

description: Library name: Fos_ETPx4rec_3

value: Fos promoter


title: Ovary tissue, OCCC_EMS EMS 3

description: Library name: Sample 5


title: Ovary tissue, OCCC_EMS OCCC 2

description: Library name: Sample 4


title: D10-3

description: orthotopic glioma model, day 10 after tumor innoculation

value: GL261 glioma day 10


title: Capture-C in E14 (TOT2N variant) cells with rTetR-MybTA construct +30min doxcycline, replicate 2

description: Library name: r30_2

tag: cell line

value: E14 (TOT2N variant) containing stable integration of rTetR-MybTA constuct

tag: treatment

value: Doxycycline 1 µg/ml


title: primary cortical neurons, 24hrs post 4 rounds of 1hr ETP treatment, rep2, Fos

description: Library name: Fos_ETPx4rec_2

tag: bait

tag: genotype


title: D20-3

description: orthotopic glioma model, day 20 after tumor innoculation

value: GL261 glioma day 20


title: Female_3_PFF_Injected_W_0

value: cortex

tag: Sex

value: Female

tag: timepoint (month_post_injection)

tag: injection

value: PFF

tag: hemisphere

value: Injected

tag: cage

value: W

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: volume to_genomics


title: Female_1_PFF_Non-injected_V_10

tag: tissue

value: Non-injected

value: V

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: rna date_isolated

tag: case id


title: Neural Stem Cells - APLP1-/-

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

institute: German Cancer Research Center

description:
long (150 bp paired-end) reads to capture 3'UTRs
Sample 4

data_processing:
Library strategy: CITE-seq
mapping with bowtie2 to the mm10 genome (local mode, paired)
compressing SAM to BAM (samtools)
sorting the BAM files by region (samtools)
Hash tag oligos (HTOs) very counted by regular expression using custom R scripts for every possible cell barcode.
genes counted with 10X Genomics cellranger for Sample 1 & 2, with custom R scripts for Samples 3 to 4 and with Bioconductor R assays(summarizeOverlaps(mm10_gns, reads,mode="Union")) for samples 7 to 14
immunoprecipitation samples were mapped with bowtie2 (end-to-end alignment)
Genome_build: Mus Musculus (mm 10)
Supplementary_files_format_and_content: gene count tables

source_name: Neural Stem Cells

growth_protocol: Neural stem cells were isolated from the sub-ventricular zone of adult mice

extract_protocol:
10X genomics, oligo(dT) capturing (Hash tag oligos conjugated to anti-MHC1 and anti-CD45; HTO_1: 155803 TotalSeq™-A0302 anti-mouse Hashtag 2 Antibody BioLegend, HTO_2: 155805 TotalSeq™-A0303 anti-mouse Hashtag 3 Antibody BioLegend, HTO_3: 155807 TotalSeq™-A0304 anti-mouse Hashtag 4 Antibody BioLegend)
10X Genomics library preparation

treatment_protocol: cultured NSC were treated either with BMP4 for 3 days or EGF

value: Neural Stem Cells

tag: nsc isolation

value: freshly isolated

tag: treatment

value: no treatment

tag: genotype

tag: sequenced molecule

value: mRNA


title: Ovary tissue, OCCC_EMS EMS 2

description: Library name: Sample 3

value: Ovary tissue


title: Female_3_PFF_Non-injected_W_10

tag: cell line

tag: Sex

tag: timepoint (month_post_injection)

tag: injection

tag: hemisphere

tag: cage

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)


title: Female_1_PFF_Injected_V_10

tag: tissue

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: volume to_genomics


title: primary cortical neurons, 24hrs post 4 rounds of 1hr ETP treatment, rep1 , Fos

description: Library name: Fos_ETPx4rec_1

value: primary cortical neurons

tag: bait

value: Fos promoter

tag: genotype

value: WT Swiss Webster Mice


title: Ovary tissue, OCCC_EMS EMS 1

description: Library name: Sample 2


title: Ovary tissue, OCCC_EMS OCCC 1

description: Library name: Sample 1


title: primary cortical neurons, control, Exp2, rep3, Fos

description: Library name: Fos_Control_Exp2_3


title: Female_3_PFF_Injected_W_1

tag: cell line

tag: Sex

tag: timepoint (month_post_injection)

tag: injection

tag: mg of_tissue

tag: rna date_isolated

tag: case id


title: Female_1_PFF_Non-injected_V_3

tag: tissue

tag: hemisphere

tag: cage

tag: animal

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)


title: B cell progenitor and precursor populations, IkBKO-Young_GEX

city: Los Angeles

first: Yu-Sheng

last: Lin

state: California

address: 611 Charles E. Young Drive East

department: MIMG

institute: University of California, Los Angeles

data_processing:
I1 read: contains the sample index.
R1 read: contains the cell barcode (first 16 nt) and UMI (next 10 nt).
R2 read: contains the RNA sequence.
For the gene expression(GEX) libraries, Novaseq 6000 S2 pair-ended sequencing(2x50) was used and the resulting bcl2 files were demultiplexed and processed by cellranger mkfastq program. Fastq outputs from gene expression libraries were then processed by cellranger count program to determine the gene expression counts based on the high-quality reads mapped to mm10 reference genome.
For the VDH(Immune profiling) libraries, NextSeq 500 High Output pair-ended sequencing(2x150) was used and the resulting bcl2 files were demultiplexed and processed by cellranger mkfastq program to generate the fastq outputs. Fastq outputs from VDJ libraries were then processed by cellranger vdj program to filter low-quality reads and assemble the contigs in immunoglobulin genes.
Genome_build: mm10
Supplementary_files_format_and_content: For the gene expression(GEX) library, the processed data contains the matrix files which were indexed based on the cell barcode and feature lists from the outputs of cellranger count program. The GEX processed data are in tsv and mtx formats compressed to gz files. For the VDJ(Immune profiling) library, the processed data include the mapped contig for immunoglobulin genes and the resulting clonotypes from the outputs of cellranger vdj program. The VDJ(immune profiling) processed data are in csv format.

source_name: Mouse B lymphoid progenitor and precursor populations

growth_protocol: The sample were prepared directly from primary cells isolated from mouse bone marrow without further growth.

extract_protocol:
CD3e-CD8a-CD11b-F4/80-Gr-1-CD49b-B220+IgM-IgD- populations were sorted from pooled, purified, and enriched mouse bone marrow cells from two mice per group . The sorted cells from different genotypes were then subjected to 10X Genomics Single-cell immune-profiling with Chromium Single Cell V(D)J Enrichment Kit workflows for single-cell gene expression and immune profiling library construction.
Library construction is based on the standard protocol in 10X genomics Chromium Single Cell V(D)J Reagent Kits.

treatment_protocol: The sample were prepared directly from primary cells isolated from mouse bone marrow without further treatment.

tag: age

value: 12 weeks old

tag: strain

value: nfkbie-/-nfkbib-/-nfkbia+/-

tag: cell type


title: primary cortical neurons, control, Exp2, rep2, Fos

description: Library name: Fos_Control_Exp2_2

tag: bait

tag: genotype


title: Female_1_PFF_Injected_V_3

value: cortex

tag: cell line

tag: Sex

tag: timepoint (month_post_injection)

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: volume to_genomics


title: primary cortical neurons, NMDA 10min stim 20min recovery, after a 24hr rec. period, rep3, Fos

description: Library name: Fos_ETPNMDA_3

tag: tissue


title: B cell progenitor and precursor populations, WT-Aged_GEX

value: 100 weeks old

value: WT

value: B lymphoid progenitor and precursor populations


title: primary cortical neurons, control, Exp2, rep1, Fos

description: Library name: Fos_Control_Exp2_1


title: U87-MGcell,ZNF25,siRNA ,siZNF25-3

city: Chengdu

first: Xiaohong

middle: Huang

last: Yi

state: Sichuan

address: 1166 Liutai Avenue, Wenjiang District, Chengdu City

department: School of Basic Medical Science

institute: CDUTCM

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < researchspecies > was sequenced run with Illumina NovaseqTM 6000 sequence platform.
Using the Illumina paired-end RNA-seq,approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.
get high quality clean reads, reads were further filtered by Cutadapt,(https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9).including the Q20, Q30 and GC-content of the clean data.
The raw sequence data have been extractd and normolizated.
Assembly: GRCh38
Supplementary files format and content: text file including raw read counts for each sample
Supplementary files format and content: text file including raw fpkm values for each sample

source_name: brain

growth_protocol: lioma cells U87-MG were obtained from ATCC (Manassas, USA). Cell lines were maintained in DMEM medium (Gibco, ThermoFisher, China) supplemented with 100U/ml penicillin-streptomycin (HyCloneTM, Utah, USA) and 10% fetal bovine serum (FBS, ExCell, China), at 37 ℃ in a 5% CO2 incubator.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: ZNF25-siRNA (siZNF25)/NC-siRNA (siNC) and transfection reagent (Dharma FECT1, Dharmacon Reagents, USA)  were mixed and left to stand for 30 minutes. The resulting mixture was then evenly added to the bottom of a 10cm plate, with 7× 105 cells seeded in each plate. After 72 hours of transfection, the total mRNA was extracted and the transfection efficiency of siRNA was measured.

value: brain

value: glioma

value: ZNF25 knockdown

tag: treatment

value: knock-down


title: Female_1_PFF_Injected_V_1

value: Female

tag: injection

value: PFF

tag: hemisphere

value: Injected

tag: cage

value: V

tag: animal

tag: mg of_tissue

tag: rna date_isolated

tag: case id

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)


title: U87-MGcell,ZNF25,siRNA ,siZNF25-1

tag: cell line

tag: cell type

tag: genotype


title: B cell progenitor and precursor populations, WT-Young_GEX

tag: age

tag: strain


title: U87-MGcell,ZNF25,siRNA ,siZNF25-2

tag: tissue


title: Female_1_PFF_Non-injected_V_0

tag: Sex

tag: timepoint (month_post_injection)

value: Non-injected

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: notes

value: note reverse order on non vs. injected

tag: volume to_genomics


title: primary cortical neurons, NMDA 10min stim 20min recovery, after a 24hr rec. period, rep2, Fos

description: Library name: Fos_ETPNMDA_2

value: primary cortical neurons

tag: bait

value: Fos promoter

value: WT Swiss Webster Mice


title: U87-MGcell,ZNF25,siRNA ,NC3

tag: cell line

tag: treatment


title: Female_1_PFF_Non-injected_V_1

value: cortex

tag: injection

tag: hemisphere

tag: cage

tag: animal

tag: mg of_tissue

tag: rna date_isolated

tag: case id

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)


title: primary cortical neurons, NMDA 10min stim 20min recovery, after a 24hr rec. period, rep1, Fos

description: Library name: Fos_ETPNMDA_1

tag: tissue

tag: genotype


title: U87-MGcell,ZNF25,siRNA ,NC1

tag: cell type


title: U87-MGcell,ZNF25,siRNA ,NC2


title: Female_1_PFF_Injected_V_0

tag: Sex

tag: timepoint (month_post_injection)

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: volume to_genomics


title: UACC-257, H3K27ac, replicate 3 (ChIP)

city: Suzhou

first: Gongjie

last: Wu

address: Renai Road

institute: Xi'an Jiaotong-Liverpool University

description: Library name: M20-H3K27ac-3

data_processing:
Bowtie2 aligner (v2.4.2), MACS2 peak caller (v.2.1.1.20160309)
Assembly: GRCh38/hg38
Supplementary files format and content: Bigwig

source_name: Skin

growth_protocol: Melanoma cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, High glucose, Biosharp) supplemented with 10% fetal bovine serum (VivaCell), Penicillin-Streptomycin 100 X solution (Hyclone) in a standard incubator with 5% CO2 at 37°C. Cells were passaged every two to three days by Trypsin-EDTA solution (Sigma-Aldrich) after washing with 1 x PBS.

extract_protocol:
Nuclei were sonicated in a Bioruptor to yield chromatin fragments of ~200-500 bp, as confirmed by agarose gel electrophoresis.
ChIP-seq libraries were prepared and sequenced using single-end 50 bp sequencing (SE50) on the BGISEQ-500 platform (BGI, Wuhan, China).

treatment_protocol: Cells were crosslinked in 1% formaldehyde for 10 min at room temperature, quenched with 125 mM glycine, washed in cold PBS and lysed in a high-salt lysis buffer.

value: Skin

tag: cell line

value: Melanoma


title: UACC-257, H3K27ac, replicate 2 (ChIP)

description: Library name: M20-H3K27ac-2

value: WT


title: UACC-257, H3K27ac, replicate 1 (ChIP)

description: Library name: M20-H3K27ac-1


title: UACC-257, H3K9me3, replicate 3 (ChIP)

description: Library name: M20-H3K9me3-3


title: Female_3_PBS_Non-injected_Q_10

tag: injection

value: PBS

tag: hemisphere

tag: cage

value: Q

tag: animal

tag: mg of_tissue

tag: rna date_isolated

tag: case id


title: primary cortical neurons, 24hrs post 1hr ETP treatment, rep2, Fos

description: Library name: Fos_ETP_rec_2

tag: tissue

tag: bait

tag: genotype


title: Female_3_PBS_Injected_Q_10

tag: Sex

tag: timepoint (month_post_injection)

tag: gaby's id

tag: tube weight

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)


title: primary cortical neurons, 24hrs post 1hr ETP treatment, rep1, Fos

description: Library name: Fos_ETP_rec_1


title: UACC-257, H3K9me3, replicate 2 (ChIP)

description: Library name: M20-H3K9me3-2

tag: cell line

tag: cell type


title: primary cortical neurons, NMDA 10min stim 20min recovery, rep3, Fos

description: Library name: Fos_NMDA_3


title: Female_3_PBS_Non-injected_Q_3

tag: injection

tag: hemisphere

tag: cage

tag: tube +_sample_weight

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: volume to_genomics


title: UACC-257, replicate 3 (Input)

description: Library name: M20-H-Input-3

tag: tissue

tag: genotype


title: Female_3_PBS_Injected_Q_3

tag: Sex

tag: timepoint (month_post_injection)

tag: animal

tag: gaby's id

tag: mg of_tissue

tag: rna date_isolated

tag: case id


title: Wild-type plus JQ1 treated 1

city: Quebec City

first: Jean-Philippe

last: Lambert

state: QC

address: 2705, boulevard Laurier

department: Molecular Medicine

institute: Université Laval

data_processing:
Data cleaning: Trim Galore/Cutadapt
Quality control: FastQC and MultiQC
Pseudo-alignment: Kallisto
Normalization and Differential analyses: tximport/DESeq2
Assembly: GRCh38.p10
Supplementary files format and content: raw_counts.csv: comma separated values containing raw counts as called by tximport
Supplementary files format and content: normalized_counts.csv: comma separated values containing DESeq2 normalized counts

source_name: Wild-type plus JQ1 treated 1

growth_protocol: A375 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics (Pen/Strep) in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNAs were extracted using the RNeasy plus mini kit from QIAGEN according to the manufacturer’s instructions. 1 ug of RNA depleted of rRNA was used for the construction of sequencing libraries
The NEBNext Ultra II directional RNA library prep kit for Illumina (New Englands Biolabs Inc., Ipswich, MA, USA) was used to prepare RNA sequencing libraries, according to manufacturer’s instruction.

treatment_protocol: 500 nM JQ1 or DMSO control were used for 48 hours treatments

tag: cell line

tag: cell type

value: Malignant melanoma

tag: treatment

value: 500 nM JQ1

tag: time


title: Wild-type untreated 3

source_name: Wild-type untreated 3

value: DMSO


title: Wild-type plus JQ1 treated 3

source_name: Wild-type plus JQ1 treated 3


title: Wild-type plus JQ1 treated 2

source_name: Wild-type plus JQ1 treated 2


title: UACC-257, replicate 2 (Input)

description: Library name: M20-H-Input-2


title: primary cortical neurons, NMDA 10min stim 20min recovery, rep2, Fos

description: Library name: Fos_NMDA_2

source_name: primary cortical neurons

tag: bait


title: primary cortical neurons, NMDA 10min stim 20min recovery, rep1, Fos

description: Library name: Fos_NMDA_1


title: UACC-257, H3K9me3, replicate 1 (ChIP)

description: Library name: M20-H3K9me3-1


title: Female_3_PBS_Injected_Q_1

source_name: cortex

value: Female

tag: injection

tag: hemisphere

tag: cage

tag: tube weight

tag: tube +_sample_weight

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)

tag: volume (ul)

tag: total (ug)


title: UACC-257, replicate 1 (Input)

description: Library name: M20-H-Input-1

tag: tissue

tag: genotype


title: Wild-type untreated 2

source_name: Wild-type untreated 2

tag: cell line


title: Female_3_PBS_Non-injected_Q_0

tag: Sex

tag: timepoint (month_post_injection)

tag: animal

tag: gaby's id

tag: mg of_tissue

tag: rna date_isolated

tag: case id

tag: ug/mg tissue

tag: volume to_genomics


title: Wild-type untreated 1

source_name: Wild-type untreated 1

tag: cell type

tag: treatment

tag: time


title: primary cortical neurons, ETP 30min, rep3, Fos

description: Library name: Fos_ETP_3

tag: bait


title: MK2 KO plus JQ1 treated 3

source_name: MK2 KO plus JQ1 treated 3

value: MAPKAPK2 knockout


title: SK-Mel-103, H3K27ac, replicate 3 (ChIP)

description: Library name: M9-H3K27ac-3


title: primary cortical neurons, ETP 30min, rep2, Fos

description: Library name: Fos_ETP_2


title: SK-Mel-103, H3K27ac, replicate 2 (ChIP)

description: Library name: M9-H3K27ac-2


title: Female_3_PBS_Injected_Q_0

tag: injection

tag: hemisphere

value: Injected

tag: cage

tag: tube weight

tag: tube +_sample_weight

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)

tag: volume (ul)

tag: total (ug)


title: primary cortical neurons, ETP 30min, rep1, Fos

description: Library name: Fos_ETP_1

tag: tissue

tag: genotype


title: MK2 KO plus JQ1 treated 2

source_name: MK2 KO plus JQ1 treated 2

tag: cell line


title: MK2 KO plus JQ1 treated 1

source_name: MK2 KO plus JQ1 treated 1

tag: cell type


title: Female_1_PBS_Injected_P_10

tag: Sex

tag: timepoint (month_post_injection)

value: P

tag: animal

tag: gaby's id

tag: mg of_tissue

tag: rna date_isolated

tag: case id

tag: ug/mg tissue

tag: volume to_genomics


title: SK-Mel-103, H3K27ac, replicate 1 (ChIP)

description: Library name: M9-H3K27ac-1


title: primary cortical neurons, control, Exp1, rep3, Fos

description: Library name: Fos_Control_Exp1_3

tag: bait


title: MK2 KO untreated 3

source_name: MK2 KO untreated 3

tag: treatment

tag: time


title: primary cortical neurons, control, Exp1, rep2, Fos

description: Library name: Fos_Control_Exp1_2


title: Female_1_PBS_Non-injected_P_10

tag: injection

tag: hemisphere

value: Non-injected

tag: cage

tag: tube weight

tag: tube +_sample_weight

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)

tag: volume (ul)

tag: total (ug)


title: SK-Mel-103, H3K9me3, replicate 3 (ChIP)

description: Library name: M9-H3K9me3-3

tag: tissue

tag: cell line

tag: cell type

tag: genotype


title: Female_1_PBS_Non-injected_P_3

tag: Sex

tag: timepoint (month_post_injection)

tag: animal

tag: gaby's id

tag: mg of_tissue

tag: rna date_isolated

tag: case id

tag: ug/mg tissue

tag: volume to_genomics


title: SK-Mel-103, H3K9me3, replicate 2 (ChIP)

description: Library name: M9-H3K9me3-2


title: MK2 KO untreated 2

source_name: MK2 KO untreated 2

tag: treatment

tag: time


title: SK-Mel-103, H3K9me3, replicate 1 (ChIP)

description: Library name: M9-H3K9me3-1