title: MRE11_CRE1_2hr_MRE11

data_processing:
For CUT&RUN samples, quality read trimming was performed using trimmomatic/0.36 using the following command: java -jar trimmomatic-0.33.jar PE -phred33 [FASTQ_FILE] ILLUMINACLIP:/n/app/trimmomatic/0.36/bin/adapters/TruSeq3-PE.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25. Adapters were further trimmed according to pipeline and script (kseq_test).
Paired-end reads were mapped to the mouse genome using the bowtie2/2.2.9 with the following command: bowtie2 --local --very-sensitive-local --no-unal -x mm10 --dovetail --no-mixed --no-discordant --phred33 -I 10 -X 700. Yeast spike-in reads were mapped using the following command: bowtie2 --local --very-sensitive-local --no-unal –x sacCer3 --no-overlap --no-dovetail --no-mixed --no-discordant --phred33 -I 10 -X 700.
Read depth (normalized to 1000000) or spike (normalized to 1) normalized bedgraph files were created using custom scripts modified from Spike_in_Calibration_v2.csh
bedGraphToBigWig (ucsc-tools/363) was used to generate the bigWig files from either read depth or yeast spike-in normalized begraph files.
All peak calling was performed using SEACR_1.1.sh. For H3K27ac and FOS CUT&RUN datasets, peak calling on individual replicates was performed using the spikein normalized bedgraph files based on fragments 1 to 1000 bp in length with the following command: SEACR_1.1.sh [target bedgraph] [control bedgraph] norm stringent. Paired control samples (either IgG or KO control) are listed in Extended Data Table 1 of associated manuscript. To identify reproducible peak sets, SEACR peaks found in 3 of 3 replicates were intersected using bedtools/2.27.1 intersect bed. Peaks within 150 bp were merged. For NPAS4, ARNT2, EP400, MRE11, and ETL4 CUT&RUN datasets, peak calling on individual replicates was performed using SEACR_1.1.sh using the spikein normalized bedgraph files based on fragments 1 to 1000 bp in length with the following command: SEACR_1.1.sh [target bedgraph] [control bedgraph] norm relaxed. Paired control samples (either IgG or KO control) are listed in Extended Data Table 1 of manuscript. To identify reproducible peak sets, SEACR peaks found in 4 of 5 NPAS4 replicates (2hr KA stimulation), 2 of 2 NPAS4 replicates (0hr KA stimulation), 2 of 2 ARNT2 replicates (2hr KA stimulation), 2 of 2 EP400 replicates (0 and 2hr KA stimulation; Abcam antibody), 2 of 2 MRE11 replicates (0 and 2hr KA stimulation), 2 of 2 ETL4 replicates (0hr KA stimulation) and 3 of 4 ETL4 replicates (2hr KA stimulation) were intersected using bedtools/2.27.1 intersect bed. Peaks within 150 bp were merged. Finally, the maxima of CUT&RUN signal within 100 bp windows for each peak was calculated from spikein normalized bigWig files using custom scripts. For FOS, ARNT2, EP400, ETL4, NPAS4 and MRE11, final peak calls were extended 200 base pairs up and downstream from this 100bp peak maxima to generate 500 base pair peak calls for each factor and timepoint. Mm10 blacklisted regions 78 were filtered out using the following command: bedops/2.4.30 –not-element-of 1 [BLACKLIST_BED]. NPAS4 peaks were also extended to 1 kb, as we found maximal enrichment for the Ebox (CAGATG) motif and bHLH/PAS motif (CGTG) in 1 kb regions extended from peak maxima.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: Table_Extracted_transcription_factor_CUTRUN_counts across regulatory regions in WT hippocampus
Supplementary files format and content: Table of DeSeq2_MRE11_CUTRUN_normalized read counts across regulatory regions in hippocampus_Mre11_inNpas4cKO_Mice
Supplementary files format and content: Table of DeSeq2_EP400_CUTRUN_normalized read counts across regulatory regions in hippocampus_Ep400_inNpas4cKO_Mice
Supplementary files format and content: Table of DeSeq2_H3K27ac_CUTRUN_normalized read counts across regulatory regions in WT hippocampus
Supplementary files format and content: SEACR peaks merged replicates; see processing steps

source_name: Hippocampal tissue

extract_protocol:
Briefly, fresh hippocampal tissue pooled from 4-5 mice was placed into 5 mL of buffer HB (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, pH 7.8, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine) and dounced 15X with a tight pestle. 5% IGEPAL CA-630 (320 µL) was added prior to douncing with a tight pestle 5 more times, and the sample was filtered through a 40-µm strainer into a 15 mL conical collection tube. 5 mL of working solution (50% iodixanol, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, pH 7.8, supplemented with protease inhibitors, DTT, spermine and spermidine) was added to the sample. Homogenized tissue was gently added on top of 2 ml of 30%/40% iodixanol layers. Samples were centrifuged at 10,000g for 18 min, and 1 mL of nuclei was collected from the 30/40% iodixanol interface. Nuclei were counted and evenly distributed across unstimulated and stimulated conditions in the following amounts: FOS (in house), H3K27ac (Abcam ab4729): 75,000 nuclei; NPAS4 (in house), EP400 (Bethyl Laboratories, A300541A; Abcam ab5201), ARNT2 (in house): 1,000,000 nuclei; MRE11 (Novus Biologicals, Novus NB100-142), RAD50(Novus Biologicals NB100-154), CTCF (Active Motif 61311), ETL4 (Bethyl Laboratories, A304-928A): 500,000 nuclei. For samples FACS-isolated from Npas4-cKO mice, MRE11 and EP400 CUT&RUN was performed with 100,000 nuclei. Replicates consist of independent pools of 2-3 mice.
Equal numbers of nuclei between unstimulated (PBS-injected mice) and stimulated conditions (2hr KA-injected mice) were aliquoted into 1 ml of CUT&RUN Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.2% Tween-20, 1 mg ml−1 BSA, 10 mM sodium butyrate and 0.5 mM spermidine supplemented with protease inhibitors). Magnetic concanavalin-A (ConA) beads (Bangs Laboratories) that had been washed with CUT&RUN binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2) were added to each sample to bind nuclei. ConA-bead-bound nuclei were incubated overnight at 4°C in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.2% Tween-20, 1 mg mL−1 BSA, 0.1% Triton X-100 and 2 mM EDTA,10 mM sodium butyrate and 0.5 mM spermidine supplemented with protease inhibitors) containing 1:50 dilution of the aforementioned antibodies.
After overnight incubation with antibodies, ConA-bead-bound nuclei were washed with CUT&RUN antibody buffer and resuspended in CUT&RUN Triton-wash buffer (CUT&RUN wash buffer supplemented with 0.1% Triton X-100). Protein-A-MNase was added at a final concentration of 700 ng mL−1, and samples were incubated at 4°C for 1 hr. ConA-bead-bound nuclei were next washed twice with CUT&RUN Triton-wash buffer and resuspended in 100 μL of CUT&RUN Triton-wash buffer. After the addition of 3μL of 100 mM CaCl2, samples were incubated on ice for 30 min. To stop the MNase reaction, 100 μL of 2X STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.04% Triton X-100, 20 pg mL−1 yeast spike-in DNA, and 0.1 μg mL−1 RNase A) was added to each sample prior to incubation at 37°C for 20 min. Following incubation, a magnet was used to capture Con-A-beads, and supernatants containing DNA fragments released by protein-A-MNase were collected. 2 μL of 10% SDS and 2 μL of 20 mg mL−1 proteinase-K were added to supernatants followed by incubation at 65°C with gentle shaking for 1 h. Standard phenol/chloroform extraction with ethanol precipitation was used to precipitate DNA.
Sequencing libraries from precipitated DNA suspend in TE buffer were generated as previously described in (Hainer et al., 2019), with the following changes: Rapid T4 DNA ligase (Enzymatics) was used to perform adapter ligation onto end-repaired, and A-tailed DNA. Adaptor dimers were removed from PCR-amplified libraries using a 1.1X ratio of AMPure XP beads. CUT&RUN libraries were sequenced on Illumina NextSeq 500 using 40-bp paired-end reads.

treatment_protocol: Nuclei were collected from 4 week old wildtype mice. Postnatal day 21 day mice were injected with AAVs expressing either CRE virus (to remove the protein of interest) or DELCRE ('called DEL'), a nuclease deficient CRE. Mice were sacrificed 10 days later. To induce synchronous neuronal activity, mice were injected with 12 mg/kg kainic acid (KA).  Hippocampal tissue was harvested 0 or 2 hours later as indicated. In the case of CRE or DEL-CRE infected tissue, nuclei expressing CRE-mCherry or DEL-CRE-GFP were FACS sorted using a SONY SH800.

value: FACS sorted mCherry+ nuclei from hippocampal tissue

value: 2 hour post KA stimulation

tag: antibody

value: MRE11 Novus Biologicals, Novus NB100-142


title: MRE11_DEL3_2hr_MRE11

status: Public on Dec 16 2022

type: SRA

city: BOSTON

first: ELIZABETH

last: POLLINA

state: MA

address: 220 LONGWOOD AVENUE, GOLDENSON 405

department: Neurobiology

country: USA

institute: HARVARD MEDICAL SCHOOL

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell/tissue type

value: FACS sorted GFP+ nuclei from hippocampal tissue

tag: mouse strain

tag: treatment


title: CD8nv-38

type: genomic

city: Lebanon

first: Lucas

middle: A.

last: Salas

state: NH

address: 1 Medical Center Dr, DHMC

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

description:
205689130135_R02C01
CD8nv

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2
matrix processed value definition: SeSAMe Processed Average Beta
matrix signal intensities value definition: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

organism: Homo sapiens

source_name: isolated CD8 naive; leukoreduction filter 38

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: age

tag: purity

tag: ethnicity

tag: arraytypes

value: IlluminaHumanMethylationEPIC


title: round_spermatids3 (RS3), MeRIP-seq

city: Yangling

first: Xiaoxu

last: Chen

address: Litai street

country: China

institute: Northwest A&F University

description:
m6A modification
Methylated_RNA_sites.mRNA

library_source: transcriptomic

data_processing:
RNA-seq: After raw data process, high quality clean reads were aligned to the reference genome (susScr3) with hisat2 software (v2.0.4). Then, cuffdiff software (part of cufflinks) was used to get the gene level FPKM based on the Ensembl gtf gene annotation file. The differentially expressed mRNA were identified and used for further analysis.
MeRIP-seq: After quality controlled by Q30, 3’ adaptor and low quality reads were removed by cutadapt software (v1.9.3). Clean reads of all libraries were aligned to the reference genome (SusScr3) by Hisat2 software (v2.0.4). Methylated sites were identified by MACS software and further used for differentially methylation analysis. Gene ontology analysis were performed by the differentially methylated protein coding genes.
Genome_build: SusScr3
Supplementary_files_format_and_content: abundance measurements - Methylated_RNA_sites.mRNA.xlsx, mRNA Expression Profiling.xlsx

molecule: total RNA

organism: Sus scrofa

source_name: germ cells

extract_protocol:
Fractions with high purity of spermatogonia, pachytene spermatocytes and round spermatids were resuspended with Trizol (Invitrogen, USA) and total RNA was extracted for further analysis.
RNA seq: The rRNAs were removed from total RNA by using NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer’s instruction. NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) was used to construct RNA libraries. Library quality were confirmed by BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an Illumina Hiseq 4000 with 150 bp paired end reads.
MeRIP-seq: In brief, total RNA was extracted by using TRIzol Reagent (Invitrogen, USA). Denaturing agarose electrophoresis was used for confirming RNA integrity. Then, mRNA was isolated from total RNA by using Seq-Star T M poly(A) mRNA Isolation Kit (Arraystar, MD, USA). The m6A RNA immunoprecipitation was conducted by using GenSeq™ m6A RNA IP Kit (GenSeq Inc., China) according to the manufacturer’s instructions. Libraries were constructed from the samples with and without m6A immunoprecipitation by using NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., MA, USA). Library was evaluated by the BioAnalyzer 2100 system (Agilent Technologies Inc., CA, USA) and sequenced on an Illumina Hiseq 4000 with 150 bp paired-end reads.  After quality controlled by Q30, 3’ adaptor and low quality reads were removed by cutadapt software (v1.9.3). Clean reads of all libraries were aligned to the reference genome (SusScr3) by Hisat2 software (v2.0.4). Methylated sites were identified by MACS software and further used for differentially methylation analysis. Gene ontology analysis were performed by the differentially methylated protein coding genes.

tag: cell type

value: round spermatids


title: Npas4_7_delcre

description: Single nucleus RNA-seq (10X) from deltacre infected hippocampal nuclei

library_source: transcriptomic single cell

data_processing:
FASTQ files were created using the standard bcl2fastq pipeline from Illumina. FASTQ files were concatenated across flowcell lanes and and across four sequencing runs.
Gene expression tables for each nuclear barcode were generated via the CellRanger 3.0.0 pipeline as designed by 10X Genomics. Samples were demultiplexed, and all Npas4fl/fl or Tip60fl/fl samples were merged using the CellRanger aggr function using default parameters.
The datasets were loaded into R and analyzed using the Seurat (v3) and Monocle3 packages. Nuclei were removed from the dataset if they contained fewer than 500 detected genes, displayed more than 5% of reads mapping to mitochondrial genes, or had RNA counts detected at a level greater than 2 standard deviations higher than the mean value in their assigned cell type.
Assembly: mm10
Supplementary files format and content: h5 filtered feature barcode matrices generated by Cellranger 3.0

source_name: Hippocampus

extract_protocol:
To isolate hippocampal nuclei, we placed flash-frozen hippocampal tissue in 0.5mL of buffer HB (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, pH 7.8, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine) and dounced 5X with a loose pestle and 10X with a tight pestle. 5% IGEPAL CA-630 (32 µL) was added prior to douncing with a tight pestle 5-8 more times and filtering through a 40-µm strainer into a 15 mL conical collection tube. Buffer HB (3.5 mL) and 5 mL working solution (50% iodixanol, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, pH 7.8, supplemented with protease inhibitors, DTT, spermine and spermidine) were added. Homogenized tissue was gently layered on top of 1 mL of 30% iodixanol on top of a layer of 1 mL of 40% iodixanol (diluted from working solution). Samples were centrifuged at 10,000g for 18 min and 70 µL of nuclei was collected from the 30/40% iodixanol interface.
SnRNA-seq was performed using the 10X Genomics Chromium Single Cell Kit (v3). Each reaction lane was loaded with up to 10,000 nuclei from one hippocampal hemisphere (infected with either Cre-mCherry or ΔCre-GFP) from one mouse. Subsequent steps for cDNA amplification and library preparation were conducted according to the manufacturer’s protocol (10X Genomics). Samples were sequenced using Illumina NextSeq500 with 28 bp (R1), 56 bp (R2), and 8 bp(index).
Single nucleus RNA-seq (10X)

treatment_protocol: Postnatal day 21 day mice were injected with AAVs expressing either CRE virus (to remove the protein of interest) or DELCRE ('called DEL'), a nuclease deficient CRE. Mice were sacrificed 10 days later. To induce synchronous neuronal activity, mice were injected with 12 mg/kg kainic acid (KA).  Hippocampal tissue was harvested 6 hours later.

value: 6 hour post kainate stim

value: Hippocampal nuclei


title: Genomic DNA from invasive tumor front (ITF) of lung metastatic uterine leiomyosarcoma 23

city: Santiago de Compostela

first: Angel

last: Diaz-Lagares

state: A Coruña

address: C/ Choupana s/n

department: ONCOMET

country: Spain

institute: Health Research Institute of Santiago (IDIS)

description: Invasive tumor front (ITF) of lung metastatic uterine leiomyosarcoma

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to human Infinium MethylationEPIC BeadChip (Illumina) using standard Infinium HD FFPE Methylation Protocol (Illumina).

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting

data_processing: RnBeads package in R environment (v4.1.1)

source_name: Lung Metastasis from uterine leiomyosarcoma 23

label_protocol: Standard Infinium HD FFPE Methylation Protocol from Illumina

extract_protocol: Genomic DNA was isolated from FFPE tissue sections of microdissected invasive tumor front (ITF) of lung metastasis (LM) from uterine adenocarcinomas (uADC) and leiomyosarcomas (uLMS) using the AllPrep DNA/RNA FFPE Kit (Qiagen) and following the manufacturer’s instructions.

tag: gender

value: Female

tag: tissue

value: Lung metastasis

tag: tumor type

value: Uterine adenocarcinoma

tag: tumor area

value: Invasive tumor front


title: Npas4_6_delcre


title: CD8nv-36

description:
205689130135_R04C01
CD8nv

source_name: isolated CD8 naive; leukoreduction filter 36


title: round_spermatids1 (RS1), MeRIP-seq


title: MRE11_CRE3_2hr_MRE11


title: pachytene_spermatocytes1 (PS1), MeRIP-seq

value: pachytene spermatocytes


title: Genomic DNA from invasive tumor front (ITF) of lung metastatic uterine leiomyosarcoma 15

source_name: Lung Metastasis from uterine leiomyosarcoma 15


title: MRE11_CRE2_2hr_MRE11


title: Genomic DNA from invasive tumor front (ITF) of lung metastatic uterine leiomyosarcoma 17

source_name: Lung Metastasis from uterine leiomyosarcoma 17


title: pachytene_spermatocytes3 (PS3), MeRIP-seq


title: Genomic DNA from invasive tumor front (ITF) of lung metastatic uterine leiomyosarcoma 19

source_name: Lung Metastasis from uterine leiomyosarcoma 19


title: spermatogonia3 (SPG3), MeRIP-seq

value: spermatogonia


title: CD8EM-39

description:
205689130106_R06C01
CD8em

source_name: isolated CD8 effector memory; leukoreduction filter 39


title: MRE11_CRE1_2hr_IgG

value: IgG (CST 2729S)


title: Genomic DNA from invasive tumor front (ITF) of lung metastatic uterine leiomyosarcoma 13

source_name: Lung Metastasis from uterine leiomyosarcoma 13


title: MRE11_DEL3_2hr_IgG


title: CD8nv-30

description:
205624860032_R01C01
CD8nv

source_name: isolated CD8 naive; leukoreduction filter 30


title: Genomic DNA from invasive tumor front (ITF) of lung metastatic uterine leiomyosarcoma 21

source_name: Lung Metastasis from uterine leiomyosarcoma 21


title: pachytene_spermatocytes2 (PS2), MeRIP-seq


title: spermatogonia1 (SPG1), MeRIP-seq


title: Genomic DNA from invasive tumor front (ITF) of lung metastatic uterine leiomyosarcoma 5

source_name: Lung Metastasis from uterine leiomyosarcoma 5


title: CD8EM-32

description:
205689130135_R01C01
CD8em

source_name: isolated CD8 effector memory; leukoreduction filter 32


title: CHD4_A_Reh

city: Cambridge

first: Fadi

middle: John

last: Najm

state: Massachusetts

address: 415 Main Street 6043

department: Epigenomics

institute: Broad Institute

description: Column name in the processed data file: MR68

data_processing:
Data were aligned with STAR aligner 43 to the hg38 genome assembly using the “Basic” two-pass mode. The option “--outFilterScoreMinOverLread“ was set to 0.2 to allow the mapping of shorter fragments
Raw gene counts were obtained using STAR aligner by adding the option “--quantMode GeneCounts” to the mapping script. NCBI RefSeq GTF file was used for gene counting purposes.
The merged length of all exons for each protein-coding gene was used to correct raw counts. TPM was calculated using the following formula in R: “tpm.mat <- t( t(x) * 1e6 / colSums(x) )” where x is the gene length-corrected expression matrix
Assembly: hg38
Supplementary files format and content: Tab-delimited text file including TPM valuies for each gene in all processed mRNA-Seq libraries

molecule: polyA RNA

source_name: Reh

growth_protocol: Cells were continuously cultured in RPMI 1640 supplemented with 10% FBS and penicilin/streptomycin.

extract_protocol:
RNA was isolated with Qiagen RNeasy Plus Micro kit according to the manufacturer's protocol and ensuring RIN values were greater than 7.
Libraries were prepared first with Poly-A enrichment using magnetic oligo(dT)-beads (Invitrogen), then ligated to RNA adaptors for sequencing.

treatment_protocol: Cells were transduced with lentivirus delivering CRISPR-Cas9, guide, and fluorescent reporter. After 7 days, cells were flow analyzed, sorted, and collected for RNA extraction.

tag: cell line

value: Reh

value: cell line

value: CHD4 KO


title: CD8EM-31

description:
205689130135_R07C01
CD8em

source_name: isolated CD8 effector memory; leukoreduction filter 31


title: Genomic DNA from invasive tumor front (ITF) of lung metastatic uterine adenocarcinoma 29

description: Invasive tumor front (ITF) of lung metastatic uterine adenocarcinoma

source_name: Lung Metastasis from uterine adenocarcinoma 29


title: Genomic DNA from invasive tumor front (ITF) of lung metastatic uterine adenocarcinoma 38

source_name: Lung Metastasis from uterine adenocarcinoma 38


title: NPAS4_CRE3_2hr_EP400

source_name: Hippocampal tissue

value: FACS sorted mCherry+ nuclei from hippocampal tissue

value: 2 hour post KA stimulation

value: EP400 Abcam ab5201


title: CD8nv-29

description:
205624860032_R04C01
CD8nv

source_name: isolated CD8 naive; leukoreduction filter 29

value: IlluminaHumanMethylationEPIC


title: Genomic DNA from invasive tumor front (ITF) of lung metastatic uterine leiomyosarcoma 7

source_name: Lung Metastasis from uterine leiomyosarcoma 7


title: Genomic DNA from invasive tumor front (ITF) of lung metastatic uterine leiomyosarcoma 20

source_name: Lung Metastasis from uterine leiomyosarcoma 20


title: MRE11_DEL2_2hr_MRE11

value: FACS sorted GFP+ nuclei from hippocampal tissue

value: MRE11 Novus Biologicals, Novus NB100-142


title: Genomic DNA from invasive tumor front (ITF) of lung metastatic uterine adenocarcinoma 28

source_name: Lung Metastasis from uterine adenocarcinoma 28


title: Genomic DNA from invasive tumor front (ITF) of lung metastatic uterine adenocarcinoma 30

source_name: Lung Metastasis from uterine adenocarcinoma 30


title: MRE11_DEL1_2hr_MRE11


title: Genomic DNA from invasive tumor front (ITF) of lung metastatic uterine adenocarcinoma 6

source_name: Lung Metastasis from uterine adenocarcinoma 6


title: round_spermatids3 (RS3), RNA-seq

description: mRNA Expression Profiling

source_name: germ cells

value: round spermatids


title: round_spermatids2 (RS2), RNA-seq

description: mRNA Expression Profiling


title: MRE11_CRE3_2hr_IgG


title: NPAS4_CRE2_2hr_EP400


title: CD8EM-40

description:
205689130106_R03C01
CD8em

source_name: isolated CD8 effector memory; leukoreduction filter 40


title: Genomic DNA from invasive tumor front (ITF) of lung metastatic uterine adenocarcinoma 39

source_name: Lung Metastasis from uterine adenocarcinoma 39

value: Female


title: NPAS4_DEL3_2hr_EP400


title: NPAS4_CRE1_2hr_EP400


title: NPAS4_DEL1_2hr_EP400


title: CD8CM-40

description:
205624860032_R02C01
CD8cm

source_name: isolated CD8 central memory; leukoreduction filter 40


title: CD8CM-41

description:
205689130106_R01C01
CD8cm

source_name: isolated CD8 central memory; leukoreduction filter 41


title: MRE11_CRE2_2hr_IgG


title: NPAS4_DEL2_2hr_EP400


title: MRE11_DEL2_2hr_IgG


title: MRE11_DEL1_2hr_IgG


title: CD8CM-42

description:
205689130135_R03C01
CD8cm

source_name: isolated CD8 central memory; leukoreduction filter 42


title: NPAS4_CRE4_2hr_EP400


title: NPAS4_DEL4_2hr_IgG


title: spermatogonia2 (SPG2), MeRIP-seq


title: pachytene_spermatocytes2 (PS2), RNA-seq

description: mRNA Expression Profiling


title: NPAS4_CRE3_2hr_MRE11


title: NPAS4_CRE6_2hr_IgG


title: pachytene_spermatocytes3 (PS3), RNA-seq

description: mRNA Expression Profiling


title: CD8CM-39

description:
205624860032_R06C01
CD8cm

source_name: isolated CD8 central memory; leukoreduction filter 39


title: round_spermatids1 (RS1), RNA-seq

description: mRNA Expression Profiling


title: spermatogonia3 (SPG3), RNA-seq

description: mRNA Expression Profiling


title: NPAS4_DEL3_2hr_MRE11


title: NPAS4_CRE1_2hr_MRE11


title: NPAS4_DEL2_2hr_MRE11


title: CD4CM-9

description:
CD4CM
204373100025_R06C01

source_name: Human Peripheral Blood CD4+ CD45RO+ CD45RA- CD62L+ CD197+ Central memory T cells from leukoreduction filter

value: WHITE

tag: smoker

tag: bmi

tag: Sex

value: M

value: FACS isolated cells

tag: array

tag: slide


title: CD4EM-4

description:
CD4EM
204373100025_R08C01

source_name: Human Peripheral Blood CD4+ CD45RO+ CD45RA- CD62L- CD197- Effector memory T cells from leukoreduction filter


title: NPAS4_DEL1_2hr_MRE11

tag: cell/tissue type

tag: mouse strain

tag: antibody


title: NPAS4_CRE4_2hr_IgG

tag: treatment


title: NPAS4_CRE2_2hr_MRE11


title: spermatogonia2 (SPG2), RNA-seq

description: mRNA Expression Profiling


title: Bmem07

description:
205624860110_R01C01
Bmem

source_name: Human Peripheral blood, CD19+ CD27+ B cells, Frozen

tag: age

tag: purity

tag: ethnicity


title: pachytene_spermatocytes1 (PS1), RNA-seq

description: mRNA Expression Profiling

tag: cell type

value: pachytene spermatocytes


title: NPAS4_CRE5_2hr_IgG

source_name: Hippocampal tissue


title: CD4EM-6

description:
CD4EM
204373100025_R03C01

value: BLACK OR AFRICAN AMERICAN

tag: arraytypes


title: spermatogonia1 (SPG1), RNA-seq

description: mRNA Expression Profiling

value: spermatogonia


title: NPAS4_CRE1_2hr_IgG

value: IgG (CST 2729S)


title: Bepridil_1295U_3

city: Shanghai

first: Xinrui

last: Wang

address: 197 Ruijin Rd II

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads  containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat2.
Read counts for each gene were carried out using HT-Seq using the GRCz11 refSeq refFlat GTF file.
Genes with adjusted P-value < 0.05 and foldChange >2 were defined as differentially expressed genes (DEGs).
Genome_build: GRCz11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Danio rerio

source_name: Embryo

extract_protocol:
The total RNA of zebrafish larvae at 120 hpf in each group was isolated using RNAiso Plus (TakaRa, 9108) and stored at -80℃. The concentration and purity of RNA were determined using a NanoPhotometer (ThermoFisher Scientific Intertek, Cat. 3100668). Each individual mRNA was isolated with 15 zebrafish larvae.
RNA purification, cDNA synthesis and RNA-Seq of each group (n = 3) were performed by Oebiotech company (Shang hai, China). RNA integrity was analyzed through the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara). The RNA integrity number ≥ 7 were subjected to the following analysis. The cDNA libraries were constructed through TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA).

tag: strain

value: AB

tag: tissue

value: Embryo

value: post fertilization hour 120

value: 1295 ng/mL bepridil treatment


title: CD4CM-11

description:
CD4CM
204373100025_R01C01

value: F


title: NPAS4_DEL3_2hr_IgG

value: 2 hour post KA stimulation


title: CD8CM-31

description:
205689130135_R06C01
CD8cm

source_name: isolated CD8 central memory; leukoreduction filter 31

value: IlluminaHumanMethylationEPIC


title: Bepridil_1295U_2


title: CD4CM-10

description:
CD4CM
204372030109_R07C01


title: NPAS4_DEL2_2hr_IgG

value: FACS sorted GFP+ nuclei from hippocampal tissue


title: NPAS4_DEL1_2hr_IgG


title: CD4EM-5

description:
CD4EM
204372030109_R06C01


title: Bepridil_1295U_1


title: KA_2hr_HIP_CTCF_Rep3

value: Hippocampal tissue

value: CTCF Active Motif 61311


title: KA_2hr_HIP_CTCF_Rep2


title: Bepridil_750U_3

value: 750 ng/mL bepridil treatment


title: KA_2hr_HIP_CTCF_Rep1


title: NPAS4_CRE2_2hr_IgG

value: FACS sorted mCherry+ nuclei from hippocampal tissue


title: NPAS4_CRE3_2hr_IgG


title: Unstim_HIP_CTCF_Rep3

value: Unstim (Saline-injected)


title: Bepridil_750U_2


title: Unstim_HIP_CTCF_Rep2


title: Unstim_HIP_CTCF_Rep1


title: Bepridil_750U_1


title: CD4CM-8

description:
CD4CM
204372030109_R04C01

value: WHITE

value: M

value: FACS isolated cells


title: KA_2hr_HIP_Rad50_Rep4

value: RAD50 Novus Biologicals, Novus NB100-154


title: CD4EM-8

description:
CD4EM
204373100002_R08C01


title: KA_2hr_HIP_Rad50_Rep3


title: KA_2hr_HIP_Rad50_Rep2


title: Bepridil_250U_3

value: AB

value: 250 ng/mL bepridil treatment


title: CD4EM-11

description:
CD4EM
204373100002_R06C01


title: KA_2hr_HIP_Rad50_Rep1


title: CD4CM-6

description:
CD4CM
204373100002_R05C01

value: BLACK OR AFRICAN AMERICAN


title: Bepridil_250U_1

value: Embryo

value: post fertilization hour 120


title: CD4CM-7

description:
CD4CM
204373100002_R02C01


title: Bepridil_0U_3

value: 0 ng/mL bepridil treatment


title: Unstim_HIP_Rad50_Rep1


title: Tn0018

description:
CD8nv
203028210044_R01C01

source_name: Human Peripheral Blood CD8+ CD45RA+ T Cells, Frozen

value: Indo-European

value: Caucasian

value: No

value: Obese

value: F

value: Cell Pellet

value: IlluminaHumanMethylationEPIC


title: KA_2hr_HIP_Mre11_Novus_Rep2

value: Hippocampal tissue

value: 2 hour post KA stimulation

value: MRE11 Novus Biologicals, Novus NB100-142


title: Unstim_HIP_Mre11_Novus_Rep1

value: Unstim (Saline-injected)


title: KA_2hr_HIP_Mre11_Novus_Rep1


title: Unstim_HIP_Mre11_Novus_Rep2


title: CD4EM-7

description:
CD4EM
204372030109_R01C01

value: WHITE

value: M

value: FACS isolated cells


title: KA_2hr_HIP_ETL4_Bethyl_Rep3

value: ETL4  Bethyl Laboratories, A304-928A


title: Tn0049

description:
CD8nv
203027390100_R06C01

value: Overweight


title: Bepridil_0U_2

value: AB

value: Embryo

value: post fertilization hour 120

value: 0 ng/mL bepridil treatment


title: Tn0979

description:
CD8nv
203027390094_R05C01

value: Indo-European

value: Caucasian

value: No

value: Normal


title: KA_2hr_HIP_ETL4_Bethyl_Rep4

value: Hippocampal tissue


title: KA_2hr_HIP_ETL4_Bethyl_Rep2

value: 2 hour post KA stimulation


title: Bepridil_0U_1


title: Unstim_HIP_ETL4_Bethyl_Rep1


title: Unstim_HIP_ETL4_Bethyl_Rep2


title: KA_2hr_HIP_ETL4_Bethyl_Rep1


title: KA_2hr_HIP_p400_Abcam_Rep2

value: EP400 Abcam ab5201


title: Tn0043

description:
CD8nv
203027390051_R01C01

value: F

value: Cell Pellet

value: IlluminaHumanMethylationEPIC


title: KA_2hr_HIP_p400_Abcam_Rep1


title: Bepridil_250U_2

value: 250 ng/mL bepridil treatment


title: Tn0073

description:
CD8nv
203027390092_R03C01

value: WHITE

value: M


title: Unstim_HIP_Rad50_Rep2

value: Unstim (Saline-injected)

value: RAD50 Novus Biologicals, Novus NB100-154


title: tumor_wt, sctcr_seq

city: Oxford

first: Audrey

last: Gerard

address: Roosevelt Dr.

country: United Kingdom

institute: The Kennedy Institute of Rheumatology

description:
10X Genomics
targeted RNA

data_processing:
Sequence reads were mapped using CellRanger multi (version 6.0.0) with the 10x mouse reference transcriptome (version 2020-A).
Paired chain TCR sequences were obtained through targeted amplification of full-length V(D)J segments during library preparation. Sequence assembly and clonotype calling was done through cellranger’s immune profiling pipeline (cellranger multi).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scTCR-seq

source_name: Tumor

extract_protocol:
Tumors and draining lymph nodes (LNs) from 3 controls (CD8-Cre-Rosa26Tomato) and 3 CD8-IFNγRKO(CD8-Cre-Rosa26Tomato-IFNgR1flox/flox) mice were harvested. Tumors were then dilacerated, incubated 30 minutes at 37C in 5% CO2 in R10 containing Liberase TL at 1mg/mL (Roche) and DNase I at 10ug/mL (Roche), and run through a 70μm cell strainer (Falcon). Cells were either undergoing Ficoll to obtain live immune cells.  LNs were directly smashed through a 70μm cell strainer and resuspended in PBS. All cells were stained with CD45, CD3, CD8, without fixation step. Cells were then sorted based on expression of CD45, CD3, CD8, and Tomato using a FACSAria™ II (BD). Approximately 20,000 cells per sample were loaded onto the 10X Genomics Chromium Controller (Chip K).
Gene expression, feature barcoding and TCR sequencing libraries were prepared using the 10x Genomics Single Cell 5' Reagent Kits v2 (Dual Index) following manufacturer user guide (CG000330 Rev B). The final libraries were diluted to ~10nM for storage. The 10nM library was denatured and further diluted prior to loading on the NovaSeq6000 sequencing platform (Illumina, v1.5 chemistry, 28bp/98bp paired end for gene expression and feature barcoding, 150bp paired end for TCR libraries).

value: Tumor

value: CD8 T cells

tag: genotype

value: CD8-Cre Rosa26Tomato

value: Mice were engrafted with B16-OVA tumor line


title: Unstim_HIP_Rad50_Rep3


title: tumor_ko, sctcr_seq

description:
10X Genomics
targeted RNA

value: CD8-Cre IFNgR1flox/flox Rosa26Tomato


title: cd8_ln_ko_s06, scrna_seq

description: 10X Genomics

data_processing:
Sequence reads were mapped using CellRanger multi (version 6.0.0) with the 10x mouse reference transcriptome (version 2020-A).
Paired chain TCR sequences were obtained through targeted amplification of full-length V(D)J segments during library preparation. Sequence assembly and clonotype calling was done through cellranger’s immune profiling pipeline (cellranger multi).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: draining lymph node

value: draining lymph node


title: Tn0082

description:
CD8nv
203013220070_R01C01

value: Indo-European

value: Caucasian

tag: smoker

value: No

value: Normal


title: Unstim_HIP_p400_Abcam_Rep2

value: Hippocampal tissue

value: EP400 Abcam ab5201


title: Unstim_HIP_p400_Abcam_Rep1


title: CD4nv1217

description:
CD4nv
204237140015_R08C01

source_name: Human Peripheral Blood CD4+ CD45RA+ T Cells, Frozen

value: Yes

tag: bmi

value: Cell Pellet

value: IlluminaHumanMethylationEPIC


title: cd8_tumor_ko_s08, scrna_seq

description: 10X Genomics


title: CD4nv1876

description:
CD4nv
204237140014_R06C01

value: WHITE

tag: Sex

value: M


title: cd8_ln_wt_s05, scrna_seq

description: 10X Genomics


title: KA_2hr_HIP_Arnt2_Rep2

value: 2 hour post KA stimulation

value: ARNT2 (in house)


title: KA_2hr_HIP_Arnt2_Rep1


title: KA_2hr_HIP_Npas4_Rep8

value: NPAS4 (in house)


title: cd8_tumor_wt_s07, scrna_seq

description: 10X Genomics

value: Tumor

value: CD8 T cells

value: CD8-Cre Rosa26Tomato

value: Mice were engrafted with B16-OVA tumor line


title: CD4nv1906

description:
CD4nv
204237140014_R03C01

value: Indo-European

value: Caucasian

value: Obese

tag: array


title: KA_2hr_HIP_Npas4_Rep7

value: Hippocampal tissue


title: CD4nv 1945

description:
CD4nv
204237140013_R03C01

value: Normal

tag: slide


title: KA_2hr_HIP_Npas4_Rep6

tag: cell/tissue type


title: Unstim_HIP_p400_Bethyl_Rep1

tag: mouse strain

value: Unstim (Saline-injected)

value: EP400 Bethyl Laboratories, A300541A


title: KA_2hr_HIP_p400_Bethyl_Rep1

tag: antibody


title: KA_2hr_HIP_Npas4_Rep4

tag: treatment


title: KA_2hr_HIP_Npas4_Rep3


title: KA_2hr_HIP_Npas4_Rep1


title: HC, replicate 1, scRNAseq

city: Changsha

first: Yu

last: Zhang

address: No. 138 Tongzipo Road

department: Transplantation Center

institute: The Third Xiangya Hospital, Central South University

data_processing:
Basecalls performed using bcl2fastq V2.19.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Quantify gene expression using read2 by featureCounts software
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
The livers obtained from fibrotic liver of S. japonicum-induced mouse and healthy liver of normal mouse. The fresh tissues were stored in the sCelLiveTM Tissue Preservation Solution (Singleron) on ice as quickly as possible. After washed with Hanks Balanced Salt Solution (HBSS) for three times, the specimens were minced into small pieces. To dissociated into single-cell suspensions, the specimens then digested with 3 mL sCelLiveTM Tissue Dissociation Solution (Singleron) by Singleron PythoN™ Tissue Dissociation System at 37 °C for 15 min. After filtered through a 40-micron sterile strainer, the cell was added the GEXSCOPE® red blood cell lysis buﬀer (RCLB, Singleron), which was incubated at room temperature for 5-8 min to remove red blood cells. Centrifugation was performed at 300 × g 4 ℃ for 5 mins to remove supernatant and single cells were resuspended softly in PBS.
Single cell suspension was loaded onto microwell chip  and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron GEXSCOPE Single Cell RNAseq Library

value: Liver

value: male

tag: age

value: 17 weeks old

value: control


title: KA_2hr_HIP_Npas4_Rep2

value: 2 hour post KA stimulation


title: KA_2hr_HIP_Npas4_Rep5

value: NPAS4 (in house)


title: Bn0139

description:
Bnv
203991450045_R07C01

source_name: Human Peripheral blood, CD19+ CD27- B cells, Frozen

tag: purity

value: Mixed

value: Hispanic

value: WHITE

value: No

value: F

value: Cell Pellet

value: IlluminaHumanMethylationEPIC


title: KA_2hr_HIP_Npas4_KO_Rep2

value: Hippocampal tissue

value: Npas4 KO (Lin et al 2008)


title: SJ, replicate 1, scRNAseq

value: S. japonicum-infected


title: CD4nv 1969

description:
CD4nv
204237140011_R01C01

value: Indo-European

value: Caucasian

value: Overweight

value: M


title: Adipose EC, Control, Male, replicate 4

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

description:
SP flowcell
23B

data_processing:
The expression levels of each sample were normalized as Transcripts Per Kilobase Per Million (TPKM) by dividing the read count of each transcript model with its length and scaling the total per sample to one million using Kalisto V0.4.4. Quality control of raw and mapped reads was done using FastQC version 0.11.8.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: id tpm short.csv - xomma separated file. Features correspond to row indices with given ID, name and type
Supplementary files format and content: id counts short.csv - xomma separated file. Features correspond to row indices with given ID, name and type

source_name: white adipose tissue

extract_protocol:
Rneasy Mini column purification (Qiagen).  TruSeq Ribozero Gold Library kit was used to generate ribosomal RNA-depleted cDNA-libraries
Paired-end

treatment_protocol:
All mice were fed a high fat  (60% kCal from fat) Surwit diet for 7 weeks
Endothelial cells were isolated from white adipose tissue

value: endothelial

value: white adipose tissue

value: Male

value: 14 weeks old


title: CD4nv 2081

description:
CD4nv
204237140011_R04C01

value: Yes

value: Obese


title: Adipose EC, Control, Female, replicate 4

description:
SP flowcell
84C

value: Female


title: KA_2hr_HIP_Npas4_KO_Rep1

value: 2 hour post KA stimulation

value: NPAS4 (in house)


title: Bn0150

description:
Bnv
203991450045_R06C01

value: WHITE

value: No

value: Normal

value: F

value: Cell Pellet

value: IlluminaHumanMethylationEPIC


title: Adipose EC, Control, Female, replicate 3

description:
SP flowcell
86D


title: Unstim_HIP_Npas4_Rep2

value: Hippocampal tissue

value: Unstim (Saline-injected)


title: Unstim_HIP_Npas4_Rep1


title: Adipose EC, Control, Male, replicate 3

description:
SP flowcell
89A

value: endothelial


title: KA_2hr_HIP_IgG_O

value: IgG (CST 2729S)


title: Adipose EC, Control, Male, replicate 2

description:
SP flowcell
90C

value: white adipose tissue

value: Male


title: KA_2hr_HIP_IgG_N


title: KA_2hr_HIP_IgG_M


title: Bn0067

description:
Bnv
203991450040_R07C01

value: African-American

value: African American

value: BLACK OR AFRICAN AMERICAN

value: Yes

value: M


title: KA_2hr_HIP_IgG_L

value: 2 hour post KA stimulation


title: Bn0149

description:
Bnv
203991450040_R04C01

value: Indo-European

value: Caucasian

value: WHITE

value: No

value: Obese


title: KA_2hr_HIP_IgG_K

value: Hippocampal tissue


title: Adipose EC, Control, Female, replicate 2

description:
SP flowcell
92A

value: Female

value: 14 weeks old


title: Adipose EC, Control, Female, replicate 1

description:
SP flowcell
93A

value: endothelial


title: Bmem0031

description:
Bmem
203991450045_R08C01

value: F

value: Cell Pellet

value: IlluminaHumanMethylationEPIC


title: KA_2hr_HIP_IgG_G

value: IgG (CST 2729S)


title: KA_2hr_HIP_IgG_F


title: KA_2hr_HIP_IgG_H


title: KA_2hr_HIP_IgG_E


title: Bmem0187

description:
Bmem
203991450045_R05C01

value: African-American

value: BLACK OR AFRICAN AMERICAN

value: Overweight


title: Bn0188

description:
Bnv
203991450045_R04C01

value: African American

value: Yes

value: M


title: Unstim_HIP_Npas4_Rep3

value: Unstim (Saline-injected)

value: NPAS4 (in house)


title: Bmem0055

description:
Bmem
203991450045_R03C01

value: Indo-European

value: Caucasian

value: WHITE

value: No

value: Obese


title: 104150-001-108

city: Leiden

first: Eveline

last: Gart

state: Zuid Holland

address: Sylviusweg 71

department: MHR

country: Netherlands

institute: TNO

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: Mus_musculus.GRCm38.gencode.vM19
Supplementary files format and content: The count files contain the reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package.

growth_protocol: All animal care and experimental procedures were approved by the Ethical Committee on Animal Care and Experimentation (Zeist, The Netherlands; approval reference numbers TNO-436, date: 17th of September 2019, and TNO-440, date: 24th of October 2019), and were in compliance with European Community specification regarding the use of laboratory animals.   Ten-week-old male C57BL/6J mice were obtained from Charles River Laboratories (L’Arbresle, France) and were kept on chow maintenance diet (Ssniff Spezialdieten GmbH, Soest, Germany). Mice were housed individually in a temperature-controlled room on a 12h light-dark cycle and had free access to food (unless mentioned otherwise) and water. At the age of 12 weeks, ad libitum caloric intake was determined for each mouse separately by measuring normal individual baseline caloric intake over three periods of 3 days.

extract_protocol:
Quadriceps muscles from sacrificed animals were frozen in liquid nitrogen for transcriptome analysis. Total RNA was extracted from individual quadriceps muscle samples using glass beads and RNA-Bee (Campro Scientific, Veenendaal, The Netherlands). RNA integrity was examined using the RNA 6000 nano Lab-on-a-Chip kit and a bioanalyzer 2100 (Agilent Technologies, Amstelveen, The Netherlands).
Next Generation Sequencing was performed at Genome Scan (Leiden the Netherlands). For this strand-specific cDNA libraries were generated from RNA using oligo-dT magnetic beads mRNA fragmentation NEBNext Ultra Directional RNA Library Prep Kit from Illumina NEB  E7420S/L resulting in 300–500 bp amplified libraries/sample. Libraries were multiplexed clustered and sequenced on a NovaSeq6000 system for Illumina (New England Biolabs Inc. Ipswich MA USA) with a paired-end 150 bp sequencing protocol yielding 15-32 million reads per sample  and indexing (however, 2 samples had 13 and 111 Mreads per sample).
Clustering and DNA sequencing using the NovaSeq6000 v1.5 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis base calling and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: At the age of 14 weeks, mice were matched for body weight and lean body mass and sub-divided into four groups. One control group (n=12) remained on ad libitum chow, one CR group (n=12) received 60% of the kcal (chow) normally consumed under ad libitum conditions, one immobilized group (n=12) remained on ad libitum chow, but right hindleg was immobilized, and one combination (CR + immobilization) group (n=12) received 60% of the kcal (chow) normally consumed under ad libitum conditions and their right hindleg was immobilized as well. This period of caloric restriction (CR) and/or immobilization lasted for 14 days. Immobilization was achieved through fixation of the right hindleg using adhesive bandage and surgical tape and resulted in a fixation of the knee joint at 180°. The adhesive bandage and surgical tape were checked daily and replaced on day 5 and day 10 of immobilization, and on another day if the bandage became loose.  For reference, naturally aged mice were used. To do so, 13 months (58 weeks) old male C57BL/6J mice were obtained from Charles River Laboratories and were kept on chow maintenance diet (Ssniff Spezialdieten GmbH, Soest, Germany). Mice were housed individually in a temperature-controlled room on a 12h light-dark cycle and had free access to food and water. At 17 months of age (74 weeks), all mice were matched for body weight and lean body mass and subdivided in two groups; one 17 months (76 weeks) and one 21 months (92 weeks) old group.

value: quadriceps left muscle

tag: mouse id

tag: time point

value: Ctrl

tag: group


title: 104150-001-107


title: KA_2hr_HIP_IgG_D

value: Hippocampal tissue

value: 2 hour post KA stimulation


title: Bmem0192

description:
Bmem
203991450040_R08C01

value: F

value: Cell Pellet

tag: arraytypes

value: IlluminaHumanMethylationEPIC


title: KA_2hr_HIP_IgG_B

value: IgG (CST 2729S)


title: KA_2hr_HIP_IgG_A


title: 104150-001-106

tag: tissue


title: Bn0046

description:
Bnv
203991450045_R01C01

value: Overweight


title: 104150-001-105


title: KA_2hr_HIP_IgG_I


title: Unstim_HIP_IgG_N


title: 104150-001-104


title: Adipose EC, Control, Male, replicate 1

description:
SP flowcell
91A

tag: cell type

value: endothelial

value: white adipose tissue

tag: strain

value: Male

value: 14 weeks old


title: Bmem0017

description:
Bmem
203991450040_R06C01

value: Indo-European

value: Caucasian

tag: smoker

tag: bmi

value: M


title: Unstim_HIP_IgG_M

value: Unstim (Saline-injected)


title: KA_2hr_HIP_IgG_J


title: Bmem0008

description:
Bmem
203991450040_R01C01

value: WHITE

value: No

tag: Sex

tag: array


title: 104150-001-103

value: quadriceps left muscle

value: Ctrl


title: Unstim_HIP_IgG_K

tag: cell/tissue type

value: Hippocampal tissue


title: Unstim_HIP_IgG_L

tag: mouse strain


title: KA_2hr_HIP_IgG_C

value: 2 hour post KA stimulation

tag: antibody


title: 104150-001-102

tag: treatment


title: Unstim_HIP_IgG_I


title: 104150-001-101


title: LB17_KO_GW

city: Dallas

first: Lara

last: Bideyan

state: TX

address: 5323 Harry Hines Blvd., MC: 9077 Y6.314

department: Internal Medicine

institute: UT Southwestern

description:
resKOvsControlGW.csv
resGWvsDMSOKO.csv

data_processing:
Data quality analysis was performed via FastQC
The reads were aligned to the mm10 genome using STAR (version 2.6.0c).
Differential expression analysis was performed with DESeq2 and genes were classified as significantly regulated if adjusted P value < 0.05.
Normalized counts were extracted from DESeq2.
Assembly: mm10
Supplementary files format and content: csv (normalized counts, FDR for pairwise comparisons and interaction between genotype and treatment)

growth_protocol: Gata4 fl/fl mice were injected with AAV8-Tbg-Cre or an empty AAV8 at 10 weeks of age.

extract_protocol:
Total RNA from frozen tissue was extracted through TRIzol (Invitrogen) and Qiagen RNeasy Mini Kit.
Libraries were made with KAPA mRNA Hyperprep Kit

treatment_protocol: 1 week after AAV injection, were gavaged with 40 mg/kg GW3965 prepared in canola oil at 17 h, and then 8 h before before sacrifice. Mice were 4 h fasted at the time of killing (3-5pm). Dimethylsulfoxide in canola oil was used as vehicle control

value: mixed

value: Liver

value: male

tag: age

value: 11 weeks old

tag: genotype

value: Gata4LKO (Gata4fl/fl; AAV8-Tbg-Cre)

value: LXR Agonist GW3965


title: LB18_KO_GW

description:
resKOvsControlGW.csv
resGWvsDMSOKO.csv


title: Unstim_HIP_IgG_J

value: IgG (CST 2729S)


title: Unstim_HIP_IgG_H


title: Unstim_HIP_IgG_G


title: LB15_KO_GW

description:
resKOvsControlGW.csv
resGWvsDMSOKO.csv


title: Unstim_HIP_IgG_E


title: Unstim_HIP_IgG_C


title: Unstim_HIP_IgG_F


title: Unstim_HIP_IgG_D


title: LB16_KO_GW

description:
resKOvsControlGW.csv
resGWvsDMSOKO.csv


title: Unstim_HIP_IgG_B


title: LB14_KO_GW

description:
resKOvsControlGW.csv
resGWvsDMSOKO.csv


title: Unstim_HIP_IgG_A


title: KA_2hr_HIP_Fos_Rep1

value: FOS (in house)


title: LB12_Cntrl_GW

description:
resKOvsControlGW.csv
resGWvsDMSOControl.csv

value: Control (Gata4fl/fl; Empty AAV8)

value: DMSO Vehicle


title: 104150-001-098

tag: mouse id


title: 104150-001-097

tag: time point


title: KA_2hr_HIP_Fos_Rep2


title: LB13_Cntrl_GW


title: KA_2hr_HIP_H3K27ac_Rep3

value: H3K27ac Abcam ab4729


title: KA_2hr_HIP_Fos_Rep3


title: LB10_Cntrl_GW


title: 104150-001-100

tag: group


title: KA_2hr_HIP_H3K27ac_Rep1


title: 104150-001-095


title: LB9_Cntrl_GW


title: 104150-001-096


title: 104150-001-094


title: Unstim_HIP_Fos_Rep3

value: Unstim (Saline-injected)


title: Unstim_HIP_Fos_Rep2


title: 104150-001-099


title: LB8_KO_DMSO

description:
resKOvsControlDMSO.csv
resGWvsDMSOKO.csv


title: 104150-001-093


title: Unstim_HIP_H3K27ac_Rep3


title: Unstim_HIP_H3K27ac_Rep1


title: LB6_KO_DMSO


title: 104150-001-092


title: WT_HIP_10hrKA-10

data_processing:
Mapping pipeline was cloned from git clone https://github.com/BiCroLab/blissNP.git.
The software package homer(v4.9) was used to create tag directories for all replicates per factor for a given timepoint. For sBLISS samples, bed files generated from the pipeline described in (https://github.com/BiCroLab/blissNP.git) were expanded such that each UMI at each location was counted individually. For sBLISS samples, the –len 0 tag was added for creation of tag directories to account for the fact that sBLISS mapping generates bed files with single base pair ends of cut sites.
Raw read counts were extracted using homer(v4.9)’s annotatePeaks.pl function with the following command: annotatePeaks.pl [bed file] mm10 -size given -noann –noadj. For sBLISS signal, the –len 0 parameter was included to quantify only the cut site end (1 bp) and to prevent read shifting based on estimated fragment sizes. Raw signal counts were imported in R, and the normalized signals were generated using DeSeq2’s function counts(dds, normalized=TRUE))
sBLISS peaks were called on UMI deduplicated bed files in which the single cut site had been extended by the length of the sequencing read, 75 bp.  Peaks were called using MACS2 (v 2.1.0) with the following peak parameters: macs2 callpeak --nomodel --keep-dup all --format BED -g mm -p 1e-5. Reproducible peaks were considered those that overlap in 5 of 8 replicates. Final peak sets were extended 500 bp from the maximal sBLISS summit in a reproducible peak.
Assembly: mm10
Supplementary files format and content: Table of DeSeq2 normalized read counts across regulatory regions in hippocampus
Supplementary files format and content: Bigwig file of mapped reads.  For WT timecourse samples, all replicates per timepoint have been pooled.  Reads were downsampled to match the lowest number across all samples to allow for comparison across timepoints
Supplementary files format and content: MACS2 peaks merged replicates; see processing steps

extract_protocol:
For sBLISS-seq performed on Npas4/Tip60 WT or cKO nuclei, hippocampal tissue was dissected and quickly examined under a florescent scope to detect GFP (ΔCre) or mCherry (Cre). Tissue that was uninfected, or in rare cases showed infection of both fluorophores in a single hemisphere, was discarded. Replicates consist of individual mice.Tissue was not sorted so as to minimize stress on the nuclei that could induce ectopic DNA breaks. Hippocampi were placed in 1 mL of buffer HB (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, pH 7.8, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine) and dounced 5X with a loose pestle and 10X with a tight pestle. 5% IGEPAL CA-630 (32 µL) was added prior to douncing with a tight pestle 5-8 more times and filtering through a 40-µm strainer. To preserve DNA breaks for the remainder of the protocol, nuclei were fixed with 2% paraformaldehyde (Electron Microscopy Sciences, cat. no. 15710) followed by quenching with 125 mM Glycine. Fixed nuclei were gently pelleted by spinning at 500 g. To remove excess debris and myelin, fixed nuclei were run through a modified iodixanol gradient. Pelleted nuclei were resuspended in 1 mL of 22% iodixanol, laid on top of 100 µL of 43% iodixanol. Nuclei were then centrifuged at 1,500g for 15 min in an Eppendorf Centrifuge 5804R in a swinging bucket rotor. Nuclei (100 µL), which settle at the 43%/22% interface, were collected and transferred to a Protein Low-Bind tube. Nuclei were washed once with ice-cold PBS/1% BSA followed by 2 washes with ice-cold 1X PBS. Fixed nuclei were counted, and ~250,000 nuclei (for Npas4fl/fl and wild-type datasets) and ~100,000 nuclei (for Tip60fl/fl datasets) were transferred to a fresh tube to begin adapter ligation. To isolate nuclei from cultured neurons plated in 6-well dishes, neurons were washed with ice-cold PBS to remove debris and 1 mL of HB + 32 µL of 5% IGEPAL CA-630 was added to each well. Cells were incubated for 10 min in HB with gentle rotation at 4°C before removal by gentle scraping and transfer to Eppendorf tubes. Nuclei from cultured neurons were fixed with 2% paraformaldehyde (Electron Microscopy Sciences, 15710) followed by quenching with 125 mM Glycine and gently pelleted by spinning at 500 g. The aforementioned gradient was omitted due to lack of debris/myelin in neuronal cultures. Nuclei were washed once with ice-cold PBS/1% BSA followed by 2 washes with ice-cold 1X PBS.
Fixed nuclei were incubated for 1 hour at 37°C in LB2 (10 mM Tris-HCl, 150 mM NaCl, 0.3% SDS). Nuclei were washed twice in CutSmart Wash Buffer (1X CutSmart (New England Biolabs; B7204), 0.1% TritonX100). At room temperature, nuclei were blunted using Quick Blunting Kit (New England Biolabs, E1201) for 1 hour. Following two washes with CutSmart Wash Buffer, adapters were ligated onto free DNA ends in intact nuclei using T4 DNA ligase (5 U/mL, Thermo Fisher Scientific, EL0011). Ligation reactions were carried out for ~18 hours at 16°C in a Thermomixer. The following day, nuclei were washed twice with CutSmart Wash Buffer and incubated overnight in 100 µL of DNA extraction buffer (10 mM Tris–HCl, 100 mM NaCl, 10 mM EDTA, 0.5% SDS) containing 10 µL of Proteinase K (20 mg/mL,New England Biolabs). DNA was extracted using a standard Phenol:Chloroform extraction and resuspended in 18 µL of ultrapure Dnase/Rnase free water for subsequent fragmentation.  Cultured neuron samples were fragmented using a Bioruptor 30 s ON, 60 s OFF, HIGH intensity, for 35-40 cycles. Due to limited input from in vivo samples, we found that using enzymatic fragmentation preserved fragmented DNA better than sonication. As a result, all samples from hippocampal tissue were fragmented using NEB Fragmentase for 40-50 min at 37°C. This treatment resulted in fragments 400-800 bp in size, with the average library size approximately 650 bp. Following fragmentation and clean-up, 100 ng (for cultured neuron samples) or 35 ng (hippocampal samples) was reverse transcribed using MegaClear IVT kit (Thermo Fisher, AMB13345). Libraries from IVT products were produced as described without deviation from the protocol described in 43. Briefly, template DNA was removed by incubation of IVT products with 2 μL of DNaseI (Thermo Fisher, AM2222) for 15 min, and RNA was purified using RNAXP clean beads. RA3 adapter (/5rApp/TGGAATTCTCGGGTGCCAAGG/3SpC3/) was ligated onto RNA using T4 RNA Ligase 2, truncated (New England Biolabs, M0242L). RNA was then reverse transcribed using the reverse primers RTP (GCCTTGGCACCCGAGAATTCCA) and the SuperScript IV Reverse Transcriptase kit (Thermo Fisher,18090200). Finally, DNA was amplified using NEBNext Ultra II Q5 Master Mix (New England Biolabs, M0544L) in 8 reactions of 50 μL each. Libraries were sequenced using single-end 75-bp reads on a NextSeq 500.
sBLISS-seq

treatment_protocol: Postnatal day 21 day mice were injected with AAVs expressing either CRE virus (to remove the protein of interest) or DELCRE ('called DEL'), a nuclease deficient CRE. Mice were sacrificed 10 days later. To induce synchronous neuronal activity, mice were injected with 12-15 mg/kg kainic acid (KA).  Hippocampal tissue was harvested 0, 2, or 10 hours later.

value: wildtype C57BL6

value: 10 hour post KA stimulation


title: 104150-001-091

value: quadriceps left muscle

value: Ctrl


title: LB5_KO_DMSO


title: WT_HIP_10hrKA-8

value: Hippocampal tissue


title: KA_2hr_HIP_H3K27ac_Rep2

value: 2 hour post KA stimulation


title: LB4_Cntrl_DMSO

description:
resKOvsControlDMSO.csv
resGWvsDMSOControl.csv

value: mixed

value: Liver


title: WT_HIP_10hrKA-7


title: WT_HIP_10hrKA-6


title: 104150-001-090


title: WT_HIP_10hrKA-5


title: Unstim_HIP_Fos_Rep1


title: 104150-001-089


title: LB3_Cntrl_DMSO

value: male

value: 11 weeks old


title: 104150-001-088


title: LB2_Cntrl_DMSO


title: WT_HIP_10hrKA-3


title: WT_HIP_10hrKA-4


title: LB7_KO_DMSO

value: Gata4LKO (Gata4fl/fl; AAV8-Tbg-Cre)

value: LXR Agonist GW3965


title: 104150-001-087


title: Unstim_HIP_H3K27ac_Rep2


title: WT_HIP_10hrKA-2


title: WT_HIP_2hrKA-8


title: WT_HIP_10hrKA-1


title: 104150-001-086


title: LB1_Cntrl_DMSO


title: KO_6594 (RNA-seq)

description: RNA-Seq

data_processing:
Data quality analysis was performed via FastQC
The reads were aligned to the mm10 genome using STAR (version 2.6.0c).
Differential expression analysis was performed with DESeq2 and genes were classified as significantly regulated if adjusted P value < 0.05.
Normalized counts were extracted from DESeq2.
Assembly: mm10
Supplementary files format and content: csv and xlsx (normalized counts and FDR)

growth_protocol: Gata4 fl/fl mice were injected with AAV8-Tbg-Cre or an empty AAV8 at 8 weeks of age. 7 days later mice were euthanized.

extract_protocol:
Total RNA from frozen tissue was extracted through TRIzol (Invitrogen) and Qiagen RNeasy Mini Kit.
Libraries were made with KAPA Stranded kit with mRNA capture

treatment_protocol: They were put on western diet from Research Diets (D12079B) for 3 weeks. On the say of the euthanization, they were fasting for 6 hours starting at 8 - 9am .

tag: diet

value: Western Diet for 3 weeks


title: WT_HIP_2hrKA-7


title: 104150-001-085

tag: tissue


title: WT_HIP_2hrKA-6


title: WT_HIP_2hrKA-5


title: WT_HIP_2hrKA-4


title: KO_6593 (RNA-seq)

description: RNA-Seq


title: WT_HIP_2hrKA-3


title: Control_6628 (RNA-seq)

description: RNA-Seq

value: Control (Gata4fl/fl; Empty AAV8)


title: WT_HIP_0hrKA-10


title: WT_HIP_2hrKA-1


title: WT_HIP_0hrKA-9


title: 104150-001-048

value: CR+IR


title: 104150-001-047


title: 104150-001-046


title: Control_6626 (RNA-seq)

description: RNA-Seq


title: 104150-001-045


title: WT_HIP_0hrKA-8


title: WT_HIP_0hrKA-6


title: WT_HIP_10hrKA-9


title: Control_6625 (RNA-seq)

description: RNA-Seq


title: WT_HIP_0hrKA-5


title: WT_HIP_0hrKA-7


title: 104150-001-044


title: WT_HIP_0hrKA-2


title: 104150-001-043


title: WT_HIP_0hrKA-1


title: 104150-001-042


title: 2hrKA_WT_CRE3


title: Refed7 (RNA-seq)

description: RNA-Seq

data_processing:
Data quality analysis was performed via FastQC
The reads were aligned to the mm9 genome using STAR (version 2.6.0c).
Reads were quantified through Seqmonk. Differential expression analysis was performed with DESeq2 and genes were classified as significantly regulated if adjusted P value < 0.05.
Assembly: mm9
Supplementary files format and content: xlsx (RPKM and FDR)

extract_protocol:
Total RNA from frozen tissue was extracted through TRIzol (Invitrogen) and Qiagen RNeasy Mini Kit.
Libraries were made with Universal Plus mRNA-Seq kit

treatment_protocol: Refed group were fasted for 12h starting at 10am and refed with High sucrose diet (69% sucrose, 10% fat D07042201 from Research Diets) for 12h starting at 10pm. Fasted group started fasting for 12h at 10pm. All mice were euthanized at 10am the following day.

value: 8 weeks old

value: Refed


title: KO_6635 (RNA-seq)

description: RNA-Seq


title: 2hrKA_WT_CRE2

value: wildtype C57BL6


title: 2hrKA_WT_CRE1


title: Refed8 (RNA-seq)

description: RNA-Seq


title: Refed5 (RNA-seq)

description: RNA-Seq


title: 104150-001-041


title: 2hrKA_WT_DEL3


title: WT_HIP_2hrKA-2


title: 104150-001-040


title: 2hrKA_WT_DEL2


title: Fasted3 (RNA-seq)

description: RNA-Seq

value: Fasted


title: 10hrKA_TIP60_CRE6

value: 10 hour post KA stimulation


title: Fasted1 (RNA-seq)

description: RNA-Seq


title: 2hrKA_WT_DEL1


title: 10hrKA_TIP60_CRE3


title: 104150-001-038

value: quadriceps left muscle


title: 10hrKA_TIP60_CRE2

value: Hippocampal tissue


title: 10hrKA_TIP60_DEL6


title: 10hrKA_TIP60_DEL5


title: input-2417RLL_KO_Refed

description: ChIP-Seq

data_processing:
samples were demultiplexed and quality control was done using FastQC.
Trimgalore was used to trim adapters.
Trimmed sequences were aligned to the mm9 mouse genome assembly using bowtie2.
Mitochondrial, unmapped, multi-mapped and duplicate reads were removed using samtools.
Peaks were called using MACS2. Consensus peaks were made using bedtools.
Quantitated across samples using Diffbind. Differentially accessible peaks were identified using EdgeR module.
Peaks were annotated to genomic features and nearest promoter via Homer.
Bam files were merged using samtools. Bigwigs created via deeptools.
Assembly: mm9
Supplementary files format and content: bw (merged and individual, for visualization), xlsx and txt (normalized counts and FDR KO vs Control in Fasted or in Refed, or Genotype or Interaction between Genotype and Nutrition)

extract_protocol:
Chromatin was prepared from frozen tissue using truChIP Chromatin Shearing Tissue Kit (Covaris). Chromatin was sheared using Diagenode Bioruptor Pico for 30 s ON/ 30 s OFF 10 cycles in SDS lysis buffer (1% SDS, 10 mM EDTA pH 8.1; 50 mM Tris-HCl, pH 8.1) supplemented with protease inhibitor cocktail. Input were decrosslinked overnight at 65C in elution buffer (0.1M NaHCO3; 0.1% SDS; 200mM NaCl) followed by treatment with RNAseA (0.125ug/ml) and Proteinase K (0.1mg/ml). Chromatin was purified using QIAQuick PCR Purification Kit and quantified using Qubit (dsDNA HS). Dynabeads Protein A (Invitrogen) were preincubated with 4 ug of H3K27Ac (ab4729, Abcam) or Rabbit anti-GATA4 Antibody (A303-503A, Fortis Life Sciences) in ChIP dilution buffer (0.01% SDS; 1.1% Triton X-100; 1mM EDTA, pH 8.1; 16.7 mM Tris-HCl, pH 8.1; 167 mM NaCl + proteinase inhibitor) for 1.5 hours at room temperature. 7 -– 10 ug of chromatin were incubated overnight with the corresponding antibody-bound beads with rotation for immunoprecipitation (IP). IP samples were washed with low salt wash buffer (0.1% SDS; 1% Triton X-100; 2 mM EDTA pH 8.1; 20mM Tris-HCl pH 8.1; 150 mM NaCl), followed by high salt wash buffer (0.1% SDS; 1% Triton X-100; 2 mM EDTA pH 8.1; 20mM Tris-HCl pH 8.1; 500 mM NaCl), LiCl wash buffer (250 mM LiCl; 1% deoxycholic acid; 1mM EDTA pH 8.1, 10 mM Tris-HCl pH 8.1; 1% Igepal) and finally 2 washes with TE Buffer (1 mM EDTA pH 8.1; 10 mM Tris-HCl pH 8.1) (Ferrari et al. 2017). IP samples were de-crosslinked and purified as described for the input above.
Libraries were made with KAPA DNA HyperPrep kit

treatment_protocol: Refed group were fasted for 12h starting at 9 - 10am and refed with High sucrose diet (69% sucrose, 10% fat D07042201 from Research Diets) for 12h starting at 9 - 10pm. Fasted group started fasting for 12h at 9 - 10pm. All mice were euthanized at 9 - 10am the following day.

value: 9 weeks old


title: input-2417B_KO_Refed

description: ChIP-Seq


title: 104150-001-039


title: 104150-001-036

value: IR


title: 10hrKA_TIP60_DEL3


title: input-2417L_KO_Refed

description: ChIP-Seq

value: Liver


title: input-2416L_Control_Refed

description: ChIP-Seq

value: male


title: 104150-001-035


title: 10hrKA_NPAS4_CRE2


title: 10hrKA_NPAS4_CRE4


title: 104150-001-034


title: input-2416R_Control_Refed

description: ChIP-Seq


title: 10hrKA_NPAS4_CRE1


title: Fasted4 (RNA-seq)

description: RNA-Seq


title: 10hrKA_TIP60_CRE5


title: 104150-001-033


title: 10hrKA_NPAS4_DEL4


title: 10hrKA_NPAS4_DEL5


title: 104150-001-037


title: input-2416N_Control_Refed

description: ChIP-Seq


title: input-2419L_KO_Fasted

description: ChIP-Seq


title: 10hrKA_NPAS4_DEL2


title: 10hrKA_NPAS4_DEL1


title: 104150-001-032


title: 10hrKA_NPAS4_DEL3


title: 104150-001-031


title: 2hrKA_NPAS4_CRE5

value: 2 hour post KA stimulation


title: input-2419R_KO_Fasted

description: ChIP-Seq

value: Gata4LKO (Gata4fl/fl; AAV8-Tbg-Cre)


title: 10hrKA_NPAS4_CRE5


title: 104150-001-030


title: 2hrKA_NPAS4_CRE4


title: 10hrKA_TIP60_DEL2


title: 10hrKA_NPAS4_CRE3


title: input-2419N_KO_Fasted

description: ChIP-Seq


title: 2hrKA_NPAS4_CRE3


title: 2hrKA_NPAS4_CRE2


title: 2hrKA_NPAS4_CRE1


title: 2hrKA_NPAS4_DEL5


title: input-2436L_Control_Fasted

description: ChIP-Seq


title: 104150-001-029


title: 2hrKA_NPAS4_DEL4


title: input-2436R_Control_Fasted

description: ChIP-Seq


title: 2hrKA_NPAS4_DEL3


title: 104150-001-028


title: 104150-001-027


title: 2hrKA_NPAS4_DEL2


title: 2hrKA_NPAS4_DEL1


title: 104150-001-026


title: input-2436N_Control_Fasted

description: ChIP-Seq


title: H3K-2417RLL_KO_Refed (ChIP)

description: ChIP-Seq


title: PBS_NPAS4_CRE5

value: Unstim (Saline-injected)


title: PBS_NPAS4_CRE4


title: H3K-2417B_KO_Refed (ChIP)

description: ChIP-Seq


title: PBS_NPAS4_CRE3


title: PBS_NPAS4_CRE1


title: PBS_NPAS4_DEL4


title: H3K-2416L_Control_Refed (ChIP)

description: ChIP-Seq


title: H3K-2417L_KO_Refed (ChIP)

description: ChIP-Seq


title: 104150-001-025


title: PBS_NPAS4_DEL2


title: PBS_NPAS4_DEL3


title: 104150-001-024

value: CR


title: 104150-001-023


title: 104150-001-022


title: PBS_NPAS4_DEL1


title: CRISPR_Neuron_Rep4

source_name: Cultured cortical neurons

value: E16-E17 cortices; cultured neurons

value: wildtype

value: Infected with pool of LENTICRISPRv2 + gRNA


title: 104150-001-021


title: H3K-2416R_Control_Refed (ChIP)

description: ChIP-Seq

value: Control (Gata4fl/fl; Empty AAV8)

value: Refed


title: CRISPR_Neuron_Rep2


title: H3K-2416N_Control_Refed (ChIP)

description: ChIP-Seq


title: H3K-2419L_KO_Fasted (ChIP)

description: ChIP-Seq

value: Fasted


title: 104150-001-020


title: 104150-001-019


title: CRISPR_Neuron_Rep1


title: EV_Neuron_Rep2

value: Infected with LENTICRISPRv2- no guide


title: PBS_NPAS4_CRE2


title: 104150-001-018

value: quadriceps left muscle


title: Lgr5-Abx

city: Hangzhou

first: Lijiang

last: Fei

address: 866 Yuhangtang Rd

institute: Zhejiang University

description: EGFP+ cells

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed.
ScRNA-seq reads were aligned to the Mus_musculus.GRCm38.88 genome assembly using STAR with default configurations.
Each aligned exonic read was tagged with a gene name. A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes. The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample.
Genome_build: Mus_musculus.GRCm38.88 genome
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes. And the annotation files is  for each cell identity.

source_name: Intestinal Lgr5-EGFP+ cells

extract_protocol:
Tissue was collected from male mouse. Crypts were collected by EDTA shaking, and were digested with digestion buffer (Protease, dispase, DANase). Single cells wer sorted for EGFP+ cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Antibiotics treated Intestine

tag: allele

tag: developmental stage

value: Postnatal day 17


title: H3K-2419N_KO_Fasted (ChIP)

description: ChIP-Seq

tag: strain

value: 9 weeks old


title: EV_Neuron_Rep3


title: EV_Neuron_Rep1


title: 104150-001-017


title: PBS_NPAS4_DEL5

value: Hippocampal tissue


title: H3K-2436L_Control_Fasted (ChIP)

description: ChIP-Seq

value: Liver

value: male


title: Lgr5-Control

description: EGFP+ cells

value: Normal Intestine


title: 104150-001-016


title: H3K-2436R_Control_Fasted (ChIP)

description: ChIP-Seq


title: CRISPR_Neuron_Rep3


title: Abx

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12 (https://github.com/broadinstitute/Drop-seq/files/2425535/Drop-seqAlignmentCookbookv1.2Jan2016.pdf ). The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed.
ScRNA-seq reads were aligned to the Mus_musculus.GRCm38.88 genome assembly using STAR with default configurations.
Each aligned exonic read was tagged with a gene name. A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes. The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample.
Genome_build: Mus_musculus.GRCm38.88 genome
tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes. And the annotation files is  for each cell identity.

source_name: Antibiotics treated group

extract_protocol:
Macrophages were collected from the 1/3 portion of distal part intestine of the pups from postnatal day 17. Epithelial cells were removed by EDTA shaking, and stroma was digested with digestion buffer (Protease, dispase, DANase). Single cells wer sorted for Csfr1-GFP positive cells.
RNA libraries were prepared for sequencing using standard Illumina protocols
Drop-seq, Single cell RNA-Seq

tag: strain background

tag: mouse model

value: Macrophage Fas-Induced Apoptosis (MaFIA) mouse

tag: cell type

value: Intestinal macrophages

tag: genotype/variation

value: Csfr1-GFP positive macrophage


title: 104150-001-015

value: CR


title: WT_27mon_182_amplicon_seq

data_processing:
Samples were trimmed remove these adapters with the following trimming command: java -jar trimmomatic-0.33.jar SE -threads 1 -phred33 [FASTQ_FILE] ILLUMINACLIP:[ADAPTER_FILE]:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:120. FASTQ files containing only trimmed, adapter-removed reads are provided in GEO submission. Full FASTQ files will be provided upon request.
Mapping using BWA was performed using the default parameters outlined in package Debarcer_v0.3.1 (https://github.com/oicr-gsi/debarcer/releases/tag/v0.3.1).
Debarcer output (“bamPositionComposition”) tables were obtained from the package Debarcer_v0.3.1 (https://github.com/oicr-gsi/debarcer/releases/tag/v0.3.1). These tables document the number of consensus 10 families (i.e. groups of 10 reads with the same UMI in which all 10 reads show the same base changes (or lack thereof)) for each base in a given amplicon. These tables also calculate the total number of UMI families that either match the reference genome or show a change from the reference. To include a given amplicon in the analysis, the amplicon was required to be present in greater than 1/3 of all samples and the average number of consensus 10 families across all bases in the amplicons was >100.
Assembly: mm10
Supplementary files format and content: Debarcer output (“bamPositionComposition”) for consensus10 families provided for each sample.

extract_protocol:
Flash frozen hippocampal tissue from mice of different ages was placed in 1 mL of buffer HB (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, pH 7.8, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine) and dounced 5X with a loose pestle and 10X with a tight pestle. 5% IGEPAL CA-630 (32 µL) was added prior to douncing again with a tight pestle 5-8 times. The nuclei suspension in HB was filtered through a 40-µm strainer. Nuclei were then pelleted by centrifugation at 500 rcf for 5 min and resuspended in 400 µL of FACS Block/Stain Buffer (1% BSA, 0.05% Igepal-630, 3 mM MgCl2 in 1X PBS). Nuclei were incubated for 15 min with gentle rotation at 4°C. Following this blocking step, nuclei were pelleted and resuspended in FACS Block/Stain Buffer containing 1:1000 dilution of mouse anti-NeuN-Alexa488 (Millipore; MAB377X). An isotype control Mouse IgG-Alexa488 (Life Technologies; MA518167) was included as a negative control along with an unstained sample. Samples were incubated in antibody mix for 1 hour with gentle rotation at 4°C. Nuclei were washed 1X with FACS Block/Stain Buffer, and DRAQ5 nuclear dye was added (1:500) prior to sorting. NeuN-high-expressing nuclei were separated from NeuN-low-expressing nuclei using a SONY SH800. Nuclei were sorted directly into ATL lysis buffer provided in QIAamp DNA Micro Kit. DNA was extracted using the QIAamp DNA Micro Kit (Qiagen; 56304) according to the manufacturer’s protocol and stored at -80°C until amplicon library preparation.
Amplicons of interest were divided into pools of 15 primer sets. For each primer pool, 20-30 ng of DNA isolated from the FACS-isolated NeuN+ nuclei were first amplified with Phusion Hot Start II high-fidelity DNA polymerase (Thermo Fisher Scientific, F-549L) to append UMI sequences to DNA templates. The final concentration of each primer in the reaction was 40 nM. PCR parameters for these 4 cycles were (98°C, 30 s, 4 cycles of [98°C, 10 s, 62°C, 6 min 72°C, 30 s], followed by 65°C 15 min, 95°C, 15 min). During the 65°C incubation, the PCR reaction was terminated by incubation with 10 µL of protease (Sigma-Aldrich, P5147-100MG; used at a final concentration of 0.06 µg/µL). For each primer pool, 10 µL of initial product were next amplified using Phusion Hot Start II high-fidelity DNA polymerase with the following parameters (98°C, 3 min, 2–35 cycles [98°C, 10 s 80°C, 1 s; 72°C, 30 s; 76°C, 30 s. All with ramping at 0.2°C/s]). Duplicate reactions were performed for each primer pool to increase the diversity of UMI sampling in the final libraries. Samples were size-selected to include products approximately 275 to 650 bp in length. Analysis was conducted using Debarcer_v0.3.1 (https://github.com/oicr-gsi/debarcer/releases/tag/v0.3.1)
Amplicon-sequencing

treatment_protocol: Hippocampal tissue was harvested from animals of different ages and neuronal nuclei were FACS-sorted as described in the Extraction Protocol.

tag: cell/tissue type

value: NeuN+ nuclei

tag: mouse strain

value: Npas4 WT littermate

value: aged


title: WT_23mon_174_amplicon_seq


title: H3K-2436N_Control_Fasted (ChIP)

description: ChIP-Seq

tag: Sex

value: Control (Gata4fl/fl; Empty AAV8)

tag: treatment

value: Fasted


title: WT_23mon_173_amplicon_seq

tag: age


title: WT_12mon_4273_amplicon_seq

value: middle age


title: 104150-001-014

value: quadriceps left muscle

tag: mouse id


title: WT_12mon_3459_amplicon_seq


title: 104150-001-012

tag: time point

value: Ctrl


title: H3K-2419R_KO_Fasted (ChIP)

description: ChIP-Seq

value: 9 weeks old

tag: genotype

value: Gata4LKO (Gata4fl/fl; AAV8-Tbg-Cre)


title: 104150-001-013

tag: group


title: EHE26_2

city: Cleveland

first: Brian

middle: P

last: Rubin

state: OH

address: 9620 Carnegie Ave NE2-215

department: Cancer Biology

institute: Cleveland Clinic

data_processing:
Gapped aligment was performed to the mm10 genomie with HISAT2
Raw counts were created with Featurescounts
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: EHE Cell line

extract_protocol:
Cells were washed with cold PBS and total RNA was extracted with the RNeasy Mini (Qiagen) kit.
Generation of a cDNA library was performed with polyA tail selection using the NEBNext Ultra II RNA Library Prep kit (NEB E7770).

tag: cell line


title: WT_12mon_2013_amplicon_seq


title: EHE17_3


title: EHE17_2


title: EHE17_1


title: 104150-001-011

tag: tissue


title: EHE6_3


title: EHE26_1


title: WT_3mon_4970_amplicon_seq

value: young


title: WT_12mon_2007_amplicon_seq


title: 104150-001-009


title: Control

source_name: control group

value: Postnatal day 17


title: WT_3mon_4966_amplicon_seq


title: EHE6_2


title: WT_3mon_4668_amplicon_seq


title: 104150-001-007


title: 104150-001-008


title: WT_3mon_4292_amplicon_seq


title: 104150-001-006


title: 104150-001-005


title: Refed5 (ATAC)

description: ATAC-Seq

data_processing:
samples were demultiplexed and quality control was done using FastQC.
Cutadapt was used to trim adapters.
Trimmed sequences were aligned to the mm9 mouse genome assembly using bowtie2.
Mitochondrial, unmapped, multi-mapped and duplicate reads were removed using samtools.
Peaks were called using MACS2.
Quantitated across samples using Seqmonk and normalized to million reads per sample. Differentially accessible peaks were identified using DESeq2 module.
Peaks were annotated to genomic features and nearest promoter via Homer.
Bam files were merged using samtools. Bedgraphs were created using Homer.
Assembly: mm9
Supplementary files format and content: BigWig.gz (merged and individual, for visualization), xlsx (normalized counts and FDR)

extract_protocol:
Approximately 50 -100 mg of fresh tissue was homogenized via dounce homogenizer in 1 ml of nuclear isolation buffer (20 mM Tris-HCl, 50 mM EDTA, 5 mM Spermidine, 0.15 mM Spermine, 0.1% mercaptoethanol, 40% glycerol, 1mM EGTA, 60 mM KCl, 1% IGEPAL pH 7.5) and filtered through a 40 M nylon filter. Samples were centrifuged at 4 °C at 1000 × g for 10 min and the pellet was resuspended with 1 ml cold resuspension buffer (RSB) (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, pH 7.4). Approximately 50,000 nuclei from these samples were removed and centrifuged at 4 °C at 500 × g for 5 min. Supernatant was removed and the transposase reaction was performed immediately as described in Buenrosto et al., 2015.
For ATAC-Seq, size selection was done with AMPure XP magnetic beads. Libraries were quantified by qPCR using NEBNext Library Quant Kit for Illumina

value: Liver

value: male

value: 8 weeks old

value: Refed


title: 104150-001-004


title: 104150-001-010


title: 104150-001-003


title: Fasted3 (ATAC)

description: ATAC-Seq


title: CamkIIa_2hr_yH2AX_Rep4

data_processing:
For ChIP-seq samples (e.g., NPAS4 ChIP and γH2AX ChIP) quality trimming of sequencing reads was performed with trimmomatic/0.3679 using the following command: java -jar trimmomatic-0.33.jar SE -threads 1 -phred33 [FASTQ_FILE] ILLUMINACLIP:[ADAPTER_FILE]:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:35.TruSeq adapters were specified for ChIP-seq samples.
Samples were subsequently aligned to the mm10 genome using the Bowtie alignment software (vbowtie2/2.2.9) with the –very-sensitive setting. Reads mapping to the mitochrondrial genome were removed.
Duplicate reads were marked with Picard/2.8.0 with the commandL java -jar $PICARD/picard-2.8.0.jar MarkDuplicates REMOVE_DUPLICATES=false. Duplicates were subsequently removed using samtools/1.3.1 samtools view -b -F 1796.
Peak calling on ChIP samples was performed using MACS2 (macs2/2.1.1 ) using the following command macs2 callpeak –t (experimental bam) –c (input bam) -f BAM -g mm -p 1e-5.
To generate bigWig files, 75 bp reads were extended in the 3’ direction to 200 bp (average fragment length for ChIP-seq experiments as measured by bioAnalyzer) with the bedtools slop command using the following parameters: -l 0 -r 125 -s. Mm10 blacklisted regions (Consortium, 2012) were filtered out using the following command: bedops –not-element-of 1 [BLACKLIST_BED]. The filtered BED files were converted to coverageBED format using the bedtools genomecov command with the following options: -scale [NORM_FACTOR] to scale each library to 20M reads for ChIP. Finally, bedGraphToBigWig (ucsc-tools/363) was used to generate the bigWig files.
To compare ChIP-seq signal across timepoints and conditions (e.g. different genotypes), raw read counts were extracted using homer(v4.9)’s annotatePeaks.pl function with the following command: annotatePeaks.pl [bed file] mm10 -size given -noann –noadj. Raw signal counts were imported in R, and the normalized signals were generated using DeSeq2’s function counts(dds, normalized=TRUE))
Assembly: mm10
Supplementary files format and content: bigWig fies for replicates and merged replicates
Supplementary files format and content: Table of DeSeq2 normalized read counts across regulatory regions in hippocampus
Supplementary files format and content: MACS2 generated ChIP-seq peaks for Npas4

source_name: CamkIIa+ Hippocampal nuclei

extract_protocol:
For ChIP-seq of NPAS4 from hippocampal tissue, 10-15 hippocampi were dounced in 5 ml of 1X PBS containing protease inhibitor cocktail (Roche). 1% formaldehyde was added to tissue homogenate and incubated for 10 min at room temperature, followed by by the addition of 0.125 M glycine for 5 min at room temperature. For ChIP of γH2AX from CamkIIa-expressing CA1 pyramidal neurons, nuclei were isolated from Camk2a-Cre; Sun1fl/+ mice using the INTACT method. Following isolation, nuclei with attached beads were crosslinked with 1% formaldehyde in 1 ml of 1X PBS for 10 min at room temperature. Crosslinking was quenched by the addition of 0.125 M glycine for 5 min at room temperature. Crosslinked nuclei were frozen and stored at -80°C before proceeding the protocol outlined below.  Nuclei were release from tissue by 10 minute incubation in lysis buffer 1 (in mM: 100 HEPES-NaOH pH 7.5, 280 NaCl, 2 EDTA, 2 EGTA, 0.5% Triton X-100, 1% NP-40, 20% Glycerol) followed by washing in buffer containing 10 mM Tris-HCl pH 8.0, 200 mM NaCl. Chromatin was sheared using a Bioruptor (Diagenode) on high power mode for 40-42 cycles with 30 sec pulses in sonication buffer (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-Lauroylsarcosine).   Following sonication, 1.5 ml of chromatin from hippocampal tissue (~60 µg) was supplemented with 1% Triton and incubated overnight at °C with 4 µg NPAS4 (in house) coupled to 15 µl Protein A Dynabeads (Invitrogen). For γH2AX ChIP, 1.5 ml of chromatin released from ~100,000 purified nuclei was incubated with 2 µl of anti- γH2AX (Abcam, ab2893) coupled to 15 µl Protein A Dynabeads. ChIPs were washed twice sequentially in 0.5 mL of the following buffers: low salt buffer (20mM Tris pH 8,150mM NaCl, 2mM EDTA,1% Triton X-100, 0.1% SDS), high salt buffer (20mM Tris pH 8, 500mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), LiCl wash buffer (10mM Tris pH 8, 1mM EDTA, 1% NP-40, 250mM LiCl, 1% Na-deoxycholate), followed by a wash in 1 ml of TE Buffer. Protein:DNA complexes were eluted off the beads by incubation with 200 μL of TE + 1% SDS for 30 min at 65°C. Crosslinked DNA was reversed by incubation overnight at 65°C. The following day, RNA and protein was digested away by the addition of 10 μg of RNase A and 5-7 μL of Proteinase K (New England Biolabs, P8107S). DNA was purified by standard phenol:chloroform extraction.
ChIP-seq libraries were generated using the Ovation Ultralow V2 kit (Nugen, 0344-32) according to the manufacturer’s instructions and PCR amplified for 13-16 cycles, depending on antibody.

treatment_protocol: To induce synchronous neuronal activity, mice were injected with 12-15 mg/kg kainic acid (KA).  Hippocampal tissue was harvested 2 hours later.

value: Excitatory CamkIIa-Cre expressing nuclei

value: B6;129-Gt(ROSA)26Sor<tm5(CAG-Sun1/sfGFP)Nat>/J (Jackson labs Stock 021039) X B6.Cg-Tg(Camk2a-cre)T29-1Stl/J (Jackson labs Stock 005329)

value: 2 hour post KA stimulation

tag: chip antibody

value: yH2AX (Abcam 8293)


title: Npas4_ChIP

source_name: Mouse hippocampal tissue

value: Mouse hippocampal tissue

value: Npas4 (in house)


title: CamkIIa_2hr_yH2AX_Rep3


title: Npas4_ChIP_Input


title: Fasted4 (ATAC)

description: ATAC-Seq

tag: strain

value: Fasted


title: 104150-001-002

value: quadriceps left muscle


title: K4me3 Epigenomic MERFISH

city: Stanford

first: Cheen Euong

last: Ang

state: CA

address: 265 Campus Drive, G3145

institute: Stanford University

description: CUT&Tag reaction (ChIP-seq) with a T7 sequence added to transposed adapter to amplify the tagged region (with the histone marks). The resulting RNA is subjected to reverse transcription and followed by PCR for RNA-sequencing. Detailed protocol from the paper attached as a supplementary PDF file.

data_processing:
Sequencing reads were mapped using Bowtie 2.1.041 with an additional -5 10 parameter to remove the low-quality bases and the following additional option (--very-sensitive)
Mitochondrial reads were then removed (awk '\$3!="chrM"'). Reads were subsequently deduplicated using the rmdup option in samtools
Peak calling was performed using MACS 2.1.142 using the default options outlined in the vignette with the significant value cut-off at q<0.1
Assembly: hg19
Supplementary files format and content: narrowPeak

source_name: hTERT immortalized RPE1 cells

growth_protocol: RPE1 cells were DMEM-F12 media with 10% FBS and 1%PenStrep

extract_protocol:
RNA were extracted using Zymo RNA kit
Reverse transcription was performed on the RNA using Maxima RT kit. The cDNA was amplified adding in the illumina adapters.

treatment_protocol: No treatment was done on the RPE1 cells. The cells were plated at a density of 1 million on silanized coverslip.

tag: histone mark


title: 104150-001-001

value: Ctrl


title: 2417RLL_KO_Refed (RNA-seq)

description: RNA-Seq

extract_protocol:
Total RNA from frozen tissue was extracted through TRIzol (Invitrogen) and Qiagen RNeasy Mini Kit.
Libraries were made with KAPA Stranded RNA-seq kit

value: 9 weeks old


title: CamkIIa_0hr_yH2AX_Rep4

value: Unstim (Saline-injected)


title: EHE6_1


title: K27me3 Epigenomic MERFISH Rep2


title: Fasted1 (ATAC)

description: ATAC-Seq


title: 30h_3

city: Chicago

first: Peng

last: Ji

state: Illinois

address: Ward Building Room 3-230/45, 303 E Chicago Avenue

department: Pathology

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: mouse fetal liver cell

growth_protocol: E13.5 fetal liver cells were harvested and purified for Ter-119 negative cells. Purified cells were then cultured in EPO containing medium for analysis.

extract_protocol:
Total RNA was purified with Qiagen Rneasy purification kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DMSO or Z-VAD-FMK were added at 24h and cells were havested at 30h for RNA-seq.

value: progenitor cells

value: DMSO


title: CamkIIa_2hr_yH2AX_Rep1


title: CamkIIa_0hr_yH2AX_Rep3


title: 2417L_KO_Refed (RNA-seq)

description: RNA-Seq

value: Liver

value: Gata4LKO (Gata4fl/fl; AAV8-Tbg-Cre)


title: K27me3 Epigenomic MERFISH Rep1


title: Refed8 (ATAC)

description: ATAC-Seq

value: male

value: 8 weeks old


title: Refed7 (ATAC)

description: ATAC-Seq

value: Refed


title: 30h_2


title: K27ac Epigenomic MERFISH Rep2


title: CamkIIa_0hr_yH2AX_Rep1

value: Excitatory CamkIIa-Cre expressing nuclei

value: B6;129-Gt(ROSA)26Sor<tm5(CAG-Sun1/sfGFP)Nat>/J (Jackson labs Stock 021039) X B6.Cg-Tg(Camk2a-cre)T29-1Stl/J (Jackson labs Stock 005329)


title: 30h_1


title: 2417B_KO_Refed (RNA-seq)

description: RNA-Seq


title: K27ac Epigenomic MERFISH Rep1


title: 2416RLL_Control_Refed (RNA-seq)

description: RNA-Seq

value: Control (Gata4fl/fl; Empty AAV8)


title: CamkIIa_2hr_ChIP_Input_Rep2

value: 2 hour post KA stimulation

value: yH2AX (Abcam 8293)


title: day0_3

value: no treatment


title: 2416L_Control_Refed (RNA-seq)

description: RNA-Seq


title: HEK293T DICER AA rescue AQ-seq replicate 2

city: Seoul

first: Haedong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

description: AQ-seq

data_processing:
The TruSeq 3′ adapter sequence was removed using cutadapt. For AQ-seq data, 4 nt-long degenerate sequences at the 3′ and 5′ end were trimmed using the FASTX-Toolkit. Reads shorter than 18 nt, low-quality reads (phred quality <20 or <30 in >95% or >50% of nucleotides, respectively), and artifact reads were discarded using the FASTX-Toolkit.
Preprocessed reads were first aligned to the spike-in sequences by BWA with an option of -n 3. Reads mapped to spike-in sequences perfectly or with a single mismatch were considered as reliable spike-in reads.
Reads unmapped to spike-in sequences by BWA with an option of -n 3 were subsequently mapped to the mouse genome (mm10) with the same option. For multi-mapped reads, we selected the alignment results which have the best alignment score, allowing mismatches only at the 3′ end of reads using custom scripts.
Reads were classified into annotations from miRBase release 21 (from www.mirbase.org), RefSeq, RepeatMasker (from UCSC genome browser), GtRNAdb (from gtrnadb.ucsc.edu), and Rfam (from rfam.sanger.ac.uk) by intersectBed in BEDTools.
Assembly: hg38
Supplementary files format and content: Tab-separated values (tsv) files containing sequence variants and corresponding read counts.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen).
Total RNAs were subjected to AQ-seq (Kim et al., 2019) except that 100 µg of total RNAs were used for library construction, and that cDNAs were amplified with NEBNext Ultra II Q5 Master Mix (NEB). The libraries were sequenced on the NovaSeq 6000 platform.


title: HEK293T DICER AA rescue AQ-seq replicate 1

description: AQ-seq


title: 2416R_Control_Refed (RNA-seq)

description: RNA-Seq


title: day0_1


title: CamkIIa_2hr_ChIP_Input_Rep1


title: day0_2


title: CamkIIa_0hr_ChIP_Input_Rep2


title: HEK293T DICER ΔdsRBD rescue AQ-seq replicate 2

description: AQ-seq


title: 2419B_KO_Fasted (RNA-seq)

description: RNA-Seq

value: Fasted


title: HEK293T DICER ΔdsRBD rescue AQ-seq replicate 1

description: AQ-seq


title: HEK293T DICER WT rescue AQ-seq replicate 2

description: AQ-seq


title: 2416N_Control_Refed (RNA-seq)

description: RNA-Seq


title: CamkIIa_0hr_ChIP_Input_Rep1


title: Healthy donors (DS13) in day 9

city: Mulhouse

first: Anne

last: ARIES

address: 87 Av d'Alkirch

country: France

institute: IRHT

data_processing:
The normalization and differential expression analysis was performed with  the R/Bioconductor package edgeR v.3.28.1, for the genes annotated in the reference  genome. Lowly expressed genes were filtered, keeping genes that are expressed at a  reasonable level (10 counts in at least 7 samples). The filtered data were normalized  by the library size.
Assembly: GRCh38.p13
Supplementary files format and content:  normalized counts

source_name: ProtheraCytes (expanded CD34+ cells)

extract_protocol:
Total RNA was purified from ProtheraCytes® collected from 7 Frozen healthy donor and 8 Acute myocardiac infarcted  patients using RNAeasy plus minikit (QIAGEN,Courtabeuf, France). Briefly, sample  quality was assessed using a DNA High sensitivity chip (Agilent Technologies).
Single end 50 reads barcoded RNA-Seq sequencing library was performed on an Illumina HiSeq4000 with the TruSeq SBS v3 chemistry.

tag: individual

tag: condition

value: Healthy

value: ProtheraCytes (expanded CD34+ cells)


title: Healthy donors (DS14) in day 9

tag: cell type


title: CamkIIa+Hip neurons- ATAC_Rep3

city: BOSTON

first: ELIZABETH

last: POLLINA

address: 220 LONGWOOD AVENUE, GOLDENSON 405

institute: HARVARD MEDICAL SCHOOL

data_processing:
For ATAC-seq samples, quality trimming of sequencing reads was performed with trimmomatic/0.3679 using the following command: java -jar trimmomatic-0.33.jar SE -threads 1 -phred33 [FASTQ_FILE] ILLUMINACLIP:[ADAPTER_FILE]:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:35. Nextera adapters were specificed for ATAC seq.
Samples were subsequently aligned to the mm10 genome using the Bowtie alignment software (vbowtie2/2.2.9) with the –very-sensitive setting. Reads mapping to the mitochrondrial genome were removed.
Duplicate reads were marked with Picard/2.8.0 with the commandL java -jar $PICARD/picard-2.8.0.jar MarkDuplicates REMOVE_DUPLICATES=false. Duplicates were subsequently removed using samtools/1.3.1 samtools view -b -F 1796.
ATAC-seq enriched peaks were determined using MACS2 (v 2.1.0) parameters –shift 100 -p 1e-5 --nolambda --keep-dup all --slocal 10000.  ATAC-seq peaks overlapping mm10 Blacklist regions were removed.
To generate bigWig files for ATAC-seq, 75 bp reads were extended in the 3’ direction to 200 bp (average fragment length for ATAC-seq experiments as measured by bioAnalyzer) with the bedtools slop command using the following parameters: -l 0 -r 125 -s. Mm10 blacklisted regions (Consortium, 2012) were filtered out using the following command: bedops –not-element-of 1 [BLACKLIST_BED]. The filtered BED files were converted to coverageBED format using the bedtools genomecov command with the following options: -scale [NORM_FACTOR] to scale each library to 20M reads for ATAC. Finally, bedGraphToBigWig (ucsc-tools/363) was used to generate the bigWig files.
To compare ATAC-seq signal across timepoints and conditions (e.g. different genotypes), raw read counts were extracted using homer(v4.9)’s annotatePeaks.pl function with the following command: annotatePeaks.pl [bed file] mm10 -size given -noann –noadj. Raw signal counts were imported in R, and the normalized signals were generated using DeSeq2’s function counts(dds, normalized=TRUE)).
Assembly: mm10
Supplementary files format and content: Table of DeSeq2 normalized read counts across regulatory regions in hippocampus
Supplementary files format and content: bigWig fies for replicates
Supplementary files format and content: MACS2 generated union of ATAC peaks across replicates and timepoint

extract_protocol:
For ATAC-seq libraries generated from hippocampal neuronal subtypes in vivo, CamkIIa-expressing CA1 pyramidal neurons were isolated from Camk2a-Cre; Sun1fl/+ mice using the INTACT method. Briefly, hippocampi were dounced 15X in buffer HB (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, pH 7.8, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine) to release nuclei. Nuclei were purified by spinning through an iodixanol gradient at 10,000 rcf (see above description for nuclear isolation in CUT&RUN experiments). Nuclei expressing SUN1-GFP on the nuclear membrane in a Cre-dependent manner were isolated by incubating the nuclear suspension with 10 μg of anti-GFP antibody (Invitrogen G10362) for 30 min at 4°C. Antibody-coated nuclei were subsequently captured by incubation with magnetic Protein G Dynabeads (Thermo Fisher). Following nuclear isolation and counting, approximately 30,000-40,000 nuclei per condition were resuspended in L1 lysis buffer (100 mM HEPES-NaOH pH 7.5, 280 mM NaCl, 2 mM EGTA, 2 mM EDTA, 0.5% Triton X-100, 1% NP-40, 20% Glycerol), followed by 5 minute incubation in L2 lysis buffer (10 mM Tris-HCl pH 8.0, 200 mM NaCl) and 5 minute incubation in ATAC lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal-630).
Nuclei were transposed using the Nextera DNA Library Prep Kit (Illumina, FC-121-1030). Transposition was carried out for 30 min at 37ºC. Transposed DNA fragments from individual samples were purified, independently barcoded, and amplified for 8-11 cycles. ATAC-seq libraries were selected for fragments ranging 200-1000 bp by gel electrophoresis and sequenced on the Illumina Nextseq 500 with 75 bp single-end reads.
Nextera ATAC-seq

tag: cell/tissue type

value: Unstim (Saline-injected)


title: CamkIIa+Hip neurons- 2KA_ATAC_Rep3

tag: mouse strain


title: CamkIIa+Hip neurons- 2KA_ATAC_Rep2


title: CamkIIa+Hip neurons- ATAC_Rep2


title: HEK293T DICER WT rescue AQ-seq replicate 1

description: AQ-seq


title: 2419R_KO_Fasted (RNA-seq)

description: RNA-Seq

tag: Sex

value: 9 weeks old


title: 2419L_KO_Fasted (RNA-seq)

description: RNA-Seq

tag: treatment


title: Healthy donors (DS12) in day 9


title: HCT116 DICER AA rescue AQ-seq replicate 1

description: AQ-seq


title: CamkIIa+Hip neurons- 2KA_ATAC_Rep1


title: Healthy donors (DS10) in day 9


title: Healthy donors (DS9) in day 9


title: 2436B_Control_Fasted (RNA-seq)

description: RNA-Seq

tag: age


title: Healthy donors (DS8) in day 9


title: CamkIIa+Hip neurons- ATAC_Rep1


title: 2436L_Control_Fasted (RNA-seq)

description: RNA-Seq


title: 2436R_Control_Fasted (RNA-seq)

description: RNA-Seq


title: HCT116 DICER ΔdsRBD rescue AQ-seq replicate 1

description: AQ-seq


title: AMI Patient (PE16) in day 9

value: AMI


title: Healthy donors (DS11) in day 9


title: 2436N_Control_Fasted (RNA-seq)

description: RNA-Seq

value: Liver


title: AMI Patient (PE15) in day 9


title: HCT116 DICER WT rescue AQ-seq replicate 1

description: AQ-seq